@article {pmid39045014,
year = {2024},
author = {Chien, YC and Valencia, CA and Lee, HY and Yoon, GM and Kim, D},
title = {DNA-encoded probe-based assay for profiling plant kinase activities.},
journal = {PNAS nexus},
volume = {3},
number = {7},
pages = {pgae281},
pmid = {39045014},
issn = {2752-6542},
abstract = {Elucidating kinase-substrate relationships is pivotal for deciphering cellular signaling mechanisms, yet it remains challenging due to the complexity of kinase networks. Herein, we report the development of a versatile DNA-based kinase assay platform for high-throughput profiling of plant protein kinase activities and substrate preferences. Our approach employs DNA-linked peptide substrates, facilitating quantitative and specific kinase activity detection through next-generation DNA sequencing. Leveraging DNA barcodes as quantitative readouts, our approach establishes a high-throughput, sensitive, and specific platform for dissecting kinase-substrate networks in plants, representing a powerful tool for elucidating signaling mechanisms in plants.},
}

@article {pmid39044181,
year = {2024},
author = {Askari, F and Paksa, A and Shahabi, S and Saeedi, S and Sofizadeh, A and Vahedi, M and Soltani, A},
title = {Population genetic structure and phylogenetic analysis of Anopheles hyrcanus (Diptera: Culicidae) inferred from DNA sequences of nuclear ITS2 and the mitochondrial COI gene in the northern part of Iran.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {724},
pmid = {39044181},
issn = {1471-2334},
support = {30181//Shiraz University of Medical Sciences/ ; },
mesh = {Animals ; Iran ; *Phylogeny ; *Anopheles/genetics/classification ; *Electron Transport Complex IV/genetics ; *Mosquito Vectors/genetics/classification ; Haplotypes ; Genetic Variation ; Genetics, Population ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; },
abstract = {BACKGROUND: The Anopheles hyrcanus group is distributed throughout the Oriental and Palaearctic regions and can transmit diseases such as malaria, Japanese encephalitis virus, and filariasis. This investigation marks the inaugural comprehensive study to undertake a phylogenetic analysis of the constituents of this malaria vector group in the northeastern region of Iran, juxtaposed with documented occurrences from different areas within Iran and worldwide.

METHODS: Mosquitoes were collected using various methods from nine different locations in Golestan province from April to December 2023. The collected mosquitoes were identified morphologically using valid taxonomic keys. DNA was isolated using the Sambio™ Kit. COI and ITS2 primers were designed using Oligo7 and GeneRunner. PCR and purification were performed with the Qiagen kit. Subsequently, sequencing was carried out at the Mehr Mam GENE Center using an Applied Biosystems 3730XL sequencer. The nucleotide sequences were then analyzed and aligned with GenBank data using BioEdit. Kimura 2-parameter was Utilized for base substitutions. DNA models were selected based on AIC and BIC criteria. Bayesian and Maximum Likelihood trees were constructed, along with a haplotype network. Molecular diversity statistics computed using DnaSP software.

RESULTS: In this study, a total of 819 adult mosquitoes were collected. An. hyrcanus was the second most abundant species, predominantly found in Kalaleh and Turkman counties. The sequenced and edited COI and ITS2 sequences were deposited in GenBank under specific accession numbers. Phylogenetic analyses using ML, BI, and NJ methods confirmed a monophyletic lineage for An. hyrcanus with strong support. Molecular analysis of Iranian An. hyrcanus found 11 diverse haplotypes, with the COI gene displaying low diversity. The ITS2 gene revealed two clades - one associating with Iran, Europe, and Asia; the other originating from southwestern Iran. The haplotype network showed two main groups - one from southwest Iran and the other from north Iran. Iran exhibited six distinct haplotypes, while Turkey showcased the highest diversity.

CONCLUSIONS: An. hyrcanus in southwestern Iran exhibits a distinct haplogroup, suggesting possible subspecies differentiation. Additional studies are required to validate this phenomenon.},
}

Animals
Iran
*Phylogeny
*Anopheles/genetics/classification
*Electron Transport Complex IV/genetics
*Mosquito Vectors/genetics/classification
Haplotypes
Genetic Variation
Genetics, Population
Sequence Analysis, DNA
DNA, Ribosomal Spacer/genetics

@article {pmid39041315,
year = {2024},
author = {Titus, BM and Gibbs, HL and Simões, N and Daly, M},
title = {Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syae045},
pmid = {39041315},
issn = {1076-836X},
abstract = {Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.},
}

@article {pmid39041198,
year = {2024},
author = {McGee, RS and Kinsler, G and Petrov, D and Tikhonov, M},
title = {Improving the accuracy of bulk fitness assays by correcting barcode processing biases.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae152},
pmid = {39041198},
issn = {1537-1719},
abstract = {Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce non-uniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here we develop a computational method, REBAR, for inferring the effects of barcode processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to two independent data sets, and demonstrate that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. REBAR mitigates bias and improves fitness estimates in high-throughput assays without introducing additional complexity to the experimental protocols, with potential applications in a range of experimental evolution and mutation screening contexts.},
}

@article {pmid39041008,
year = {2024},
author = {Allison, PF and Pickich, ET and Barnett, ZC and Garrick, RC},
title = {DNA barcoding is currently unreliable for species identification in most crayfishes.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e70050},
pmid = {39041008},
issn = {2045-7758},
abstract = {DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.},
}

@article {pmid39040809,
year = {2024},
author = {Alojayri, G and Al-Quraishy, S and Al-Shaebi, E and Mohammed, OB and Abdel-Gaber, R},
title = {Morphological and genetic identification of the gill monogenean parasite (Diclidophora merlangi) that infects Twobar Seabream Fish (Acanthopagrus bifasciatus) in the Arabian Gulf, Saudi Arabia.},
journal = {Helminthologia},
volume = {61},
number = {2},
pages = {184-193},
pmid = {39040809},
issn = {0440-6605},
abstract = {Ectoparasites, particularly monogeneans, negatively affect fish health and growth. This study identified monogenean parasites in the twobar seabream, Acanthopagrus bifasciatus (Sparidae), inhabited the Arabian Gulf (Saudi Arabia). Following that, forty A. bifasciatus fish samples were visually examined for monogeneans. Parasite species were collected from the gills and then analyzed morphometrically, morphologically, and molecularly using the partial regions of the large subunit of ribosomal RNA (28S rRNA) and mitochondrial cytochrome C oxidase subunit I (COI) genes. Fish species were also identified using a DNA barcoding approach based on the COI gene. The monogenean species of Diclidophora merlangi (Diclidophoridae) were found in 45% of the fish species studied. The generic features of the Diclidophora genus distinguish this species. This species discriminated itself from congeners by having a muscular bulb with 17 grooved and recurved hooks, 218±10 (184-267) post-ovarian testes, and four pairs of pedunculated clamps of relative sizes. Partial 28S rRNA sequencing from monogeneans revealed that they grouped with members of the genus Diclidophora, forming a monophyletic group that supported the morphological descriptions. Molecular identification revealed that D. merlangi has a unique barcode made up of a COI sequence. The host identity was established as A. bifasciatus based on the COI gene sequences. Furthermore, a molecular phylogenetic study was performed to determine the phylogenetic affinity of parasite species and fish hosts. This study on Diclidophora species is considered the first record of this genus in the examined area.},
}

@article {pmid39037657,
year = {2024},
author = {Handly-Santana, A and Oren, Y},
title = {Characterizing Rare Dormant and Cycling Lineages Using the Watermelon System.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2811},
number = {},
pages = {165-175},
pmid = {39037657},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Humans ; Cell Proliferation/genetics ; Sequence Analysis, RNA/methods ; RNA, Messenger/genetics ; },
abstract = {Barcode-based lineage tracing approaches enable molecular characterization of clonal cell families. Barcodes that are expressed as mRNA can be used to deconvolve lineage identity from single-cell RNA sequencing transcriptional data. Here we describe the Watermelon system, which facilitates the simultaneous tracing of lineage, transcriptional, and proliferative state at a single cell level.},
}

*Single-Cell Analysis/methods
*Cell Lineage/genetics
Humans
Cell Proliferation/genetics
Sequence Analysis, RNA/methods
RNA, Messenger/genetics

@article {pmid39032368,
year = {2024},
author = {Kwon, YL and Shin, KJ},
title = {Unique molecular identifier-based amplicon sequencing of microhaplotypes for background noise mitigation.},
journal = {Forensic science international. Genetics},
volume = {72},
number = {},
pages = {103096},
doi = {10.1016/j.fsigen.2024.103096},
pmid = {39032368},
issn = {1878-0326},
abstract = {Microhaplotypes (MHs), comprising two or more single-nucleotide polymorphisms in a short fragment, are promising forensic markers owing to their remarkable polymorphic nature. Several studies have demonstrated the utility of MHs through massively parallel sequencing (MPS). Nevertheless, the background noise level associated with MHs in MPS, which imposes a practical detection limit for the system, remains uninvestigated. Currently, unique molecular identifier (UMI) systems are known to effectively mitigate background noise by tracking original DNA molecules and facilitating PCR and MPS error corrections. Hence, this study aimed to design a UMI-based amplicon sequencing system, designated MH-UMIseq, which can amplify 46 MHs simultaneously and generate MPS libraries in four steps: barcoding PCR, nuclease reaction, boosting PCR, and indexing PCR. The performance of the MH-UMIseq system was evaluated using the Illumina NextSeq 550 and MiniSeq systems with 31 sets for 5 ng, 1 ng, and 200 pg of input DNA. The fgbio toolkit was used in conjunction with STRait Razor 3.0 and Visual Microhap to analyze the UMI data on MHs. The corresponding average not suppressed noise proportion of MH-UMIseq were 0.1 %, 0.3 %, and 0.7 % for 5 ng, 1 ng, and 200 pg of DNA, respectively, which substantially suppressed the background noise for more than 1 ng of DNA. Interestingly, the proportion of not suppressed noise in MH-UMIseq notably decreased as the amount of input DNA increased. The number of UMI families was proportional to the copy number of the template DNA and closely correlated with the system resolution. Therefore, the resolution of MH-UMIseq system is expected to be higher than that of conventional MPS for the deconvolution of mixtures containing more than 1 ng of DNA.},
}

@article {pmid39031987,
year = {2024},
author = {Wang, H and Zhan, Q and Ning, M and Guo, H and Wang, Q and Zhao, J and Bao, P and Xing, S and Chen, S and Zuo, S and Xia, X and Li, M and Wang, P and Lu, ZJ},
title = {Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.},
journal = {Clinical and translational medicine},
volume = {14},
number = {7},
pages = {e1760},
pmid = {39031987},
issn = {2001-1326},
support = {32170671//National Natural Science Foundation of China/ ; 82371855//National Natural Science Foundation of China/ ; 82341101//National Natural Science Foundation of China/ ; 81902384//National Natural Science Foundation of China/ ; CFH 2022-2-4075//Capital's Funds for Health Improvement and Research/ ; 2022ZD0117700//National Key Research and Development Plan of China/ ; 2021GQG1020//Tsinghua University Guoqiang Institute/ ; 2022ZLA003//Tsinghua University Initiative Scientific Research Program of Precision Medicine/ ; //Institute of Health and Medicine, Hefei Comprehensive National Science Center/ ; //Bayer Micro-funding/ ; //Bio-Computing Platform of Tsinghua University Branch of China National Center for Protein Sciences/ ; },
mesh = {Humans ; *Extracellular Vesicles/genetics/metabolism ; *Cell-Free Nucleic Acids/blood/analysis/genetics ; *Sequence Analysis, RNA/methods ; },
abstract = {BACKGROUND: Cell-free long RNAs in human plasma and extracellular vesicles (EVs) have shown promise as biomarkers in liquid biopsy, despite their fragmented nature.

METHODS: To investigate these fragmented cell-free RNAs (cfRNAs), we developed a cost-effective cfRNA sequencing method called DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing). DETECTOR-seq utilised a meticulously tailored set of customised guide RNAs to remove large amounts of unwanted RNAs (i.e., fragmented ribosomal and mitochondrial RNAs) in human plasma. Early barcoding strategy was implemented to reduce costs and minimise plasma requirements.

RESULTS: Using DETECTOR-seq, we conducted a comprehensive analysis of cell-free transcriptomes in both whole human plasma and EVs. Our analysis revealed discernible distributions of RNA types in plasma and EVs. Plasma exhibited pronounced enrichment in structured circular RNAs, tRNAs, Y RNAs and viral RNAs, while EVs showed enrichment in messenger RNAs (mRNAs) and signal recognition particle RNAs (srpRNAs). Functional pathway analysis highlighted RNA splicing-related ribonucleoproteins (RNPs) and antimicrobial humoral response genes in plasma, while EVs demonstrated enrichment in transcriptional activity, cell migration and antigen receptor-mediated immune signals. Our study indicates the comparable potential of cfRNAs from whole plasma and EVs in distinguishing cancer patients (i.e., colorectal and lung cancer) from healthy donors. And microbial cfRNAs in plasma showed potential in classifying specific cancer types.

CONCLUSIONS: Our comprehensive analysis of total and EV cfRNAs in paired plasma samples provides valuable insights for determining the need for EV purification in cfRNA-based studies. We envision the cost effectiveness and efficiency of DETECTOR-seq will empower transcriptome-wide investigations in the fields of cfRNAs and liquid biopsy.

KEYPOINTS: DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing) enabled efficient and specific depletion of sequences derived from fragmented ribosomal and mitochondrial RNAs in plasma. Distinct human and microbial cell-free RNA (cfRNA) signatures in whole Plasma versus extracellular vesicles (EVs) were revealed. Both Plasma and EV cfRNAs were capable of distinguishing cancer patients from normal individuals, while microbial RNAs in Plasma cfRNAs enabled better classification of cancer types than EV cfRNAs.},
}

Humans
*Extracellular Vesicles/genetics/metabolism
*Cell-Free Nucleic Acids/blood/analysis/genetics
*Sequence Analysis, RNA/methods

@article {pmid39031978,
year = {2024},
author = {Bañón, R and de Carlos, A and Comesaña, ÁS and Barreiro Vázquez, JD and Baldó, F},
title = {Second world record for Barathronus roulei Nielsen, 2019 (Ophidiiformes, Bythitidae), from the Porcupine Bank (Northeast Atlantic).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.15878},
pmid = {39031978},
issn = {1095-8649},
support = {PORCUDEM-20233FMP001//European Maritime, Fisheries and Aquaculture Fund/ ; },
abstract = {Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)-DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species.},
}

@article {pmid39031483,
year = {2024},
author = {Gil, F and Beroiz, B and Ballesteros, I and Horreo, JL},
title = {Can consumers avoid mislabelling? Genetic species identification provides recommendations for shrimp/prawn products.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.13771},
pmid = {39031483},
issn = {1097-0010},
abstract = {BACKGROUND: Crustaceans of the superfamily Penaeoidea (e.g., shrimps and prawns) are among the most commercially available aquatic products worldwide. However, there are few studies regarding not only the presence but also the characteristics of mislabelling in these food products. Such information would be helpful for consumers in order to avoid the typical problems associated with mislabelling (e.g., health and economic issues). For this reason, this work considers Penaeoidea mislabelling by comparing different products (frozen, fresh, boiled), and sources (hypermarkets, supermarkets and fishmongers) from Spain (Europe).

RESULTS: A total of 94 samples from 55 different products were collected, representing 19 different species from 13 genera. Mitochondrial DNA (COI gene) was amplified, revealing mislabelling in almost 30% of supermarket products and almost exclusively found in frozen samples (95% of the total) regardless of its price. In addition, products from the Pacific Ocean seem to be particularly susceptible to mislabelling.

CONCLUSIONS: All in all, recommendations for the consumer in order to avoid mislabelling of prawns include purchasing them fresh from fishmongers; aquaculture products must not be avoided. This study represents, to our knowledge, the first attempt to provide recommendations to consumers based on DNA analyses in order to avoid mislabelling in food products. Further research is therefore required to provide such recommendations in different food products, particularly those that are processed, packaged and/or frozen. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid39027082,
year = {2024},
author = {Changbunjong, T and Weluwanarak, T and Laojun, S and Duvallet, G and Chaiphongpachara, T},
title = {Genetic and morphometric differentiation between two morphs of Haematobosca sanguinolenta (Diptera: Muscidae) from Thailand.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {6},
number = {},
pages = {100186},
pmid = {39027082},
issn = {2667-114X},
abstract = {Haematobosca is a genus of biting fly within the subfamily Stomoxyinae of the family Muscidae. It is currently recognized to include 16 species worldwide. These species, acting as ectoparasites, are considered to have significant importance in the veterinary and medical fields. To address the color polymorphism related to the genus Haematobosca in Thailand, herein, we focused on the normal (legs mainly black) and yellow (legs mainly yellow) morphs of Haematobosca sanguinolenta and examined them for genetic differences using three molecular markers: the cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes from the mitochondrial genome as well as the internal transcribed spacer 2 (ITS2) region from the nuclear ribosomal DNA. In addition, we analyzed wing differences between the two morphs using geometric morphometrics (GM). The genetic divergences between the two morphs showed that cytb gene showed the greatest divergence, for which the average distance was 5.6%. This was followed by the combination of cox1-cytb-ITS2, exhibiting an average divergence of 4.5%, ITS2 with a divergence of 4.1%, and finally cox1, showing the lowest divergence of 3.5%. Phylogenetic analyses distinctly separated the two morphs of H. sanguinolenta; this separation was supported by high bootstrap values (97-100%). These results were further corroborated by three species delimitation methods, i.e. assemble species by automatic partitioning (ASAP), automated barcode gap discovery (ABGD), and Poisson tree processes (PTP), all of which suggested that the two morphs likely represent separate species. In addition, a GM study identified a statistically significant difference in wing shape between the two morphs of H. sanguinolenta (P < 0.05). This combination of genetic and morphometric results strongly supports the existence of two distinct species within H. sanguinolenta in Thailand.},
}

@article {pmid39027045,
year = {2024},
author = {Götz, TI and Cong, X and Rauber, S and Angeli, M and Lang, EW and Ramming, A and Schmidkonz, C},
title = {A novel Slide-seq based image processing software to identify gene expression at the single cell level.},
journal = {Journal of pathology informatics},
volume = {15},
number = {},
pages = {100384},
doi = {10.1016/j.jpi.2024.100384},
pmid = {39027045},
issn = {2229-5089},
abstract = {Analysis of gene expression at the single-cell level could help predict the effectiveness of therapies in the field of chronic inflammatory diseases such as arthritis. Here, we demonstrate an adopted approach for processing images from the Slide-seq method. Using a puck, which consists of about 50,000 DNA barcode beads, an RNA sequence of a cell is to be read. The pucks are repeatedly brought into contact with liquids and then recorded with a conventional epifluorescence microscope. The image analysis initially consists of stitching the partial images of a sequence recording, registering images from different sequences, and finally reading out the bases. The new method enables the use of an inexpensive epifluorescence microscope instead of a confocal microscope.},
}

@article {pmid39026955,
year = {2024},
author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S},
title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11584},
doi = {10.1002/ece3.11584},
pmid = {39026955},
issn = {2045-7758},
abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.},
}

@article {pmid39026715,
year = {2024},
author = {Chamberlin, JT and Gillen, AE and Quinlan, AR},
title = {Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.07.10.602909},
pmid = {39026715},
issn = {2692-8205},
abstract = {Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site, which is expected to be the poly(A) tail or a genomic adenine homopolymer. Direct sequencing across this priming site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the "barcode" end. Here, we evaluate the capability of "avidity base chemistry" DNA sequencing from Element Biosciences to sequence through this homopolymer accurately, and the impact of the additional cDNA sequence on read alignment and precise quantification of polyadenylation site usage. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The resulting paired-end alignments enable direct and independent assignment of reads to polyadenylation sites, which bypasses complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and arrive at an adjusted adapter trimming and alignment workflow that significantly improves the alignment of sequence data from Element and Illumina, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site analyses but do not rule out the potential for similar performance from other emerging platforms.},
}

@article {pmid39024335,
year = {2024},
author = {Gul, A and Shah, SHJ and Faris, S and Qazi, J and Qazi, A and Dey, SK},
title = {An analysis of morphological and genetic diversity of mango fruit flies in Pakistan.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0304472},
pmid = {39024335},
issn = {1932-6203},
mesh = {Animals ; *Tephritidae/genetics/classification ; Pakistan ; *Mangifera/parasitology/genetics ; *Genetic Variation ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Phylogeny ; },
abstract = {Fruit flies of genus Bactrocera are important insect pests of commercially cultivated mangos in Pakistan limiting its successful production in the country. Despite the economic risk, the genetic diversity and population dynamics of this pest have remained unexplored. This study aimed to morphologically identify Bactrocera species infesting Mango in major production areas of the country and to confirm the results with insect DNA barcode techniques. Infested mango fruits from the crop of 2022, were collected from 46 locations of 11major production districts of Punjab and Sindh provinces, and first-generation flies were obtained in the laboratory. All 10,653 first generation flies were morphologically identified as two species of Bactrocera; dorsalis and zonata showing geography-based relative abundance in the two provinces; Punjab and Sindh. Morphological identification was confirmed by mitochondrial cytochrome oxidase gene subunit I (mt-COI) based DNA barcoding. Genetic analysis of mtCOI gene region of 61 selected specimens by the presence of two definite clusters and reliable intraspecific distances validated the results of morphological identification. This study by morphological identification of a large number of fruit fly specimens from the fields across Pakistan validated by insect DNA barcode reports two species of Bactrocera infesting mango in the country.},
}

Animals
*Tephritidae/genetics/classification
Pakistan
*Mangifera/parasitology/genetics
*Genetic Variation
*DNA Barcoding, Taxonomic
*Electron Transport Complex IV/genetics
Phylogeny

@article {pmid39023176,
year = {2024},
author = {Zhang, LJ and Liu, Y and Wang, YL and Xie, LL and Wang, XY and Ma, YS},
title = {Population genetic diversity and structure of Tephritis angustipennis and Campiglossa loewiana (Diptera: Tephritidae) based on COI DNA barcodes in the three-river source region, China.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
doi = {10.1093/jisesa/ieae075},
pmid = {39023176},
issn = {1536-2442},
support = {2024-SF-101//Qinghai Science and Technology Department/ ; },
mesh = {Animals ; *Tephritidae/genetics ; China ; *Electron Transport Complex IV/genetics ; *Genetic Variation ; *DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; Insect Proteins/genetics ; },
abstract = {Tephritis angustipennis (Diptera: Tephritidae) and Campiglossa loewiana (Diptera: Tephritidae) are phytophagous pests in China. Their damage has significantly impacted the collection and cultivation of germplasm resources of native Asteraceae plants. However, the genetic characteristics and structure of their population are unclear. This study focused on the highly damaging species of T. angustipennis and C. loewiana collected from the three-river source region (TRSR). We amplified the mitochondrial cytochrome C oxidase subunit I (mtCOI) gene sequences of these pests collected from this area and compared them with COI sequences from GenBank. We also analyzed their genetic diversity and structure. In T. angustipennis, 5 haplotypes were identified from 5 geographic locations; the genetic differentiation between France population FRPY (from Nylandia, Uusimaa) and China populations GLJZ (from Dehe Longwa Village, Maqin County), GLDR (from Zhique Village, Dari County), and GLMQ (from Rijin Village, Maqin County) was the strongest. GLJZ exhibited strong genetic differentiation from GLDR and GLMQ, with relatively low gene flow. For C. loewiana, 11 haplotypes were identified from 5 geographic locations; the genetic differentiation between the Chinese population GLMQ-YY (from Yangyu Forest Farm, Maqin County) and Finnish population FDNL (from Nylandia, Uusimaa) was the strongest, with relatively low gene flow, possibly due to geographical barriers in the Qinghai-Tibet plateau. Only 1 haplotype was identified across GLDR, GLMQ, and GLBM. High gene flow between distant locations indicates that human activities or wind dispersal may facilitate the dispersal of fruit flies and across different geographic. Geostatistical analysis suggested a recent population expansion of these 2 species in TRSR. Our findings provide technical references for identifying pests in the TRSR region and theoretical support for managing resistance, monitoring pest occurrences, analyzing environmental adaptability, and formulating biological control strategies for Tephritidae pests on Asteraceae plants.},
}

Animals
*Tephritidae/genetics
China
*Electron Transport Complex IV/genetics
*Genetic Variation
*DNA Barcoding, Taxonomic
Haplotypes
Phylogeny
Insect Proteins/genetics

@article {pmid39020177,
year = {2024},
author = {Chen, W and Choi, J and Li, X and Nathans, JF and Martin, B and Yang, W and Hamazaki, N and Qiu, C and Lalanne, JB and Regalado, S and Kim, H and Agarwal, V and Nichols, E and Leith, A and Lee, C and Shendure, J},
title = {Symbolic recording of signalling and cis-regulatory element activity to DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39020177},
issn = {1476-4687},
abstract = {Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter[1], we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.},
}

@article {pmid39018572,
year = {2024},
author = {Khumalo, N and Chaisi, M and Magoro, RK and Mwale, M},
title = {An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2024-0052},
pmid = {39018572},
issn = {1480-3321},
abstract = {Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. Approximately over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma, and Argas species had multiple barcode Index Numbers (BINs), suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives.},
}

@article {pmid39018344,
year = {2024},
author = {Todisco, V and Basu, DN and Prosser, SWJ and Russell, S and Mutanen, M and Zilli, A and Huertas, B and Kunte, K and Vane-Wright, R},
title = {DNA barcodes from over-a-century-old type specimens shed light on the taxonomy of a group of rare butterflies (Lepidoptera: Nymphalidae: Calinaginae).},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305825},
doi = {10.1371/journal.pone.0305825},
pmid = {39018344},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics/classification/anatomy & histology ; *Phylogeny ; Wings, Animal/anatomy & histology ; Electron Transport Complex IV/genetics ; },
abstract = {We analyzed COI barcode sequences from 138 over-a-century old specimens of Calinaga including 36 name-bearing type specimens stored at the Natural History Museum London. These new data, combined with previously available RPS5 sequences, divide the Calinaga samples into four well-supported mitochondrial lineages that together with a novel wing-pattern analysis, support the recognition of six species (lhatso, buddha, brahma, aborica, formosana and davidis), with all other names subsumed either as subspecies or synonyms. One new taxon is described, Calinaga aborica naima Vane-Wright, ssp. n.},
}

Animals
*DNA Barcoding, Taxonomic
*Butterflies/genetics/classification/anatomy & histology
*Phylogeny
Wings, Animal/anatomy & histology
Electron Transport Complex IV/genetics

@article {pmid39018276,
year = {2024},
author = {de Almeida, LH and Gonçalves, MC and da Conceição Bispo, P},
title = {An integrative approach to the study of Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) from Brazil: Support for the description of four new species and a basis for future studies.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305824},
doi = {10.1371/journal.pone.0305824},
pmid = {39018276},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Phylogeny ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Bayes Theorem ; Insecta/classification/genetics/anatomy & histology ; Neoptera/genetics/classification/anatomy & histology ; Species Specificity ; Female ; },
abstract = {Kempnyia (Plecoptera: Perlidae) is an endemic genus of Brazilian stoneflies that has 36 valid species and is distributed primarily in the Atlantic Forest and the mountainous areas of Central Brazil, particularly in Goiás and Tocantins states. Despite being the Brazilian genus with the most DNA sequences available on GenBank, integrative studies on the genus began only recently, in 2014. In this context, herein we studied the morphology and molecular data of Kempnyia specimens deposited in the Aquatic Biology Laboratory (UNESP, Assis) and the Entomology Museum of the Federal University of Viçosa (UFVB, Viçosa) collections. For the integrative approach adopted, in addition to studying the specimens morphologically, we used sequences of the COI mitochondrial gene combined with the following species delimitation methods: Automatic Barcode Gap Discovery (ABGD), both primary (ABGDp) and recursive (ABGDr) partitions; Assemble Species by Automatic Partitioning (ASAP); Poisson Tree Processes (PTP) and the Bayesian implementation of the Poisson Tree Processes (bPTP). As a result, we provided 28 new COI sequences of 21 species and support the description of four new species, namely, K. guarani sp. nov., K. tupiniquim sp. nov., K. una sp. nov., and K. zwickii sp. nov., consequently increasing the known diversity of the genus to 40 species. We also discuss the morphological variations observed in other species of the genus and provide several new geographic records. Therefore, our study brings new insights into the values of intra- and interspecific molecular divergence within Kempnyia, serving as a basis for new studies.},
}

Animals
Brazil
*Phylogeny
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic
Bayes Theorem
Insecta/classification/genetics/anatomy & histology
Neoptera/genetics/classification/anatomy & histology
Species Specificity
Female

@article {pmid39015799,
year = {2024},
author = {Xiaoqi, M and Zhang, T and Wang, C},
title = {Description of two species of the orb-weaver spider genus Argiope Audouin, 1826 (Araneae, Araneidae) from Xizang, China.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e125601},
pmid = {39015799},
issn = {1314-2828},
abstract = {BACKGROUND: The spider genus Argiope Audouin, 1826, comprises 88 species worldwide, including 23 species occurring in China. Two Argiope species were collected by the spider survey on Yarlung Zangbo Grand Canyon National Nature Reserve, Xizang, southwest China, conducted in 2023.

NEW INFORMATION: Two species of the orb-weaver spider genus Argiope from Xizang, China are described, including a new species, A.beibeng Mi & Wang, sp. nov. (♂♀) and a known species, A.caesarea Thorell, 1897 (♂♀). The unknown male of A.caesarea is described for the first time.},
}

@article {pmid39015529,
year = {2024},
author = {Lee, S and Hwang, S and Lee, M and Seung, J and Choi, W and Bai, M},
title = {DNA barcoding reveals a taxonomic fraud: Note on validity of Propomacrusmuramotoae (Coleoptera, Scarabaeidae).},
journal = {ZooKeys},
volume = {1206},
number = {},
pages = {181-190},
pmid = {39015529},
issn = {1313-2989},
abstract = {Until the early 2000s, the genus Propomacrus was known to comprise two species, occurring in the Eastern Mediterranean and Southeast China. The discovery of Propomacrusmuramotoae Fujioka in Tibet and subsequently in Bhutan and Nepal, might play a crucial role in bridging the geographical distribution gap of the Euchirini tribe between the Mediterranean and Central China, offering profound insights into its evolution and biogeography. However, all specimens, including the holotype specimen, were sourced from a single insect vendor, with no further specimens found or catalogued in museum collections thereafter. During our examination of a P.muramotoae specimen from a private collection in South Korea, we found its COI gene sequence to be identical to that of P.bimucronatus (Pallas) from Turkey, a species known for its wide distribution and genetic variability across regional populations. This overlap in genetic identity raised significant doubts, further compounded by our detection of deliberate modifications in essential diagnostic features during morphological examination. All three specimens we examined showed crude modifications, including staining and artificial grinding. Despite our inability to access the P.muramotoae type specimens for direct examination-a challenge we attempted to overcome through various means-it is evident that significant fraudulent tampering has occurred with the P.muramotoae specimens. Therefore, a new synonymy is proposed: Propomacrusbimucronatus Pallas, 1781 = P.muramotoae Fujioka, 2007 (syn. nov.). We also advocate for a straightforward verification of the type specimen through molecular analysis of the COI barcode region and morphological re-examination under a microscope for those who have access to the type specimens.},
}

@article {pmid39014300,
year = {2024},
author = {Darabi, A and Sobhani, S and Aghdam, R and Eslahchi, C},
title = {AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {241},
pmid = {39014300},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; *Algorithms ; Nucleotides/genetics ; High-Throughput Nucleotide Sequencing/methods ; Software ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Cluster Analysis ; Contig Mapping/methods ; Metagenome/genetics ; },
abstract = {BACKGROUND: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.

RESULTS: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.

CONCLUSION: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.

AVAILABILITY: A python package is available at: https://github.com/SayehSobhani/AFITBin .},
}

*Metagenomics/methods
*Algorithms
Nucleotides/genetics
High-Throughput Nucleotide Sequencing/methods
Software
Microbiota/genetics
Sequence Analysis, DNA/methods
Cluster Analysis
Contig Mapping/methods
Metagenome/genetics

@article {pmid39012608,
year = {2024},
author = {Albrecht, C and Bashtrykov, P and Jeltsch, A},
title = {Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2842},
number = {},
pages = {405-418},
pmid = {39012608},
issn = {1940-6029},
mesh = {*DNA Methylation ; *Sulfites/chemistry ; *High-Throughput Nucleotide Sequencing/methods ; *Polymerase Chain Reaction/methods ; Humans ; DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Epigenesis, Genetic ; Epigenomics/methods ; },
abstract = {DNA methylation is an important epigenetic modification that regulates chromatin structure and the cell-type-specific expression of genes. The association of aberrant DNA methylation with many diseases, as well as the increasing interest in modifying the methylation mark in a directed manner at genomic sites using epigenome editing for research and therapeutic purposes, increases the need for easy and efficient DNA methylation analysis methods. The standard approach to analyze DNA methylation with a single-cytosine resolution is bisulfite conversion of DNA followed by next-generation sequencing (NGS). In this chapter, we describe a robust, powerful, and cost-efficient protocol for the amplification of target regions from bisulfite-converted DNA, followed by a second PCR step to generate libraries for Illumina NGS. In the two consecutive PCR steps, first, barcodes are added to individual amplicons, and in the second PCR, indices and Illumina adapters are added to the samples. Finally, we describe a detailed bioinformatics approach to extract DNA methylation levels of the target regions from the sequencing data. Combining barcodes with indices enables a high level of multiplexing allowing to sequence multiple pooled samples in the same sequencing run. Therefore, this method is a robust, accurate, quantitative, and cheap approach for the readout of DNA methylation patterns at defined genomic regions.},
}

*DNA Methylation
*Sulfites/chemistry
*High-Throughput Nucleotide Sequencing/methods
*Polymerase Chain Reaction/methods
Humans
DNA/genetics
Sequence Analysis, DNA/methods
Computational Biology/methods
Epigenesis, Genetic
Epigenomics/methods

@article {pmid39011841,
year = {2024},
author = {Berteloot, OH and Peusens, G and Beliën, T and De Clercq, P and Van Leeuwen, T},
title = {Unveiling the diet of two generalist stink bugs, Halyomorpha halys and Pentatoma rufipes (Hemiptera: Pentatomidae), through metabarcoding of the ITS2 region from gut content.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8287},
pmid = {39011841},
issn = {1526-4998},
support = {LA-traject HBC.2018.2224//VLAIO (Flanders Innovation and Entrepreneurship)/ ; },
abstract = {BACKGROUND: The use of DNA metabarcoding has become an increasingly popular technique to infer feeding relationships in polyphagous herbivores and predators. Understanding host plant preference of native and invasive herbivore insects can be helpful in establishing effective integrated pest management (IPM) strategies. The invasive Halyomorpha halys and native Pentatoma rufipes are piercing-sucking stink bug pests that are known to cause economic damage in commercial fruit orchards.

RESULTS: In this study, we performed molecular gut content analysis (MGCA) on field-collected specimens of these two herbivorous pentatomids using next-generation amplicon sequencing (NGAS) of the internal transcribed spacer 2 (ITS2) barcode region. Additionally, a laboratory experiment was set up where H. halys was switched from a mixed diet to a monotypic diet, allowing us to determine the detectability of the initial diet in a time series of ≤3 days after the diet switch. We detected 68 unique plant species from 54 genera in the diet of two stink bug species, with fewer genera found per sample and a smaller diet breadth for P. rufipes than for H. halys. Both stink bug species generally prefer deciduous trees over gymnosperms and herbaceous plants. Landscape type significantly impacted the observed genera in the diet of both stink bug species, whereas season only had a significant effect on the diet of H. halys.

CONCLUSION: This study provides further insights into the dietary composition of two polyphagous pentatomid pests and illustrates that metabarcoding can deliver a relevant species-level resolution of host plant preference. © 2024 Society of Chemical Industry.},
}

@article {pmid39008212,
year = {2024},
author = {Wengrat, APGS and Carvalho, LC and Pietrowski, V and Schoeninger, K and Costa, VA and Johnson, NF},
title = {First Record of Telenomus dilophonotae (Hymenoptera, Scelionidae), Parasitizing Eggs of Erinnyis ello (Lepidoptera, Sphingidae) in Western Paraná, Brazil, with Molecular Characterization and Records of Occurrences.},
journal = {Neotropical entomology},
volume = {},
number = {},
pages = {},
pmid = {39008212},
issn = {1678-8052},
support = {152666/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2020/16051-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/50334-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/18965-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 65562/2014-0//Instituto Nacional de Ciência e Tecnologia de Hymenoptera Parasitoides/ ; 2018/02317-5//São Paulo Advanced Research Center for Biological Control/ ; },
abstract = {There are few records for Telenomus dilophonotae Cameron, 1913 (Hymenoptera, Scelionidae) from South America. In Brazil, the first occurrence was reported in Bahia in rubber crops, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. - Arg., there parasitizing eggs of Erinnyis ello Linnaeus, 1758 (Lepidoptera, Sphingidae). It was also found parasitizing the same host in cassava, Manihot esculenta Crantz (Euphorbiaceae). This is the first record of occurrence of T. dilophonotae in the state of Paraná, parasitizing eggs of E. ello in areas of cassava production in the western region of Paraná, this being the southernmost record of the species. Here, photographs, the first sequence of DNA barcode of this species of parasitoid wasp, and a distribution map are provided.},
}

@article {pmid39007612,
year = {2024},
author = {Bomidi, C and Zeng, XL and Poplaski, V and Coarfa, C and Estes, MK and Blutt, SE},
title = {Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {208},
pages = {},
doi = {10.3791/66749},
pmid = {39007612},
issn = {1940-087X},
mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestine, Small/cytology/metabolism ; *Single-Cell Analysis/methods ; *Intestinal Mucosa/cytology/metabolism ; Gene Expression Profiling/methods ; Transcriptome/genetics ; },
abstract = {Single cell transcriptomics has revolutionized our understanding of the cell biology of the human body. State-of-the-art human small intestinal organoid cultures provide ex vivo model systems that bridge the gap between animal models and clinical studies. The application of single cell transcriptomics to human intestinal organoid (HIO) models is revealing previously unrecognized cell biology, biochemistry, and physiology of the GI tract. The advanced single cell transcriptomics platforms use microfluidic partitioning and barcoding to generate cDNA libraries. These barcoded cDNAs can be easily sequenced by next generation sequencing platforms and used by various visualization tools to generate maps. Here, we describe methods to culture and differentiate human small intestinal HIOs in different formats and procedures for isolating viable cells from these formats that are suitable for use in single-cell transcriptional profiling platforms. These protocols and procedures facilitate the use of small intestinal HIOs to obtain an increased understanding of the cellular response of human intestinal epithelium at the transcriptional level in the context of a variety of different environments.},
}

Humans
*Organoids/cytology/metabolism
*Intestine, Small/cytology/metabolism
*Single-Cell Analysis/methods
*Intestinal Mucosa/cytology/metabolism
Gene Expression Profiling/methods
Transcriptome/genetics

@article {pmid39006907,
year = {2024},
author = {Kantelinen, A and Svensson, M and Malíček, J and Vondrák, J and Thor, G and Palice, Z and Svoboda, S and Myllys, L},
title = {A phylogenetic study of Micareamelaeniza and similar-looking species (Pilocarpaceae) unveils hidden diversity and clarifies species boundaries and reproduction modes.},
journal = {MycoKeys},
volume = {106},
number = {},
pages = {327-354},
pmid = {39006907},
issn = {1314-4049},
abstract = {Micarea (Ascomycota, Pilocarpaceae) is a large cosmopolitan genus of crustose lichens. We investigated molecular systematics and taxonomy of the poorly known Micareamelaeniza group focussing on M.melaeniza, M.nigella and M.osloensis. A total of 54 new sequences were generated and using Bayesian and maximum likelihood analysis of two markers (nuITS and mtSSU), we discovered two previously unrecognized phylogenetic lineages, one of which is described here as Micareaeurasiatica Kantelinen & G. Thor, sp. nov., morphologically characterized by pycnidia that are sessile to emergent, cylindrically shaped, with greenish-black K+ olive green, wall pigmentation and containing large mesoconidia up to 6 µm in length. The species is known from Japan and Finland. In addition, we show that the reproduction biology of M.osloensis has been poorly understood and that the species often occurs as an anamorph with stipitate pycnidia. We present a species synopsis and notes on pigments. Our research supports previous results of asexuality being an important reproductive strategy of species growing on dead wood.},
}

@article {pmid39005645,
year = {2024},
author = {Wattanasatja, V and Phisutrattanaporn, J and Doenphai, N and Sirinual, S and Kanjanabuch, T},
title = {Peritoneal dialysis-associated peritonitis due to infected umbilicus.},
journal = {Medical mycology case reports},
volume = {45},
number = {},
pages = {100654},
pmid = {39005645},
issn = {2211-7539},
abstract = {We provide the first case report of peritoneal dialysis (PD)-associated peritonitis due to Lasiodiplodia theobromae, a known plant pathogen causing rotting and dieback in post-harvest citrus fruit, in immunocompetent patient with fungal colonization inside the PD catheter lumen. A root cause analysis suspected the patient's umbilical infection as the source of contamination. The fungal infection was established through microscopic examination of the PD catheter lumen and galactomannan testing in both serum and effluent. The species of pathogen was confirmed by DNA barcoding. The patient responded well to timely PD catheter removal and a 2-week course of oral voriconazole. Preventive strategies should prioritize hygiene practices, including umbilical care, to mitigate the risk of contamination and subsequent infections of fungal pathogens.},
}

@article {pmid39000014,
year = {2024},
author = {Kartavtsev, YP and Masalkova, NA},
title = {Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae).},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000014},
issn = {1422-0067},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Phylogeny ; *Evolution, Molecular ; Mytilidae/genetics/classification ; RNA, Transfer/genetics ; Bivalvia/genetics/classification ; Mytilus/genetics/classification ; },
abstract = {Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.},
}

Animals
*Genome, Mitochondrial/genetics
*Phylogeny
*Evolution, Molecular
Mytilidae/genetics/classification
RNA, Transfer/genetics
Bivalvia/genetics/classification
Mytilus/genetics/classification

@article {pmid38997781,
year = {2024},
author = {Jiang, K and Liu, T and Kales, S and Tewhey, R and Kim, D and Park, Y and Jarvis, JN},
title = {A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes.},
journal = {BMC medical genomics},
volume = {17},
number = {1},
pages = {185},
pmid = {38997781},
issn = {1755-8794},
support = {R21-AR071878//National Institutes of Health (USA)/ ; R21 AR076948/NH/NIH HHS/United States ; UL1TR001412/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Haplotypes ; *Arthritis, Juvenile/genetics ; K562 Cells ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Although genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes.

METHODS: We used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180 bp oligonucleotide reporters ("oligos") in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve > 20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs.

RESULTS: We identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total = 84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants.

CONCLUSION: Using MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.},
}

Humans
*Polymorphism, Single Nucleotide
*Haplotypes
*Arthritis, Juvenile/genetics
K562 Cells
*Genetic Predisposition to Disease
Genome-Wide Association Study

@article {pmid38996389,
year = {2024},
author = {Baxter, JR and Kotze, A and de Bruyn, M and Matlou, K and Labuschagne, K and Mwale, M},
title = {DNA barcoding of southern African mammal species and construction of a reference library for forensic application.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2023-0050},
pmid = {38996389},
issn = {1480-3321},
abstract = {Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of Cytochrome c oxidase subunit 1 (COI) and Cytochrome b (Cyt b) sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.},
}

@article {pmid38993689,
year = {2024},
author = {Shim, J and Song, JH},
title = {A taxonomic review of the order Mantodea in Korea based on morphology and DNA barcodes.},
journal = {ZooKeys},
volume = {1206},
number = {},
pages = {1-43},
doi = {10.3897/zookeys.1206.123355},
pmid = {38993689},
issn = {1313-2989},
abstract = {A taxonomic study of Korean Mantodea using morphological and molecular characters (COI) is presented. Eight species [Amantisnawai (Shiraki, 1908), Acromantisjaponica Westwood, 1889, Mantisreligiosasinica Bazyluk, 1960, Statiliamaculata (Thunberg, 1784), Tenoderaangustipennis Saussure, 1869, T.sinensis Saussure, 1871, Hierodulachinensis Werner, 1929, H.patellifera (Audinet-Serville, 1838)] belonging to six genera in three families are recognized. Interspecific genetic divergence of COI using uncorrected p-distance ranged from 6.7% to 22.4%, while intraspecific divergence ranged from 0% to 2.2% among eight Korean Mantodea species. All eight species were each strongly supported as a single lineage using COI on both neighbor-joining and parsimony trees. An illustrated key, redescriptions, habitus photographs, and illustrations of diagnostic characters of the species of Korean Mantodea are provided to facilitate identification.},
}

@article {pmid38989842,
year = {2024},
author = {Slusher, EK and Cottrell, T and Gariepy, T and Acebes-Doria, A and Querejeta Coma, M and Toledo, PFS and Schmidt, JM},
title = {A molecular approach to unravel trophic interactions between parasitoids and hyperparasitoids associated with pecan aphids.},
journal = {Journal of insect science (Online)},
volume = {24},
number = {4},
pages = {},
pmid = {38989842},
issn = {1536-2442},
mesh = {Animals ; *Aphids/parasitology/genetics ; *Food Chain ; *Host-Parasite Interactions ; Carya/parasitology ; DNA Barcoding, Taxonomic ; Wasps/physiology/genetics ; },
abstract = {Advances in molecular ecology can overcome many challenges in understanding host-parasitoid interactions. Genetic characterization of the key-players in systems helps to confirm species and identify trophic linkages essential for ecological service delivery by biological control agents; however, relatively few agroecosystems have been explored using this approach. Pecan production consists of a large tree perennial system containing an assortment of seasonal pests and natural enemies. As a first step to characterizing host-parasitoid associations in pecan food webs, we focus on aphid species and their parasitoids. Based on DNA barcoding of field-collected and reared specimens, we confirmed the presence of 3 species of aphid, one family of primary parasitoids, and 5 species of hyperparasitoids. By applying metabarcoding to field-collected aphid mummies, we were able to identify multiple species within each aphid mummy to unravel a complex food web of 3 aphids, 2 primary parasitoids, and upward of 8 hyperparasitoid species. The results of this study demonstrate that multiple hyperparasitoid species attack a single primary parasitoid of pecan aphids, which may have negative consequences for successful aphid biological control. Although further research is needed on a broader spatial scale, our results suggest multiple species exist in this system and may suggest a complex set of interactions between parasitoids, hyperparasitoids, and the 3 aphid species. This was the first time that many of these species have been characterized and demonstrates the application of novel approaches to analyze the aphid-parasitoid food webs in pecans and other tree crop systems.},
}

Animals
*Aphids/parasitology/genetics
*Food Chain
*Host-Parasite Interactions
Carya/parasitology
DNA Barcoding, Taxonomic
Wasps/physiology/genetics

@article {pmid38989789,
year = {2024},
author = {Ansai, E and Nitta, M and Saito, T and Kojima, Y and Waki, T},
title = {The first intermediate host of the invasive frog trematode Glypthelmins quieta in Japan.},
journal = {Diseases of aquatic organisms},
volume = {159},
number = {},
pages = {9-14},
doi = {10.3354/dao03799},
pmid = {38989789},
issn = {0177-5103},
mesh = {Animals ; Japan ; *Trematoda/genetics ; *Snails/parasitology ; Introduced Species ; Host-Parasite Interactions ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Glypthelmins quieta is a frog trematode native to North and Central America. This trematode was recently detected in Japan in the American bullfrog Lithobates catesbeianus, which was introduced from North America to Japan. As the first intermediate host of G. quieta, typically a snail, has not yet been identified in Japan, we conducted a snail survey in eastern Japan to screen for an intermediate host using DNA barcoding based on the nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1. We sampled 3 different snail species, Orientogalba ollula, Physella acuta, and Sinotaia quadrata histrica (157 individuals in total), and only the freshwater snail Physella acuta, which is also believed to have been introduced from North America to Japan, had sporocysts of G. quieta in its hepatopancreas. The introduction of the intermediate and definitive hosts from North America may have facilitated the invasion of G. quieta into Japan.},
}

Animals
Japan
*Trematoda/genetics
*Snails/parasitology
Introduced Species
Host-Parasite Interactions
RNA, Ribosomal, 28S/genetics

@article {pmid38988805,
year = {2024},
author = {, and Bragard, C and Baptista, P and Chatzivassiliou, E and Di Serio, F and Gonthier, P and Jaques Miret, JA and Justesen, AF and Magnusson, CS and Milonas, P and Navas-Cortes, JA and Parnell, S and Potting, R and Reignault, PL and Stefani, E and Thulke, HH and Van der Werf, W and Vicent Civera, A and Yuen, J and Zappalà, L and Grégoire, JC and Malumphy, C and Gobbi, A and Golic, D and Kertesz, V and Sfyra, O and MacLeod, A},
title = {Pest categorisation of Monema flavescens.},
journal = {EFSA journal. European Food Safety Authority},
volume = {22},
number = {7},
pages = {e8831},
pmid = {38988805},
issn = {1831-4732},
abstract = {The EFSA Panel on Plant Health performed a pest categorisation of Monema flavescens (Lepidoptera, Limacodidae), following the commodity risk assessment of Acer palmatum plants grafted on A. davidii from China, in which M. flavescens was identified as a pest of possible concern to the European Union. This species can be identified by morphological taxonomic keys and by barcoding. The adults of the overwintering generation emerge from late June to late August. The eggs are laid in groups on the underside of the host-plant leaves, on which the larvae feed throughout their six to eight larval instars. Pupation occurs in ovoid cocoons at the junction between twigs and branches, or on the trunk. Overwintering occurs as fully grown larvae or prepupae in their cocoon. There are one or two generations per year. M. flavescens is polyphagous and feeds on broadleaves; it has been reported on 51 plant species belonging to 24 families. It mainly occurs in Asia (Bhutan, China, the Democratic People's Republic of Korea, Japan, Nepal, the Republic of Korea), Russia (Eastern Siberia) and Taiwan. It is also present in the USA (Massachusetts). The pest's flight capacities are unknown. The main pathway for entry and spread is plants for planting with cocoons attached. This is partially closed by prohibition of some hosts. In several EU member states climatic conditions are conducive for establishment and many host plants are widespread. Introduction of M. flavescens may result in defoliations influencing tree health and forest diversity. The caterpillars also have urticating spines affecting human health. Phytosanitary measures are available to reduce the likelihood of entry, establishment and spread, and there is a definite potential for classical biological control. Recognising that natural enemies prevent M. flavescens being regarded as a pest in Asia, there is uncertainty regarding the magnitude of potential impact in EU depending on the influence of natural enemies. All criteria assessed by EFSA for consideration as a potential quarantine pest are met.},
}

@article {pmid38988182,
year = {2024},
author = {Chen, MY and Tu, YC and Shyu, HY and Lin, TA and Juan, CP and Wu, FC},
title = {Using rDNA ITS2 barcoding to identify kratom (Mitragyna speciosa) from the genus Mitragyna and Neolamarckia cadamba.},
journal = {Electrophoresis},
volume = {},
number = {},
pages = {},
doi = {10.1002/elps.202400003},
pmid = {38988182},
issn = {1522-2683},
abstract = {This study collected 80 samples of suspected kratom plant powder. A polymerase chain reaction sequence analysis was conducted using two sets of DNA barcode primers for plant ribosomal (r)DNA internal transcribed spacers (ITSs), namely, ITS3/ITS4 and ITS-p3/ITS-u4. Among the 80 samples, 40 were analyzed using the ITS3/ITS4 primer pair, and then DNA sequences were subjected to a National Center for Biotechnology Information-Basic Local Alignment Search Tool (NCBI-BLAST) comparison. Results showed that 29 samples had a 100% match (364/364) with Mitragyna speciosa (kratom), and 6 samples had a 99.73% match (363/364) with M. speciosa, whereas 5 samples had disordered and unreadable sequences. The 5 unreadable samples and an additional 40 suspected kratom samples were then analyzed using the ITS-p3/ITS-u4 primer pair, followed by an NCBI-BLAST comparison. Among these, 32 samples had a 100% match (404/404) with M. speciosa, and 11 samples had a 99.75% match (403/404) with M. speciosa. Among the samples with sequences matching M. speciosa, three distinct types were observed (no variance/404, 287M/404, and 287A/404). One sample had a 99.51% match (404/406) with Neolamarckia cadamba, and another sample had a sequencing length of 305 bp, with 25 positions showing mixed base pairs, indicating a mixture of different species. Analysis of the mixed base pair pattern suggested a possible mixture of M. speciosa and N. cadamba. Actually, M. speciosa and N. cadamba have very similar external morphologies. This indicates that the ITS-p3/ITS-u4 primer pair is effective in distinguishing mixtures of M. speciosa and N. cadamba and is thus more suitable than ITS3/ITS4 for identifying and analyzing samples of suspected kratom plant powder.},
}

@article {pmid38987689,
year = {2024},
author = {Wu, X and Wang, M and Li, X and Chen, Y and Liao, Z and Zhang, D and Wen, Y and Wang, S},
title = {Identification and characterization of a new species of Taxus - Taxus qinlingensis by multiple taxonomic methods.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {658},
pmid = {38987689},
issn = {1471-2229},
support = {CX2018B435//Hunan Provincial Innovation Foundation for Postgraduate/ ; 31470666//National Natural Science Foundation of China/ ; },
mesh = {*Taxus/genetics/anatomy & histology/classification ; *Phylogeny ; *Plant Leaves/anatomy & histology/genetics ; *DNA Barcoding, Taxonomic ; China ; DNA, Plant/genetics ; Phenotype ; },
abstract = {BACKGROUND: The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.

RESULTS: Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500 m.

CONCLUSIONS: Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen & X. T. Wu, sp. nov.},
}

*Taxus/genetics/anatomy & histology/classification
*Phylogeny
*Plant Leaves/anatomy & histology/genetics
*DNA Barcoding, Taxonomic
China
DNA, Plant/genetics
Phenotype

@article {pmid38985195,
year = {2024},
author = {Corradini, B and Gianfreda, D and Ferri, G and Ferrari, F and Borciani, I and Santunione, AL and Cecchi, R},
title = {Forensic species identification: practical guide for animal and plant DNA analysis.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {38985195},
issn = {1437-1596},
abstract = {The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.},
}

@article {pmid38984293,
year = {2024},
author = {Ollinger, N and Malachova, A and Sulyok, M and Krska, R and Weghuber, J},
title = {Mycotoxin contamination in moldy slices of bread is mostly limited to the immediate vicinity of the visible infestation.},
journal = {Food chemistry: X},
volume = {23},
number = {},
pages = {101563},
pmid = {38984293},
issn = {2590-1575},
abstract = {Bread is an important staple food that is susceptible to spoilage, making it one of the most wasted foods. To determine the safety of partially moldy bread, five types of bread were inoculated with common mold species. After incubation, the metabolite profile was determined in and under the inoculation spot, as well as at a lateral distance of 3 cm from the moldy spot. The result showed that the metabolites were exclusively concentrated in the inoculation area and directly below the inoculation area. The only exception was citrinin, a mycotoxin produced by Penicillia such as Penicillium citrinum, which was detected in almost all tested bread areas when inoculated with the corresponding strains. The results of our study suggest that the removal of moldy parts may be a solution to reduce food waste if the remaining bread is to be used, for example for insect farming to produce animal feed.},
}

@article {pmid38982951,
year = {2024},
author = {Yang, S and Xu, Y and Lin, R and Feng, X and Wang, K and Wang, Z and Cui, K and Chen, S and Wang, Z and Wang, X and Chen, S and Zhang, W and Zhu, C and Gao, Z},
title = {Conformation-Driven Responsive 1D and 2D Lanthanide-Metal-Organic Framework Heterostructures for High-Security Photonic Barcodes.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2402890},
doi = {10.1002/smll.202402890},
pmid = {38982951},
issn = {1613-6829},
support = {22275104//National Natural Science Foundation of China/ ; ZR2021YQ06//Shandong Provincial Natural Science Foundation/ ; tsqn202306255//Taishan Scholar Program of Shandong Province/ ; kq2206026//The Training Program for Excellent Young Innovators of Changsha/ ; },
abstract = {Development of luminescent segmented heterostructures featuring multiple spatial-responsive blocks is important to achieve miniaturized photonic barcodes toward anti-counterfeit applications. Unfortunately, dynamic manipulation of the spatial color at micro/nanoscale still remains a formidable challenge. Here, a straightforward strategy is proposed to construct spatially varied heterostructures through amplifying the conformation-driven response in flexible lanthanide-metal-organic frameworks (Ln-MOFs), where the thermally induced minor conformational changes in organic donors dramatically modulate the photoluminescence of Ln acceptors. Notably, compositionally and structurally distinct heterostructures (1D and 2D) are further constructed through epitaxial growth of multiple responsive MOF blocks benefiting from the isomorphous Ln-MOF structures. The thermally controlled emissive colors with distinguishable spectra carry the fingerprint information of a specific heterostructure, thus allowing for the effective construction of smart photonic barcodes with spatially responsive characteristics. The results will deepen the understanding of the conformation-driven responsive mechanism and also provide guidance to fabricate complex stimuli-responsive hierarchical microstructures for advanced optical recording and high-security labels.},
}

@article {pmid38979326,
year = {2024},
author = {Hotinger, JA and Campbell, IW and Hullahalli, K and Osaki, A and Waldor, MK},
title = {Quantification of Salmonella enterica serovar Typhimurium Population Dynamics in Murine Infection Using a Highly Diverse Barcoded Library.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.28.601246},
pmid = {38979326},
issn = {2692-8205},
abstract = {UNLABELLED: Murine models are often used to study the pathogenicity and dissemination of the enteric pathogen Salmonella enterica serovar Typhimurium. Here, we quantified S. Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverse S . Typhimurium barcoded library containing ∼55,000 unique strains distinguishable by genomic barcodes by enumerating S . Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen's colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed that Salmonella re-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding of Salmonella population dynamics.

SIGNIFICANCE STATEMENT: Salmonella is a prevalent food-borne pathogen that infects hundreds of millions of people worldwide. Here, we created a highly complex barcoded Salmonella enterica serovar Typhimurium library containing ∼55,000 barcodes to further understand and quantify Salmonella population dynamics in experimental murine infection. Through comparisons of barcode abundance and frequency in different samples and following different routes of inoculation, we quantify key facets of Salmonella infection, including bottleneck sizes and dissemination patterns, and uncover hidden routes of spread that drive heterogeneity in infection outcome. These observations provide a detailed map of Salmonella infection and demonstrate the power of high-diversity barcoded libraries in deciphering microbial population dynamics.},
}

@article {pmid38979006,
year = {2024},
author = {Ren, J and Ren, L and Zhang, R},
title = {Delimiting species, revealing cryptic diversity, and population divergence in Qinghai-Tibet Plateau weevils through DNA barcoding.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11592},
pmid = {38979006},
issn = {2045-7758},
abstract = {The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.},
}

@article {pmid38979002,
year = {2024},
author = {Nakagawa, K and Ogino, K and Katoh, TK and Kono, N},
title = {Species identification of livefood flightless fly (Torinido-shoujoubae) through DNA barcoding.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11622},
pmid = {38979002},
issn = {2045-7758},
abstract = {Torinido-shoujoubae, as it is called in Japanese, is a flightless Drosophila sp. that is sold commercially in Japan. This Drosophila sp. is often used as feeds for model organisms such as reptiles and spiders. There is no scientific name provided for the fruit fly that is known as Torinido-shoujoubae, as well as any historical background or data behind this species. There has been a previous study that was conducted through morphological characteristics analysis of the body as well as the male copulatory organ and has been estimated as Drosophila hydei. The objective of this study was to determine the species of this unidentified fly known as Torinido-shoujoubae based on a molecular evidence with a DNA barcoding. Samples were purchased from four separate suppliers to examine whether there are any differences between them. COI regions were amplified using PCR and the sequenced results were aligned against two databases, NCBI and BOLD. Torinido-shoujoubae samples provided from all suppliers were confirmed to be D. hydei.},
}

@article {pmid38973066,
year = {2024},
author = {Kumano, S and Tanaka, K and Akahori, R and Yanagiya, A and Nojima, A},
title = {Using peptide barcodes for simultaneous profiling of protein expression from mRNA.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {38},
number = {18},
pages = {e9867},
doi = {10.1002/rcm.9867},
pmid = {38973066},
issn = {1097-0231},
support = {//Hitachi Ltd/ ; //ARCALIS Inc./ ; },
mesh = {*RNA, Messenger/genetics/analysis ; *Green Fluorescent Proteins/genetics/chemistry/metabolism ; *Peptides/chemistry/analysis/genetics/metabolism ; Humans ; Mass Spectrometry/methods ; Gene Expression Profiling/methods ; },
abstract = {RATIONALE: mRNA technology has begun to play a significant role in the areas of therapeutic intervention and vaccine development. However, optimizing the mRNA sequence that influences protein expression levels is a resource-intensive and time-consuming process. This study introduces a new method to accelerate the selection of sequences of mRNA for optimal protein expression.

METHODS: We designed the mRNA sequences in such a way that a unique peptide barcode, corresponding to each mRNA sequence, is attached to the expressed protein. These barcodes, cleaved off by a protease and simultaneously quantified by mass spectrometry, reflect the protein expression, enabling a parallel analysis. We validated this method using two mRNAs, each with different untranslated regions (UTRs) but encoding enhanced green fluorescence protein (eGFP), and investigated whether the peptide barcodes could analyze the differential eGFP expression levels.

RESULTS: The fluorescence intensity of eGFP, a marker of its expression level, has shown noticeable changes between the two UTR sequences in mRNA-transfected cells when measured using flow cytometry. This suggests alterations in the expression level of eGFP due to the influence of different UTR sequences. Furthermore, the quantified amount of peptide barcodes that were released from eGFP showed consistent patterns with these changes.

CONCLUSIONS: The experimental findings suggest that peptide barcodes serve as a valuable tool for assessing protein expression levels. The process of mRNA sequence selection, aimed at maximizing protein expression, can be enhanced by the parallel analysis of peptide barcodes using mass spectrometry.},
}

*RNA, Messenger/genetics/analysis
*Green Fluorescent Proteins/genetics/chemistry/metabolism
*Peptides/chemistry/analysis/genetics/metabolism
Humans
Mass Spectrometry/methods
Gene Expression Profiling/methods

@article {pmid38972989,
year = {2024},
author = {Ng, DYM and Sun, W and Sit, THC and Brackman, CJ and Tse, ACN and Bui, CHT and Tang, AWY and Wong, ANC and Tsang, ATL and Koo, JCT and Cheng, SMS and Peiris, M and Chin, AWH and Poon, LLM},
title = {Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong.},
journal = {Virology journal},
volume = {21},
number = {1},
pages = {153},
pmid = {38972989},
issn = {1743-422X},
support = {U01AI151810//Division of Microbiology and Infectious Diseases/ ; T11-705/21-N//Research Grants Council, University Grants Committee/ ; },
mesh = {Animals ; Hong Kong ; *Phylogeny ; *Genetic Variation ; *Birds/virology ; *Genome, Viral ; *Feces/virology ; *Astroviridae Infections/veterinary/virology ; Animals, Wild/virology ; Bird Diseases/virology ; High-Throughput Nucleotide Sequencing ; Avastrovirus/genetics/classification/isolation & purification ; RNA, Viral/genetics ; Open Reading Frames ; Astroviridae/genetics/isolation & purification/classification ; },
abstract = {Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.},
}

Animals
Hong Kong
*Phylogeny
*Genetic Variation
*Birds/virology
*Genome, Viral
*Feces/virology
*Astroviridae Infections/veterinary/virology
Animals, Wild/virology
Bird Diseases/virology
High-Throughput Nucleotide Sequencing
Avastrovirus/genetics/classification/isolation & purification
RNA, Viral/genetics
Open Reading Frames
Astroviridae/genetics/isolation & purification/classification

@article {pmid38972540,
year = {2024},
author = {Mizuno, T and Tokoro, M and Yagi, T and Wada, E and Yamadori, I and Arai, M},
title = {Infant gastrointestinal canthariasis caused by cigarette beetle (Lasioderma serricorne).},
journal = {Parasitology international},
volume = {},
number = {},
pages = {102921},
doi = {10.1016/j.parint.2024.102921},
pmid = {38972540},
issn = {1873-0329},
abstract = {Diseases caused by beetle larvae infestation are known as intestinal canthariasis. Canthariasis from the cigarette beetle, Lasioderma serricorne, is quite rare; however, with the accumulation of genetic references, such cases of accidental pseudo-parasitism have been increasingly recognized. Here, we describe a case of asymptomatic gastrointestinal passage of L. serricorne in a 4-year-old male. Larval identification was conducted by PCR-sequencing targeting cytochrome c oxidase subunit 1 using DNA extracted from the larvae. Due to the difficulty of differential identification of beetles using larval morphology, DNA barcoding is essential.},
}

@article {pmid38969342,
year = {2024},
author = {Serio, RN and Scheben, A and Lu, B and Gargiulo, DV and Patruno, L and Buckholtz, CL and Chaffee, RJ and Jibilian, MC and Persaud, SG and Staklinski, SJ and Hassett, R and Brault, LM and Ramazzotti, D and Barbieri, CE and Siepel, AC and Nowak, DG},
title = {Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-23-1332},
pmid = {38969342},
issn = {2159-8290},
abstract = {The patterns by which primary tumors spread to metastatic sites remain poorly understood. Here, we define patterns of metastatic seeding in prostate cancer (PCa) using a novel injection-based mouse model - EvoCaP (Evolution in Cancer of the Prostate), featuring aggressive metastatic cancer to bone, liver, lungs, and lymph nodes. To define migration histories between primary and metastatic sites, we used our EvoTraceR pipeline to track distinct tumor clones containing recordable barcodes. We detected widespread intratumoral heterogeneity from the primary tumor in metastatic seeding, with few clonal populations (CPs) instigating most migration. Metastasis-to-metastasis seeding was uncommon, as most cells remained confined within the tissue. Migration patterns in our model were congruent with human PCa seeding topologies. Our findings support the view of metastatic PCa as a systemic disease driven by waves of aggressive clones expanding their niche, infrequently overcoming constraints that otherwise keep them confined in the primary or metastatic site.},
}

@article {pmid38968228,
year = {2024},
author = {Chaumeau, V and Piarroux, M and Kulabkeeree, T and Sawasdichai, S and Inta, A and Watthanaworawit, W and Nosten, F and Piarroux, R and Nabet, C},
title = {Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0305167},
pmid = {38968228},
issn = {1932-6203},
mesh = {*Anopheles/genetics/classification ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Animals ; Mosquito Vectors/genetics/classification ; Malaria/transmission ; Asia, Southeastern ; Species Specificity ; DNA Barcoding, Taxonomic/methods ; Thailand ; Southeast Asian People ; },
abstract = {Malaria elimination in Southeast Asia remains a challenge, underscoring the importance of accurately identifying malaria mosquitoes to understand transmission dynamics and improve vector control. Traditional methods such as morphological identification require extensive training and cannot distinguish between sibling species, while molecular approaches are costly for extensive screening. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and cost-effective tool for Anopheles species identification, yet its current use is limited to few specialized laboratories. This study aimed to develop and validate an online reference database for MALDI-TOF MS identification of Southeast Asian Anopheles species. The database, constructed using the in-house data analysis pipeline MSI2 (Sorbonne University), comprised 2046 head mass spectra from 209 specimens collected at the Thailand-Myanmar border. Molecular identification via COI and ITS2 DNA barcodes enabled the identification of 20 sensu stricto species and 5 sibling species complexes. The high quality of the mass spectra was demonstrated by a MSI2 median score (min-max) of 61.62 (15.94-77.55) for correct answers, using the best result of four technical replicates of a test panel. Applying an identification threshold of 45, 93.9% (201/214) of the specimens were identified, with 98.5% (198/201) consistency with the molecular taxonomic assignment. In conclusion, MALDI-TOF MS holds promise for malaria mosquito identification and can be scaled up for entomological surveillance in Southeast Asia. The free online sharing of our database on the MSI2 platform (https://msi.happy-dev.fr/) represents an important step towards the broader use of MALDI-TOF MS in malaria vector surveillance.},
}

*Anopheles/genetics/classification
*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Animals
Mosquito Vectors/genetics/classification
Malaria/transmission
Asia, Southeastern
Species Specificity
DNA Barcoding, Taxonomic/methods
Thailand
Southeast Asian People

@article {pmid38966247,
year = {2024},
author = {Turanov, SV and Koltsova, MA and Rutenko, OA},
title = {Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11631},
doi = {10.1002/ece3.11631},
pmid = {38966247},
issn = {2045-7758},
abstract = {Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at the within-species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode.},
}

@article {pmid38965520,
year = {2024},
author = {, },
title = {Retraction Note: DNA barcoding detects contamination and substitution in North American herbal products.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {279},
doi = {10.1186/s12916-024-03504-x},
pmid = {38965520},
issn = {1741-7015},
}

@article {pmid38965405,
year = {2024},
author = {LeSavage, BL and Zhang, D and Huerta-López, C and Gilchrist, AE and Krajina, BA and Karlsson, K and Smith, AR and Karagyozova, K and Klett, KC and Huang, MS and Long, C and Kaber, G and Madl, CM and Bollyky, PL and Curtis, C and Kuo, CJ and Heilshorn, SC},
title = {Engineered matrices reveal stiffness-mediated chemoresistance in patient-derived pancreatic cancer organoids.},
journal = {Nature materials},
volume = {},
number = {},
pages = {},
pmid = {38965405},
issn = {1476-4660},
support = {R01 EB027171/EB/NIBIB NIH HHS/United States ; DP1CA238296//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U01CA217851//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U01CA217851//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U54CA224081//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; CBET 2033302//National Science Foundation (NSF)/ ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is characterized by its fibrotic and stiff extracellular matrix. However, how the altered cell/extracellular-matrix signalling contributes to the PDAC tumour phenotype has been difficult to dissect. Here we design and engineer matrices that recapitulate the key hallmarks of the PDAC tumour extracellular matrix to address this knowledge gap. We show that patient-derived PDAC organoids from three patients develop resistance to several clinically relevant chemotherapies when cultured within high-stiffness matrices mechanically matched to in vivo tumours. Using genetic barcoding, we find that while matrix-specific clonal selection occurs, cellular heterogeneity is not the main driver of chemoresistance. Instead, matrix-induced chemoresistance occurs within a stiff environment due to the increased expression of drug efflux transporters mediated by CD44 receptor interactions with hyaluronan. Moreover, PDAC chemoresistance is reversible following transfer from high- to low-stiffness matrices, suggesting that targeting the fibrotic extracellular matrix may sensitize chemoresistant tumours. Overall, our findings support the potential of engineered matrices and patient-derived organoids for elucidating extracellular matrix contributions to human disease pathophysiology.},
}

@article {pmid38963889,
year = {2024},
author = {Wu, R and Liu, L and Zhang, L and Bogan, AE and Niu, G and Jin, D and Wu, X and Liu, X},
title = {Taxonomic revision of two species in the genus Ptychorhynchus Simpson, 1900 (Bivalvia: Unionidae: Gonideinae), with description of a new species.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS24014},
pmid = {38963889},
issn = {1447-2600},
mesh = {Animals ; *Phylogeny ; *Unionidae/genetics/classification/anatomy & histology ; *Species Specificity ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Accurate identification and precise classification of freshwater mussel species that are among the most threatened freshwater taxa in the world, play a crucial role in informing conservation and management efforts for these organisms. However, due to the variability in shell morphology, relying solely on shell characteristics for species taxonomy poses significant challenges, thereby impeding effective conservation planning and management. The freshwater mussel genus Ptychorhynchus Simpson, 1900 is one such group in need of study. We integrate molecular phylogeny, shell morphology and soft-body anatomy to examine the classification of Ptychorhynchus denserugata (Haas, 1910) and Ptychorhynchus resupinatus (von Martens, 1902). The COI barcoding data support the clustering of P. denserugata and Nodularia douglasiae within a single clade, and P. denserugata shares the diagnostic feature of the genus Nodularia , i.e. knobs or bumps on the inner mantle surface in the excurrent aperture. Therefore, by integrating molecular data and anatomical characteristics, we confirm that the nominal species P. denserugata syn. nov. is a new synonym for N. douglasiae . The multi-locus (COI + ND1 + 16S rRNA + 18S rRNA + 28S rRNA) phylogeny and mitochondrial phylogenomics support the transfer of P. resupinatus from Ptychorhynchus to the newly elevated genus Cosmopseudodon stat. rev., as Cosmopseudodon resupinatus stat. rev. that is still considered the designated type species. We also describe a new species based on integrative taxonomy, i.e. Cosmopseudodon wenshanensis sp. nov. The comprehensive understanding of the taxonomy and diversity of the revised Cosmopseudodon species, and shell heteromorphism of N. douglasiae (=P. denserugata syn. nov.), will serve as a crucial foundation for further scientific assessment and conservation strategies pertaining to these taxa. ZooBank: urn:lsid:zoobank.org:pub:E48968B1-DF0F-42AD-8F31-B8C95F23CE57.},
}

Animals
*Phylogeny
*Unionidae/genetics/classification/anatomy & histology
*Species Specificity
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic

@article {pmid38962025,
year = {2024},
author = {Mamadashvili, G and Brin, A and Chumak, M and Diedus, V and Drössler, L and Förster, B and Georgiev, KB and Ghrejyan, T and Hleb, R and Kalashian, M and Kamburov, I and Karagyan, G and Kevlishvili, J and Khutsishvili, Z and Larrieu, L and Mazmanyan, M and Petrov, PI and Tabunidze, L and Bässler, C and Müller, J},
title = {Drivers of wood-inhabiting fungal diversity in European and Oriental beech forests.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11660},
pmid = {38962025},
issn = {2045-7758},
abstract = {The hyperdiverse wood-inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood-drilling samples in 18 forests from France to Armenia and identified fungi by meta-barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old-growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old-growth forests.},
}

@article {pmid38962021,
year = {2024},
author = {Ma, Y and López-Pujol, J and Yan, D and Zhou, Z and Deng, Z and Niu, J},
title = {Complete chloroplast genomes of the hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11677},
pmid = {38962021},
issn = {2045-7758},
abstract = {The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".},
}

@article {pmid38959129,
year = {2024},
author = {Luo, J and Walsh, E and Faulborn, A and Gao, K and White, J and Zhang, N},
title = {Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/00275514.2024.2363084},
pmid = {38959129},
issn = {1557-2536},
abstract = {Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.},
}

@article {pmid38958078,
year = {2024},
author = {Xu, Z and Chen, L and Lin, X and Lyu, Y and Zhou, M and Chen, H and Zhang, H and Zhang, T and Chen, Y and Suo, Y and Liang, Q and Qin, Z and Wang, Y},
title = {Single Nucleus Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Gliomas.},
journal = {Small methods},
volume = {},
number = {},
pages = {e2301801},
doi = {10.1002/smtd.202301801},
pmid = {38958078},
issn = {2366-9608},
support = {32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; 82200977//National Natural Science Foundation of China/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//"Pioneer" R&D programs of Zhejiang Province/ ; 2024SSYS0022//Key R&D Program of Zhejiang/ ; Y-zai2021/qn-0204//Beijing Xisike Clinical Oncology Research Foundation/ ; Y-zai2021/zd-0207//Beijing Xisike Clinical Oncology Research Foundation/ ; },
abstract = {Gliomas, the predominant form of brain cancer, comprise diverse malignant subtypes with limited curative therapies available. The insufficient understanding of their molecular diversity and evolutionary processes hinders the advancement of new treatments. Technical complexities associated with formalin-fixed paraffin-embedded (FFPE) clinical samples hinder molecular-level analyses of gliomas. Current single-cell RNA sequencing (scRNA-seq) platforms are inadequate for large-scale clinical applications. In this study, automated snRandom-seq is developed, a high-throughput single-nucleus total RNA sequencing platform optimized for archival FFPE samples. This platform integrates automated single-nucleus isolation and droplet barcoding systems with the random primer-based scRNA-seq chemistry, accommodating a broad spectrum of sample types. The automated snRandom-seq is applied to analyze 116 492 single nuclei from 17 FFPE samples of various glioma subtypes, including rare clinical samples and matched primary-recurrent glioblastomas (GBMs). The study provides comprehensive insights into the molecular characteristics of gliomas at the single-cell level. Abundant non-coding RNAs (ncRNAs) with distinct expression profiles across different glioma clusters and uncovered promising recurrence-related targets and pathways in primary-recurrent GBMs are identified. These findings establish automated snRandom-seq as a robust tool for scRNA-seq of FFPE samples, enabling exploration of molecular diversities and tumor evolution. This platform holds significant implications for large-scale integrative and retrospective clinical research.},
}

@article {pmid38956928,
year = {2024},
author = {Doorenweerd, C and San Jose, M and Leblanc, L and Barr, N and Geib, SM and Chung, AYC and Dupuis, JR and Ekayanti, A and Fiegalan, E and Hemachandra, KS and Hossain, MA and Huang, CL and Hsu, YF and Morris, KY and Maryani A Mustapeng, A and Niogret, J and Pham, TH and Thi Nguyen, N and Sirisena, UGAI and Todd, T and Rubinoff, D},
title = {Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13987},
doi = {10.1111/1755-0998.13987},
pmid = {38956928},
issn = {1755-0998},
support = {8130-0565//United States Department of Agriculture/ ; 8130-0665//United States Department of Agriculture/ ; 8130-0893//United States Department of Agriculture/ ; HAW00942-H//United States Department of Agriculture/ ; },
abstract = {The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.},
}

@article {pmid38955202,
year = {2024},
author = {Nath, A and Gangopadhayya, A and Ghuge, O and Kumar, S and Ramdasi, A and Karlekar, S and Sudeep, AB and Lole, KS},
title = {Determination of Species Identity and Genetic Diversity of Aedes aegypti and Other Medically Important Mosquitoes of India Using DNA Barcoding.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.23-0471},
pmid = {38955202},
issn = {1476-1645},
abstract = {Aedes aegypti-borne viruses (i.e., dengue, chikungunya, and Zika) have become endemic to India, posing a severe threat to public health. Vector control remains the mainstay of disease management due to nonavailability of licensed vaccines/therapeutics. Conventional morpho-taxonomical methods cannot differentiate between closely related sibling species or species complexes, and hence we evaluated two molecular markers, mitochondrial cytochrome c oxidase subunit 1 (Cox1) and nuclear DNA internal transcribed spacer 2 (-2) gene sequences, to characterize seven populations of Ae. aegypti and four medically important mosquito species (Aedes albopictus, Anopheles stephensi, Culex tritaeniorhyncus, and Culex murrelli). DNA extracted from the 11 mosquito populations (two mosquitoes per population) was polymerase chain reaction amplified, sequenced, and analyzed. Molecular characterization was found to be congruent with morphological identification, suggesting no variants or cryptic species exist in Ae. aegypti and the other mosquitoes studied. Phylogenetic analysis with sequences obtained with Cox1 gene of Ae. aegypti and other Aedes and non-Aedes mosquito species showed clustering of sequences from different species representing different clades, distinctly separating one taxon from the other, whereas ITS-2 sequences of Aedes aegypti from across the world clustered tightly. Nucleotide divergence values revealed a low percentage of intraspecies variation and a higher percentage of interspecies variation. The present study authenticates the applicability of Cox1 and ITS-2 in the precise identification of Ae. aegypti mosquitoes against cryptic or sibling species. Cox1 appeared to be a more reliable marker because it showed distinct clustering of mosquito species, and some sequence variations to represent genetic diversity.},
}

@article {pmid38949306,
year = {2024},
author = {Higgins, SA and Kara Murdoch, F and Clifton, JM and Brooks, JH and Fillinger, KL and Middleton, JK and Heater, BS},
title = {CRISPR-Cas9-mediated barcode insertion into Bacillus thuringiensis for surrogate tracking.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0000324},
doi = {10.1128/spectrum.00003-24},
pmid = {38949306},
issn = {2165-0497},
abstract = {UNLABELLED: The use of surrogate organisms can enable researchers to safely conduct research on pathogens and in a broader set of conditions. Being able to differentiate between the surrogates used in the experiments and background contamination as well as between different experiments will further improve research efforts. One effective approach is to introduce unique genetic barcodes into the surrogate genome and track their presence using the quantitative polymerase chain reaction (qPCR). In this report, we utilized the CRISPR-Cas9 methodology, which employs a single plasmid and a transformation step to insert five distinct barcodes into Bacillus thuringiensis, a well-established surrogate for Bacillus anthracis when Risk Group 1 organisms are needed. We subsequently developed qPCR assays for barcode detection and successfully demonstrated the stability of the barcodes within the genome through five cycles of sporulation and germination. Additionally, we conducted whole-genome sequencing on these modified strains and analyzed 187 potential Cas9 off-target sites. We found no correlation between the mutations observed in the engineered strains and the predicted off-target sites, suggesting this genome engineering strategy did not directly result in off-target mutations in the genome. This simple approach has the potential to streamline the creation of barcoded B. thuringiensis strains for use in future studies on surrogate genomes.

IMPORTANCE: The use of Bacillus anthracis as a biothreat agent poses significant challenges for public health and national security. Bacillus anthracis surrogates, like Bacillus thuringiensis, are invaluable tools for safely understanding Bacillus anthracis properties without the safety concerns that would arise from using a virulent strain of Bacillus anthracis. We report a simple method for barcode insertion into Bacillus thuringiensis using the CRISPR-Cas9 methodology and subsequent tracking by quantitative polymerase chain reaction (qPCR). Moreover, whole-genome sequencing data and CRISPR-Cas9 off-target analyses in Bacillus thuringiensis suggest that this gene-editing method did not directly cause unwanted mutations in the genome. This study should assist in the facile development of barcoded Bacillus thuringiensis surrogate strains, among other biotechnological applications in Bacillus species.},
}

@article {pmid38949302,
year = {2024},
author = {Kramara, J and Kim, M-J and Ollinger, TL and Ristow, LC and Wakade, RS and Zarnowski, R and Wellington, M and Andes, DR and Mitchell, AG and Krysan, DJ},
title = {Systematic analysis of the Candida albicans kinome reveals environmentally contingent protein kinase-mediated regulation of filamentation and biofilm formation in vitro and in vivo.},
journal = {mBio},
volume = {},
number = {},
pages = {e0124924},
doi = {10.1128/mbio.01249-24},
pmid = {38949302},
issn = {2150-7511},
abstract = {Protein kinases are critical regulatory proteins in both prokaryotes and eukaryotes. Accordingly, protein kinases represent a common drug target for a wide range of human diseases. Therefore, understanding protein kinase function in human pathogens such as the fungus Candida albicans is likely to extend our knowledge of its pathobiology and identify new potential therapies. To facilitate the study of C. albicans protein kinases, we constructed a library of 99 non-essential protein kinase homozygous deletion mutants marked with barcodes in the widely used SN genetic background. Here, we describe the construction of this library and the characterization of the competitive fitness of the protein kinase mutants under 11 different growth and stress conditions. We also screened the library for protein kinase mutants with altered filamentation and biofilm formation, two critical virulence traits of C. albicans. An extensive network of protein kinases governs these virulence traits in a manner highly dependent on the specific environmental conditions. Studies on specific protein kinases revealed that (i) the cell wall integrity MAPK pathway plays a condition-dependent role in filament initiation and elongation; (ii) the hyper-osmolar glycerol MAPK pathway is required for both filamentation and biofilm formation, particularly in the setting of in vivo catheter infection; and (iii) Sok1 is dispensable for filamentation in hypoxic environments at the basal level of a biofilm but is required for filamentation in normoxia. In addition to providing a new genetic resource for the community, these observations emphasize the environmentally contingent function of C. albicans protein kinases.IMPORTANCECandida albicans is one of the most common causes of fungal disease in humans for which new therapies are needed. Protein kinases are key regulatory proteins and are increasingly targeted by drugs for the treatment of a wide range of diseases. Understanding protein kinase function in C. albicans pathogenesis may facilitate the development of new antifungal drugs. Here, we describe a new library of 99 protein kinase deletion mutants to facilitate the study of protein kinases. Furthermore, we show that the function of protein kinases in two virulence-related processes, filamentation and biofilm formation, is dependent on the specific environmental conditions.},
}

@article {pmid38948916,
year = {2024},
author = {Dreyling, L and Boch, S and Lumbsch, HT and Schmitt, I},
title = {Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces.},
journal = {MycoKeys},
volume = {106},
number = {},
pages = {153-172},
pmid = {38948916},
issn = {1314-4049},
abstract = {Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.},
}

@article {pmid38948467,
year = {2024},
author = {Shen, L and Zhang, M and Qiu, Y and Yang, L and Lu, Y and Li, H and Zhang, L and Tang, F and Wang, F and Zhu, C and Bao, H and Ding, Y},
title = {DNA barcoding combined with high-resolution melting analysis to discriminate rhubarb species and its traditional Chinese patent medicines.},
journal = {Frontiers in pharmacology},
volume = {15},
number = {},
pages = {1371890},
pmid = {38948467},
issn = {1663-9812},
abstract = {Introduction: Rhubarb is a frequently used and beneficial traditional Chinese medicine. Wild resources of these plants are constantly being depleted, meaning that rhubarb products have been subjected to an unparalleled level of adulteration. Consequentially, reliable technology is urgently required to verify the authenticity of rhubarb raw materials and commercial botanical drugs. Methods: In this study, the barcode-DNA high-resolution melting (Bar-HRM) method was applied to characterize 63 rhubarb samples (five Polygonaceae species: Rheum tanguticum, Rh. palmatum, Rh. officinale, Rumex japonicus and Ru. sp.) and distinguish the rhubarb contents of 24 traditional Chinese patent medicine (TCPM) samples. Three markers, namely ITS2, rbcL and psbA-trnH, were tested to assess the candidate DNA barcodes for their effectiveness in distinguishing rhubarb from its adulterants. A segment from ITS2 was selected as the most suitable mini-barcode to identify the botanical drug rhubarb in TCPMs. Then, rhubarbs and TCPM samples were subjected to HRM analysis based on the ITS2 barcode. Results: Among the tested barcoding loci, ITS2 displayed abundant sites of variation and was effective in identifying Polygonaceae species and their botanical origins. HRM analysis based on the ITS2 mini-barcode region successfully distinguished the authenticity of five Polygonaceae species and eight batches of TCPMs. Of the 18 TCPM samples, 66.7 % (12 samples) were identified as containing Rh. tanguticum or Rh. officinale. However, 33.3 % were shown to consist of adulterants. Conclusions: These results demonstrated that DNA barcoding combined with HRM is a specific, suitable and powerful approach for identifying rhubarb species and TCPMs, which is crucial to guaranteeing the security of medicinal plants being traded internationally.},
}

@article {pmid38947432,
year = {2024},
author = {Frigerio, J and Campone, L and Giustra, MD and Buzzelli, M and Piccoli, F and Galimberti, A and Cannavacciuolo, C and Ouled Larbi, M and Colombo, M and Ciocca, G and Labra, M},
title = {Convergent technologies to tackle challenges of modern food authentication.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32297},
pmid = {38947432},
issn = {2405-8440},
abstract = {The authentication process involves all the supply chain stakeholders, and it is also adopted to verify food quality and safety. Food authentication tools are an essential part of traceability systems as they provide information on the credibility of origin, species/variety identity, geographical provenance, production entity. Moreover, these systems are useful to evaluate the effect of transformation processes, conservation strategies and the reliability of packaging and distribution flows on food quality and safety. In this manuscript, we identified the innovative characteristics of food authentication systems to respond to market challenges, such as the simplification, the high sensitivity, and the non-destructive ability during authentication procedures. We also discussed the potential of the current identification systems based on molecular markers (chemical, biochemical, genetic) and the effectiveness of new technologies with reference to the miniaturized systems offered by nanotechnologies, and computer vision systems linked to artificial intelligence processes. This overview emphasizes the importance of convergent technologies in food authentication, to support molecular markers with the technological innovation offered by emerging technologies derived from biotechnologies and informatics. The potential of these strategies was evaluated on real examples of high-value food products. Technological innovation can therefore strengthen the system of molecular markers to meet the current market needs; however, food production processes are in profound evolution. The food 3D-printing and the introduction of new raw materials open new challenges for food authentication and this will require both an update of the current regulatory framework, as well as the development and adoption of new analytical systems.},
}

@article {pmid38946964,
year = {2024},
author = {Rossouw, L and Ngcobo, N and Clouse, K and Nattey, C and Technau, KG and Maskew, M},
title = {Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.19.24309149},
pmid = {38946964},
abstract = {BACKGROUND: The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information.

METHODS: We explored an alternative method to examine patient files from a large administrative dataset in South Africa (the National Health Laboratory Services, or NHLS), by linking external data to the NHLS database using specimen barcodes associated with laboratory tests. This offers us with a deterministic way of performing data linkages without accessing demographic information. In this paper, we quantify the performance metrics of this approach.

RESULTS: The linkage of the large NHLS data to external hospital data using specimen barcodes achieved a 95% success. Out of the 1200 records in the validation sample, 87% were exact matches and 9% were matches with typographic correction. The remaining 5% were either complete mismatches or were due to duplicates in the administrative data.

CONCLUSIONS: The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective tool for deterministic linking in health data, and may provide a method of creating large, linked data sets without compromising patient confidentiality.},
}

@article {pmid38943817,
year = {2024},
author = {Piersanti, S and Rebora, M and Turchetti, B and Salerno, G and Ruscetta, M and Zucconi, L and D'Alò, F and Buzzini, P and Sannino, C},
title = {Microplastics in the diet of Hermetia illucens: Implications for development and midgut bacterial and fungal microbiota.},
journal = {Waste management (New York, N.Y.)},
volume = {186},
number = {},
pages = {259-270},
doi = {10.1016/j.wasman.2024.06.021},
pmid = {38943817},
issn = {1879-2456},
abstract = {In a world with a population exceeding 8 billion people and continuing to grow, pollution from food and plastic waste is causing long-term issues in ecosystems. Potential solutions may be found by exploiting insect-based bioconversion. In this context, we investigated the impact of polyvinyl chloride microparticles (PVC-MPs) on the development of Hermetia illucens (black soldier fly; BSF) and its midgut bacterial and fungal microbiota. The impact of PVC-MPs was evaluated feeding BSF larvae with a PVC-MPs-supplemented diet. The larvae exposed to different PVC-MPs concentrations (2.5%, 5%, 10% and 20% w/w) developed into adults with no significant increase in pupal mortality. Faster development and smaller pupae were observed when 20% PVC-MPs was provided. The BSF larvae ingest PVC-MPs, resulting in a reduction in MPs size. Larvae exposed to PVC-MPs did not exhibit differences in gut morphology. Regarding the impact of PVC-MPs on the structure of both bacterial and fungal communities, the overall alpha- and beta-diversity did not exhibit significant changes. However, the presence of PVC-MPs significantly affected the relative abundances of Enterobacteriaceae and Paenibacillaceae among the bacteria and of Dipodascaceae and Plectospharellaceae among the fungi (including yeast and filamentous life forms), suggesting that PVC-MP contamination has a taxa-dependent impact. These results indicate that BSF larvae can tolerate PVC-MPs in their diet, supporting the potential use of these insects in organic waste management, even in the presence of high levels of PVC-MP contamination.},
}

@article {pmid38943640,
year = {2024},
author = {Xiao, S and Yadav, S and Jayant, K},
title = {Probing multiplexed basal dendritic computations using two-photon 3D holographic uncaging.},
journal = {Cell reports},
volume = {43},
number = {7},
pages = {114413},
doi = {10.1016/j.celrep.2024.114413},
pmid = {38943640},
issn = {2211-1247},
abstract = {Basal dendrites of layer 5 cortical pyramidal neurons exhibit Na[+] and N-methyl-D-aspartate receptor (NMDAR) regenerative spikes and are uniquely poised to influence somatic output. Nevertheless, due to technical limitations, how multibranch basal dendritic integration shapes and enables multiplexed barcoding of synaptic streams remains poorly mapped. Here, we combine 3D two-photon holographic transmitter uncaging, whole-cell dynamic clamp, and biophysical modeling to reveal how synchronously activated synapses (distributed and clustered) across multiple basal dendritic branches are multiplexed under quiescent and in vivo-like conditions. While dendritic regenerative Na[+] spikes promote millisecond somatic spike precision, distributed synaptic inputs and NMDAR spikes regulate gain. These concomitantly occurring dendritic nonlinearities enable multiplexed information transfer amid an ongoing noisy background, including under back-propagating voltage resets, by barcoding the axo-somatic spike structure. Our results unveil a multibranch dendritic integration framework in which dendritic nonlinearities are critical for multiplexing different spatial-temporal synaptic input patterns, enabling optimal feature binding.},
}

@article {pmid38943021,
year = {2024},
author = {Farzad, N and Enninful, A and Bao, S and Zhang, D and Deng, Y and Fan, R},
title = {Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38943021},
issn = {1750-2799},
abstract = {Spatial epigenetic mapping of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue environment. Here we outline a complete procedure for two spatial epigenomic profiling methods: spatially resolved genome-wide profiling of histone modifications using in situ cleavage under targets and tagmentation (CUT&Tag) chemistry (spatial-CUT&Tag) and transposase-accessible chromatin sequencing (spatial-ATAC-sequencing) for chromatin accessibility. Both assays utilize in-tissue Tn5 transposition to recognize genomic DNA loci followed by microfluidic deterministic barcoding to incorporate spatial address codes. Furthermore, these two methods do not necessitate prior knowledge of the transcription or epigenetic markers for a given tissue or cell type but permit genome-wide unbiased profiling pixel-by-pixel at the 10 μm pixel size level and single-base resolution. To support the widespread adaptation of these methods, details are provided in five general steps: (1) sample preparation; (2) Tn5 transposition in spatial-ATAC-sequencing or antibody-controlled pA-Tn5 tagmentation in CUT&Tag; (3) library preparation; (4) next-generation sequencing; and (5) data analysis using our customed pipelines available at: https://github.com/dyxmvp/Spatial_ATAC-seq and https://github.com/dyxmvp/spatial-CUT-Tag . The whole procedure can be completed on four samples in 2-3 days. Familiarity with basic molecular biology and bioinformatics skills with access to a high-performance computing environment are required. A rudimentary understanding of pathology and specimen sectioning, as well as deterministic barcoding in tissue-specific skills (e.g., design of a multiparameter barcode panel and creation of microfluidic devices), are also advantageous. In this protocol, we mainly focus on spatial profiling of tissue region-specific epigenetic landscapes in mouse embryos and mouse brains using spatial-ATAC-sequencing and spatial-CUT&Tag, but these methods can be used for other species with no need for species-specific probe design.},
}

@article {pmid38940749,
year = {2024},
author = {Nolan, D and DaRoza, J and Brody, R and Ganta, K and Luzuriaga, K and Huston, C and Rosenthal, S and Lamers, S and Rose, R},
title = {Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1 gp160 Single Template Amplicons.},
journal = {AIDS research and human retroviruses},
volume = {},
number = {},
pages = {},
doi = {10.1089/AID.2024.0012},
pmid = {38940749},
issn = {1931-8405},
abstract = {Our goal was to assess the accuracy of next generation sequencing (NGS) compared to Sanger. We performed single genome amplification (SGA) of HIV-1 gp160 on extracted tissue DNA from two HIV+ individuals. Amplicons (n=30) were sequenced with Sanger, or re-amplified with barcoded primers and pooled before sequencing using Oxford Nanopore Technologies [ONT] and Pacific Bioscience [PB]. For each amplicon, a consensus sequence for NGS reads was obtained by (1) mapping reads to the Sanger sequence when available ("reference-based") or (2) mapping reads to a "pseudo-reference" sequence, i.e., a consensus sequence of a subset of NGS reads ("reference-free"). PB reads were clustered based on genetic similarity. A Sanger consensus sequence was obtained for 23/30 amplicons, for which all NGS consensus sequences were identical [n=9] or nearly identical [n=14] compared to Sanger. For the nine mismatches between Sanger/NGS, the nucleotide in the NGS sequence matched all other sequences from that patient. Of the 7/30 amplicons without a Sanger sequence, NGS sequences had (?)35 ambiguous calls in five amplicons, and 0 ambiguities in two amplicons. Analysis of the electropherograms showed failure of a single sequencing primer for the latter two amplicons (consistent with a single template), and overlapping peaks for the other five (consistent with multiple templates). Clustering results closely followed the Sanger/NGS consensus results, where amplicons derived from a single template also had a single cluster, and vice versa (with one exception, which could be the result of barcode misidentification). Representative sequences from the clusters contained 2 -13 differences compared to Sanger/NGS. In summary, we show that both ONT and PB can produce amplicon consensus sequences with similar or higher accuracy compared to Sanger, and importantly, without the need for a known reference sequence. Clustering could be useful in some circumstances to predict or confirm the presence of multiple starting templates.},
}

@article {pmid38935254,
year = {2024},
author = {Saathoff, S and Goodman, CL and Haas, E and Mettelmann, I and Stanley, D},
title = {A cell line derived from the black soldier fly, Hermetia illucens (Diptera: Stratiomyidae).},
journal = {In vitro cellular & developmental biology. Animal},
volume = {},
number = {},
pages = {},
pmid = {38935254},
issn = {1543-706X},
support = {5070-22000-038-000-D//Agricultural Research Service/ ; },
abstract = {Insect cell lines are effective tools used in industry and academia. For example, they are used in screening potential insecticides, in making certain proteins for biomedical applications, and in basic research into insect biology. So far, there are no cell lines derived from the black soldier fly, Hermetia illucens (BSF). This may become an issue because BSFs are employed in a range of industrial and household processes. BSFs are used in producing biodiesel, in developing cosmetics and skin creams, and in the production of some medicines and animal feeds. BSF larvae process waste streams from a variety of sources into food for some animals and are also used in household composting. Our BSF cell line, designated BCIRL-HiE0122021-SGS, was developed from eggs using the medium CLG#2 (50% L-15 + 50% EX-CELL 420, with 9% FBS and antibiotics), with many other media being tested. This cell line consists of attached cells with a variety of morphologies and its identity was authenticated using CO1 barcoding. A growth curve was generated and the resulting doubling time was 118 h. We quantified the fatty acid methyl esters (FAMES) and recorded the expected range of saturated, monounsaturated, and polyunsaturated FAMEs, with only trace levels of lauric acid being noted. The BSF cell line is available free of charge by request.},
}

@article {pmid38933488,
year = {2024},
author = {Kurata, S and Mano, S and Nakahama, N and Hirota, SK and Suyama, Y and Ito, M},
title = {Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e117014},
pmid = {38933488},
issn = {1314-2828},
abstract = {Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.},
}

@article {pmid38927697,
year = {2024},
author = {Kim, JE and Kim, KM and Kim, YS and Chung, GY and Che, SH and Na, CS},
title = {Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060761},
pmid = {38927697},
issn = {2073-4425},
support = {2021400B10-2425-CA02//Korea Forestry Promotion Institute/ ; },
mesh = {*Vitis/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; Evolution, Molecular ; Genetic Variation ; Republic of Korea ; Chloroplasts/genetics ; Genome, Plant ; },
abstract = {The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.},
}

*Vitis/genetics
*Genome, Chloroplast/genetics
*Phylogeny
Evolution, Molecular
Genetic Variation
Republic of Korea
Chloroplasts/genetics
Genome, Plant

@article {pmid38927627,
year = {2024},
author = {Li, H and Miao, X and Wang, R and Liao, Y and Wen, Y and Zhang, R and Lin, L},
title = {Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060691},
pmid = {38927627},
issn = {2073-4425},
support = {IRASCC01-02-02&02-02//Chinese Arctic and Antarctic Administration, Ministry of Natural Resources of the People's Republic of China/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Antarctic Regions ; *Electron Transport Complex IV/genetics ; Phylogeny ; Oceans and Seas ; },
abstract = {The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/genetics/classification
*Biodiversity
Antarctic Regions
*Electron Transport Complex IV/genetics
Phylogeny
Oceans and Seas

@article {pmid38927625,
year = {2024},
author = {Karbarz, M and Szlachcikowska, D and Zapał, A and Leśko, A},
title = {Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/genes15060689},
pmid = {38927625},
issn = {2073-4425},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; *Endangered Species ; Phylogeny ; DNA, Plant/genetics ; },
abstract = {Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.},
}

*DNA Barcoding, Taxonomic/methods
*Orchidaceae/genetics/classification
*Endangered Species
Phylogeny
DNA, Plant/genetics

@article {pmid38927245,
year = {2024},
author = {Sutula, M and Kakanay, A and Tussipkan, D and Dzhumanov, S and Manabayeva, S},
title = {Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers.},
journal = {Biology},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/biology13060365},
pmid = {38927245},
issn = {2079-7737},
support = {BR18574125//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; OR11465422//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.},
}

@article {pmid38926630,
year = {2024},
author = {Liu, H},
title = {Bacterial barcoding facilitates plant microbiome studies.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {38926630},
issn = {1740-1534},
}

@article {pmid38926392,
year = {2024},
author = {Li, S and Xv, Y and Sun, Y and Shen, Z and Hao, R and Yan, J and Liu, M and Liu, Z and Jing, T and Li, X and Zhang, X},
title = {Macrophage-derived CD36 + exosome subpopulations as novel biomarkers of Candida albicans infection.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14723},
pmid = {38926392},
issn = {2045-2322},
mesh = {*Exosomes/metabolism ; *Candida albicans ; *Biomarkers/metabolism ; *Macrophages/metabolism/microbiology/immunology ; *CD36 Antigens/metabolism ; *Candidiasis/diagnosis/microbiology/metabolism/immunology ; Humans ; Animals ; Mice ; },
abstract = {Invasive candidiasis (IC) is a notable healthcare-associated fungal infection, characterized by high morbidity, mortality, and substantial treatment costs. Candida albicans emerges as a principal pathogen in this context. Recent academic advancements have shed light on the critical role of exosomes in key biological processes, such as immune responses and antigen presentation. This burgeoning body of research underscores the potential of exosomes in the realm of medical diagnostics and therapeutics, particularly in relation to fungal infections like IC. The exploration of exosomal functions in the pathophysiology of IC not only enhances our understanding of the disease but also opens new avenues for innovative therapeutic interventions. In this investigation, we focus on exosomes (Exos) secreted by macrophages, both uninfected and those infected with C. albicans. Our objective is to extract and analyze these exosomes, delving into the nuances of their protein compositions and subgroups. To achieve this, we employ an innovative technique known as Proximity Barcoding Assay (PBA). This methodology is pivotal in our quest to identify novel biological targets, which could significantly enhance the diagnostic and therapeutic approaches for C. albicans infection. The comparative analysis of exosomal contents from these two distinct cellular states promises to yield insightful data, potentially leading to breakthroughs in understanding and treating this invasive fungal infection. In our study, we analyzed differentially expressed proteins in exosomes from macrophages and C. albicans -infected macrophages, focusing on proteins such as ACE2, CD36, CAV1, LAMP2, CD27, and MPO. We also examined exosome subpopulations, finding a dominant expression of MPO in the most prevalent subgroup, and a distinct expression of CD36 in cluster14. These findings are crucial for understanding the host response to C. albicans and may inform targeted diagnostic and therapeutic approaches. Our study leads us to infer that MPO and CD36 proteins may play roles in the immune escape mechanisms of C. albicans. Additionally, the CD36 exosome subpopulations, identified through our analysis, could serve as potential biomarkers and therapeutic targets for C. albicans infection. This insight opens new avenues for understanding the infection's pathology and developing targeted treatments.},
}

*Exosomes/metabolism
*Candida albicans
*Biomarkers/metabolism
*Macrophages/metabolism/microbiology/immunology
*CD36 Antigens/metabolism
*Candidiasis/diagnosis/microbiology/metabolism/immunology
Humans
Animals
Mice

@article {pmid38925122,
year = {2024},
author = {Zhang, Z and Melzer, ME and Arun, KM and Sun, H and Eriksson, CJ and Fabian, I and Shaashua, S and Kiani, K and Oren, Y and Goyal, Y},
title = {Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100592},
doi = {10.1016/j.xgen.2024.100592},
pmid = {38925122},
issn = {2666-979X},
abstract = {Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.},
}

@article {pmid38922410,
year = {2024},
author = {Sakae, K and Kawai, S and Kitagami, Y and Matsuo, N and Selosse, MA and Tanikawa, T and Matsuda, Y},
title = {Effects of fungicide treatments on mycorrhizal communities and carbon acquisition in the mixotrophic Pyrola japonica (Ericaceae).},
journal = {Mycorrhiza},
volume = {},
number = {},
pages = {},
pmid = {38922410},
issn = {1432-1890},
support = {2023-4099//Japan Science Society/ ; 25304026//Japan Society for the Promotion of Science/ ; },
abstract = {Pyrola japonica, a member of the family Ericaceae, is a mixotroph that grows on forest floors and obtains carbon (C) from both its photosynthesis and its mycorrhizal fungi. Its mycorrhizal community is dominated by Russulaceae. However, the mechanism of its C acquisition and its flexibility are not well understood. Our aim was to assess the impact of disturbance of the mycorrhizal fungal communities on C acquisition by P. japonica. We repeatedly applied a fungicide (Benomyl) to soils around P. japonica plants in a broad-leaved forest of central Japan, in order to disturb fungal associates near roots. After fungicide treatment, P. japonica roots were collected and subjected to barcoding by next-generation sequencing, focusing on the ITS2 region. The rate of mycorrhizal formation and α-diversity did not significantly change upon fungicide treatments. Irrespective of the treatments, Russulaceae represented more than 80% of the taxa. Leaves and seeds of the plants were analysed for [13]C stable isotope ratios that reflect fungal C gain. Leaf and seed δ[13]C values with the fungicide treatment were significantly lower than those with the other treatments. Thus the fungicide did not affect mycorrhizal communities in the roots, but disturbed mycorrhizal fungal pathways via extraradical hyphae, and resulted in a more photosynthetic behaviour of P. japonica for leaves and seeds.},
}

@article {pmid38921121,
year = {2024},
author = {Ganbaatar, B and Li, Q and Xi, O and Cao, H and Zhu, C},
title = {One Step beyond Species Description: Unveiling a Fine-Scale Diversity within the Genus Dzhanokmenia Kostjukov (Hymenoptera: Eulophidae).},
journal = {Insects},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/insects15060406},
pmid = {38921121},
issn = {2075-4450},
support = {32330013//the National Natural Science Foundation of China/ ; 2008DP173354//the Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences/ ; },
abstract = {Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar & Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia.},
}

@article {pmid38920364,
year = {2024},
author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E},
title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0080024},
doi = {10.1128/aem.00800-24},
pmid = {38920364},
issn = {1098-5336},
abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.},
}

@article {pmid38919770,
year = {2024},
author = {Vogel, J and Sauren, J and Peters, RS},
title = {New evidence on the identity of the European Helorus species (Hymenoptera, Proctotrupoidea, Heloridae).},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e122523},
pmid = {38919770},
issn = {1314-2828},
abstract = {BACKGROUND: Species of Helorus Latreille 1802 are rarely collected endoparasitoids of Chrysopidae larvae (Neuroptera). Previous work on the limits between the European species of this species-poor genus, based on morphology only, has left some uncertainties. Here, we approach these cases and revisit previous taxonomic decisions using freshly collected and museum material.

NEW INFORMATION: We generated the first large-scale Heloridae DNA barcode dataset, combined these with morphological data in an integrative taxonomic approach, and added information from studying all relevant type material. We found five species, Helorusanomalipes (Panzer, 1798), H.coruscus Haliday, 1857 stat. rev., H.nigripes Förster, 1856, H.ruficornis Förster, 1856, and H.striolatus Cameron, 1906, for which we provide an updated identification key. DNA barcode data are added to publicly available DNA barcode reference databases, for all species, except H.nigripes.},
}

@article {pmid38918858,
year = {2024},
author = {Cardoso, SF and Guesser, JVC and Rodrigues, AAF and Brazil, RP and Rona, LDP and Pitaluga, AN},
title = {Leishmania infantum detection in Nyssomyia neivai and dogs in Southern Brazil.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {269},
pmid = {38918858},
issn = {1756-3305},
support = {16/2014//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; Dogs ; *Leishmania infantum/genetics/isolation & purification ; Brazil/epidemiology ; *Psychodidae/parasitology/classification ; *Dog Diseases/parasitology/epidemiology ; *Leishmaniasis, Visceral/veterinary/epidemiology/parasitology/transmission ; Female ; *Insect Vectors/parasitology ; Polymerase Chain Reaction ; Male ; },
abstract = {BACKGROUND: The sand fly Nyssomyia neivai is one of the most abundant species in Southern Brazil. It is frequently found in areas that are foci of visceral leishmaniasis in the state of Santa Catarina, caused by Leishmania infantum. In this region, the main vector of L. infantum, Lutzomyia longipalpis, has not been detected. In the absence of L. longipalpis, this study aimed to identify the sand fly fauna and diagnose any potential Leishmania spp. infection in sand flies and in dogs in a region of Southern Brazil that experienced a recent canine visceral leishmaniasis outbreak.

METHODS: This report includes a survey of the sand fly fauna at the Zoonosis Control Center of the Municipality of Tubarão (Santa Catarina, Brazil). Molecular tests were conducted to investigate Leishmania spp. natural infection in sand flies using polymerase chain reaction (PCR). In positive females, in addition to morphological identification, molecular analysis through DNA barcoding was performed to determine the sand fly species. Additionally, the dogs were tested for the presence of Leishmania spp. using a non-invasive technique for the collection of biological material, to be assessed by PCR.

RESULTS: A total of 3419 sand flies, belonging to five genera, were collected. Nyssomyia neivai was the most abundant species (85.8%), followed by Migonemyia migonei (13.3%), Pintomyia fischeri (0.8%), Evandromyia edwardsi (< 0.1%), and species of the genus Brumptomyia. (0.1%). Out of the 509 non-engorged females analyzed by PCR, two (0.4%) carried L. infantum DNA. The naturally infected females were identified as Ny. neivai, in both morphological and molecular analysis. In addition, two out of 47 conjunctival swabs from dogs tested positive for L. infantum, yielding an infection rate of 4.2%.

CONCLUSIONS: These results confirm the presence of Ny. neivai naturally infected with L. infantum in an area where dogs were also infected by the parasite, suggesting its potential role as a vector in Southern Brazil.},
}

Animals
Dogs
*Leishmania infantum/genetics/isolation & purification
Brazil/epidemiology
*Psychodidae/parasitology/classification
*Dog Diseases/parasitology/epidemiology
*Leishmaniasis, Visceral/veterinary/epidemiology/parasitology/transmission
Female
*Insect Vectors/parasitology
Polymerase Chain Reaction
Male

@article {pmid38918509,
year = {2024},
author = {Bauer, N and Oberist, C and Poth, M and Stingele, J and Popp, O and Ausländer, S},
title = {Genomic barcoding for clonal diversity monitoring and control in cell-based complex antibody production.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14587},
pmid = {38918509},
issn = {2045-2322},
mesh = {CHO Cells ; *Cricetulus ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Clone Cells ; Genomics/methods ; Antibodies, Monoclonal/genetics ; },
abstract = {Engineered mammalian cells are key for biotechnology by enabling broad applications ranging from in vitro model systems to therapeutic biofactories. Engineered cell lines exist as a population containing sub-lineages of cell clones that exhibit substantial genetic and phenotypic heterogeneity. There is still a limited understanding of the source of this inter-clonal heterogeneity as well as its implications for biotechnological applications. Here, we developed a genomic barcoding strategy for a targeted integration (TI)-based CHO antibody producer cell line development process. This technology provided novel insights about clone diversity during stable cell line selection on pool level, enabled an imaging-independent monoclonality assessment after single cell cloning, and eventually improved hit-picking of antibody producer clones by monitoring of cellular lineages during the cell line development (CLD) process. Specifically, we observed that CHO producer pools generated by TI of two plasmids at a single genomic site displayed a low diversity (< 0.1% RMCE efficiency), which further depends on the expressed molecules, and underwent rapid population skewing towards dominant clones during routine cultivation. Clonal cell lines from one individual TI event demonstrated a significantly lower variance regarding production-relevant and phenotypic parameters as compared to cell lines from distinct TI events. This implies that the observed cellular diversity lies within pre-existing cell-intrinsic factors and that the majority of clonal variation did not develop during the CLD process, especially during single cell cloning. Using cellular barcodes as a proxy for cellular diversity, we improved our CLD screening workflow and enriched diversity of production-relevant parameters substantially. This work, by enabling clonal diversity monitoring and control, paves the way for an economically valuable and data-driven CLD process.},
}

CHO Cells
*Cricetulus
Animals
*DNA Barcoding, Taxonomic/methods
*Clone Cells
Genomics/methods
Antibodies, Monoclonal/genetics

@article {pmid38918059,
year = {2024},
author = {Belford, SG},
title = {Combining morphological characteristics and DNA barcoding techniques confirm sea urchins of the genus Echinometra (Echinodermata: Echinoidea) in marine habitat located at extreme regions of the Caribbean Sea.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icae083},
pmid = {38918059},
issn = {1557-7023},
abstract = {Echinometra spp. are pantropical echinoids found in benthic marine habitat throughout the Caribbean, Atlantic, and Indo-West Pacific oceanic regions. Currently, morphology and molecular data is sparse for echinoids observed along the northeastern coast of Toco, Trinidad where they are relatively common. Additionally, accurate species identity for Echinometra spp. remains dynamic at both northernmost and southernmost parts of the Caribbean Sea. Although distribution of sea urchins in the genus Echinometra have extensively been studied throughout the Atlantic and Indo-West Pacific, information on its range of distribution at the edge of the Caribbean Sea is lacking. In this study, the mitochondrial Cytochrome c Oxidase subunit I (mt COI) gene was amplified using polymerase chain reaction, then sequenced. Based on successfully obtained gene sequences for 581 base pairs, the echinoid species E. lucunter and E. viridis were identified for black and red color morphotypes from Trinidad (n = 23) and Key Largo, Florida (n = 6) respectively. Furthermore, these specimens were genetically identical to species identified in other studies for Puerto Rico, Panamá, Honduras, and Belize. Although morphological variations, such as spine and test color occur throughout Echinometra spp., molecular identification using the barcoding technique confirmed E. lucunter color morphs for the first time in Trinidad. Since the status of E. lucunter populations, specifically at the most northern and southern regions of the Caribbean Sea is dynamic, further studies using gene markers are essential in determining species distribution, in light of current trends in climate change.},
}

@article {pmid38915710,
year = {2024},
author = {Trende, R and Darling, TL and Gan, T and Wang, D and Boon, ACM},
title = {Barcoded SARS-CoV-2 viruses define the impact of time and route of transmission on the transmission bottleneck in a Syrian hamster model.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.06.08.597602},
pmid = {38915710},
abstract = {The transmission bottleneck, defined as the number of viruses that transmit from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, SARS-CoV-2's transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. In airborne-exposed hamsters, the transmission bottleneck increased with longer exposure durations. We found that direct contact exposure produced the largest transmission bottleneck (average 27 BCs), followed by airborne exposure (average 16 BCs) then fomite exposure (average 8 BCs). Interestingly, we detected unique BCs in both the upper and lower respiratory tract of contact animals from all routes of exposure, suggesting that SARS-CoV-2 can directly infect hamster lungs. Altogether, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission. In the future, barcoded SARS-CoV-2 will strengthen studies of immune factors that influence virus transmission.},
}

@article {pmid38912975,
year = {2024},
author = {Zahn, FE and Jiang, H and Lee, YI and Gebauer, G},
title = {Mode of carbon gain and fungal associations of Neuwiedia malipoensis within the evolutionary early diverging orchid subfamily Apostasioideae.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcae097},
pmid = {38912975},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: The earliest diverging orchid lineage Apostasioideae consists only of two genera: Apostasia and Neuwiedia. Previous report of Apostasia nipponica indicated a symbiotic association with an ectomycorrhiza-forming Ceratobasidiaceae clade and partial utilization of fungal carbon during the adult stage. However, the trophic strategy of Neuwiedia throughout its development remains unidentified. To further improve our understanding of mycoheterotrophy in the Apostasioideae, this study focused on Neuwiedia malipoensis examining both the mycorrhizal association and the physiological ecology of this orchid species across various development stages.

METHODS: We identified the major mycorrhizal fungi of N. malipoensis protocorm, leafy seedling and adult stages using molecular barcoding. To reveal nutritional resources utilized by N. malipoensis, we compared stable isotope natural abundance (δ13C, δ15N, δ2H, δ18O) of different developmental stages to autotrophic reference plants.

KEY RESULTS: Protocorms exhibited an association with saprotrophic Ceratobasidiaceae rather than ectomycorrhiza-forming Ceratobasidiaceae and 13C signature was characteristic of their fully mycoheterotrophic nutrition.Seedlings and adults predominantly associated with saprotrophic fungi belonging to the Tulasnellaceae. While 13C and 2H stable isotope data revealed partial mycoheterotrophy of seedlings, it is unclear to what extent the fungal carbon supply is reduced in adult N. malipoensis. However, the 15N enrichment of mature N. malipoensis suggests partially mycoheterotrophic nutrition.Our data indicated a transition in mycorrhizal partners during ontogenetic development with decreasing dependency of N. malipoensis on fungal nitrogen and carbon.

CONCLUSIONS: The divergence in mycorrhizal partners between N. malipoensis and A. nipponica indicates different resource acquisition strategies and allows for various habitat options in the earliest diverging orchid lineage Apostasioideae. While A. nipponica relies on the heterotrophic C gain from its ectomycorrhizal fungal partner and thus on forest habitats, N. malipoensis rather relies on own photosynthetic C gain as adult allowing it to establish in habitats as widely distributed as those where Rhizoctonia fungi occur.},
}

@article {pmid38911824,
year = {2024},
author = {Nassiri, I and Kwok, AJ and Bhandari, A and Bull, KR and Garner, LC and Klenerman, P and Webber, C and Parkkinen, L and Lee, AW and Wu, Y and Fairfax, B and Knight, JC and Buck, D and Piazza, P},
title = {Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae085},
pmid = {38911824},
issn = {2635-0041},
abstract = {MOTIVATION: Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps.

RESULTS: We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells.

EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).},
}

@article {pmid38909361,
year = {2024},
author = {Fei, L and Zhang, K and Hautaniemi, S and Sahu, B},
title = {Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach.},
journal = {STAR protocols},
volume = {5},
number = {3},
pages = {103148},
doi = {10.1016/j.xpro.2024.103148},
pmid = {38909361},
issn = {2666-1667},
abstract = {Ectopic expression of lineage-specific transcription factors (TFs) of another cell type can induce cell fate reprogramming. However, the heterogeneity of reprogramming cells has been a challenge for data interpretation and model evaluation. Here, we present a protocol to characterize cells expressing defined factors during direct cell reprogramming using a factor-indexing approach based on single-nuclei multiome sequencing (FI-snMultiome-seq). We describe the steps for barcoding TFs, converting human fibroblasts to pancreatic ductal-like cells using defined TFs, and preparing library for FI-snMultiome-seq analysis. For complete details on the use and execution of this protocol, please refer to Fei et al.[1].},
}

@article {pmid38907922,
year = {2024},
author = {Bell, CM},
title = {Single-Cell Sequencing of 3' RNA Transcripts.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2822},
number = {},
pages = {227-243},
pmid = {38907922},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; Humans ; *3' Untranslated Regions ; *RNA, Messenger/genetics ; *Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; Animals ; High-Throughput Nucleotide Sequencing/methods ; Poly A/genetics ; Transcriptome/genetics ; },
abstract = {Single-cell RNA sequencing (scRNA-seq) enables the measurement of RNA expressed from individual cells within a tissue or population. RNA expression profiles may be used to draw conclusions about cellular states, cell subtypes within the population, responses to perturbations, and cellular behavior in the context of disease. Here we describe a method for scRNA-seq via single-cell encapsulation and capture of the polyadenosine tails at the 3' end of mRNA transcripts combined with cell and molecular barcoding, allowing for the sequencing of 3' untranslated regions in order to identify expressed genes from a cell.},
}

*Single-Cell Analysis/methods
Humans
*3' Untranslated Regions
*RNA, Messenger/genetics
*Sequence Analysis, RNA/methods
Gene Expression Profiling/methods
Animals
High-Throughput Nucleotide Sequencing/methods
Poly A/genetics
Transcriptome/genetics

@article {pmid38907921,
year = {2024},
author = {Orzolek, LD},
title = {Sequencing: 10X Genomics 3' HT Assay for Gene Expression.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2822},
number = {},
pages = {207-226},
pmid = {38907921},
issn = {1940-6029},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; *Gene Library ; *Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; DNA, Complementary/genetics ; },
abstract = {Single-cell RNA sequencing supports the isolation of individual cells and barcoding of cDNA, specific to each cell of origin. Subsequent sequencing of the generated library yields both the gene expression sequences and the cellular barcode, allowing distinction of gene expression patterns across individual cells. The 10X Genomics 3' HT assay uses a droplet-based method to isolate individual cells within oil emulsions, combined with a gel bead coated in uniquely barcoded primers, specific to each bead. The high-throughput, HT, assay is similar to its predecessor (3' v3.1) in reaction chemistry but utilizes (a) higher numbers of cellular barcodes, (b) a new, proprietary chip designed to target up to 60,000 cells per lane, and (c) captures up to 16 samples per run. The 3' HT assay supports whole cells and nuclei as input, with an approximate 60% capture rate. Here we describe the methods for sample quality control (QC) assays, loading and operation of the Chromium X instrument for cell capture, and cDNA synthesis and library preparation for downstream Illumina sequencing.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Genomics/methods
*Gene Library
*Single-Cell Analysis/methods
Sequence Analysis, RNA/methods
Gene Expression Profiling/methods
DNA, Complementary/genetics

@article {pmid38906909,
year = {2024},
author = {Wang, T and Li, X and Tang, C and Cao, Z and He, H and Ma, X and Li, Y and De, K},
title = {Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14357},
pmid = {38906909},
issn = {2045-2322},
support = {LHZX-2022-01//The Chinese Academy of Sciences - People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 2021-SF-A4//The major science and technology projects of Qinghai Province/ ; },
mesh = {*Phylogeny ; *Genome, Chloroplast ; *Pedicularis/genetics/classification ; *Microsatellite Repeats/genetics ; RNA, Transfer/genetics ; },
abstract = {The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced, assembled, and annotated. Their chloroplast (cp) genome lengths were 146,452 bp, and 146,852 bp, respectively; 120 and 116 genes were identified, comprising 75 and 72 protein-coding genes (PCGs), 37 and 36 transfer RNA (tRNA) genes, and 8 and 8 ribosomal RNA (rRNA) genes, for P. chinensis and P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences were mainly composed of mononucleotide repeats (A/T motif) and dinucleotide repeats (AT/TA motif). Comparative genomics identified several variant genes (rpl22, rps19, rpl12, ycf1, trnH, psbA, and ndhH) and variant regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, and rpl32-trnL) with a high Pi, indicating the potential to serve as deoxyribo nucleic acid (DNA) barcodes for Pedicularis species identification. The results show that the cp genomes of P. chinensis and P. kansuensis were the same as those of other plants in Pedicularis, with different degrees of AT preference for codons. Large differences in the number of SSRs and the expansion of the inverted repeat (IR) region showed strong variability and interspecific differentiation between these two species and other species represented in the genus Pedicularis. A phylogenetic analysis showed that P. kansuensis had the closest relationship with P. oliveriana, and P. chinensis had the closest relationship with P. aschistorhyncha. These results will facilitate the study of the phylogenetic classification and interspecific evolution of Pedicularis plants.},
}

*Phylogeny
*Genome, Chloroplast
*Pedicularis/genetics/classification
*Microsatellite Repeats/genetics
RNA, Transfer/genetics

@article {pmid38903959,
year = {2024},
author = {Ferreira, S and Corley, MFV and Nunes, J and Rosete, J and Vasconcelos, S and Mata, VA and Veríssimo, J and Silva, TL and Sousa, P and Andrade, R and Grosso-Silva, JM and Pinho, CJ and Chaves, C and Martins, FM and Pinto, J and Puppo, P and Muñoz-Mérida, A and Archer, J and Pauperio, J and Beja, P},
title = {The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e117169},
pmid = {38903959},
issn = {1314-2828},
abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.

NEW INFORMATION: The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).},
}

@article {pmid38901752,
year = {2024},
author = {Negi, N and Krishna, R and Meena, RK and Bhandari, MS and Pandey, S},
title = {Discovery of Botryosphaeria eucalypti sp. nov. from blighted Eucalyptus leaves in India.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106756},
doi = {10.1016/j.micpath.2024.106756},
pmid = {38901752},
issn = {1096-1208},
abstract = {Eucalyptus spp. are undoubtedly one of the most favored plantation trees globally. Accurately identifying Eucalyptus pathogens is therefore crucial for timely disease prevention and control. Recently, symptoms of a leaf blight disease were observed on Eucalyptus trees in plantations at Jhajjhar and Karnal in the state of Haryana, northern India. Asexual morphs resembling the features of the Botryosphaeriaceae were consistently isolated from the symptomatic leaves. Morphological features coupled with DNA sequence analysis confirmed a novel species, which is described and illustrated here as Botryosphaeria eucalypti sp. nov. Conidia of the new taxon are longer and wider than those of its phylogenetic neighbors. A distinct phylogenetic position for the new taxon was established through combined analysis of the internal transcribed spacer (ITS), partial translation elongation factor-1α (tef1) and partial β-tubulin (tub2) regions. Recombination analysis provided additional support for the new species hypothesis. The pathogenicity of the novel species was proved on Eucalyptus leaves, and Koch's postulates were fulfilled. The discovery of new Botryosphaeria species is important because it will help in understanding the species diversity, host range, possible threats, new phylogenetic neighbors and disease control in the long run.},
}

@article {pmid38900825,
year = {2024},
author = {Rewicz, A and Monzalvo, R and Myśliwy, M and Tończyk, G and Desiderato, A and Ruchisansakun, S and Rewicz, T},
title = {Pollination biology of Impatiens capensis Meerb. in non-native range.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0302283},
pmid = {38900825},
issn = {1932-6203},
mesh = {*Pollination/physiology ; Animals ; *Impatiens/physiology/genetics ; *Introduced Species ; Diptera/physiology/anatomy & histology ; Poland ; DNA Barcoding, Taxonomic ; Hymenoptera/physiology ; },
abstract = {Pollination biology in the widespread species Impatiens capensis Meerb. has only been studied in America, specifically in zones of the U.S.A. and Canada. In this study, we investigated the pollination biology of I. capensis using an integrative identification approach using morphological and molecular tools in four populations of Northwest Poland. We also determined and compared the functional characteristics of the pollinators of the introduced species from the study sites and the native ones reported, for the latter collecting information from bibliographic sources. Visitors were identified using standard morphological keys, including identifying and classifying insect mouthparts. Molecular identification was carried out using mitochondrial DNA's cytochrome oxidase subunit I (COI). We morphologically identified 20 species of visitors constituted by 17 pollinators and three nectar robbers. DNA barcoding of 59 individuals proved the identification of 18 species (also 18 BINs). The frequency of pollinator species was primarily made up of representatives of both Hymenoptera (75%) and Diptera (21%). The morphological traits, such as the chewing and sucking mouthparts, small and big body height, and robber and pollinator behavior explained mainly the native and introduced visitors' arrangements that allow pollination success. However, to understand the process comprehensively, further investigation of other causalities in pollination success and understanding the diversity of pollinators in outer native ranges are necessary.},
}

*Pollination/physiology
Animals
*Impatiens/physiology/genetics
*Introduced Species
Diptera/physiology/anatomy & histology
Poland
DNA Barcoding, Taxonomic
Hymenoptera/physiology

@article {pmid38900631,
year = {2024},
author = {Li, H and Humphreys, BD},
title = {Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing.},
journal = {STAR protocols},
volume = {5},
number = {3},
pages = {103049},
doi = {10.1016/j.xpro.2024.103049},
pmid = {38900631},
issn = {2666-1667},
abstract = {Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys with SHARE-seq. We describe steps for processing fixed nuclei for SHARE-seq split-pool barcoding and library preparation. We also detail how to determine the optimal working concentration of Tn5 transposase for transposition and tagmentation. This protocol allows researchers to generate large-scale single-cell multiomics data at low reagent cost. For complete details on the use and execution of this protocol, please refer to Li et al.[1].},
}

@article {pmid38899721,
year = {2024},
author = {Veltman, MA and Anthoons, B and Schrøder-Nielsen, A and Gravendeel, B and de Boer, HJ},
title = {Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13986},
doi = {10.1111/1755-0998.13986},
pmid = {38899721},
issn = {1755-0998},
support = {765000//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; },
abstract = {Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.},
}

@article {pmid38899428,
year = {2024},
author = {Laifi-Necibi, N and Amor, N and Merella, P and Mohammed, OB and Medini, L},
title = {DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/24701394.2024.2363350},
pmid = {38899428},
issn = {2470-1408},
abstract = {Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.},
}

@article {pmid38898172,
year = {2024},
author = {Liu, Y and Sundah, NR and Ho, NRY and Shen, WX and Xu, Y and Natalia, A and Yu, Z and Seet, JE and Chan, CW and Loh, TP and Lim, BY and Shao, H},
title = {Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {38898172},
issn = {2157-846X},
support = {MOH-000564; MOH-000541; MOH-000206//MOH | National Medical Research Council (NMRC)/ ; NRF-CRP29-2022-0001//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; DTC-RGC-09//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; T2EP20121-0040//Ministry of Education - Singapore (MOE)/ ; },
abstract = {Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.},
}