@article {pmid40271218,
year = {2025},
author = {Tomsia, M and Grzywacz, A and Szpila, K and Walczak, K and Mahlerová, K and Vaněk, D and Matuszewski, S},
title = {Human costal cartilage, tooth cavities, and femur nutrient canals-new niches for insects used in forensic entomology.},
journal = {Forensic sciences research},
volume = {10},
number = {2},
pages = {owae028},
doi = {10.1093/fsr/owae028},
pmid = {40271218},
issn = {2471-1411},
abstract = {UNLABELLED: The study aimed to analyze the entomological material collected during 13 autopsies performed on the unidentified cadavers revealed at different stages of decay in the Upper Silesia Region (Poland) over 2016-2022. During the preparation of human tissues for genetic identification, we revealed larvae, puparia, and adult insects in previously undescribed locations: costal cartilage, femur nutrient canals (foramen nutrients), and tooth cavities. The taxonomical assessment was done using morphological examination or DNA barcoding, where necessary. Based on our observations, we conclude that the apical constriction, foramen, and cavities may serve as migration paths inside teeth, and the femur nutrient canals to the bone marrow. The study also revealed that the beetle Necrobia ruficollis (Fabricius, 1775) and the moth family Pyralidae Latreille, 1802 (Phycitinae) moths can form pupal chambers inside the costal cartilage, indicating that these insects can complete their life cycle inside this cache. We believe that the newly reported locations of carrion insects in human remains may be relevant to forensic entomology, as they provide new opportunities to collect insect evidence.

KEY POINTS: Costal cartilage may serve as an occasional cache for adults and immatures of carrion insects.Tooth cavities and apical foramen may serve as entryways for necrophilous insect larvae.Insect larvae use nutrient canals as migratory pathways to the bone marrow.},
}

@article {pmid40270798,
year = {2025},
author = {Kireta, D and van Dijk, KJ and Crotty, S and Malik, A and Bell, K and Hogendoorn, K and Lowe, AJ},
title = {A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture-Based DNA Metabarcoding.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71311},
doi = {10.1002/ece3.71311},
pmid = {40270798},
issn = {2045-7758},
abstract = {Pollen identification (ID) and quantification is important in many fields, including pollination ecology and agricultural sciences, and efforts to explore optimal molecular methods for identifying low concentrations of DNA from plant mixtures are increasing, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy is time-consuming, requires expertise and has limited accuracy and throughput. Molecular barcoding approaches being explored offer improved accuracy and throughput. The common approach, amplicon sequencing, employs PCR amplification to isolate DNA barcodes, but introduces significant bias, impairing downstream quantification. We apply a novel molecular hybrid capture approach to artificial pollen mixtures to improve upon current taxon ID and quantification methods. The method randomly fragments DNA and uses RNA baits to capture DNA barcodes, which allows for PCR duplicate removal, reducing downstream quantification bias. Four reference databases were used to explore identification and quantification. A restricted matK database containing only mixture species yielded sequence proportions highly correlated with input pollen proportions, demonstrating the potential usefulness of hybrid capture for metabarcoding and quantifying pollen mixtures. Identification power was further tested using two reference libraries constructed from publicly available sequences: the matK plastid barcode and RefSeq complete chloroplast references. Single barcode-based taxon ID did not consistently resolve to species or genus level. The RefSeq chloroplast database performed better qualitatively but had limited taxon coverage (relative to species used here) and introduced ID issues. At the family level, both databases yielded comparable qualitative results, but the RefSeq database performed better quantitatively. Whilst the method developed here has tremendous potential, the choice and expansion of reference databases remains one of the most important factors allowing qualitative and quantitative accuracy using the full set of genomic regions screened by this hybrid capture method.},
}

@article {pmid40270465,
year = {2025},
author = {Borer, G and Monteiro, C and Lima, FP and Martins, FMS},
title = {Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14115},
doi = {10.1111/1755-0998.14115},
pmid = {40270465},
issn = {1755-0998},
support = {BIOINTERACT/https://doi.org/10.54499/2022.02887//Fundação para a Ciência e a Tecnologia/ ; CEECInd/10.54499/CEECIND/03185/2018/CP1546/CP164//Fundação para a Ciência e a Tecnologia/ ; OceanLog/10.54499/PTDC/BIA-BMA/4848/2021//Fundação para a Ciência e a Tecnologia/ ; ANERIS/101094924//Horizon 2020 Framework Programme/ ; FutureMares/869300//Horizon 2020 Framework Programme/ ; NORTE-01-0246-FEDER-000063//European Commission/ ; },
abstract = {Large biogeographical shifts in marine communities are taking place in response to climate change and biological invasions yet we still lack a full understanding of their diversity and distribution. An important example of this is turf and foliose algae that are key coastal primary producers in several regions and are expanding into new environments. Traditionally, monitoring turf and foliose algae communities involves species identification based on morphological traits, which is challenging due to their reduced dimensions and highly variable morphology. Molecular methods promise to revolutionise this field, but their effectiveness in detecting turf and foliose algae has yet to be tested. Here, we evaluate the performance of DNA metabarcoding (COI and rbcL markers) and morphological identification (in situ and photoquadrat) to describe intertidal turf and foliose algae communities along the Portuguese coast. Both molecular markers detected more taxa than the morphological methods and showed greater discrimination of turf and foliose algae communities between regions, matching our knowledge of the geographical and climatic patterns for the region. In sum, our multi-marker metabarcoding approach was more efficient than morphology-based methods in characterising turf and foliose algae communities along the Portuguese coast, differentiating morphologically similar species, and detecting unicellular organisms. However, certain taxa that were identified by in situ and photoquadrat approaches were not detected through metabarcoding, partly due to lack of reference barcodes or taxonomic resolution. Metabarcoding emerges as a valuable tool for monitoring these communities, particularly in long-term programmes requiring accuracy, speed, and reproducibility.},
}

@article {pmid40270210,
year = {2025},
author = {Pedersen, FB and Hauge, AW and Hansen, JF and Andersen, LS and Blomsterberg, S and Bruunsgaard, H},
title = {Cost-Effective and Highly Scalable Typing of HLA Classes I and II Genes of up to 96 Individuals Using Nanopore Sequencing.},
journal = {HLA},
volume = {105},
number = {4},
pages = {e70164},
doi = {10.1111/tan.70164},
pmid = {40270210},
issn = {2059-2310},
support = {FF 2022/01//Bloddonorernes Forskningsfond/ ; },
mesh = {Humans ; *Histocompatibility Testing/methods/economics ; *Nanopore Sequencing/economics/methods ; Cost-Benefit Analysis ; Alleles ; *Histocompatibility Antigens Class II/genetics ; Multiplex Polymerase Chain Reaction/economics ; },
abstract = {HLA typing of large donor registries and biobanks as well as acute single patient/donor samples remains expensive, slow and logistically challenging, despite recent developments in the field. We have tested and validated a cost-effective, accurate and highly scalable method for typing specific genes in the HLA region. This enables HLA typing from 1 to 96 individuals simultaneously, using a targeted PCR and Native Barcoding kit from Oxford Nanopore Technologies. A primer set for seven HLA genes (HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1) was developed to work in a multiplex PCR reaction. The resulting amplicons provide a possible four-field resolution of the HLA Class I genes and G-group resolution of the HLA Class II genes. The entire process, from DNA to HLA typing result, takes a total of 5.5-10.5 h depending on the number of samples processed simultaneously. Data analysis was conducted using NGSEngine-Turbo from GenDx (Utrecht, The Netherlands), with analysis time ranging from 1 to 5 min per sample. Samples from 96 Danish registered stem cell donors were typed using this method. One allele out of 1128 analysed alleles was inaccurately called homozygous, leading to an accuracy of 99.91%. The rapid turnaround, low cost and high accuracy make this new method highly relevant for HLA typing of large biobanks and donor registries, as well as for acute single samples. HLA typing can be obtained within 1 day, with a cost per sample of approximately €7 when 96 samples are sequenced simultaneously.},
}

Humans
*Histocompatibility Testing/methods/economics
*Nanopore Sequencing/economics/methods
Cost-Benefit Analysis
Alleles
*Histocompatibility Antigens Class II/genetics
Multiplex Polymerase Chain Reaction/economics

@article {pmid40269967,
year = {2025},
author = {Isiye, E and Valcarcel Olmeda, A and Curran, T and O'Neill, D and de Waal, T and Barry, G and O'Hanlon, A and O'Shaughnessy, J and Keohane McCarthy, N and Vellinga, A and Jenkinson, A and Johnson, A and Barrett, D and Costello, S and Zintl, A and O'Meara, D},
title = {Molecular characterisation of common Culicoides biting midges (Diptera: Ceratopogonidae) in Ireland.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {149},
pmid = {40269967},
issn = {1756-3305},
mesh = {Animals ; *Ceratopogonidae/genetics/classification/virology ; Ireland ; *Insect Vectors/genetics/classification/virology ; DNA Barcoding, Taxonomic ; Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Bluetongue virus ; Bluetongue/transmission ; Female ; },
abstract = {BACKGROUND: Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques.

METHODS: Adult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. In addition, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland.

RESULTS: DNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides spp. that could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector.

CONCLUSIONS: DNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.},
}

Animals
*Ceratopogonidae/genetics/classification/virology
Ireland
*Insect Vectors/genetics/classification/virology
DNA Barcoding, Taxonomic
Phylogeny
Electron Transport Complex IV/genetics
Genetic Variation
Bluetongue virus
Bluetongue/transmission
Female

@article {pmid40266812,
year = {2025},
author = {Wu, Y and Liu, Y and Huang, Z and Yin, H and Xu, X},
title = {New Species of the Purse-Web Spider Genus Atypus Latreille, 1804 from Southern China (Araneae, Atypidae), with the General Natural History of Atypus Spiders.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030301},
pmid = {40266812},
issn = {2075-4450},
support = {32070429/31772423/31471963/31372160//National Natural Sciences Foundation of China/ ; 2023JJ30399//Hunan Provincial Natural Science Foundation of China/ ; CX20230525//Hunan Provincial Innovation Foundation for Postgraduate/ ; },
abstract = {Three species of the purse-web spider genus Atypus Latreille, 1804, collected from Hunan and Sichuan Provinces of China, are diagnosed and described as new to science: A. yaozu sp. nov. (♂♀), A. siyiensis sp. nov. (♂♀) and A. yanjingensis sp. nov. (♂♀). Detailed descriptions, photographs and DNA barcodes of the three new species and a distribution map of Atypus species in China are provided. Additionally, we enrich the general natural history of the genus Atypus through a decade of observation.},
}

@article {pmid40265169,
year = {2025},
author = {Renou, L and Sun, W and Friedrich, C and Galant, K and Conrad, C and Consalus, A and Plantier, E and Schallmoser, K and Krisch, L and Barroca, V and Devanand, S and Dechamps, N and Reinisch, A and Martinovic, J and Magnani, A and Faivre, L and Lewandowski, D and Calvo, J and Perie, L and Kosmider, O and Pflumio, F},
title = {Orchestration of human multi-lineage hematopoietic cell development by humanized in vivo bone marrow models.},
journal = {HemaSphere},
volume = {9},
number = {4},
pages = {e70120},
pmid = {40265169},
issn = {2572-9241},
abstract = {Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate the differentiation and preservation of hematopoietic stem and progenitor cells (HSPCs). Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, but the physiology of these models is questioned as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h) in vivo BM model, developed from fetal (F/) and post-natal (P-N/) mesenchymal stromal cell (MSC) differentiation (called hOssicles [hOss]), in which human hematopoietic cells are generated following the transplantation of CD34[+] cells. Serial isolation and transplant experiments of hMSCs and HSPCs from hOss revealed the dynamic nature of these hBM niches. hOss modified human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels, with no major transcriptional changes in HSPCs at the single-cell level. Clonal tracking using genetic barcodes highlighted hematopoietic cell cross-talks between the endogenous murine BM and hOss and differences in clonal myeloid/multipotent cell production between F/hOss and P-N/hOss, uncovering ontogeny-related impact of the BM on human hematopoietic cell production.},
}

@article {pmid40263935,
year = {2025},
author = {Becker, J and Domenger, C and Choksi, P and Krämer, C and Baumgartl, C and Maiakovska, O and Kim, JJ and Weinmann, J and Huber, G and Schmidt, F and Thirion, C and Müller, OJ and Willenbring, H and Grimm, D},
title = {Identification of a robust promoter in mouse and human hepatocytes by in vivo biopanning of a barcoded AAV library.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2025.04.027},
pmid = {40263935},
issn = {1525-0024},
abstract = {Recombinant adeno-associated viruses (AAV) are leading vectors for in vivo human gene therapy. An integral vector element are promoters, which control transgene expression in either a ubiquitous or cell-type-selective manner. Identifying optimal capsid-promoter combinations is challenging, especially when considering on- versus off-target expression. Here, we report a pipeline for in vivo promoter biopanning in AAV building on our AAV capsid barcoding technology and illustrate its potential by screening 53 promoters in 16 murine tissues using an AAV9 vector. Surprisingly, the 2.2 kb human glial fibrillary acidic protein (GFAP) promoter was the top hit in the liver, where it outperformed robust benchmarks such as the human alpha-1-antitrypsin promoter or the clinically used liver-specific promoter 1 (LP1). Analysis of hepatic cell populations revealed preferred GFAP promoter activity in hepatocytes. Notably, the GFAP promoter also surpassed the LP1 and cytomegalovirus (CMV) promoters in human hepatocytes engrafted in an immune-deficient mouse. These findings establish the GFAP promoter as an exciting alternative for research and clinical applications requiring efficient and specific transgene expression in hepatocytes. Our pipeline expands the arsenal of technologies for high-throughput in vivo screening of viral vector components and is compatible with capsid barcoding, facilitating the combinatorial interrogation of complex AAV libraries.},
}

@article {pmid40263541,
year = {2025},
author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and McCrea, EM and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD},
title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.},
journal = {Cell death and differentiation},
volume = {},
number = {},
pages = {},
pmid = {40263541},
issn = {1476-5403},
support = {R35CA197591//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; T32CA009302//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 28IP-0037//Tobacco-Related Disease Research Program (TRDRP)/ ; T31DT1713//Tobacco-Related Disease Research Program (TRDRP)/ ; },
abstract = {TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq[Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.},
}

@article {pmid40263346,
year = {2025},
author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N},
title = {Non-invasive molecular species identification using spider silk proteomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13844},
pmid = {40263346},
issn = {2045-2322},
support = {23K21203//Japan Society for the Promotion of Science/ ; },
abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.},
}

@article {pmid40262372,
year = {2025},
author = {Finney, J and Kuraoka, M and Song, S and Watanabe, A and Liang, X and Liao, D and Moody, MA and Walter, EB and Harrison, SC and Kelsoe, G},
title = {Fluorescence-barcoded cell lines stably expressing membrane-anchored influenza neuraminidases.},
journal = {Vaccine},
volume = {56},
number = {},
pages = {127157},
doi = {10.1016/j.vaccine.2025.127157},
pmid = {40262372},
issn = {1873-2518},
abstract = {The discovery of broadly protective antibodies to the influenza virus neuraminidase (NA) has raised interest in NA as a vaccine target. However, recombinant, solubilized tetrameric NA ectodomains are often challenging to express and isolate, hindering the study of anti-NA humoral responses. To address this obstacle, we established a panel of 22 non-adherent cell lines stably expressing native, historical N1, N2, N3, N9, and NB NAs anchored on the cell surface. The cell lines are barcoded with fluorescent proteins, enabling high-throughput, 16-plex analyses of antibody binding with commonly available flow cytometers. The cell lines were at least as efficient as a Luminex multiplex binding assay at identifying NA antibodies from a library of unselected clonal IgGs derived from human memory B cells. The cell lines were also useful for measuring the magnitude and breadth of the serum antibody response elicited by experimental infection of rhesus macaques with influenza virus. The membrane-anchored NAs are catalytically active and are compatible with established sialidase activity assays. NA-expressing K530 cell lines therefore represent a useful tool for studying NA immunity and evaluating influenza vaccine efficacy.},
}

@article {pmid40262024,
year = {2025},
author = {Tong, Y and Wang, H and Li, H and Jia, Y and Zhou, Z},
title = {Molecular Diet Analysis of Leaf-Grazing Katydids Based on DNA Barcoding.},
journal = {Archives of insect biochemistry and physiology},
volume = {118},
number = {4},
pages = {e70062},
doi = {10.1002/arch.70062},
pmid = {40262024},
issn = {1520-6327},
support = {//This study was supported by Engineering Research Center of Ecological Safety and Conservation in Beijing-Tianjin-Hebei (Xiong'an New Area) of MOE, China (2024-11)./ ; },
abstract = {The diversity of herbivorous insects is associated with host plant diversity. The determination of dietary profile is a central topic in insect ecology. DNA barcoding, that is, taxon identification using a standardized DNA region, have been important to the recent advances in food web understandings. In this study, three commonly plant barcoding loci (i.e., rbcL, matK, and trnH-psbA) were chosen for screening of ingested plant DNA in 207 specimens of 18 leaf-grazing katydid species representing 4 subfamilies in China. The obtained sequences were queried against the Barcode of Life Database (BOLD) and GenBank for taxa identification. The results of identification were as follow: 3 Conocephalinae species consumed 10 plant families, with preference for Poaceae; 1 Mecopodinae species consumed 18 plant families, with preference for Fabaceae and Vitaceae; 11 Phaneropterinae species consumed 43 plant families, with preference for Juglandaceae; 3 species Pseudophyllinae species consumed 9 plant families, with preference for Balsaminaceae. Among these, only 81 out of 207 samples were identified at the species level when compares with NCBI and BOLD database. Our study added a significant amount of dietary information for leaf-grazing katydids in China. It is crucial to fully understand coevolution of katydids and plant, katydids diet resource requirements, and best practices for habitat conservation.},
}

@article {pmid40261157,
year = {2025},
author = {Kumar, A and Mishra, DK and Kanojiya, S},
title = {Identification of Botanicals Based on Their Mass Spectrum Fingerprints Using Ultra-Performance Liquid Chromatography-Mass Spectrometry.},
journal = {Journal of mass spectrometry : JMS},
volume = {60},
number = {5},
pages = {e5131},
doi = {10.1002/jms.5131},
pmid = {40261157},
issn = {1096-9888},
support = {YSS/2015/001048//Science & Engineering Research Board (SERB) DST Government of India/ ; },
mesh = {Chromatography, High Pressure Liquid/methods ; *Mass Spectrometry/methods ; *Plants, Medicinal/chemistry/classification ; *Plant Extracts/chemistry/analysis ; Liquid Chromatography-Mass Spectrometry ; },
abstract = {In the current scenario, herbal raw materials are identified via morphotaxonomy, microscopic pharmacognosy, or DNA barcoding. However, these methods do not reveal their chemical integrity, while plant raw materials play a crucial role in the quality of plant-based medicine. To overcome this limitation, we used a mass spectrometry-based method to identify 30 botanicals. This assay followed a standard operating procedure (SOP) from sample preparation to the reference library's mass spectrum fingerprint (MSFP) search. The MS1 score showed a similarity index between the input data and the reference mass spectrum. A more than 50% MS1 score was the critical threshold for accurately identifying botanicals based on their chemical integrity. Interestingly, the analysis of 30 different plant species yielded no false results. The results were 100% accurate and selective for tested botanical samples. However, we found that the standard deviation of analytical assays and biological replicates was ± 3.5 and ± 6.3 (MS1 score) for all analyzed samples, respectively. Intraspecies variability showed MS1 scores > 50% ± 10, whereas interspecies variability was observed with MS1 scores < 50% ± 10. The MS1 score was observed, dependent on the plant species, ranging from 53.00% (± 2.65) to 89.76% (± 4.08). In addition, the method was tested to see how seasonal and geographical changes affected search results. The MS1 score changed by less than 15%. We simultaneously created a chemical barcode (unique molecular weight sequence) for each plant species to validate search results and ensure the reliable identification of botanicals.},
}

Chromatography, High Pressure Liquid/methods
*Mass Spectrometry/methods
*Plants, Medicinal/chemistry/classification
*Plant Extracts/chemistry/analysis
Liquid Chromatography-Mass Spectrometry

@article {pmid40260151,
year = {2025},
author = {Shapkin, V and Caboň, M and Kolařík, M and Adamčíková, K and Baldrian, P and Michalková, T and Větrovský, T and Adamčík, S},
title = {Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71352},
pmid = {40260151},
issn = {2045-7758},
abstract = {The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.},
}

@article {pmid40260148,
year = {2025},
author = {Wong, A and Eizirik, E and Koepfli, KP and de Ferran, V and Shihepo, T and Lay, AR and Zumbroich, J and Rooney, N and Marker, L and Schmidt-Küntzel, A},
title = {Identifying Cryptic Mammals With Non-Invasive Methods: An Effective Molecular Species Identification Tool to Survey Southern African Terrestrial Carnivores.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71223},
pmid = {40260148},
issn = {2045-7758},
abstract = {Carnivores play a vital role in ecosystem health and are thus an important focus for conservation management. Non-invasive methods have gained traction for carnivore monitoring as carnivores are often elusive and wide-ranging, making visual counts particularly difficult. Faecal mini-barcoding combines field collection of scats with genetic analysis for species identification. Here, we assessed the applicability of a mini-barcode based on the mitochondrial ATP6 gene in southern Africa. We predicted amplification success based on in silico evaluation of reference sequences from 34 of the 42 terrestrial carnivore species existing in southern Africa, including the Congo clawless otter (Aonyx congicus) for which we contributed a mitochondrial assembly. We further tested amplification success on available reference samples of 23 species. We expanded the existing ATP6 mini-barcode reference database by contributing additional sequences for 22 species, including the Cape genet (Genetta tigrina) and the side-striped jackal (Lupulella adusta) for which no complete mini-barcode sequences were available on GenBank, and compiled a representative reference dataset of 61 unique sequences as a tool for species identification. As a proof of principle, we applied the ATP6 mini-barcode to a small scat-based carnivore survey conducted in Namibia 13 years prior, which showed a 95% identification success and detected six species among 157 samples collected. With southern Africa's mammalian carnivores facing escalating threats, this robust mini-barcode offers a vital tool for accurate species identification from non-invasive samples, enabling crucial monitoring and conservation efforts.},
}

@article {pmid40259706,
year = {2025},
author = {Woodford, DJ and Magoro, M and Kadye, WT and Scheepers, M and Sithole, Y and Mutizwa, TI and Ntokoane, T and Chakona, A},
title = {Freshwater fishes of the Waterberg aquatic ecoregion, South Africa: Diversity, taxonomic conflicts and conservation concerns.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70007},
pmid = {40259706},
issn = {1095-8649},
support = {FBIP-211006643719//National Research Foundation/ ; IBIP-BS13100251309//National Research Foundation/ ; FBIC200227507229//National Research Foundation/ ; },
abstract = {Southern Africa is a region denoted by both high levels of fish diversity, some of it cryptic and unrecognised by current taxonomy, and severely threatened freshwater ecosystems. The Waterberg, a key aquatic ecoregion of the greater Limpopo River basin in South Africa, represents an area with high terrestrial conservation value but is lacking in aquatic biodiversity information. This study characterised this unique aquatic ecoregion's fish diversity, their biogeographic patterns and threats to this biodiversity. A total of 29 fish species (11 families, 19 genera) were identified, with many distinct upland fish communities occurring within the high-altitude headwaters of the ecoregion, whereas lowland fish communities tended to be more homogeneous. Mitochondrial CO1 barcoding revealed genetically distinct lineages in four presumed-widespread southern African species: the shortfin barb, Enteromius brevipinnis (Jubb, 1966); hyphen barb, Enteromius bifrenatus (Fowler, 1935); straightfin barb, Enteromius paludinosus (Peters, 1852) and snake catfish, Clarias theodorae Weber, 1897, that were restricted to the Waterberg aquatic ecoregion. The level of genetic divergence suggests that these four Waterberg-restricted lineages are likely new candidate species. These findings indicate the Waterberg to be a biogeographic island within the greater Zambezian ichthyofaunal region of southern Africa, which should be prioritised for aquatic ecosystem conservation. Current terrestrial conservation structures in the region, encapsulated within the Waterberg Biosphere Reserve, appear to protect this distinct ichthyofauna from human land-use-derived impacts. Nonetheless, the presence of the invasive predatory largemouth bass (Micropterus nigricans) inside the biosphere represents a credible conservation threat. Engagement with biosphere stakeholders will be critical for managing this threat to the Waterberg's unique ichthyofauna going forward.},
}

@article {pmid40258808,
year = {2025},
author = {van der Toorn, W and Bohn, P and Liu-Wei, W and Olguin-Nava, M and Gribling-Burrer, AS and Smyth, RP and von Kleist, M},
title = {Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3742},
pmid = {40258808},
issn = {2041-1723},
support = {390685689//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KI2016//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 955974//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; VH-NG-1347//Helmholtz Association/ ; ANR 20-SFRI-0012//Université de Strasbourg (University of Strasbourg)/ ; },
mesh = {*SARS-CoV-2/genetics ; RNA, Viral/genetics ; Humans ; *Sequence Analysis, RNA/methods ; *Nanopore Sequencing/methods ; COVID-19/virology ; *Nanopores ; Software ; Algorithms ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing rapid phenotypic profiling of different SARS-CoV-2 viruses through multiplexed sequencing of longitudinal samples on a single flowcell, identifying systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX represents a broadly applicable, high-performance, economical multiplexing solution for dRNA-seq, facilitating advanced (epi-) transcriptomic research.},
}

*SARS-CoV-2/genetics
RNA, Viral/genetics
Humans
*Sequence Analysis, RNA/methods
*Nanopore Sequencing/methods
COVID-19/virology
*Nanopores
Software
Algorithms
Machine Learning
High-Throughput Nucleotide Sequencing/methods

@article {pmid40258437,
year = {2025},
author = {Kioulos, I and Grigoriadou, AM and Papadakis, A and Vontas, J and Mavridis, K},
title = {Molecular genotyping of pyrethroid resistant mutations and their haplotypes in bed bug populations from Greece.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107624},
doi = {10.1016/j.actatropica.2025.107624},
pmid = {40258437},
issn = {1873-6254},
abstract = {The resurgence of bed bugs poses significant risks to public health and tourism-driven economies in Southern Europe, including Greece. Control efforts largely rely on pyrethroids; however, the widespread selection of knockdown resistance (kdr) mutations has compromised their effectiveness. Molecular monitoring is therefore essential for accurate species identification and resistance surveillance to support evidence-based pest management strategies. In this study, we analyzed bed bug populations collected from Athens, Thessaloniki, and Heraklion between 2021 and 2024. Species identification was performed via DNA barcoding of the cytochrome oxidase I (COI) gene, while kdr mutations in the voltage-gated sodium channel (VGSC) gene-specifically V419L, L925I, and I936F-were assessed to determine their frequencies and haplotype distributions. All specimens were identified as Cimex lectularius. The L925I mutation reached fixation (100%) in Thessaloniki and Heraklion, while V419L was detected at frequencies of 30.00% and 50.00%, respectively; I936F was not detected in these populations. In Athens, L925I was highly prevalent (98.40%), while V419L (5.27%) and I936F (0.60%) were detected at lower frequencies. Haplotype analysis revealed Haplotype B (L925I only) as the most common in Athens (91.20%) and Thessaloniki (60.0%), while Haplotype C (L925I + V419L) predominated in Heraklion (76.92%). Additional haplotypes were identified in Athens, including Haplotype B[b] (L925I + I936F), marking its first detection in Europe. These findings highlight the widespread presence of kdr mutations and underscore the urgent need for integrated pest management (IPM) strategies, incorporating resistance monitoring, alternative insecticides, and non-chemical control methods to mitigate the growing challenge of pyrethroid resistance in bed bugs.},
}

@article {pmid40257565,
year = {2025},
author = {Marsolier, J and Moutaux, E and Grosselin, K and Griffiths, A and Vallot, C},
title = {Single-cell Epigenomic Profiling with High-throughput Droplet scChIP-seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2919},
number = {},
pages = {213-239},
pmid = {40257565},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Epigenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Histones/genetics ; Microfluidics/methods ; *Epigenesis, Genetic ; },
abstract = {Our high-throughput scChIP-seq approach combines droplet microfluidics with single-cell DNA barcoding to study the heterogeneity of epigenomes (H3K27me3, H3K4me3, H3K27Ac, H3K4me1) in a cellular population of several thousand cells with a coverage of up to 10,000 unique loci per cell.},
}

*Single-Cell Analysis/methods
*Epigenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Humans
Histones/genetics
Microfluidics/methods
*Epigenesis, Genetic

@article {pmid40253081,
year = {2025},
author = {Llera-Oyola, J and Pérez-Moraga, R and Parras, M and Rosón, B},
title = {How to view the female reproductive tract through single-cell looking glasses.},
journal = {American journal of obstetrics and gynecology},
volume = {232},
number = {4S},
pages = {S21-S43},
doi = {10.1016/j.ajog.2024.08.040},
pmid = {40253081},
issn = {1097-6868},
mesh = {Female ; Humans ; *Single-Cell Analysis/methods ; *Genitalia, Female/cytology ; Sequence Analysis, RNA ; Pregnancy ; },
abstract = {Single-cell technologies have emerged as an unprecedented tool for biologists and clinicians, allowing them to assess organs and tissues at the level of individual cells. In the field of women's reproductive biology, single-cell studies have provided insights into the cellular and molecular processes that regulate reproductive and obstetrical functions in health and disease. The knowledge that these studies generate is helping clinicians to improve the understanding and diagnosis of infertility related issues or pregnancy complications and to find new avenues for their treatment. However, navigating the expansive landscape of this type of transcriptomic data analysis represents a pivotal challenge in current research. Single cell RNA sequencing involves isolating cells into droplets, reverse transcribing RNA to generate complementary DNA, with each droplet content uniquely labeled by a barcode. Upon sequencing the complementary DNAs, the barcodes enable the reassignment of sequencing reads to individual droplets, facilitating the reconstruction of the cellular landscape of the sample obtained from a tissue or organ and beyond. Researchers, equipped with the metaphorical 'single-cell glasses,' must adequately choose from a plethora of strategies to dissect and interpret cellular information. Sophisticated algorithms and the decision-making process are often underestimated, resulting in artefactual or cumbersome interpreted results. Computational biologists apply and innovate computational tools designed to process, model, and interpret expansive datasets. The ramifications of their work extend far beyond the realm of data processing; they give shape to the outcome of analyses, playing a pivotal role in drawing meaningful conclusions from the wealth of information garnered. In this review, we describe the wide variety of approaches and analytical steps available with enough detail to gain a concise picture of what a complete examination of a single-cell dataset would be. We commence with a discussion on key points in experimental design, highlighting crucial questions one should consider. Following this, we delve into the various preprocessing and quality control steps essential for any single-cell dataset. The subsequent section offers a detailed guide on constructing a single-cell atlas, exploring nuances such as differential characteristics in visualization and clustering techniques, as well as strategies for assigning identity to cell populations through gene marker annotations. Moving beyond the creation of an atlas, we explore methods for investigating pathological conditions. This involves conducting cell population comparison tests between conditions and analyzing specific cell-to-cell communications and cellular differentiation trajectories in both health and disease scenarios. This work aims to furnish a newcomer researcher and/or clinician with essential guidelines to embark on a single-cell adventure without succumbing to common pitfalls. By bridging the gap between theory and practice, it facilitates the translation of single-cell technologies into clinically relevant applications. Throughout the manuscript, practical examples of its usage in women's reproductive health studies are provided. Various sections delve into specific clinical scenarios, demonstrating how these guidelines can be instrumental in unraveling the molecular landscapes of diseases and physiological processes related to women's reproduction.},
}

Female
Humans
*Single-Cell Analysis/methods
*Genitalia, Female/cytology
Sequence Analysis, RNA
Pregnancy

@article {pmid40248651,
year = {2025},
author = {Liu, WW and Yin, CZ and Zhang, ZX and Wang, XS and Meng, Z and Zhang, XG and Wang, S},
title = {Four new species of Beltraniella (Amphisphaeriales, Beltraniaceae) revealed by morphology and phylogenetic analyses from China.},
journal = {MycoKeys},
volume = {116},
number = {},
pages = {125-144},
pmid = {40248651},
issn = {1314-4049},
abstract = {Beltraniella is a widely-distributed genus on Earth, although its abundance is relatively limited in relation to other dematiaceous hyphomycetes. In the present study, diseased leaves of Myristicafragrans and decaying leaves were collected from Hainan and Sichuan Province. Fungal DNA was amplified and sequenced using two barcodes, the internal transcribed spacer (ITS) and large subunit of ribosomal RNA (LSU), and phylogenetic analyses were conducted through maximum likelihood (ML) and Bayesian inference (BI) algorithms. Four new species of Beltraniella, B.dujiangyanensis, B.jianfengensis, B.myristicae, and B.xinglongensis are identified through phylogenetic analyses and morphological comparison during a survey of fungal diversity in Hainan and Sichuan Provinces, China. Detailed descriptions of the morphological characteristics of these four new species are provided and illustrated with figures.},
}

@article {pmid40248647,
year = {2024},
author = {Wibisana, JN and Plessy, C and Dierckxsens, N and Masunaga, A and Miao, J and Luscombe, NM},
title = {The complete mitogenome of an unidentified Oikopleura species.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {1357},
pmid = {40248647},
issn = {2046-1402},
mesh = {*Genome, Mitochondrial ; Animals ; *Urochordata/genetics/classification ; Japan ; Sequence Analysis, DNA ; },
abstract = {Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of Oikopleura dioica. This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.},
}

*Genome, Mitochondrial
Animals
*Urochordata/genetics/classification
Japan
Sequence Analysis, DNA

@article {pmid40248491,
year = {2025},
author = {Fulci, V},
title = {Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf044},
pmid = {40248491},
issn = {2631-9268},
mesh = {*Software ; *Gene Expression Profiling/methods ; *Transcriptome ; Humans ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Recently, several protocols repurposing the Illumina flow cells or DNA nanoballs as an RNA capture device for spatial transcriptomics have been reported. These protocols yield high volumes of sequencing data which are usually analyzed through the use of high-performance computing clusters. I report Fast analysis of Spatial Transcriptomic (FaST), a novel pipeline for the analysis of subcellular resolution spatial transcriptomics datasets based on barcoding. FaST is compatible with OpenST, seq-scope, Stereo-seq, and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of >500 M million reads in as little as 1 h on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented Spatial Transcriptomics datasets suitable for subsequent analysis through commonly used packages (e.g scanpy or seurat). Notably, the pipeline I present relies on the spateo-release package for RNA segmentation and does not require hematoxylin/eosin or any other imaging procedure to guide cell segmentation. Nevertheless, integration with other software for imaging-guided cell segmentation is still possible. FaST is publicly available on github (https://github.com/flcvlr/FaST).},
}

*Software
*Gene Expression Profiling/methods
*Transcriptome
Humans
Sequence Analysis, RNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid40248452,
year = {2025},
author = {Hrivniak, Ľ and Sroka, P and Godunko, RJ and Martynov, AV and Palatov, DM and Bojková, J},
title = {Discovering diversity of Central Asian and Himalayan Epeorus (Caucasiron) mayflies (Ephemeroptera, Heptageniidae) using DNA barcoding and morphology.},
journal = {ZooKeys},
volume = {1234},
number = {},
pages = {89-125},
pmid = {40248452},
issn = {1313-2989},
abstract = {The mayflies of the genus Epeorus Eaton, 1881 subgenus Caucasiron Kluge, 1997 are distributed from the eastern Mediterranean to the mountains of south-west China. In contrast to the Caucasus, the Mediterranean and Irano-Anatolian regions, where E. (Caucasiron) represents one of the most extensively studied mayfly taxa, the species diversity in the more eastern mountains of Asia has been studied only sporadically. In this study, the species diversity of E. (Caucasiron) from the mountains of Central Asia (Pamir, Tian Shan) and the western part of the Himalayas was analysed using DNA barcoding and the morphology of larvae and adults. The distance- and phylogenetic tree-based molecular species delimitation analyses revealed five E. (Caucasiron) species occurring in the study area. Three of them did not correspond morphologically to any known species of the genus Epeorus. These species were described herein as E. (C.) himalayensis Hrivniak & Sroka, sp. nov., E. (C.) lanceolatus Hrivniak & Sroka, sp. nov. and E. (C.) lineatus Hrivniak & Sroka, sp. nov. All new species were compared with other representatives of the subgenus and other related species of the genus Epeorus, and appropriate morphological diagnostic characters were provided. Morphological revision, main diagnostic characters, and information on the distribution of E. (C.) guttatus Braasch & Soldán, 1979 and two other potentially related Epeorus species from the area, E.psi Eaton, 1885 and E.suspicatus (Braasch, 2006), are also given.},
}

@article {pmid40247933,
year = {2025},
author = {Moulin, N},
title = {MANGF: a reference library of DNA barcodes for Mantodea from French Guiana (Insecta, Dictyoptera).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e149486},
pmid = {40247933},
issn = {1314-2828},
abstract = {BACKGROUND: Mantodea plays a special role in the food chain as a group charismatic generalist predators. They regulate invertebrate populations while themselves being prey for many larger animals such as reptiles and birds. The present study focuses on Fench Guiana where about 78 species are known within eight families. This diversity represents a challenge for specimen identification.

NEW INFORMATION: The MANGF project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of mantises as indicators in ecological studies. As a first step towards that goal, we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 425 records representing 68 species in eight different families. Species were identified by expert taxonomists and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.},
}

@article {pmid40246065,
year = {2025},
author = {Oskolas, H and Nogueira, FCN and Domont, GB and Yu, KH and Semenov, YR and Sorger, P and Steinfelder, E and Corps, L and Schulz, L and Wieslander, E and Fenyö, D and Kárpáti, S and Holló, P and Kemény, LV and Döme, B and Megyesfalvi, Z and Pawłowski, K and Nishimura, T and Kwon, H and Encarnación-Guevara, S and Szasz, AM and Veréb, Z and Gyulai, R and Németh, IB and Appelqvist, R and Rezeli, M and Baldetorp, B and Horvatovich, P and Malmström, J and Pla, I and Sanchez, A and Knudsen, B and Kiss, A and Malm, J and Marko-Varga, G and Gil, J},
title = {Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105442},
doi = {10.1016/j.jprot.2025.105442},
pmid = {40246065},
issn = {1876-7737},
abstract = {This white paper presents a comprehensive biobanking framework developed at the European Cancer Moonshot Lund Center that merges rigorous sample handling, advanced automation, and multi-omic analyses to accelerate precision oncology. Tumor and blood-based workflows, supported by automated fractionation systems and standardized protocols, ensure the collection of high-quality biospecimens suitable for proteomic, genomic, and metabolic studies. A robust informatics infrastructure, integrating LIMS, barcoding, and REDCap, supports end-to-end traceability and realtime data synchronization, thereby enriching each sample with critical clinical metadata. Proteogenomic integration lies at the core of this initiative, uncovering tumor- and blood-based molecular profiles that inform cancer heterogeneity, metastasis, and therapeutic resistance. Machine learning and AI-driven models further enhance these datasets by stratifying patient populations, predicting therapeutic responses, and expediting the discovery of actionable targets and companion biomarkers. This synergy between technology, automation, and high-dimensional data analytics enables individualized treatment strategies in melanoma, lung, and other cancer types. Aligned with international programs such as the Cancer Moonshot and the ICPC, the Lund Center's approach fosters open collaboration and data sharing on a global scale. This scalable, patient-centric biobanking paradigm provides an adaptable model for institutions aiming to unify clinical, molecular, and computational resources for transformative cancer research.},
}

@article {pmid40245615,
year = {2025},
author = {Wu, Q and Nakano, T and Ishida, S and Komai, T and Fujiwara, Y and Yoshida, T and Kawato, M and Oka, SI and Fujikura, K and Miya, M and Minamoto, T},
title = {Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107094},
doi = {10.1016/j.marenvres.2025.107094},
pmid = {40245615},
issn = {1879-0291},
abstract = {Cephalopods play crucial roles in marine ecosystems, acting as both predators and prey for apex predators, thereby contributing to the distribution of energy and nutrients across the food web. Traditional net capture methods are often ineffective for studying cephalopods owing to their wide distribution in marine environments, necessitating the development of simple and efficient surveying techniques to assess cephalopod diversity. Therefore, in this study, we aimed to establish universal polymerase chain reaction primers specifically targeting mitochondrial 16S rRNA genes for environmental DNA metabarcoding in cephalopods. Two primer sets, Cep16S_D and Cep16S_O, were designed for squids and octopuses, respectively. Taxonomic specificity, resolution, and coverage of these primers were evaluated via in silico and in vitro analyses. Additionally, efficiency of these primer sets was assessed using tissue samples and mock communities. Finally, their applicability and performance were tested at various depths. The developed primers exhibited a relatively large amplification size with mixed bases that enhanced their amplification efficiency and sensitivity for cephalopod detection. We successfully identified cephalopod species with different body sizes, from small species, such as Heteroteuthis dagamensis, to large species, such as Architeuthis dux, at varying water depths. Overall, the primer sets established in this study serve as powerful tools to study cephalopod diversity and exhibit great potential for barcoding and genetic diversity investigations.},
}

@article {pmid40242636,
year = {2025},
author = {Munkhtulga, D and Baasanmunkh, S and Nyamgerel, N and Park, JH and Tsegmed, Z and Tojibaev, KS and Choi, HJ},
title = {Morphological and phylogenetic analysis approach to three new species and a new section of Astragalus (Fabaceae) from Mongolia.},
journal = {PhytoKeys},
volume = {255},
number = {},
pages = {51-73},
pmid = {40242636},
issn = {1314-2011},
abstract = {Astragalus L. is the largest genus worldwide, comprising more than 3,100 species belonging to 250 sections. In Mongolia, approximately 130 species, including 15 endemic and 25 subendemic species have been previously recognized from 42 sections and 6 subgenera. In this study, we investigated several species within section Laguropsis in Mongolia based on extensive morphological analyses and molecular evidence. Based on these results, we describe three new species and a new section. Two of the newly described species, A.oyunicus and A.teshigicus, belong to the section Laguropsis, whereas the remaining species, A.uvsicus, is the type species of the new section Uvsicus. Furthermore, our findings revealed that (i) A.tamiricus, previously considered endemic to Mongolia, is an additional synonym of A.laguroides, and (ii) A.gobi-altaicus, previously a synonym of A.laguroides, is an independent species. Finally, we provide taxonomic nomenclature, morphological observations, distribution maps and wild photo illustrations of each species.},
}

@article {pmid40238250,
year = {2025},
author = {Zhao, J and Yang, W and Cai, H and Cao, G and Li, Z},
title = {Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071116},
pmid = {40238250},
issn = {2304-8158},
support = {Grant No. ZDYF2024GXJS316//Key Research and Development Projects in Hainan Province/ ; },
abstract = {Addressing the pervasive issue of food adulteration and fraud driven by economic interests has long presented a complex challenge. Such adulteration not only compromises the safety of the food supply chain and destabilizes the market economy but also poses significant risks to public health. Food adulteration encompasses practices such as substitution, process manipulation, mislabeling, the introduction of undeclared ingredients, and the adulteration of genetically modified foods. Given the diverse range of deceptive methods employed, genomics-based identification techniques have increasingly been utilized for detecting food adulteration. Compared to traditional detection methods, technologies such as polymerase chain reaction (PCR), next-generation sequencing (NGS), high-resolution melt (HRM) analysis, DNA barcoding, and the CRISPR-Cas system have demonstrated efficacy in accurately and sensitively detecting even trace amounts of adulterants. This paper provides an overview of genomics-based approaches for identifying food adulteration, summarizes the latest applications in certification procedures, discusses current limitations, and explores potential future trends, thereby offering new insights to enhance the control of food quality and contributing to the development of more robust regulatory frameworks and food safety policies.},
}

@article {pmid40237570,
year = {2025},
author = {Bignotto, TS and de Souza, HB and da Silva Bronzim, RC and Maniglia, TC and Baumgartner, D},
title = {Integrative morphometric and molecular analyses reveal possible genetic contamination of silver catfish populations of the genus Rhamdia in Neotropical River basins.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70057},
pmid = {40237570},
issn = {1095-8649},
abstract = {Rhamdia quelen, Rhamdia branneri and Rhamdia voulezi are morphologically similar species that, until recently, were considered synonymous. Although R. quelen has wide distribution in the Neotropical region, R. branneri and R. voulezi are sympatric and endemic species of the Iguaçu River basin. We used an integrative approach, including morphometric and molecular data (barcodes DNA, COI gene), to assist in the identification and delimitation of these species. We also intended to investigate genetic contamination of the Paraná III and lower Iguaçu River basins, as silver catfish production has increased in southern Brazil, and accidental or occasional escapes to nature may pose risks to the genetic integrity of native populations. COI sequences and morphometric data were efficient in the characterization and differentiation of Rhamdia species and may be helpful tools in correctly identifying R. quelen, R. branneri and R. voulezi. Both morphometric and molecular analyses indicated the segregation of specimens into three groups. Although this separation coincided with the taxonomy and the collection site in the morphometric analyses, the taxonomic identification of most samples did not coincide with the molecular identification. This fact may be due to (i) incorrect morphological identification and/or (ii) escapes of pure species and/or interspecific hybrids from fish farms. The detection of COI haplotypes of R. quelen in the lower Iguaçu River, as well as COI haplotypes of R. branneri and R. voulezi in the Paraná III basin, combined with the morphometric and morphological characteristics of the specimens, reinforces the occurrence of hybrid specimens in these river basins. These results reveal the importance of characterizing species and interspecific hybrids of Rhamdia and the urgency to regulate aquaculture activities.},
}

@article {pmid40236044,
year = {2025},
author = {Blois, S and Goetz, BM and Mojumder, A and Sullivan, CS},
title = {Shedding dynamics of a DNA virus population during acute and long-term persistent infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.31.646279},
pmid = {40236044},
issn = {2692-8205},
abstract = {UNLABELLED: Although much is known of the molecular mechanisms of virus infection within cells, substantially less is understood about within-host infection. Such knowledge is key to understanding how viruses take up residence and transmit infectious virus, in some cases throughout the life of the host. Here, using murine polyomavirus (muPyV) as a tractable model, we monitor parallel infections of thousands of differentially barcoded viruses within a single host. In individual mice, we show that numerous viruses (>2600) establish infection and are maintained for long periods post-infection. Strikingly, a low level of many different barcodes is shed in urine at all times post-infection, with a minimum of at least 80 different barcodes present in every sample throughout months of infection. During the early acute phase, bulk shed virus genomes derive from numerous different barcodes. This is followed by long term persistent infection detectable in diverse organs. Consistent with limited productive exchange of virus genomes between organs, each displays a unique pattern of relative barcode abundance. During the persistent phase, constant low-level shedding of typically hundreds of barcodes is maintained but is overlapped with rare, punctuated shedding of high amounts of one or a few individual barcodes. In contrast to the early acute phase, these few infrequent highly shed barcodes comprise the majority of bulk shed genomes observed during late times of persistent infection, contributing to a stark decrease in bulk barcode diversity that is shed over time. These temporally shifting patterns, which are conserved across hosts, suggest that polyomaviruses balance continuous transmission potential with reservoir-driven high-level reactivation. This offers a mechanistic basis for polyomavirus ubiquity and long-term persistence, which are typical of many DNA viruses.

AUTHOR SUMMARY / IMPORTANCE: Polyomavirus infections, mostly benign but potentially fatal for immunocompromised individuals, undergo acute and long-term persistent infections. Typically, polyomavirus-associated diseases arise due to virus infection occurring in the context of a persistently infected individual. However, little is understood regarding the mechanisms of how polyomaviruses establish, maintain, and reactivate from persistent infection. We developed a non-invasive virus shedding assay combining barcoded murine polyomavirus, massively parallel sequencing technology, and novel computational approaches to track long-term infections in mice. We expect these methods to be of use not only to the study of DNA viruses but also for understanding persitent infection of diverse microbes. The study revealed organ-specific virus reservoirs and two distinct shedding patterns: constant low-level shedding of numerous barcodes and episodic high-level shedding of few barcodes. Over time, the diversity of shed barcodes decreased substantially. These findings suggest a persistent low-level infection in multiple reservoirs, with occasional bursts of replication in a small subset of infected cells. This combination of broad reservoirs and varied shedding mechanisms may contribute to polyomavirus success in transmission and maintaining long-term infections.},
}

@article {pmid40236020,
year = {2025},
author = {Tasca, JA and Doherty, JF and Shields, EJ and Mudiyanselage, SD and Reich, LN and Sarma, K and Garcia, BA and Bonasio, R},
title = {Pooled scanning of protein variants identifies novel RNA-binding mutants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.02.646914},
pmid = {40236020},
issn = {2692-8205},
abstract = {Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying separation-of-function mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein for its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein-RNA interactions.},
}

@article {pmid40235722,
year = {2025},
author = {Chai, Y and Tian, T and Wang, L and Wei, J and Xu, Y and Liu, P and Xiang, C and Yue, M},
title = {Using Plant DNA Barcodes and Functional Traits to Assess Community Assembly of Quercus Forests at Different Scales in the Semiarid Loess Plateau of China.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71103},
pmid = {40235722},
issn = {2045-7758},
abstract = {Trait and evolutionary differences among coexisting species are increasingly used to comprehend the processes shaping communities. However, they do not consistently yield congruent insights due to methodological limitations and scale dependence. Utilizing two plastid DNA genes (rbcL and matK) and one nuclear DNA gene (internal transcribed spacer, ITS), we first constructed the phylogenies of 147 woody species from 98 line transects in the forest areas of the Loess Plateau and subsequently measured three functional traits. Five plots (2500 m[2]) were constructed within Quercus forests to analyze the functional and phylogenetic structures at three spatial scales (100, 400, 2500 m[2]) and two vertical structural layers (tree colonization and shrub layer). In contrast to the phylogenetic convergence observed at the genus level, using plant DNA barcodes, we found that the entire forest communities and the tree layer exhibited phylogenetic randomness across all three spatial scales; even the shrub layer showed phylogenetic overdispersion with increasing scale. Specific leaf area (SLA) exhibited functional convergence in both the shrub and tree layers. In contrast, seed mass (SM) and plant height (PH) displayed distinct functional structures. In the tree layer, these traits showed phylogenetic overdispersion, while in the shrub layer, they demonstrated functional convergence. This contrast highlights the different ecological roles and processes at play in the two layers. Specifically, the scale dependency of assembly patterns in the shrub layer was more pronounced than in the tree layer for both functional and phylogenetic structures. Our findings underscore the significance of employing DNA barcodes to assess the phylogenetic structure of communities with closely related coexisting species and emphasize niche-based functional assembly and multi-process phylogenetic assembly among vertical structural layers in the Quercus community. Decoupling functional and phylogenetic disparities between species could facilitate the understanding of complex species differences influencing community assembly.},
}

@article {pmid40234750,
year = {2025},
author = {Shen, X and Li, Y and Liu, Y and Jiang, D},
title = {Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {475},
pmid = {40234750},
issn = {1471-2229},
support = {2021C02071-4-2//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; },
abstract = {BACKGROUND: Cherries, a subgenus of Cerasus within Rosaceae, as fruit trees with high economic value and elegant garden plants, have broad prospects for development and utilization. However, traditional morphology and molecular data have struggled to accurately identify cherry species due to their extensive overlap in the distribution, frequent hybridization, both open and closed flowers, hysteranthy and limited species coverage, hindering the advancement of the cherry industry. In this study, 61 well-documented cherry species were collected and whole chloroplast genome data was used to develop an effective DNA identification system for precise species identification.

RESULTS: 36 new cherry chloroplast genomes were added to the public database, resulting in the most comprehensive phylogenetic relationship of cherry species to date. While whole chloroplast genome data achieved an 85.26% species identification success rate, it did not fully resolve all species identification. Relying solely on whole chloroplast genome data is resource-intensive. Therefore, we explored using highly variable regions, species-specific SNPs, and structural variations for accurate species identification. This study revealed that 14 newly developed DNA barcodes could identify 71.88% of cherry samples, while 106 SNPs and Indels allowed for precise identification of 59 out of 61 cherry species.

CONCLUSIONS: This study not only clarified the phylogenetic relationships of major cherry species but also developed a precise identification system, providing a robust tool for accurate species identification and laying a solid foundation for breeding and the broader promotion of cherry species.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid40231940,
year = {2025},
author = {Grbin, D and Zrnčić, S and Oraić, D and Alfier, M and Cindrić, M and Jović, L and Sučec, I and Zupičić, IG},
title = {Seafood Labeling in Croatia: Molecular Evidence and Regulatory Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14060917},
pmid = {40231940},
issn = {2304-8158},
support = {Project MetaPatvor NPOO.C3.2.R3-I1.04.0122//European Union NextGenerationEU/ ; },
abstract = {Fisheries and aquaculture play a crucial role in global food security, yet species mislabeling remains a persistent challenge, undermining consumer trust and market transparency. Proper food labeling is essential for protecting public health due to the presence of unknown toxic or allergenic substances and preventing illegally sourced products from entering the market. Despite extensive research across Europe, seafood mislabeling in Croatia has remained unexplored. This study aims to provide the first comprehensive assessment of seafood labeling accuracy in Croatia, where fisheries are integral to the coastal economies and tourism. Using DNA barcoding of the COI gene, 109 seafood samples were collected over two years from various sources, including restaurants, markets, and fishing vessels, and analyzed for potential mislabeling. Results revealed a mislabeling rate of 3% among fish samples and 20% among cephalopods, with notable substitutions, such as the yellowfin tuna mislabeled as bigeye tuna and Bluefin tuna and the European squid mislabeled as Patagonian squid. Additionally, 38.5% of samples were partially labeled, while 32% lacked clear country-of-origin information, complicating traceability. While the findings align with the mislabeling rates in other European countries, this study underscores the ongoing challenges in seafood labeling compliance. Establishing standardized monitoring protocols will be essential for improving comparability and effectively addressing seafood fraud.},
}

@article {pmid40228207,
year = {2025},
author = {Leibovich, N and Goyal, S},
title = {Limitations and optimizations of cellular lineages tracking.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012880},
doi = {10.1371/journal.pcbi.1012880},
pmid = {40228207},
issn = {1553-7358},
mesh = {*Cell Lineage/genetics ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Cell Tracking/methods ; Humans ; Animals ; },
abstract = {Tracking cellular lineages using genetic barcodes provides insights across biology and has become an important tool. However, barcoding strategies remain ad hoc. We show that elevating barcode insertion probability and thus increasing the average number of barcodes within the cells, adds to the number of traceable lineages but may decrease the accuracy of lineages inference due to reading errors. We establish the trade-off between accuracy in tracing lineages and the total number of traceable lineages, and find optimal experimental parameters under limited resources concerning the populations size of tracked cells and barcode pool complexity.},
}

*Cell Lineage/genetics
Computational Biology/methods
*DNA Barcoding, Taxonomic/methods
*Cell Tracking/methods
Humans
Animals

@article {pmid40226864,
year = {2025},
author = {Huang, Y and Zhang, Z and Yang, T and Zhang, Y and Cheng, X and Kang, Y and Guang, Y and Zou, Y and Zhang, X and Luo, Z and Chen, J and Cheng, W},
title = {Gemini Molecular Assembly Colocalization (GOAL): Accurate and Efficient Fusion Genotyping for Chronic Myeloid Leukemia Intelligent Diagnosis.},
journal = {Small methods},
volume = {},
number = {},
pages = {e2500194},
doi = {10.1002/smtd.202500194},
pmid = {40226864},
issn = {2366-9608},
support = {82372334//National Natural Science Foundation of China/ ; 82302621//National Natural Science Foundation of China/ ; U24A20751//National Natural Science Foundation of China/ ; KJZD-K202200404//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; KJQN202300435//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; CSTB2023NSCQ-LZX0022//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0183//Future Medical Youth Innovation Team Development Support Program Project of Chongqing Medical University/ ; CYYY-DSTDXM-202305//The First Affiliated Hospital of Chongqing Medical University Graduate Tutor Team Building Project Grants/ ; CYYY-YJSJXCX-202303//The First Affiliated Hospital of Chongqing Medical University Graduate Teaching Innovation Team Project Grants/ ; },
abstract = {RNA small fragment aberrances are associated with diseases by mediating a range of pathogenesis and pathological processes. DNA assembly-based barcoding and amplification technologies are currently being actively explored for RNA in situ analysis. However, these modular integrated DNA assembly processes are inevitably accompanied with false positive signals caused by unexpected misassembly. Completely avoiding this phenomenon through simple and universal methods is challenging. Here, a novel dual-input to dual-output in situ analysis paradigm is proposed, aiming to improve target specificity through co-recognition (dual-input) and to eliminate false positive misassembly through fluorescent signal co-localization (dual-output). Based on this paradigm, Gemini molecular assembly co-localization (GOAL) in situ imaging system is launched to accurately distinguish the fusion gene subtypes associated with chronic myeloid leukemia (CML), and to precisely report the proportion of minimum residual cancer cells in clinical samples by intelligent co-localization counting and sorting. GOAL achieves highly sensitive and accurate genotyping recognition of 0.01% CML tumor cells and realizes fully automatic rapid diagnosis with a customized Intelligent Cell Image Sorter (iCis). iCis-assisted GOAL represents an innovative and versatile molecular toolkit for accurate, rapid, user-friendly, and professional-independent profiling of cancer cells with RNA small fragment aberrances, providing efficient clinical decision support for disease diagnosis.},
}

@article {pmid40221509,
year = {2025},
author = {Siriwan, W and Charoenlappanit, S and Phaonakrop, N and Thaisakun, S and Roytrakul, S},
title = {Identification of peptidome-based biomarkers of cassava mosaic disease resistance in different cassava varieties.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12653},
pmid = {40221509},
issn = {2045-2322},
support = {FF(KU)18.65//Kasetsart University Research and Development (KURDI)/ ; },
mesh = {*Manihot/virology/metabolism/genetics ; *Disease Resistance ; Biomarkers/metabolism/analysis ; *Plant Diseases/virology/genetics ; *Peptides/metabolism/analysis ; Tandem Mass Spectrometry ; Chromatography, Liquid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Plant Proteins/metabolism ; Proteomics/methods ; },
abstract = {Cassava, a major economic crop in Thailand, yielded over 3 million USD in exports in 2023. However, its production has been declining since 2021 due to cassava mosaic disease (CMD) outbreaks, which affect cassava plantations. CMD infections have recently increased due to the scarcity of healthy stems and CMD-resistant varieties, the latter being key to controlling its spread. Developing novel methods is critical for accelerating the cultivation of high-yield, CMD-resistant varieties. In this study, signature peptide patterns were determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem MS (LC-MS/MS) to screen for CMD-resistant varieties. Peptide mass fingerprint (PMF) analyses revealed distinct peptide barcodes across 11 varieties, clearly delineating CMD-resistant and CMD-tolerant phenotypes. LC-MS/MS and orthogonal partial least squares-discriminant analysis (OPLS-DA) further demonstrated clear distinctions between the peptide profiles of different phenotypes. Heatmap and PMF analyses consistently revealed unique peptide patterns across the varieties. Volcano plot analysis identified seven upregulated peptides-TATTVAGS, PAAGGGGG, PNELLSYSE, SSIEEGGS, GGGVGGPL, NNGGGFSV, and GPGPAPAA-in CMD-resistant plants. These peptides were associated with proteins containing CONSTANS-like zinc finger, C2H2-type, GST N-terminal, Tubby-like F-box, nuclear-localized AT-hook motif, auxin response factor, and C2 domains. Altogether, this study identified peptidome-based biomarkers for screening CMD-resistant varieties; however, further validation using larger samples is necessary.},
}

*Manihot/virology/metabolism/genetics
*Disease Resistance
Biomarkers/metabolism/analysis
*Plant Diseases/virology/genetics
*Peptides/metabolism/analysis
Tandem Mass Spectrometry
Chromatography, Liquid
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Plant Proteins/metabolism
Proteomics/methods

@article {pmid40221395,
year = {2025},
author = {Huayamares, SG and Lian, L and Rab, R and Hou, Y and Radmand, A and Kim, H and Zenhausern, R and Achyut, BR and Gilbert Ross, M and Lokugamage, MP and Loughrey, D and Peck, HE and Echeverri, ES and Da Silva Sanchez, AJ and Shajii, A and Li, A and Tiegreen, KE and Santangelo, PJ and Sorscher, EJ and Dahlman, JE},
title = {Nanoparticle delivery of a prodrug-activating bacterial enzyme leads to anti-tumor responses.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3490},
pmid = {40221395},
issn = {2041-1723},
support = {R01DE026941//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Prodrugs/administration & dosage/metabolism/pharmacology ; *Purine-Nucleoside Phosphorylase/genetics/metabolism ; *Nanoparticles/chemistry/administration & dosage ; Mice ; Humans ; Cell Line, Tumor ; Escherichia coli/enzymology/genetics ; *Antineoplastic Agents/pharmacology/administration & dosage ; Vidarabine/analogs & derivatives/metabolism/pharmacology/administration & dosage ; Female ; Vidarabine Phosphate/analogs & derivatives/pharmacology/metabolism ; Xenograft Model Antitumor Assays ; RNA, Messenger/metabolism/genetics ; *Head and Neck Neoplasms/drug therapy ; Drug Delivery Systems ; *Escherichia coli Proteins/genetics/metabolism ; },
abstract = {Most cancer patients diagnosed with late-stage head and neck squamous cell carcinoma are treated with chemoradiotherapy, which can lead to toxicity. One potential alternative is tumor-limited conversion of a prodrug into its cytotoxic form. We reason this could be achieved by transient and tumor-specific expression of purine nucleoside phosphorylase (PNP), an Escherichia coli enzyme that converts fludarabine into 2-fluoroadenine, a potent cytotoxic drug. To efficiently express bacterial PNP in tumors, we evaluate 44 chemically distinct lipid nanoparticles (LNPs) using species-agnostic DNA barcoding in tumor-bearing mice. Our lead LNP, designated LNP intratumoral (LNP[IT]), delivers mRNA that leads to PNP expression in vivo. Additionally, in tumor cells transfected with LNP[IT], we observe upregulated pathways related to RNA and protein metabolism, providing insight into the tumor cell response to LNPs in vivo. When mice are treated with LNP[IT]-PNP, then subsequently given fludarabine phosphate, we observe anti-tumor responses. These data are consistent with an approach in which LNP-mRNA expression of a bacterial enzyme activates a prodrug in solid tumors.},
}

Animals
*Prodrugs/administration & dosage/metabolism/pharmacology
*Purine-Nucleoside Phosphorylase/genetics/metabolism
*Nanoparticles/chemistry/administration & dosage
Mice
Humans
Cell Line, Tumor
Escherichia coli/enzymology/genetics
*Antineoplastic Agents/pharmacology/administration & dosage
Vidarabine/analogs & derivatives/metabolism/pharmacology/administration & dosage
Female
Vidarabine Phosphate/analogs & derivatives/pharmacology/metabolism
Xenograft Model Antitumor Assays
RNA, Messenger/metabolism/genetics
*Head and Neck Neoplasms/drug therapy
Drug Delivery Systems
*Escherichia coli Proteins/genetics/metabolism

@article {pmid40220447,
year = {2025},
author = {Duft, RG and Griffin, JL and Stead, DA},
title = {MEATiCode: A comprehensive proteomic LC-MS/MS method for simultaneous species identification in meat authentication.},
journal = {Food chemistry},
volume = {483},
number = {},
pages = {144231},
doi = {10.1016/j.foodchem.2025.144231},
pmid = {40220447},
issn = {1873-7072},
abstract = {Food fraud in the meat industry threatens consumer trust, market stability, and public health. Traditional methods like DNA barcoding are limited, especially for processed foods where DNA is often degraded. This paper introduces the workflow MEATiCode, a comprehensive proteomic liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the simultaneous identification of species in meat authentication. Application of a novel database search approach - MEATiCode - enabled the differentiation of meat species (as demonstrated for beef, pork, chicken and lamb) in raw and cooked food products following a simple sample preparation procedure and LC-MS/MS analysis of extracted meat peptides. The efficacy of the MEATiCode method was demonstrated through its application to a range of meat products, achieving high sensitivity (0.5 % Limit of Detection (LoD)) and reliability in the detection of adulteration, even in highly processed or cooked meats.},
}

@article {pmid40218301,
year = {2025},
author = {Yang, S and Zhao, Z and Xu, Z and Liu, Y and Jiang, M and Fu, L and Zhang, J and Jing, Z and Pang, X and Shao, W and Zhang, C and Li, Y and Du, X and Wu, J},
title = {Identification of Hybrid Sturgeon (Acipenser baerii × Acipenser schrenckii) from Their Parents Using Germplasm.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070907},
pmid = {40218301},
issn = {2076-2615},
support = {2021YFYZ0015//the Sichuan Science and Technology Program/ ; SCCXTD-2024-15//Project of Sichuan Innovation Team of National Modern Agricultural Industry Technology System/ ; kczx2023-2025-19//2023 Aquaculture Breeding Research Project, Integration and application demonstration of key technologies for sturgeon breeding/ ; },
abstract = {The hybrid sturgeon Acipenser baerii × A. schrenckii is the most widely cultured commercial sturgeon in China. However, its morphological similarity to the parental species frequently leads to misuse of germplasm in the breeding process, resulting in a decline in the quality of the sturgeon production. In this study, we have developed a protocol by using mitochondrial DNA barcoding and microsatellite locus analysis for the accurate identification of sturgeon species. Genetic distance and phylogenetic analysis based on the mitochondrial COI segment showed that A. baerii exhibited the closest genetic relationship with orthogonal individuals A. baerii (♀) × A. schrenckii (♂). Conversely, A. schrenckii displayed the highest genetic similarity with reciprocal individuals A. schrenckii (♀) × A. baerii (♂). Additionally, genetic structure analysis and factor correlation analysis (FCA) were conducted using six microsatellite loci among 100 samples, including eight species and two hybrid sturgeon. The results showed that all samples, encompassing both hybrid sturgeon (A. baerii × A. schrenckii) and their parental species, were accurately grouped into ten clusters, thereby validating the precision of this species assignment method.},
}

@article {pmid40212379,
year = {2025},
author = {Qiu, Y and Fan, D and Wang, J and Zhou, X and Teng, X and Rao, C},
title = {High throughput construction of species characterized bacterial biobank for functional bacteria screening: demonstration with GABA-producing bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1545877},
pmid = {40212379},
issn = {1664-302X},
abstract = {Bacteria and their metabolites exhibit remarkable diversity, offering substantial potential for industrial biotechnology. However, the low throughput for constructing and screening bacterial biobanks limits the exploration and utilization of this diversity. In this study, we developed a cost-effective, high-throughput platform for bacterial biobank construction and functional screening. We employed a double-ended barcoding strategy, enabling thousands of bacterial isolates to be pooled for simultaneous Nanopore sequencing of full-length 16S rDNA for species identification. This approach demonstrated 99% accuracy compared to Sanger sequencing while reducing per-sample costs to under 10%. Using this platform, we established a bacterial biobank comprising 15,337 bacterial isolates derived from fermented foods and infant feces collected across China. To identify functional bacteria within the biobank, we designed a versatile fluorescence-based biosensor system employing dual plasmids to decouple metabolite sensing from signal reporting. This modular biosensor framework can be readily adapted for detecting diverse metabolites. As a proof-of-concept, we screened 1,740 isolates and identified 46 with high γ-aminobutyric acid (GABA)-producing capacity, demonstrating potential for probiotic development. Together, our integrated bacterial identification and functional screening platform provides an efficient pipeline for the discovery of functional bacteria, advancing industrial biotechnology through synthetic biology.},
}

@article {pmid40208941,
year = {2025},
author = {Zhao, X and Zhao, Y and Li, Z and Liu, H and Fu, W and Chen, F and Sun, Y and Song, D and Fan, C and Zhao, Y},
title = {Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {15},
pages = {e2425000122},
doi = {10.1073/pnas.2425000122},
pmid = {40208941},
issn = {1091-6490},
support = {22125404//MOST | National Natural Science Foundation of China (NSFC)/ ; 22004096//MOST | National Natural Science Foundation of China (NSFC)/ ; 22474107//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023YFB3210103//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023JC-JQ-23//Natural Science Foundation of Shaanxi Province (Shaanxi Natural Science Foundation)/ ; 2023-CX-TD-62//Innovation Capability Support Program of Shaanxi/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Membrane Proteins/genetics/metabolism ; *Sequence Analysis, DNA/methods ; Breast Neoplasms/genetics/metabolism ; Epithelial Cell Adhesion Molecule/metabolism/genetics ; Receptor, ErbB-2/metabolism/genetics ; DNA Probes/genetics ; Cell Line, Tumor ; Female ; DNA, Single-Stranded/genetics ; },
abstract = {Cellular structure maintenance and function regulation critically depend on the composition and spatial distribution of numerous membrane proteins. However, current methods face limitations in spatial coverage and data scalability, hindering the comprehensive analysis of protein interactions in complex cellular nanoenvironment. Herein, we introduce proximity-activated DNA scanning encoded sequencing (PADSE-seq), an innovative technique that utilizes flexible DNA probes with adjustable lengths. These dynamic probes are anchored at a single end, enabling free swings within a nanoscale range to perform global scanning, recording, and accumulating of information on diverse proximal proteins in random directions along unrestricted paths. PADSE-seq leverages the autonomous cyclic cleavage of single-stranded DNA to sequentially activate encoded probes distributed throughout the local area. This process triggers strand displacement amplification and bidirectional extension reactions, linking proteins barcodes with molecular barcodes in tandem and further generating millions to billions of amplicons embedded with the combinatorial identifiers for next-generation sequencing analysis. As a proof of concept, we validated PADSE-seq for mapping the distribution of over a dozen kinds of proteins, including HER1, EpCAM, and PDL1, in proximity to HER2 in breast cancer cell lines, demonstrating its ability to decode multiplexed protein proximities at the nanoscale. Notably, we observed that the spatial distribution of proximal proteins around low-abundance target proteins exhibited greater diversity across regions with variable proximity ranges. This method offers a massive access for high-resolution and comprehensive mapping of cellular molecular interactions, paving the way for deeper insights into complex biological processes and advancing the field of precision medicine.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Membrane Proteins/genetics/metabolism
*Sequence Analysis, DNA/methods
Breast Neoplasms/genetics/metabolism
Epithelial Cell Adhesion Molecule/metabolism/genetics
Receptor, ErbB-2/metabolism/genetics
DNA Probes/genetics
Cell Line, Tumor
Female
DNA, Single-Stranded/genetics

@article {pmid40208109,
year = {2025},
author = {Stevenson, ZC and Laufer, E and Estevez, AO and Robinson, K and Phillips, PC},
title = {Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkaf081},
pmid = {40208109},
issn = {2160-1836},
abstract = {A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode fitness experiment within an animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, with the frequency of each barcode then being measured at multiple time points via sequencing at deep coverage and used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.},
}

@article {pmid40204808,
year = {2025},
author = {Xu, S and Ouyang, Y and Qin, Y and Chen, D and Duan, Z and Song, D and Harries, D and Xia, F and Willner, I and Huang, F},
title = {Spatiotemporal dynamic and catalytically mediated reconfiguration of compartmentalized cyanuric acid/polyadenine DNA microdroplet condensates.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3352},
pmid = {40204808},
issn = {2041-1723},
support = {21874121//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*DNA/chemistry ; Catalysis ; *Triazines/chemistry ; *Poly A/chemistry ; *Artificial Cells/chemistry/metabolism ; },
abstract = {Native cells possess membrane-bound subcompartments, organelles, such as mitochondria and lysosomes, that intercommunicate and regulate cellular functions. Extensive efforts are directed to develop synthetic cells, or protocells, that replicate these structures and functions. Among these approaches, phase-separated coacervate microdroplets composed of polymers, polysaccharides, proteins, or nucleic acids are gaining interest as cell-mimicking systems. Particularly, compartmentalization of the synthetic protocell assemblies and the integration of functional constituents in the containments allowing signaling, programmed transfer of chemical agents, and spatiotemporal controlled catalytic transformations across the protocell subdomains, are challenging goals in developing artificial cells. Here, we report the assembly of compartmentalized, phase-separated cyanuric acid/polyadenine coacervate microdroplets. Hierarchical, co-centric compartmentalization is achieved through the dynamic and competitive spatiotemporal occupation of pre-engineered barcode domains within the polyadenine microdroplet framework by invading DNA strands. By encoding structural and functional information within these DNA-invaded compartments, the light-triggered, switchable reconfiguration of compartments, switchable catalytic reconfiguration of containments, and reversible aggregation/deaggregation of the compartmentalized microdroplets are demonstrated.},
}

*DNA/chemistry
Catalysis
*Triazines/chemistry
*Poly A/chemistry
*Artificial Cells/chemistry/metabolism

@article {pmid40204203,
year = {2025},
author = {Zhou, X and Faust, K},
title = {A high-throughput and time-efficient Nanopore full-length 16S rRNA gene sequencing protocol for synthetic microbial communities.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2025.04.003},
pmid = {40204203},
issn = {1095-9130},
abstract = {Next-generation sequencing (NGS) has transitioned from primarily research-focused applications to a mature technology. However, resolving microbial community composition on the species level based on the 16S rRNA gene is impeded by several critical bottlenecks that limit the efficiency and scalability of analyses. Specifically, standard MiSeq sequencing suffers from read-length limitation; library preparation requires multiple labour-intensive steps from DNA isolation to amplification and barcoding; and prolonged turnaround times delay results. These challenges underscore the need for improved methods, which our study aims to address. Recent advancements in Oxford Nanopore long-read sequencing technology (ONT), including a smaller and cheaper benchtop instrument and support for diverse sample types, have enabled faster sequencing in-house with reduced costs. To address the need for standardized, reproducible workflows, we present an optimized and state-of-the-art protocol for full-length 16S rRNA gene sequencing using the ONT MinION sequencing device. Furthermore, we quantified the reproducibility and accuracy of our protocol and compared it with the previous MiSeq results. The results showed that the accuracy of our sequencing pipeline for synthetic communities is significantly higher than for MiSeq pipeline. In summary, our protocol elucidates the composition of synthetic microbial communities in an easy, fast and accurate manner while ensuring reproducible results.},
}

@article {pmid40202150,
year = {2025},
author = {Tnah, LH and Ahmad-Farhan, NR and Nur-Nabilah, A and Soo, P and Hazwani-Humaira', Z and Ng, K and Lee, C and Ng, C and Lee, S},
title = {Genetic insights: integrating DNA barcoding with taxonomy in the study of Baccaurea (Phyllanthaceae).},
journal = {Genome},
volume = {68},
number = {},
pages = {1-7},
doi = {10.1139/gen-2024-0105},
pmid = {40202150},
issn = {1480-3321},
mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA, Plant/genetics ; },
abstract = {Traditional taxonomic revisions based on macromorphological and leaf anatomical traits may have limitations in accurately distinguishing certain species within the genus. To improve taxonomic clarity, this study applied DNA barcoding to enhance the understanding of the taxonomy and phylogeny of Baccaurea Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including rbcL, ITS2, and trnH-psbA, were used to analyze 64 samples representing 19 Baccaurea species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of rbcL, ITS2, trnH-psbA, and their combinations rbcL + ITS2 and rbcL + ITS2 + trnH-psbA as 21.1%, 89.5%, 87.5%, 89.5%, and 89.5%, respectively. The Neighbor-Joining tree revealed well-defined, monophyletic species clusters that largely align with phylogenetic positions based on macromorphological features. Notably, our results indicate that Baccaurea parviflora and the synonymized Baccaurea scortechinii are distinct species, recommending the re-establishment of B. scortechinii as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.},
}

*DNA Barcoding, Taxonomic/methods
Phylogeny
DNA, Plant/genetics

@article {pmid40202117,
year = {2025},
author = {Shapiro, JR and Simard, N and Bolotin, S and Watts, TH},
title = {Fluorescent Cell Barcoding of Peripheral Blood Mononuclear Cells for High-Throughput Assessment of Vaccine-Induced T Cell Responses in Low-Volume Research Samples.},
journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology},
volume = {},
number = {},
pages = {},
doi = {10.1002/cyto.a.24933},
pmid = {40202117},
issn = {1552-4930},
support = {//Donation from Juan and Stefania Speck/ ; //Canadian Immunization Research Network/ ; /CAPMC/CIHR/Canada ; },
abstract = {T cell responses are rarely measured in large-scale human vaccine studies due to the sample volumes required, as well as the logistical, technical, and financial challenges associated with available assays. Fluorescent cell barcoding has been proposed in other contexts to allow for more high-throughput flow cytometry-based assays. Here, we aimed to expand on existing barcoding approaches to develop a reagent and sample-sparing assay for in-depth assessment of T cell responses to vaccine antigens. By using various concentrations of two fixable viability dyes in a matrix format, up to 25 samples that were pooled and acquired together could be successfully deconvoluted based on their unique fluorescent signature. This fluorescent cell barcoding approach was then combined with extracellular and intracellular staining to identify functional (i.e., producing at least one cytokine) and polyfunctional (i.e., producing multiple cytokines) T cells in response to vaccine antigen stimulation. As a proof-of-concept, we plated just 200,000 peripheral blood mononuclear cells (PBMC) per condition, and by staining and acquiring only two pooled samples, we were able to detect rare antigen-specific T cell responses in eight donors to four stimulants each. The frequencies of antigen-induced cytokine-positive cells detected in barcoded samples with 200,000 input PBMC were strongly correlated with those detected in non-barcoded samples from the same donors with 1 million input PBMC, demonstrating the validity of this approach. In conclusion, by reducing the number of PBMC needed by five-fold, and the volume of staining reagents needed by 25-fold, this assay has widespread potential applications to human vaccine studies.},
}

@article {pmid40201216,
year = {2025},
author = {Huang, MC and Kawai, T},
title = {A new species of supergiant Bathynomus A. Milne-Edwards, 1879 (Isopoda: Cirolanidae) from the Paracel Islands, South China Sea.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e144238},
pmid = {40201216},
issn = {1314-2828},
abstract = {BACKGROUND: Bathynomusparacelensis sp. nov., a medium-sized supergiant Bathynomus, is described from specimens obtained at Zhengbin fishing port in Keelung, Taiwan and had been caught in the water near Paracel Islands, South China Sea. Due to its similar shape to B.jamesi, this species has often been mistaken for juveniles or immatures of B.jamesi by fishermen working in this area. Species of Bathynomus can be distinguished morphologically and genetically. The differences from B.jamesi are in the shorter body, clypeus shape, uropod endopod and gene sequence. The difference from B.vaderi is in the body shape, clypeus shape, hook number of maxilliped endite and spines number of maxilulla. Based on the morphological and genetic data results, the specimen is a hitherto undescribed species. The samples were collected as a bycatch species in the deep-sea bottom trawl fishery. The distribution area and depth of this new species and population size are still unclear.

NEW INFORMATION: B.paracelensis sp. nov. is the third supergiant Bathynomus discovered in the South China Sea after B.jamesi and B.vaderi. Its remarkable feature is its short body length and sub-parallel shape. In addition, it is different from B.jamesi and B.vaderi in features such as clypeus shape, number of maxillula keratinised spine and pleotelson spine almost straight. Phylogenetic and barcoding gap analyses confirm that B.paracelensis sp. nov. is not the same species as B.jamsei. Many morphological differences also indicate that it should be a different species from B.vaderi. B.paracelensis sp. nov. may be an intermediate species between giant and supergiant, possessing characteristics of both categories, which can increase researchers' understanding of Bathynomus biodiversity.},
}

@article {pmid40201215,
year = {2025},
author = {Fetnassi, N and Er-Rguibi, O and Aglagane, A and Ghamizi, M and Õunap, E},
title = {Updates to the checklist of nocturnal Macroheterocera (Lepidoptera) of the Central High Atlas of Morocco: One new species added for Morocco.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e137839},
pmid = {40201215},
issn = {1314-2828},
abstract = {BACKGROUND: This paper provides updates to the checklist of Macroheteroceran moths (Lepidoptera) of the central High Atlas of Morocco, following the initial inventory conducted by Charles Rungs nearly five decades ago. Sampling was carried out using sugar bait traps deployed across various habitat types in the region (natural, semi-natural and agricultural lands). Identification of the collected specimens involved a comprehensive approach, including examination of external morphology, dissections of genitalia and DNA barcoding.

NEW INFORMATION: In this study, we recorded a total of 123 species belonging to the families Noctuidae, Erebidae, Geometridae, Eutelidae and Drepanidae. Euxoacos (Noctuidae) was recorded as a new species for Morocco. The presence of Apameamaroccana (Noctuidae) and Chersotisrungsi (Noctuidae), both endemic to Morocco, was verified in the study area. Four of the 123 species were only identified at the genus level. Our inventory also sheds light on species that were previously not known to occur within our study area, reporting twelve species from the High Atlas Mountains for the first time. We also suggest omitting Eupitheciafarinosa (Geometridae) from the Moroccan Lepidoptera list. This study significantly contributes to uncovering an overlooked aspect of Lepidopteran biodiversity in Morocco, which is crucial for future conservation efforts.},
}

@article {pmid40201154,
year = {2025},
author = {Li, Y and Lu, JJ and An, YB and Jiang, L and Wu, HJ and Wang, K and Phurbu, D and Luobu, J and Ma, C and Yang, RH and Dong, CH and Yao, YJ},
title = {An attempt of DNA barcodes based geographical origin authentication of the Chinese caterpillar fungus, Ophiocordycepssinensis.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e144783},
pmid = {40201154},
issn = {2210-6340},
abstract = {Ophiocordycepssinensis is one of the best-known traditional Chinese medicines with distribution confined to the Tibetan Plateau and its surrounding regions. Harvesting the fungus contributes greatly to the livelihood of local communities. The quality and price varies amongst different production regions, usually resulting in an intentional mix-up of its production locality during trading processes, which leads to a demand of developing a reliable way that can trace the geographical origin of this fungus. In the present study, a DNA barcoding-based method applying two universal DNA barcodes for identifying fungal and insect, respectively i.e. the nuclear ribosomal internal transcribed spacer (ITS) and the mitochondrial cytochrome oxidase I (COI), was evaluated and used for geographical origin authentication of O.sinensis. A total of 24 ITS and 78 COI haplotypes were recognised from 215 individuals collected from 75 different geographic localities (county level). Ninety-nine haplotypes were defined using the combination of ITS and COI, discriminating the 75 investigated production counties into 99 distinct regions. A "core" production region was recognised which covers areas of Nagqu and Qamdo in Xizang, Yushu and Guoluo in Qinghai, Gannan (Maqu and Xiahe) in Gansu and certain regions in Nyingch (Bomi and Zayü) and Lhasa (Damxung) in Xizang and Garzê (Sêrxü) in Sichuan Province. Haplotype analyses using the combined barcodes of ITS and COI showed an excellent performance in the geographical origin authentication of O.sinensis and the definition of "core" and "non-core" production region.},
}

@article {pmid40200683,
year = {2025},
author = {Wang, Y and Ma, J and Cai, W and Song, M and Wang, Z and Xu, Z and Shen, Y and Zheng, S and Zhang, S and Tang, Z and Wang, Y},
title = {Fast Encapsulation of Microbes into Dissolvable Hydrogel Beads Enables High-Throughput Microbial Single-Cell RNA Sequencing of Clinical Microbiome Samples.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2500481},
doi = {10.1002/adma.202500481},
pmid = {40200683},
issn = {1521-4095},
support = {32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; 52203282//National Natural Science Foundation of China/ ; LY23B040002//Natural Science Foundation of Zhejiang Province/ ; 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/ ; },
abstract = {Microbial single-cell RNA-seq (mscRNA-seq) can achieve resolution at the cellular level, enhancing the understanding of microbial communities. However, current high-throughput mscRNA-seq methods are limited by multiple centrifugation steps, which can lead to microbial loss and bias. smGel-seq is reported, a high-throughput single-microbe RNA sequencing method for clinical microbiome samples that employs hydrogel beads to encapsulate individual microbes to reduce microbial loss and input requirements. In this method, a novel microchannel array device is implemented for encapsulating single microbe in dissolvable hydrogel beads (smDHBs), along with an optimized automated microfluidic platform to co-encapsulate barcoded beads and smDHBs, enabling high-throughput barcoding of individual microbes. smGel-seq significantly increases the microbial recovery rate in a gut microbiome sample from 8.8% to 91.8%. Furthermore, this method successfully processes clinical microbiome samples with microbial inputs 20 times lower than those required by previous methods. Notably, smGel-seq enables the first mscRNA-seq in a clinical sputum microbiome sample, revealing a specific microbial subpopulation that may play a key role in environmental adaptability, antibiotic resistance, and pathogenicity. These results highlight the compatibility of smGel-seq with clinical microbiome samples and demonstrate its potential for widespread application in diverse clinical and research settings.},
}

@article {pmid40200529,
year = {2025},
author = {Barro, SG and Ouattara, TA and Staccini, P},
title = {Assignment of Unique Specimen IDs and Barcodes to Pathology Image Samples in Medical Laboratories in Burkina Faso.},
journal = {Studies in health technology and informatics},
volume = {323},
number = {},
pages = {458-462},
doi = {10.3233/SHTI250132},
pmid = {40200529},
issn = {1879-8365},
mesh = {Burkina Faso ; Humans ; *Specimen Handling/methods ; *Laboratories, Clinical/organization & administration ; *Patient Identification Systems/methods ; *Clinical Laboratory Information Systems/organization & administration ; },
abstract = {The accurate and efficient assignment of unique identifiers to biomedical specimens, along with the generation of barcodes for pathology samples, are crucial elements in ensuring the quality and reliability of medical diagnostics. In Burkina Faso, the adoption of an automated system for these tasks marks a significant advancement in laboratory management. This article explores the impact of this automation on reducing human errors, improving sample traceability, and optimizing operational processes. Indeed, the integration of AJAX queries for the dynamic management of specimen numbers allows for real-time updates and reduces the risks of duplication or incorrect assignment. Furthermore, the use of specialized libraries for the automatic generation of barcodes ensures a unique and secure identification of each sample, thereby facilitating its tracking throughout the analysis process. This modernization of sample management practices not only improves the efficiency of laboratories but also optimizes processing times, thus enhancing the quality of care and diagnostics provided to patients.},
}

Burkina Faso
Humans
*Specimen Handling/methods
*Laboratories, Clinical/organization & administration
*Patient Identification Systems/methods
*Clinical Laboratory Information Systems/organization & administration

@article {pmid40198433,
year = {2025},
author = {Watanabe, K and Imanishi, S and Kayukawa, T and Tateishi, K},
title = {Establishment of 27 cell lines derived from various insects.},
journal = {In vitro cellular & developmental biology. Animal},
volume = {},
number = {},
pages = {},
pmid = {40198433},
issn = {1543-706X},
support = {20K06083//Japan Society for the Promotion of Science/ ; 23K05264//Japan Society for the Promotion of Science/ ; },
abstract = {Insect cell lines are valuable for basic and applied biological research. In this study, we established 27 cell lines from various insect species, including Hemiptera: Nilaparvata lugens, Coleoptera: Sitophilus oryzae, Hymenoptera: Allantus luctifer and Trichogramma ssp., Diptera: Culicoides oxystoma, Lepidoptera: Spodoptera litura, Mythimna separata, Bombyx mori, Agrius convolvuli, Plodia interpunctella, and Cryptophlebia horii. This is the first report of cell lines derived from A. luctifer, C. oxystoma, A. convolvuli, and C. horii. Additionally, cell lines from S. litura and M. separata were established from different tissues including the hemocytes, fat bodies, embryos, and Malpighian tubules. Eighteen cell lines were successfully adapted to commercial culture media, with the population doubling time ranging from 1 to 8 d. The identities of the cell lines were confirmed using DNA barcoding. These established cell lines could be valuable for various research applications.},
}

@article {pmid40197720,
year = {2025},
author = {Snoeck, HW},
title = {Direct megakaryopoiesis.},
journal = {Current opinion in hematology},
volume = {},
number = {},
pages = {},
pmid = {40197720},
issn = {1531-7048},
abstract = {PURPOSE OF REVIEW: Megakaryocytes are large, polyploid cells that produce platelets and originate from hematopoietic stem cells (HSCs) in the bone marrow. While in the classical paradigm, megakaryocytes are generated in a stepwise fashion through increasingly committed progenitor stages, studies using in-vivo barcoding, transplantation, and in-vitro culture have suggested that, in addition, a more direct pathway existed. The relevance of this direct pathway and its functional and phenotypic characteristics were unclear, however.

RECENT FINDINGS: Recent publications using fate-mapping and single-cell transplantation now unequivocally demonstrate the existence of a direct megakaryocyte differentiation pathway, provide molecular characterization, and indicate distinct roles and regulation of both pathways. The direct pathway originates from a separate subset of 'top' HSCs, is enhanced by hematopoietic stress, inflammation and aging, bypasses multipotential progenitors, may be more active in myeloproliferative neoplasms, and generates phenotypically distinct megakaryocyte progenitors and more reactive platelets.

SUMMARY: Novel insights into the direct megakaryocyte differentiation pathway provide a deeper understanding of HSC biology, hematological recovery after myeloablation, and aging of the hematopoietic system, and suggest that this pathway may contribute to the increase in thrombotic incidents with age and in myeloproliferative neoplasms.},
}

@article {pmid40197053,
year = {2025},
author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A},
title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0116624},
doi = {10.1128/msystems.01166-24},
pmid = {40197053},
issn = {2379-5077},
abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.

IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.},
}

@article {pmid40196009,
year = {2025},
author = {Smolka, M and Comstock, W and Navarro, M and Maybee, D and Rho, Y and Wagner, M and Wang, Y},
title = {Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6220494/v1},
pmid = {40196009},
issn = {2693-5015},
abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo . In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.},
}

@article {pmid40191542,
year = {2025},
author = {Liu, B},
title = {Contribution to the knowledge of the genus Calcyopa Stüning, 2000 (Lepidoptera, Geometridae, Ennominae, Boarmiini), with description of a new species.},
journal = {ZooKeys},
volume = {1233},
number = {},
pages = {125-138},
pmid = {40191542},
issn = {1313-2989},
abstract = {The genus Calcyopa Stüning, 2000, is briefly reviewed. A new species, Calcyopahainana Liu, sp. nov., is described from Hainan Province, China. Within the genus Calcyopa, two species groups are identified, characterized by shared traits yet distinguished by a set of consistent features. The difoveata-group, comprises C.difoveata, C.fansipana and C.hainana sp. nov., and the rosearia-group, includes C.rosearia, C.prasina and C.subprasina. The relationship of both species groups is discussed, and an identification key of all known Calcyopa species is presented. Illustrations are provided for adult males and females of the difoveata-group, along with their genitalia, except for C.fansipana, which is known only from males. DNA barcodes are provided for the type species and the newly described species.},
}

@article {pmid40190802,
year = {2025},
author = {McCulloch, GA and Pohe, SR and Wilkinson, SP and Drinan, TJ and Waters, JM},
title = {Targeted eDNA Metabarcoding Reveals New Populations of a Range-Limited Stonefly.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71244},
pmid = {40190802},
issn = {2045-7758},
abstract = {Understanding the geographic distributions of rare species can be crucial for conservation management. New environmental DNA (eDNA) technologies offer the potential to efficiently document the distributions of endangered species, but to date, such screening has focused largely on vertebrate taxa. Here we use freshwater eDNA to assess the geographic distribution of the Maungatua stonefly, Zelandoperla maungatuaensis, a flightless insect previously known from only a handful of streams draining a 4-km section of the Maungatua mountain range in southern New Zealand. We analyzed freshwater eDNA from 12 stream localities across the Maungatua range. Screening with commercial eDNA COI primers failed to detect the focal species Z. maungatuaensis. However, newly designed species-specific primers detected this taxon from four adjacent east-flowing streams known to contain Z. maungatuaensis, and two streams from which it had not previously been detected. Subsequent manual surveys confirmed the presence of two newly discovered Z. maungatuaensis populations, with COI barcoding revealing that they together represent a previously unknown, genetically divergent subclade. Our results illustrate the potential of eDNA metabarcoding to help delineate the geographic ranges of rare taxa, and highlight the importance of primer specificity when screening for rare taxa. These findings also have considerable implications for commercial companies offering biodiversity and stream health eDNA services targeting invertebrates.},
}

@article {pmid40188161,
year = {2025},
author = {Ramesh, KB and Mahendra, C and Gouda, MNR and Salim, R and Subramanian, S},
title = {Genetic structure and haplotype analysis of predominant genetic group of Bemisia tabaci Asia II 1 from Asia and India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11672},
pmid = {40188161},
issn = {2045-2322},
mesh = {Animals ; *Hemiptera/genetics/classification ; *Haplotypes ; India ; Genetic Variation ; Phylogeny ; Asia ; },
abstract = {Whitefly, Bemisia tabaci is a globally recognized invasive cryptic pest species complex and a primary vector for 90% of begomoviruses. Understanding the species composition and diversity within the B. tabaci cryptic species complex is essential for developing effective pest management strategies. The Asia II 1 genetic group of B. tabaci is notably widespread in India and across Asia, demonstrating significant genetic diversity. Our study investigates the haplotype diversity of Asia II 1 using the mtCOI barcoding gene, analyzing 676 sequences from various Asian countries and 190 sequences from India. We identified 241 distinct haplotypes in Asia II 1 across Asia, with the highest haplotype diversity in China (Hd: 1.000) and the lowest in Vietnam (Hd: 0.667). Nucleotide diversity peaked in Pakistan (pi: 0.0145) and was lowest in Vietnam (pi: 0.0010). In India, we identified 77 haplotypes with a diversity of 0.926 and nucleotide diversity of 0.0076. When grouped by hostplant families, 79 haplotypes were recorded, with the highest diversity in Cucurbitaceae and the lowest in Solanaceae. Our findings suggest that hostplants and geographical location significantly influence genetic group development, offering novel insights into Asia II 1's genetic structure and evolution. This marks the first comprehensive study of Asia II 1 genetic diversity in Asia and India.},
}

Animals
*Hemiptera/genetics/classification
*Haplotypes
India
Genetic Variation
Phylogeny
Asia

@article {pmid40187791,
year = {2025},
author = {He, Z and Wang, H and Chen, Y and Chen, N},
title = {Comparative genomic and phylogenetic analysis of mitochondrial genomes of the Pseudo-nitzschia HAB species.},
journal = {Harmful algae},
volume = {144},
number = {},
pages = {102829},
doi = {10.1016/j.hal.2025.102829},
pmid = {40187791},
issn = {1878-1470},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Diatoms/genetics/classification ; DNA, Mitochondrial/genetics ; Harmful Algal Bloom ; Genomics ; },
abstract = {The genus Pseudo-nitzschia within Bacillariophyta (diatoms) is best known for its rich collection of toxigenic harmful algal bloom (HAB) species capable of producing the neurotoxin domoic acid (DA), which causes amnesic shellfish poisoning (ASP) in humans. Molecular markers such as 18S rDNA, ITS1, and ITS2 have been applied to facilitate Pseudo-nitzschia species identification because morphology-based methods often could not adequately distinguish different species due to their morphological similarities and plasticity. In this study, we constructed mitochondrial genomes (mtDNAs) for 11 Pseudo-nitzschia species and assessed their utility as "super-barcodes" for species identification and evolutionary analysis. These mtDNAs exhibited conserved genome structures despite variability in repeat regions. A potential tatA-tatC gene fusion event was observed in a single Pseudo-nitzschia species P. brasiliana. We also observed intron variability in cox1 genes. Phylogenetic analyses of mtDNAs, chloroplast genomes (cpDNAs), and nuclear ribosomal DNA (nrDNA) arrays revealed consistent results, supporting the closely related but distinct clustering of the genera Fragilariopsis and Pseudo-nitzschia. We further designed a high-resolution molecular marker tatA for species identification based on the comparative analysis of these mtDNAs, which could be used to track Pseudo-nitzschia diversity. These findings offer new genome resources and new insights into the genetic evolution and classification of Pseudo-nitzschia, underscoring the need for continued research in this field.},
}

*Genome, Mitochondrial
*Phylogeny
*Diatoms/genetics/classification
DNA, Mitochondrial/genetics
Harmful Algal Bloom
Genomics

@article {pmid40187273,
year = {2025},
author = {Prasetyo, DB and Yean, S and Boyer, S},
title = {Reevaluating the presence of Rhipicephalus australis (Acari: Ixodidae) in Southeast Asia: A phylogenetic approach based on Cambodian tick samples.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {3},
pages = {102478},
doi = {10.1016/j.ttbdis.2025.102478},
pmid = {40187273},
issn = {1877-9603},
abstract = {Morphological variability between Rhipicephalus australis and R. microplus has led to taxonomic ambiguity, leading to species misidentification. Rhipicephalus australis is reported to have a distribution range in Pacific Ocean region extending to several Southeast Asian countries, including Cambodia, although its presence in continental Southeast Asia has not been supported by molecular data. With growing evidence of conflicting morphological characters, this study aimed to evaluate the presence of R. australis in Cambodia using both morphological and molecular identification. Tick specimens were collected from cattle across 21 provinces of Cambodia, and a subset of 95 R. microplus complex (37 morphologically identified as R. australis, 39 R. microplus, and 19 nymphs) was selected for molecular analysis. DNA barcoding of the cox1 gene was performed, and a maximum likelihood phylogenetic tree revealed that all specimens clustered within R. microplus clade A. These findings, along with previous observations from other regions, suggest that, in the absence of molecular data, there is no definitive evidence to support the presence of R. australis in continental Southeast Asia, particularly in Cambodia.},
}

@article {pmid40186944,
year = {2025},
author = {Solbach, MD and Siemensma, F and Holzmann, M},
title = {A remarkable new monothalamid (Rhizaria, Foraminifera) from the shoreline of Livingston Island, Antarctica.},
journal = {European journal of protistology},
volume = {99},
number = {},
pages = {126148},
doi = {10.1016/j.ejop.2025.126148},
pmid = {40186944},
issn = {1618-0429},
abstract = {In this study, we describe a novel monothalamous Foraminifera, discovered in shoreline sediment samples from the Southern Ocean. The individuals, approximately 75 μm in diameter, are relatively small for Foraminifera, mostly spherical, with an organic-walled test. Notably, these Foraminifera exhibit a unique behavior in culture: they surround themselves in planktonic diatoms, enabling them to float in the water column. This floating behavior is unusual for Foraminifera, which are often larger and possess a thick test made of calcite or agglutinated particles. We hypothesize that the small size of the organism, its lightweight organic test, and the habit of surrounding itself with centric diatoms may enable the floating behavior observed in culture and potentially aid dispersal in nature. Phylogenetic analysis of the 18S rDNA barcoding fragment places this undescribed organism as an independent lineage among monothalamid Foraminifera. We erect the novel genus Pensilisphaera with its type species Pensilisphaera antarcticaensis.},
}

@article {pmid40185067,
year = {2025},
author = {Papapetrou, EP},
title = {The clones have STRACK: Tracing responses to leukemic mutations.},
journal = {Cell stem cell},
volume = {32},
number = {4},
pages = {499-501},
doi = {10.1016/j.stem.2025.03.001},
pmid = {40185067},
issn = {1875-9777},
mesh = {Animals ; *Mutation/genetics ; *Leukemia/genetics/pathology ; Clone Cells/pathology ; Mice ; *Hematopoietic Stem Cells/metabolism/pathology ; Humans ; },
abstract = {Rodriguez-Fraticelli and colleagues combine genetic barcoding with ex vivo expansion and sister-cell analysis of murine hematopoietic stem cells (HSCs) carrying inducible leukemia driver mutations. This approach allows them to capture the intrinsic heterogeneity of clonal cell behaviors and study how these impact cell fates upon acquisition of leukemia driver mutations.},
}

Animals
*Mutation/genetics
*Leukemia/genetics/pathology
Clone Cells/pathology
Mice
*Hematopoietic Stem Cells/metabolism/pathology
Humans

@article {pmid40183470,
year = {2025},
author = {Haley, RM and Padilla, MS and El-Mayta, RD and Joseph, RA and Weber, JA and Figueroa-Espada, CG and Mukalel, AJ and Ricciardi, AS and Palanki, R and Geisler, HC and Jester, MT and Davidson, BL and Mitchell, MJ},
title = {Lipid Nanoparticles for In Vivo Lung Delivery of CRISPR-Cas9 Ribonucleoproteins Allow Gene Editing of Clinical Targets.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.4c16617},
pmid = {40183470},
issn = {1936-086X},
abstract = {In the past 10 years, CRISPR-Cas9 has revolutionized the gene-editing field due to its modularity, simplicity, and efficacy. It has been applied for the creation of in vivo models, to further understand human biology, and toward the curing of genetic diseases. However, there remain significant delivery barriers for CRISPR-Cas9 application in the clinic, especially for in vivo and extrahepatic applications. In this work, high-throughput molecular barcoding techniques were used alongside traditional screening methodologies to simultaneously evaluate LNP formulations encapsulating ribonucleoproteins (RNPs) for in vitro gene-editing efficiency and in vivo biodistribution. This resulted in the identification of a lung-tropic LNP formulation, which shows efficient gene editing in endothelial and epithelial cells within the lung, targeting both model reporter and clinically relevant genomic targets. Further, this LNP shows no off-target indel formation in the liver, making it a highly specific extrahepatic delivery system for lung-editing applications.},
}

@article {pmid40182483,
year = {2025},
author = {Kipkoech, A and Li, K and Milne, RI and Oyebanji, OO and Wambulwa, MC and Fu, XG and Wakhungu, DA and Wu, ZY and Liu, J},
title = {An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae).},
journal = {Plant diversity},
volume = {47},
number = {2},
pages = {229-243},
doi = {10.1016/j.pld.2024.11.004},
pmid = {40182483},
issn = {2468-2659},
abstract = {Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.},
}

@article {pmid40181733,
year = {2025},
author = {Congrains, C and Bremer, F and Dupuis, JR and Barr, NB and Garzón-Orduña, IJ and Rubinoff, D and Doorenweerd, C and Jose, MS and Morris, K and Kauwe, A and Geib, S},
title = {CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14113},
doi = {10.1111/1755-0998.14113},
pmid = {40181733},
issn = {1755-0998},
support = {8130-0565-CA//U.S. Department of Agriculture-Animal and Plant Health Inspection Service/ ; 8130-0984-IA//U.S. Department of Agriculture-Animal and Plant Health Inspection Service/ ; },
abstract = {DNA sequencing technology has undergone substantial improvements in recent years, to the extent that Third Generation Sequencing platforms are capable of massively generating long-reads. Amplicon sequencing has been among the most popular techniques due to its wide application in diverse fields of biological sciences. However, there is a lack of software specifically designed to analyse intra-individual genetic variation using amplicon long-read data. Here, we present CCS-consensuser, an end-to-end pipeline that generates consensus sequences from amplicon sequencing using high-fidelity reads produced by PacBio circular consensus sequencing (CCS). We evaluated the concordance of the results produced using CCS + CCS-consensuser and other sequencing platforms (Illumina and Sanger), as well as accuracy using a simulated dataset. This assessment showed that CCS amplicon data coupled with CCS-consensuser can produce high-quality sequences (PHRED > 30). The pipeline resulted in high proportions of identical sequence bins for real data, achieving up to 94.94% concordance with COI Sanger sequences and 92.61% with nuclear loci Illumina sequences (considering heterozygous loci), and 95.55% with a fully phased nuclear simulated dataset. Furthermore, our pipeline can be used to detect heteroplasmy in mtDNA, cross-contamination, resolve the phase of nuclear genes in diploid organisms, and conceivably for multi-copy gene systems such as rDNA. These results not only support its potential for application in studies using haploid data such as DNA barcoding, but also demonstrate its unique capacity to explore within individual haplotype variation. Therefore, our strategy shows promise for a broad range of applications in biology and medicine that have been challenging to assess using traditional techniques.},
}

@article {pmid40180452,
year = {2025},
author = {Schares, HAM and Hayes, MJ and Balsamo, JA and Thirman, HL and Bachmann, BO and Irish, JM},
title = {Multiplexed cytometry for single cell chemical biology.},
journal = {Methods in cell biology},
volume = {195},
number = {},
pages = {143-172},
doi = {10.1016/bs.mcb.2023.03.007},
pmid = {40180452},
issn = {0091-679X},
mesh = {Humans ; *Flow Cytometry/methods ; *Single-Cell Analysis/methods ; Animals ; Mice ; Small Molecule Libraries ; Histones/metabolism ; DNA Damage ; },
abstract = {Flow cytometry has great potential for screening in translational research areas due to its deep quantification of cellular features, ability to collect millions of cells in minutes, and consistently expanding suite of validated antibodies that detect cell identity and functions. However, cytometry remains under-utilized in discovery chemical biology due to the differences in expertise between chemistry groups developing chemical libraries and cell biologists developing single cell assays. This chapter is designed to bridge this gap by providing a detailed protocol aimed at both chemistry and biology audiences with the goal of helping train novice researchers. Assay users select from three elements: a small molecule input, a target cell type, and a module of cytometry readouts. For each, we explore basic and advanced examples of inputs, including screening fractionated microbial extracts and pure compounds, and target cells, including primary human blood cells, mouse cells, and cancer cell lines. One such module of cytometry readouts focuses on cell function and measures DNA damage response (γH2AX), growth (phosphorylated S6), DNA content, apoptosis (cleaved Caspase3), cell cycle M phase (phosphorylated Histone H3), and viability (membrane permeabilization). The protocol can also be adapted to measure different functional readouts, such as cell identity or differentiation and contrasting cell injury mechanisms. The protocol is designed to be used in 96-well plate format with fluorescent cell barcoding and the debarcodeR algorithm. Ultimately, the goal is to encourage the next generation of chemical biologists to use functional cell-based cytometry assays in discovery and translational research.},
}

Humans
*Flow Cytometry/methods
*Single-Cell Analysis/methods
Animals
Mice
Small Molecule Libraries
Histones/metabolism
DNA Damage

@article {pmid40179197,
year = {2025},
author = {de Haan, S and He, J and Corbat, AA and Belicova, L and Ratz, M and Vinsland, E and Frisén, J and Kelley, MW and Andersson, ER},
title = {Ectoderm barcoding reveals neural and cochlear compartmentalization.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {60-68},
doi = {10.1126/science.adq9248},
pmid = {40179197},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Ectoderm/embryology/cytology ; Cell Lineage ; *Cochlea/embryology/cytology ; *Neural Crest/embryology/cytology ; *DNA Barcoding, Taxonomic/methods ; Single-Cell Analysis ; Cell Differentiation ; Neurogenesis ; *Nervous System/embryology ; },
abstract = {Placodes and the neural crest are defining features of vertebrates. In this study, we investigate their lineages in mice using in utero approaches. We demonstrated that nanoinjection at embryonic day 7.5 targeted the ectoderm, including the future nervous system, placodes, and neural crest, allowing highly efficient manipulation of the future nervous system and inner ear. By using heritable DNA barcodes and high-throughput next-generation single-cell lineage tracing, we elucidated convergent differentiation pathways and identified distinct nervous system-, neural crest-, and otic placode-derived lineages. Clonal analyses identified early neural and cochlear compartmentalization, linking differentiated cell types to their progenitors or cellular siblings. This provides foundational insights for neuroscience and developmental biology.},
}

Animals
Mice
*Ectoderm/embryology/cytology
Cell Lineage
*Cochlea/embryology/cytology
*Neural Crest/embryology/cytology
*DNA Barcoding, Taxonomic/methods
Single-Cell Analysis
Cell Differentiation
Neurogenesis
*Nervous System/embryology

@article {pmid40179100,
year = {2025},
author = {Long, Z and Yu, J and Bing, T},
title = {Theoretical Basis for the Highly Efficient Aptamer Selection Using Unique Molecular Identifiers.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c00118},
pmid = {40179100},
issn = {1520-6882},
abstract = {Rapid selection methods are crucial for promoting the discovery and application of aptamers across various fields. We previously reported a highly efficient aptamer selection strategy by using unique molecular identifiers (UMIs), enabling the efficient isolation of aptamers from a single cell by only one round. The strategy integrates an ultrasensitive DNA barcoding technology with high-throughput sequencing to accurately quantify aptamer candidates, thereby mitigating issues such as PCR bias and sequence overenrichment that are inherent in traditional multiround selection. Here, we conduct a systematically theoretical analysis of this strategy in the elucidation of the theoretical basis, advantages, and applicability. The feasibility and advantages of isolating aptamers from low-enriched DNA libraries was investigated at a theoretical level, showing that this strategy is effective in reducing nonspecific binding and thus increasing the success of selecting high-affinity aptamers. Our theoretical analysis supports the broad applicability of the strategy for the single-round aptamer selection, paving the way for its widespread adoption in high-efficiency aptamer discovery and aptamer-based cell atlas.},
}

@article {pmid40177347,
year = {2025},
author = {Gong, L and Zhong, Y},
title = {Re-description of Sinopodacurva Zhong, Jäger, Chen & Liu, 2019 (Araneae, Sparassidae), with a first description of the female.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e152100},
doi = {10.3897/BDJ.13.e152100},
pmid = {40177347},
issn = {1314-2828},
abstract = {BACKGROUND: Sinopoda Jäger, 1999 is a relatively large spider genus that currently comprises 141 species distributed worldwide. However, the genus remains inadequately studied because nearly half of the species are known from a single sex or juvenile specimens. Sinopodacurva Zhong, Jäger, Chen & Liu, 2019 was described, based on two male specimens from Damingshan National Nature Reserve, Guangxi Zhuang Autonomous Region, China and no additional specimens have been recorded since.

NEW INFORMATION: Recently, new materials of huntsman spiders have been collected from Mt. Wuyishan, including specimens of both sexes. Several males were identified as S.curva, based on morphological comparison with the holotype. Based on morphological characters and DNA barcodes, we confidently matched the females and males as S.curva. Herein, S.curva is re-described, based on these new materials and the female is described and illustrated for the first time.},
}

@article {pmid40174196,
year = {2025},
author = {Kohlmann, B and Solís, Á},
title = {A review of the species groups of the Western Hemisphere Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae) using COI barcoding and gene trees.},
journal = {Zootaxa},
volume = {5604},
number = {4},
pages = {401-447},
doi = {10.11646/zootaxa.5604.4.1},
pmid = {40174196},
issn = {1175-5334},
abstract = {Species groups of Western Hemispheric Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) are suggested using COI barcoding and gene trees and supported by congruence with external morphology, behavior, ecology, and biogeographic evidence. New species groups, complexes, and taxonomic statuses are offered, and other preexisting proposals are confirmed. No barcoding gap w as found between the intragroup and intergroup genetic distance blocks, but the average intragroup (8.38%) and intergroup (13.88%) Kimura-two-parameter distances are statistically different. The following seven preexisting species groups were supported by the congruence between the mtDNA barcode analysis and other independent evidence: O. chevrolati, O. clypeatus, O. dicranius, O. gazellinus, O. hircus, O. landolti, and O. mexicanus. Eight new species groups are suggested: O. crinitus, O. curvicornis, O. eulophus, O. hecate, O. hoepfneri, O. marginatus, O. nasutus, and O. velutinus. Possible behavioral/ecological adaptations of morphological characters are also discussed. New biogeographic and evolutionary hypotheses are also advanced. An identification key for species groups is presented.},
}

@article {pmid40174133,
year = {2025},
author = {Mori, E and Viviano, A and Baratti, M and Serafini, E and Gabbrielli, B and Picchi, MS and Giannetti, D and Mascalchi, C and Ancillotto, L},
title = {A light in the dark: DNA barcoding provides new data about the taxonomy of the Italian Luciola (Coleoptera, Lampyridae) fireflies.},
journal = {Zootaxa},
volume = {5609},
number = {4},
pages = {525-536},
doi = {10.11646/zootaxa.5609.4.4},
pmid = {40174133},
issn = {1175-5334},
abstract = {Environmental pollution and agricultural intensification are threatening insects worldwide, and reliable taxonomy is pivotal to protect these taxa, particularly endemic species. Despite their wide distribution, lampyrid beetles (Lampyridae)-well-known as fireflies-are poorly studied in terms of taxonomy, particularly in Europe. Accordingly, as for almost all insects, the description of most species is only based on a few morphological featuresSince genetic analyses can provide valuable support in taxonomic studies, in this work, we investigated the species identity of an Italian endemic firefly, Luciola pedemontana (Curtis, 1843), with respect to other congeneric species, namely Luciola italica (Linnaeus, 1767) and Luciola lusitanica (Charpentier, 1825) by applying Barcoding technique. Particularly, L. pedemontana has been for long considered as a synonym of L. lusitanica or as a subspecies of L. italica. Italy hosts the highest diversity of firefly species in Europe, but the Luciola inter-specific phylogenetic relationships and species delimitations are still poorly known. With the aim to assist morphological analyses in the taxonomic characterization of species of the genus Luciola in Italy, we sequenced the cytochrome oxidase subunit I gene (COI) fragment of 40 individuals from 18 sites in Central Italy. Our analysis confirmed L. pedemontana as a well-supported monophyletic clade and as the sister taxon of L. italica. Furthermore, a low intraspecific genetic variation was found between L. lusitanica and L. pedemontana and between Luciola unmunsana + Luciola papariensis. Genetic data obtained for the Luciola species can help to improve conservation measures for L. pedemontana, strongly required to protect this Italian endemic taxon, which is currently threatened by light pollution and environmental alterations.},
}

@article {pmid40174117,
year = {2025},
author = {Girdley, J and Garre, M and Rubio, RM and Ortiz, AS},
title = {Eucosma callei sp. nov.-a new species of Olethreutinae from South-eastern Iberian Peninsula (Lepidoptera, Tortricidae).},
journal = {Zootaxa},
volume = {5583},
number = {1},
pages = {186-194},
doi = {10.11646/zootaxa.5583.1.11},
pmid = {40174117},
issn = {1175-5334},
abstract = {Eucosma callei sp. nov. is described and illustrated from the Iberian Peninsula. It differs from its Iberian congener, Eucosma gonzalezalvarezi Agenjo, 1970, in external appearance and genitalia. The 5' barcode fragments of the mitochondrial gene COI (the DNA barcode) are presented and confirms the description of this new species.},
}

@article {pmid40174108,
year = {2025},
author = {Cava, S and Rijllo, G and Zucco, G and Scalercio, S},
title = {Revisiting the genus Diplodoma Zeller, 1852 in Europe: DNA barcoding reveals the presence of an undescribed species from forested habitats of southern Italy (Lepidoptera: Psychidae).},
journal = {Zootaxa},
volume = {5583},
number = {2},
pages = {371-382},
doi = {10.11646/zootaxa.5583.2.8},
pmid = {40174108},
issn = {1175-5334},
abstract = {Diplodoma Zeller, 1852 is a Eurasian genus belonging to the family Psychidae Boisduval, 1829 of which three species are known in Europe: Diplodoma adspersella Heinmann, 1870, D. laichartingella (Goeze, 1783), and D. taurica Zagulajev, 1986. Some authors have argued that Diplodoma adspersella may be a subspecies or even a form of D. laichartingella. The revision of literature and the study of DNA barcoding fragments confirmed the inconsistency of D. adspersella as a valid species, and therefore we propose the new synonymy of Diplodoma adspersella with D. laichartingella (syn. nov.). During recent surveys in southern Italy, three specimens of Diplodoma were collected. DNA barcoding and morphological analyses showed that COI sequences and male genitalia significantly differ from any previously studied specimen. As a result, we described Diplodoma giulioregenii sp. nov., leaving unaltered the number of species belonging to this genus known from Europe.},
}

@article {pmid40174101,
year = {2025},
author = {Thiel, R and Knebelsberger, T and Chernova, N and Eidus, I},
title = {Two new species of eelpout genus Lycenchelys (Perciformes: Zoarcidae) from the Kuril-Kamchatka Trench, based on morphological and molecular evidence.},
journal = {Zootaxa},
volume = {5583},
number = {3},
pages = {491-508},
doi = {10.11646/zootaxa.5583.3.4},
pmid = {40174101},
issn = {1175-5334},
abstract = {Two new species of eelpout genus Lycenchelys Gill, 1884 are described based on eight specimens caught at a depth between 3517 and 3580 m at the western slope of the upper margin of the Kuril-Kamchatka Trench, relatively close to the Bussol Strait and Simushir Island in the center of the Kuril Islands chain. Lycenchelys delanglei sp. nov. differs from its congeners by the following combination of characters: vertebrae 28-29 + 91-93 = 120-121; interorbital and occipital pores absent; postorbital pores 4; suborbital pores 10-12; preoperculomandibular pores 4 + 5; gill rakers 11-16; dorsal-fin rays 114-117, 2-3 free pterygiophores at the beginning of dorsal fin; anal-fin rays 96-98; pelvic-fin rays 2; pectoral-fin rays 16-17, ray tips of the pectoral fin exserted, especially the middle and lower ones; lateral line absent; pyloric caeca not developed. Lycenchelys renatae sp. nov. differs from its congeners by the following combination of characters: vertebrae 26-27 + 99-103 = 125-130; interorbital pores 0-1; occipital pores absent; postorbital pores 1-4; suborbital pores 6-9; preoperculomandibular pores 3-4 + 5; gill rakers 13-15; dorsal-fin rays 115-122, 1-3 free pterygiophores at the beginning of dorsal fin; anal-fin rays 102-106; pelvic-fin rays two; pectoral-fin rays 16-17, ray tips of the pectoral fin exserted, the middle and lower ones more so than the upper ones; lateral line mediolateral, poorly developed; pyloric caeca not developed. For each of the two described new species four mitochondrial COI sequences were analysed and share the same haplotype within species. The obtained DNA barcodes allowed discrimination of L. delanglei sp. nov. and L. renatae sp. nov. from each other and exhibit a genetic distance of 2,61%. The closest match of L. delanglei sp. nov. with already published sequences was Lycenchelys lenzeni with a sequence similarity of 98.47%, whereas the closest match of L. renatae sp. nov. with already published sequences was Lycenchelys jordani with a similarity of 98.62%. A new analysis of radiographs of the type specimens confirmed that L. birsteini should be considered as synonym of L. plicifera, especially due to similar numbers of free pterygiophores at the beginning of dorsal fin.},
}

@article {pmid40174087,
year = {2025},
author = {Luengo, E and Genis-Armero, R and Clark, PF and Palero, F},
title = {Final stage phyllosoma of Galearctus sp. (Decapoda: Scyllaridae) from the Coral Sea.},
journal = {Zootaxa},
volume = {5584},
number = {1},
pages = {101-112},
doi = {10.11646/zootaxa.5584.1.6},
pmid = {40174087},
issn = {1175-5334},
abstract = {Larval stages are known for only four out of eight Galearctus Holthuis, 2002 (Crustacea: Scyllaridae) species, a slipper lobster genus widely distributed throughout the Indo-Pacific region. DNA barcoding analyses of phyllosomae collected from the Coral Sea by the Australian Institute of Marine Science suggest the presence of two new genetic clades in the area, for which larvae cannot be discriminated morphologically. The last instar larva of an unknown species of Galearctus is described and illustrated in detail here. It is possible that this larval material may be assigned to G. umbilicatus, the only species of the genus lacking a DNA barcode. Morphological analyses and a literature review allowed the re-evaluation of previous Galearctus larval studies, identifying several misidentifications and inconsistencies. Further morphological and molecular revision of adult Galearctus species is required to confirm larval identities, but the results presented here indicate that the diversity of Galearctus may be underestimated.},
}

@article {pmid40174058,
year = {2025},
author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Hendrix, SV and Helmick, EE and Bahder, BW},
title = {A new species of Cyclopoliarus (Hemiptera: Auchenorrhyncha: Fulgoromorpha: Cixiidae) from American oil palms (Elaeis oleifera) in Caño Negro, Costa Rica.},
journal = {Zootaxa},
volume = {5584},
number = {4},
pages = {523-538},
doi = {10.11646/zootaxa.5584.4.4},
pmid = {40174058},
issn = {1175-5334},
abstract = {Recent palm survey work in Costa Rica focusing on planthoppers has resulted in the discovery of several new taxa, primarily in Cixiidae and Derbidae. Here a new species of Cyclopoliarus Fennah, C. nigelwatsoni sp. nov., is described from Caño Negro, Limón Province, Costa Rica. The new species is compared with C. omani, the only other described Central American Cyclopoliarus. Supplemental molecular data is presented for the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and D9 to D10 expansion region of the 28S rRNA gene. A phylogeny is presented to place the new species relative to other available taxa.},
}

@article {pmid40174054,
year = {2025},
author = {Lukhtanov, VA and Makhov, IA and Gagarina, AV and Romanovich, AE},
title = {Taxonomy of the West Palaearctic butterfly genus Palaeophilotes Forster, 1938 (Lepidoptera: Lycaenidae) based on combined analysis of COI barcodes and multilocus nuclear markers.},
journal = {Zootaxa},
volume = {5584},
number = {4},
pages = {570-580},
doi = {10.11646/zootaxa.5584.4.8},
pmid = {40174054},
issn = {1175-5334},
abstract = {Based on molecular phylogenetic analysis of all relevant taxa, we propose to consider the species previously classified as members of Pseudophilotes, Palaeophilotes, Rubrapterus, and Inderskia as belonging to a single genus, the valid name of which is Palaeophilotes. This genus can be divided into two subgenera: Rubrapterus with species P. bavius and P. fatma, and Palaeophilotes sensu stricto. The latter subgenus includes four lineages and nine species: (1) the P. abencerragus lineage (single species P. abencerragus), (2) P. barbagiae lineage (single species P. barbagiae), (3) P. panope lineage (P. panope and P. triphysina), and (4) P. baton lineage (P. panoptes, P. baton, P. vicrama, P. jacuticus and P. sinaicus). The name Borisinia Korb, 2013, syn. nov. is shown to be an objective synonym of Palaeophilotes Forster, 1938. The previously proposed synonymy of P. svetlana and P. marina with P. panope is supported by the identity of their DNA-barcodes. Palaeophilotes panope is reported for the Kazakhstan part of the Altai mountains for the first time. Palaeophilotes jacuticus is confirmed for the Lake Baikal region in Siberia.},
}

@article {pmid40174049,
year = {2025},
author = {Serbina, LŠ and Malenovský, I and Queiroz, DL and Burckhardt, D},
title = {Jumping plant-lice of the tribe Paurocephalini (Hemiptera: Psylloidea: Liviidae) in Brazil.},
journal = {Zootaxa},
volume = {5585},
number = {1},
pages = {1-164},
doi = {10.11646/zootaxa.5585.1.1},
pmid = {40174049},
issn = {1175-5334},
abstract = {The predominantly tropical tribe Paurocephalini of jumping plant-lice currently consists of seven genera and 94 described species worldwide, of which the genera Klyveria Burckhardt et al. and Melanastera Serbina et al. have been recorded from Brazil with two and one species, respectively. Here we review the taxonomy of the Brazilian species based on material collected from extensive fieldwork carried out in 15 states over the last decade. One species of Klyveria and 59 species of Melanastera are newly described, bringing the number of extant Klyveria spp. to three (both in Brazil and worldwide) and that of extant Melanastera spp. to 69 (60 in Brazil, 67 in the Neotropical region and one each in the Afrotropical and Oriental regions). The new species are described and illustrated, and identification keys for the Brazilian species are provided for adults and last instar immatures. The most diagnostically important structures are the distal segment of the aedeagus and the paramere, the forewing (shape, venation, surface spinules and colour pattern) and the female terminalia in the adults, and the chaetotaxy, tarsal arolium and shape of the additional pore fields on the caudal plate in the last instar immatures. The species descriptions are complemented by mitochondrial DNA barcodes (COI and cytB) and information on host plants. Klyveria spp. are restricted to Luehea (Malvaceae), while in Brazil 28 Melanastera spp. develop or are likely to develop on Melastomataceae, 18 spp. on Annonaceae, four spp. each on Asteraceae and Myristicaceae, and one species on Cannabaceae. Only three of the 63 species of Paurocephalini reported here from Brazil, are also known from other countries: two from Paraguay and one from Trinidad. Probably many more species of Melanastera are yet to be discovered and described. Priority in fieldwork should be given to areas that are at high risk of destruction or degradation by human activities, such as the Amazon rainforest, the Atlantic Forest and the Cerrado.},
}

@article {pmid40174044,
year = {2024},
author = {Borkent, A and Spinelli, GR and Díaz, F and Steinke, D and Perez, KHJ and Stur, E and Hallwachs, W and Janzen, DH},
title = {Looking Into the Abyss-How Many Species of Biting Midges (Diptera: Ceratopogonidae) Are There? Their Remarkable Diversity in Costa Rica and Elsewhere.},
journal = {Zootaxa},
volume = {5555},
number = {3},
pages = {331-384},
doi = {10.11646/zootaxa.5555.3.3},
pmid = {40174044},
issn = {1175-5334},
abstract = {The biting midges (Ceratopogonidae) are one of the most species-rich families of insects on the planet with over 6,200 named species. However, their true diversity is unknown and this paper is the first to address the question. Our systematic study of the family in Costa Rica indicates that 192 species were present in a four hectare area of cloudforest at Zurquí de Moravia, at 1,600 m after a year of intensive sampling. Combined with a collection from a single Malaise trap at Tapantí for one year, about 40 kms away and also at 1,600 m, the total was 245 species with significant differences between the two areas and with the strong majority unnamed. This compares to 430 named species for all of Costa Rica and 1,314 for the entire Neotropical Region. Barcoding of 221,407 specimens from Costa Rica similarly indicates large numbers of unnamed species with 4,023 BINs present. On this basis, we project at least 5,000 species in Costa Rica and using ratios of named species here and elsewhere, we suggest that nearly 73,000 are present worldwide. Details from Malaise traps in the Área de Conservación Guanacaste also indicate various levels of endemism. Samples from Bolivia support an interpretation of high diversity. The diversification of the family was examined by comparing phyletic lineages, rather than merely comparing numbers of species in various genera, providing insight as to why some lineages are more diverse than others. Zoogeographic patterns of named species suggest stronger southern connections for Costa Rican Ceratopogonidae in both cloudforest habitats as well as the country as a whole, although many are also more broadly distributed north and south of the country. Comparisons between various collecting methods at Zurquí de Moravia indicate the efficacy of Malaise traps but also the importance of light traps and other methods in sampling adults of Ceratopogonidae. Phenological data from the Malaise traps in the Área de Conservación Guanacaste suggest some patterns of emergence of adults in Costa Rica, the first for any tropical country anywhere.},
}

@article {pmid40173973,
year = {2025},
author = {Huber, BA and Meng, G},
title = {Like grains of sand: Ninetis spiders on the Arabian Peninsula (Araneae, Pholcidae).},
journal = {Zootaxa},
volume = {5563},
number = {1},
pages = {290-335},
doi = {10.11646/zootaxa.5563.1.19},
pmid = {40173973},
issn = {1175-5334},
abstract = {Ninetinae is a group of small to tiny, short-legged daddy-longlegs spiders (Pholcidae) that has its highest diversity in the New World. Only two genera are known to occur in the Old World: the nominotypical genus Ninetis Simon, 1890 on the Arabian Peninsula and in Africa, and the monotypic genus Magana Huber, 2019 in Oman. Here we redescribe the type species of Ninetis, N. subtilissima Simon, 1890, and describe three new species from the Arabian Peninsula: N. amoud sp. nov. from Saudi Arabia, N. marnif sp. nov. and N. samail sp. nov. from Oman. All species descriptions are based on males and females, supported by CO1 barcodes, and accompanied by SEM photographs. While N. amoud sp. nov. is morphologically and genetically similar to N. subtilissima (and to the known African species, of which no CO1 barcodes are available), the two new Omani species are morphologically very distinct. Intraspecific genetic (K2P) distances are partly very high, in particular in N. amoud sp. nov. (up to 17%) and N. marnif sp. nov. (up to 13%). An exploratory species delimitation analysis suggests that these two nominal species might in fact represent several cryptic species each. No corresponding morphological variation was detected.},
}

@article {pmid40173932,
year = {2025},
author = {Zuñiga, R and Valerio, AA and Hanson, P and Hallwachs, W and Janzen, DH},
title = {Endoparasitoid wasps of the genus Cubus (Hymenoptera, Ichneumonidae, Metopiinae) reared from caterpillars of Área de Conservación Guanacaste, Costa Rica.},
journal = {Zootaxa},
volume = {5590},
number = {3},
pages = {365-385},
doi = {10.11646/zootaxa.5590.3.4},
pmid = {40173932},
issn = {1175-5334},
abstract = {As a result of COI barcoding over 200 reared specimens of what appeared to be Cubus validus from northwestern Costa Rica, and matching them with their host caterpillars and morphological traits, we describe eleven new sympatric species. All are endoparasitoids of leaf-rolling Crambidae (Lepidoptera). The new species, authored by Zúñiga, Valerio & Hanson, are: Cubus alanflemingi, C. christhompsoni, C. curtsabrowskyi, C. duvalierbricenoi, C. gracewoodae, C. jeffcummingi, C. jimoharai, C. johnstiremani, C. manuelzumbadoi, C. montywoodi, and C. normwoodleyi. We also provide an illustrated key, a table of key morphological characters of each species, and a table of host records.},
}

@article {pmid40173915,
year = {2025},
author = {Brodin, Y},
title = {Procladius (Diptera, Chironomidae) of Europe and a global view.},
journal = {Zootaxa},
volume = {5591},
number = {1},
pages = {1-127},
doi = {10.11646/zootaxa.5591.1.1},
pmid = {40173915},
issn = {1175-5334},
abstract = {A project initiated in 1991 to untangle species-taxonomy of European Procladius (Chironomidae) has been accomplished. Increasing amount of material, loans and especially the development of barcodes and the BIN-system of BOLD, made finalization possible after about 33 years. An iterative process based on detailed studies of male morphology and barcode clusters, BINs, resulted in identification of 27 species present in Europe, most of them also in Asia (China, Japan, Mongolia and Russia) and North America (Canada and the United States). One hundred morphological characters were adopted for species identification of which the 30 most important ones were used to construct a species key and an additional helpdesk. The key contains three characters for each species separation as this is frequently needed for reliable identification. The ratio GspR, the outer length of the gonostylus process versus length of outer margin in gonostylus, proved to be the most important character for species identification. All but two of the 27 species have barcodes and BINs. All but one BIN contained only one species. The exception is a BIN that previously was divided into two BINs each containing one morphologically distinct species. Intraspecific divergence within the species ranged from 0‒3.3% and interspecific divergence from 2.0‒8.8%. Four new species are presented. These are P. exilis Brodin, new species, P. gemma Brodin, new species, P. saeticubitus Brodin, new species and P. tenebricosus Brodin & Hellberg, new species. The other 23 species presented are as follows with new synonyms within brackets: P. appropinquatus (Lundström, 1916) [P. ruris Roback, 1971], P. bellus (Loew, 1866) [Tanypus rufovittatus van der Wulp, 1874, P. latifrons Kieffer, 1922, P. leucocoma Kieffer, 1922, P. profundorum Kieffer, 1923], P. breviatus Remmert, 1953, P. choreus (Meigen, 1804) [Chironomus incomptus Walker, 1856], P. clavus Roback, 1971, P. crassinervis (Zetterstedt, 1838) [Tanypus pectinatus Kieffer, 1909, P. bifasciatus Goetghebuer, 1936, P. cinereus Goetghebuer, 1936, P. abetus Roback, 1971], P. culiciformis (Linnaeus, 1767) [Tanypus sagittalis Kieffer, 1909, Trichotanypus scapularis Kieffer, 1924, P. freemani Sublette, 1964 in part], P. dentus Roback, 1971, P. ferrugineus (Kieffer, 1918) [Trichotanypus parvulus Kieffer, 1918, Trichotanypus fulvus Kieffer, 1924, Trichotanypus profundorum Kieffer, 1924, P. rugulosus Saether 2010], P. fimbriatus Wülker, 1959, P. flavifrons Edwards, 1929, P. floralis Kieffer, 1915, P. frigidus (Holmgren, 1869) [P. gretis Roback, 1971], P. imicola Kieffer, 1922 [P. bathyphilus Kieffer, 1922, P. nietus Roback, 1971], P. islandicus (Goetghebuer, 1931) [P. fuscus Brundin, 1949, P. vesus Roback, 1971], P. longistilus (Kieffer, 1916) [P. suecicus Brundin, 1949], P. lugens Kieffer, 1915 [P. macrotrichus Roback, 1971], P. lugubris (Zetterstedt, 1850) [P. barbatus Brundin, 1949, P. johnsoni Roback, 1980], P. nudipennis Brundin, 1947, P. pruinosus (Kieffer, 1924), P. signatus (Zetterstedt, 1850) [Trichotanypus nigriventris Kieffer, 1924, P. denticulatus Sublette, 1964 in part], P. simplicistilus Freeman, 1948, P. tatrensis Gowin, 1944. In addition, 12 species of Procladius not found in Europe are briefly described and it is indicated where they appear in the species-key. Species of Procladius have been reported from 133 countries or autonomies worldwide. As many as 12 species have been found in extreme cold places of the northern hemisphere, with mean annual temperature ‒10 C or more. Altitude records are at 4 730 m above sea level in the Himalayas. Larvae of most European species are known to be omnivorous, although predation might be more beneficial for growth. Synonyms and dubious names reduce the number of valid (accepted) species of Procladius according to Catalogue of Life and Systema Dipterorum with 34% worldwide. After the inclusion of four new species of the present study and two others from Asia the number or valid species of Procladius worldwide land on 69.},
}

@article {pmid40173762,
year = {2025},
author = {Wang, M and Lai, Y and Liu, X},
title = {The green lacewing genus Kuwayamachrysa Tsukaguchi & Tago, 2018 from China, with description of two new species based on morphological and molecular evidence.},
journal = {Zootaxa},
volume = {5570},
number = {1},
pages = {138-150},
doi = {10.11646/zootaxa.5570.1.6},
pmid = {40173762},
issn = {1175-5334},
abstract = {Previously, Kuwayamachrysa Tsukaguchi & Tago, 2018 (Neuroptera: Chrysopidae: Chrysopinae) was known as a monotypic green lacewing genus from the Palearctic region. Here we described two new species of Kuwayamachrysa from China: Kuwayamachrysa wujiaoensis sp. nov. and Kuwayamachrysa neptuna sp. nov. Also, Mallada qinlingensis Yang, 1989, currently named as Apertochrysa qinlingensis (Yang, 1989), is recognized as a junior synonym of Kuwayamachrysa kichijoi (Kuwayama, 1936). A key to the Kuwayamachrysa species is provided. The standard DNA barcoding region of cytochrome c oxidase subunit I (COI) of these species was sequenced for the verification of the new species.},
}

@article {pmid40173760,
year = {2025},
author = {Słomczyński, K and Matera, T and Brodecki, J and Gadawski, P and Płóciennik, M},
title = {The first report from Poland and larvae description of Eukiefferiella dittmari Lehmann, 1972 (Diptera: Chironomidae) based on morphological and molecular characteristics.},
journal = {Zootaxa},
volume = {5570},
number = {1},
pages = {169-178},
doi = {10.11646/zootaxa.5570.1.8},
pmid = {40173760},
issn = {1175-5334},
abstract = {Eukiefferiella is a large genus in the family Chironomidae with over 50 species worldwide. Their immature stages have so far been described in many species in the western Palearctic. Nevertheless, some species are still known only from adult males. Presented below is a description of Eukiefferiella dittmari Lehmann, 1972 larvae first recorded in Poland in the pristine river Rawka. The larvae were collected from water moss and identified to the species level using a DNA barcode from BOLD database. E. dittmari larvae belong to E. ilkleyensis group having bifid SIII seta, and mentum with wide central tooth and four pairs of lateral teeth. At the genetic and morphological level, E. dittmari is a sister species to Nearctic E. endobryonia, also an aquatic moss dweller. The phylogenetic relation of these two species should be further investigated.},
}

@article {pmid40173718,
year = {2025},
author = {Verdone, CJ and Williams, BW and Beaty, SR and Holland, VB and Grubbs, SA and Dewalt, RE},
title = {The adults, larvae, and systematics of the Nearctic Oemopteryx Klapálek, 1902 (Plecoptera: Taeniopterygidae).},
journal = {Zootaxa},
volume = {5595},
number = {1},
pages = {1-94},
doi = {10.11646/zootaxa.5595.1.1},
pmid = {40173718},
issn = {1175-5334},
abstract = {The adult and larval life stages of the Nearctic species of Oemopteryx Klapálek, 1902 (Plecoptera: Taeniopterygidae) are reviewed using color images, scanning electron microscopy photomicrographs, variation in the barcode region of the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene, and distributional information. Two new species are described from the southeast Nearctic region. Adult and larval keys to Oemopteryx species are presented in addition to revised keys to genera for Nearctic Taeniopterygidae.},
}

@article {pmid40173671,
year = {2024},
author = {Eiseman, CS and Feldman, TS and Palmer, MW},
title = {New larval host records, parasitoid records, and DNA barcoding data for North American leaf-mining leaf beetles (Coleoptera: Chrysomeloidea).},
journal = {Zootaxa},
volume = {5549},
number = {1},
pages = {1-60},
doi = {10.11646/zootaxa.5549.1.1},
pmid = {40173671},
issn = {1175-5334},
abstract = {We discuss 46 species of North American leaf-mining leaf beetles (Coleoptera: Chrysomelidae, Megalopodidae), plus one external feeder observed to spin its cocoon within the leaf mine of another insect. For each species, we review previous records of larval and adult hosts and associated hymenopteran parasitoids, augmenting these with our own observations, including the first accounts of oviposition and larval habits for many species. We present the first rearing records for 12 of these species: Anisostena californica Van Dyke, A. funesta (Baly), A. lecontii (Baly), A. perspicua (Horn), Microrhopala excavata (Olivier), Odontota floridana Butte, Stenopodius lateralis (Schaeffer), Altica lazulina LeConte, Dibolia obscura Parry, Monoxia inornata Blake, Zeugophora puberula Crotch, and Z. varians Crotch; as well as 18 new state and provincial records for chrysomeloids, although some of these are based on tentative identifications. We also present original DNA barcoding data showing intra- and interspecific variation among 18 species of hispines (Chrysomelidae: Chalepini). Our data do not provide evidence for cryptic species within Baliosus nervosus (Panzer), Sumitrosis inaequalis (Weber), and S. rosea (Weber) hypothesized based on differences in larval hosts and leaf mines. However, they do suggest the possibility of cryptic species within Tilia-feeding B. nervosus, as well as within S. ancoroides (Schaeffer) and perhaps Microrhopala excavata and Odontota horni Smith. Our barcoding data also support the recognition of the Silphium-feeding M. laetula LeConte as distinct from the Solidago-feeding M. vittata (Fabricius).},
}

@article {pmid40173657,
year = {2024},
author = {Loh, KH and Poong, SW and DU, J and Ong, JJL and Zheng, X and Li, Y and Hu, W},
title = {First record of the blue-and-yellow grouper Epinephelus flavocaeruleus (Lacepède 1802) (Perciformes: Epinephelidae) from the Borneo waters, Malaysia.},
journal = {Zootaxa},
volume = {5550},
number = {1},
pages = {133-144},
doi = {10.11646/zootaxa.5550.1.14},
pmid = {40173657},
issn = {1175-5334},
abstract = {Groupers of the family Epinephelidae constitute a diverse and commercially valuable group of reef fishes globally. They comprise an assemblage of carnivorous marine fishes, comprising more than 177 species across 16 genera. The epinephelid genus Epinephelus, which consists of over 90 species, is found worldwide in the tropics and subtropics. To date, the ichthyofauna of Malaysia has documented a total of 43 epinephelid species. Apart from these, Epinephelus flavocaeruleus (Lacepède, 1802), commonly known as the blue-and-yellow grouper, is rarely reported in the Indo-Pacific Ocean. The present study extends the documented distribution range of E. flavocaeruleus eastwards from the Andaman Sea to the Borneo waters of Sabah, Malaysia. Five specimens of the blue-and-yellow grouper were collected from a local fish market. Species identification was confirmed by the color patterns and DNA barcoding of 630 base pairs of the cytochrome C oxidase I gene for all E. flavocaeruleus specimens, Epinephelus cyanopodus (Richardson, 1846), and 10 closely related Epinephelus species. The interspecies genetic distance ranged from 0.002-0.168. Results from the Templeton, Crandall, and Sing (TCS) haplotype network analysis and maximum likelihood phylogeny based on the COI marker indicate a close genetic relationship between E. flavocaeruleus and E. cyanopodus. However, we refrain from proposing any taxonomic revisions given that more in-depth studies using multiple molecular markers or phylogenomic analysis on a larger sample size are necessary to confirm the taxonomic status of both species. This study significantly contributes to a better understanding of the taxonomy, phylogenetic relationship, and genetic diversity of E. flavocaeruleus.},
}

@article {pmid40173619,
year = {2024},
author = {Leong, WI and Yu, JK and Tsai, IJ and Kaczmarek, Ł and Lee, YC and Lin, CP},
title = {Echiniscus gemmatussp. nov. (Heterotardigrada: Echiniscidae; the spinulosus morphogroup) from Macau, China.},
journal = {Zootaxa},
volume = {5551},
number = {2},
pages = {333-352},
doi = {10.11646/zootaxa.5551.2.5},
pmid = {40173619},
issn = {1175-5334},
abstract = {The study of tardigrades in urban environments, particularly in natural areas within cities, has been significantly overlooked. A recent discovery of a new species of tardigrade in lichens collected from Mong Há Hill Municipal Park in Macau provides new insights into the population of tardigrades within the city. Echiniscus gemmatus sp. nov. was identified based on distinct morphological characters, morphometric measurements, and DNA sequences of nuclear (18S rRNA, 28S rRNA, ITS-1, and ITS-2), as well as a mitochondrial (COI) markers. Our research indicates that Ech. gemmatus sp. nov. belongs to the Echiniscus spinulosus morphogroup and is most similar to Ech. tropicalis, as confirmed by both qualitative characters and DNA barcoding. Notably, Echiniscus gemmatus sp. nov. exhibits distinct characteristics that differentiate it from other members of the Ech. spinulosus morphogroup, including (1) often asymmetrical short spines B, C, Cd, Dd, and E, and (2) larger and more visible pores tend to be concentrated in the median and posterior portions of the first and second paired plates, with their visibility gradually decreasing towards the anterior and lateral suture regions.},
}

@article {pmid40173612,
year = {2024},
author = {Jiang, ZH and Li, T and Yan, M and Wang, JX and Zheng, XY and Hu, SJ},
title = {The life history of Smerinthus minor Mell, 1937, with a review of the East Asian species of the genus Smerinthus Latreille, 1802 (Lepidoptera: Sphingidae).},
journal = {Zootaxa},
volume = {5551},
number = {3},
pages = {453-478},
doi = {10.11646/zootaxa.5551.3.2},
pmid = {40173612},
issn = {1175-5334},
abstract = {The six species of the genus Smerinthus Latreille, 1802 known from China, namely S. caecus Ménétriés, 1857, S. kindermannii Lederer, 1853, S. minor Mell, 1937, S. ocellata (Linnaeus, 1758), S. planus Walker, 1856, and S. szechuanus (Clark, 1938) (Lepidoptera, Sphingidae, Smerinthinae, Smerinthini), are examined and illustrated, including the first description of the life history and female genitalia of S. minor. Diagnostic features and distribution maps of all Smerinthus species in East Asia are provided, together with a phylogenetic analysis based on DNA barcode sequences and a global checklist of all Smerinthus species.},
}

@article {pmid40173608,
year = {2024},
author = {Kodama, M and Kodama, N and Mukaida, Y and Hosoki, TK and Nakamoto, K and Tanita, I and Yamada, H},
title = {First record of the genus Cymadusa Savigny, 1816 (Crustacea: Amphipoda: Ampithoidae) from Japan, with redescription and DNA barcoding for C. imbroglio Rabindranath, 1972.},
journal = {Zootaxa},
volume = {5551},
number = {3},
pages = {556-568},
doi = {10.11646/zootaxa.5551.3.6},
pmid = {40173608},
issn = {1175-5334},
abstract = {The ampithoid amphipod Cymadusa imbroglio Rabindranath, 1972 was collected from Ishigaki Island, southwest Japan, as the first Japanese record of the genus. The specimens collected from Ishigaki Island also represent the northernmost record of the species. We herein provide a detailed description and illustration of the specimens from Ishigaki Island. Sequences of COI were determined from two specimens for DNA barcoding and future taxonomic studies.},
}

@article {pmid40173599,
year = {2024},
author = {Eiseman, CS and Lonsdale, O and Montgomery, GA and Jacobsen, JM and Kahn, EX and Rosati, MC and Hauser, M and Parikh, GR and Yu, D},
title = {Invasive Cape ivy (Asteraceae: Delairea odorata Lem.) confirmed as a host for the North American leafminer Liriomyza temperata Spencer (Diptera: Agromyzidae).},
journal = {Zootaxa},
volume = {5555},
number = {1},
pages = {24-34},
doi = {10.11646/zootaxa.5555.1.2},
pmid = {40173599},
issn = {1175-5334},
abstract = {A leafminer reared in California from Cape ivy (Asteraceae: Delairea odorata Lem.), an invasive plant introduced from South Africa, is identified as Liriomyza temperata Spencer (Diptera: Agromyzidae). This is believed to be a novel host association for a native Nearctic fly, which appears to have been introduced in Hawaii along with Cape ivy. Liriomyza tricornis Lonsdale syn. nov. is treated as a junior synonym of L. temperata. There are no previous host records for either taxon. We review previously published rearing records of North American Liriomyza spp. from other plants in the tribe Senecioneae, as well as observations of unidentified Liriomyza mines on these plants. We also discuss the leaf mine and DNA barcode of an undetermined Trypeta sp. (Diptera: Tephritidae) found mining leaves of Cape ivy in California.},
}

@article {pmid40173572,
year = {2025},
author = {Ps, FP and Arjunan, JK and Venu, S and Eranhottu, S and Ummath, A and Kalita, S and Pv, MR and Sadaka, S},
title = {Taxonomic redescription and molecular confirmation of Lutjanus rufolineatus (Acanthuriformes: Lutjanidae) from the Andaman Islands, India.},
journal = {Zootaxa},
volume = {5566},
number = {2},
pages = {370-380},
doi = {10.11646/zootaxa.5566.2.7},
pmid = {40173572},
issn = {1175-5334},
abstract = {We provide a detailed taxonomic redescription of Lutjanus rufolineatus, based on six specimens collected from the Andaman Islands, India. The species' taxonomic status and distribution have historically been misinterpreted within Indian waters due to close similarities with congeners, leading to frequent misidentification. To address this, we performed comprehensive morphological and molecular analyses, including DNA barcoding and phylogenetic reconstruction, to confirm the identity of L. rufolineatus and clarify its relationships with related species. Our findings emphasize the value of thorough taxonomic assessment in delineating species boundaries, particularly for understudied marine fauna. Additionally, this research fills critical gaps in the taxonomy of Indian marine fishes, addressing past ambiguities and enhancing regional biodiversity records. By integrating morphological and molecular data, this study underscores the importance of precise species identification for improved biodiversity conservation and management efforts in the Indo-Pacific.},
}

@article {pmid40173511,
year = {2025},
author = {Zaldívar-Riverón, A and Castañeda-Osorio, R and Shaw, SR},
title = {Three new species and phylogenetic affinity of the neotropical genus Sericobracon Shaw (Braconidae: Doryctinae).},
journal = {Zootaxa},
volume = {5613},
number = {1},
pages = {171-185},
doi = {10.11646/zootaxa.5613.1.9},
pmid = {40173511},
issn = {1175-5334},
abstract = {Sericobracon Shaw is a small doryctine genus which was erected based on two species from Trinidad and the U.S. Virgin Islands (St. Croix) in the Caribbean Sea (S. arimaensis Shaw and S. evansi Shaw). Its type species, S. arimaensis, was reported as endoparasitoid of an Embioptera species, which is a unique biology for known Braconidae. Here we describe three new species of Sericobracon from Costa Rica: S. paulmarshi Zaldívar-Riverón & Shaw, S. puravida Zaldívar-Riverón & Shaw, and S. zunigai Zaldívar-Riverón & Shaw. The former species is characterized with DNA barcoding, providing the first such molecular data for any species in this genus. We also investigated the phylogenetic affinity of the genus within the subfamily Doryctinae based on nuclear UCE data. Sericobracon was recovered within the main Neotropical doryctine clade closely related to Bolivar Zaldívar-Riverón & Rodríguez-Jiménez and Parallorhogas Marsh. We discuss the higher taxonomic classification of Sericobracon and the latter two genera within the Doryctinae based on these relationships recovered and their shared morphological features. A key to species and digital photographs of the five described species of Sericobracon are provided.},
}

@article {pmid40173502,
year = {2025},
author = {Jaroenchaiwattanachote, C and Pramual, P and Wangwasit, K and Bunchalee, P and Thanee, I},
title = {Integrative taxonomy and DNA barcoding of Thai Caddisflies (Trichoptera), with the description of a new Species.},
journal = {Zootaxa},
volume = {5613},
number = {2},
pages = {307-322},
doi = {10.11646/zootaxa.5613.2.6},
pmid = {40173502},
issn = {1175-5334},
abstract = {Caddisflies (Trichoptera) are abundant and diverse aquatic insects. Their immature stages inhabit a wide range of aquatic environments, making them ideal candidates for water quality biomonitoring. However, the limited morphological characteristics available for species identification in the immature stages pose a significant challenge to their application in biomonitoring. In this study, we evaluated the effectiveness of DNA barcoding, based on mitochondrial cytochrome c oxidase I (COI) sequences, for species identification of caddisflies in Thailand. A total of 1,487 adult specimens were collected and morphologically identified into 13 species across 8 genera and 4 families. From these taxa, 88 COI sequences were generated from representative specimens. Maximum intraspecific genetic divergence ranged from 0% to 3.08%. Only three species were successfully matched to COI sequences in the BOLD database, while nine species are reported here for the first time, and one species remained ambiguous. Integrating COI barcoding sequences with morphological data revealed that one species, morphologically similar to Triplectides indicus (Walker 1852), represents a novel species, Triplectides buengkanensis sp. nov. We provide a detailed description, illustrations, diagnostic features, and DNA barcoding sequences for this new species.},
}

@article {pmid40173501,
year = {2025},
author = {Kerkig, P and Quicke, DLJ and Latibari, MH and Butcher, BA},
title = {World checklist of the genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with description of a new species from Thailand.},
journal = {Zootaxa},
volume = {5613},
number = {2},
pages = {323-336},
doi = {10.11646/zootaxa.5613.2.7},
pmid = {40173501},
issn = {1175-5334},
abstract = {We describe and illustrate a new species of the aphidiine braconid genus Lipolexis Förster, Lipolexis khaoyaiensis sp. nov., from Thailand, using an integrative approach. Morphologically, the new species is similar to L. peregrinus Tomanović and Kocić, 2020, but molecular analysis showed clear separation of at least 27 independent Lipolexis lineages, only eight of which correspond to previously known species, plus the one which represents the new species described here. A molecular phylogeny based on all available barcodes support that the genus comprises two well supported clades, with L. khaoyaiensis sp. nov. being recovered in the gracilis species-group with strong support (100% ultrafast bootstrap). A modified section of the identification key to species of Lipolexis is added to include the new species. Reported host associations for each of the described species as well as a distribution map of all records of species plus provenances of all barcoded specimens is provided.},
}

@article {pmid40173486,
year = {2025},
author = {Lee, DJ and Roh, SJ},
title = {A new species of the genus Unilepidotricha (Lepidoptera, Meessiidae) from Ulleungdo island, Korea.},
journal = {Zootaxa},
volume = {5613},
number = {3},
pages = {585-592},
doi = {10.11646/zootaxa.5613.3.10},
pmid = {40173486},
issn = {1175-5334},
abstract = {In this study, we describe a new species, Unilepidotricha ulleungensis sp. nov., from Korea. All available information on U. ulleungensis is presented, including collecting locations and illustrations of adult and male genitalia. Additionally, DNA barcodes for the species are provided.},
}

@article {pmid40170826,
year = {2025},
author = {Liu, Y and Liu, K and Dong, W and Dong, S and Wang, Y and Xu, C and Li, E and Sun, J},
title = {Chloroplast Genome Evolution of Hamamelidaceae at Subfamily Level.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71141},
pmid = {40170826},
issn = {2045-7758},
abstract = {The Hamamelidaceae is significant for its contributions to construction, furniture making, and ornamental use, including 26 genera and 119 species. However, complete chloroplast genome sequences of Hamamelidaceae species have been reported less frequently. In this study, five species were newly sequenced, and seven others available complete chloroplast genomes were added to compare the chloroplast genome evolution in Hamamelidaceae at the subfamily level. The results indicated that the chloroplast genome size ranged from 158,116 to 159,941 bp, encoding 79 to 81 protein-coding genes, four ribosomal RNA genes, and 30 to 31 transfer RNA genes. A robust phylogenetic tree of Hamamelidaceae was obtained using complete chloroplast genomes, supporting that all Hamamelidaceae species formed a monophyletic group and divided into four subfamilies. Exbucklandioideae was the first diverged group within Hamamelidaceae, followed by Mytilarioideae, Disanthoideae, and Hamamelidoideae, which formed a clade. Furthermore, three new potential DNA barcodes were provided: trnH-psbA, psbJ-petA, and ycf1. This study confirms that the complete chloroplast genome data provide a more accurate and confident resolution of the phylogenetic relationships within the Hamamelidaceae. These new genomic data not only enhance the understanding of genome evolution but also provide a better understanding of the phylogenetic relationships of Hamamelidaceae.},
}

@article {pmid40170416,
year = {2025},
author = {Surmacz, B and Vecchi, M and Fontaneto, D and Budzik, K and Godziek, J and Matsko, Y and Stec, D},
title = {COI Metabarcoding With a Curated Reference Database and Optimized Protocol Provides a Reliable Species-Level Diversity Assessment of Tardigrades.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12972},
pmid = {40170416},
issn = {1749-4877},
support = {2022/45/N/NZ8/01992//the National Science Centre, Poland/ ; 2022/44/C/NZ8/00050//the National Science Centre, Poland/ ; //the National Biodiversity Future Centre (NBFC)/ ; CN00000033//the Italian Ministry of University and Research, PNRR, Missione 4 Componente 2, "Dalla ricerca all'impresa," Investimento 1.4/ ; },
abstract = {DNA metabarcoding is revolutionizing biodiversity research by providing rapid and efficient ways of collecting species occurrence data. However, it has not yet been effectively applied to many taxonomic groups, mainly due to a significant lack of reference sequences and dedicated protocols. One such group is the tardigrades-a charismatic phylum of microinvertebrates known for their extremophilic and cryptobiotic capabilities. In this study, we provide the first curated database of 3194 tardigrade COI sequences sourced from public databases and supplemented with newly produced barcodes. We demonstrate tardigrade metabarcoding in action with optimized PCR primers and a sample processing protocol using 78 samples collected in Poland and Italy. The metabarcoding revealed the presence of more than a hundred operational taxonomic units classified as Tardigrada, representing 23 genera. We compared the metabarcoding results with a morphological survey, which revealed the presence of the same genera, but a lower number of species-level taxa identified morphologically. We observed congruent patterns of tardigrade species richness and taxonomic composition between metabarcoding and morphological surveys in both within-sample and regional fauna composition levels. The metabarcoding had a higher discriminatory power, revealing cryptic diversity, and distinguishing species belonging to taxonomically challenging species complexes. By combining metabarcoding with morphological study, we were able to find rare taxa, including novel biogeographic records and putative species new to science, showing also that this approach can be extremely powerful and effective in meiofauna research.},
}