@article {pmid41924242,
year = {2026},
author = {Li, W and Miao, B and Wan, S},
title = {A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.},
journal = {Bio-protocol},
volume = {16},
number = {6},
pages = {e5636},
pmid = {41924242},
issn = {2331-8325},
abstract = {Extrachromosomal circular DNA (eccDNA) is a type of circular DNA that exists independently of chromosomes and has garnered significant attention in various fields, particularly in the context of smaller eccDNAs, which have considerable roles in gene regulation through various mechanisms. Current methods such as Circle-Seq and 3SEP can enrich small eccDNAs during sample preparation, but most bioinformatics pipelines remain challenging, exhibiting low accuracy and efficiency. This protocol describes the detailed workflow of a newly developed bioinformatics analysis pipeline, named EccDNA Caller based on Consecutive Full Pass (ECCFP), to accurately identify eccDNA from long-read Nanopore sequencing data. Compared to other pipelines, ECCFP significantly improves detection sensitivity, accuracy, and runtime efficiency. The process includes raw data quality control, trimming of adapters and barcodes, alignment to a reference genome, and identification of eccDNA, with detailed results encompassing accurate positioning of eccDNA, consensus sequences, and variants of individual eccDNA. Key features • This protocol provides a beginner-friendly, step-by-step workflow that enables researchers without bioinformatics experience to successfully execute the entire eccDNA identification process. • It offers an efficient computational pipeline for eccDNA detection from Nanopore sequencing data, integrating quality control, trimming, alignment, and eccDNA identification. • ECCFP exhibits sensitivity, accuracy, high efficiency, and low false-positive rates compared to existing long-read-based tools.},
}

@article {pmid41924441,
year = {2026},
author = {St Laurent, RA and Wehrly, S and Slotten, J},
title = {A new species of sack-bearer moth (Lepidoptera, Mimallonidae) from Florida.},
journal = {ZooKeys},
volume = {1273},
number = {},
pages = {287-306},
pmid = {41924441},
issn = {1313-2989},
abstract = {A rarely reported new species of Mimallonidae from Florida, USA, is described. Remarkably, the distinctive new species has not been seen across much of its historical range since the 1960s, and all records come from six somewhat isolated white sand Florida Scrub habitats, one of which is completely destroyed and most others clearly imperiled. DNA barcoding sequences from the disparate populations suggest notable genetic diversity in the few known populations, meaning extirpation of any of them could signal loss of critical population structure of an already narrowly endemic species. Cicinnus albarenicolus St Laurent, sp. nov. is compared to the only other similar species in North America, C. melsheimeri (Harris in Doubleday), a common denizen of oak forests throughout the eastern United States, including Florida, southern Canada, and the Rocky Mountains. Until its distribution and life history are more well-understood, C. albarenicolus will remain an enigmatic taxon of major conservation concern.},
}

@article {pmid41925123,
year = {2026},
author = {van der Burgt, YEM and Cobbaert, CM},
title = {Next-generation proteomics in medical laboratories: metrologically sound quantitative protein tests vs. innovative and personalized proteome patterns.},
journal = {Clinical chemistry and laboratory medicine},
volume = {},
number = {},
pages = {},
pmid = {41925123},
issn = {1437-4331},
abstract = {In precision medicine protein phenotypes are foreseen that combined with pattern recognition tools exhibit great potential in guaranteeing safe and accurate test results for patient management and intervention. For discovery purposes novel high-throughput technologies have emerged and this has led to a resurging interest in plasma proteomics. These next-generation proteomics technologies pursue enhanced speed and robustness of proteome readouts and have therefore been designed in combination with machine learning tools for pattern recognition to allow large-scale population studies. In the proximity extension assay two antibodies with single-stranded DNA tags are applied that hybridize upon binding to their target proteins. The second affinity-based assay relies on DNA-based aptamers with specific binding shape complementarity to their target proteins. In both assays the resulting protein-DNA barcodes are quantified through next-generation sequencing. On the one hand the ease of data analysis and integration with genomic and transcriptomic data is attractive compared to complex MS-based proteomics datasets. On the other hand MS allows an unequivocal characterization of the protein of interest and its proteoforms. Laboratory professionals now face the following protein diagnostics dilemma: either hold firm to metrologically sound protein or proteoform quantification by mass spectrometry or pursue individual protein profiles combined with machine learning algorithms without detailing various proteoforms. The first strategy has proven slow and may not be sustainable for all biomarkers, whereas the latter approach clearly requires concerted efforts from all stakeholders involved in medical test development before these can be adapted into medical laboratories.},
}

@article {pmid41925564,
year = {2026},
author = {Goyette, MA and Graser, C and Seehawer, M and Patmanidis, A and Rojas Jimenez, E and Kamat, A and Yan, P and Fassl, A and Foidart, P and Li, Z and James, A and Sflomos, G and Brisken, C and Sicinski, P and Michor, F and Polyak, K},
title = {HER2 heterogeneous breast cancer models reveal novel therapeutic targets and subclonal dynamics during evolution to resistance to HER2-targeted therapies.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-25-1459},
pmid = {41925564},
issn = {2159-8290},
abstract = {Intratumor heterogeneity for HER2 in HER2-positive breast cancer is a driver of resistance to HER2-targeted therapies. The advancement of treatments for HER2 heterogeneous tumors has been hindered by the lack of preclinical models that accurately mimic the human disease. Here we describe human HER2 heterogeneous breast cancer models composed of ERBB2 amplified (HER2hi) and non-amplified (HER2lo) cell populations derived from the same tumor. Utilizing these models, together with cellular barcoding, we demonstrate subclonal cooperation between HER2hi and HER2lo subpopulations. Furthermore, HER2lo cells drive resistance to HER2-targeting antibody-drug conjugates (ADC) like T-DXd but are sensitive to HER2 kinase inhibitors. CRISPR screens in heterogeneous co-cultures identified sensitizers of HER2lo cells to T-DXd including ABCC1 and USP9X. USP9X inhibition enhances the lysosomal targeting of HER2, thereby potentiating ADC payload release and reducing tumor recurrence after T-DXd treatment. Our results elucidate the functional relevance of HER2 heterogeneity and propose improved therapies for these tumors.},
}

@article {pmid41925998,
year = {2026},
author = {Laakkonen, L and Kvarnström, K and Janhunen, K and Linden-Lahti, C and Kuitunen, S},
title = {Facilitators and barriers in using barcode technology to ensure safe medication dispensing, preparation, and administration in a children's hospital: a focus group study for clinical pharmacists.},
journal = {International journal of clinical pharmacy},
volume = {},
number = {},
pages = {},
pmid = {41925998},
issn = {2210-7711},
abstract = {INTRODUCTION: Barcode technology is widely used in hospitals to improve medication safety. Although this technology is considered effective for making system-wide improvements, its implementation faces several challenges. Hospital pharmacists play a key role in supporting this process.

AIM: To explore clinical pharmacists' perceptions of the facilitators and barriers to using barcode technology in a pediatric hospital setting.

METHOD: A qualitative focus group study. Fourteen clinical pharmacists working in the pediatric department of a university hospital were chosen for the focus groups (n = 3) using purposive sampling to identify the individuals who regularly use barcode technology in clinical practice. The focus group discussions, guided by a semi-structured interview guide with six questions, were recorded and transcribed verbatim. Two researchers independently conducted inductive content analysis, which was later thoroughly reviewed by the entire research group.

RESULTS: The data revealed four main themes: factors encouraging the adoption of barcode technology, factors complicating barcode workflow, ideas to improve workflow efficiency, and at-risk behaviors. Factors encouraging the adoption of barcode technology were associated with the benefits and usability of barcode technology, increased expertise and teamwork, positive user experience, and supportive functions of the electronic health record (EHR) system. Factors complicating barcode workflow included deficiencies related to barcodes in labels and drug packages, negative attitudes of users, organizational factors, the use of the EHR system, and deficiencies in workstations and equipment. These factors were found to contribute to at-risk behaviors, while ideas to improve workflow efficiency focused on removing factors complicating barcode workflow and reducing at-risk behaviors.

CONCLUSION: Various factors can influence the implementation of barcode technology in clinical practice, underscoring the importance of an organizational process to identify system deficiencies and continuously improve usability. Building on previous studies, our research emphasized the issues related to dispensing and preparation workflows, as well as the need for pediatric-specific EHR system customization as key development areas. Our findings can guide risk management efforts in implementing and maintaining barcode technology in hospitals.},
}

@article {pmid41928916,
year = {2024},
author = {Le Cadre, J and Klemp, FL and Bálint, M and Scheu, S and Schaefer, I},
title = {Applicability and perspectives for DNA barcoding of soil invertebrates.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17709},
pmid = {41928916},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Soil ; Electron Transport Complex IV/genetics ; Phylogeny ; *Invertebrates/genetics/classification ; *Arthropods/genetics/classification ; },
abstract = {Belowground invertebrate communities are dominated by species-rich and very small microarthropods that require long handling times and high taxonomic expertise for species determination. Molecular based methods like metabarcoding circumvent the morphological determination process by assigning taxa bioinformatically based on sequence information. The potential to analyse diverse and cryptic communities in short time at high taxonomic resolution is promising. However, metabarcoding studies revealed that taxonomic assignment below family-level in Collembola (Hexapoda) and Oribatida (Acariformes) is difficult and often fails. These are the most abundant and species-rich soil-living microarthropods, and the application of molecular-based, automated species determination would be most beneficial in these taxa. In this study, we analysed the presence of a barcoding gap in the standard barcoding gene cytochrome oxidase I (COI) in Collembola and Oribatida. The barcoding gap describes a significant difference between intra- and interspecific genetic distances among taxa and is essential for bioinformatic taxa assignment. We collected COI sequences of Collembola and Oribatida from BOLD and NCBI and focused on species with a wide geographic sampling to capture the range of their intraspecific variance. Our results show that intra- and interspecific genetic distances in COI overlapped in most species, impeding accurate assignment. When a barcoding gap was present, it exceeded the standard threshold of 3% intraspecific distances and also differed between species. Automatic specimen assignments also showed that most species comprised of multiple genetic lineages that caused ambiguous taxon assignments in distance-based methods. Character-based taxonomic assignment using phylogenetic trees and monophyletic clades as criteria worked for some species of Oribatida but failed completely for Collembola. Notably, parthenogenetic species showed lower genetic variance in COI and more accurate species assignment than sexual species. The different patterns in genetic diversity among species suggest that the different degrees of genetic variance result from deep evolutionary distances. This indicates that a single genetic threshold, or a single standard gene, will probably not be sufficient for the molecular species identification of many Collembola and Oribatida taxa. Our results also show that haplotype diversity in some of the investigated taxa was not even nearly covered, but coverage was better for Collembola than for Oribatida. Additional use of secondary barcoding genes and long-read sequencing of marker genes can improve metabarcoding studies. We also recommend the construction of pan-genomes and pan-barcodes of species lacking a barcoding gap. This will allow both to identify species boundaries, and to cover the full range of variability in the marker genes, making molecular identification also possible for species with highly diverse barcode sequences.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Soil
Electron Transport Complex IV/genetics
Phylogeny
*Invertebrates/genetics/classification
*Arthropods/genetics/classification

@article {pmid41929110,
year = {2026},
author = {Siepel, A and Hassett, R and Staklinski, SJ},
title = {VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.24.696405},
pmid = {41929110},
issn = {2692-8205},
abstract = {Bayesian methods are now widely used in reconstructing both species and cell-lineage phylogenies, but they remain heavily reliant on computationally intensive Markov chain Monte Carlo sampling. Phylogenetic variational inference (VI) circumvents this dependency but so far has been limited in speed and scalability. Here we introduce Variational Inference with Node Embeddings (V ine), a computational method that combines an embedding of taxa in a high-dimensional space and a distance-based "decoder" with several algorithmic innovations to dramatically improve phylogenetic VI. V ine supports both standard DNA substitution models and CRISPR barcode-mutation models for inference of cell-lineage trees and tissue-migration histories. In extensive simulation experiments, we show that V ine is comparable in accuracy to the best available Bayesian methods with speeds orders of magnitude faster. We then apply V ine to ∼1,000 complete SARS-CoV-2 genomes and ∼900 lung-cancer cell barcodes, showing reductions in compute time from days to hours or minutes.},
}

@article {pmid41929850,
year = {2026},
author = {Andrade, LF and Jażdżewska, AM},
title = {Two new abyssal Harpiniinae Barnard & Drummond, 1978 (Amphipoda, Phoxocephalidae) from the Clarion-Clipperton Zone.},
journal = {ZooKeys},
volume = {1274},
number = {},
pages = {103-118},
pmid = {41929850},
issn = {1313-2989},
abstract = {Two new species of the phoxocephalid subfamily Harpiniinae are described from the easternmost sector of the Clarion-Clipperton Zone. The material examined was collected with epibenthic sledges during the projects ABYSSLINE-2, MANGAN 2016 and MANGAN 2018 from depths ranging from 4133 to 4359 metres. Harpinia lobata sp. nov. is mainly characterized by: head anteroventral corner with a small projection; gnathopod 1 coxa anteroventrally produced; pereopod 6 basis with posterior proximal expanded lobe; and epimeron 3 posteroventral corner rounded. Harpiniopsis pedro sp. nov. can be diagnosed by: head anteroventral corner with a large projection; mandible palp article 2 shorter than article 3; gnathopods 1-2 palm defined by a subacute hump; pereopod 6 basis with a posterior distal lobe reaching the apex of ischium; and epimeron 3 posteroventral corner produced as a slightly curved spine. Here, we provide the deepest record of the known Harpinia species and the first Harpiniopsis record from the Pacific abyssal plain.},
}

@article {pmid41917196,
year = {2026},
author = {Son, S and Lyden, A and Ng, CF and Dextre, A and Shu, J and Stephens, SI and Fozouni, P and Knott, GJ and Smock, DCJ and Liu, TY and Boehm, D and Simoneau, C and Kumar, GR and Doudna, JA and Ott, M and Fletcher, DA},
title = {Programmable kinetic barcoding for multiplexed RNA detection with Cas13a.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {41917196},
issn = {2157-846X},
abstract = {Rapid identification of viral infections and specific variants in patient samples requires a simple and multiplexed RNA detection method that does not rely on DNA sequencing. Although recent direct detection assays based on CRISPR-Cas13a offer rapid RNA detection by avoiding reverse transcription and DNA amplification required of gold-standard PCR assays, these assays are not easily multiplexed to detect multiple viruses or variants without dividing the sample into separate reactions. Here we show that Cas13a acting on single-target RNAs exhibits variable nuclease activity that depends on the interaction between the target RNA and crRNA. To exploit this feature for multiplexed detection, we devised a crRNA modification strategy that enables programmable tuning of Cas13a's nuclease enzymatic rates. Using a droplet-based Cas13a assay, we demonstrate that kinetic signatures can be harnessed to differentiate among respiratory viruses and SARS-CoV-2 variants in contrived and clinical samples. This kinetic barcoding strategy can be extended to additional RNA targets through simple modification of crRNAs.},
}

@article {pmid41919838,
year = {2026},
author = {Sousa, RN and Santos, GG and Fernandes, GC and Figueredo, SA and Tchaicka, L and Barros, JRS},
title = {DNA Barcoding applied to the identification of Meliponini in the Lençóis Maranhenses microregion, Brazil.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e295935},
doi = {10.1590/1519-6984.295935},
pmid = {41919838},
issn = {1678-4375},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Brazil ; Bees/genetics/classification ; Phylogeny ; Genetic Variation/genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Haplotypes ; DNA, Mitochondrial/genetics ; },
abstract = {Stingless bees (Meliponini) are essential pollinators widely distributed in tropical regions, playing a crucial role in ecosystem maintenance. In Brazil, they are found throughout the national territory. DNA barcoding has emerged as an effective tool for species identification and genetic diversity assessment, especially in areas affected by anthropogenic activities. This study aimed to identify and characterize local stingless bee species at the molecular level. A total of 32 specimens were collected from three communities in Tutóia, Maranhão (MA). Samples were processed at the LabWick/UEMA, with DNA extracted using the phenol-chloroform method and amplification of the COI region via PCR. Sequence analyses were performed using dedicated software. The mitochondrial COI marker enabled the identification of eight stingless bee species distributed across seven distinct genera. The DNA fragments analyzed averaged 450 bp in length, with a predominance of adenine (A) and thymine (T). Sequence similarity with the NCBI database ranged from 96.33% to 98.93%, with Melipona fuliginosa showing the highest match. A total of 25 haplotypes were identified, 10 belonging to the Melipona genus and 15 to other genera. Phylogenetic analysis revealed four groupings within Melipona and six among the remaining genera. The geographic isolation of the sampled communities may have limited species distribution across the study area. Despite the effectiveness of COI, the absence of a clear barcode gap and the scarcity of reference data in databases such as GenBank limit identification accuracy for certain genera. This study underscores the importance of DNA barcoding in contributing genetic data to repositories like NCBI and enhancing the known species diversity in the Lençóis Maranhenses microregion.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Brazil
Bees/genetics/classification
Phylogeny
Genetic Variation/genetics
Polymerase Chain Reaction
Sequence Analysis, DNA
Haplotypes
DNA, Mitochondrial/genetics

@article {pmid41919997,
year = {2026},
author = {Zhang, M and Chen, C and Wu, M and Copley, JT and Poitrimol, C and Alfaro-Lucas, JM and Watanabe, HK and Zhang, R and Zhou, Y},
title = {Global barcoding of the deep-sea snail genus Phymorhynchus reveals surprising distribution ranges and genetic diversity.},
journal = {Biology letters},
volume = {22},
number = {4},
pages = {},
doi = {10.1098/rsbl.2025.0685},
pmid = {41919997},
issn = {1744-957X},
support = {//the Foundation of China Ocean Mineral Resources R & D Association/ ; //Japan Agency for Marine-Earth Science and Technology/ ; //ANR 'CERBERUS'/ ; //the French Oceanographic Fleet/ ; //Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; //the UK Natural Environment Research Council (NERC)/ ; //the China Deep Ocean Affairs Administration/ ; //the United Nations Ocean Decade Programme Digital DEPTH/ ; //the National Key Research and Development Program of China/ ; //University of Victoria/ ; },
mesh = {Animals ; *Snails/genetics/classification/anatomy & histology ; *Genetic Variation ; DNA Barcoding, Taxonomic ; *Animal Distribution ; Phylogeny ; Pacific Ocean ; Indian Ocean ; Atlantic Ocean ; },
abstract = {For rare fauna inhabiting insular habitats, specimens from geographically distant locations are often assumed to be distinct species without a detailed assessment of their genetic diversity. The raphitomid snail genus Phymorhynchus includes a species complex considered endemic to deep-sea hot vents and cold seeps. Despite small morphological differences, existing species hypotheses largely relied on geographic distance to support separation. Here, we present a molecular barcoding study for this complex with a total of 180 specimens sampled across the Atlantic, Pacific and Indian oceans. Our delimitation analyses identified six distinct species supported by morphology, notably egg-capsule characters. They have broader distributions than previously realized, with P. starmeri ranging across the Indo-West Pacific and P. moskalevi apparently cosmopolitan, both showing complex genetic subgroupings. These species are probably also distributed outside vents and seeps, supported by several ambient records. Our results challenge the assumption of fine-scale geographic separation in species inhabiting deep-water insular habitats.},
}

Animals
*Snails/genetics/classification/anatomy & histology
*Genetic Variation
DNA Barcoding, Taxonomic
*Animal Distribution
Phylogeny
Pacific Ocean
Indian Ocean
Atlantic Ocean

@article {pmid41922718,
year = {2026},
author = {Phan, QT and Nguyen, HN and Dinh, KV},
title = {Vietnamese Odonata: bridging global biodiversity, ecological, and conservation gaps in a changing world.},
journal = {npj biodiversity},
volume = {5},
number = {1},
pages = {},
pmid = {41922718},
issn = {2731-4243},
abstract = {Vietnam is a global hotspot, hosting 493 Odonata species, with ~95% evaluated by the IUCN. Odonata species play vital ecological roles in aquatic and terrestrial ecosystems; yet, they face escalating threats from climate change, habitat loss, and pollution. Adult taxonomy has dominated research; yet, critical eco-evolutionary, ecotoxicological, and conservation studies are lacking. This synthesis of 200 years of Vietnamese Odonata research bridges knowledge gaps, offering insights into tropical ecosystem vulnerability in a changing world. We propose an integrative framework scalable to all aquatic invertebrates and understudied tropical regions to advance research and conservation: (1) enhance larval and adult taxonomy and phylogeny using morphology, DNA barcoding (COI gene), and whole genome sequencing for ecologically important, critically endangered or rare species; (2) implement monitoring programmes with eDNA metabarcoding, remote sensing, automated imaging, and citizen science to track distributions, phenology, and traits; (3) conduct eco-evolutionary and ecotoxicological studies with multi-omics to elucidate mechanisms underlying ecophysiology and evolutionary responses; and (4) apply machine learning to project distributions and responses to environmental changes. This framework aligns with global biodiversity and sustainability policy agendas, including the Convention on Biological Diversity and SDGs 14: Life Below Water, and 15: Life on Land, and offers actionable solutions for protecting vulnerable ecosystems.},
}

@article {pmid41922758,
year = {2026},
author = {Vong, KI and Alvarez, YD and Zhang, Q and Weng, J and Noel, G and Barton, ST and Chung, C and Howarth, R and Meave, N and Jiwani, F and Patarlapalli, SB and Yao, F and Zhu, F and Barrows, C and Patel, A and Wang, JX and Chi, NC and Kingsmore, SF and White, MD and Yang, X and Gleeson, JG},
title = {Developmental organization of sensory and sympathetic ganglia.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41922758},
issn = {1476-4687},
abstract = {The neural crest generates a broad spectrum of cell types that migrate across the body plan to populate multiple tissues[1]. However, the relationship between lineages of neural crest derivatives remains unclear, and the extent to which neural crest cells delaminated from the neural tube have specified fates remains debated. Here, leveraging CRISPR barcoding in mice and mosaic variant barcode analysis in humans, we demonstrate robust bilateral progenitor clonal spread of neural crest progenitors along the rostrocaudal axis but limited clonal overlap between sensory and sympathetic lineages. Computational modelling of mosaic variants suggests that most neural crest cells show strong fate restriction before delamination. Real-time imaging of quail embryos further shows a fibroblast-growth-factor-dependent rostrocaudal dispersion of neural crest cells across multiple axial levels. These findings support a model in which neural crest fate bias predominantly emerges within the neural tube, with only a minor subset of delaminated progenitors retaining multipotency to generate both sensory and sympathetic derivatives.},
}

@article {pmid41915710,
year = {2026},
author = {Kim, JY and Lee, YK and Shin, HY and Kim, YJ and Jeon, MA and Yang, W and Jun, A and Kim, K and Cho, H and Kim, MA and Kim, JH},
title = {Biobanking of gynecologic cancer biospecimens: Development, quality control, and translational applications.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0345861},
pmid = {41915710},
issn = {1932-6203},
mesh = {Humans ; Female ; *Biological Specimen Banks/standards ; Quality Control ; *Genital Neoplasms, Female/pathology/genetics ; Translational Research, Biomedical ; Animals ; Cell Line, Tumor ; Republic of Korea ; Ovarian Neoplasms/pathology/genetics ; Mice ; Specimen Handling ; Whole Genome Sequencing ; },
abstract = {INTRODUCTION: This study presents a nationwide infrastructure for the collection and utilization of gynecologic cancer biospecimens, established through the Korea Biobank Project. We comprehensively describe the biobanking strategy, quality control protocols, and development of secondary resources to support future translational and discovery-based research.

METHODS: We established a gynecologic cancer biobank within the Korea Biobank Project (KBP) through a multi-institutional consortium. Biospecimens, including blood, tumor tissue, urine, and ascites, were collected from 294 patients with endometrial, cervical, or ovarian cancers. Pre-analytical variables were documented using the Standard PREanalytical Code (SPREC), and all samples were tracked with 2D barcodes. Secondary resources were developed, including whole-genome sequencing (WGS) datasets, immortalized human ovarian surface epithelial (IHOSE) cell lines, patient-derived xenografts (PDX), tumor organoids, and tissue microarrays (TMAs).

RESULTS: A total of 6,168 biospecimens were archived. WGS was performed on 386 cancer samples, including 172 paired tumor-normal sets. Four IHOSE cell lines were authenticated and validated for stability, 14 PDX models retained histological fidelity across passages, and patient-derived ovarian cancer organoids demonstrated drug sensitivity consistent with clinical response patterns. TMAs were constructed from 519 tumors, supporting large-scale molecular profiling. Industry collaborations further highlighted the translational utility of these resources.

CONCLUSIONS: This study describes the development and application of a gynecologic cancer biobank that integrates standardized biospecimen collection, rigorous QC, and the generation of diverse secondary resources. By linking these resources with clinical and epidemiological data, the biobank provides a scalable and accessible platform for precision oncology and academic-industry collaboration.},
}

Humans
Female
*Biological Specimen Banks/standards
Quality Control
*Genital Neoplasms, Female/pathology/genetics
Translational Research, Biomedical
Animals
Cell Line, Tumor
Republic of Korea
Ovarian Neoplasms/pathology/genetics
Mice
Specimen Handling
Whole Genome Sequencing

@article {pmid41916275,
year = {2026},
author = {Schaff, DL and White, PE and Cote, CJ and Watterson, GE and Lin, KZ and Fasse, AJ and Zhang, NR and Shaffer, SM},
title = {Pre-existing cell states predict resistance to multiple treatments.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101191},
doi = {10.1016/j.xgen.2026.101191},
pmid = {41916275},
issn = {2666-979X},
abstract = {Pre-existing differences between individual cancer cells can predict which cells will become resistant to treatment. DNA barcoding methods that track clones and their cell states during treatment have furthered this understanding, previously focusing on resistance to single treatments. Here, we performed multi-treatment, high-throughput clonal tracking and single-cell RNA sequencing to trace rare clones through resistance development across many treatments in parallel, identifying cell states associated with multi-treatment resistance. We found that clones resistant to one treatment had an increased chance of separately developing resistance to other treatments. We identified high CD44 expression in treatment-naive cells as a predictor of future multi-treatment resistance. Additionally, we found that differences in pre-treatment gene expression states can lead cells within the same treatment condition to follow divergent paths toward their ultimate resistance fate. This work provides a framework for extracting targetable gene expression states from complex resistance dynamics to eliminate multi-treatment resistance.},
}

@article {pmid41917119,
year = {2026},
author = {Jhawar, K and Chu, XL and DeGrandchamp, JB and Yin, Y and Peddibhotla, LA and Banu, S and Mohd Hatta, FNN and Wang, Y and Török, P and Wang, L},
title = {Morphology-guided deep learning for nanoparticle agglomeration diagnostic assays.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45423-2},
pmid = {41917119},
issn = {2045-2322},
support = {EDUNC-33-18-279-V12//Institute for Digital Molecular Analytics and Science, NTU/ ; },
}

@article {pmid41917144,
year = {2026},
author = {Tekle, YI and Wang'ondu, VW and Ghebezadik, S and Cooper, KS},
title = {Quantifying genus-level divergence using 18S rDNA and its application to heterolobosea with discovery of a novel genus from Mombasa Kenya.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45864-9},
pmid = {41917144},
issn = {2045-2322},
support = {2401946//Directorate for Biological Sciences/ ; SFA-23-5//Simons Foundation Fellow Award/ ; },
abstract = {The phylum Heterolobosea comprises a morphologically diverse and ecologically versatile assemblage of free-living microbial eukaryotes, yet genus-level boundaries remain difficult to resolve due to limited diagnostic characters and extensive phenotypic plasticity. Here, we apply a reproducible 18S rDNA divergence framework to quantify genus-level divergence in Heterolobosea and to evaluate taxonomic placement of a newly discovered isolate from coastal sediments of Mombasa, Kenya. Microscopic observations reveal a highly plastic amoeba exhibiting monopodial limax-type locomotion, episodic eruptive activity, and the formation of large multinucleate and polyploid stages that fragment into smaller cells, suggesting an unusual parasexual-like life cycle. Phylogenetic analyses recover the isolate in a strongly supported clade with Orodruina flavescens and an uncultured environmental lineage from the Lost City hydrothermal field. Pairwise 18S rDNA distance analyses show a clear bimodal separation between intragenus and intergenus comparisons with divergence values among these lineages consistently exceed empirical intrageneric thresholds across multiple analytical frameworks. Substitution saturation diagnostics confirm that these divergences occur within the phylogenetically informative region of the SSU rDNA gene. Together, the molecular, morphological, and ecological evidence support recognition of the Mombasa lineage as a distinct genus and species, Mombasina parasexualis gen. nov. et sp. nov., within Orodruinidae. This study reveals previously underappreciated diversity within Tetramitia and demonstrates the broader utility of quantitative divergence-based frameworks for resolving genus-level boundaries in microbial eukaryotes.},
}

@article {pmid41907722,
year = {2026},
author = {Fan, X and Shen, F and Luan, Y and Dong, T and Zhang, C and Gou, F and Han, Y and Yao, W and Wang, L and Wang, X and Zhu, Z and Liu, Y and Li, L and Zhao, J and Li, Z and Jiang, S and Bai, X and Shi, S},
title = {Identification of intraspecific cultivar Melia azedarach 'Mizhi' based on complete chloroplast genome data and leaf anatomy.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1783041},
pmid = {41907722},
issn = {1664-462X},
abstract = {The Melia azedarach 'Mizhi' (cultivar 'Mizhi') is a recently developed cultivar within the genus Melia. It has an elegant tree form, dense foliage, and notable ornamental, ecological, and potential medicinal value, offering broad market prospects. As the number of cultivar Melia continues to increase, accurate identification of these cultivars becomes increasingly critical to ensure its proper utilization and successful large-scale promotion. This study aims to provide more evidence for cultivar identification, development and protection by analyzing shallow whole-genome sequencing data, leaf epidermal and cross-sectional structure. Finally, four complementary approaches: nuclear gene fragments, complete chloroplast genome data, leaf epidermal structure (include micromorphological and ultrastructural characteristic), and leaf cross-sectional structure, were used in this study. The results show that the Melia azedarach 'Mizhi' exhibits its uniqueness in all of the above aspects. Moreover, the SNP based on the chloroplast genome can directly reveal the differences between Melia azedarach 'Mizhi' and others. Overall, this study provides precise molecular markers for the identification and protection of Melia azedarach 'Mizhi', offering new technical tools and theoretical support for the sustainable development and utilization of Melia species. The standardized molecular markers and multi-scale phenotypic data generated in this study also provide high-quality source data for future AI-assisted and automated cultivar identification. This work lays a solid foundation for the development of objective, scalable, and data-driven identification systems in plant cultivar research.},
}

@article {pmid41909257,
year = {2026},
author = {Cukusic, A and Karwautz, C and Murhammer, C and Rasch, G and Biletska, M and Griebler, C},
title = {Dynamic changes in protist community composition along a surface water-groundwater transect in the Danube wetland Lobau, Vienna, Austria.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1749803},
pmid = {41909257},
issn = {1664-302X},
abstract = {Groundwater remains an underexplored habitat for protistan diversity and community dynamics relative to better-studied surface aquatic environments. To address this knowledge gap, we compared protistan communities at two sites, a wetland surface water body and a nearby shallow aquifer, using molecular analysis, to shed light on environmental drivers of both total and active protist communities. The 2-year time series with monthly sampling provided insight into seasonal patterns, and barcoding enabled taxonomic assignment. Our study identified differences in community composition and trophic modes associated with habitat type. Protistan communities in shallow groundwater exhibited pronounced seasonal dynamics, apparently temporally linked to their surface water counterparts. Higher absolute water levels in the backwater than in groundwater, along with a significant fraction of phototrophic protists sampled from the shallow aquifer, are consistent with groundwater recharge from surface water influencing the groundwater protistan community composition.},
}

@article {pmid41910177,
year = {2026},
author = {Sokolova, AI and Galaktionov, KV and Gonchar, A},
title = {Microphallus pseudopygmaeus (Digenea) infects phylogenetically distant gastropods, with signs of host-linked genetic divergence.},
journal = {Parasite (Paris, France)},
volume = {33},
number = {},
pages = {15},
pmid = {41910177},
issn = {1776-1042},
support = {23-14-00329//Russian Science Foundation/ ; 125012800903-5//State Academic Program, Russia/ ; },
mesh = {Animals ; *Trematoda/genetics/classification/physiology/isolation & purification ; Phylogeny ; *Gastropoda/parasitology/classification ; *Host Specificity/genetics ; *Genetic Variation ; RNA, Ribosomal, 28S/genetics ; Haplotypes ; Host-Parasite Interactions/genetics ; DNA, Helminth/genetics/chemistry ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Host-switching between distantly related host species offers rare insight into how parasites overcome compatibility barriers and initiate evolutionary divergence. Microphallus pseudopygmaeus is exceptional among digeneans in its ability to infect gastropods from two distantly related subclasses, Vetigastropoda and Caenogastropoda. This study aimed to test the hypothesis about the species status of M. pseudopygmaeus and clarify its host range. We obtained partial sequences of the cox1 gene, 28S rDNA and ITS2 for M. pseudopygmaeus from nine host species, including Margarites spp. (Vetigastropoda). The data on the conservative and variable markers, phylogenetic and barcoding gap analyses, supported the unity of the species and its broad specificity to the first intermediate hosts. The cox1-based haplotype network revealed host-associated genetic divergence, particularly in isolates from Margarites spp. and Cryptonatica affinis. This pattern may result from localized circulation of the parasite in the regions where certain host species, such as Margarites spp., dominate in the absence of periwinkles, creating ecological conditions that could promote reproductive isolation and incipient speciation. This work opens up the prospects of using M. pseudopygmaeus as a model for studying host-switching and speciation in parasites.},
}

Animals
*Trematoda/genetics/classification/physiology/isolation & purification
Phylogeny
*Gastropoda/parasitology/classification
*Host Specificity/genetics
*Genetic Variation
RNA, Ribosomal, 28S/genetics
Haplotypes
Host-Parasite Interactions/genetics
DNA, Helminth/genetics/chemistry
DNA, Ribosomal Spacer/genetics

@article {pmid41910863,
year = {2026},
author = {Shoukat, S and Mehmood, N and Ghuffar, S and Bibi, S and Rauf, M and Irshad, G and Khan, GE and Maqsood, S and Anwar, T and Qureshi, H and Rebouh, NY and Yunusov, S and Ziyadov, S and Muminov, MM},
title = {Diversity of wild Morchella (Ascomycota) revealed by integrated morphological and molecular analyses.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41910863},
issn = {1874-9356},
}

@article {pmid41912001,
year = {2026},
author = {Rodrigues, BL and de Oliveira, AG and de Souza Pinto, I and Galati, EAB},
title = {The challenge of species delimitation in Brumptomyia sand flies (Diptera: Psychodidae) from Brazil.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108075},
doi = {10.1016/j.actatropica.2026.108075},
pmid = {41912001},
issn = {1873-6254},
abstract = {Species delimitation has been facilitated by the utilization of molecular markers, which, within the framework of integrative taxonomy, has contributed to a more profound comprehension of biodiversity. The analysis of DNA sequences of sand flies has yielded significant progress in species identification, sex association, and the description of species complexes, but has been overlooked concerning Brumptomyia França & Parrot, 1921 genus. Here, we assessed the molecular taxonomy of some Brumptomyia species, highlighting the challenges encountered in delimiting these taxa by different methods. We have sequenced and analyzed the DNA barcoding fragment of the cytochrome c oxidase subunit I (COI) gene, in addition to a nuclear DNA marker of the paralytic (PARA) gene. The final dataset encompasses 11 Brumptomyia species, 149 COI sequences, and 30 PARA fragments. A set of different discovery and validation species-delimitation approaches were performed, including single-locus heuristic ones, and an approach based on the multispecies coalescent model (MSC). Interspecific pairwise genetic distances were found to be lower than intraspecific distances. In a similar manner, the species pairs B. avellari/B. brumpti, B. cavicola/B. troglodytes, and B. nitzulescui/B. mangabeirai were merged into a single genetic cluster for each pair. Consequently, only five Brumptomyia taxa could be unambiguously identified using the standard DNA barcoding approach. However, the validation analysis under the MSC indicates that nearly all nominal species represent independent taxa, except for B. avellari and B. brumpti. These two latter, although closely-related, are well recognized by their morphology, and possibly more molecular markers, individuals, and populations are needed to understand their taxonomic status and evolutionary relationship. The species delimitation of Brumptomyia remains challenging, and further genomic assessments are necessary to advance our understanding of its diversity.},
}

@article {pmid41913691,
year = {2026},
author = {Erens, J and Heine, C and Lötters, S and Krehenwinkel, H and Crawford, AJ and Rueda-Solano, LA and Plewnia, A},
title = {A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70122},
doi = {10.1111/1755-0998.70122},
pmid = {41913691},
issn = {1755-0998},
support = {//Ministerium für Wirtschaft, Verkehr, Landwirtschaft und Weinbau Rheinland-Pfalz/ ; //Deutsche Gesellschaft für Herpetologie und Terrarienkunde/ ; //Forschungsfonds of Trier University/ ; //Forschungsinitiative Rheinland-Pfalz through Trier University/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; *Amphibians/classification/genetics ; *DNA, Environmental/genetics ; Workflow ; *Metagenomics/methods ; },
abstract = {Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots-particularly in remote and resource-limited tropical regions-to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Biodiversity
*Amphibians/classification/genetics
*DNA, Environmental/genetics
Workflow
*Metagenomics/methods

@article {pmid41914723,
year = {2026},
author = {Falke, LP and Rowe, S and Liu, Y and Sheehan, TF},
title = {DNA-based identification of anadromous fishes (Alosa spp., Family Clupeidae) in stomach contents of marine groundfish.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70415},
pmid = {41914723},
issn = {1095-8649},
support = {NA22NMF4540361//National Oceanic and Atmospheric Administration/ ; },
abstract = {Using DNA techniques for prey identification is an emerging approach for enhancing the precision and accuracy of trophic information. We evaluated the effectiveness of DNA-based prey identification in conjunction with visual stomach content analysis of commercially important groundfish in the nearshore Gulf of Maine, with a focus on distinguishing consumed anadromous (Alosa spp.) and closely related marine prey (Atlantic herring Clupea harengus, Atlantic menhaden Brevoortia tyrannus). DNA barcoding of 179 consumed prey specimens provided species- or genus-level identification in 122 cases (68.2%), including 104 improvements to taxonomic resolution and three conflicting results compared to visual identifications. Combining DNA-based identifications of partially or well-digested prey with the broader visual analysis substantially improved quantification of a diet metric, frequency occurrence, as a proxy for the relative diet contributions of anadromous and marine clupeids. Body size measurements of consumed Alosa spp. identified using DNA were consistent with year-0 or year-1 juvenile life stages. Possible limitations to success rates of DNA assignment included the quality of sample preservation (ethanol), reference database quality (accuracy of voucher specimen identification) and sequencing errors (miscalling of nucleotide bases). Despite this, the integration of molecular methods substantially improved the interpretability of trophic interactions involving morphologically similar prey with ecologically important differences in life history. These results highlight how the targeted application of DNA-based prey identification can complement conventional diet analyses by improving the quantification of trophic interactions that ultimately govern ecosystem processes.},
}

@article {pmid41915473,
year = {2026},
author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C},
title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117166},
doi = {10.1016/j.celrep.2026.117166},
pmid = {41915473},
issn = {2211-1247},
abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.},
}

@article {pmid41899006,
year = {2026},
author = {Chang, K and Guo, Y and Dewer, Y and Chen, X and Shang, S},
title = {Determination of the Morphometric Characteristics of Larval Instars in the Sap Beetle Urophorus humeralis (Coleoptera: Nitidulidae).},
journal = {Insects},
volume = {17},
number = {3},
pages = {},
pmid = {41899006},
issn = {2075-4450},
support = {GAU-KYQD-2021-26//The Scientific research Start-up Funds for Openly-recruitment recruited Doctors of Gansu Agricultural University/ ; },
abstract = {Effective integrated pest management (IPM) relies on precise knowledge of pest developmental biology, particularly the identification of larval instars, which is fundamental for predicting population dynamics and timing control interventions. This study established a morphometric framework for the larval staging of a sap beetle pest infesting pear orchards. Specimens were collected and reared under laboratory conditions, with their identity confirmed as Urophorus humeralis through integrated morphological and molecular (COI barcoding) analysis. To determine the number of larval instars, head capsule width (HCW), inter-antennal distance (IAD), and inter-caudal distance (ICD) were measured. Frequency distribution analysis and validation using Dyar's rule via linear regression revealed three distinct larval instars. Head capsule width was identified as the most reliable and consistent morphological character for instar discrimination. This study reports for the first time the infestation of pear fruits by U. humeralis and provides detailed morphometric criteria for larval staging, delivering essential baseline data for the biology of Nitidulidae and a scientific basis for developing stage-specific pest management strategies.},
}

@article {pmid41902267,
year = {2026},
author = {Mojumder, A and Nguyen, KW and Sullivan, CS},
title = {Divergent Fates of Kidney-Resident Polyomaviruses: Stable Shedding Versus Near-Silent Persistence.},
journal = {Viruses},
volume = {18},
number = {3},
pages = {},
pmid = {41902267},
issn = {1999-4915},
support = {R21AI188807//National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Virus Shedding ; *Kidney/virology ; *Polyomavirus Infections/virology/urine ; Mice ; *Polyomavirus/genetics/physiology ; Genome, Viral ; *Persistent Infection/virology ; Mice, Inbred C57BL ; Female ; },
abstract = {Polyomaviruses establish long-term infection in the kidney and are intermittently shed in urine. However, the relationship between kidney-resident viral genomes and urinary shedding during persistent infection remains poorly defined. Using a genetically barcoded murine polyomavirus library, we tracked thousands of viral lineages in vivo by pairing longitudinal urine sampling with endpoint barcode sequencing of kidney tissue in four mice. Across all animals, kidney infection consistently resolved into two stable viral populations, with near-silent persistence as the dominant fate. Most kidney-resident barcodes were never detected in late urine at late stages of infection, even though many reached substantial abundance within the kidney, demonstrating that kidney viral genome levels alone do not predict urinary shedding. In contrast, only a small minority of kidney barcodes contributed disproportionately to urine virus output at late timepoints, and these barcodes exhibited stable longitudinal behavior, with repeated detection in urine over time and markedly higher peak urine abundance than late non-shed or random barcode controls. Shedding behavior was not explained by input virus stock abundance, barcode sequence features, predicted miRNA targeting, or ongoing reseeding from blood or other tissues. Instead, barcodes that ultimately dominated late urine already showed elevated urine detection early after infection, indicating that shedding fate is established early and maintained throughout persistent infection. Together, these findings reveal that persistent kidney infection is a structured reservoir composed of a large population of deeply restricted viral genomes and a smaller, stable subset that repeatedly produces urine-detectable viruses, with concurrent smoldering infections and latency-like restriction representing one possible model to explain the sharply different probabilities of shedding among kidney-resident genomes.},
}

Animals
*Virus Shedding
*Kidney/virology
*Polyomavirus Infections/virology/urine
Mice
*Polyomavirus/genetics/physiology
Genome, Viral
*Persistent Infection/virology
Mice, Inbred C57BL
Female

@article {pmid41903168,
year = {2026},
author = {Edwards, ML and Blacket, MJ and Rodoni, BC and Lye, JC and Martoni, F},
title = {Assessing collection and trapping methods for diagnostics and surveillance of psyllids (Hemiptera: Psylloidea) in and around citrus orchards.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag066},
pmid = {41903168},
issn = {1938-291X},
support = {//Agriculture Victoria Research (DEECA) and Citrus Australia Limited/ ; },
abstract = {The economic impacts of Huanglongbing disease have prompted global surveillance of citrus psyllid vectors. While yellow sticky traps (YSTs) are widely used to detect pests such as the African citrus psyllid (Trioza erytreae) and the Asian citrus psyllid (Diaphorina citri), alternative methods may capture unique species and greater taxa richness and abundance, which could impact downstream species identification and diagnostics. We assessed psyllid richness and abundance across 4 sites within major citrus-growing regions of eastern Australia, and found that combining hand sampling with YSTs captured more species compared to light trapping and pan traps, but all sampling techniques collected unique taxa. Species were identified via an integrative taxonomy approach combining host plant data, morphology, and DNA sequences. We generated 196 cytochrome oxidase reference sequences from 87 species, 27 genera, and 5 families. Of these, 65 morphospecies and a described species were previously unrecorded in public DNA databases. This allowed us to build a baseline reference for eastern Australian native psyllids found around citrus orchard environments, thereby enhancing species-level molecular identification, and strengthening surveillance and biosecurity in Australia.},
}

@article {pmid41905555,
year = {2026},
author = {Martin, KE and Sábato, F and Lynch, J and Ferreira-Gonzalez, A and Barrie, ES},
title = {Performance evaluation of a PCR/Nanopore assay for carrier screening for cystic fibrosis, spinal muscular atrophy, and fragile X syndrome.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmoldx.2026.03.003},
pmid = {41905555},
issn = {1943-7811},
abstract = {Cystic Fibrosis, Spinal Muscular Atrophy, and Fragile X Syndrome are among the most common inherited genetic disorders making carrier screening essential for identifying at-risk couples. Traditional screening often involves multiple workflows and may miss rare variants. Comprehensive sequencing offers broader variant detection across diverse populations. We validated a PCR/Nanopore-based assay for comprehensive assessment of CFTR, SMN1/2, and FMR1. Samples included anonymized DNA from: whole blood (archival clinical samples, n = 53), cell lines (n = 19), and residual CAP proficiency testing material (n = 3). Using the AmplideX Nanopore Carrier Plus reagents, gene specific PCR was performed, followed by barcoding and sequencing on MinION flow cells. Data were analyzed using the AmplideX One Reporter software. Results for SMN1/2 and FMR1 showed 100% concordance with orthogonal methods (PCR/fragment analysis lab-developed tests) and 97% for CFTR. These results were reproducible between inter- and intra- run repeats. Here, we show that the PCR/Nanopore-based assay is accurate and reproducible for identifying pathogenic variants and poly-T size in CFTR; SMN1/2 copy number and SNP detection; and FMR1 CGG repeat sizes and AGG interruptions. The assay was also able to detect mosaicism as low as 10% for FMR1. This single workflow enables accurate, reproducible screening for multiple disorders, with the ability to identify more CFTR variants than traditional genotyping panels.},
}

@article {pmid41906122,
year = {2026},
author = {Diaz, D and Kniha, E and Koblmüller, S and Studentsky, L and Elbaz, SL and Ben Avi, I and Shilo, S and Kalmus, S and Akad, F and Naveh, I and Reicher, S and Davidovich-Cohen, M and Orshan, L and Kirstein, OD},
title = {First record of Phlebotomus (Larroussius) orientalis (Parrot, 1936) (Diptera: Psychodidae) in Israel: phylogeographic placement and implications for leishmaniasis surveillance.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07358-5},
pmid = {41906122},
issn = {1756-3305},
support = {101057690//HORIZON EUROPE Framework Programme/ ; 10038150//UK Research and Innovation/ ; },
abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are the principal vectors of Leishmania spp., the causative agents of leishmaniasis. Since 2008, the Ministry of Health and the Ministry of Environmental Protection of Israel have conducted nationwide, periodic sand fly surveys. Initially, these surveys focused on localities with known endemic transmission of cutaneous leishmaniasis, but in recent years, entomological trapping has expanded to areas where prior information on sand flies was unavailable. Here we report the first confirmed occurrence of Phlebotomus (Larroussius) orientalis (Parrot, 1936) in Israel and place the Israeli material in a comparative phylogeographic context.

METHODS: Entomological surveys by CO2 trapping were conducted in the Negev Desert, southern Israel, between 2020 and 2024. Morphological sand fly identification was confirmed by sequencing fragments of the mitochondrial COI and Cytb/NADH1 genes. For a newly reported species, we inferred intraspecific phylogenetic relationships and divergence times between major clades. A subset of females was additionally screened for Leishmania DNA and vertebrate blood-meal sources by real-time polymerase chain reaction (PCR) coupled with high-resolution melt analysis.

RESULTS: Targeted surveys and routine surveillance in the Negev region between 2020 and 2024 yielded 269 Phlebotomus orientalis (96 males, 173 females) among other species of local sand fly fauna from multiple wadi systems in the central Negev. These detections constitute the first confirmed records of Ph. orientalis in Israel. Species identification was confirmed through both morphological examination and molecular analyses of partial COI and Cytb/NADH1 genes. Phylogenetic analysis indicated that the Israeli Ph. orientalis specimens constitute a distinct lineage that diverged from East African conspecifics during the Early to Middle Pleistocene. Blood-meal analysis of engorged Ph. orientalis females identified the European hare as a vertebrate host, and none of the tested Ph. orientalis specimens were positive for Leishmania DNA.

CONCLUSIONS: Phlebotomus orientalis is a confirmed vector of L. donovani, the main agent of visceral leishmaniasis in East Africa. Its detection as a distinct and apparently long-established lineage in the Negev, in a region where parasites of the L. donovani complex are already involved in cutaneous leishmaniasis transmission, highlights the need to clarify the distribution, ecology, and host preferences of Ph. orientalis in Israel. Further studies are required to characterize its spatial and seasonal occurrence, evaluate its vector competence for L. donovani and L. infantum, and assess its potential contribution to current and future leishmaniasis transmission risks.},
}

@article {pmid41907444,
year = {2026},
author = {Wang, J and Deng, J and Xiao, T and Meng, W},
title = {Decoding chemerin proteolytic processing and isoform signaling across disease contexts.},
journal = {iScience},
volume = {29},
number = {4},
pages = {115259},
pmid = {41907444},
issn = {2589-0042},
abstract = {Chemerin (RARRES2) is a multifunctional adipokine widely implicated in metabolic, inflammatory, cardiovascular, and neoplastic diseases, yet its clinical interpretation remains confounded by reliance on "total chemerin" measurements that obscure its proteoform-specific signaling. This single value is mechanistically misleading because chemerin is secreted as an inactive precursor and undergoes extracellular proteolytic processing into C-terminal isoforms with graded receptor potency and compartment-specific distribution. This review decodes chemerin's functional duality through three integrated layers: (1) protease-encoded isoform "barcodes" that dictate bioactivity, (2) compartment-specific isoform landscapes in human biofluids and disease microenvironments, and (3) receptor context across CMKLR1, GPR1, and CCRL2 that shapes signaling output. We provide a conceptual roadmap for translating chemerin biology, emphasizing isoform-resolved quantification via targeted /MRM-MS and a compartment-aware framework for interpreting clinical associations. This framework helps interpret heterogeneous disease associations and highlights testable entry points for context-specific targeting.},
}

@article {pmid41898899,
year = {2026},
author = {Sadat-Shojaei, M and Dabert, M and Akrami, MA and Sadeghi, S and Dabert, J},
title = {Second Palearctic Record of the Genus Stereoglyphus Berlese (Acari: Acaridae) with Morpho-Molecular Description of a New Species from Zagros Mountains, Iran.},
journal = {Insects},
volume = {17},
number = {3},
pages = {},
pmid = {41898899},
issn = {2075-4450},
abstract = {In this study, the astigmatid mite genus Troglocoptes Fain, 1966 is proposed as a junior synonym of Stereoglyphus Berlese, 1923. As a part of the project concerning identification of cave-dwelling mites in the Zagros Mountains, all ontogenetic instars of Stereoglyphus iranensis sp. nov. (Sarcoptiformes: Acaridae) are described from Doroodzan Cave, Fars Province, Iran. This is the second record of the genus in caves in the Palearctic region and the fifth described species worldwide. The morphological description is supplemented with DNA barcode data based on the mitochondrial cytochrome c oxidase subunit I (COI) gene, representing the first molecular data for this genus. Additionally, the first Asian record of Stereoglyphus longibursatus (Fain et Mahunka, 1990) is reported from Sahlak Cave, Fars Province, Iran. An identification key to the known species of the genus is provided. The troglobitic status of the new species is discussed, and the modifications of the anterior legs and tarsal setae, along with the partial reduction of idiosomal setation, are interpreted as adaptations to burrowing in bat guano.},
}

@article {pmid41898953,
year = {2026},
author = {Huang, B and Wu, L and Ni, T and Su, R and Song, H and Wang, R},
title = {Molecular Techniques and Ecological Data for Taxonomically Difficult Groups: A Case Study of a Morphologically Variable New Species in the Genus Chrysobothris (Coleoptera: Buprestidae).},
journal = {Insects},
volume = {17},
number = {3},
pages = {},
pmid = {41898953},
issn = {2075-4450},
abstract = {Morphological characters of beetles can differ greatly, even within a single species, necessitating the integration of molecular techniques and ecological data for accurate taxonomical delineation, particularly within taxonomically challenging groups. Chrysobothris, a world-distributed genus of considerable size with a homonymy rate exceeding 1/5, frequently presents ambiguities in species boundaries. In this research, a series of Chrysobothris specimens collected from southern China were segregated into four sharply contrasting external morphotypes. A taxonomic ambiguity was initially posed: whether they represented several species, intraspecific polymorphism within a single species, or geographic/intraspecific variants of the similar species Chrysobothris violacea Kerremans, 1892. COI barcoding and phylogenetic analyses supported the conspecificity of these morphotypes and confirmed their distinction from C. violacea at the species level. Based on integrated evidence, we describe these specimens as Chrysobothris borealina Huang, Wu & Song, sp. nov., provide diagnostic characters with illustrations, and compare the new species with C. violacea. The species occurs in mid- to high-elevation pine and pine-broadleaf mixed forests and differs from C. violacea in both elevational range and phenology, indicating potential ecological differentiation. Additionally, we document a rare instance of a nymphal parasitengone mite (cf. Erythraeidae) attached to one female specimen.},
}

@article {pmid41898975,
year = {2026},
author = {Zhao, C and Balkcom, KS},
title = {First Molecular Verification of the Two-Spot Cotton Leafhopper Amrasca biguttula (Hemiptera: Cicadellidae) in the United States.},
journal = {Insects},
volume = {17},
number = {3},
pages = {},
pmid = {41898975},
issn = {2075-4450},
abstract = {This report contains the first molecular record of the two-spot cotton leafhopper, Amrasca biguttula (Ishida) (Hemiptera: Cicadellidae), in the United States. Nymphs of multiple instars and adult specimens were collected from a cotton (Gossypium hirsutum) field in Macon County, Alabama, in August 2025. While distinct paired dark spots were observed on the forewings of adult specimens, this trait was inconsistently present on nymphal wing pads. Cytochrome oxidase I (COI) DNA barcoding confirmed the specimen identity. The United States sequence shared > 99% identity with Asian A. biguttula references, and phylogenetic analysis placed it within the A. biguttula clade with 100% posterior probability support. Although this pest was previously reported in 2023 from Puerto Rico based solely on morphological traits, our findings provide the first DNA-confirmed evidence of its presence in the United States. Given its well-documented role in damaging cotton across Asia and Africa, this report underscores the urgent need for monitoring and development of management strategies in United States cotton-growing regions.},
}

@article {pmid41892277,
year = {2026},
author = {Peng, W and Yu, J and Wang, Z and Li, Z and Miao, X and Liu, J and Zhang, J and Xie, L and Ding, W and Ma, K and Yang, M},
title = {Characterization and Comparative Analyses of Nuclear Mitochondrial DNAs in Genomes of the Leaf-Roller Moths (Lepidoptera: Tortricidae).},
journal = {Biology},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biology15060517},
pmid = {41892277},
issn = {2079-7737},
support = {31702046//Natural Science Foundation of China/ ; 2021M692244//China Postdoctoral Science Foundation/ ; 2020GGJS211//Young Backbone Teacher Guiding Foundation in Colleges and Universities in Henan Province/ ; 24A180030//Key Scientific Research projects of Colleges and Universities in Henan Province/ ; 26B210032//Key Scientific Research projects of Colleges and Universities in Henan Province/ ; },
abstract = {During eukaryotes evolution, mitochondrial DNA (mtDNA) fragments integrate into nuclear genomes, forming nuclear mitochondrial DNA sequences (Numts). Tortricidae (Lepidoptera), a species-rich and economically critical family, lacks systematic characterization of Numts, which hinders reliable molecular research. Here, we systematically characterized Numts in 27 Tortricidae species spanning two subfamilies via genome download, mitochondrial genome annotation, and Numt identification and characterization. With each species' mtDNA as query, Numt identification was performed with an E-value threshold of 10[-4] and a sequence similarity cut-off of >60%, with a minimum length of 50 bp to exclude spurious hits. Results showed that all species contained Numts, with copy numbers varying drastically (9-208). Numt numbers positively correlated with nuclear genome length, but not mitochondrial genome length. Numts insertion flanking regions had significantly higher AT content than nuclear genome, indicating the insertion preference for AT-rich regions. Numts were predominantly derived from the mitochondrial cox1 gene, highlighting the risk of co-amplification when cox1 is used as a DNA barcode for species identification or phylogenetic studies. This study represents a systematic charaterizition of copy number, length distribution, insertion sequence preferences, and mitochondrial gene origins of Numts in Tortricidae, offering valuable references for refining molecular systematics, comparative genomics, and pest management in Tortricidae and related lepidopteran groups.},
}

@article {pmid41893143,
year = {2026},
author = {Cruz, D and Suárez, JP and Chamba, A and Duque-Sarango, P and Espinosa, L and Vandregrift, R},
title = {Morphological Diversity and Preliminary DNA Barcoding of Xylaria (Xylariales) from Estación Científica San Francisco, Including Xylaria aenea as a New Record for Ecuador.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/jof12030211},
pmid = {41893143},
issn = {2309-608X},
abstract = {The genus Xylaria comprises numerous species, particularly prevalent in tropical ecosystems such as those of Ecuador. Despite its ecological importance, the taxonomy of the genus remains challenging, and much of its diversity in the Neotropics remains under-documented. This study provides a preliminary characterization of the Xylaria diversity at the Estación Científica San Francisco, an Andean biodiversity hotspot in Southern Ecuador. Through an integrated approach including detailed macro- and micro-morphological descriptions and nuclear ribosomal DNA (nrDNA ITS and LSU) phylogenetic analyses, 20 Xylaria specimens were examined. As a result, ten species were recognized: Xylaria adscendens, X. cf. anisopleura, X. apiculata, X. curta, X. enterogena, X. fissilis, X. globosa, X. aff. telfairii, X. tuberoides, and X. aenea, the latter representing a new record for Ecuador. The phylogenetic analysis presented here serves as a preliminary systematic positioning of these specimens within the genus rather than a comprehensive global reconstruction. While these ribosomal markers provided preliminary insights into species relationships, partial incongruence with morphospecies highlights the evolutionary complexity of certain lineages and underscores the need for future multilocus studies. Furthermore, four additional phylotypes found in their anamorphic state are documented, suggesting that local diversity exceeds current records. By providing detailed morphological documentation supported by preliminary barcode data from a poorly sampled region, this study contributes vital information to the global understanding of Xylaria and underscores the importance of Southern Ecuador as a reservoir of fungal diversity.},
}

@article {pmid41894059,
year = {2026},
author = {Shah, P and Jain, N and Gawande, N and Sharma, T and Devanathan, K and Sankaranarayanan, S and Balaji, R},
title = {Advancing plant DNA barcoding: integrating chloroplast genome sequencing, cryptic diversity discovery and machine learning.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41894059},
issn = {1573-4978},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Genome, Chloroplast/genetics ; *Machine Learning ; *Plants/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; Sequence Analysis, DNA/methods ; DNA, Plant/genetics ; Phylogeny ; },
abstract = {Accurate plant species identification underpins taxonomy, conservation, ecological monitoring, and the authentication of medicinal and food resources. While classical morphology-based approaches often struggle with cryptic or closely related taxa, DNA barcoding has emerged as a standardized molecular framework for species identification. In plants, core plastid markers such as rbcL and matK, together with nuclear regions like ITS and ITS2, have been widely adopted, yet species-level resolution remains limited in recently diverged or hybridizing lineages. Recent advances in high-throughput sequencing have enabled chloroplast genome sequencing and plastome-scale "super-barcoding," substantially improving discriminatory power and facilitating the derivation of lineage-specific and mini-barcodes. Concurrently, multi-locus barcoding, metabarcoding, and environmental DNA (eDNA) approaches are revealing cryptic diversity and reshaping our understanding of plant community structure and species interactions. Emerging machine-learning methods further enhance barcode-based classification, reference-library curation, and integrative species delimitation. This review synthesizes developments in plastome-guided barcoding, cryptic diversity discovery, and data-driven analytics, outlining methodological advances, practical constraints, and future directions. We emphasize that continued expansion and rigorous curation of reference libraries, combined with transparent benchmarking of computational models, are essential for reliable, scalable, and genome-aware plant identification systems in the genomic era.},
}

*DNA Barcoding, Taxonomic/methods
*Genome, Chloroplast/genetics
*Machine Learning
*Plants/genetics/classification
High-Throughput Nucleotide Sequencing/methods
Genetic Variation
Sequence Analysis, DNA/methods
DNA, Plant/genetics
Phylogeny

@article {pmid41894564,
year = {2026},
author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S},
title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70130},
doi = {10.1111/1755-0998.70130},
pmid = {41894564},
issn = {1755-0998},
support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; Puerto Rico ; *Anthozoa/genetics/classification ; *Genetic Variation ; *Metagenomics/methods ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Animals
*DNA, Environmental/genetics
Puerto Rico
*Anthozoa/genetics/classification
*Genetic Variation
*Metagenomics/methods
RNA, Ribosomal, 28S/genetics

@article {pmid41895431,
year = {2026},
author = {Ceruti, A and Bisia, M and Balatsos, G and Kobialka, RM and Zamil, MF and Hasan, A and Truyen, U and Lucati, F and Sanpera-Calbet, I and Palmer, JRB and Alam, MS and Michaelakis, A and Wahed, AAE},
title = {MosquitoID: Rapid metagenomic sequencing for offline mosquito surveillance.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108071},
doi = {10.1016/j.actatropica.2026.108071},
pmid = {41895431},
issn = {1873-6254},
abstract = {Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning systems. In this study, a portable metagenomic sequencing approach using Oxford Nanopore Technologies (ONT) for field-based mosquito analysis (MosquitoID protocol) was developed, enabling species and host feeding patterns identification, and pathogen detection all coming from a single amplification-free workflow. DNA was extracted from 62 mosquito samples (Aedes albopictus, Aedes cretinus, Culex pipiens, Culiseta longiareolata) from Greece and Spain, either single-species pools (1-19 specimens),mixed-species pools, wirth reverse purification method or archived samples. Additionally, 30 pooled Aedes aegypti samples from Bangladesh underwent cDNA reverse purification. All samples were sequenced using ONT rapid barcoding kits. Offline bioinformatics analysis via Geneious screened custom BLAST databases for species, host, and virus identification. MosquitoID accurately identified mosquito species in 89% of samples overall, with main discrepancies in Aedes cretinus. Virus screening detected Phasi Charoen-like virus in cDNA samples. Host DNA sequences identified multiple species including horses, cattle, and ducks. This study demonstrates metagenomic ONT sequencing's effectiveness for rapid host, species, and virus identification. After further benchmarking, the approach shows potential for real-time disease monitoring and enhanced surveillance systems. Integrating portable next-generation sequencing with offline bioinformatics tools could significantly strengthen mosquito-borne disease prevention strategies, particularly for non-bioinformaticians and in resource-limited settings.},
}

@article {pmid41897682,
year = {2026},
author = {Sommeregger, P and Pallua, N and Zelger, B and Kahlil, R and Pallua, JD},
title = {Digital Specimen Tracking- and ISO 15189-Oriented Risk Management in Anatomic Pathology: A Qualitative Study of Expert Perspectives in Western Austria.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/diagnostics16060949},
pmid = {41897682},
issn = {2075-4418},
abstract = {Background: Breakpoints in the pre-examination processes and at organizational interfaces are a significant source of failures in specimen identification and tracking in anatomic pathology. While ISO 15189 emphasizes end-to-end traceability and risk-based quality management, implementing these principles in complex, multi-actor specimen pathways remains challenging. This study explores expert perspectives on specimen process chains, tracking mechanisms, and ISO 15189-oriented quality and risk management in pathology. Methods: We conducted 10 semi-structured expert interviews across three settings. Interviews were audio-recorded, transcribed, pseudonymized, and analyzed using structured qualitative content analysis (Mayring) supported by MAXQDA. A deductive category system derived from the theoretical framework and interview guide comprised six main categories and twelve subcategories. Results: Across 512 coded text segments, participants identified several factors as critical for effective implementation, including: (i) interface management along the specimen pathway, with recurrent vulnerabilities at handovers between operating theater/ward/transport and accessioning; (ii) the central role of barcode-based identification and the need for closed-loop traceability; (iii) the importance of measurable quality indicators and incident learning systems to operationalize risk management; (iv) persistent paper-digital handoffs and heterogeneous IT landscapes that undermine data integrity; (v) the need for clearly assigned responsibilities, training, and SOP governance; and (vi) implementation barriers including resources, change management, and vendor integration, alongside practical enablers such as incremental roll-out and cross-professional governance. Conclusions: Experts converge on a pragmatic ISO 15189-aligned roadmap: prioritize interface risks, standardize identifiers and handover rules, define a minimal KPI set for tracking and misidentification events, and reduce paper-digital handoffs by interoperable IT. Future work should quantify baseline error rates and evaluate the impact of digital tracking interventions on patient safety and turnaround times.},
}

@article {pmid41898805,
year = {2026},
author = {Vella, N and Zorrilla García, M and Vella, A},
title = {Molecular Taxonomy of Geckos Reveals a Second Tarentola Species (Reptilia: Squamata) on the Maltese Islands.},
journal = {Genes},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/genes17030271},
pmid = {41898805},
issn = {2073-4425},
support = {grant No. I18LU06-01//University of Malta/ ; },
mesh = {Animals ; *Lizards/genetics/classification ; Malta ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Electron Transport Complex IV/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Background/Objectives: The Maltese islands, situated in the Sicilian Channel, are known to host two gecko species, Hemidactylus turcicus and Tarentola mauritanica. However, gecko taxonomy is complicated by cryptic lineages within species complexes, requiring molecular approaches for accurate identification. Methods: In this study, we investigated species diversity using opportunistic sampling of 30 dead gecko specimens, including road-killed individuals, from across the Maltese islands. Due to the degraded condition of most samples, morphological identification was limited; therefore, mitochondrial markers (12S, 16S and COI) were employed to assign species identity. Results: Our analyses revealed the first records of the Tarentola fascicularis/deserti complex in Malta. This finding extends the known distribution of this complex and complements records from neighbouring islands in the Sicilian Channel, where T. mauritanica and T. fascicularis/deserti lineages occur in sympatry. Conclusions: Given the greater ecological affinity of the T. fascicularis/deserti complex for arid environments, these findings emphasise the importance of continued monitoring to clarify the dynamics of sympatry, potential ecological displacement, and the long-term effects of climate change and anthropogenic activity on the central Mediterranean herpetofauna.},
}

Animals
*Lizards/genetics/classification
Malta
Phylogeny
RNA, Ribosomal, 16S/genetics
Electron Transport Complex IV/genetics
DNA, Mitochondrial/genetics

@article {pmid41877864,
year = {2026},
author = {Suwannasaeng, T and Hiengrach, P and Kuwatjanakul, W and Samerpitak, K and Faksri, K and Payungporn, S and Sangsiwarit, P and Budmala, P and Visedthorn, S and Ruengket, P and Srisak, K and Chitcharoen, S},
title = {Identification of pathogenic fungi causing ocular infections using full rRNA operon sequencing with Oxford Nanopore Technologies.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20997},
pmid = {41877864},
issn = {2167-8359},
mesh = {Humans ; Thailand ; Phylogeny ; *Eye Infections, Fungal/microbiology/diagnosis ; *Fungi/genetics/isolation & purification/classification ; *rRNA Operon/genetics ; *Nanopore Sequencing/methods ; },
abstract = {Although fungal eye infections are a major cause of visual impairment worldwide, standard clinical laboratory methods remain slow, insensitive, and limited in their taxonomic resolution. Sequencing of the full ribosomal RNA (rRNA) operon provides a comprehensive marker for fungal identification. In this study, twenty fungal isolates associated with ocular infections were obtained from Srinagarind Hospital, Thailand, and characterized using four identification approaches. Initial hospital-based routine identification relied on conventional morphological methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). To enhance resolution and to develop a comprehensive analytical pipeline, we further employed full rRNA operon sequencing using Oxford Nanopore Technologies (ONT), analyzed through three bioinformatic pipelines: EPI2ME/Minimap2, NGSpeciesID with BLASTn, and internal transcribed spacer (ITS)-based phylogenetic analysis coupled with phylogenetic analysis. All isolates yielded complete operon sequences, thus ensuring comprehensive coverage of the target regions. NGSpeciesID produced high-confidence consensus sequences and species-level classifications for nearly all isolates (except one Candida specimen). Of these, 15 of the 20 isolates showed exhibited concordance with hospital identifications at the genus level (≥97% identity). This approach successfully resolved closely related Aspergillus taxa (i.e., A. terreus, A. luchuensis, A. oryzae), reclassified Curvularia isolates as Bipolaris maydis, and confirmed species-level assignments for Fusarium and Rhodotorula. By contrast, the EPI2ME workflow produced more variable classifications, providing species-level assignments for Aspergillus and Rhodotorula but mixed genus/species profiles for several isolates, including seven isolate assignments unique to this method. ITS-based phylogenetic reconstruction recovered all expected clades, with Curvularia isolates clustering within their genus. However, node support varied substantially, highlighting the limited discriminatory power of ITS alone, which constrains taxonomic resolution to the species-complex level rather than consistently achieving the species-level identification of Aspergillus isolates. Overall, ONT-based full-operon sequencing demonstrates strong potential for fungal diagnostics, its performance depends on bioinformatic pipelines, database quality, and sequencing errors. Species-level resolution is particularly limited in Aspergillus, while incomplete reference datasets hinder the classification of isolates such as Curvularia. To improve reliability and clinical application, it will be essential to expand curated full-length rRNA references, integrate complementary loci, and refine analytical strategies.},
}

Humans
Thailand
Phylogeny
*Eye Infections, Fungal/microbiology/diagnosis
*Fungi/genetics/isolation & purification/classification
*rRNA Operon/genetics
*Nanopore Sequencing/methods

@article {pmid41878470,
year = {2026},
author = {Millan Arias, P and Sadjadi, N and Safari, M and Gong, Z and Wang, AT and Haurum, JB and Zarubiieva, I and Steinke, D and Kari, L and Chang, AX and Lowe, SC and Taylor, GW},
title = {BarcodeBERT: transformers for biodiversity analyses.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag054},
pmid = {41878470},
issn = {2635-0041},
abstract = {MOTIVATION: In the global effort to characterize biodiversity, short species-specific genomic sequences known as DNA barcodes enable fine-grained comparisons among organisms within the same kingdom of life. Although machine learning algorithms specifically designed for the analysis of DNA barcodes are becoming more popular, most existing methodologies rely on generic supervised training algorithms.

RESULTS: We introduce BarcodeBERT, a family of models tailored to biodiversity analysis and trained exclusively on data from a reference library of 1.5 M invertebrate DNA barcodes. We evaluate BarcodeBERT on taxonomic identification tasks against a spectrum of machine learning approaches, including supervised training of classical neural architectures and fine-tuning of general DNA foundation models. Our self-supervised pretraining strategies on domain-specific data outperform fine-tuned foundation models, especially in identification tasks involving lower taxa such as genera and species. Compared with BLAST, a widely used sequence-search tool, BarcodeBERT achieves comparable species-level classification accuracy while being 55× faster. Our analysis of masking and tokenization strategies also provides practical guidance for building customized DNA language models, emphasizing the importance of aligning model training strategies with dataset characteristics and domain knowledge.

The code repository is available at https://github.com/bioscan-ml/BarcodeBERT.},
}

@article {pmid41879721,
year = {2026},
author = {Séguigne, CJM and Pupier, CA and Chand, T and Grall, J and Guillaume, T and Robert, K and Azam, CS and Buray, N and Jeandel, JM and Mataarere, A and Trinh, AM and Rummer, J},
title = {First genetic confirmation of the smooth hammerhead shark (Sphyrna zygaena, Linnaeus, 1758) in French Polynesian waters.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70432},
pmid = {41879721},
issn = {1095-8649},
support = {2024A69//European Union (BESTLIFE2030)/ ; //Direction des Ressources Marines (DRM)/ ; //Institut pour la Recherche sur les Écosystèmes Mésophotiques et Profonds (IREMP)/ ; },
abstract = {The smooth hammerhead shark (Sphyrna zygaena) has never been formally confirmed in French Polynesian waters. Observations of solitary hammerhead sharks suggested the presence of an unrecorded species. Two specimens captured off Tahiti were morphologically and genetically examined. Both matched traits of the smooth hammerhead and COI barcoding confirmed >99% similarity to reference sequences in the NCBI and BOLD databases. This record extends the known range of S. zygaena to the central South Pacific and highlights the role of citizen observations in detecting rare oceanic sharks, which is important to regional conservation frameworks.},
}

@article {pmid41881357,
year = {2026},
author = {Schumacher, GA and Minchella, DJ},
title = {DIVERSITY, HOST RANGE, AND SPECIFICITY OF ECHINOSTOMES (FAMILY ECHINOSTOMATIDAE; LOOSS, 1899) IN THE MIDWESTERN UNITED STATES.},
journal = {The Journal of parasitology},
volume = {112},
number = {2},
pages = {170-182},
doi = {10.1645/24-138},
pmid = {41881357},
issn = {1937-2345},
mesh = {Animals ; *Echinostomatidae/genetics/classification/physiology ; *Snails/parasitology ; Phylogeny ; *Host Specificity ; Midwestern United States/epidemiology ; DNA, Helminth/isolation & purification/chemistry ; RNA, Ribosomal, 28S/genetics ; Humans ; DNA, Ribosomal Spacer/chemistry ; },
abstract = {Trematodes in the family Echinostomatidae (Looss, 1899) are globally distributed parasites of both humans and wildlife. In North America, echinostomes are nearly ubiquitous in freshwater systems, where they commonly parasitize snails as their first intermediate hosts, aquatic hosts such as snails or tadpoles as second intermediate hosts, and waterfowl and semi-aquatic mammals as their definitive hosts. Our study expands on sampling efforts in the midwestern United States and contributes novel ND1, ITS2, and 28S sequences from 12 lineages of echinostomes in the genera Echinostoma, Echinoparyphium, and Hypoderaeum. Additionally, COI barcoding and phylogenetic analysis of snail first intermediate hosts elucidated novel host-parasite combinations. Finally, we demonstrate that echinostomes are often not specific to 1 species of snail first intermediate host but rather to a family of aquatic snails, and we suggest that first intermediate hosts may drive echinostome speciation.},
}

Animals
*Echinostomatidae/genetics/classification/physiology
*Snails/parasitology
Phylogeny
*Host Specificity
Midwestern United States/epidemiology
DNA, Helminth/isolation & purification/chemistry
RNA, Ribosomal, 28S/genetics
Humans
DNA, Ribosomal Spacer/chemistry

@article {pmid41883558,
year = {2026},
author = {Theuer, T and Faber, K and Oberli, L and Schweingruber, T and Fraiture, MA and Roosens, N and Kindler, A and Rudiger, A and Leist, R and Vanhee, C},
title = {When herbal supplements cause heart problems: Clinical case report and forensic toxicological analysis.},
journal = {Toxicology reports},
volume = {16},
number = {},
pages = {102239},
pmid = {41883558},
issn = {2214-7500},
abstract = {The global expansion of travel and online supplement markets has eliminated traditional geographic barriers to toxic plant exposures. We report a case of a 42-year-old female presenting with digoxin-like intoxication symptoms, including nausea, vomiting, and hypotension. Electrocardiography revealed sinus bradycardia (51/min), first-degree AV block, and downsloping ST-segment depressions with reverse tick morphology. Upon further comprehensive anamnesis, the patient revealed the consumption of a weight-loss supplement labeled as "Tejocote root" (Crataegus mexicana), purchased during a travel to the USA. Serum digoxin assays yielded conflicting results across different platforms. The patient was managed with supportive care, including fluid replacement and antiemetics. Bradycardia persisted for five days, with complete resolution of symptoms and ECG abnormalities by day nine. Subsequent forensic toxicological analysis using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) and DNA barcoding confirmed the presence of yellow oleander (Thevetia peruviana) in the supplement, with no detection of the advertised Crataegus mexicana. While standard toxicological screening panels do not include plant-derived cardiac glycosides, cross-reactivity in digoxin assays may aid early diagnosis. Clinicians should maintain high suspicion for exotic plant poisonings in patients presenting cardiac glycoside-like symptoms, particularly following use of imported or online-purchased supplements. This case underscores the critical importance of multidisciplinary collaboration in determining the root cause of intoxication and highlights significant gaps in current forensic analytical capabilities for detecting botanical adulterants with public health implications.},
}

@article {pmid41890610,
year = {2026},
author = {Wanke, D and Müller, S and Noori, S and Pereira, RJ and Rajaei, H and Sihvonen, P and Lee, KM},
title = {Integration of morphologic and genetic data clarifies the evolution and species boundaries within a Nychiodes Lederer, 1853 species complex (Lepidoptera, Geometridae).},
journal = {ZooKeys},
volume = {1273},
number = {},
pages = {167-183},
pmid = {41890610},
issn = {1313-2989},
abstract = {Young species radiations are valuable from an evolutionary perspective, as they can reveal traits involved in species formation, but they are challenging for taxonomists due to discordance among independent lines of evidence. The present study integrates morphologic, ecological, and phylogenetic data to resolve delimitation of species within the geometrid moth genus Nychiodes Lederer, 1853, with a particular focus on the closely related species pair N. divergaria Staudinger, 1892 and N. subvirida Brandt, 1938. Our findings revealed significant ecological niche differentiation across the Iranian mountain ranges between the range of taxa distinguished by morphology and DNA barcodes. While individual gene trees from mtCOI and nuclear loci showed conflicting results regarding species boundaries, our multispecies coalescent analyses support the distinction of taxa with different female genitalia characters. Our study highlights how the combination of morphological, genetic, and ecological data helps to define the boundaries between closely related species, to solve taxonomic uncertainties in regions with a complex evolutionary background.},
}

@article {pmid41875072,
year = {2026},
author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT},
title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70127},
pmid = {41875072},
issn = {1755-0998},
support = {LP190100555//Australia Research Council Linkage Project/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; },
abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.},
}

*DNA Barcoding, Taxonomic/methods
*DNA Primers/genetics
*DNA, Environmental/genetics
*Electron Transport Complex IV/genetics
Animals
Biodiversity
*Metagenomics/methods

@article {pmid41868791,
year = {2026},
author = {Özdemir Değirmenci, F},
title = {Evaluating SSR marker transferability and plastid barcode variation in native Populus and Salix species of Türkiye.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20936},
pmid = {41868791},
issn = {2167-8359},
mesh = {*Populus/genetics/classification ; *Salix/genetics/classification ; *Microsatellite Repeats/genetics ; *DNA Barcoding, Taxonomic/methods ; *Plastids/genetics ; *Genetic Variation ; Phylogeny ; Genetic Markers ; DNA, Plant/genetics ; },
abstract = {Populus and Salix species are key components of forest and riparian ecosystems and hold substantial economic value in forestry, bioenergy, and restoration practices. In Türkiye, these genera are widely distributed across diverse ecological zones, yet regional molecular data remain limited. In this study, I examined genetic relationships among six native species-Populus nigra L., Populus alba L., Populus tremula L., Populus euphratica Olivier, Salix alba L., and Salix caprea L.-using an integrative molecular approach. Twelve nuclear microsatellite (simple sequence repeats; SSR) markers and three plastid DNA barcode regions (matK, rbcL, trnH-psbA) were employed to assess marker performance, genetic variation, and species-level relationships. The analyses revealed clear genetic differentiation between Populus and Salix and substantial variation among Populus species. SSR loci detected both conserved and lineage-specific alleles, with limited allele sharing between genera, while plastid barcodes showed marker-specific patterns of sequence variation and phylogenetic resolution. Among the plastid regions, matK provided the strongest discriminatory signal, whereas rbcL was more conservative and trnH-psbA exhibited higher variability. P. tremula and P. nigra displayed higher levels of sequence and allelic variation compared with the other taxa, whereas P. euphratica showed a more distinct genetic profile. The combined use of nuclear SSRs and plastid barcodes provided complementary insights into genetic structure and evolutionary relationships among selected Populus and Salix species. Although limited in taxon and marker coverage, this study contributes regionally focused molecular data from a biogeographically underrepresented area and provides a foundation for future multilocus and genome-wide investigations of Salicaceae diversity in Türkiye.},
}

*Populus/genetics/classification
*Salix/genetics/classification
*Microsatellite Repeats/genetics
*DNA Barcoding, Taxonomic/methods
*Plastids/genetics
*Genetic Variation
Phylogeny
Genetic Markers
DNA, Plant/genetics

@article {pmid41869962,
year = {2026},
author = {Yang, L and Tan, H and Wang, Y and Zhang, J and Meng, X and Liu, X and Hou, T and Chen, W and Li, F},
title = {Fluidly Confined CRISPR-Magnetic Microbots Empowered Homogeneous Electrochemical Biosensor for Amplified Detection and Discrimination of Cancer-Derived Extracellular Vesicle Subtypes.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.6c00448},
pmid = {41869962},
issn = {1520-6882},
abstract = {Accurate identification and profiling of multiple protein biomarkers on tumor-derived extracellular vesicles (tEVs) are crucial for noninvasive cancer subtyping diagnosis but remain technically challenging due to their high heterogeneity, low abundance in biofluids, and preisolation/purification processes. Herein, we developed a homogeneous electrochemical biosensor empowered by fluidly confined CRISPR-magnetic microbots for the amplified detection and sensitive discrimination of tEV subtypes. The CRISPR-magnetic microbots were constructed by engineering CRISPR/Cas12a and DNA icosahedra/doxorubicin (DNA-ICOS/DOX) on intracellularly gelated magnetic cells (IGMCs). Benefiting from the synergistic effects of spatial confinement and membrane fluidity to elevate the local concentration and collision efficiency, the activity of CRISPR/Cas12a was found to be greatly enhanced on IGMCs. For selective sorting of tEVs, a logic-gated aptamer system was used to orthogonally label tEV subpopulations, which further triggers the trans-cleavage activity of CRISPR/Cas12a, resulting in the release of massive DNA-ICOS/DOX into solution. After magnetic separation, the liberated DOX molecules generate a strong electrochemical signal. Particularly, the CRISPR-magnetic microbots could efficiently reduce the background signal, endowing a significantly improved signal-to-noise ratio. Therefore, by combining the CRISPR-magnetic microbots with the dual-target-guided orthogonal barcoding strategy in a homogeneous electrochemical biosensor, precise identification and sensitive detection of tEVs were successfully achieved. More significantly, this assay achieves accurate cancer subtyping in clinical samples, demonstrating its potential as a robust, noninvasive tool for high-accuracy disease screening, classification, and progression monitoring.},
}

@article {pmid41872204,
year = {2026},
author = {LaTurner, ZW and Dysart, MJ and Schwartz, SK and Zeng, E and Chappell, J and Silberg, JJ and Stadler, LB},
title = {Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70995-y},
pmid = {41872204},
issn = {2041-1723},
support = {2237052//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; },
abstract = {Bacteriophages (phages) facilitate gene transfer and microbial evolution in all ecosystems and have applications as tools for engineering microbiomes and as antimicrobials. Historic efforts to map phage hosts, such as plaque assays, are limited to cultured bacteria, are low throughput, and are hard to apply in microbial communities and environmentally-relevant contexts. To overcome these limitations, we integrate a synthetic ribozyme that stores information about participation in horizontal gene transfer in 16S ribosomal RNA (rRNA) into the phage-plasmid P1, and perform targeted 16S rRNA sequencing following transduction to identify phage-host interactions. Experiments in synthetic and wastewater communities reveal Aeromonadales as a previously unreported P1 host order and show P1 transduction into pathogens. In wastewater, host range varies across phagemids having different origins of replication and phage-derived particles having different tail fibers. This work shows how autonomous barcoding can be used in phages to identify the molecular controls on their host range in microbial communities.},
}

@article {pmid41873564,
year = {2026},
author = {Fu, X and Bai, SY and Chen, L and Lv, C and He, YX and Li, YP and Liu, YQ},
title = {DNA barcoding-assisted classification of the genus Actias (Lepidoptera: Saturniidae).},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-17},
doi = {10.1017/S0007485326100893},
pmid = {41873564},
issn = {1475-2670},
abstract = {The classification of the species in the genus Actias Leach, 1815 (Lepidoptera: Saturniidae) is challenging because many species have a highly similar morphology, while differences in database classification standards also provoke identification problems. To help resolve these issues, we conducted an integrative analysis of 741 cytochrome oxidase subunit I (COI) barcode sequences available by combining phylogenetic reconstruction, population genetic (Fst) metrics, and biogeographic data. This approach delineated 44 molecular operational taxonomic units (MOTUs) and established a genus-specific, empirical genetic distance threshold of 2.05% from a baseline of 29 morphologically validated MOTUs. These 29 MOTUs/morphospecies were then utilized to assess the interspecific genetic distance gap of this genus and further used as the species-level genetic distance to delimit the remaining morphospecies. Applying this multi-evidence framework allowed us to propose a significant re-evaluation of species boundaries, including several taxonomic reclassifications, and to generate the molecular inventory for Actias. Our study illustrates the power of an integrated molecular approach to resolve complex taxonomic issues and provides a robust, data-driven foundation for future research on Actias.},
}

@article {pmid41867886,
year = {2025},
author = {Zia, M and Suwayyid, F and Hozumi, Y and Wee, J and Feng, H and Wei, GW},
title = {CAP: Commutative algebra prediction of protein-nucleic acid binding affinities.},
journal = {Machine learning: science and technology},
volume = {6},
number = {4},
pages = {},
pmid = {41867886},
issn = {2632-2153},
support = {R35 GM148196/GM/NIGMS NIH HHS/United States ; },
abstract = {An accurate prediction of protein-nucleic acid binding affinity is vital for deciphering genomic processes, yet existing approaches often struggle in reconciling high accuracy with interpretability and computational efficiency. In this study, we introduce commutative algebra prediction (CAP) framework, which couples persistent Stanley-Reisner theory with advanced sequence embedding for predicting protein-nucleic acid binding affinities. CAP encodes proteins through transformer-learned embeddings that retain long-range evolutionary context, and represents DNA and RNA with k-mer algebra embeddings derived from persistent facet ideals, which capture fine-scale nucleotide geometry. We demonstrate that CAP surpasses the SVSBI protein-nucleic acid benchmark and, in a further test, maintains reasonable performance on newly curated protein-RNA and protein-nucleic acid datasets. Leveraging only primary sequences, CAP generalizes to any protein-nucleic acid pair with minimal preprocessing, enabling genome-scale analyses without 3D structural data and promising faster virtual screening for drug discovery and protein engineering.},
}

@article {pmid41868278,
year = {2026},
author = {Ju, J and Ma, J and Xu, P and Mao, L and Weng, Z and Xu, Q},
title = {Application of Supply Processing and Distribution Model in Interventional Consumables Management Based on Whole-Process Coding Technology.},
journal = {Risk management and healthcare policy},
volume = {19},
number = {},
pages = {546711},
pmid = {41868278},
issn = {1179-1594},
abstract = {OBJECTIVE: To explore the application effectiveness of the integration of the whole-process coding technology and Supply Processing and Distribution (SPD) supply chain management model in the management of interventional consumables.

METHODS: Based on the original SPD management mode of interventional consumables in a tertiary hospital, a standardized classification and coding system was constructed, and a basic database of consumables with a unique identification code was established and integrated into various information management platforms to achieve the whole - process code management. Comparison and analysis were made on the changes in key indicators such as the timely supply rate of interventional consumables, the traceability accuracy of barcodes, the matching accuracy between consumables and pricing items, the information registration accuracy, and the billing - outbound matching rate before and after the application of the system.

RESULTS: After the implementation of the integrated management model, all measured indicators demonstrated statistically significant improvements (p<0.05). The timeliness of consumable supply increased from 81.53% to 95.69%, traceable barcode accuracy from 85.28% to 96.39%, correct match rate between consumables and pricing items from 92.08% to 99.17%, accuracy of consumable information registration from 94.17% to 99.31%, and consistency rate between consumable pricing and inventory outflow from 96.39% to 99.58%. Staff satisfaction also significantly rose from 64.33% to 93.33% (all p<0.05).

CONCLUSION: This integrated management model significantly improves the lean and intelligent management of interventional consumables and demonstrates strong potential for clinical application and broader adoption.},
}

@article {pmid41868409,
year = {2026},
author = {Singo, L and Matthee, CA and Chaisi, ME and Stekolnikov, AA and Ueckermann, EA and Matthee, S},
title = {Diversity of ectoparasites associated with Rhabdomys pumilio and Rhabdomys intermedius (Muridae) in the Fynbos, Succulent Karoo and Nama-Karoo biomes of South Africa.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {29},
number = {},
pages = {101217},
pmid = {41868409},
issn = {2213-2244},
abstract = {Rodent species within the southern African genus Rhabdomys are ecologically flexible, exhibit opportunistic behaviour, and are adapted to a wide range of habitat types. They comprise four morphologically cryptic species that are, however, strictly confined to different vegetation types represented by distinct biomes. Descriptive ectoparasite data on the diversity of lice, fleas, mesostigmatic mites, and ticks are currently limited to Rhabdomys pumilio in the Fynbos biome, and narrative data on trombiculid mites are absent. To address these gaps in ectoparasitic knowledge, the present study was extended across a broader geographic scale and included R. pumilio from the Succulent Karoo biome, as well as R. intermedius occurring in the Nama-Karoo biome. The complete ectoparasite assemblage associated with 237 Rhabdomys individuals (171 R. pumilio and 66 R. intermedius) trapped at 12 localities during the spring-summer seasons of 2023 to 2025 yielded more than 10 000 ectoparasite individuals representing five taxonomic groups: lice, fleas, mesostigmatic mites, trombiculid mites, and ticks. Overall, 46 ectoparasitic species were recorded, comprising one louse species, nine flea species, nine mesostigmatic mite species, five tick species, and 22 trombiculid mite species. Rhabdomys pumilio harboured 42 ectoparasite species across the Fynbos and Succulent Karoo biomes, while R. intermedius in the Nama-Karoo biome harboured 21 species. The study provides detailed data on the prevalence, and localization on the host body of 14 chigger species described as new in separate taxonomic papers or awaiting description. Additional contributions include 36 new locality records across ectoparasite taxa, 14 new host associations and 24 mtDNA COI barcodes for flea species, which complement morphological identifications. This study highlights that more extensive geographic sampling of rodent host species can substantially enhance our understanding of the true diversity of rodent ectoparasites in South Africa.},
}

@article {pmid41851307,
year = {2026},
author = {Zheng, L and Sun, Y and Hein, LA and Eisenstein, M and Soh, HT},
title = {Single-molecule peptide sequencing through reverse translation of peptides into DNA.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41851307},
issn = {1546-1696},
abstract = {Despite advances in mass spectrometry and emerging single-molecule approaches, sequencing peptides at the single-molecule level remains a central challenge in proteomics. Here we present a 'reverse translation' strategy that enables single-molecule peptide sequencing with single-amino-acid resolution. In this approach, peptides undergo a modified Edman degradation that iteratively releases N-terminal amino acids tagged with peptide-specific DNA barcodes. Antibody-mediated proximity extension assays identify these barcoded amino acids and generate PCR-amplifiable DNA reporters that record the identity, position and originating peptide of each amino acid. The resulting DNA library is directly read by high-throughput sequencing, converting peptide sequences into digital DNA outputs. Using this approach, we demonstrate true single-molecule peptide sequencing, achieving full sequence coverage in millions of reads and accurate differentiation of both native and post-translationally modified peptides. These results establish a framework that redefines protein sequencing as a DNA sequencing problem and lays the foundation for high-throughput, de novo single-molecule protein sequencing.},
}

@article {pmid41852582,
year = {2026},
author = {Wang, Q and Baikeli, M and Luo, Y and Wang, X and Zhang, Y and Zhao, J and Tuerhong, R and Xiaokaiti, M and Rehemu, A and Wang, X and Mou, W},
title = {Molecular identification and phylogenetic analysis of marmots in the Xinjiang's Altai Mountains, a newly discovered plague focus of China.},
journal = {Biochemistry and biophysics reports},
volume = {46},
number = {},
pages = {102539},
pmid = {41852582},
issn = {2405-5808},
abstract = {The Altai Mountains in Xinjiang have been recognized as a new plague focus in China since 2023. Although previous morphological studies suggested that marmots in this region belong to Marmota baibacina, this classification remained unconfirmed at the molecular level. In this study, 37 marmot samples were collected: including 10 M. baibacina from the northern Tianshan Mountains, 9 M. baibacina from the southern Tianshan Mountains, and 18 unverified individuals from the Altai Mountains. The COI, Cytb, and D-loop gene fragments were sequenced and subjected to phylogenetic analysis. Homology comparisons revealed greater than 95% sequence identity across all samples, with all matches corresponding to marmot populations. Genetic distances between groups (1%-7%) exceeded those within groups (0%-2%). F st values among populations ranged from 0.55780 to 0.98449, indicating significant differentiation, particularly between the southern Tianshan population and the other two groups. In contrast, genetic divergence between the Altai and northern Tianshan populations was minimal. Maximum likelihood trees based on COI and Cytb sequences strongly supported a close phylogenetic relationship between the northern Tianshan and Altai marmots, which clustered together, while the southern Tianshan population formed a separate clade. The D-loop region provided lower phylogenetic resolution. Based on these results, we confirm that the marmots in the Altai Mountains belong to M. baibacina and classify this plague focus as a M. baibacina-Spermophilus undulatus focus, given that S. undulatus is also a documented reservoir host in the area. These findings provide a molecular basis for targeted plague surveillance and control. The close genetic affinity between the northern Tianshan and Altai populations further suggests they may represent the same subspecies.},
}

@article {pmid41853872,
year = {2026},
author = {Koong, JET and Shafique, A and Md Nasir, ND and Han, A and Harada, O and Lee, S and Nishimura, R and Ohi, Y and Tizhoosh, HR and Tan, PH},
title = {Artificial intelligence modelling in grading breast phyllodes tumours.},
journal = {Histopathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/his.70144},
pmid = {41853872},
issn = {1365-2559},
abstract = {BACKGROUND: Breast phyllodes tumours (PT) are rare biphasic neoplasms consisting of epithelial and stromal components. They are classified into benign, borderline and malignant categories. Diagnosing and grading PTs present a challenge for pathologists, as there are multiple histological parameters and their own tiers. We aim to investigate the potential role of artificial intelligence (AI) as a diagnostic aid in determining PT grade.

MATERIALS AND METHODS: We investigated 15 PT whole slide images (WSIs), comprising 5 benign, 5 borderline and 5 malignant cases. We sought to classify and retrieve the most relevant WSIs by matching histological features at different patch sizes, using the Yottixel framework for WSI processing. Patches were extracted at a 20× magnification level. We then used the KimiaNet to extract feature vectors and transformed these into barcode representations. Barcodes of a query WSI were compared with those of others in the archive, allowing us to identify the most similar WSI and determine the PT grades from histological similarities.

RESULTS: We utilized 'majority-n accuracy' as a measure of correctness, that is when the majority of the top-n search results have the correct diagnosis as the query patient. We achieved a maximum reported accuracy of 67%, with a 3000 × 3000 patch size when grading PT at majority voting with n = 4.

CONCLUSION: Despite the small sample size and absence of fine-tuning, our study demonstrated the potential of AI-based PT grade stratification using various patch sizes through histological matching. This serves as a preliminary proof of concept, with the prospect of refinement for potential routine clinical application.},
}

@article {pmid41860223,
year = {2026},
author = {Hemraj-Naraine, D and Taphorn, D and Torres-Pineda, P and Hughes, LC and Kolmann, MA},
title = {Ichthyofaunal diversity of the Canje River (Guyana): A distinctive lowland fauna between the Berbice and Corentyne Rivers, supported by a DNA barcode repository.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70391},
pmid = {41860223},
issn = {1095-8649},
support = {40787-1//Rufford Foundation/ ; //University of Louisville/ ; //Friends of the North Carolina Museum of Natural Sciences/ ; },
abstract = {Guyana, and the Guianas more generally, exhibit some of the highest examples of biodiversity and regional endemism in the Neotropics. However, much of this diversity is still unknown, with the first modern list of freshwater fishes from Guyana compiled only in 2022. We continue to build on prior efforts in Guyana and provide an annotated list of fishes collected from the Canje River, a lowland tributary of the Berbice River. The Canje is also adjacent to the Corentyne River, raising the question of whether the Canje's fauna more closely resembles the Berbice or the Corentyne. A total of 92 sites were sampled in the Canje River during both high and low water seasons in 2023, 2024, and 2025. These expeditions yielded 87 species from 63 genera representing 28 families and seven orders. Characiformes dominated collections in terms of species. In addition to collecting several taxa once thought to be endemic only to the upper Berbice River, we report the first record of Sternopygus sabaji in Guyana, as well as several likely undescribed taxa. Contrary to expectations, the Canje was not particularly similar in faunal overlap to either the Berbice or the Corentyne, providing an example of high endemicity and beta diversity in neotropical lowland rivers.},
}

@article {pmid41863034,
year = {2026},
author = {de Melo, MRS and Masumoto, FT and Caixeta, HC and Dos Reis Júnior, MR and Oliveira, C},
title = {Range extension and first records of Coryphaenoides striaturus Barnard, 1925 and Coryphaenoides subserrulatus Makushok, 1976 (Macrouridae: Gadiformes) in Brazilian waters, Southwest Atlantic, using integrative taxonomy.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70401},
pmid = {41863034},
issn = {1095-8649},
support = {2017/12909-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/13433-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/05619-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 88887.824037/2023-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88887.644858/202100//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 433050/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306054/2006-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 403380/2022-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Coryphaenoides Gunnerus, 1765 comprises 66 valid species of deep-sea fishes commonly known as grenadiers, with 6 previously reported from Brazilian waters. Here, we make the first records for Coryphaenoides striaturus and Coryphaenoides subserrulatus on the Brazilian continental slope. Both species are distributed in the subtropical regions of the Southern Hemisphere, and the former is being reported for the first time in the Southwest Atlantic, and the latter has its distribution range extended northward. The identifications were confirmed by a unique combination of morphological characters and DNA barcoding using the cytochrome oxidase subunit 1 (COI) gene.},
}

@article {pmid41851179,
year = {2026},
author = {Venkatramani, A and Ciftci, D and Pham, K and Cohen, L and Sepulveda, L and Li, C and Zhuang, X},
title = {Multiplexed optical barcoding and sequencing for spatial omics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41186-y},
pmid = {41851179},
issn = {2045-2322},
}

@article {pmid41851241,
year = {2026},
author = {Saengprajak, J and Phetsom, J and Sangdee, A and Saengprajak, A and Thanyasiriwat, T and Mahakham, W},
title = {Phylogenetic relationship based on DNA barcodes and comparative analysis of phytochemical contents among Rhynchostylis orchids in Thailand.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44785-x},
pmid = {41851241},
issn = {2045-2322},
}

@article {pmid41850290,
year = {2026},
author = {Su, C and Ryu, HS and Chandradoss, KR and Malachowski, T and Boya, R and Zhou, L and Nguyen, HE and Mazzoni, EO and Brennand, KJ and Phillips-Cremins, JE},
title = {MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101341},
doi = {10.1016/j.crmeth.2026.101341},
pmid = {41850290},
issn = {2667-2375},
abstract = {More than 60 human disorders are caused by unstable expansion of short tandem repeat (STR) tracts. These can exhibit cell-type-specific mosaicism in several repeat expansion disorders and remain difficult to characterize due to technical challenges intrinsic to highly repetitive sequences. Long-read approaches can measure STR length and DNA methylation on the same single molecule but are low-throughput and cost-prohibitive across multiple experimental conditions or patient samples. Here, we present MASTR-seq, multiplexed analysis of short tandem repeats with sequencing, for cost-effective, high-throughput, accurate measurement of STR genotype and DNA methylation at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, size selection, and PCR-free multiplexed barcoding to increase on-target read proportion for 8-12 pooled samples in a single MinION flow cell. MASTR-seq quantifies tract length and DNA methylation status for CGG, GGGGCC (G4C2), and CAG STR tracts in normal-length and mutation-length samples.},
}

@article {pmid41840711,
year = {2026},
author = {Vila-Farré, M and Brand, JN and Boothe, T and Brockmeyer, M and Ficze-Schmidt, F and Grohme, MA and Weill, U and Kluiver, KH and Gąsiorowski, L and Kauf, L and Kanana, Y and Bilandžija, H and Riutort, M and Rink, JC},
title = {An integrative taxonomic approach reveals unexplored diversity in Croatian planarians.},
journal = {Frontiers in zoology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12983-026-00603-8},
pmid = {41840711},
issn = {1742-9994},
support = {TTP-2018-07-9675//Evolution in the Dark, Croatian-Swiss Research Programme./ ; },
abstract = {BACKGROUND: Freshwater ecosystems are among the most endangered habitats on Earth, with approximately one-fourth of aquatic species at risk of extinction. Effective conservation efforts require comprehensive monitoring and accurate species identification, including often overlooked groups. Planarian flatworms are one such group that, although commonly present in freshwater ecosystems worldwide, remains understudied even in species-rich areas, e.g. Croatia. As a result, the true extent of planarian diversity often remains underappreciated.

RESULTS: With the goal of characterising the Croatian planarian diversity, we used an integrative approach combining barcoding and classical taxonomy methods. Motivated by the highly skewed representation of planarian diversity in current GenBank records of the barcoding gene cytochrome c oxidase subunit I (COI), we first optimised primer design and amplification protocols. Applying these approaches to field-collected material from Croatia, we substantially expanded the number of taxonomically curated COI barcode sequences for European dugesiids, dendrocoelids and planariids. In addition, our efforts resulted in the description of a new pigmented Dendrocoelum species, Dendrocoelum pigmentatum Vila-Farré, sp. nov., the discovery of two highly differentiated haplotypic clades in Schmidtea lugubris, and the rediscovery of Polycladodes alba in Croatia after a century.

CONCLUSIONS: Overall, our effort integrates Croatia as an underexplored but planaria species-rich region into the endeavour to systematically describe the planarian fauna of Europe. The expansion of a known number of Croatian planarian species from eight to sixteen and the discovery of a new, large planarian species in continental Europe, Dendrocoelum pigmentatum, demonstrate the effectiveness of our integrative approach. Overall, our work highlights the underappreciated diversity of planarians, even in continental Europe and supports practical conservation efforts to preserve aquatic biodiversity.},
}

@article {pmid41842855,
year = {2026},
author = {Hemprich-Bennett, DR and Donkor, E and Adams, B and Acquaah, NA and Ofori, ED and Anie-Amoah, S and Bailey, A and Godfray, HCJ and Lewis, OT and Aboagye-Antwi, F and Hackett, TD},
title = {Characterising a species-rich and understudied tropical insect fauna using DNA barcoding.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag028},
pmid = {41842855},
issn = {2047-217X},
abstract = {BACKGROUND: West Africa has high biodiversity that is relatively understudied, especially for insects. Studies of West African arthropod diversity can therefore help address important questions regarding conservation, ecosystem services, and insecticide use and other species-control interventions in agriculture and disease management. We intensively sampled arthropods in Ghana using complementary trapping methods, generated DNA barcodes, and classified sequences by Barcode Index Numbers (BINs, a species proxy). Using this dataset, we investigate assemblage composition, temporal activity patterns, and the state of regional biodiversity sampling.

RESULTS: Sequencing DNA from 95,996 individuals captured using Malaise, yellow pan, pitfall, Heath and Centre for Disease Control (CDC) traps, we identified 10,120 unique BINs. The rate of species accumulation did not approach an asymptote for any taxonomic group or trap type, indicating high biodiversity. The different trap types sampled different subsets of the local community, with greatest similarity between yellow pan and pitfall traps. More insects and species (BINs) were trapped during the day than at night. Our dataset shared more BINs in the Barcode of Life Database with South Africa than with any other country, although this predominantly reflects the limited sampling and DNA sequencing campaigns in Africa.

CONCLUSIONS: This study more than doubles the published BINs for West Africa, offering insights into the biodiversity of an ecologically important but understudied taxon and region. Using multiple trap types allowed a more complete assessment of the local arthropod assemblage. The public release of these data will support and stimulate further taxonomic and ecological work in the region.},
}

@article {pmid41843053,
year = {2026},
author = {Mohd-Redzuan, MAA and Rajasegaran, P and Husin, NA and Syarriman AbdulRahim, MH and AbdulHalim, AA and Halim, MRA and Abdullah, NA and Jiliun, EA and Khoo, JJ and AbuBakar, S and Makepeace, BL and Ya'cob, Z},
title = {DNA barcoding reveals cryptic diversity in chiggers (Trombiculidae) parasitizing small mammals across Peninsular Malaysia.},
journal = {Experimental & applied acarology},
volume = {96},
number = {3},
pages = {},
pmid = {41843053},
issn = {1572-9702},
abstract = {UNLABELLED: Chiggers (Acariformes: Trombiculidae) are ectoparasites of small mammals and important vectors of scrub typhus, yet their taxonomy and molecular diversity in Southeast Asia remain poorly resolved. This study represents the first DNA barcoding and phylogenetic assessment of chiggers from small mammals across Peninsular Malaysia, integrating mitochondrial (COI) and nuclear (28 S rDNA) genes. A total of 192 chiggers representing 11 morphospecies from six genera were sequenced, with tree topologies inferred using maximum likelihood and supported by multiple species delimitation methods. The COI gene discriminated five species as monophyletic, while analysis of the 28 S rDNA gene clarified phylogenetic relationships within Walchia and Leptotrombidium. Discordance between morphological and molecular boundaries in several taxa, particularly Gahrliepia fletcheri, Leptotrombidium deliense, and Walchiella oudemansi, suggests the existence of cryptic lineages and potential regional diversification. Importantly, this study provides the first molecular records for eight species, including the only barcodes from the genera Gahrliepia and Walchiella worldwide. These findings provide important resources for the molecular identification of Southeast Asian chiggers and underscore the need for integrative approaches combining morphology, molecular data, and biogeography to resolve complex species boundaries and improve vector surveillance for mite-borne diseases.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10493-026-01128-9.},
}

@article {pmid41843159,
year = {2026},
author = {Redkina, VV and Krivina, ES and Soromotin, AV and Temraleeva, AD},
title = {First records of cyanobacteria and microalgae in sand dunes of the Russian high north: morphological and DNA barcoding evidence.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41843159},
issn = {1432-072X},
support = {24-16-00163//Russian Science Foundation/ ; },
mesh = {*Cyanobacteria/genetics/classification/isolation & purification ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Microalgae/genetics/classification/isolation & purification/cytology ; Russia ; *Soil Microbiology ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {This study presents the first integrated analysis of cyanobacterial and microalgal diversity in soils and biological soil crusts from the sand dunes of the Russian High North, combining morphological characterization with DNA barcoding of cultured isolates. We identified 33 taxa across four phyla, dominated by Chlorophyta (Trebouxiophyceae and Chlorophyceae). Although ITS2 sequencing is widely used for phylogenetic studies, only approximately 35% of eukaryotic algal strains in our study could be confidently identified to the species level, underscoring both the limitations of this marker for certain taxonomic groups and the ongoing challenges in algal systematics. ITS2 sequencing limitations as a single-locus marker were revealed when analyzing phylogenetically complex genera, including Asterochloris, Klebsormidium, Interfilum, and Vischeria, where robust classification required integration of additional genetic markers. Phylogenies revealed taxonomic gaps in several algal lineages (Spongiococcum, Myrmecia, Leptosira, and the Radiococcaceae family), exacerbated by critical gaps in reference databases. We identified eight novel candidates via concordant molecular and morphological divergence, including one potential new genus. Ecological roles varied, ranging from free-living soil crust formers (Klebsormidium spp., Kalymmatonema sp.) to lichen symbionts (Asterochloris spp., Myrmecia israelensis). Remarkably, we documented the rare cyanobacterium Dapisostemon apicaliramis in these sand dunes, expanding its known range beyond Brazil. Our findings demonstrate the necessity of multi-locus approaches to resolve taxonomic uncertainties in understudied genera, while emphasizing the crucial role these microbial communities play in stabilizing fragile northern taiga ecosystems in Western Siberia.},
}

*Cyanobacteria/genetics/classification/isolation & purification
*DNA Barcoding, Taxonomic
Phylogeny
*Microalgae/genetics/classification/isolation & purification/cytology
Russia
*Soil Microbiology
Biodiversity
Sequence Analysis, DNA

@article {pmid41848558,
year = {2026},
author = {Liu, FT and Sun, RB and Zhang, XR and Ding, ZX and Zhang, TQ and Hou, HJ and Wang, YF and Zhang, H and Li, SY and Yang, WB and Zhang, M and Qian, C and Chen, YH and Song, HP},
title = {An Integrated Identification Strategy for Closely Related Plants Mahonia bealei, Mahonia fortunei, and Berberis soulieana Using Microscopic Characterization, HPLC-QTOF-MS/MS, and DNA Barcoding: A Controversial Case on the Taxonomy of Mahonia and Berberis.},
journal = {Phytochemical analysis : PCA},
volume = {},
number = {},
pages = {},
doi = {10.1002/pca.70066},
pmid = {41848558},
issn = {1099-1565},
support = {RC230846//Shenyang Youth Science and Technology Innovation Talent Cultivation Project-U35 Top Youth Project/ ; 2024-MSLH-297//Liaoning Natural Science Foundation/ ; 2025-BS-0706//Liaoning Natural Science Foundation/ ; 2025-DxkjcU45-19-03//Under-45 Multidisciplinary Team for Innovation in Traditional Chinese Medicine Science and Technology/ ; 22KJB360002//Jiangsu Provincial University Natural Science Research Project/ ; //National Traditional Chinese Medicine Veteran (Kang Ting-Guo) Heritage Studio Construction Project/ ; },
abstract = {INTRODUCTION: The taxonomic boundary between Mahonia and Berberis has long been controversial. Mahonia bealei (Fort.) Carr. (MB) and Mahonia fortunei (Lindl.) Fedde (MF) are representative species of Mahonia, while Berberis soulieana Schneid. (BS) represents Berberis. These three plants are often confused in practical medicinal use.

OBJECTIVE: This study aims to elucidate the diagnostic characteristics and taxonomic relationships among MB, MF, and BS. It seeks to provide a potential basis for generic realignment.

METHODOLOGY: Their structural differences were compared based on macro-morphological features of leaves and microscopic characteristics of roots. Qualitative and quantitative analyses of the chemical components in the three samples were carried out using HPLC-QTOF-MS/MS, followed by a comparison of their chemical fingerprints and the content of major components. Based on multiple DNA barcoding, interspecific genetic distances were calculated and RNA secondary structures were predicted.

RESULTS: The differences in the root transverse sections provided a basis for distinguishing the three samples. A total of 67 compounds were identified using HPLC-QTOF-MS/MS, with 24 of these being common to all three samples. While their chemical fingerprints were highly similar, berberine content served as a key differentiating marker. Among DNA barcodes, PsbA3 exhibited the highest sequence variation and largest inter-species genetic distance. These properties made it the optimal barcode for discrimination. Notably, its secondary structure was relatively conserved, exhibiting a unique phenomenon of highly variable sequences with conserved structures.

CONCLUSION: Although several diagnostic features were identified, the marked chemical similarities, conserved DNA barcodes, and shared microscopic characteristics provided novel insights into the taxonomic relationship between the genera Mahonia and Berberis.},
}

@article {pmid41838382,
year = {2026},
author = {Saini, K and Singh, R},
title = {Regulatory Approaches to Electronic Labelling in the USA, EU, and India: A Comparative Overview.},
journal = {Therapeutic innovation & regulatory science},
volume = {},
number = {},
pages = {},
pmid = {41838382},
issn = {2168-4804},
abstract = {OBJECTIVE: In this era of growth, e-labelling is becoming increasingly important as the labels are important sources of information for patients. However, regulations governing e-labeling for pharmaceuticals and medical equipment varies throughout the countries. This review compares the e-labelling regulation approaches in EU, USA, and India.

SCOPE: The regulations have been initiated by appropriate governments and/or health authorities of EU, USA, and India in collaboration with key stakeholders, including patients, healthcare providers, pharmaceutical companies, environmental and regulatory agencies. EU and USA have established the digital labelling but India still relies on paper instruction manuals with limited digital systems.

METHODOLOGY: The regulatory information and current trends of e-labelling in EU, US, and India were studied and compared for electronic prescribing and electronic decision support systems with health record. Regulatory information was recognized through a structured review of official regulatory agency websites (FDA, EMA, CDSCO), international organizations (WHO, ICH), and peer-reviewed literature accessed through databases such as PubMed and Google Scholar. Eligible sources comprised official regulations, guidance documents, policy reports, and peer-reviewed articles specifically addressing pharmaceutical e-labelling, while draft policies and unrelated documents were excluded. Data were synthesized using qualitative thematic analysis, and cross-jurisdictional comparisons were structured across predefined domains including regulatory scope, legal status, implementation stage, digital infrastructure, and stakeholder accessibility.

KEY FINDINGS: Common challenges include maintaining authenticity, readability, and interoperability of e-labels. Technologies like QR codes, barcoding, and decision support tools increase safety and access. However, digital implementation and regulatory maturity differ generally between the developed and developing nations.},
}

@article {pmid41840192,
year = {2026},
author = {Gülmez, İ and Dönmez, AA and Aydın, ZU},
title = {Comparative chloroplast genome analysis of Polygala species: insights into evolution, phylogeny, and DNA barcoding.},
journal = {Planta},
volume = {263},
number = {4},
pages = {},
pmid = {41840192},
issn = {1432-2048},
support = {118 Z 708//TUBITAK/ ; },
mesh = {*Genome, Chloroplast/genetics ; Phylogeny ; *DNA Barcoding, Taxonomic ; *Polygala/genetics/classification ; Evolution, Molecular ; Genetic Variation ; },
abstract = {Polygala species are rich in saponin molecules and are traditionally used for medical purposes. Research on the chloroplast (cp) genome of Polygala is crucial to understanding its phylogenetics, biogeography, and species identification. In this study, the tetraploid Polygala vulgaris chloroplast genome was reported for the first time via various assembly and annotation tools. By combining these new data with the published cp genomes of 12 Polygala taxa from NCBI, we conducted a comparative analysis of nucleotide diversity, repeat sequences, genome synteny, phylogenetic relationships and DNA barcoding. The final assembled chloroplast genome sizes for the studied Polygala taxa ranged from 165,246 bp to 168,779 bp, with a total of 174 genes annotated, including 102 protein-coding genes, 63 transfer RNA genes, and 13 ribosomal RNA genes in Polygala vulgaris. A total of nine highly divergent genes were identified, including the CDS gene rpl32 as well as the intergenic spacer regions matK-trnK, trnL-trnF, trnH-psbA, trnQ-psbK, ndhI-ndhF, ndhF-rpl32, ccsA-ndhD, and ndhG-ndhI. Phylogenetic relationships were reconstructed based on Bayesian inference and maximum likelihood analyses using ortholog-based and concatenated datasets derived from the identified hypervariable regions separately. The topological structure of the constructed phylogenetic tree showed biogeographic disjunction, and the most similar relative of Polygala vulgaris was one of the European taxa, P. amerella, based on high support values. The analysis of relative synonymous codon usage revealed that a codon usage pattern largely consistent with that observed across other Polygala species. A total of three types of repeat sequences, forward, palindromic, and reverse, were identified across the chloroplast genomes of the analyzed species. These findings provide a valuable reference for phylogenomic and evolution of Polygala taxa as well as to develope molecular markers for DNA barcoding.},
}

*Genome, Chloroplast/genetics
Phylogeny
*DNA Barcoding, Taxonomic
*Polygala/genetics/classification
Evolution, Molecular
Genetic Variation

@article {pmid41835227,
year = {2026},
author = {Sun, L and Zheng, H and Huang, Y and Huang, X and Yan, K and Wang, Z and Yang, L and Yue, Y and Gou, X and Du, G and Wang, Y and Wu, X and Liu, H and Chen, H and Ma, D and Han, Y and Dai, J and Cao, G},
title = {Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq.},
journal = {National science review},
volume = {13},
number = {5},
pages = {nwag004},
pmid = {41835227},
issn = {2053-714X},
abstract = {Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and its underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate an integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of the mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated the projectomic atlas with its distinct spectrum of neurotransmitters/neuropeptides with their receptor-related gene profiles in order to demonstrate the PFC neural signal transmission network, by which means we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information. As a proof of concept, we used this model to predict projections of fear recall engram neurons. This study facilitates our understanding of the brain multi-modal network and neural computation.},
}

@article {pmid41835454,
year = {2026},
author = {Walterspiel, F and Ugarte-Uribe, B and Terjung, S and Cabrera, A and Khan, AUM and Deo, C},
title = {Photoclickable Halotag ligands for spatiotemporal multiplexed protein labeling on living cells.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41835454},
issn = {2633-0679},
abstract = {Precise spatiotemporal control over fluorescence labeling is a powerful approach for selective marking and tracking of proteins of interest within living systems. Here, we report a photoclickable labeling platform based on the 2,3-diaryl-indanone epoxide (DIO) photoswitch scaffold and the self-labeling protein HaloTag. Upon illumination, the protein-bound DIO undergoes reversible photoisomerization to form a metastable oxidopyrylium ylide (PY) that reacts with ring-strained dipolarophiles via [5 + 2] cycloaddition, enabling covalent spatiotemporal labeling. We synthesize and characterize a library of DIO-HaloTag and DIO-SNAP-tag ligands, systematically examining the effects of linker architecture and scaffold substitution on the photoswitching and photoclick reactivity in vitro and on living cells. We identify a naphthyl-substituted DIO ligand exhibiting superior photoswitching and photoclick efficiency, allowing fast, selective labeling of HaloTagged proteins on the surface of living cells using visible light activation (405 nm). Using this system, we achieve two- and three-color labeling of defined cell surface regions with excellent spatial and temporal precision, additionally allowing combinatorial labeling. Together, this work establishes a versatile framework for multiplexed, light-directed protein labeling compatible with living systems, with promising future applications including multiplexed long-term tracking and cellular barcoding.},
}

@article {pmid41836496,
year = {2024},
author = {Miller, DR and Jacobs, JT and Rockefeller, A and Singer, H and Bollinger, IM and Conway, J and Slot, JC and Cliffel, DE},
title = {Cultivation, chemistry, and genome of Psilocybe zapotecorum.},
journal = {Journal of psychedelic studies},
volume = {8},
number = {1},
pages = {63-81},
pmid = {41836496},
issn = {2559-9283},
abstract = {Psilocybe zapotecorum is a strongly blue-bruising psilocybin mushroom used by indigenous groups in southeastern Mexico and beyond. While this species has a rich history of ceremonial use, research into its chemistry and genetics has been limited. Herein, we report on mushroom morphology, cultivation parameters, chemical profile, and the full genome sequence of P. zapotecorum. First, we detail growth and cloning methods that are simple, and reproducible. In combination with high resolution microscopic analysis, the strain was identified by DNA barcoding, confirming the field identification. Full genome sequencing reveals the architecture of the psilocybin gene cluster in P. zapotecorum, and can serve as a reference genome for Psilocybe clade I. Characterization of the tryptamine profile revealed a psilocybin concentration of 17.9 ± 1.7 mg/g, with a range of 10.6-25.7 mg/g (n = 7), and similar tryptamines (psilocin, baeocystin, norbaeocystin, norpsilocin, aeruginascin, and 4-HO-tryptamine) in lesser concentrations for a combined tryptamine concentration of 22.5 ± 3.2 mg/g. These results show P. zapotecorum to be a potent and chemically variable Psilocybe mushroom. Chemical profiling, genetic analysis, and cultivation assist in demystifying these mushrooms. As clinical studies with psilocybin gain traction, understanding the diversity of Psilocybe expands the conversation beyond the molecule.},
}

@article {pmid41837206,
year = {2026},
author = {Kočárek, P and Fontana, P and Kočárková, I and Bonczek, V},
title = {A new cryptic species of Chelidurella Verhoeff, 1902 (Dermaptera, Forficulidae) from the Italian Alps: molecular evidence reveals hidden diversity in a high-altitude refugium.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {173-188},
pmid = {41837206},
issn = {1313-2989},
abstract = {The cryptic diversity within the earwig genus Chelidurella Verhoeff, 1902 remains underestimated despite growing evidence from molecular phylogenetic studies. During recent collecting efforts in the Adamello-Presanella Alps, a population of Chelidurella specimens that morphologically resemble C. mutica (Krauss, 1886) but exhibit distinct molecular divergence was discovered. Based on integrative taxonomic analysis combining molecular evidence with detailed morphological examination, Chelidurella maccagnoae Kočárek & Fontana, sp. nov. is described. Despite sharing the diagnostic shortened pygidium with C. mutica, phylogenetic analysis reveals that C. maccagnoae Kočárek & Fontana, sp. nov. is more closely related to the C. vignai / C. pseudovignai species complex, indicating convergent evolution of this character rather than shared ancestry. An updated identification key to Chelidurella males is provided and the biogeographic implications for understanding Quaternary diversification patterns in flightless Alpine arthropods discussed.},
}

@article {pmid41837210,
year = {2026},
author = {Ponce, P and Cevallos, V and Carrazco-Montalvo, A and Gallardo-Cóndor, J and Arévalo, V and Galarza, X and Coloma, J},
title = {An updated checklist of mosquitoes (Diptera, Culicidae) of Ecuador: new records and public health significance.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {67-136},
pmid = {41837210},
issn = {1313-2989},
abstract = {Mosquitoes are major vectors of human and animal diseases, making their accurate identification essential for vector surveillance and control. However, morphological identification has often been challenging, requiring taxonomic expertise and well-preserved specimens. Molecular markers, particularly DNA barcoding, offer an effective alternative for identifying both adult and immature stages. Ecuador is one of the most biodiverse countries in the world, a diversity that is also evident in its Culicidae fauna. This study provides a comprehensive revision of Ecuadorian mosquitoes, updating the national checklist and emphasizing species of public health importance. For species identification, an integrative approach was used combining morphology and DNA barcoding (COI and ITS2 regions). We list 266 species in 22 genera, of which 17 species are new national records, and 33 species are validated through molecular analysis. The updated checklist highlights Ecuador's Culicidae diversity across its biogeographic regions, which represent 7% of the world's mosquito diversity. These findings provide a critical foundation for future entomological research and vector control in the country.},
}

@article {pmid41822874,
year = {2026},
author = {van der Nol, E and Luo, Z and Gao, QQ and Haupt, NA and Böcker, S and Pomplun, S},
title = {Integration of palladium-catalyzed C-N coupling into self-encoded libraries for accelerated hit discovery.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41822874},
issn = {2633-0679},
abstract = {Affinity screenings with encoded libraries are transformative tools for rapid hit discovery from vast compound collections. Yet the adaptation of established chemical reactions to DNA-encoded libraries (DELs) remains challenging due to DNA-compatibility constraints and mismatches between barcode and chemical structure in case of incomplete reactions or side product formation. Recently, we introduced self-encoded libraries (SELs) as a barcode-free alternative to DELs. The SEL platform offers unmatched flexibility in reaction conditions and decodes screening hits directly from their chemical structure, avoiding the problem of mismatched barcode-compound pairs. Here, we expand the SEL platform to Buchwald-Hartwig aminations, enabling the construction of new high diversity SELs. We performed a thorough reaction condition optimization and tested a scope of >170 different building blocks. We adapted our automated MS/MS-based decoding methodology SIRIUS-COMET to the resulting scaffolds, enabling accurate compound decoding from complex mixtures. A 25 725-member library was synthesized and screened all at once against carbonic anhydrase IX (CAIX), resulting in robust enrichment of hits with specific building block patterns and yielding several nanomolar-affinity binders. This work showcases the seamless integration of palladium-catalyzed cross-couplings into SELs, expanding the chemical space of this technology and accelerating hit discovery with high synthetic versatility.},
}

@article {pmid41823389,
year = {2026},
author = {Ogola, EO and Slothouwer, I and Rotich, G and Kopp, A and Bastos, ADS and Getugi, C and Melchert, J and Jones, TC and Omoga, DCA and Sang, R and Torto, B and Tchouassi, DP and Junglen, S},
title = {Identification and full genome sequencing of previously unknown sandfly-borne phleboviruses using a newly established capture-based next-generation sequencing approach.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0108225},
doi = {10.1128/jcm.01082-25},
pmid = {41823389},
issn = {1098-660X},
abstract = {Sandfly-borne phleboviruses cause febrile illness and neuroinvasive disease in humans. While infections are reported in the Mediterranean region, the discovery of previously unknown phleboviruses in sandflies from Kenya suggests a wider geographic distribution. Detection and characterization of novel phleboviruses are often hindered by low-quality and low-viral-load samples. We developed a capture-based target enrichment next-generation sequencing approach that showed a 99%-100% fold enrichment of viral genomes from primary material and provides a robust tool for generating complete genomes of both known and previously unknown viruses. From a collection of 15,652 sandflies in Kenya, we recovered seven complete coding sequences of Embossos, Bogoria, and Kiborgoch viruses, and of two previously unknown phleboviruses, which were named Sosoik and Shable viruses. Sosoik virus shared 83% amino acid identity in its RdRp gene with that of Bogoria virus, while Shable virus shared ca. 88% amino acid identity with viruses of the Salehabad serocomplex. Additionally, a reassortant of Shable virus was detected that possessed an M segment from an undescribed Ponticelli-like virus. DNA barcoding of blood-fed sandflies revealed several potentially novel Sergentomyia species and evidence of host-feeding on humans, livestock, and reptiles, suggesting possibilities for zoonotic transmission. Overall, our findings increase the known genetic diversity of Old World sandfly-borne phlebovirus species from 18 to 25 (by 38.9%), including the detection of viruses from all pathogenic sandfly-borne phlebovirus serocomplexes in East Africa, opening new horizons in disease ecology research.IMPORTANCEKnowledge of the genetic diversity of circulating pathogens is crucial for providing appropriate diagnostics and disease management. This study established a novel capture-based target enrichment next-generation sequencing approach that enabled the near-complete viral genome recovery from primary samples, while native NGS yielded negative or poor-quality results. In addition to the five recently discovered sandfly-borne phleboviruses in Kenya, two previously unknown phleboviruses were detected in sandflies from the same region. The viruses were detected in several sandfly species, which showed diverse host-feeding behaviors, including mixed feeding on humans and chickens. The study significantly advances the understanding of sandfly-borne phleboviruses by uncovering their broader geographic distribution and genetic diversity, particularly in East Africa, highlighting the importance of expanding surveillance efforts beyond traditionally studied regions.},
}

@article {pmid41823847,
year = {2026},
author = {Bunchom, N and Kongim, B and Manphae, A and Pilap, W and Andrews, RH and Tantrawatpan, C and Saijuntha, W},
title = {Morphological Differentiation Among Three Mitochondrial Lineages of Hydrobioides nassa Theobald, 1865 (Gastropoda: Bithyniidae) from Thailand.},
journal = {Biology},
volume = {15},
number = {5},
pages = {},
pmid = {41823847},
issn = {2079-7737},
support = {//Mahasarakham University/ ; },
abstract = {The identification of species complexes in freshwater snails remains challenging due to limited diagnostic morphological characters and incomplete taxonomic knowledge in many taxa. Within the family Bithyniidae, species have traditionally been classified using shell morphology and genital anatomy to distinguish intraspecific variation from interspecific differences. However, extensive morphological plasticity has hindered reliable species delimitation, and the presence of cryptic diversity further complicates taxonomy. Recent DNA barcoding studies of Hydrobioides have provided evidence of such cryptic diversity, highlighting the need for taxonomic reassessment within the genus. In the present study, we examined morphological variation in Hydrobioides nassa from Thailand in conjunction with mitochondrial DNA sequence data. Molecular phylogenetic analyses based on cytochrome c oxidase subunit I (cox1) sequences revealed three well-supported genetic lineages within H. nassa, accompanied by high levels of pairwise genetic divergence. Morphological comparisons of shell, operculum, and radular characters further supported differentiation among these lineages, although some characters showed overlap. While Hydrobioides has previously been regarded as comprising a single morphologically defined species, our results demonstrate that H. nassa represents a complex of genetically distinct lineages with subtle but consistent morphological differences. This study highlights the importance of integrating molecular approaches with traditional morphological analyses to improve taxonomic resolution and to better understand biodiversity within freshwater snail groups exhibiting cryptic diversity.},
}

@article {pmid41823851,
year = {2026},
author = {Lee, SJ and Lee, EY and Kim, BY and Lee, SR},
title = {DNA Barcoding for Herbarium Specimens of the Red Alga Meristotheca pilulaora and Molecular Marker Development for Species Identification.},
journal = {Biology},
volume = {15},
number = {5},
pages = {},
pmid = {41823851},
issn = {2079-7737},
support = {NFQS2026001//National Fishery Products Quality Management Service (Development and Management of Dis-ease Control Program for Aquatic Life)/ ; NIBR202602103//National Institute of Biological Resources (NIBR)/ ; },
abstract = {The genus Meristotheca (Gigartinales, Solieriaceae) comprises edible red algae that are economically important food ingredients in Korea, Japan, and China. In Korea, two species, Meristotheca coacta and Meristotheca papulosa, have been identified, with the latter being predominantly reported. Recently, molecular phylogenetic analysis enabled the identification of Meristotheca pilulaora (Gigartinales; Solieriaceae) on Jeju Island (Korea). In this study, we used a DNA barcoding method to re-examine M. papulosa herbarium specimens deposited at the National Institute of Biological Resources (Incheon, Korea). Specimens were collected from Korean coastal regions between 2009 and 2019. Molecular analyses based on the rbcL and cox1 sequences of the "M. papulosa" herbarium specimens revealed that the specimens were of two other species, M. pilulaora and Gracilaria textorii (Gracilariales; Gracilariaceae). Our work represents a case study for establishing a misidentification at the inter-ordinal level among herbarium specimens without DNA sequence verification. Moreover, we developed a molecular marker for the effective species-level identification of M. pilulaora and G. textorii specimens. The DNA barcoding method provides useful information regarding M. pilulaora distribution and taxonomy.},
}

@article {pmid41826340,
year = {2026},
author = {Lin, BA and Leung, KT and Han, W and Liu, M and Lam, VYY and Seymour, M},
title = {Biodiversity of Hong Kong purse seine fisheries: An integrated DNA barcode reference library.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06981-2},
pmid = {41826340},
issn = {2052-4463},
abstract = {Here we present a multi-marker DNA barcoding library for Hong Kong marine fishes (Teleostei), cephalopods (Mollusca), and crustaceans (Arthropoda) frequently captured by purse seine fisheries. In total, 605 specimens were morphologically identified with 562 specimens sequenced and assigned to 185 fish species from 146 genera, 64 families, and 26 orders; 8 cephalopod species from 6 genera, 4 families and 4 orders (24 specimens); and 13 crustacean species from 10 genera, 5 families and 1 order (19 specimens). The barcode library includes mitochondrial cytochrome c oxidase subunit I (COI) and mitochondrial 12S ribosomal RNA (12S) barcodes for fishes, and COI and mitochondrial 16S ribosomal RNA (16S) barcodes for cephalopods and crustaceans. Specimens were assigned to species-level using integrated morphological and genetic assessment. The library represents the first barcode reference dataset for marine fishes, cephalopods and crustaceans from Hong Kong, increasing our knowledge of species diversity, enabling accurate identification of the three nekton groups and improving species identification reliability for eDNA metabarcoding studies in Hong Kong waters and the northern South China Sea.},
}

@article {pmid41832919,
year = {2026},
author = {Chai, MJ and Bogutskaya, NG and Reier, S and Friedrich, R and Rund, H and Wanzenböck, S and Wanzenböck, J and Glaser, F and Marcante, S and Prowatke, I and Jung, M and Mikschi, E and Palandačić, A},
title = {Data collected in a citizen scientist study uncover a new species record of Phoxinus minnow for Austria.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41832919},
issn = {1573-2959},
support = {SPSC_01_021//Federal Ministry of Women, Science and Research; Austria's Agency for Education and Internationalisation (OeAD); Sparkling Science 2.0/ ; SPSC_01_021//Federal Ministry of Women, Science and Research; Austria's Agency for Education and Internationalisation (OeAD)/ ; },
mesh = {Austria ; *Biodiversity ; *Environmental Monitoring/methods ; *Cyprinidae/classification/genetics ; Animals ; Citizen Science ; DNA Barcoding, Taxonomic ; Ecosystem ; },
abstract = {Freshwaters are among the most vulnerable ecosystems, yet the scarcity of biodiversity assessments prevents the detection of changes incurred by neobiota. Minnows of the genus Phoxinus were long thought to be represented by a single species in Eurasia, the common minnow P. phoxinus, but the genus now includes more than 25 valid species. However, their distributions do not follow drainage boundaries, there are known cases of human translocations, and morphological species assignation is difficult due to intra- and interpopulation phenotypic diversity. Hence, the species were delimited and are now determined mostly using molecular methods. In Austria, recent studies have identified at least four different species of Phoxinus, three of which are considered native and one introduced. However, more data were needed; thus, extensive collecting and DNA barcoding of minnow populations was undertaken with the help of recreational fishers, school pupils, and field biologists. DNA barcodes of museum specimens and environmental DNA collected from water samples were also included. Altogether, the genetic lineage of 258 new Phoxinus specimens was determined. The results confirmed the distribution of P. marsilii in eastern Austria, P. lumaireul in southern Austria and P. csikii in central and western Austria. Additional populations of the introduced P. phoxinus were identified. Most importantly, a new species record for Austria, P. cf. morella, was discovered, yet it is unclear whether its distribution in Austria is natural. This study also confirmed the potential of citizen science for biodiversity monitoring, with the number of specimens analyzed increasing fourfold in just two years.},
}

Austria
*Biodiversity
*Environmental Monitoring/methods
*Cyprinidae/classification/genetics
Animals
Citizen Science
DNA Barcoding, Taxonomic
Ecosystem

@article {pmid41820665,
year = {2026},
author = {Chen, D and Isakova, A and Wan, Z and Wagner, MJ and Wu, Y and Zhao, BS},
title = {Connectome-seq: high-throughput mapping of neuronal connectivity at single-synapse resolution via barcode sequencing.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41820665},
issn = {1548-7105},
abstract = {Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods particularly limited in mapping long-distance circuits and preserving cell type information. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding and parallel single-nucleus and single-synaptosome sequencing to map neuronal connectivity at single-synapse resolution. This adeno-associated virus-based approach enables simultaneous capture of both synaptic connections and molecular identities of connected neurons. We validated this approach in the mouse pontocerebellar circuit, identifying both established and potentially uncharacterized synaptic connections. Through integrated analysis of connectivity and gene expression, we identified molecular markers enriched in connected neurons, suggesting potential molecular determinants of circuit-specific connectivity. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision and gene expression information, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states.},
}

@article {pmid41819881,
year = {2026},
author = {Bhowmik, D and Rickard, JJS and Goldberg Oppenheimer, P},
title = {Advanced Real-Time, Non-Destructive Spectral Fingerprinting for Early microbial Spoilage Detection: AI-Integrated Raman Biosensing Platform for Scalable Food Safety and Quality.},
journal = {Food research international (Ottawa, Ont.)},
volume = {231},
number = {Pt 2},
pages = {118745},
doi = {10.1016/j.foodres.2026.118745},
pmid = {41819881},
issn = {1873-7145},
mesh = {*Food Safety/methods ; *Biosensing Techniques/methods ; *Food Microbiology/methods ; *Spectrum Analysis, Raman/methods ; Animals ; *Food Contamination/analysis ; Meat/analysis/microbiology ; Neural Networks, Computer ; Milk/microbiology/chemistry ; Food Quality ; },
abstract = {Food spoilage poses a global challenge, contributing to economic losses, food insecurity, and health risks from microbial contamination. Conventional detection methods are often destructive, time-consuming and ineffective at identifying early biochemical changes or stereospecific microbial by-products. We developed SkiNET-FoodSpec, a novel, non-invasive biosensor platform integrating biomolecular spectroscopy with an advanced self-organising map-based neural network (SkiNET) for rapid, real-time spoilage detection. The system achieves >93% classification accuracy across a range of food matrices, including meat, milk and leafy greens. It detects key spoilage markers, such as cadaverine in meat (LoD: 0.06875 mg/kg), D-/L-lactic acid enantiomers in milk (LoD:3 mmol/mL) and carotenoid and cellulose degradation in greens (LoD: 0.071 mg/kg). By generating matrix-specific spectral barcodes, SkiNET-FoodSpec identifies early spoilage prior to visible or olfactory cues. This advance in biotechnology enables intelligent, point-of-need diagnostics for food quality assurance, offering a powerful tool to enhance food safety, reduce waste and support resilient, sustainable food systems.},
}

*Food Safety/methods
*Biosensing Techniques/methods
*Food Microbiology/methods
*Spectrum Analysis, Raman/methods
Animals
*Food Contamination/analysis
Meat/analysis/microbiology
Neural Networks, Computer
Milk/microbiology/chemistry
Food Quality

@article {pmid41816200,
year = {2026},
author = {Srinivasan, P and Xian, PTZ and Tan Shu Ya, E and Ang, Y},
title = {A new species of Oriental-endemic Thalerosphyrus Eaton, 1881 (Ephemeroptera, Heptageniidae) from the Chinese Yunnan Oriental-Palaearctic transition zone and insights into cryptic diversity in the T. flowersi complex.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {33-45},
pmid = {41816200},
issn = {1313-2989},
abstract = {The Ephemeropteran genus Thalerosphyrus Eaton, 1881 (Heptageniidae: Ecdyonurinae) is an Oriental-endemic genus hitherto comprising ten species, distributed from Sundaland to the Western Ghats of India and northeastern Indochina. Here, Thalerosphyrus lannaae sp. nov., belonging to the T. sinuosus group, is described from Yunnan Province (China), marking the northernmost record of the genus and extending its distribution into the Oriental-Palaearctic transitional zone. We also examined existing molecular data for T. flowersi, which revealed multiple deeply divergent lineages across India and Thailand, with the new species genetically closest to one of the Thai lineages. These findings highlight unrecognised cryptic diversity within the genus and underscore the need for taxonomic revision. An updated species key to Thalerosphyrus is provided. We discuss how larval preference for moderately cool, fast-flowing streams may explain the discovery of this tropically adapted Oriental-endemic genus in such high latitudes, and we explore the importance of transitional zones for aquatic insect diversity.},
}

@article {pmid41815967,
year = {2026},
author = {Thornval, NR and Lacy-Roberts, N and Rebelo, AR and Nilsson, P and Mourão, J and Gibson, C and Hasman, H and Hendriksen, RS},
title = {Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1755877},
pmid = {41815967},
issn = {2296-2565},
mesh = {*Nanopore Sequencing/methods/economics ; Humans ; *Whole Genome Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Whole-genome sequencing (WGS) is emerging as a valuable tool for antimicrobial resistance (AMR) surveillance, yet implementation in low-resource settings remains limited by prohibitory costs and infrastructure constraints. Oxford Nanopore Technologies (ONT) offers portable sequencing platforms that can overcome these barriers, but optimal workflows for bacterial WGS are not fully standardized. We evaluated the impact of multiplexing level (12-, 24-, and 36-plex) and input DNA amounts (50 ng, 100 ng, and 200 ng) on sequencing performance using ONT's Rapid Barcoding Kit v14 and R10.4.1 flow cells. Sequencing success was defined as assemblies with ≥30 × depth of coverage, complete MLST assignment, and full AMR gene detection. Across nine run configurations, sequencing success was highest for 12-plex runs (92-100% success) and 24-plex runs (79-82% success) when using ≤100 ng DNA input. 36-plex configurations and high DNA input markedly reduced performance (as low as 2.8% success). Lower DNA input (50 ng) did not compromise outcomes and mitigated negative effects of multiplexing. Cost analysis showed per-sample costs decreased with higher multiplexing, but excessive batching compromised data quality. These findings support practical ONT workflows for decentralized AMR surveillance, recommending ≤24 samples per flow cell and ≤100 ng DNA input to balance cost-effectiveness and sequencing success in low-resource laboratory settings.},
}

*Nanopore Sequencing/methods/economics
Humans
*Whole Genome Sequencing/methods
*Drug Resistance, Bacterial/genetics

@article {pmid41815890,
year = {2026},
author = {Song, P and Su, J and Kristine Vraa, CL and Gockert, M and Fjelstrup, S and Hager, H and Kjems, J},
title = {Optimizing C14120-based LNPs for in vitro and in vivo mRNA delivery.},
journal = {Molecular therapy. Nucleic acids},
volume = {37},
number = {1},
pages = {102866},
pmid = {41815890},
issn = {2162-2531},
abstract = {Lipid nanoparticles (LNPs) have proven to be an effective delivery system for RNA therapeutics. The chemical composition of LNPs determines their functional delivery efficiency and targeting properties, which vary between in vitro and in vivo contexts. Here, we have systematically characterized and compared 25 novel C14120-based LNP formulations for mRNA delivery in vitro and assessed in vivo mRNA expression and biodistribution using deep sequencing of DNA barcodes in a pooled LNP-mRNA library. In vitro experiments showed correlations of lipid composition with particle size and mRNA transfection efficiency in 4 different cell lines of distinct tissue and species origin. In vivo experiments employed a pooled LNP delivery of luciferase mRNA in combination with a multiplexed barcode system and identified LNP compositions with organ-specific targeting properties. Individual validation of three selected LNP candidates based on mRNA expression analysis confirmed high specificity for the lung-targeting candidate, lower specificity for the liver-targeting candidate, and inconclusive results for the spleen-targeting candidate. These findings identify LNP formulations with promising potential for in vitro and in vivo organ-targeted delivery.},
}

@article {pmid41814093,
year = {2026},
author = {Jozić, A and Le Roux, C and Kim, J and Berchel, M and Sahel, DK and Bodi, EK and Palumbo, M and Vasudevan, A and Murthy, NTV and Eygeris, Y and Gautam, M and Bloom, E and Barnes, AP and Jaffrès, PA and Sahay, G},
title = {In vivo endosomal escape assay identifies mechanisms for efficient hepatic LNP delivery.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41814093},
issn = {1546-1696},
support = {HR0011-25-9-0008//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; R01EY033423//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; R01CA270783//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 2R01HL146736-06A1//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Endosomal escape is a central barrier to efficient nucleic acid delivery by lipid nanoparticles (LNPs) and remains challenging to quantify in vivo. We report a library of branched ionizable phospholipids that markedly enhance messenger RNA delivery to the liver. The lead candidate BiP-20 outperformed the clinical benchmark LP01 by eightfold for CRISPR-Cas9 editing of the TTR gene at low dose with rapid pharmacokinetics. To quantify the endosomal escape kinetics of BiP-20, we used LysoTag mice, which allow immunoisolation of liver lysosomes, and our Lysosomal Barcoding method, finding that ~8% of BiP-20 LNPs reach the cytosol within 30 min of administration. Lysosomal proteomics revealed mechanistic regulators of escape and BiP-20-induced alterations in endosomal maturation and recycling pathways. Loss of Rab7, a mediator of late endosomal maturation, increased LNP escape. These findings provide a potent class of ionizable lipids for RNA delivery, a method to quantify endosomal escape in vivo, and mechanistic insight into the endolysosomal determinants of LNP trafficking.},
}

@article {pmid41809908,
year = {2026},
author = {Ngo, DM and Vu, LT and Nguyen, HD and Vu, TTT and Chu, MH},
title = {Dataset of chloroplast DNA sequences, ndhC-trnV, rpoA, trnK-matK, and trnK-rps16 regions of Platycodon grandiflorus (Jacq.) A.DC. from Vietnam.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112627},
pmid = {41809908},
issn = {2352-3409},
abstract = {Platycodon grandiflorus (Jacq.) A.DC., a member of the Campanulaceae family, is a well-known medicinal herb traditionally used to relieve coughs, promote expectoration, reduce inflammation, and protect the respiratory system. In recent years, numerous commercial products containing Platycodon extracts have been introduced to the market. However, during processing and distribution, the morphological and anatomical features of the raw material are often lost or altered, increasing the risk of misidentification or adulteration with morphologically similar species, thereby compromising product quality and therapeutic efficacy. Therefore, the application of DNA barcode markers is essential for accurate species identification and quality control of raw materials. This study presents a dataset of P. grandiflorus samples collected from natural populations and analyzes four chloroplast DNA regions (ndhC-trnV, rpoA, trnK-matK, and trnK-rps16) to support species identification. Phylogenetic analysis based on these sequences revealed that P. grandiflorus is closely related to, and clusters within, the Campanulaceae family, with high bootstrap support values (96-100%). These four chloroplast regions are proposed as potential DNA barcodes for the reliable identification and differentiation of P. grandiflorus from related species.},
}

@article {pmid41808340,
year = {2026},
author = {Senjarini, K and Hasanah, LNU and Wathon, S and Oktarianti, R and Labes, A},
title = {Malaria Vector Surveillance in Indonesia: COX1 Phylogenetic Reveals Monophyletic Clades and Cryptic Diversity in Anopheles Mosquitoes.},
journal = {Journal of vector borne diseases},
volume = {},
number = {},
pages = {},
doi = {10.4103/jvbd.jvbd_331_25},
pmid = {41808340},
issn = {0972-9062},
abstract = {BACKGROUND OBJECTIVES: Anopheles mosquitoes are key malaria vectors, their high diversity influences transmission competence. Accurate species identification is crucial for understanding malaria epidemiology and implementing effective vector control strategies. The COX1 gene is a widely used DNA barcoding marker for Anopheles due to its high mutation rate and species-specific variations. This study evaluates the consistency of morphological and molecular identification using COX1, analyzes phylogenetic relationships, and explores the implications of these findings for malaria vector control strategies.

METHODS: Anopheles mosquitoes were collected from Bangsring, Banyuwangi, and Hargowilis, Kulonprogo, Indonesia, two geographically distinct sites with a history of malaria outbreaks. Mosquitoes were collected using human landing catches. Identification was performed morphologically and confirmed by molecular analysis based on COX1 sequences. Phylogenetic tree and genetic distances were analyzed in MEGA11 using the Neighbor-Joining method with the Kimura-2 Parameter model.

RESULTS: Morphological and COX1-based identification were mostly consistent; however, specimens identified as Anopheles (An.) aconitus and An. minimus from Hargowilis were molecularly confirmed as An. flavirostris. Phylogenetic analysis revealed eight monophyletic clades with strong bootstrap support (≥99% for six), confirming species groupings. Genetic distance analysis showed An. minimus from Hargowilis clustering more closely with An. flavirostris than with An. minimus from other Asian regions. The dominance of An. sundaicus (68%) in Bangsring and An. flavirostris (13%) in Hargowilis highlights the need for targeted vector control strategies.

INTERPRETATION CONCLUSION: Misidentification of cryptic Anopheles species may lead to ineffective vector control in specific epidemiological settings. Integrating molecular tools into malaria surveillance can support more accurate species identification and contribute to informed disease prevention strategies.},
}

@article {pmid41806682,
year = {2026},
author = {Park, SH and Na, JY and Kim, YR and Lee, H and Lee, JH and Yoon, JH and Jang, JW and Kim, MJ},
title = {Validating the Efficacy of archival microclimate proxies for indoor postmortem interval Estimation: A case study using Boettcherisca peregrina (Robineau-Desvoidy, 1830).},
journal = {Legal medicine (Tokyo, Japan)},
volume = {82},
number = {},
pages = {102831},
doi = {10.1016/j.legalmed.2026.102831},
pmid = {41806682},
issn = {1873-4162},
abstract = {Indoor death scenes challenge defensible estimation of the minimum postmortem interval (PMImin) because colonization delay, refrigeration, and poorly characterized microclimates often undermine transparency and reproducibility in medicolegal contexts. We report an indoor death investigation from Busan, Republic of Korea, in which post-feeding third-instar larvae of Boettcherisca peregrina (Diptera: Sarcophagidae) provided the principal entomological evidence. Species identity was confirmed by morphology and COI barcoding. Developmental age was estimated using an accumulated degree-hours (ADH)-only framework parameterized with species-specific constants (developmental zero, D0 = 10.87 °C). Larval thermal exposure was reconstructed using an archival indoor May temperature proxy (mean = 23.2 °C), with a ± 1 °C sensitivity envelope propagated across all calculations to reflect plausible room-scale variability. The body was removed from the scene on 16 May 2025 (∼15:00) and stored at ≤ 4 °C until autopsy on 19 May 2025 (09:00), arresting further development; thus, larval age refers exclusively to the pre-removal interval. Back-calculation from wandering-phase thresholds yielded a PMImin of 3.1-8.3 days across the ± 1 °C range. Expressed as calendar bounds, larviposition was estimated between 08 May 2025 (∼21:00) and 13 May 2025 (∼03:00 KST), with a nominal estimate of 09 May (∼12:00) to 11 May (∼01:00 KST) at 23.2 °C. These estimates are coherent with independent administrative anchors and the documented discovery-transfer-autopsy timeline. This report provides a reproducible workflow for indoor PMImin estimation that explicitly separates pre-removal development from refrigeration arrest and propagates indoor thermal uncertainty, thereby improving transparency and courtroom defensibility in constrained indoor scenes.},
}

@article {pmid41806198,
year = {2026},
author = {Iwahashi, N and Noguchi, T and Sakai, K and Yahata, T and Nishioka, K and Fujino, M and Takeda, S and Suzuki, N and Nishio, K and Ino, K},
title = {Comprehensive circulating tumor DNA mutation profiling via CAPP-Seq liquid biopsy for cervical cancer.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {41806198},
issn = {1437-7772},
support = {20K18228//Japan Society for the Promotion of Science/ ; 23K08894//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Liquid biopsy using circulating tumor DNA (ctDNA) is a minimally invasive approach for detecting tumor-associated genomic alterations. Although ctDNA analysis has been widely explored in solid tumors, its application to cervical cancer remains limited. Cancer personalized profiling by deep sequencing (CAPP-Seq) enables sensitive ctDNA profiling via molecular barcoding and digital error suppression.

METHODS: We evaluated the feasibility of ctDNA-based mutation profiling in cervical cancer using the CAPP-Seq platform by analyzing plasma samples from 38 patients.

RESULTS: The cohort included three patients with stage I disease, nine with stage II, 19 with stage III, and seven with stage IV. Somatic gene alterations were detected in 33 of the 38 cases (87%), including squamous cell carcinoma (27/29 [93%]) and adenocarcinoma (6/9 [67%]). Non-synonymous mutations were identified in 23 patients (59%), with PIK3CA being the most frequently mutated gene [13/38 (34%)]. Copy number gains of EGFR, MET, and ERBB2 were observed in 24%, 11%, and 5% of cases, respectively. The median blood tumor mutational burden was 17.7 mutations/Mb, and 50% of the patients exhibited a hypermutated phenotype. In a subset of four patients who received concurrent chemoradiotherapy, longitudinal changes in ctDNA mutation profiles between pre- and post-treatment samples were associated with treatment response.

CONCLUSIONS: This study demonstrates the feasibility of ctDNA-based mutation profiling using CAPP-Seq in cervical cancer, with a high detection rate of tumor-associated genomic alterations across histological subtypes. ctDNA analysis may represent a minimally invasive approach for the molecular characterization and disease monitoring of cervical cancer.},
}

@article {pmid41806065,
year = {2026},
author = {Guerretti, V and Abd-Ellatif, MAA and Vangone, R and Cucolo, C and De Vivo, MM and Moustafa, AA and Guerriero, G and Mansour, SR},
title = {Bird diversity and health status of bioindicator species (Coturnix coturnix, Horsfield, 1821) in Egypt's Manzala Lagoon: seasonal resilience monitoring.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41806065},
issn = {1573-2959},
mesh = {Animals ; Egypt ; *Biodiversity ; *Environmental Monitoring ; Wetlands ; Seasons ; *Birds/physiology ; DNA Damage ; },
abstract = {Manzala Lagoon, the largest coastal wetland of Egypt, lies within the Nile Delta and serves as an essential sanctuary for both resident and migratory birds. Despite its importance for regional biodiversity, the ecosystem faces significant anthropogenic pressures, with recent dredging activities constituting a major disturbance. This study aimed to evaluate dredging impacts on bird diversity and environmental health in the Ashtoum El-Gamil Protected Area. Seasonal monitoring in 2024, combining camera-based morphological identification with molecular barcoding of feathers (n = 13; cytochrome oxidase 1 gene), documented 123 species across 11 orders and 23 families, with 51 species consistently observed year-round. Health assessments in the endemic Coturnix coturnix (common quail) were conducted by measuring genotoxic damage, DNA repair capacity (via poly(ADP)-ribosylation), and total antioxidant capacity (TAC) in the gut, liver, and gonads. Results revealed reduced DNA recovery, elevated antioxidant capacity, and a prominent 40 kDa PARP immunoreactive band, particularly in gut and gonads. These oxidative stress indicators were independent of low heavy metal loads, implicating factors like rising temperatures may be the primary drivers. These findings highlight dredging's limited immediate effects on species diversity but underscore subtle health risks, advocating sustained, long-term monitoring and targeted management to safeguard wetland biodiversity.},
}

Animals
Egypt
*Biodiversity
*Environmental Monitoring
Wetlands
Seasons
*Birds/physiology
DNA Damage

@article {pmid41805294,
year = {2026},
author = {Anfang, M and Yahya, RH and Caldararu, O and Ben Yaakov, S and Landau, U and Berman, A and Hu, Y and Belew, ZM and Crocoll, C and Xu, D and Nour-Eldin, HH and Mayrose, I and Shani, E},
title = {Targeting redundant gene families: A multiplexed, tissue-specific CRISPR toolbox for Arabidopsis genetic screens.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117055},
doi = {10.1016/j.celrep.2026.117055},
pmid = {41805294},
issn = {2211-1247},
abstract = {Genome-scale targeted CRISPR libraries for forward genetic screens in plants are powerful tools for functional analysis, but they suffer from limited spatial control, single sgRNA design, and poor handling of genetic redundancy. We develop multiplexed CRISPR libraries in which each construct contains two sgRNAs that simultaneously target multiple members of a gene family. The libraries can also function at the cell-type-specific and tissue levels. A double-barcoding strategy enables efficient tracking and identification of sgRNA combinations at the plant level without individually sequencing each line. Using this platform, we generate over 1,000 Arabidopsis lines that express sgRNAs targeting 707 transporter genes across 114 gene families involved in nutrient uptake. The multiplexed design increases gene coverage and editing efficiency, underscoring its improved targeting capability to reveal hidden phenotypes. This toolbox provides a scalable resource for multi-targeted genome editing and spatially precise forward genetic screens in plants.},
}

@article {pmid41688672,
year = {2026},
author = {Di Batista Borko, Š and Grimm, J and Hahn, C and Takács, P and Greilberger, AM and Koblmüller, S and Sefc, KM},
title = {Habitat preferences and genetic diversity of the amphipod Gammarus roeselii across the Eastern Alps and western Pannonian Basin.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41688672},
issn = {2045-2322},
support = {FFT NP FTA, NP2022-II3/2022//Sustainable Development and Technologies National Program of the Hungarian Academy of Sciences/ ; C321069//Austrian Biodiversity Fund of the Federal Ministry of Agriculture and Forestry, Climate and Environmental Protection, Regions and Water Management of the Republic of Austria/ ; },
abstract = {UNLABELLED: Freshwater amphipods often exhibit cryptic diversity and are undergoing range shifts driven by environmental changes. Gammarus roeselii, a species inhabiting streams, rivers and lakes across Europe, diversified into ancient genetic lineages in the Balkan Peninsula and the Pannonian Basin, with only one lineage colonizing Central and Western Europe after the ice ages. We investigated the distribution and genetic diversity of G. roeselii by sampling over 1,000 sites across the eastern Alpine region and the Western Pannonian Basin. Cytochrome oxidase I barcoding assigned all sequenced G. roeselii (528 individuals from 174 sites) to the Central-Western European lineage. The occurrence of G. roeselii was associated with low elevation, high summer temperature and gentle stream and river slopes and was biased towards downstream reaches and rivers with large drainage sizes. Its distribution partially overlapped with G. fossarum, which predominates in cooler, faster-flowing streams. Species distribution modelling under future climate scenarios predicted a range expansion of G. roeselii into current G. fossarum habitat. Genetic diversity patterns are consistent with longstanding stable populations in the Southwestern Pannonian Basin, a post-glacial range expansion across alpine forelands, and recent colonization of some alpine valleys.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-39958-7.},
}

@article {pmid41805176,
year = {2026},
author = {Helsmoortel, M and Sentausa, E and Villain, A and Tran, V-D and Santiago-Allexant, E and Beaulieu, C and Hesketh, A and Abi-Ghanem, J and Leissner, P and Saliou, A},
title = {Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0285625},
doi = {10.1128/spectrum.02856-25},
pmid = {41805176},
issn = {2165-0497},
abstract = {The development of long-read sequencing technologies has enabled the analysis of extended nucleic acid sequences. These methods have proven their strength through their capacity to generate long reads, facilitating the analysis of complex genomic regions and rearrangements. Oxford Nanopore Technologies (ONT) offers a rapid and portable system that brings sequencing to the field. Although this is a great advantage for clinical settings, applications of long-read sequencing in this context have been limited by the high error rates reported for these methods. Here, we report an adaptation of an amplicon sequencing approach combined with unique molecular identifiers. We applied this method to whole-genome sequencing using mock community samples and human blood cultures spiked with common bloodstream infection pathogens. Our results showed a total error rate of <0.1% with V9 chemistry, which was further reduced by <0.05% when using the V14 chemistry. Our results also highlight the improvements of the V14 chemistry on the standard ONT ligation protocol and the importance of the basecalling tool for sequencing accuracy.IMPORTANCERecent advances in genome sequencing have greatly improved our ability to study microbes and detect infections. One such technology, Oxford Nanopore Technologies (ONT), can read long stretches of nucleic acids. ONT is also portable and can sequence in real time, making it useful in clinical settings. However, ONT accuracy is known to be lower than traditional short-read methods, limiting its widespread use. Fortunately, many strategies have emerged to overcome this limitation: better ONT chemistry, better basecaller, and hybrid approaches combining ONT with highly accurate short reads. Another promising method uses molecular barcodes or "Unique Molecular Identifiers" (UMIs) to make long reads at high accuracy, reaching accuracy levels similar to the existing short-read technologies. In our study, we optimized this UMI-based method and successfully applied it to human blood samples spiked with common infection-causing bacteria. The results showed a significant drop in ONT error rate, suggesting that this approach could make ONT a reliable tool for diagnosing infections and analyzing microbial DNA in clinical samples.},
}

@article {pmid41803893,
year = {2026},
author = {Andrus, PS and Han, QC and Yang, LM and Wade, CM and Qin, ZQ and Kassegne, K and Wu, XN and Guo, YH and Zhou, XN},
title = {Population genetic diversity of invasive Pomacea snails and surveillance of Angiostrongylus cantonensis in Shanghai, East China.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07224-w},
pmid = {41803893},
issn = {1756-3305},
support = {No. W2533202//National Natural Science Foundation of China/ ; TF2024012//Technology Innovation Support Program, NIPD, China CDC/ ; WSJK2024MS226//Hainan Province Health Technology Innovation Joint Project/ ; 2021YFC2300800//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Golden apple snails (Gastropoda: Ampullariidae: Pomacea) were introduced into China in the 1980s for aquaculture and have since become widespread agricultural pests across East Asia. In addition to their invasive impact, they are a key intermediate host of the rat lungworm Angiostrongylus cantonensis (Secernentea: Angiostrongylidae) in China, the causative agent of eosinophilic meningitis in humans.

METHODS: We conducted a malacological survey of 55 freshwater sites across Shanghai and neighboring East China provinces to assess Pomacea distribution, genetic diversity, and A. cantonensis infection status. A total of 700 Pomacea snails were examined for A. cantonensis using traditional lung microscopy and molecular xenomonitoring (PCR and LAMP). Mitochondrial COI barcoding was performed on 200 individuals from 20 high-density sites to assess species composition and genetic diversity.

RESULTS: Pomacea snails were found at 81.8% (45/55) of sites surveyed. No A. cantonensis infections were detected by microscopy or molecular assays. Genetic analyzes revealed three Pomacea species (P. canaliculata, P. maculata, and P. occulta) and nine distinct COI haplotypes. Pomacea canaliculata was the most common and genetically diverse species, with four unique haplotypes (H5-H8) occurring only in Shanghai, indicative of recent introductions. Overall, populations showed moderate haplotype diversity (Hd = 0.73) and population structure (FST = 0.24).

CONCLUSIONS: Although no A. cantonensis infections were detected in the snails examined in this survey, these negative findings do not preclude the possibility of low-prevalence or newly emerging infections. The wide distribution and high genetic diversity of Pomacea populations across Shanghai and East China highlight that suitable hosts are already well-established, emphasizing the ongoing risk of parasite introduction and spread into currently nonendemic regions. Continued molecular surveillance, public awareness, and strengthened biosecurity measures remain essential to effectively manage invasive snail populations and mitigate future public health threats.},
}

@article {pmid41801891,
year = {2026},
author = {Schoenefuss, P and Whatmore, P and Windell, C and Baker, AM and Hurwood, DA},
title = {Non-destructive environmental DNA extracted from owl pellet contents: A valuable tool for monitoring mammalian species richness.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344097},
pmid = {41801891},
issn = {1932-6203},
mesh = {Animals ; *Strigiformes/genetics ; *Biodiversity ; *DNA, Environmental/isolation & purification/genetics ; DNA Barcoding, Taxonomic ; *Mammals/genetics/classification ; Queensland ; },
abstract = {Environmental DNA (eDNA) offers valuable presence/absence data for populations and has been widely used in comprehensive biodiversity assessments. However, applying eDNA in terrestrial environments poses unique challenges, particularly in obtaining samples that are representative of ecological communities. eDNA extracted from top-predator dietary samples can be an effective sampling source in monitoring prey populations. In this study, we tested a novel, non-destructive protocol to assess the efficacy of eDNA from barn owl (Tyto javanica delicatula) pellets as a tool for monitoring small mammal communities in an arid environment. We assessed the species composition and abundance of small mammals from owl pellets collected in the Simpson Desert in far western Queensland, Australia, using a three-tiered approach. We extracted DNA from 50 owl pellets and targeted a 16S mini-barcode for metabarcoding. We compared species detection via genetic analysis with that of morphological analysis, and finally with historical small mammal trapping data. The DNA extraction method presented here resulted in full preservation of prey bones and fur material for museum archival. eDNA detected four mammal species that were not detected via morphological pellet analysis, three of which are significant detections that had not been observed at this location before but were expected to occur based on likely distribution ranges. However, a key limitation of the eDNA approach demonstrated in this study, is that taxonomic identification was constrained by the completeness of reference databases, which can result in false negatives or ambiguous assignments. The results of the present study demonstrate that the specificity of an eDNA approach can offer advantages compared with morphological identification of mammalian remains from owl pellets, and that genetic owl pellet analysis may be particularly useful in full vertebrate diversity assessments that include reptiles, birds and amphibians that are unidentifiable from skeletal remains.},
}

Animals
*Strigiformes/genetics
*Biodiversity
*DNA, Environmental/isolation & purification/genetics
DNA Barcoding, Taxonomic
*Mammals/genetics/classification
Queensland

@article {pmid41800390,
year = {2026},
author = {Pho, HTT and Nguyen, NTT and Sy, TD and Nguyen, QH and Chu, MH},
title = {Dataset on intergenic spacer sequences of the chloroplast genome and potential DNA barcodes of Adinandra glischroloma Hand.-Mazz. from Vietnam.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112606},
pmid = {41800390},
issn = {2352-3409},
abstract = {Adinandra glischroloma Hand.-Mazz. is a woody species of the genus Adinandra (Pentaphylacaceae), a taxonomic group in which species delimitation is often complicated by high morphological similarity. Moreover, genetic information for A. glischroloma is still scarce, limiting molecular identification and comparative studies. This article reports a dataset of nucleotide sequences from five chloroplast intergenic regions, namely rps15-ycf1, ndhF-rpl32, rpl32-trnL, accD-psaI, and petA-psbJ. These sequences were extracted from the chloroplast genome of A. glischroloma collected in Y Ty commune, Bat Xat district, Lao Cai province, Vietnam. The dataset includes voucher specimen images (AGYT03), the nucleotide sequences, fragment lengths, sampling metadata, and phylogenetic trees reconstructed separately for each intergenic region to facilitate phylogenetic interpretation within the order Ericales. These data provide a useful molecular resource for species identification, phylogenetic inference, and the evaluation of candidate DNA barcodes in Adinandra and related taxa.},
}

@article {pmid41800269,
year = {2026},
author = {Cohen, OR and Orange Kedem, R and Leites, L and Parizat, A and Jeffet, J and Laufer, L and Stern, S and Ebenstein, Y and Shechtman, Y},
title = {Compact Spectral Encoding Microscopy by Terrace Grating Optics.},
journal = {ACS photonics},
volume = {13},
number = {5},
pages = {1407-1416},
pmid = {41800269},
issn = {2330-4022},
abstract = {Spectral information is essential in microscopy, yet many multispectral imaging solutions require increased optical complexity or restrict the spectrum to a few discrete bands. In this work we introduce the Terrace grating optics family: flat, 3D-printable elements that provide continuous spectral encoding, as a plug-and-play add-on component to standard microscopes. The Terrace design preserves the illumination path in widefield operation and integrates trivially with other microscopy phase masks. We introduce two variants: a Single-order Terrace that concentrates energy into one diffraction order for high signal-to-noise ratio, and a Dual-order Terrace that adds a wavelength-independent reference spot, enabling robust color decoding. Using a Fourier-optics model, we show that the wavelength displacement is linearly controlled by the Terrace step-width and refractive-index mismatch. We validate the approach in two settings: snapshot decoding of four-color mRNA barcodes and multicolor NeuroPAL worm imaging with a single camera exposure and instantaneous color readout. Furthermore, we demonstrate continuous spectral and depth encoding masks yielding simultaneous depth and color readout via PSF shape, which remains compact and efficient. Terrace gratings thus offer a practical alternative to prisms and blazed gratings, enabling continuous multispectral encoding and straightforward integration with conventional microscopes.},
}

@article {pmid41800140,
year = {2026},
author = {Kasymova, U and Ulug, A},
title = {Genetic differentiation of morphologically similar polyploid wheat species.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20723},
pmid = {41800140},
issn = {2167-8359},
mesh = {*Triticum/genetics/classification ; *Polyploidy ; DNA, Plant/genetics ; Genetic Markers ; },
abstract = {BACKGROUND: Wheat is a globally important polyploid crop, with hexaploid bread wheat (Triticum aestivum L.) and tetraploid durum wheat (T. turgidum subsp. durum (Desf.) Husn.) as its main cultivated forms. Despite distinct end-use properties, these species are morphologically similar, making their identification difficult. Traditional phenotypic approaches often fail to resolve closely related polyploid wheats, emphasizing the need for a reliable molecular diagnostic and wheat barcoding strategy.

METHOD: This study developed and validated a multilocus molecular diagnostic framework for the discrimination of polyploid wheat species. The approach integrates plastid (rbcL, matK), nuclear ribosomal (ITS2, IGS), and nuclear-coding markers (Glu-1 and XDuPw167), all amplified using the Polymerase Chain Reaction. Validation was performed using ten experimental samples and 203 reference sequences retrieved from the NCBI GenBank database. We developed and validated a multilocus molecular diagnostic method for the reliable discrimination of wheat species.

RESULTS: Plastid loci showed limited variation, whereas the IGS region contained a diagnostic 71 bp insertion linked to the D genome, clearly distinguishing hexaploids from tetraploids. The Glu-1 and XDuPw167 loci exhibited genome-specific polymorphisms that further differentiated the two species. The multilocus diagnostic method achieved over 95% amplification success and consistent sequence profiles across replicates, confirming its accuracy and reproducibility.

CONCLUSIONS: The proposed molecular diagnostic method provides a reproducible, cost-effective, and high-resolution molecular diagnostic tool for reliable wheat species identification. By combining genome-specific nuclear and expressed sequence tag-simple sequence repeat (EST-SSR) markers, this approach establishes a robust and scalable system applicable to species authentication, seed purity testing, germplasm characterization, and genetic resource management.},
}

*Triticum/genetics/classification
*Polyploidy
DNA, Plant/genetics
Genetic Markers