@article {pmid41541251,
year = {2025},
author = {Wu, Y and Liu, R and Wang, WJ and Li, DZ and Burgess, KS and Yu, WB and Wang, H},
title = {High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites.},
journal = {Plant diversity},
volume = {47},
number = {6},
pages = {920-930},
pmid = {41541251},
issn = {2468-2659},
abstract = {Complete plastid genomes have been proposed as potential "super-barcodes" for plant identification and delineation, particularly in cases where standard DNA barcodes may be insufficient. However, few studies have systematically addressed how taxonomic complexity, especially in rapidly radiating lineages with intricate evolutionary histories, might influence the efficacy of plastome-scale barcodes. Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains, and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus. Therefore, Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity. In this study, we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes. Our results revealed that the traditional standard barcode combination (nrITS + matK + rbcL + trnH-psbA) achieved the highest discrimination rates (81.25%), closely followed by the plastid large single copy (LSC) region (80.21%), then by full plastome, the supermatrix of protein-coding genes, and hypervariable regions (79.17%). Notably, the matK and ycf1 gene alone could discriminate 78.13% of species. Key determinants of species discrimination by integrating alignment length (AL) and the proportion of parsimony-informative sites (PPIS), as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity. Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes, this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis' specific biological habits and potentially reflecting unique evolutionary patterns in the plastid genome.},
}

@article {pmid41540123,
year = {2026},
author = {Enninful, A and Zhang, Z and Klymyshyn, D and Ingalls, M and Yang, M and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Lu, Y and Bao, S and Deng, S and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R},
title = {Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41540123},
issn = {1548-7105},
support = {U54CA274509//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA245313//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54CA268083//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; UH3CA257393//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; RF1MH128876//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54AG079759//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54AG076043//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; RM1MH132648//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01CA294514//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2245575//Center for Selective C-H Functionalization, National Science Foundation/ ; 2245575//Center for Selective C-H Functionalization, National Science Foundation/ ; 2345215//National Science Foundation (NSF)/ ; 2245575//National Science Foundation (NSF)/ ; },
abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can profoundly advance our understanding of cellular heterogeneity and function. Here we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multimodal spatial omics approach combining sequencing-based spatial transcriptomics and multiplexed protein imaging on the same section, enabling both single-cell-resolution cell typing and transcriptome-wide interrogation of biological pathways. DBiTplus utilizes spatial barcoding and RNase H-mediated cDNA retrieval, preserving tissue architecture for multiplexed protein imaging. We developed computational pipelines to integrate these modalities, allowing imaging-guided deconvolution to generate single-cell-resolved spatial transcriptome atlases. We demonstrate DBiTplus across diverse samples including frozen mouse embryos, and formalin-fixed paraffin-embedded human lymph nodes and lymphoma tissues, highlighting its compatibility with challenging clinical specimens. DBiTplus uncovered mechanisms of lymphomagenesis, progression and transformation in human lymphomas. Thus, DBiTplus is a unified workflow for spatially resolved single-cell atlasing and unbiased exploration of biological mechanisms in a cell-by-cell manner at transcriptome scale.},
}

@article {pmid41539929,
year = {2026},
author = {Li, X and Zheng, J and Fang, X and Gao, W and Chen, H and Liu, Z and Li, C and Zhang, R},
title = {Multiple microRNAs analysis based on DNAzyme cascade DNA fiber barcodes for cell typing.},
journal = {Biosensors & bioelectronics},
volume = {},
number = {},
pages = {118383},
doi = {10.1016/j.bios.2026.118383},
pmid = {41539929},
issn = {1873-4235},
abstract = {Accurate tumor subtyping through multiplex miRNA profiling is critical for precision medicine but remains challenging due to limitations in current methods, including cross-reactivity, cost, and stability. Herein, we present a DNAzyme-powered DNA fiber barcode platform that combines G-quadruplex (G4)/hemin catalysis, miRNA-responsive displacement, and polydopamine (PDA)-mediated fluorescence modulation for sensitive and specific miRNA detection. The system operates via a target-dependent "switch": in the absence of target miRNAs, G4/hemin DNAzymes catalyze dopamine (DA) oxidation into PDA that efficiently quench fluorescence through Förster resonance energy transfer (FRET); when target miRNAs are present, they competitively binding to the capture strands on DNA fibers with higher affinity, displacing the G4 structures, inhibiting DNAzyme formation and preserving the fluorescence signal, with fluorescence intensity showing a positive correlation with target concentration. This mechanism enables dual qualitative and quantitative analysis with a broad linear range (50 pM-100 nM) and low detection limits (5.50 pM). Key advantages include stable, tunable G4/hemin transduction, enhanced kinetics and signal-to-noise through synergistic displacement-quenching, and multicolor barcoding for one-pot multiplex miRNA detection. Validated against qPCR with high concordance, this platform overcomes existing technical barriers to enable robust miRNA-based cell typing classification and precision diagnostics.},
}

@article {pmid41539305,
year = {2026},
author = {Kurochkin, I and Altman, AR and Caiado, I and Pértiga-Cabral, D and Halitzki, E and Minaeva, M and Zimmermannová, O and Henriques-Oliveira, L and Klein, D and Nair, M and Oliveira, D and Cajal, LR and Knittel, R and Feick, C and Ringnér, M and Martin, M and Cirovic, B and Pires, CF and Rosa, FF and Sitnicka, E and Theis, FJ and Pereira, CF},
title = {A combinatorial transcription factor screening platform for immune cell reprogramming.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101457},
doi = {10.1016/j.cels.2025.101457},
pmid = {41539305},
issn = {2405-4720},
abstract = {Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode's discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.},
}

@article {pmid41538080,
year = {2026},
author = {Juhász, A and Makaula, P and Cunningham, LJ and Nkolokosa, C and Archer, J and Jones, S and Namacha, G and Chammudzi, P and Mainga, B and Lally, D and Kayuni, SA and LaCourse, EJ and O'Ferrall, AM and Musaya, J and Stothard, JR},
title = {One Health insights into local transmission of zoonotic Schistosoma mattheei in southern Malawi.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1941},
pages = {},
doi = {10.1098/rstb.2024.0519},
pmid = {41538080},
issn = {1471-2970},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Malawi/epidemiology ; *Schistosoma/genetics/physiology ; *Schistosomiasis/transmission/veterinary/parasitology/epidemiology ; Cattle ; Humans ; *Zoonoses/transmission/parasitology/epidemiology ; *Cattle Diseases/parasitology/transmission/epidemiology ; Snails/parasitology ; Goats ; *One Health ; *Goat Diseases/parasitology/transmission/epidemiology ; Praziquantel/therapeutic use ; Prevalence ; Haplotypes ; },
abstract = {Schistosoma mattheei is a zoonotic schistosome species in central and southern Africa and is of increasing public health concern in southern Malawi. To gain insight into its local transmission, we investigated the biology of Schistosoma mattheei in southern Malawi, integrating epidemiological, environmental and genetic data within a One Health framework. Cattle, goats, humans and snails were surveyed, with DNA barcoding revealing nine mitochondrial S. mattheei haplotypes. Two haplotypes were shared across species, indicating cross-host transmission. Infected snails were detected year-round, with seasonal variation linked to vegetation cover (Normalized Difference Vegetation Index (NDVI)). Praziquantel (40 mg kg-1) treatment in selected cattle herds reduced infection prevalence over 12 weeks. These findings highlight the zoonotic potential of S. mattheei and the need for integrated control strategies. This article is part of the Royal Society Science+ meeting issue 'Parasite evolution and impact in action: exploring the importance and control of hybrid schistosomes in Africa and beyond'.},
}

Animals
Malawi/epidemiology
*Schistosoma/genetics/physiology
*Schistosomiasis/transmission/veterinary/parasitology/epidemiology
Cattle
Humans
*Zoonoses/transmission/parasitology/epidemiology
*Cattle Diseases/parasitology/transmission/epidemiology
Snails/parasitology
Goats
*One Health
*Goat Diseases/parasitology/transmission/epidemiology
Praziquantel/therapeutic use
Prevalence
Haplotypes

@article {pmid41538056,
year = {2026},
author = {Rehman, U and Sarfraz, M and Bibi, F and Noor, A and Ullah, M and Tarafder, E and Shinwari, ZK},
title = {DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {2},
pages = {40},
pmid = {41538056},
issn = {1572-9699},
mesh = {*DNA Barcoding, Taxonomic/methods/trends ; *Phylogeny ; *Agaricales/genetics/classification ; Genomics/methods ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Metabolomics ; },
abstract = {Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.},
}

*DNA Barcoding, Taxonomic/methods/trends
*Phylogeny
*Agaricales/genetics/classification
Genomics/methods
Genome, Fungal
High-Throughput Nucleotide Sequencing
Metabolomics

@article {pmid41536623,
year = {2026},
author = {Noenrimnong, C and Suttinun, C and Tungpairojwong, N and Boonsoong, B},
title = {Taxonomic insights into the diversity of Cloeon Leach, 1815 (Ephemeroptera, Baetidae) in Thailand.},
journal = {ZooKeys},
volume = {1266},
number = {},
pages = {1-39},
pmid = {41536623},
issn = {1313-2989},
abstract = {Four species of the genus Cloeon have previously been reported in Thailand: C. bicolor Kimmins, 1947, C. bimaculatum Eaton, 1885, C. harveyi (Kimmins, 1947) and C. marginale Hagen, 1858. However, since 1961, no systematic studies or investigations of this genus have been conducted in that country. This study reviews Cloeon Leach, 1815 in Thailand and investigates five species-C. bengalense, C. bicolor, C. harveyi, C. rubellum, and C. viridulum-based on morphological, molecular, and taxonomic analyses. Three species (C. bengalense, C. rubellum, and C. viridulum) are recorded for the first time in Thailand, and C. rubellum is described for the first time as a mature nymph and adult female. Additionally, the egg chorionic surface of all five species is described for the first time, and its use is demonstrated for species identification in Thailand. A key to the species of Cloeon in Thailand is provided based on the egg structure, mature nymph, and adult female and male.},
}

@article {pmid41536601,
year = {2025},
author = {Schmidt-Stohn, G and Bellanger, JM and Brandrud, TE and Bidaud, A and Oertel, B and Saar, G and Ballarà, J and Carteret, X and Reyes García, JDD and Dondl, M and Ploch, S and Thines, M and Dima, B},
title = {The big brown Telamonia unlocked: four new species in Cortinarius section Bovini (Agaricales, Basidiomycota) and a revised taxonomy of bovinoid Cortinarii.},
journal = {Persoonia},
volume = {55},
number = {},
pages = {1-57},
pmid = {41536601},
issn = {0031-5850},
abstract = {In this study, we describe four species of Cortinarius subgen. Telamonia sect. Bovini as new to science: Cortinarius acutipes, C. cepiformis, C. schistaceus and C. sericeovelatus. We also provide updated descriptions and synonymies for several known species in the section, including C. pachypus (formerly C. terribilis and C. pseudobulbosus), C. sordescens (neotypified here), C. turgidulus and C. urbis-veteris, as well as for C. hillieri, here supported as a genuine Bovini member. In addition, through DNA sequencing of its holotype, we fix here the interpretation of C. aprinus, the iconic member of a difficult group of large, fleshy, grey brown Telamonia species often referred to as Aprini or Sordescentes. We also update the taxonomy of C. diffractosuavis (sect. Sordescentes) and C. testaceomicaceus (sect. Exsulares), to yield a most comprehensive overview of phylogenetically supported "bovinoid" species from deciduous forests on calcareous soils of Europe. The habitat and distribution of all treated species are presented, and a tentative identification key is also proposed. Citation: Schmidt-Stohn G, Bellanger J-M, Brandrud TE, Bidaud A, Oertel B, Saar G, Ballarà J, Carteret X, Reyes García JdD, Dondl B, Ploch S, Thines M, Dima B (2025). The big brown Telamonia unlocked: four new species in Cortinarius section Bovini (Agaricales, Basidiomycota) and a revised taxonomy of bovinoid Cortinarii. Persoonia 55: 1-57. doi: 10.3114/persoonia.2025.55.01.},
}

@article {pmid41535733,
year = {2026},
author = {Wang, Y and Liu, H and Zhao, D and Wang, S and Wang, J and Chi, X and Zhang, C and Wang, T and Lyu, C and Kang, C and Sun, J and Guo, L and Huang, L},
title = {Assessment of suitable cultivation area for Paris polyphylla var. chinensis and var. yunnanensis under anthropogenic disturbance based on ensemble modeling and germplasm identification.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-08010-7},
pmid = {41535733},
issn = {1471-2229},
support = {2023YFC3503801//National Key Research and Development Program of China/ ; },
}

@article {pmid41534951,
year = {2026},
author = {Lichtner, V and Irnazarow, A and Bush, S and Dowding, D and Elphick, P and Franklin, BD and Jani, YH and Songhurst, M},
title = {Complexities and capabilities of Scan4Safety in NHS hospitals: a qualitative study of a national demonstrator site.},
journal = {BMJ health & care informatics},
volume = {33},
number = {1},
pages = {},
doi = {10.1136/bmjhci-2024-101366},
pmid = {41534951},
issn = {2632-1009},
mesh = {Qualitative Research ; Humans ; *State Medicine ; Interviews as Topic ; United Kingdom ; *Hospitals ; Patient Safety ; },
abstract = {OBJECTIVES: Data standards and barcoding technologies are implemented in hospitals to uniquely identify objects, people and locations; streamline the management of supplies and inventories; improve efficiency; reduce waste and improve patient safety and quality of care. This study examined the implementation of the Scan4Safety programme at one NHS demonstrator site to understand the hospital experience of adopting these standards, barcoding and related technologies.

METHODS: Exploratory case study design, informed by information infrastructure theory, at one Scan4Safety demonstrator site. Semi-structured interviews were conducted with internal and external stakeholders (n=19), and 67 documents related to the Scan4Safety programme were identified. Interview transcripts and documents underwent thematic analysis.

RESULTS: Key enablers for Scan4Safety included allocated funding, government role/regulation, executive buy-in/wide stakeholder involvement, patient focus, agile/adaptive approach and data linkage. Challenges were both internal and external, mainly pertaining to data quality, work-as-done and trade-offs. Mechanisms of anticipated positive outcomes and potential risks were also identified.

DISCUSSION: Scan4Safety benefits are delivered through tracking and tracing capabilities, and automating data capture, alerts and data linkages. For traceability of devices, the benefits depend on the extent to which items are tracked in inventory and consistent barcode scanning at the point of care.

CONCLUSIONS: Linked standards for identification of patients, products, places and procedures, across supplies and hospital processes, constitute a wide-ranging information infrastructure with the potential for significant value to patients and the whole health system.},
}

Qualitative Research
Humans
*State Medicine
Interviews as Topic
United Kingdom
*Hospitals
Patient Safety

@article {pmid41532186,
year = {2026},
author = {Mur, M and Kavčič, A and Jagodič, U and Podlipec, R and Humar, M},
title = {Two-Photon 3D Printing of Functional Microstructures Inside Living Cells.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e19286},
doi = {10.1002/adma.202519286},
pmid = {41532186},
issn = {1521-4095},
support = {851143//HORIZON EUROPE European Research Council/ ; N1-0362//The Slovenian Research and Innovation Agency/ ; P1-0099//The Slovenian Research and Innovation Agency/ ; },
abstract = {3D printing is transforming manufacturing and biomedicine, yet it has not been demonstrated inside living cells. Additionally, there is no method to deliver micron-scale, free-standing solid microstructures directly into the cytosol of non-phagocytic cells. Here, both of these challenges are addressed by fabricating custom-shaped polymeric microstructures directly inside living cells using two-photon polymerization. A bio-compatible photoresist is injected into cells and selectively polymerized with a femtosecond laser, creating intracellular structures with submicron resolution. Structures of various shapes are printed in live cells, including a 10 μ m $\umu {\rm m}$
elephant, barcodes for cell tracking, diffraction gratings for remote readout, and microlasers. The printed structures in cells can affect the cell biology. The demonstrated top-down intracellular biofabrication approach, combined with functional photoresists, may enable new applications in intracellular sensing, biomechanical manipulation, bioelectronics, and targeted drug delivery. These embedded structures could provide novel control over the intracellular environment, allowing engineering of cellular properties beyond natural limits and genetic engineering.},
}

@article {pmid41366305,
year = {2025},
author = {Tsafack, DT and Monamele, CG and Koro Koro, F and Essengue, LLM and Mounchili-Njifon, A and Esso, L and Njankouo Ripa, M and Touoyem, PI and Mouliem, JLM and Tamoufe, U and Moumbeket-Yifomnjou, MH and Njouom, R},
title = {Whole-genome analysis of influenza A(H1N1)pdm09 viruses in Cameroon (2019-2024) using nanopore sequencing.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {53},
pmid = {41366305},
issn = {1471-2334},
abstract = {BACKGROUND: Since 2019, Cameroon has reported a high number of seasonal influenza cases caused by the A(H1N1)pdm09 subtype, which remained the predominant global strain as of 2024.

METHODS: To characterize the evolutionary dynamics of circulating A(H1N1)pdm09 viruses, whole-genome sequencing was conducted using Oxford Nanopore Technologies, with multiplexing native barcode expansion kits. DNA repair and end preparation were performed using the NEBNext Ultra II End-Repair/dA-tailing kit. Phylogenetic trees for HA genes segments were inferred using the maximum likelihood (ML) method implemented in IQ-TREE v3.0.1under the LG + F + G4 substitution model. Additionally, Mutation analysis was performed across all eight gene segments using MEGA with A/Wisconsin/67/2022 (A/H1N1pdm09) serving as the reference strain. Identified amino acid substitutions were annotated and their potential phenotypic effects were evaluated using FluSurver.

RESULTS: All Cameroonian A(H1N1)pdm09 strains from 2019 to 2024 belonged to subclade 6B.1A.5a.2a. Phylogenetic analysis revealed annual divergence from Northern Hemisphere vaccine strains, suggesting a mismatch with locally circulating variants. Several functionally relevant mutations were identified in the viral genes, including A3L, A214T, and F12V in HA; R159K and A267V in PA; A241E and T137A in M2; I42L and V7I in NS1; and I84V and I33V in PB1. Many of these mutations have been associated with increased virulence. In addition, amino acid substitutions were observed in the NA protein at V13I, S200N, L339S, S37T, V80M, and I163V, relative to the 2024 vaccine strain A/Wisconsin/67/2022.Overall, the number of amino acid mutations between circulating strains and the vaccine strain was notably high, indicating that local viruses may be evolving away from the vaccine strain selected for the 2023–2024 season.

CONCLUSIONS: These findings underscore the ongoing genetic evolution of the influenza A(H1N1)pdm09 virus in Cameroon and highlight the importance of local genomic data into the selection of WHO vaccine candidate strains for the Northern Hemisphere.

CLINICAL TRIAL NUMBER: Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-12284-5.},
}

@article {pmid41531910,
year = {2026},
author = {Muirberry, J and Lancaster, LT},
title = {Global Changes in Lepidopteran Phylogenetic Diversity Across Space and Time.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72557},
doi = {10.1002/ece3.72557},
pmid = {41531910},
issn = {2045-7758},
abstract = {Amidst increasing reports of insect declines, it is ever more important to understand spatial and temporal insect diversity patterns and processes. Phylogenetic diversity (PD) is an important biodiversity metric in that it relates strongly to ecosystem processes, and it can be estimated more accurately from opportunistic occurrence data than other elements of biodiversity. Here, we assess recent changes across global variation in Lepidopteran PD, to discover overall patterns, their repeatability across regions and environmental drivers. We assess global, spatiotemporal variation in PD, as compared to null expectations given sampling effort, determining how such variation relates to region, space, time and environment. Our analysis is based on 374,749 gene sequence accessions from the barcode of life database (BOLD), representing 3158 species assemblages, spanning 62 years. We find that global variation in PD of Lepidopteran species assemblages has significantly increased over time at high latitudes while remaining relatively unchanged near the equator. This pattern exhibits parallelism across global regions, with the strongest increases in PD towards the present observed in high-latitude communities in North America and Asia, in lowland sites in Europe, and across the African continent. In contrast, PD has declined through time in wetter portions of Australasia and in Africa and South America. Our reported patterns likely reflect changes in Lepidopteran responses to tropical habitat loss and widespread range expansions to higher latitudes. However, changing clines in DNA barcoding strategies could also play a role. Detecting spatiotemporal patterns of change in PD at the global scale is enabled by the increasing use of genetic markers in taxonomy. Our replicated findings provide confidence in biogeographic interpretation, yet increased metadata on sub-sampling decisions would aid future interpretation of biodiversity trends using ecological genomics synthesis.},
}

@article {pmid41531273,
year = {2026},
author = {Lim, VC and Kanthaswamy, S and Malaivijitnond, S},
title = {DNA Barcoding Supports Mitochondrial Lineage Structure in the Genus Macaca With Implications for Biomedical Research and Laboratory Colony Management.},
journal = {Journal of medical primatology},
volume = {55},
number = {1},
pages = {e70054},
doi = {10.1111/jmp.70054},
pmid = {41531273},
issn = {1600-0684},
support = {//Second Century Fund (C2F), Chulalongkorn University/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Biomedical Research ; *Macaca/genetics/classification ; *DNA, Mitochondrial/genetics ; *Macaca fascicularis/genetics/classification ; },
abstract = {BACKGROUND: Cynomolgus macaques are widely used in biomedical research, yet the hybridisation between the subspecies M. f. fascicularis (Mff) and M. f. aurea (Mfa), and introgression from another species M. mulatta (Mm) may affect the research outcomes.

METHODS: DNA barcoding targeting COI mtDNA, as well as phylogenetic, pairwise distance and statistical analyses were employed to examine the relationships between Mff, Mfa and Mm using 52 newly sequenced and 59 public DNA barcodes representing 17 Macaca taxa and seven species groups.

RESULTS: DNA barcoding delineated the Macaca taxa, revealing genetic distinctions between Mff and Mfa greater than between Mff and Mm, as well as delineating geographical populations. This underscores the need for verification of laboratory individuals, besides genetic management of breeding colonies, as genetic differences can influence disease susceptibility and drug trial outcomes.

CONCLUSIONS: DNA barcoding offers a rapid, cost-effective tool to ensure appropriate selection and genetic management of laboratory individuals used in biomedical research.},
}

Animals
*DNA Barcoding, Taxonomic
Phylogeny
*Biomedical Research
*Macaca/genetics/classification
*DNA, Mitochondrial/genetics
*Macaca fascicularis/genetics/classification

@article {pmid41530905,
year = {2026},
author = {Kindree, K and Chochinov, CA and Bhachu, K and Cheng, Y and Caron, A and McDonald, M and Mamai, Z and Nguyen Ba, AN},
title = {Deep-mutational scanning libraries using tiled-region exchange mutagenesis.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag006},
pmid = {41530905},
issn = {2160-1836},
abstract = {The analysis of gene function frequently requires the generation of mutants. Deep-mutational scanning (DMS) has emerged as a powerful tool to decipher important functional residues within genes and proteins. However, methods for performing DMS tend to be complex or laborious. Here, we introduce Tiled-Region Exchange (T-REx) Mutagenesis, which is a multiplexed modification of the EMPIRIC mutagenesis approach. Self-encoded removal fragments are cloned in parallel in non-overlapping gene locations and pooled. In a one-pot reaction, oligonucleotides are then swapped with their corresponding self-encoded removal fragments in bulk using a single Golden Gate reaction. To aid in downstream phenotyping, the library is then fused with unique DNA barcodes using the Bxb1 recombinase. We demonstrate this approach and its optimizations, to show that it is both easy to perform and efficient. This method offers simple and expedient means to create comprehensive mutagenesis libraries.},
}

@article {pmid41528854,
year = {2026},
author = {Wang, J and Wang, B and Zhou, S and Cao, B and Li, W and Zheng, P},
title = {DNACSE: Enhancing Genomic LLMs with Contrastive Learning for DNA Barcode Identification.},
journal = {Journal of chemical information and modeling},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jcim.5c02747},
pmid = {41528854},
issn = {1549-960X},
abstract = {DNA barcoding is a powerful tool for exploring biodiversity, and DNA language models have significantly facilitated its construction and identification. However, since DNA barcodes come from a specific region of mitochondrial DNA and there are structural differences between DNA barcodes and reference genomes used to train existing DNA language models, it is difficult to directly apply the existing DNA language models to the DNA barcoding task. To address this, this paper introduces DNACSE (DNA Contrastive Learning for Sequence Embeddings), an unsupervised noise-contrastive learning framework designed to fine-tune the DNA language foundation model while enhancing the distribution of the embedding space. The results demonstrate that DNACSE outperforms the direct usage of DNA language models in DNA barcoding-related tasks. Specifically, in fine-tuning and linear probe tasks, it achieves accuracy rates of 99.17 and 98.31%, respectively, surpassing the current state-of-the-art BarcodeBERT by 6.44 and 6.44%. In zero-shot clustering tasks, it raises the adjusted mutual information (AMI) score to 92.25%, an improvement of 8.36%. In addition, zero-shot benchmarking and genomic benchmarking tests are evaluated, indicating that DNACSE enhances the performance of DNA language models in generalized genomic tasks. In summary, DNACSE has demonstrated excellent performance in DNA barcode species classification by making full use of multispecies information and DNA barcode information, providing a feasible way to further explore and protect biodiversity. The code repository is available at https://github.com/Kavicy/DNACSE.},
}

@article {pmid41528393,
year = {2026},
author = {McPhail, BA and Veinot, HES and Podruzny, A and Shen, N and Tomusiak, S and Dodds, N and Hanington, PC},
title = {Integrating eDNA, molecular cercariometry, and snail surveys enhances characterization of digenetic trematode diversity.},
journal = {Parasitology research},
volume = {125},
number = {1},
pages = {8},
pmid = {41528393},
issn = {1432-1955},
support = {2018-05209 and 2018-522661//Natural Sciences and Engineering Research Council of Canada/ ; 2078//Alberta Innovates/ ; },
mesh = {*Trematoda/genetics/classification/isolation & purification ; Animals ; *Snails/parasitology ; *DNA Barcoding, Taxonomic/methods ; Alberta ; *Biodiversity ; *DNA, Environmental/genetics ; Cercaria/genetics ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; },
abstract = {Traditional methods for studying digenetic trematode populations involve collecting the snail first intermediate hosts and either shedding larval cercariae or dissecting the snails. Because larval trematodes can be difficult to identify based on morphology alone, these methods are often supplemented with DNA sequencing. This approach can be labour-intensive, and environmentally disruptive. Metabarcoding of environmental DNA (eDNA) or cercariometry (counting of cercariae in water) samples offers an alternative method to simplify this process without negatively affecting the trematode community through the removal of parasites and hosts from the environment. Through ongoing trematode research in central Alberta, Canada, we have documented 102 trematode species infecting multiple snail species and have developed a database of sequences using several DNA barcoding genes. To understand how the trematode community composition derived from metabarcoding compares to a snail infection baseline, we examined the trematode species richness detected by each method. We also established a 16 S rDNA database using representative sequences to align our metabarcoding datasets with others in the field. We found no significant difference between eDNA and cercariometry samples regarding the ability of either method to estimate pooled trematode species richness, but cercariometry detected more species than eDNA when trematode richness was compared between sites. However, snail collections predicted lower species richness than both molecular methods. These findings indicate that the combination of these methods result in enhanced characterization of the trematode community. As more researchers adopt 16 S rDNA for digenetic trematode studies, metabarcoding will become an increasingly valuable tool for trematode surveillance and diversity assessments.},
}

*Trematoda/genetics/classification/isolation & purification
Animals
*Snails/parasitology
*DNA Barcoding, Taxonomic/methods
Alberta
*Biodiversity
*DNA, Environmental/genetics
Cercaria/genetics
DNA, Helminth/genetics
DNA, Ribosomal/genetics

@article {pmid41526574,
year = {2026},
author = {Luo, P and Ma, Z and Wu, Q and Zhao, T and Shen, X},
title = {Efficient adaptive rotated object detection for 1D and QR barcodes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34854-y},
pmid = {41526574},
issn = {2045-2322},
support = {GDRC202415//Natural Science Foundation of Top Talent of SZTU/ ; 20231128141501001//Shenzhen Science and Technology Program/ ; },
abstract = {This study introduces EA-OBB, a lightweight rotated object detection framework designed for detecting one-dimensional (1D) and Quick Response barcodes. Built upon the YOLO11 architecture, EA-OBB integrates several innovative modules-KWConv, ORPNCSPELAN, and LADH-OBB-to enhance both accuracy and computational efficiency in rotated object detection. The KWConv module utilizes a dynamic convolution kernel mechanism to improve rotational barcode feature extraction. The ORPNCSPELAN module enhances computational efficiency through multi-path feature aggregation and online re-parameterization. The LADH-OBB module decouples classification and regression tasks, improving the precision of rotation angle regression. To further adapt to resource-constrained environments, this study incorporates the Taylor Pruning algorithm, significantly reducing model parameters and computational costs. Experimental results on the RotBar dataset demonstrate the superior performance of EA-OBB, achieving an optimal balance of precision, recall, and computational complexity compared to existing methods.},
}

@article {pmid41526492,
year = {2026},
author = {Xu, W and Hu, Y and Zhang, Y and Schnepp, PM and Lo, LM and Zhang, Q and Cheng, SM and Chen, X},
title = {Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {41526492},
issn = {1750-2799},
abstract = {Multimodal profiling of different molecular layers from the same single cell enables more comprehensive characterization of cellular heterogeneity compared with conventional single-modality approaches. A key example is co-detection of chromatin accessibility and gene expression that offers the opportunity to investigate cell type-resolved gene regulatory mechanisms. Here we describe a sensitive and robust protocol for in situ sequencing hetero RNA-DNA-hybrid after assay for transposase-accessible chromatin using sequencing (ISSAAC-seq) for the concurrent measurement of chromatin accessibility and gene expression from the same single nucleus. The method begins with dual Tn5 tagging of open chromatin regions and the RNA-cDNA hybrid produced by reverse transcription that take place in bulk nuclei. Then, various single-nucleus isolation strategies, including plate and droplet barcoding-based approaches, can be used based on the experimental purpose of the user. The protocol is highly modular with a flexible throughput ranging from several hundreds to tens of thousands of nuclei. The generated data are of high quality in both modalities. The entire workflow can be finished within 1 or 2 days, and the procedures work on multiple different single-nucleus isolation and barcoding platforms.},
}

@article {pmid41524665,
year = {2026},
author = {Pibaque, P and Porporato, G and Cescutti, S and Cruz-Flores, A and Busche, T and Winker, A and Rapp, TM and Bergkamp, P and Doneva, A and Chakarov, N},
title = {Domination Versus Sisterhoods in the Blood Microbiota of Migrating Birds: Patterns of Within- and Between-Individual Blood Parasite Diversity Revealed Through Metabarcoding.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70056},
pmid = {41524665},
issn = {1749-4877},
abstract = {Avian blood parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon are typically identified through Sanger sequencing of a partial cytochrome b fragment, the MalAvi barcoding region. This approach limits the detection of mixed infections and the relative frequencies of co-infecting parasites. In contrast, next-generation sequencing (NGS) can resolve these problems but has been underused for haemosporidian lineage identification in samples from the wild. We used an improved PCR protocol and sequencing with Illumina MiSeq to determine haemosporidian assemblages in wild birds captured at a migration stopover site in Bulgaria, Europe. From 406 samples obtained from 52 bird species, we detected 81 haemosporidian lineages in 131 infected samples from 32 species (32% prevalence). On average, individuals were infected with 2.4 lineages, with 59 birds infected by a single lineage, and 21 birds infected with 5-9 lineages. A subset of samples was Illumina- and Sanger-sequenced in parallel, finding mixed infections in 72 samples and 8× higher detection rate of mixed and co-infections through high-throughput sequencing. Both methods identified the same dominant (co-infecting) lineage (91%). Metabarcoding identified common mixed infections of sister lineage groups ("sisterhoods") known for prevalent lineages and morphospecies, including Plasmodium relictum p_SGS1, Haemoproteus motacillae h_YWT2, and Haemoproteus parabelopolskyi h_SYAT01. Some other lineages appeared consistently more dominant. Our study shows that in some host communities, metabarcoding can reveal a great diversity of mixed infections. This opens new horizons to the study of assemblages of haemosporidian parasites, their interactions within individual hosts, and co-evolution with other members of the blood microbiome and the hosts.},
}

@article {pmid41522876,
year = {2025},
author = {Crous, PW and Groenewald, JZ and Bensch, K and Gené, J and Guarro, J},
title = {Genera of phytopathogenic fungi known from culture: 1-379.},
journal = {Studies in mycology},
volume = {112},
number = {},
pages = {261-633},
pmid = {41522876},
issn = {0166-0616},
abstract = {Approximately 200000 species of fungi have been described to date, representing nearly 8000 currently recognised genera. Many of these genera are regarded as plant pathogenic, as they include at least one species proven to cause pre- or postharvest plant disease. Following the abandonment of dual nomenclature and the advent of DNA sequencing and phylogenetic approaches, numerous para- and polyphyletic clades were resolved into distinct genera. These genera are now defined based on morphology, ecology, and DNA phylogeny. The present paper represents the first in a series that aims to provide descriptions, classification, illustrations, significant species, disease symptoms, and DNA data for the common genera of phytopathogenic fungi known from culture, including the first treatment of 379 genera. In addition, several new combinations, lecto-, epi-, or neotypes are also proposed. Taxonomic novelties: New combinations: Anisogramma coryli (Batsch) Crous, Helostroma bacarum (Buhagiar) Aime & Bensch, Hymenella cerealis (Ellis & Everh.) Crous & J.Z. Groenew., Hypomyces multiseptatus (de Hoog) Crous & Bensch, Hypomyces verticillatus (Link) Crous & Bensch, Mastigocladium capsici (S.Q. Tong & Y.J. Wu) Lin Zhao & Crous, Mastigocladium lepidopterorum (L.W. Hou et al.) Lin Zhao & Crous, Microstroma glucosiphilum (T. Kij. & Aime) Aime & Bensch, Paraconiothyrium coniothyrium (Fuckel) Crous & Bensch, Sclerophomella aquilegiicola (M. Petrov) Crous & Bensch, Sclerophomella clematidina (Thüm.) Crous & Bensch, Sclerophomella clematidis-rectae (Petr.) Crous & Bensch, Sclerophomella glaucii (Brunaud) Crous & Bensch, Sclerophomella humulicola (Chaiwan et al.) Crous & Bensch, Sclerophomella hydei (Maharachch. et al.) Crous & Bensch, Sclerophomella parvula (L.W. Hou et al.) Crous & Bensch, Sclerophomella petasitis (Tibpromma et al.) Crous & Bensch, Sclerophomella rosae (Qian Chen et al.) Crous & Bensch, Sclerophomella sandfjordenica (Crous & Rämä) Crous & Bensch, Sclerophomella vincetoxici (De Not.) Crous & Bensch, Sclerophomella vodakii (E. Müll.) Crous & Bensch; New name: Sclerophomella humuligena Crous & Bensch for Calophoma humuli V. Thiyag. et al. New typifications (basionyms): Ascochyta pisi Lib., Cryptosphaeria glaucopunctata Grev., Diaporthe cubensis Bruner, Geotrichum candidum Link, Hymenula cerealis Ellis & Everh., Lanosa nivalis Fr., Mauginiella scaettae Cavara, Phaeophleospora eugeniae Rangel, Pilidium acerinum Kunze, Seiridium marginatum Nees, Sphaeria melanostyla DC., Sporendonema sebi Fr., Tubercularia chaetospora Pat., Wallemia ichthyophaga Johan-Olsen. Citation: Crous PW, Groenewald JZ, Bensch K, Gené J, Guarro J (2025). Genera of phytopathogenic fungi known from culture: 1-379. Studies in Mycology 112: 261-633. doi: 10.3114/sim.2025.112.05.},
}

@article {pmid41522517,
year = {2026},
author = {Rehsen, PM and Honka, MS and Impiö, M and Madge Pimentel, I and Leese, F and Beermann, AJ},
title = {Improving taxonomic resolution, biomass and abundance assessments of aquatic invertebrates by combining imaging and DNA megabarcoding.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20501},
pmid = {41522517},
issn = {2167-8359},
mesh = {Animals ; *Biomass ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; *Aquatic Organisms/classification/genetics ; *Invertebrates/genetics/classification ; Neural Networks, Computer ; *Insecta/genetics/classification ; Ecosystem ; },
abstract = {Understanding biodiversity change requires a comprehensive assessment of not only the identity of species inhabiting an ecosystem but also their biomass and abundance. However, assessing biodiversity on the species level with precise biomass information is a time-consuming process and thus rarely applied. While DNA-based approaches like DNA barcoding offer precise species identification, they lack information on specimen size and biomass. In contrast, high-throughput imaging techniques enable rapid measurements of a specimen's size and morphological features but may have low taxonomic resolution. In this study, we combined DNA megabarcoding, i.e., high-throughput barcoding of single specimens, with semi-automated imaging and deep neural networks to produce accurate taxonomic identifications, abundance, and biomass estimations for insects. In a multiple stressor field experiment, we collected a dataset of 743 specimens from 14 species of the orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), which are routinely used as aquatic biological quality indicator taxa. Each specimen was imaged, weighed, and megabarcoded using the COI barcode gene. From the images captured using the semi-automated imaging device BIODISCOVER, we curated a final dataset of 146,439 images taken from two perpendicular cameras. We trained convolutional neural networks (CNNs) with these pictures for species identification and biomass estimation and evaluated their performance. In addition, we investigated whether models pre-trained for species identification perform better on the biomass estimation task, compared to models trained solely for biomass estimation, thus potentially reducing the need for extensive labelled data in future studies. Our findings demonstrate that combining DNA megabarcoding with automated imaging and deep neural networks enables fast, reliable, but also comprehensive assessment of species composition and biomass on the specimen level, contributing to the urgently needed methods in conservation biology, ecology, and evolution.},
}

Animals
*Biomass
*DNA Barcoding, Taxonomic/methods
Biodiversity
*Aquatic Organisms/classification/genetics
*Invertebrates/genetics/classification
Neural Networks, Computer
*Insecta/genetics/classification
Ecosystem

@article {pmid41522508,
year = {2026},
author = {Campos-Yánez, F and García-Ruilova, AB and Inclán, DJ},
title = {A new species of aposematic grasshopper of the genus Pseudoutanacris (Acrididae: Gomphocerinae) from the Andean cloud forest of the Ecuadorian Amazon basin.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20376},
pmid = {41522508},
issn = {2167-8359},
mesh = {Animals ; Ecuador ; Male ; Female ; *Grasshoppers/classification/anatomy & histology/physiology ; Forests ; Amazona ; },
abstract = {We have identified a new grasshopper species belonging to the genus Pseudoutanacris Jago, 1971, in the montane forests of the eastern Andes in Ecuador. This discovery expands the known distribution of the genus, previously limited to a single species in the Bolivian tropics, by over 2,000 kilometers. For the first time, a female of the genus is described, and notes on the ecology and natural history of the species are presented. We also provide the first barcodes of the genus Pseudoutanacris Jago, 1971. The males of a newly described species, Pseudoutanacris grilla sp. nov. shares a striking coloration pattern with their Bolivian congener, Pseudoutanacris chromobapta Jago, 1971, setting them apart from other members of the tribe Amblytropidiini. However, the females maintain a cryptic coloration pattern, similar to that of the tribe members, and display different behavior from the males. During our study, we also observed Ps. grilla sp. nov. on the same plant as Megacheilacris graminicola (Descamps & Amédégnato, 1971) (Bactrophorinae: Romaleidae), a species with similar chromatic characteristics. This finding also marks the first formal documentation of the new geographical records of M. graminicola (Descamps & Amédégnato, 1971) in Ecuador.},
}

Animals
Ecuador
Male
Female
*Grasshoppers/classification/anatomy & histology/physiology
Forests
Amazona

@article {pmid41522495,
year = {2026},
author = {Bao, S and Deng, L and Shi, Y and Duan, N},
title = {Comparative genomics and phylogenetic analysis of seven Ficus species based on chloroplast genomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20531},
pmid = {41522495},
issn = {2167-8359},
mesh = {*Ficus/genetics/classification ; *Genome, Chloroplast/genetics ; *Phylogeny ; *Genomics/methods ; },
abstract = {BACKGROUND: The genus Ficus (Moraceae) is a large and ecologically important group, known for its intricate fig-wasp pollination mutualism and role as a keystone resource in tropical ecosystems. Despite its significance, the phylogenetic relationships within Ficus remain partially unresolved, necessitating more comprehensive genomic data. Chloroplast (cp) genomes are valuable resources for plant phylogenetic and comparative genomic studies. Here, we sequenced, assembled, and comparatively analyzed the complete chloroplast genomes of seven Ficus species, including Ficus esquiroliana, Ficus pandurata, Ficus formosana, Ficus erecta, Ficus carica, Ficus hirta, and Ficus stenophylla.

RESULTS: The complete cp genomes were successfully assembled, ranging in size from 160,340 bp to 160,669 bp, and exhibited a typical quadripartite structure with highly conserved gene content and arrangement. Critically, while some of these species have previously published plastomes, our assemblies consistently encoded 130 genes, contrasting with reported gene counts (e.g., 129 for F. formosana (NC_059898), 119 for F. carica (KY635880), 131 for F. erecta (MT093220)) in earlier studies. Numerous repeat sequences and simple sequence repeats (SSRs) were identified, predominantly in non-coding regions, which serve as valuable resources for developing novel genetic markers. Analysis of codon usage revealed a strong bias towards A/T endings, a common feature in plant cp genomes. While inverted repeat (IR) boundary regions were largely conserved, minor variations, including partial gene duplications (rps19, rpl2), were observed. Comparative genome alignment and nucleotide diversity analysis showed high sequence conservation, with most variations concentrated in single-copy and non-coding regions. We identified three hypervariable regions (ccsA, ccsA - ndhD, and rpoB - trnC-GCA) with elevated nucleotide diversity (Pi > 0.012, ccsA up to 0.0141), suggesting their utility as candidate DNA barcodes for Ficus. Phylogenetic analysis using 79 protein-coding genes from 26 species robustly supported the monophyly of Ficus and resolved the seven newly sequenced species into two well-supported clades, consistent with previous classifications.

CONCLUSIONS: Our study provides new, consistently assembled and rigorously annotated chloroplast genome data for Ficus, including clarified data for previously studied species with notable gene content discrepancies. These data identify candidate molecular markers with potential applications for systematics and population genetics, and offer robust insights into relationships among sampled taxa. These data will facilitate future studies of Ficus evolution and conservation when complemented by broader taxon sampling and nuclear/mitochondrial data.},
}

*Ficus/genetics/classification
*Genome, Chloroplast/genetics
*Phylogeny
*Genomics/methods

@article {pmid41522476,
year = {2025},
author = {Seokho, S and Sohn, J and Kim, H},
title = {First records of Opius and Apodesmia (Hymenoptera, Braconidae, Opiinae) from South Korea, with descriptions of newly-recorded species.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e176155},
pmid = {41522476},
issn = {1314-2828},
abstract = {BACKGROUND: The subfamily Opiinae comprises more than 2,000 valid species worldwide. Members of this subfamily are koinobiont endoparasitoids, with parasitism generally culminating in the eventual death of the host. Several species of Opiinae have been utilised for biological control of agricultural pests. The genus Opius is the largest genus within Opiinae, with more than 1,000 valid species worldwide. It is divided into several subgenera, classification of which remains under active discussion. The genus Apodesmia was formerly regarded as a subgenus of Opius, but was elevated to genus level, based on differences in the form of the occipital carina.

NEW INFORMATION: Opius youi Li & van Achterberg, 2013 is recorded for the first time from South Korea, representing the first record of the species outside China. Apodesmia incisula Fischer, 1963 is also newly recorded from South Korea, constituting the first record of the species outside Europe, where it was previously known from Germany and the Netherlands. For each species, detailed morphological descriptions are provided, accompanied by diagnostic characters illustrated with photographs of the relevant body structures. The barcode region of mitochondrial cytochrome c oxidase I (COI) was also analysed for the species.},
}

@article {pmid41522231,
year = {2026},
author = {Gu, F and Yang, L},
title = {Structural Characteristics, Comparative Analyses, and Conservation Significance of the Complete Chloroplast Genome of the Critically Endangered Lithocarpus yongfuensis (Fagaceae).},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72833},
pmid = {41522231},
issn = {2045-7758},
abstract = {This study aims to delineate the chloroplast (cp) genome of the critically endangered Lithocarpus yongfuensis (Fagaceae), with fewer than 10 wild individuals known. Genomic information for this species is scarce, hindering conservation strategies. We sequenced, assembled, and annotated its complete cp genome, analyzed its structure, and conducted comparative and phylogenetic analyses within the genus Lithocarpus. The cp genome is 161,258 bp in length, exhibiting a typical quadripartite structure and containing 131 annotated genes (86 protein-coding, 8 rRNA, and 37 tRNA genes). Comparative analysis revealed a conserved genomic architecture across the genus, with two protein-coding genes (rpoC2 and matK) showing evidence of positive selection. The rps16-trnK-UUU intergenic spacer was identified as a potential DNA barcode for distinguishing L. yongfuensis. Phylogenetic analysis based on complete cp genomes placed L. yongfuensis within the Southeast China clade, closely allied to L. crassifolius, L. litseifolius, and L. brevicaudatus. These findings provide essential genomic resources for conservation genetics and offer insights into the adaptive evolution of this rare species.},
}

@article {pmid41520911,
year = {2026},
author = {McKenzie, M and Irac, SE and Chen, Z and Moradi, A and Jenner, A and Nguyen, Q and Rashidieh, B},
title = {Integrative Spatial Omics and Artificial Intelligence: Transforming Cancer Research with Omics Data and AI.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2026.01.002},
pmid = {41520911},
issn = {1096-3650},
abstract = {The integration of multi-omics data, including genomics, transcriptomics, proteomics, epigenomics, and metabolomics, coupled with the histological spatial data have transformed biomedical research, offering unprecedented insights into cellular functions and disease mechanisms. However, the sheer volume and complexity of these datasets present a significant challenge in terms of interpretation and clinical translation. Artificial intelligence (AI) and machine learning (ML) are revolutionizing data analysis, enabling the extraction of meaningful patterns from high-dimensional datasets and facilitating the development of predictive models. This shift is particularly transformative in cancer research, where understanding the tumor microenvironment (TME) and its spatial dynamics is crucial for improving therapeutic outcomes. This review explores recent advancements in spatial Omics (SO) including spatial transcriptomics (ST) and spatial proteomics (SP), and AI-driven computational models, focusing on their applications in oncology. We discuss key methodologies, including spatial barcoding, in situ sequencing, and digital spatial profiling, and highlight major platforms. AI-powered tools, including deep learning models and spatial graph-based analyses, enhance data interpretation, allowing for robust predictive modeling, biomarker discovery, and personalized therapeutic strategies. Despite their transformative potential, ST and AI-driven approaches face challenges, including high-dimensional data complexity, computational constraints, and standardization of analytical pipelines. Addressing these challenges requires advanced mathematical frameworks such as spatial graph theory, topological data analysis, and agent-based modeling, which refine data integration and improve biological insights. Future research should focus on enhancing spatial resolution, cross-platform data harmonization, and AI-driven predictive models to advance precision oncology. By integrating ST, SP, and AI, researchers can develop dynamic, patient-specific treatment strategies, ultimately improving clinical outcomes and deepening our understanding of cancer progression and immune system interactions.},
}

@article {pmid41518826,
year = {2026},
author = {Palm, ER and Santini, G and Niccolai, A and Vergine, M and Negro, C and Nissim, WG and Sabbatini, L and Balestrini, R and de Pinto, MC and Gohari, G and Fotopoulos, V and Mancuso, S and Luvisi, A and De Bellis, L and Rodolfi, L and Vita, F},
title = {Improving yield of a bean ecotype using biostimulants: focus on bean amino acid profiles and plant responses.},
journal = {Plant physiology and biochemistry : PPB},
volume = {231},
number = {},
pages = {110988},
doi = {10.1016/j.plaphy.2025.110988},
pmid = {41518826},
issn = {1873-2690},
abstract = {Biostimulants have emerged as having the potential to sustainably enhance crop performance as well as yield quantity and nutritional quality. Although naturally rich in lysine, beans are generally deficient in sulfur-containing amino acids like methionine and cysteine. Improving the nutritional imbalance in beans is highly desirable, especially in those with cultural and economic value, like Fagiolo di Sorana, a high-quality Protected Designation of Origin (PDO) bean variety from Pistoia, Italy. A spirulina-based (1 g/L and 3 g/L) and a commercially available (MC EXTRA; 1 g/L) biostimulant were applied as foliar sprays for two consecutive years to Fagiolo di Sorana plants grown under both open field and semi-controlled greenhouse conditions. Productivity was higher in treated plants: a 7 % increase (p-value, 0.036) was found in whole pod weight in the first year of the trial with 3 g/L and in the second year trial (p-value, 0.020) for MC EXTRA compared to the control. Improved amino acid composition of the beans were found, specifically an increase of 200 % (p-value, 0.040) and 400 % (p-value, 0.053) in methionine content with 3 g/L spirulina and MC EXTRA, respectively, compared to the control, thus addressing the bean's typical deficiency in sulfur amino acids. Bean digestibility increased 3 % (p-value, 0.013) with the higher concentration (3 g/L) of the spirulina-based biostimulant relative to the control-grown plants. Molecular barcoding identified genetic differences within a collection of ten Tuscan bean landraces, including the Fagiolo di Sorana variety, thus offering a first attempt at the genetic characterization essential for preserving landrace germplasm. These genetic data were then coupled with the assessment of protein digestibility to identify differences within the landrace collection. Thus, the use of biostimulants presents an opportunity to further enhance the yield and nutritional profile of this PDO without compromising its environmental integrity.},
}

@article {pmid41515439,
year = {2026},
author = {Ísleifsdóttir, D and Xu, M and Biwersi, M and Leblanc, MJ and Heiðmarsson, S and Pálsson, S and Sorensen, JL and Viktorsson, EÖ and Ólafsdóttir, ES},
title = {Is the Reindeer Lichen Cladonia arbuscula Really Producing Isousnic Acid? A Chemotaxonomy Query.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {1},
pages = {},
pmid = {41515439},
issn = {1420-3049},
support = {2310001-051//Icelandic Research Fund/ ; VÍS2023-93104//University of Iceland Science Park Fund/ ; 92257//University of Iceland research fund/ ; NÝR-14-2023//Landsvirkjun Fund/ ; ALLP 585977-23//Natural Sciences and Engineering Research Council of Canada Alliance International Collaboration/ ; },
mesh = {*Lichens/chemistry/metabolism/genetics/classification ; Chromatography, High Pressure Liquid ; *Ascomycota/genetics/metabolism/chemistry/classification ; DNA Barcoding, Taxonomic ; *Benzofurans/metabolism/chemistry ; *Reindeer/microbiology ; Animals ; Phylogeny ; },
abstract = {Isousnic acid (isoUA) has been detected in a few usnic acid (UA)-producing lichens with chemotaxonomic values. IsoUA was first isolated from a specimen belonging to Cladonia arbuscula s.l. (referred to as C. mitis in the publication). However, the isolation and detection of isoUA in this Cladonia species have not been reproduced and confirmed with clear evidence. This study focused on C. arbuscula s.l. collected in Iceland and aimed to (1) identify the lichen specimen using DNA barcoding and (2) investigate whether isoUA is produced using a series of chromatographic methods. The fungal nuclear ribosomal internal transcribed spacer (nrITS) barcode was sequenced, and the specimen was identified as C. arbuscula, following recent circumscription recommendations. Routine metabolite profiling did not detect isoUA, and it could only be identified after vigorous chromatographic purification and concentration steps using flash chromatography and preparative high-performance liquid chromatography. IsoUA was found in trace quantities (~24 µg/g dry weight), which likely explains its absence in routine metabolite profiling. A rapid ultra-high-performance liquid chromatography (UHPLC) method using a pentafluorophenyl column was developed to separate UA and isoUA. Our study highlights the importance of an integrative approach combining DNA barcoding and detailed chromatographic analyses for lichen chemistry research.},
}

*Lichens/chemistry/metabolism/genetics/classification
Chromatography, High Pressure Liquid
*Ascomycota/genetics/metabolism/chemistry/classification
DNA Barcoding, Taxonomic
*Benzofurans/metabolism/chemistry
*Reindeer/microbiology
Animals
Phylogeny

@article {pmid41514962,
year = {2025},
author = {Todorov, K and Antova, G and Petkova, Z and Teneva, O and Angelova-Romova, M and Mladenov, R and Naimov, S and Apostolova, E and Gyuzeleva, D and Mladenova, T and Panayotova, H and Stoyanov, P},
title = {Anatomical, Molecular-Genetic, and Phytochemical Study of Species from the Genus Equisetum in Bulgaria.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41514962},
issn = {2223-7747},
support = {project № BG-RRP-2.004-0001-C01//European Union-NextGenerationEU, through the National Recovery and Resilience Plan of the Republic of Bulgaria/ ; },
abstract = {Five species of the genus Equisetum distributed in Bulgaria were studied: four species from the subgenus Equisetum (Equisetum arvense, E. telmateia, E. sylvaticum, and E. palustre) and one from the subgenus Hippochaete (E. ramosissimum). The anatomical, taxonomic, and phylogenetic characteristics of the selected species were established. In species belonging to the subgenus Equisetum, the endodermis was arranged in the form of a continuous ring, while in the representatives of the subgenus Hippochaete, a two-layered endodermis surrounding each vascular bundle was observed. The results from the DNA barcoding supported the taxonomic treatment of the studied species. The chemical and lipid compositions of the plants were also investigated. The Equisetum species had a similar chemical composition and a high content of sterols and phospholipids. In the glyceride oils, palmitic acid predominated, ranging from 69.5% to 78.7%. β-sitosterol was the main component in the sterol fraction, while the tocopherol content was found to be remarkably low in two of the samples (37.6-82.8 mg/kg), with α-tocopherol being predominant. In the phospholipid fraction, the major classes were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and phosphatidic acids. The chemical composition of the studied species and their high biologically active lipid constituents suggested that they were suitable for application in various directions.},
}

@article {pmid41514857,
year = {2025},
author = {Zhan, Q and Tang, Y and Zhao, Y and Hou, S and Huang, Y and Zhao, X and Chen, Y and Xue, X},
title = {Complete Mitochondrial Genome Sequencing of Brachypelma albiceps and Comparative Codon Usage Bias Analysis Across Seven Mygalomorphae Species.},
journal = {Biology},
volume = {15},
number = {1},
pages = {},
pmid = {41514857},
issn = {2079-7737},
support = {LGZD202507//Fundamental Research Funds for the Central Universities/ ; 2025//Qinglan Project" of Jiangsu Province in 2025/ ; 32100366//National Natural Science Foundation of China/ ; 2022YFC2601200//National Key R&D Program of China/ ; "Public Security Technology" project (2022)//the Jiangsu Province "14th Five-Year Plan" Key Construction Discipline/ ; },
abstract = {Tarantulas (family Theraphosidae) are ecologically significant invertebrate predators in terrestrial ecosystems, but many species face threats from habitat fragmentation and unsustainable collection for the international pet trade. Brachypelma albiceps, a CITES Appendix II-listed species, lacks comprehensive mitochondrial genome characterization, limiting phylogenetic and evolutionary studies. Here, we report a complete mitochondrial genome sequence for B. albiceps (13,856 bp; GC content 32.84%) and provide detailed annotation. The genome exhibits typical metazoan mitochondrial organization, containing 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs, with an AT-rich nucleotide composition (67.16%) characteristic of arthropod mitochondria. Comparative analyses of B. albiceps and six other Mygalomorphae species revealed strong biases toward A/T-ending codons and avoidance of G/C-ending codons. ENC-GC3s, neutrality, and PR2 analyses consistently indicate that natural selection plays a dominant role in shaping synonymous codon usage, with mutation pressure also contributing. Phylogenetic reconstruction based on 10 high-quality mitochondrial protein-coding genes from 23 spider species confirmed the placement of B. albiceps within the family Theraphosidae and its close phylogenetic relationship to Cyriopagopus species. These results provide valuable genomic resources for the Theraphosidae systematics, enhance our understanding of codon bias evolution, and provide critical DNA barcode data for forensic identification of CITES-regulated specimens in the illegal wildlife trade.},
}

@article {pmid41513884,
year = {2026},
author = {Balsamo, JA and Mendoza, M and Kelly-Baker, L and G Thacker, S and Verthelyi, D},
title = {Multiplexed Immunophenotyping for Innate Activation Assessment Detects Single-Cell Responses to Immunomodulatory Nucleic Acid Impurities in Therapeutics.},
journal = {The AAPS journal},
volume = {28},
number = {1},
pages = {49},
pmid = {41513884},
issn = {1550-7416},
mesh = {Humans ; *Immunity, Innate/drug effects/immunology ; *Immunophenotyping/methods ; *Single-Cell Analysis/methods ; Flow Cytometry/methods ; *Nucleic Acids/immunology ; Oligodeoxyribonucleotides/immunology/pharmacology ; Monocytes/immunology/drug effects ; },
abstract = {Innate immune response modulating impurities (IIRMI) with adjuvant potential have emerged as important factors in the immunogenicity risk assessment of protein, peptide, and oligonucleotide therapeutics, particularly for follow-on products where minimal or no clinical studies are available. To assess the impact of differences in impurities on specific cell types, we developed a new IIRMI assay termed multiplexed immunophenotyping for innate activation assessment (MIIAA) that employs spectral flow cytometry to capture single-cell responses to drug products and potential impurities. This technique introduces a new live fluorescent cell barcoding platform that enables sample multiplexing for homogeneous staining with a single fluorescent antibody cocktail composed of identity and activation markers that are acquired simultaneously with a five laser Cytek Aurora. Samples are digitally reassigned to their original testing conditions by positive and negative gating of barcode dyes. Cellular subsets are identified by dimensionality reduction of surface markers with UMAP then gated using cell-specific markers. Here we use trace levels of TLR3, 7/8 and 9 agonists (Poly(I:C), R848, and CpG ODN) to characterize specific responses in B cells, monocytes, cDC and pDC. Importantly, MIIAA captures single-cell responses to nucleic acid impurities in the presence of therapeutic oligonucleotides or monoclonal antibodies with high sensitivity. Taken together, MIIAA offers a powerful immunophenotyping tool to characterize single-cell responses to drug products and potential immunomodulatory impurities that may find utility in drug pipelines to characterize the impact of therapeutics on specific immune cells and to interrogate immunogenic or immunomodulatory risk in comparisons between reference and follow-on products.},
}

Humans
*Immunity, Innate/drug effects/immunology
*Immunophenotyping/methods
*Single-Cell Analysis/methods
Flow Cytometry/methods
*Nucleic Acids/immunology
Oligodeoxyribonucleotides/immunology/pharmacology
Monocytes/immunology/drug effects

@article {pmid41513017,
year = {2026},
author = {Cao, J and Poyarkov, NA and Wei, P and Tie, M and Matsukoji, T and Suwannapoom, C and Ai, R and Lu, W and Sucharitakul, P and Wang, H and Chomdej, S and Yuan, Z and Yan, F},
title = {Diversity, Phylogeny, and biogeography of the subgenus Japonigekko (Gekkonidae: Gekko).},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108530},
doi = {10.1016/j.ympev.2025.108530},
pmid = {41513017},
issn = {1095-9513},
abstract = {The subgenus Japonigekko, a monophyletic lineage, represents the most ecologically and morphologically diverse group within the genus Gekko, with a wide distribution across East Asia. Given the ecological significance and high diversity of Japonigekko, understanding its true species diversity and biogeographic history is crucial for biodiversity conservation in East Asia. However, research on this subgenus remains limited compared to other well-studied vertebrate groups such as mammals and amphibians. In this study, we conducted extensive sampling and integrated molecular data from 34 of the 38 known Japonigekko species using barcoding techniques for 331 samples from 129 sites, systematically elucidating their phylogenetic relationships. Further genomic analysis addressed longstanding taxonomic controversies, revealed previously underestimated species diversity, and clarified the historical biogeography of this group. Ultimately, we identified nine candidate new species. Phylogenetic analyses and ancestral area reconstructions suggest that Japonigekko originated in the Indochina Peninsula and southern China, subsequently dispersing northward and eastward during the Miocene in response to geological events and climatic fluctuations. The recurrent formation and disappearance of land bridges between the mainland and East Asian islands provided critical opportunities for both dispersal and isolation, revealing a unidirectional mainland-to-island dispersal pattern. These findings support to the "Ancient Species Divergence Hypothesis" in East Asia.},
}

@article {pmid41510249,
year = {2025},
author = {Skene, P and Hart, M and Thomson, Z and Kaul, S and Ilkisin, S and Landreau, M and Stuckey, T and Wittig, P and Keller, M and McCann, C and Torgerson, T},
title = {Massively Scalable Single-cell Multiomic Profiling of T Cell Repertoire with REFLEX.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7915855/v1},
pmid = {41510249},
issn = {2693-5015},
abstract = {Single-cell profiling of T cell state with immune repertoire is critical for understanding heterogenous T cell phenotypes and responses to antigen, however, existing technologies struggle to generate this information at sufficient throughput to match biological complexity. We present "REFLEX", a novel single-cell method enabling highly scalable, cost-efficient, multiomic profiling with paired-chain TCR sequencing. REFLEX utilizes in-situ reverse transcription with integrated sample multiplexing barcodes in a way that merges seamlessly with the commonly used 10x FLEX platform to allow capture of TCR sequences at unprecedented scale and depth. We profile >2 million cells from CMV-peptide-pulsed T cell expansions, capturing TCR sequences and rich multiomic information from 1.4M T cells, identifying many putative novel CMV reactive clonotypes and illustrating the scale and transformative impact on our understanding of T cell mediated adaptive immunity achievable with REFLEX.},
}

@article {pmid41509721,
year = {2025},
author = {Xiong, Y and Li, D and Xu, X},
title = {Five new species of the trapdoor spider genus Latouchia Pocock, 1901 (Araneae, Halonoproctidae) from China.},
journal = {ZooKeys},
volume = {1265},
number = {},
pages = {103-127},
pmid = {41509721},
issn = {1313-2989},
abstract = {Five new species of the trapdoor spider genus Latouchia Pocock, 1901 are described from southern China based on both morphological and molecular evidence: L. jihe sp. nov. (♂♀), L. wufeng sp. nov. (♂♀), L. wuhan sp. nov. (♂♀), L. yinggen sp. nov. (♂♀), and L. zhangping sp. nov. (♂♀). The male and female of L. jinyun Hao, Yu & Zhang, 2025 are also redescribed from specimens collected in Nanchong City, Sichuan Province, China, located over 100 km from the type locality in Chongqing Municipality. Species delimitation is supported by genetic distance analyses of the mitochondrial DNA barcode gene (cytochrome c oxidase subunit I, COI), comparing the five new species with five previously described taxa. GenBank accession codes for the five new species and L. jinyun are provided to facilitate future identification and taxonomic research.},
}

@article {pmid41509719,
year = {2025},
author = {Wang, JX and Zhu, XJ and Xiao, YL},
title = {Phylogenetic analysis of the genus Semioscopis (Lepidoptera, Depressariidae), with description of a new species from China.},
journal = {ZooKeys},
volume = {1265},
number = {},
pages = {175-187},
pmid = {41509719},
issn = {1313-2989},
abstract = {This study describes Semioscopis sinicella Wang, Zhu & Xiao, sp. nov. of the genus Semioscopis Hübner, 1825 (Lepidoptera, Depressariidae) from China. The new species is similar in external morphology and male genitalia to the European S. avellanella (Hübner, 1793) and the Japanese S. similis Saito, 1989, but it can be distinguished in female genitalia mainly by the distinctly shorter sclerotised section of the ductus bursae and the length ratios of the ductus bursae and corpus bursae to the papillae anales. Morphological descriptions and illustrations of the new species are provided. Furthermore, a phylogenetic analysis based on COI gene sequences using IQ-tree supports S. sinicella sp. nov. as a monophyletic lineage and further divides the genus Semioscopis into seven species groups.},
}

@article {pmid41509718,
year = {2025},
author = {Salah, M and Baleela, R and Ahmed, EY and Isam, B and Abdalla, A and Masri, M and Elfaki, E},
title = {Paragomphus alami sp. nov. (Odonata, Gomphidae): a new dragonfly species described from the White Nile River, Sudan.},
journal = {ZooKeys},
volume = {1265},
number = {},
pages = {159-174},
pmid = {41509718},
issn = {1313-2989},
abstract = {Sudan's unique biogeographic position at the Afrotropical-Palearctic interface, coupled with the ecological gradient of the Nile River, fosters a diverse odonate fauna. Despite this, the genus Paragomphus Cowley, 1934 remains understudied in the region. This study describes Paragomphus alami sp. nov., a new species of Paragomphus from the White Nile floodplain in Sudan, based on integrated morphological and molecular evidence. Field surveys conducted between 2017 and 2022 documented adult populations across the Sudanese floodplains. Specimens were morphologically analysed using microscopy compared to congeners P. lacustris Karsch, 1890 and P. elpidius Ris, 1921. DNA barcoding (COI gene) was performed on two specimens, with maximum-likelihood phylogenetic reconstruction using 28 sequences of Paragomphus and related species in addition to an outgroup. Mean interspecific genetic distance was computed manually. Morphological comparisons with congeners revealed unique diagnostic traits in P. alami sp. nov., including short, thick cerci ending with a black tooth, and an epiproct that is noticeably shorter than those of P. lacustris and P. elpidius. The phylogenetic analysis revealed that P. alami forms a well-supported monophyletic clade (bootstrap value = 100%), which is corroborated by morphological evidence, and no observed intraspecific variation, which supports the recognition of this species as distinct; this was further supported by the mean interspecific distance of 12.34%. This discovery highlights Sudan's role as a biogeographic crossroads and the need for further research of Odonata in the region. Habitat sensitivity highlights conservation urgency. The species seasonal emergence, habitat specificity, and sensitivity to deforestation underscore its conservation importance.},
}

@article {pmid41509389,
year = {2026},
author = {Wang, CC and Dorsey, E and Wu, C},
title = {Expanding High-Fidelity Multiplexing in Ultrasensitive Single-Molecule Protein Detection via Proximity Barcoding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.03.697469},
pmid = {41509389},
issn = {2692-8205},
abstract = {The human proteome presents a vast information reservoir for basic and diagnostics research, yet the low abundances of many proteins in biofluids pose an analytical challenge. While ultrasensitive methods such as digital enzyme-linked immunosorbent assay have expanded the window of detectable proteins, multiplexing with high accuracy, sensitivity, and throughput remains limited by cross-reactivity and signal readout channels To address this challenge, we introduce PRO-MOSAIX (PROximity-barcoded Molecular On-bead Signal Amplification for Individual MultipleXing), a high-accuracy, ultrasensitive multiplex digital immunoassay platform that integrates high-throughput single-molecule protein detection with DNA barcode-based proximity ligation. PRO-MOSAIX generates "ON" signals only from matched affinity reagents in proximity, minimizing false positives from cross-reactive binding. This approach overcomes the multiplexing ceiling imposed by fluorescence spectral overlap by employing a single signal readout channel and DNA barcoding. In conjunction, we further improve multiplexing accuracy by mitigating a secondary source of false positives from DNA-based signal amplification. As a proof of principle, we establish and validate a 15-plex PRO-MOSAIX assay in human plasma, with low femtomolar sensitivities and high measurement accuracies. PRO-MOSAIX is modular and utilizes common laboratory instrumentation with a high-throughput flow cytometric readout, providing a broadly accessible tool that bridges the gap between analytical sensitivity and high-order multiplexing.},
}

@article {pmid41504599,
year = {2026},
author = {Fang, C and Lindsey, JW and Abbott, LF and Aronov, D and Chettih, SN},
title = {Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41504599},
issn = {2050-084X},
support = {DBI-1707398//National Science Foundation/ ; DP2-AG071918//NIH Office of the Director/ ; 1K99NS136846/NS/NINDS NIH HHS/United States ; DE-SC0020347//U.S. Department of Energy/ ; },
mesh = {*Hippocampus/physiology ; Animals ; *Models, Neurological ; *Neurons/physiology ; Passeriformes/physiology ; *Memory, Episodic ; *Memory/physiology ; *Nerve Net/physiology ; },
abstract = {Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an 'index' - a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ('barcodes') that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems.},
}

*Hippocampus/physiology
Animals
*Models, Neurological
*Neurons/physiology
Passeriformes/physiology
*Memory, Episodic
*Memory/physiology
*Nerve Net/physiology

@article {pmid41503923,
year = {2026},
author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H},
title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70231},
pmid = {41503923},
issn = {1744-7917},
support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; },
abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.},
}

@article {pmid41503381,
year = {2026},
author = {Zanovello, L and Eisendle, D and Casari, S and Ennemoser, M and Grund, H and Favrin, G and Rossi, S and Modesti, A and Luchelli, M and Rüber, L and Meraner, A and Gandolfi, A},
title = {Origin and Genetic Diversity of Barbatula (Cypriniformes: Nemacheilidae) in Italy.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72832},
pmid = {41503381},
issn = {2045-7758},
abstract = {Recent morphological and molecular studies suggested the existence of several undescribed species within the genus Barbatula. The stone loach (Barbatula barbatula) is considered, according to the Italian Red List, as native in Northern Italy and classified as vulnerable (VU), having a limited and fragmented distribution from Lombardy to Friuli-Venezia Giulia regions. In the present study, 248 specimens of Barbatula sp., collected from 17 sampling sites in Italy-spanning its entire known distribution area-and from one site in Austria, were analysed by sequencing the Cytochrome C Oxidase I (COI) and the Cytochrome B (CytB) mitochondrial regions. Sequencing results were then compared with reference samples from the literature. Three highly divergent mitochondrial lineages were observed in Italian populations, which can be associated with three different species: Barbatula pironae in Friuli-Venezia Giulia, Barbatula fluvicola in Trentino-Alto Adige and Lombardy, and Barbatula aff. barbatula coexisting with the latter in Lombardy. The three species, with the first having a distribution limited to the upper Adriatic area, and the other two having a wider distribution north of the Alps, should therefore be considered as different Management Units. Therefore, the integration of the Italian freshwater fish species checklist and the update of their taxonomy are strongly advised. Our data together with other available evidence suggest that the three species are likely native to Italy, and hence a revision or definition of their conservation status might be needed.},
}

@article {pmid41502534,
year = {2026},
author = {Weatherford, E and Grauer, A and Sirochinsky, C and Lehman, IF and Thummala, N and Callahan, M and Sittig, DF and Singh, H and Salmasian, H and Jurgens, M and Adelman, JS},
title = {Developing updated and new guidance to promote reliable patient identification.},
journal = {JAMIA open},
volume = {9},
number = {1},
pages = {ooaf160},
pmid = {41502534},
issn = {2574-2531},
abstract = {OBJECTIVES: To describe the process of updating the Patient Identification Safety Assurance Factors for EHR Resilience (SAFER) Guide and to review new practices and refinements to the Guide.

MATERIALS AND METHODS: We conducted a review of literature on the topic of patient identification in healthcare settings, focusing on papers published after 2016. Titles and abstracts were screened by a team of reviewers, and the full text of retained articles was used to inform the revision.

RESULTS: The updated SAFER Guide strengthens recommendations for displaying patient photographs and using electronic patient identification, including barcoding and radiofrequency identification on patient wristbands. The Guide also recommends the use of biometric identification at registration and point of care. Finally, the updated Guide removes a recommendation to restrict the number of concurrently open patient records permitted in the electronic health record.

DISCUSSION: The revised SAFER Guide includes new recommendations aimed at supporting accurate patient identification at registration, order placement, and the point of care.

CONCLUSION: The updated Patient Identification SAFER Guide provides evidence-based national recommendations to help reduce patient misidentification.},
}

@article {pmid41501532,
year = {2026},
author = {Demesa-Arevalo, E and Dӧrpholz, H and Vardanega, I and Maika, JE and Pineda-Valentino, I and Eggels, S and Lautwein, T and Kӧhrer, K and Schnurbusch, T and von Korff, M and Usadel, B and Simon, R},
title = {Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {41501532},
issn = {2055-0278},
support = {EXC2048 CEPLAS//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048 CEPLAS//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CSCS FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Grass inflorescences are composite structures, featuring complex sets of meristems as stem cell niches that are initiated in a repetitive manner. Meristems differ in identity and longevity, generate branches or split to form flower meristems that finally produce seeds. Within meristems, distinct cell types are determined by positional information and the regional activity of gene regulatory networks. Understanding these local microenvironments requires precise spatio-temporal information on gene expression profiles, which current technology cannot achieve.Here we investigate transcriptional changes during barley development, from the specification of meristem and organ founder cells to the initiation of distinct floral organs, on the basis of an imputation approach integrating deep single-cell RNA sequencing with spatial gene expression data. The expression profiles of more than 40,000 genes can now be analysed at cellular resolution in multiple barley tissues using the new web-based graphical interface BARVISTA, which enables precise virtual microdissection to analyse any sub-ensemble of cells. Our study pinpoints previously inaccessible key transcriptional events in founder cells during primordia initiation and specification, characterizes complex branching mutant phenotypes by barcoding gene expression profiles, and defines spatio-temporal trajectories during flower development. We thus uncover the genetic basis of complex developmental processes, providing novel opportunities for precisely targeted manipulation of barley traits.},
}

@article {pmid41501049,
year = {2026},
author = {Moore, ST and Lian, X and Vaidya, A and Chatterjee, S and Santelli, J and Sun, Y and Farbiak, L and Zhu, H and Siegwart, DJ},
title = {Multiplexed lipid nanoparticle barcoding reveals tissue-dynamic kinetic insights and enriched cellular tropism in hepatic zones.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68103-7},
pmid = {41501049},
issn = {2041-1723},
support = {P30CA142543//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01EB025192-06//U.S. Department of Health & Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB)/ ; },
abstract = {Lipid nanoparticles (LNPs) efficiently deliver nucleic acids to cells in vivo and facilitate clinical applications including RNA-based vaccines and therapies. Discovery and optimization of LNPs remain challenging due to the complexity of input variables and low throughput workflows. To accelerate these processes, we report a broadly compatible barcoded Cre recombinase mRNA barcode platform that enables multiplexed LNP tracking in vivo in tdTomato reporter mice. We evaluate accumulation and degradation kinetics of mRNA encapsulated in Selective Organ Targeting (SORT) LNPs in the liver, lung, and spleen, and show that functional protein activity is associated with rapid organ enrichment. We further demonstrate how barcode multiplexing can streamline systematic kinetic studies, distinguish nanoparticles with distinct biological outcomes, and differentiate subtle, yet important, variations within a series of similar formulations. Finally, we use barcoding to identify and characterize nanoparticles with hepatic zonal bias and previously overlooked extrahepatic tropism. This approach could accelerate high resolution characterization of nanoparticles with desirable properties, enable large-scale systematic studies of diverse LNPs, and provide insights into optimizable parameters of LNP-mRNA delivery.},
}

@article {pmid41500013,
year = {2025},
author = {Rani, V and Chauhan, C and Sengar, RS},
title = {DNA barcoding markers: A comprehensive review and taxonomic classification across species.},
journal = {Computational biology and chemistry},
volume = {122},
number = {},
pages = {108872},
doi = {10.1016/j.compbiolchem.2025.108872},
pmid = {41500013},
issn = {1476-928X},
abstract = {DNA barcoding has revolutionized species identification and biodiversity assessment by employing short, standardized genetic sequences as molecular markers. Since its inception by Hebert in 2003, it has become a cornerstone of taxonomy, ecology, conservation, agriculture, and medicine. This review traces the historical development of DNA barcoding, highlighting the strengths and limitations of widely used markers such as COI in animals, ITS in fungi, rbcL and matK in plants, and alternative loci in algae. The discussion emphasizes how barcoding enables accurate identification of cryptic taxa, supports food and forensic authentication, and strengthens biodiversity monitoring across ecosystems. Advancements in multi-locus strategies, genome-based markers, and DNA metabarcoding have enhanced resolution and scalability, while next-generation sequencing, environmental DNA, and nanotechnology promise to overcome persistent challenges of low variability, amplification barriers, and incomplete reference databases. Despite ongoing limitations, DNA barcoding continues to be an indispensable, cost-effective tool that bridges classical taxonomy with modern genomics. By integrating emerging technologies and fostering global collaboration, it holds immense potential for transforming biodiversity science and ensuring sustainable ecosystem management in the genomic era.},
}

@article {pmid41499369,
year = {2026},
author = {Chen, K and Luo, S and Jiang, C and Gu, S and Yang, F and Liu, X and Wang, S and Qu, X and Zhang, Q and Zhang, P and Gong, Y and Zeng, H and Qiu, D and Miao, W and Xiong, J},
title = {HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70092},
doi = {10.1111/1755-0998.70092},
pmid = {41499369},
issn = {1755-0998},
support = {2023S016//Ningbo Public Welfare Science and the Technology Program Project/ ; 2022xjkk0204//Third Xinjiang Scientific Expedition Program/ ; SNJNP2022008//Background Resources Survey in Shennongjia National Park/ ; 2019 QZKK0304//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; SNJGKL2022008//Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; 32122015//National Natural Science Foundation of China/ ; 32300355//National Natural Science Foundation of China/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Ecosystem ; *Metagenomics/methods ; *Aquatic Organisms/classification/genetics ; Fungi/genetics/classification ; Computational Biology/methods ; Bacteria/classification/genetics ; },
abstract = {Aquatic ecosystems host diverse organisms across all six life kingdoms, yet their complex interactions remain poorly understood, primarily due to limitations in transkingdom species detection methods. To address this limitation, we developed HiMBar (https://github.com/Xchenkai2019/HIFI_barcoding), a high-fidelity (HiFi) metagenomic barcoding approach that utilises long, highly accurate reads to extract multiple full-length marker genes (such as rRNA genes, COI, rbcL) directly from environmental DNA sequencing reads. These genes are subsequently clustered into operational taxonomic units (OTUs) for species identification, eliminating the need for PCR amplification or sequence assembly. HiMBar outperforms existing DNA-based methods in accuracy, recall and consistency. Applying HiMBar, we identified a stable interaction network among Cyanobacteria, Planctomycetota, Verrucomicrobiota and Fungi. Further analysis revealed that glucose metabolism plays a key role in maintaining these interactions. Our study offers a powerful tool for transkingdom species monitoring and provides a case study for exploring transkingdom interactions and their molecular mechanisms.},
}

*DNA Barcoding, Taxonomic/methods
*Ecosystem
*Metagenomics/methods
*Aquatic Organisms/classification/genetics
Fungi/genetics/classification
Computational Biology/methods
Bacteria/classification/genetics

@article {pmid41493178,
year = {2026},
author = {Piątek, M and Lutz, M and Yorou, NS and Guelly, KA and Piątek, J},
title = {Smut fungi on Trachypogon spicatus in Africa: Sporisorium trachypogonis-spicati and Tilletia afrotrachypogonis, sp. nov.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/00275514.2025.2588503},
pmid = {41493178},
issn = {1557-2536},
abstract = {Two smut fungi infecting the crinkle-awn grass Trachypogon spicatus (Poaceae) in Africa are characterized morphologically, illustrated, and linked to DNA barcodes (rDNA ITS, 28S). Sporisorium trachypogonis-spicati is reported for the first time from Benin, South Africa, and Togo, far from the previously known localities in the Democratic Republic of the Congo and Zimbabwe. This species is morphologically similar and closely related but genetically divergent to Sporisorium trachypogonicola, which infects Trachypogon spicatus in the Americas. Tilletia afrotrachypogonis is described as a new species from Togo and is also known from southeastern Africa (Malawi, Zambia). This species is morphologically almost identical to but genetically distinct from Tilletia trachypogonis, which infects Trachypogon spicatus in Mexico. The phylogenetic sister relationship, phenotype, and ecological similarity for the two species pairs Sporisorium trachypogonis-spicati/S. trachypogonicola and Tilletia afrotrachypogonis/T. trachypogonis, but occurrence in different geographic areas (Africa and the Americas/North America, respectively), suggest a common ancestral species, allopatric speciation, and duplication, i.e. speciation on the same host species.},
}

@article {pmid41490555,
year = {2026},
author = {Wei, R and Gao, Z and Cui, D and Zou, Y and Dong, Y and Tian, Q and Wen, R and Li, X and Yang, W},
title = {Aucklandia lappa, Vladimiria souliei, and Inula helenium: A comprehensive review on the ethnomedicines, phytochemicals, quality control and pharmacology of three confusable Muxiang varieties (2015-2025).},
journal = {Journal of ethnopharmacology},
volume = {360},
number = {},
pages = {121163},
doi = {10.1016/j.jep.2026.121163},
pmid = {41490555},
issn = {1872-7573},
abstract = {The dried roots of Aucklandia lappa (Mu-Xiang), Vladimiria souliei (Chuan-Mu-Xiang), and Inula helenium (Tu-Mu-Xiang), perennial species of the Asteraceae family, are commonly used in traditional Chinese medicine for their therapeutic properties.

AIM OF THE REVIEW: Morphological and phytochemical similarities among three Muxiang varieties, particularly between A. lappa and V. souliei, lead to confusion. This review aimed to provide a comprehensive analysis of their ethnomedicinal uses, phytochemistry, quality control, pharmacological properties, and modern applications.

MATERIALS AND METHODS: Relevant literatures between January 2015 and September 2025 were retrieved from the Web of Science, PubMed, ScienceDirect, and CNKI.

RESULTS: A total of 429 compounds were identified from three Muxiang varieties, mainly including the sesquiterpene lactones (SLs), monoterpenoids, triterpenoids, phenylpropanoids, and flavonoids. Among these, the contained SLs (149 compounds) were the principal bioactive constituents responsible for the effects of anticancer, anti-inflammation, gastrointestinal protection, anti-microorganism, hepatoprotection and neuroprotection. Advanced analytical methods, such as HPLC, GC-MS, DNA barcoding, and hyperspectral imaging coupled with machine learning, were established to enable accurate species differentiation and quality control. The review further provided a comparative analysis of the similarities and differences among three Muxiang varieties.

CONCLUSION: This review synthesizes the current knowledge on three Muxiang varieties, establishing a foundational resource for their botany, traditional uses, phytochemistry, pharmacology, and quality control. Despite historical confusion due to morphological and ethnopharmacological similarities, modern research has revealed differences in their chemical composition and pharmacological activities. Future validation of distinctions is essential to ensure the rational and targeted utilization of these Muxiang resources.},
}

@article {pmid41489363,
year = {2026},
author = {Pipas, JM and Sullivan, CS},
title = {mGem: Deciphering how polyomaviruses coexist with their hosts for a lifetime.},
journal = {mBio},
volume = {},
number = {},
pages = {e0231125},
doi = {10.1128/mbio.02311-25},
pmid = {41489363},
issn = {2150-7511},
abstract = {Small DNA tumor viruses such as polyomaviruses have evolved persistent, in some cases lifelong infections despite their compact genomes and host immune pressure. This review synthesizes historical and recent insights into the mechanisms underlying polyomavirus persistence and shedding, including dynamic host cell cycle regulation, viral non-coding control region modulation, and viral microRNA-mediated repression. We highlight modes of shedding consistent with concurrent latent/lytic and smoldering infections, discuss emerging evidence of reversible latency, and identify unresolved questions in viral-host interplay. Understanding these strategies is critical for managing viral reactivation and disease in immunocompromised patients and exemplifies the remarkable evolutionary success of polyomaviruses.},
}

@article {pmid41488798,
year = {2026},
author = {Yan, R and Abdullah, and Jia, J and Islam, M and Li, H and Liu, M and Yir-Erong, B and Tian, X},
title = {Characterization of Verbesina encelioides (Asteroideae, Asteraceae) Chloroplast Genome and Phylogenetic Insights.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72897},
pmid = {41488798},
issn = {2045-7758},
abstract = {Verbesina encelioides (Cav.) Benth. & Hook.f. ex A.Gray (Asteroideae, Asteraceae) is a widespread annual herb native to southwestern North America that has naturalized globally. Here, we report the first de novo assembly and comprehensive annotation of the complete chloroplast (cp) genome of V. encelioides, generated using Illumina NovaSeq sequencing. The circular genome is 152,213 bp and exhibits the characteristic quadripartite structure, comprising a large single-copy (83,911 bp) region, a small single-copy (18,248 bp) region, and two inverted repeat regions (25,027 bp each). The genome encodes 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 16 genes duplicated in the IRs. Comparative analysis with Verbesina alternifolia revealed high structural conservation regarding gene content and arrangement, codon usage, amino acid frequency, and simple sequence repeats. Codon usage showed bias toward A/T-ending codons (RSCU > 1), whereas leucine was the most abundant amino acid, and cysteine was the least frequent. Simple sequence repeat analysis predominantly identified A/T-rich mononucleotide repeats. Nucleotide diversity analysis highlighted several variable regions-including trnD-trnY, atpA-trnR, rpl32-trnL, ccsA-ndhD, and trnL-ccsA-which may serve as molecular markers. Analysis of adaptive evolution in Verbesina species and related genera identified codons under positive selection in 19 chloroplast genes: atpB, ccsA, clpP, ndhD, ndhI, psaB, psbB, rpl14, rpoB, rpoC1, rps8, ycf3, accD, matK, rbcL, ndhF, rpoC2, ycf2, and ycf1. Maximum likelihood phylogenetic analysis placed Verbesina within the tribe Heliantheae. This complete cp genome provides a valuable genetic resource for phylogenetic studies, DNA barcoding, and population genetics of Verbesina and related Asteraceae taxa.},
}

@article {pmid41484813,
year = {2026},
author = {Silva-Ramos, CR and Sierra-González, MC and Chacón Gómez, ME and Melby, PC and Aguilar, PV and Cabada, MM and Hidalgo, M},
title = {Francisella spp. as an overlooked cause of acute undifferentiated febrile illness in Colombia? Unexpected evidence from febrile patients negative for other common and neglected etiologies in Villeta municipality.},
journal = {Tropical medicine and health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s41182-025-00883-6},
pmid = {41484813},
issn = {1348-8945},
support = {D43TW010331/TW/FIC NIH HHS/United States ; },
abstract = {BACKGROUND: Acute undifferentiated febrile illness (AUFI) represents a major health challenge in tropical regions due to its wide range of etiologies. In Villeta, Colombia, previous studies investigated common causes such as malaria, arboviral diseases, leptospirosis and rickettsiosis, as well as several neglected bacterial agents. However, some patients remained without an identified etiology, underscoring the need for broader approaches to uncover other potential causes. Therefore, the aim of the present study was to investigate into other potential bacterial causes of AUFI through advanced molecular strategies utilizing 16S rRNA sequencing.

METHODS: The study analyzed AUFI patient samples previously screened for fourteen pathogens. The V3-V9 hypervariable region of the 16S rRNA gene was amplified from whole-blood DNA of unresolved cases and sequenced using the Oxford Nanopore GridION platform. Reads were filtered, quality-checked, and taxonomically classified using the SILVA database.

RESULTS: Eight samples from individuals without evidence of infection or recent exposure to previously screened pathogens were selected for 16S rRNA sequencing. DNA quality and integrity were confirmed, and enrichment produced high-quality amplicons for all samples. Sequencing generated high-quality reads overwhelmingly dominated by Francisella, representing over 93% of classified reads, followed by Coxiella and Arcobacter.

CONCLUSIONS: This study provides the first molecular evidence of Francisella in whole-blood from febrile patients in Colombia. Findings highlight its potential role in AUFI, demonstrate the value of 16S rRNA barcoding, and underscore the need for expanded surveillance of highly neglected bacterial taxa.},
}

@article {pmid41481685,
year = {2026},
author = {Harper, RL and Lelliott, PM and Bender, SB and Pinto, AR},
title = {Unraveling Cardiovascular Development and Function: Insights From Single-Cell Omics.},
journal = {Circulation research},
volume = {138},
number = {1},
pages = {e325793},
doi = {10.1161/CIRCRESAHA.125.325793},
pmid = {41481685},
issn = {1524-4571},
mesh = {Humans ; *Single-Cell Analysis/methods ; Animals ; *Cardiovascular System/metabolism/embryology/growth & development/cytology ; Transcriptome ; Cell Lineage ; *Heart/embryology ; Gene Expression Profiling ; *Genomics/methods ; },
abstract = {The cardiovascular system, composed of the heart and vasculature, is essential for blood circulation, nutrient exchange, and waste removal. In the past, our understanding of cardiovascular development and function has largely been shaped by bulk tissue analyses, which obscures cellular heterogeneity. The emergence of single-cell omics has transformed the field by enabling unbiased transcriptional profiling of individual cells, revealing the diversity of stem cells and progenitor cells driving embryogenesis, resulting in the various mature cardiovascular cell types in the adult heart and vasculature. This technology has provided unprecedented insights into the molecular mechanisms governing cardiovascular development and function by identifying novel cell subpopulations, characterizing their unique properties, and tracing their temporal evolution through advanced analytical approaches. In this review, we discuss how single-cell omics has reshaped our understanding of cardiovascular developmental biology, highlight key analytical tools and emerging approaches, examine preclinical models that have facilitated these discoveries, and explore how these technologies have defined the cellular landscape of the heart and vasculature. We conclude by looking ahead to emerging technologies such as spatial transcriptomics and clonal barcoding for lineage tracing, as well as new strategies in addressing the gender gap in cardiovascular research.},
}

Humans
*Single-Cell Analysis/methods
Animals
*Cardiovascular System/metabolism/embryology/growth & development/cytology
Transcriptome
Cell Lineage
*Heart/embryology
Gene Expression Profiling
*Genomics/methods

@article {pmid41481464,
year = {2026},
author = {Ashok, Y and Bubb, KL and Oy, C and Gorjifard, S and Cuperus, JT and Queitsch, C and Fields, S},
title = {Dosa: A method to covalently barcode proteins for high-throughput biochemistry.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2529762123},
doi = {10.1073/pnas.2529762123},
pmid = {41481464},
issn = {1091-6490},
support = {RM1HG010461//HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; R21HG013504//HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; },
mesh = {Escherichia coli/genetics/metabolism ; Humans ; *Escherichia coli Proteins/genetics/metabolism/chemistry ; *tRNA Methyltransferases/genetics/metabolism/chemistry ; RNA, Transfer/genetics/metabolism ; },
abstract = {Deep mutational scanning couples a protein's activity to DNA sequencing for high-throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like cell proliferation, as proxy for protein activity. Here, we covalently link variant proteins in vivo to an RNA barcode by fusing them to Escherichia coli tRNA (m5U54) methyltransferase TrmA (E358Q). This methyltransferase mutant forms a covalent bond with a tRNA T-arm stem-loop sequence, which we embed in an RNA along with a unique barcode. Following cell lysis, variant proteins are separated in vitro according to their biochemical properties and identified by sequencing their covalently linked barcodes. The in vitro assays can be carried out in highly denaturing conditions, such as 8 M urea, due to the covalent RNA-protein linkage. We use this method, Dosa, to analyze a large pool of FLAG epitope variants for binding to an anti-FLAG-antibody, to profile substrate variants for their cleavage by enteropeptidase and human rhinovirus 3C protease, and to measure the solubility of several hundred Aβ(1-42) variants. This method should be amenable to numerous biochemical assays with proteins produced in E. coli or mammalian cells.},
}

Escherichia coli/genetics/metabolism
Humans
*Escherichia coli Proteins/genetics/metabolism/chemistry
*tRNA Methyltransferases/genetics/metabolism/chemistry
RNA, Transfer/genetics/metabolism

@article {pmid41478996,
year = {2026},
author = {Fanli, M},
title = {Single-Cell 3' mRNA Sequencing with 10× Chromium Gel Beads-in-Emulsion (GEM) Kits.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2983},
number = {},
pages = {473-492},
pmid = {41478996},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; Humans ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; *RNA, Messenger/genetics ; *Sequence Analysis, RNA/methods ; Emulsions ; Chromium/chemistry ; Gene Expression Profiling/methods ; },
abstract = {Single-cell RNA sequencing is widely used in developmental biology, immunology, cancer research, and clinical applications, providing a scalable and reliable approach for single-cell transcriptomics. The Chromium Next GEM Single Cell 3' Reagent kits by 10× Genomics provide an advanced method for generating single-cell gene expression libraries using microfluidic partitioning and barcoding technology. These kits enable the profiling of thousands of individual cells in a single experiment by encapsulating single cells with uniquely barcoded Gel Beads-in-Emulsion (GEMs). Reverse transcription (RT) occurs within each GEM, producing barcoded cDNA, which is subsequently purified, amplified, and converted into a dual-indexed sequencing library. The workflow consists of four major steps: GEM generation and barcoding, post-GEM-RT cleanup and cDNA amplification, 3' gene expression library construction, and sequencing. Quality control measures, including SPRIselect bead cleanup, Bioanalyzer/TapeStation validation, and PCR optimization, ensure high-quality sequencing results. The final library is compatible with Illumina sequencing platforms, allowing researchers to analyze cellular heterogeneity, gene expression dynamics, and rare cell populations. This protocol is based on the 10× Chromium Single Cell 3' Reagent Kits user guide (v3.1-Dual Index), which can be downloaded from the 10× Genomics website (https://www.10xgenomics.com). It is recommended to refer to the original official guide for more details when carrying out the experiments with these kits, ensuring you stay updated with any revisions or updates.},
}

*Single-Cell Analysis/methods
Humans
Gene Library
*High-Throughput Nucleotide Sequencing/methods
*RNA, Messenger/genetics
*Sequence Analysis, RNA/methods
Emulsions
Chromium/chemistry
Gene Expression Profiling/methods

@article {pmid41478954,
year = {2026},
author = {Dong, X and Edwards, S and Deng, YM and Dapat, C and Hirankitti, A and Barr, IG},
title = {Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {149-163},
pmid = {41478954},
issn = {1940-6029},
mesh = {Humans ; *Genome, Viral ; *Whole Genome Sequencing/methods ; *Respiratory Syncytial Virus, Human/genetics ; *Respiratory Syncytial Virus Infections/virology ; *Nanopore Sequencing/methods ; *High-Throughput Nucleotide Sequencing/methods ; Multiplex Polymerase Chain Reaction/methods ; Nanopores ; },
abstract = {Respiratory syncytial virus (RSV) infection continues to be a significant burden on public health care systems and is a global health concern. Whole genome sequencing (WGS) provides a useful tool to better understand the viral transmission and emerging mutations that may impact antibody treatments, antiviral drug sensitivity, and vaccine effectiveness. Here, we describe a rapid and sensitive protocol for sequencing clinical samples of both human RSV-A and RSV-B viruses based on the Oxford Nanopore Technology (ONT) sequencing platform. It involves long amplicon generation by setting up two one-step multiplex reverse-transcription polymerase chain reactions (mRT-PCR) for each sample, library preparation with the ONT rapid barcoding kit and NGS data analysis with the ARTIC pipeline.},
}

Humans
*Genome, Viral
*Whole Genome Sequencing/methods
*Respiratory Syncytial Virus, Human/genetics
*Respiratory Syncytial Virus Infections/virology
*Nanopore Sequencing/methods
*High-Throughput Nucleotide Sequencing/methods
Multiplex Polymerase Chain Reaction/methods
Nanopores

@article {pmid41477882,
year = {2026},
author = {Campbell, IW and Hullahalli, K and Waldor, MK},
title = {Quantifying host-microbe interactions with bacterial lineage tracing.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6780},
pages = {34-40},
doi = {10.1126/science.adx5362},
pmid = {41477882},
issn = {1095-9203},
mesh = {*Host Microbial Interactions/genetics ; *Bacteria/genetics/classification ; *DNA Barcoding, Taxonomic ; Animals ; Humans ; *Host-Pathogen Interactions ; *Bacterial Infections/microbiology ; },
abstract = {Using genomic barcodes to trace bacterial lineages within a host reveals previously unobservable dynamics of infection, including the impact of infection bottlenecks, routes of bacterial dissemination, and patterns of within-host evolution. Barcoding introduces trackable diversity to otherwise isogenic bacterial populations. Comparing the barcodes within an inoculum to those within the host quantifies the "founding population," which reveals the magnitude of population collapse caused by host bottlenecks. Furthermore, comparisons of the founders between tissues can reveal the patterns of pathogen dissemination. On longer timescales, the emergence of dominant barcoded lineages can also be used to detect within-host evolution. Collectively, barcoding studies quantify the hidden parameters that underlie bacterial colonization and create a quantitative framework for modeling and preventing infectious disease.},
}

*Host Microbial Interactions/genetics
*Bacteria/genetics/classification
*DNA Barcoding, Taxonomic
Animals
Humans
*Host-Pathogen Interactions
*Bacterial Infections/microbiology

@article {pmid41476166,
year = {2025},
author = {Chen, Q and Sriram, A and Das, A and Matic, K and Hendija, M and Tonry, K and Ross, JL and Das, M and McGorty, RJ and Robertson-Anderson, RM and Valentine, MT},
title = {BARCODE: high throughput screening and analysis of soft active materials.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67963-3},
pmid = {41476166},
issn = {2041-1723},
support = {NSF DMR-2119663//National Science Foundation (NSF)/ ; NSF DMR-2118403//National Science Foundation (NSF)/ ; NSF DMR-2118449//National Science Foundation (NSF)/ ; NSF DMR-1933487//National Science Foundation (NSF)/ ; CS-PBP-2023-019//Research Corporation for Scientific Advancement (RCSA)/ ; },
abstract = {Active, responsive, non-equilibrium materials-at the forefront of materials engineering-offer dynamical restructuring, mobility and other complex life-like properties. Yet, this enhanced functionality comes with significant amplification of the size and complexity of the datasets needed to characterize their properties, thereby challenging conventional approaches to analysis. To meet this need, we present BARCODE: Biomaterial Activity Readouts to Categorize, Optimize, Design and Engineer, an open-access software that automates high throughput screening of microscopy video data to enable non-equilibrium material optimization and discovery. BARCODE produces a unique fingerprint or 'barcode' of performance metrics that visually and quantitatively encodes dynamic material properties with minimal file size. Using three complementary material-agnostic analysis branches, BARCODE significantly reduces data dimensionality and size, while providing rich, multiparametric outputs and rapid tractable characterization of activity and structure. We analyze a series of datasets of cytoskeleton networks and cell monolayers to demonstrate BARCODE's abilities to accelerate and streamline screening and analysis, reveal unexpected correlations and emergence, and enable broad non-expert data access, comparison, and sharing.},
}

@article {pmid41474525,
year = {2025},
author = {Unitt, A and Krisna, MA and Parfitt, KM and Jolley, KA and Maiden, MCJ and Harrison, OB},
title = {Neisseria gonorrhoeae LIN codes provide a robust, multi-resolution lineage nomenclature.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41474525},
issn = {2050-084X},
support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10.35802/218205/WT_/Wellcome Trust/United Kingdom ; 10.35802/214374/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Neisseria gonorrhoeae/genetics/classification ; Multilocus Sequence Typing/methods ; *Terminology as Topic ; Phylogeny ; Gonorrhea/microbiology ; Humans ; *DNA Barcoding, Taxonomic/methods ; },
abstract = {Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to consistently identify N. gonorrhoeae lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect N. gonorrhoeae strain taxonomy in a reliable and stable manner. Here, a N. gonorrhoeae genomic lineage nomenclature, based on the barcoding system of Life Identification Number (LIN) codes, was developed using a refined 1430 core gene MLST (cgMLST). This hierarchical LIN code nomenclature conveys lineage information at multiple levels of resolution within one code, enabling it to provide immediate context to an isolate's ancestry, and to relate to familiar, previously used typing schemes such as Ng cgMLST v1, 7-locus MLST, or NG-STAR clonal complex (CC). Clustering with LIN codes accurately reflects gonococcal diversity and population structure, providing insight into associations between genotype and phenotype for traits such as antibiotic resistance. These codes are automatically assigned and publicly accessible via the https://pubmlst.org/organisms/neisseria-spp database.},
}

*Neisseria gonorrhoeae/genetics/classification
Multilocus Sequence Typing/methods
*Terminology as Topic
Phylogeny
Gonorrhea/microbiology
Humans
*DNA Barcoding, Taxonomic/methods

@article {pmid41472846,
year = {2025},
author = {Wang, G and Zhao, L and Shi, Y and Qu, F and Ding, Y and Liu, W and Liu, C and Luo, G and Li, M and Bai, X and Li, L and Wang, L and Wong, CC and Ho, YP and Yu, J},
title = {High-throughput generic single-entity sequencing using droplet microfluidics.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70087},
pmid = {41472846},
issn = {2770-596X},
abstract = {Single-cell sequencing has revolutionized our understanding of cellular heterogeneity by providing a micro-level perspective in the past decade. While heterogeneity is fundamental to diverse biological communities, existing platforms are primarily designed for eukaryotic cells, leaving significant gaps in the study of other single biological entities, such as viruses and bacteria. Current methodologies for single-entity sequencing remain limited by low throughput, inefficient lysis, and highly fragmented genomes. Here, we present the Generic Single-Entity Sequencing (GSE-Seq), a versatile and high-throughput framework that overcomes key limitations in single-entity sequencing through an integrated workflow. GSE-Seq combines (1) one-step generation of massive barcodes, (2) degradable hydrogel-based in situ sample processing and whole genome amplification, (3) integrated in-droplet library preparation, and (4) long-read sequencing. We applied GSE-Seq to profile viral communities from human fecal and marine sediment samples, generating thousands of high-quality single-entity genomes and revealing that most are novel. GSE-Seq identified not only dsDNA and ssDNA viruses, but also hard-to-detect giant viruses and crAssphages. GSE-Seq of bacterial genomes also revealed putative novel bacterial species, validating the versatility of this platform across different microbial kingdoms. Collectively, GSE-Seq represents a robust framework that addresses persistent challenges in high-throughput profiling for generic applications and holds immense promise for single-cell deconvolution of diverse biological entities.},
}

@article {pmid41472828,
year = {2025},
author = {Bonet, DF and Blumenthal, JI and Lang, S and Dahlberg, SK and Hoffecker, IT},
title = {Spatial coherence in DNA barcode networks.},
journal = {Patterns (New York, N.Y.)},
volume = {6},
number = {12},
pages = {101428},
pmid = {41472828},
issn = {2666-3899},
abstract = {DNA barcode networks are the basis of sequencing-based microscopy, an emerging family of chemical imaging methods aiming to reconstruct spatial information, without optics, using sequencing technology. These methods capture microscopic spatial information by forming networks composed of many local chemical interactions, each marked by a unique, DNA-based barcode. However, the fundamental laws governing such networks are not yet understood, and spatial barcode networks are influenced by structural distortions such as false or shortcut edges. Current methods lack ground-truth-free tools to validate spatial quality, and we address this with a framework for topology-based quality control. We define a fundamental feature of spatial networks, spatial coherence, which quantifies geometric self-consistency in a network. By formalizing this relationship into quantitative metrics adapted from classical geometric rules, we could quantify spatial distortions by using only network data and show how these can be used as an optimization criterion to iteratively improve spatial reconstruction.},
}

@article {pmid41472539,
year = {2025},
author = {Gustafsson, DR and Lee, L and Grossi, AA and Zou, F and Tan, DJX and Song, HW and Meier, R},
title = {From host to host, and continent to continent: Two phoresy-enabled Guimaraesiella hitchhiker louse species revealed by integrative taxonomy (Phthiraptera: Ischnocera).},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70045},
pmid = {41472539},
issn = {1365-2915},
support = {GIABR-GJRC201701//Introduction of Full-Time High-Level Talent Fund of the Institute of Zoology, Guangdong Academy of Sciences/ ; 31961123003//National Natural Science Foundation of China/ ; 32001098//National Natural Science Foundation of China/ ; //Foreign Young Talent Plan/ ; //Guangdong Academy of Sciences Special Project of Science and Technology Development/ ; //Pearl River Talent Recruitment Program of Guangdong Province/ ; },
abstract = {The 'core Guimaraesiella' comprise a morphologically rather homogeneous group of avian chewing lice (Phthiraptera), most of which remain undescribed. Based on an integrative approach combining morphological characters and analyses of COI barcoding sequences, we here describe two new species within this group: Guimaraesiella impiger new species and Guimaraesiella stellana new species. Both species were collected from hippoboscid flies in Singapore, suggesting that they are capable of moving phoretically between hosts. In at least G. impiger, this was confirmed as louse specimens from another 30 host species that were found to be conspecific with the holotype of G. impiger in our mOTU analysis. This, together with limited morphological variability between species, highlights the need to combine genetic and morphological data when identifying 'core Guimaraesiella' species from southeast Asia. Moreover, both louse species appear to be able to cross vast geographical distances. Guimaraesiella impiger is known from across southeast Asia as well as in Malawi, despite none of the known hosts occurring in both Asia and Africa. Guimaraesiella stellana is known from two host species, one in Singapore and one in Australia, separated by several known biogeographical barriers, which seem to have limited the range of all known closely related species to the Australo-Papuan region; how G. stellana arrived in Singapore on a nonmigratory host is presently unknown. These cases highlight that comparisons with only locally occurring louse species may not be a valid identification method for this group. As both species described here are morphologically similar, identification of cryptic species of lice in this group within Guimaraesiella may need to rely on COI barcodes or other molecular markers.},
}

@article {pmid41471855,
year = {2025},
author = {Cova, BO and Saranholi, BH and Gestich, CC and Machado, PR and Monte-Alegre, AF and Schriefer, A},
title = {Invertebrate-Derived DNA (iDNA) to Identify Sand Flies' Bloodmeal: A Molecular Approach to Identifying Hosts in Blood-Feeding Vectors of Leishmaniasis.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471855},
issn = {2076-2607},
support = {1U01AI136862-18/NH/NIH HHS/United States ; },
abstract = {DNA metabarcoding data obtained by next generation sequencing (NGS) has been used to identify species in mixed biological samples, such as DNA from the gut content of invertebrates that feed on vertebrates (invertebrate-derived DNA, iDNA). This investigation employed DNA metabarcoding approach to determine vertebrate hosts of female phlebotomine sand flies, blood-feeding leishmaniasis vectors. We evaluated performance across three mitochondrial markers: a mammal-specific mini-barcode (16S rRNA), a pan-vertebrate mini-barcode (12S rRNA), and a standard CytB barcode region. Phlebotomine sand flies collections occurred in the Cacao Region of Southeastern Bahia, Brazil, an American Tegumentary Leishmaniasis (ATL) endemic zone. Our analysis examined iDNA from forty female specimens pooled in thirteen samples of seven sand fly species, including confirmed ATL vectors. Metabarcoding-derived operational taxonomic units (OTUs) underwent taxonomic assignment through comparison with GenBank NCBI[®] reference databases. Results identified twenty vertebrate OTUs: primates (four OTUs), rodents (four), ungulates (five), marsupials (one), plus a domestic dog and a chicken. Notably, non-mammalian taxa, including reptiles (one OTU) and amphibians (three), were detected. The iDNA metabarcoding approach allowed us to accurately sample the diversity of phlebotomine sandflies' bloodmeals in a single specimen of a non-engorged female sand fly with mixed feeding.},
}

@article {pmid41471226,
year = {2025},
author = {Apaa, TT and Oke, PO and Shima, FK and Fidelis, GA and Dunham, S and Tarlinton, R},
title = {Canine Ticks, Tick-Borne Pathogens and Associated Risk Factors in Nigeria.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121271},
pmid = {41471226},
issn = {2076-0817},
support = {00000//University of Nottingham/ ; },
mesh = {Animals ; Dogs ; Nigeria/epidemiology ; *Dog Diseases/epidemiology/parasitology/microbiology ; Risk Factors ; *Tick-Borne Diseases/epidemiology/veterinary/parasitology ; *Tick Infestations/veterinary/epidemiology/parasitology ; Male ; *Ticks/microbiology/parasitology ; Female ; Prevalence ; Ehrlichia/isolation & purification/genetics ; Anaplasma/isolation & purification ; Rhipicephalus sanguineus ; Babesia/isolation & purification/genetics ; },
abstract = {Tick-borne pathogens (TBPs) pose a significant threat to canine health in Nigeria. Despite this, there is little data on the molecular identification of ticks and TBPs of dogs in Nigeria. This study assessed the prevalence of ticks and TBPs in Nigerian dogs, along with associated risk factors. A total of 259 dogs were enrolled in the study, from which 112 adult ticks were collected. Of these, 40 were characterized by molecular barcoding confirming Rhipicephalus sanguineus (R. sanguineus, 35/40) and Haemphysalis leachi (H. leachi, 5/40) infestations. Nucleotide sequences showed high percentage similarity to R. sanguineus tropical lineage and H. leachi sequences from Chad. Point-of-care (POC) testing of 259 dogs detected antibodies to TBPs in 40.9% of blood samples, with Ehrlichia (29.7%), Anaplasma (10.8%), and Dirofilaria (0.4%) species identified. PCR assays revealed a prevalence of 58.7% for TBPs, including Ehrlichia (40.5%) and Babesia (17.4%), with 7.3% co-infected. Risk factor analysis showed that adult dogs and those infested with ticks had a higher likelihood of TBP seropositivity. Exotic breeds and dogs examined during the rainy season were more likely to test positive for TBPs via PCR. Overall, this study demonstrates the high prevalence of diverse TBPs in Nigerian dogs and suggests that dog breed may play a role in susceptibility to diseases.},
}

Animals
Dogs
Nigeria/epidemiology
*Dog Diseases/epidemiology/parasitology/microbiology
Risk Factors
*Tick-Borne Diseases/epidemiology/veterinary/parasitology
*Tick Infestations/veterinary/epidemiology/parasitology
Male
*Ticks/microbiology/parasitology
Female
Prevalence
Ehrlichia/isolation & purification/genetics
Anaplasma/isolation & purification
Rhipicephalus sanguineus
Babesia/isolation & purification/genetics

@article {pmid41470621,
year = {2025},
author = {Krivina, E and Sinetova, M and Starikov, A and Portnov, A and Temraleeva, A},
title = {Evaluating Species Delimitation Methods in Chloroidium (Trebouxiophyceae, Chlorophyta): Efficacy of DNA Barcodes and Description of Chloroidium pseudoellipsoideum sp. nov. from Arctic Soils.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
pmid = {41470621},
issn = {2223-7747},
support = {# 075-15-2025-485//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Despite extensive research into green microalgae belonging to the genus Chloroidium, their species diversity and biotechnological potential remain poorly characterized. The strain VKM Al-418, the subject of this study, was isolated from the soil of Duvannyi Yar (Russian Federation). The independent species status of this strain is supported by distinct morphological characteristics, robust phylogenetic placement based on the 18S-ITS1-5.8S-ITS2 fragment, and unique features in the secondary structures of both ITS1 and ITS2, including one compensatory base change (CBC) in the highly conserved helix III of ITS2. Additionally, the species delimitation was also confirmed using five independent algorithmic approaches analyzing four different DNA barcodes. The concatenated ITS1-5.8S-ITS2 fragment is more reliable for species discrimination than the individual ITS1 or ITS2 barcodes. Of the species delimitation methods evaluated, ASAP (Assemble Species by Automatic Partitioning) and GMYC (Generalized Mixed Yule Coalescent) performed best in distinguishing Chloroidium species across multiple barcode regions in our analysis. The fatty acid profile of strain VKM Al-418 was analyzed at 9 °C, 22 °C, and 27 °C and exhibited high plasticity in response to temperature, indicative of an adaptive strategy to its harsh environment. Using this integrative taxonomic approach, we describe Chloroidium pseudoellipsoideum sp. nov., a new species with a distinct phylogenetic positioning and promising biotechnological properties.},
}

@article {pmid41470043,
year = {2025},
author = {Martin, PA and Pacheco-Sierra, G and Mestre, AP and Siroski, P and Amavet, PS},
title = {DNA Barcoding for Species Identification and Conservation of Caimans (Crocodilia: Alligatoridae).},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.70060},
pmid = {41470043},
issn = {2471-5646},
support = {//Student Research Assistance Scheme (SRAS)/ ; PICT-2013-1402//Agencia (FONCyT)/ ; },
abstract = {Systematics has become an essential aspect of managing and conserving species from the order Crocodilia. All members of the group are listed in CITES appendices, and to control illegal traffic of animals and subproducts, we must be able to correctly assess the specific identity of the samples. Genetic DNA barcoding is a very efficient tool for species identification in the animal kingdom, based on the sequencing of a region of a mitochondrial gene, the Cytochrome oxidase subunit I (COI). Our principal aims were to design specific primers that allow obtaining this sequence from the genetic material of the caiman species and test the potential utility of barcoding in forensic studies, as well as verify the correct identification of different collections. We successfully obtained barcodes using our designed primers to amplify caiman samples, studying a fragment of 610 bp. We also compared sequences (N = 290) from public databases of all the species included in the Order Crocodilia, obtaining a tree that resulted in a similar current crocodilian phylogeny. The primers designed can be applied to obtain barcodes from samples of other crocodilian species, and this information can contribute significantly to forensic and systematic studies.},
}

@article {pmid41469971,
year = {2025},
author = {Bradley, DD and Schimke, EJ and Alvey, AP and Hofmann, HA and Solomon-Lane, TK},
title = {Tagging Very Small Fish: Two Effective and Low Impact Methods.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.70058},
pmid = {41469971},
issn = {2471-5646},
support = {IOS-1354942//NSF/ ; #947 (2016)//BEACON Center for the Study of Evolution in Action/ ; #1081 (2017, 2018)//BEACON Center for the Study of Evolution in Action/ ; IOS-2341006//NSF/ ; //Department of Natural Sciences/ ; },
abstract = {Identifying individuals over time and across contexts is essential in many scientific fields. There are a variety of well-established methods for uniquely marking individuals (e.g., visible implant elastomer, barcodes, paint). However, for some species, life history stages, and/or experiments, existing methods are not sufficient. Here, we describe procedures for how two tagging methods-a tattoo ink injection method and a fishing line piercing method - can be used with the youngest, smallest juveniles of the African cichlid fish, Astatotilapia burtoni, which are too small for the methods used with adults. With the tattoo method, we injected tattoo ink into the dorsal muscle. Different colors and injection locations can be used to distinguish among individuals over a period of weeks (up to 4 weeks, average 2.5-3 weeks under our conditions). Because fish this young and small are sensitive to handling and injection, we also include physiological data showing fish recover well from anesthetization and tagging. With the piercing method, very thin fishing line is threaded through the dorsal muscle and tied into a barbell or loop. Unique colors and patterns can be used to distinguish among individuals over a period of months. Because a physical tag might impede normal movement in a very small fish, we also include data from an open field exploration test showing similar behavior between tagged and control (non-tagged) juveniles. We expect these effective and inexpensive methods to be useful for a variety of small species and will facilitate early-life, developmental, and longitudinal research.},
}

@article {pmid41465714,
year = {2025},
author = {Rincón, JA and Del Río, MG and Marvaldi, AE},
title = {Taxonomic Revision of the South American Genus Eudius and First Insights into the Phylogeny of the Tribe Eudiagogini (Curculionidae: Entiminae).},
journal = {Insects},
volume = {16},
number = {12},
pages = {},
pmid = {41465714},
issn = {2075-4450},
support = {PIP 3108//CONICET/ ; },
abstract = {The genus Eudius Schoenherr is classified in the broad-nosed weevil tribe Eudiagogini (Entiminae) and harbors two species, Eudius quadrisignatus Gyllenhal and Eudius jocosus Fahraeus, which are only known from their original descriptions. It is endemic to the Brazilian Atlantic Forest, which is one of the most threatened biomes in the world despite being a biodiversity hotspot. In this contribution, and as part of a wider systematic and phylogenetic study on tribe Eudiagogini, we performed a taxonomic revision of the genus Eudius and made preliminary phylogenetic analyses of Eudiagogini based on morphology and molecular evidence. Specimens from seven collections in Argentina, Brazil, and Europe were examined. Diagnosis and redescription of the genus and its species are provided, along with photographs of habits, and illustrations of diagnostic characters and new geographic distribution data. Additionally, a lectotype is designated for each species. The morphology-based phylogenetic analysis was performed under maximum parsimony, using 60 characters from adults coded for representative species from eight genera of Eudiagogini and other related tribes of Entiminae. As a result, monophyly of the genus Eudius and its placement within the tribe Eudiagogini are confirmed, while placement of the genus Chileudius Kuschel in Eudiagogini is refuted. A first molecular phylogenetic analysis of the tribe was also designed, using DNA sequences (of the COI barcode and two ribosomal markers) available for some representatives of Eudiagogini and outgroup taxa, analyzed under parsimony and maximum likelihood. The molecular results are consistent with morphology in recovering a monophyletic tribe Eudiagogini, excluding the genus Chileudius, which is now placed as incertae sedis in Entiminae, pending further analyses. Informative characters within the tribe are discussed, with Eudius supported as a clade by the basally connate tarsal claws and by the sclerites present in the bursa of female genitalia. Synapomorphies justifying the revised concept of Eudiagogini as a natural tribe are highlighted, like the presence of a cavernous prementum and the metaventrite with a spine-like swelling anterior to each metacoxa.},
}

@article {pmid41465705,
year = {2025},
author = {Shapoval, NA and Nokkala, S and Nokkala, C and Shapoval, GN and Labina, ES and Romanovich, AE and Kuznetsova, VG},
title = {Genetic Differentiation of Bisexual and Parthenogenetic Populations of Plant Louse Cacopsylla ledi (Hemiptera, Psylloidea).},
journal = {Insects},
volume = {16},
number = {12},
pages = {},
pmid = {41465705},
issn = {2075-4450},
support = {FZMW-2023- 0006//Ministry of Science and Higher Education of the Russian Federation/ ; 125012901042-9//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {The psyllid genus Cacopsylla comprises mainly bisexually reproducing species; however, some members of this genus exhibit a unisexual mode of reproduction. Using an integrative approach that combines molecular and cytogenetic methods, as well as Wolbachia screening, we conducted a comprehensive study of the Palaearctic species C. ledi. We show that this species uses various reproductive strategies (bisexual and parthenogenetic) across its distribution range. Our findings indicate that the bisexual mode of reproduction has emerged at least twice in the evolutionary history of C. ledi. Bisexual populations in southern Fennoscandia are of ancestral origin, whereas the bisexual mode of reproduction observed in northern Fennoscandia represents a recent secondary transition from parthenogenesis. We report that in the first case, parthenogenetic and bisexual lineages can be easily distinguished not only cytogenetically but also by DNA barcoding, while in the second case, "bisexual" individuals share DNA barcodes with parthenogenetic ones. A comprehensive Wolbachia screening (1140 specimens across the entire distribution range) revealed Wolbachia infection in every specimen of C. ledi, indicating a significant role of the endosymbiont in the biology and evolution of this species.},
}

@article {pmid41465176,
year = {2025},
author = {Budowle, B and Sajantila, A and Vanek, D},
title = {Animal Species and Identity Testing: Developments, Challenges, and Applications to Non-Human Forensics.},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
pmid = {41465176},
issn = {2073-4425},
support = {VJ01010026//Ministry of Interior, Czech Republic/ ; },
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Forensic Genetics/methods ; Humans ; *DNA Barcoding, Taxonomic/methods ; Species Specificity ; Genetic Markers ; },
abstract = {Biological samples of non-human origin, commonly encountered in wildlife crime investigations, present distinct challenges regarding forensic DNA analysis efforts. Although the types of samples encountered in human identity testing can vary to some degree, analyzing DNA from one species is facilitated by unified processes, common genetic marker systems, and national DNA databases. In contrast, non-human animal species identification is confounded by a diverse range of target species and a variety of sampling materials, such as feathers, processed animal parts in traditional medicine, and taxidermy specimens, which often contain degraded DNA in low quantities, are contaminated with chemical inhibitors, and may be comingled with other species. These complexities require specialized analytical approaches. Compounding these issues is a lack of validated non-human species forensic sampling and typing kits, and the risk of human DNA contamination during evidence collection. Markers residing on the mitochondrial genome (mtDNA) are routinely sought because of the large datasets available for comparison and their greater sensitivity of detection. However, the barcoding results can be complicated at times for achieving species-level resolution, the presence of nuclear inserts of mitochondrial DNA (NUMTs), and the limitation of mtDNA analysis alone to detect hybrids. Species-specific genetic markers for identification have been developed for a few high-profile species; however, many CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora)-listed organisms lack specific, validated forensic analytical tools, creating a significant gap in investigative enforcement capabilities. This deficiency stems in part from the low commercial nature of wildlife forensics efforts, a government research-driven field, the difficulty of obtaining sufficient reference samples from wild populations, limited training and education infrastructure, and inadequate funding support.},
}

Animals
DNA, Mitochondrial/genetics
*Forensic Genetics/methods
Humans
*DNA Barcoding, Taxonomic/methods
Species Specificity
Genetic Markers

@article {pmid41465154,
year = {2025},
author = {Xu, D and Zhang, L and Zhang, C and Song, L and Qian, W and Luo, H and Zhao, Q},
title = {Comparative Analysis and Characterization of Plastid Genomes of Mycetia (Rubiaceae).},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
pmid = {41465154},
issn = {2073-4425},
support = {32200169//National Natural Science Foundation of China/ ; },
mesh = {*Genome, Plastid ; Phylogeny ; Microsatellite Repeats/genetics ; *Rubiaceae/genetics/classification ; Base Composition ; Genome, Chloroplast ; Codon Usage ; Evolution, Molecular ; Plastids/genetics ; },
abstract = {BACKGROUND: Mycetia, a subshrub genus within the subfamily Rubioideae (Rubiaceae), is predominantly distributed in tropical Asia, lacking comprehensive plastid genomic resources. This study aimed to characterize the complete plastid genomes of two Mycetia species and explore their structural features and evolutionary relationships.

METHODS: The plastid genomes of Mycetia hirta and Mycetia sinensis were sequenced and assembled. We analyzed genome structure, simple sequence repeats (SSRs), long repeats, codon usage, nucleotide diversity (π), and Ka/Ks and conducted phylogenetic analysis.

RESULTS: Both genomes exhibited a typical quadripartite structure (153,989-154,588 bp; GC content 37.7-37.8%), encoding 126 genes (86 protein-coding, 8 rRNA, and 32 tRNA). Both chloroplast genomes contained 52-60 SSRs and three repeat types with minor interspecific differences. Junction regions and codon usage were highly conserved, with slight variations in RSCU values. The average π was 0.0096, and the non-coding trnE-trnT (π = 0.0817) emerged as a potential DNA barcode. The average Ka/Ks was 0.2900, indicating purifying selection. Phylogenetic analysis confirmed the monophyly of Mycetia within Argostemmateae.

CONCLUSIONS: This study provides the first comparative plastid genomic analysis for Mycetia, enhancing our understanding of its genetic diversity and supporting future phylogenetic and taxonomic research on the genus.},
}

*Genome, Plastid
Phylogeny
Microsatellite Repeats/genetics
*Rubiaceae/genetics/classification
Base Composition
Genome, Chloroplast
Codon Usage
Evolution, Molecular
Plastids/genetics

@article {pmid41465096,
year = {2025},
author = {Karbarz, M and Lebioda, E and Leśko, A},
title = {DNA Barcoding Protocol for Masdevallia Orchids: A Tool for CITES-Based Identification and Trade Control.},
journal = {Genes},
volume = {16},
number = {12},
pages = {},
pmid = {41465096},
issn = {2073-4425},
support = {Agreement No. RID/SP/0010/2024/1//Minister of Science of the Republic of Poland under the Program "Regional Initiative of Excellence"/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; Endangered Species ; DNA, Plant/genetics ; Conservation of Natural Resources ; },
abstract = {Background: Orchids of the Masdevallia genus are characterized by their beautiful esthetic qualities. However, they are vulnerable to habitat destruction, illegal harvesting, tourism and climate change. These extinction threats have led to the listing of all Masdevallia species in Appendix II of CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) and their selection by the IUCN (International Union for Conservation of Nature). Orchids are sold in various forms, e.g., stems or tubers, rendering them impossible to identify based on morphology alone. DNA barcoding is a method that enables reliable identification of organisms using DNA barcodes, and it offers an excellent solution to the need for efficient identification of Masdevallia orchids. The aim of this study was to determine the most effective locus for DNA barcode identification of Masdevallia orchids in order to develop a quick and practical identification method for this genus. Such a method can be used by CITES verification authorities to detect illegal trade. This is the first focused study to validate a DNA barcoding protocol for Masdevallia for CITES enforcement purposes. Methods: Three genetic regions were analyzed: matK, rbcL, and ITS. The effectiveness of identification was verified based on results obtained from the new version of the BOLD Systems v.5 reference database. Results: Although Masdevallia is not well represented in this database, successful identification to the genus level was achieved. Conclusions: The highest identification efficiency at the genus level was achieved for the ITS region (91%).},
}

*DNA Barcoding, Taxonomic/methods
*Orchidaceae/genetics/classification
Endangered Species
DNA, Plant/genetics
Conservation of Natural Resources

@article {pmid41463928,
year = {2025},
author = {Barua, S and Tarannum, A and Rupprecht, CE and Simonis, MC and Barrantes Murillo, DF and Willoughby, JR and Wang, C},
title = {A Simple Yet Reliable 12S rRNA-Based Molecular Approach for Identifying Bat Species.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
doi = {10.3390/ani15243643},
pmid = {41463928},
issn = {2076-2615},
support = {G0018155//Alabama Department of Conservation & natural Resources/ ; },
abstract = {Bats (Chiroptera) represent nearly one-fifth of all mammalian species and play vital ecological roles as pollinators, pest controllers, and reservoirs of zoonotic pathogens. Accurate identification of bat species is essential for biodiversity monitoring, conservation, and disease surveillance. Traditional methods based on morphology or acoustic calls are often limited by overlapping features, while DNA barcoding using the cytochrome oxidase I (COI) gene can be hindered by sequence variability. In this study, we developed a simple, single-step PCR assay targeting a short, variable region of the mitochondrial 12S rRNA gene. Alignment of sequences from 232 bat species allowed the design of a single primer pair producing a 203-224 bp amplicon that successfully distinguished all species analyzed. The assay achieved 100% amplification success across 241 bat samples, with 97.2% concordance between molecular and morphological identification. Two samples showed sequence divergence suggestive of an undescribed species. Overall, ten bat species from six genera were identified, with Eptesicus fuscus being the most frequent. This assay offers a practical and robust approach for bat identification, supporting biodiversity assessment and pathogen surveillance in ecological and public health research.},
}

@article {pmid41460495,
year = {2025},
author = {Podlipec, R and Krišelj, A and Zorc, M and Matjan Štefin, P and Usaar, S and Humar, M},
title = {Nanometer-Precision Tracking of Adipocyte Dynamics via Single Lipid Droplet Whispering-Gallery Optical Resonances.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.5c03272},
pmid = {41460495},
issn = {2379-3694},
abstract = {Biophotonics─and more recently, biointegrated photonics─offer transformative tools for probing cellular processes with unprecedented precision. Among these, whispering-gallery-mode (WGM) resonators (optical microcavities formed in spherical structures) have emerged as powerful biosensors and intracellular barcodes. Lipid droplets (LDs), with their high refractive index and intrinsic spherical geometry, are ideal candidates for supporting intracellular lasing. Although lasing in LDs has been previously demonstrated, it has not yet been harnessed to study live-cell biology. Here, we report the first use of WGM resonances in LDs of live primary adipocytes, employing a continuous-wave (CW) laser at powers below the biological damage threshold. By measuring these resonances, we achieved nanometer-scale precision in size estimation, enabling real-time observation of rapid LD dynamics and deformations on the minute scale─far beyond the spatiotemporal resolution of conventional microscopy. We systematically characterized this photonic sensing approach, demonstrating its ability to resolve adipocyte heterogeneity, monitor lipolytic responses to forskolin and isoproterenol, and detect early signs of cell viability loss─well before conventional assays. This proof-of-concept establishes intracellular LD WGM resonances as a robust platform for investigating live single-cell metabolism. The technique enables rapid, cost-effective assessment of adipocyte function, reveals cell-to-cell variability obscured by bulk assays, and lays the foundation for high-throughput analysis of metabolism- and obesity-related diseases at both the cellular and tissue levels.},
}

@article {pmid41459143,
year = {2025},
author = {Fleming, AJ and Smith, MA and Hallwachs, W and Janzen, D},
title = {A new genus and a new species in the tribe Eryciini (Diptera, Tachinidae) from Area de Conservación Guanacaste in north-western Costa Rica.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e161853},
pmid = {41459143},
issn = {1314-2828},
abstract = {BACKGROUND: A new genus and species of within the tribe Eryciini are described from the Area de Conservación Guanacaste (ACG) in north-western Costa Rica. Specimens were reared from wild-caught caterpillars collected during an ongoing biodiversity inventory within the ACG. An integrative taxonomic approach was used to characterise the new taxa, incorporating morphological analysis, life history data and DNA barcodes, supported by high-resolution photographs. Furthermore, two new combinations are proposed and the associated species are re-described. A lectotype is designated for Exorista loxostegae (Reinhard, 1922) and an identification key to the species of the new genus is provided.

NEW INFORMATION: The description of the new genus Santarosamyia Fleming and Wood, 2024 gen. nov. along with the new species: Santarosamyia woodorum Fleming & Wood sp. nov. are provided.The following new combinations are proposed: Nilea erecta (Coquillett, 1902) as Santarosamyia erecta (Coquillett, 1902) comb. nov.; Nilea uniplilum (Aldrich & Webber, 1924) as Santarosamyia unipilum (Aldrich & Webber, 1924) comb. nov.A lectotype is designated for Exorista loxostegae (Reinhard, 1922).Tachinidae, Diptera, Costa Rica, CO1, Parasitoid, Guanacaste.},
}

@article {pmid41458355,
year = {2025},
author = {Qian, Y and Wang, F and Gao, J and Jiang, Z and Gao, X and Chen, Z},
title = {Integrating Extracellular Vesicles Proteomics and Clinical Parameters to Develop a High-Precision Predictive Model for Severe Asthma.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {17945-17960},
pmid = {41458355},
issn = {1178-7031},
abstract = {INTRODUCTION: This study aimed to identify biomarkers and develop a predictive model for distinguishing severe asthma (SA) from non-severe asthma (NSA) by integrating clinical data and extracellular vesicles (EVs) proteomics.

METHODS: Plasma-derived EVs were isolated from 44 individuals, including 15 healthy controls, 15 SA patients, and 14 NSA patients. Proteomic profiling of EVs was performed using proximity barcoding assay (PBA). Clinical indicators such as FEV1/FVC ratio, DLCO% predicted, and blood neutrophil count were recorded. A multivariate model incorporating both clinical and EV-derived protein data was constructed and evaluated using ROC curve analysis. Candidate biomarkers were further validated in cell-based and murine SA models.

RESULTS: Although total EV counts and protein load did not differ significantly across groups, specific EV proteins (eg, SELL, PECAM1, ITGB3, CD9) were consistently elevated. Notably, protein combinations such as ITGB3&CLDN1 and ESAM&ITGA6 showed strong discriminatory power between SA and NSA (AUC > 0.8). The integrative model combining clinical metrics and EV proteins (IL6, NGFR, NFASC, PCDHA1) achieved a high predictive accuracy (AUC = 0.97 ± 0.075). Expression of IL6, NGFR, and NFASC was significantly upregulated in SA cellular and animal models, aligning with patient data.

CONCLUSION: This study presents a reliable multi-parameter model for distinguishing severe from non-severe asthma, leveraging both clinical indicators and EV proteomics. These findings support the potential of EV-based biomarkers in early diagnosis and personalized management of SA.},
}

@article {pmid41455508,
year = {2025},
author = {Bassini-Silva, R and da Cruz, LF and Carvalho, JT and de Souza Mello-Oliveira, V and Pesenato, IP and Calchi, AC and Castro-Santiago, AC and de Oliveira Andrade, L and da Silva Zampim, G and de Oliveira Bonaldo, R and Miranda, LFD and Subutzki, MEBS and Perrone, RF and de Quadros, RM and Ueno, TEH and Hoppe, EGL and André, MR and Duarte, JMB and Dos Santos Cruz Piveta, C and Labruna, MB and Barros-Battesti, DM and Dowling, APG and de Castro Jacinavicius, F},
title = {Sleeping with the enemy II: Expanding the ecological, molecular, and epidemiological knowledge of the tropical fowl mite, Ornithonyssus bursa (Berlese, 1888).},
journal = {Parasitology international},
volume = {},
number = {},
pages = {103226},
doi = {10.1016/j.parint.2025.103226},
pmid = {41455508},
issn = {1873-0329},
abstract = {Ornithonyssus bursa (Berlese), the tropical fowl mite from the family Macronyssidae, is a hematophagous ectoparasite of birds with increasing importance in human and animal health. This study reports new cases of human parasitism associated with O. bursa in Brazil, involving direct contact with avian hosts or their nests. These cases include new geographic records in the states of São Paulo and Santa Catarina, and new associations with bird species, including the first known record in Amazona aestiva (Psittaciformes). Molecular analysis was performed on individual mites to characterize the species and investigate associated microorganisms. This study provides the first partial sequence of the cox1 gene for O. bursa and the first phylogenetic analysis for the family using this marker. Additionally, we report the first detection of Ehrlichia and Wolbachia in Brazilian specimens. Phylogenetic analyses based on the 16S rRNA sequences placed the Ehrlichia haplotype close to strains previously detected in Haemaphysalis spp. ticks and the Wolbachia haplotype within supergroup E. These findings expand our understanding of the ecological and microbial diversity of O. bursa, highlighting its public health relevance, and emphasize the need for further studies on its vector potential and evolutionary relationships.},
}

@article {pmid41453807,
year = {2025},
author = {Hanna, AR and Shepherd, SJ and Datto, GA and El-Mayta, R and Anderson, T and Navarro, IB and Ricciardi, AS and Padilla, MS and Srikumar, N and Zhang, S and Yamagata, HM and Meng, NY and Buser, JR and Alameh, MG and Mitchell, MJ and Issadore, DA},
title = {Automated and Parallelized Microfluidic Generation of Large and Precisely Defined Lipid Nanoparticle Libraries.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c15613},
pmid = {41453807},
issn = {1936-086X},
abstract = {Lipid nanoparticles (LNPs) are being developed for a broad set of therapeutic applications by changing both the structures of the lipids used to formulate each LNP and their relative proportions. Because lipid synthesis and in vivo screening have been parallelized using combinatorial chemistry and LNP barcoding, respectively, the manual and sequential microfluidic formulation of LNPs remains the primary rate-limiting step during early-stage discovery. In this work, we present a parallelized, automated microfluidic platform capable of generating large, precisely defined LNP libraries in parallel, with throughput on the order of 1000 distinct formulations per hour. Each formulation is defined by varying the reagent flow ratios into one of eight microscale mixers using lithographically encoded fluidic resistors and dynamically controlled external pressure supplies. The microfluidic chip is integrated with custom robotic plate handling for the rapid collection of each distinct formulation. To evaluate this platform, we characterized 96 formulations generated on-chip in terms of both physicochemical properties and transfection efficiency in vitro. We further validated our lead candidate against the state of the art in vivo. We demonstrate the ability to rapidly discover a formulation and scale its production to liters per hour under identical mixing conditions, bridging from early discovery to manufacturing through microfluidic parallelization.},
}

@article {pmid41452897,
year = {2025},
author = {Fontaine, A and Djigo, OKM and Gomez, N and Boukhary, AOMS and Basco, L and Briolant, S},
title = {Amplicon-based DNA sequencing to characterize Duffy antigen polymorphisms and analysis of Duffy blood system and glucose-6-phosphate dehydrogenase deficiency in Mauritania.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {12},
pages = {e0013882},
doi = {10.1371/journal.pntd.0013882},
pmid = {41452897},
issn = {1935-2735},
abstract = {BACKGROUND: Both Duffy blood antigen expression and G6PD deficiency are known to be associated with ethnic origin. Updates in epidemiological data on the prevalence of polymorphisms in these two human genes are key information for guiding national programs to eliminate Plasmodium vivax malaria.

METHODS: Duffy genotypes and their predicted phenotypes were determined in 943 blood samples from Mauritanian patients belonging to different ethnic groups (n = 432 White Moors and n = 511 individuals of black African ancestry) with a known G6PD genotype determined by PCR-restriction fragment length polymorphism in our previous study, using a cost-saving multiplexed barcoding technique that allows simultaneous analysis of a large number of samples and next-generation DNA sequencing (NGS).

RESULTS: Duffy-negative phenotype predicted from Duffy genotype was predominant in individuals with black African ancestry (65-88%), while 16% of white Moors were Duffy-negative. Among 432 samples with interpretable Duffy sequence data from white Moors, 7/356 (2.0%) were Duffy-positive and G6PD A- deficient; 8/76 (10.5%) were Duffy-negative and G6PD A- deficient, mostly (n = 6) in heterozygous females. By contrast, among 511 patients of black African ancestry, 13 (13/140, 9.3% including heterozygous females) were Duffy-positive and G6PD A- deficient; 65 (65/371, 17.5%) were Duffy-negative and G6PD A- deficient, mostly (n = 44) in heterozygous females.

CONCLUSION: A large majority of white Moors are Duffy-positive and susceptible to P. vivax infection, but most are eligible for anti-hypnozoite therapy with primaquine at the standard dose. About 15.4% of individuals with black African ancestry were affected by G6PD A- deficiency, independently of their Duffy receptor status. This population requires G6PD screening before primaquine therapy in rare cases of P. vivax infection. These results provide important clues about the feasibility to implement an efficient anti-hypnozoite treatment in Mauritania and identify priority areas for targeted interventions against P. vivax malaria.},
}

@article {pmid41446374,
year = {2025},
author = {Fan, Y and Chen, L and Wu, Y and Wang, X and Tian, W and Ge, M and Li, C and Xie, Y},
title = {The Complete Chloroplast Genome of Synotis solidaginea and Phylogenetic Analysis.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72806},
pmid = {41446374},
issn = {2045-7758},
abstract = {Synotis is an important genus within the Asteraceae family. The genus comprises numerous species, many of which exhibit highly similar morphology, making identification using traditional taxonomic methods challenging. Therefore, developing a scientifically sound and effective identification method for Synotis plants is of significant importance. In this study, the complete chloroplast (cp) genome of Synotis solidaginea was sequenced using the Illumina HiSeq 4000 platform, analyzed, and compared with its closely related species. The results revealed that the complete chloroplast genome of S. solidaginea is 150,899 bp in length with a GC content of 37.47%. It exhibits the typical quadripartite structure, consisting of a large single-copy (LSC) region (83,338 bp), a small single-copy (SSC) region (17,885 bp), and two inverted repeat (IR) regions (each 24,838 bp). The genome encodes a total of 127 genes, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Thirty-two simple sequence repeats (SSRs) were identified. Four highly variable regions (trnG-UCC, ndhC-trnV-UAC_2, trnY-GUA-trnE-UUC, and trnH-GUG-psbA) were identified as potential DNA barcodes for species identification. Phylogenetic analysis revealed that S. solidaginea is closely related to its congeneric species Synotis cavaleriei, Synotis erythropappa, Synotis duclouxii, and Synotis nagensium. This study provides a reference for the phylogenetic analysis of Synotis using chloroplast genomics, and offers data support for the hybrid breeding of S. solidaginea to cultivate desirable ornamental traits or stress resistance traits. Furthermore, chloroplast genome research can also assist researchers in gaining a deeper understanding of the species origin of S. solidaginea and contribute to the study of species conservation and utilization.},
}

@article {pmid41446238,
year = {2025},
author = {Sohn, S and Morgan, D and Callahan, C and Dockery, K and Brock, A and Zoldan, J},
title = {Cell Barcoding Reveals Lineage-dependent Outcomes in hiPSC Cardiac Differentiation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.12.694049},
pmid = {41446238},
issn = {2692-8205},
abstract = {UNLABELLED: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have potential applications in treating cardiovascular disease but are currently limited in their clinical translation. A primary limitation is the poor clinical scalability of hiPSC-CMs, with the heterogeneity of hiPSC cardiac differentiation significantly contributing to this limitation. We hypothesize that clinical scalability can be improved by tracking and controlling hiPSC clonal heterogeneity, a variable often overlooked in current differentiation approaches. "Fate priming", wherein clonal lineage identity determines differentiation fate, has been demonstrated in other stem cell differentiation pathways. We investigated fate priming in hiPSC cardiac differentiation using the ClonMapper cell barcoding platform to label, track, and isolate distinct hiPSC lineages from the same cell line. We show that certain hiPSC lineages preferentially differentiate into hiPSC-CMs or non-CMs. After isolating lineages with apparent fate priming, we found significant differences in cardiac differentiation outcomes between these single-clone populations and heterogeneous, multi-clone hiPSC populations. These findings indicate that lineage identity influences hiPSC cardiac differentiation outcomes.

SIGNIFICANCE STATEMENT: Cardiovascular disease is a significant global health concern that can be addressed by engineering artificial tissues to develop new treatments for heart disease or to directly replace damaged heart tissue. Stem cells are a useful tool for engineering these tissues because of their ability to become cardiomyocytes. However, their clinical translation is limited by variability in the process of differentiating stem cells into cardiomyocytes. This article reports findings that show different lineages of genetically identical human induced pluripotent stem cells have different capacities for differentiating into cardiomyocytes, which may contribute to the variability observed.},
}

@article {pmid41444830,
year = {2025},
author = {Yang, Z and Zhang, Y and Fang, Y and Zhang, Y and Du, J and Shen, X and Zhang, K and Zou, P and Chen, Z},
title = {Spatial barcoding reveals reaction radii and contact-dependent mechanism of proximity labeling.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41444830},
issn = {1552-4469},
support = {2022YFA1304700//Chinese Ministry of Science and Technology | Department of S and T for Social Development (Department of S&T for Social Development)/ ; 32088101//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Proximity labeling techniques such as TurboID and APEX2 have become pivotal tools for studying protein interactions. However, the spatial patterns of labeling methods within the submicrometer range remain poorly understood. Here we used DNA nanostructure platforms to precisely measure the labeling radii of TurboID and APEX2 through in vitro assays. Our DNA nanoruler design enables the deployment of oligonucleotide-barcoded labeling targets with nanometer precision near the enzymes. By quantifying labeling yields using qPCR and mapping them against target distances, we uncovered surprising insights into the labeling mechanisms. Contrary to the prevailing diffusive labeling model, our results demonstrate that TurboID primarily operates through contact-dependent labeling. Similarly, APEX2 shows high labeling efficiency within its direct contact range. In parallel, it exhibits low-level diffusive labeling toward more distant phenols. These findings reframe our understanding in the mechanism of proximity labeling enzymes while highlighting the potential of DNA nanotechnology in spatially profiling reactive species.},
}

@article {pmid41440705,
year = {2025},
author = {Tangthirasunun, N and Gautier, V and Lalanne, C and Bonometti, L and Cros-Arteil, S and Hayes, RD and Calhoun, S and Riley, R and Pangilinan, J and Lipzen, A and Ng, V and Grigoriev, IV and Gladieux, P and Giraud, T and Silar, P},
title = {Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {41440705},
issn = {2309-608X},
support = {DOE DE-AC02-05CH11231//the U.S. Department of Energy Joint Genome Institute/ ; KREF206612//King Mongkut's Institute of Technology Ladkrabang/ ; },
abstract = {Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type locus. In vitro fruiting was obtained for 16 strains, enabling the definition of seven new species, namely Pseudorhypophila gallica, Pseudorhypophila guyanensis Rhypophila alpibus, Rhypophila brasiliensis, Rhypophila camarguensis, Rhypophila reunionensis and Rhypophila thailandica, as well as two new combinations, namely Pseudorhypophila latipes and Pseudorhypophila oryzae. Eight strains for which in vitro fruiting was not obtained may belong to additional new species. These results expand the known diversity of the Naviculisporaceae and greatly enlarge the genomic data available for the family.},
}

@article {pmid41438958,
year = {2025},
author = {Zhou, C and Ma, K and Wang, T and Tang, Y and Zhang, M and Yu, J and Liu, R and Ding, Q and Qiu, S and Li, Y and Ma, Z and Nie, G},
title = {Assessing Current Fish Diversity in the Yellow River Basin by Integrating Large-Scale Barcoding and Morphological Data.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72617},
pmid = {41438958},
issn = {2045-7758},
abstract = {In recent years, fish populations in the Yellow River (YR) basin have declined sharply due to human activities. Some studies even suggest that nearly half of the native fish species in the YR have disappeared. There are also significant differences among the literature on the systematic discussion of fish species in the Yellow River Basin. The construction of a standardized and complete DNA barcode database for YR fish is urgently needed. In this study, 127 sampling points were sampled in the YR basin from 2013 to 2023, and a DNA barcode database of 3011 sequences and 110 species was constructed. A total of 124 operable taxonomic units (OTUs) were identified via four sequence-based species classification methods. The barcode and morphological results of 84 (77.1%) species remained consistent. Some species cannot be described in the literature and are assigned to unique OTUs, and some widely distributed species are also assigned multiple OTUs. These findings indicate that the fish diversity in the YR basin has been severely underestimated, and more detailed investigations and further research are needed. This study constructed the first fish DNA barcode database in the YR basin and provided new insights for the study of fish diversity in the region.},
}

@article {pmid41438953,
year = {2025},
author = {Schoenemann, K and Lim, HC and Keady, MM and Carr, DE},
title = {Pollen Foraging by Bumble Bee Queens During a Critical Nesting Period Revealed by DNA Metabarcoding.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72733},
pmid = {41438953},
issn = {2045-7758},
abstract = {The nest-founding stage represents an especially vulnerable period of the bumble bee (Bombus) life cycle, during which solitary queens must locate and collect sufficient foraging resources to sustain themselves and their brood. Yet, we lack contemporary information about floral foraging resources used by queens in early spring. Here, we use next-generation sequencing to characterize the floral species used by queens for pollen provisions during early nest establishment. We collected pollen loads from over 100 wild bumble bee queens at working farms, rural and city parks, and nature preserves across the Piedmont region of Virginia, USA. Using metabarcoding of two universal DNA barcodes for plants, ITS2 and rbcL, we determined the taxonomic composition of pollen used by queens. Pollen loads contained native and non-native woody (e.g., Cercis: Fabaceae, Prunus: Rosaceae, Salix: Salicaceae), herbaceous (e.g., Lamium: Lamiaceae, Viola: Violaceae), and vine (e.g., Lonicera: Caprifoliaceae) taxa. The non-native Lamium and Elaeagnus (Elaeagnaceae) most frequently hosted foraging queens, owing in part to their abundance across sites and the season. Pollen composition varied more over time than among bumble bee species or across sites, but land cover predicted a small amount of variation in pollen composition. Specifically, the percentage of crop land within 1 km increased the representation of Lamium in queen pollen loads, likely reflecting the abundance of the disturbance-adapted flower in fallow cornfields. Finally, the pollen communities detected by rbcL were twice as diverse as those by ITS2, perhaps owing to the better taxonomic resolution afforded by the fast-evolving rbcL marker. This study demonstrates that queens are flexible foragers and that among the most common Bombus species, plant phenology drives pollen use more than species identity. Further, this study highlights the importance of monitoring pollen diets to inform regional management strategies and considerations about metabarcoding techniques.},
}

@article {pmid41435415,
year = {2025},
author = {Argue, BM and Gate, D},
title = {Basic Science and Pathogenesis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 1},
number = {Suppl 1},
pages = {e100419},
doi = {10.1002/alz70855_100419},
pmid = {41435415},
issn = {1552-5279},
mesh = {Humans ; *Alzheimer Disease/cerebrospinal fluid/genetics/blood ; *Cognitive Dysfunction/cerebrospinal fluid/genetics/blood ; Aged ; Male ; Protein Isoforms/genetics/cerebrospinal fluid ; Female ; Single-Cell Analysis ; },
abstract = {BACKGROUND: Single-cell long-read sequencing was performed on immune cells from cerebrospinal fluid (CSF) and blood to assess isoform diversity in healthy aging individuals and those diagnosed with mild cognitive impairment (MCI) or Alzheimer's disease (AD).

METHOD: cDNA from single-cell experiments was subjected to long-read sequencing using Oxford Nanopore Technologies. The dataset included immune cells from CSF (45 controls, 13 MCI/AD) and blood (22 controls, 28 AD). Computational analysis incorporated scNanoGPS for extracting cell barcodes and mapping reads to the genome, IsoQuant for isoform modeling, and SQANTI3 for filtering artifacts.

RESULTS: Single-cell long-read sequencing identified 97,920 unique transcripts, with half of all genes exhibiting multiple isoforms. Notably, 20% of the detected isoforms were previously unannotated in the human genome. Novel isoforms were observed in AD-associated genes, including BIN1 and PTK2B, with BIN1 displaying lymphoid cell-specific isoforms.

CONCLUSION: Human immune cells demonstrate extensive isoform diversity, including previously unannotated isoforms, particularly in genes implicated in AD.},
}

Humans
*Alzheimer Disease/cerebrospinal fluid/genetics/blood
*Cognitive Dysfunction/cerebrospinal fluid/genetics/blood
Aged
Male
Protein Isoforms/genetics/cerebrospinal fluid
Female
Single-Cell Analysis

@article {pmid41432445,
year = {2025},
author = {Giorgio, RT and Le, MT and Zhang, T and Holmes, CL and Hullahalli, K},
title = {Accurate interpretation of within-host dissemination using barcoded bacteria.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0146025},
doi = {10.1128/msystems.01460-25},
pmid = {41432445},
issn = {2379-5077},
abstract = {Bacterial dissemination across tissues is a critically important process influencing infection outcomes. Monitoring within-host dissemination is challenging because conventional measures of bulk bacterial burden cannot distinguish between lineages that are shared between tissues and those that replicate locally. This limitation can be overcome using barcoded bacteria, where deep sequencing of the barcode locus and comparisons of barcodes between tissues define which lineages spread within the host. Numerous studies have used barcoded bacteria to generate high-resolution maps of dissemination. However, since multiple cells in the infectious inoculum can contain identical barcodes, inferences about dissemination can be confounded when distinct lineages from the inoculum with identical barcodes are observed in different tissues. Thus, even though the same barcodes can be observed in different tissues, dissemination between these tissues may not have occurred. Here, we aimed to develop an approach that would provide a solution to this confounding effect. We developed a simulation-based distance metric that quantifies the significance of observing shared barcodes between tissues. We validated this approach using simulated data sets spanning three orders of magnitude in barcode diversities and on three published experimental infection data sets. Our reanalysis reveals previously unappreciated patterns of Escherichia coli spread during liver abscess formation, clarifies the role of the Muc2 mucin in Listeria monocytogenes systemic spread, and quantifies how Klebsiella pneumoniae replication in the lungs drives systemic dissemination. As barcoding studies expand across diverse infection models, this approach provides an essential tool for accurate interpretation of within-host bacterial dissemination.IMPORTANCEHow microbes move between tissues in the host is an important factor that controls the outcome and severity of infections. A powerful method to monitor within-host microbial dissemination is the use of barcoded bacteria and lineage tracing. Comparisons of barcodes between tissues enable inferences of microbial dissemination, and this method has been applied to diverse contexts of bacterial infections. Here, we demonstrate that inferences of microbial dissemination are confounded, where observing identical barcodes in different tissues does not always signify that dissemination has occurred. To overcome this limitation, we define a metric to quantify the extent to which sharing of barcodes is meaningful and provide new insights into previous barcoding studies in Escherichia coli, Listeria monocytogenes, and Klebsiella pneumoniae. As bacterial lineage tracing continues to be applied across diverse models, our method will help ensure accurate interpretations of microbial dissemination.},
}

@article {pmid41431142,
year = {2025},
author = {Shaw, AJ and Duffy, AM and Aguero, B and Nieto-Lugilde, M and Imwattana, K and Robinson, SC and Schuette, S and Wilkens, RT and Yavitt, J and Weston, DJ and Piatkowski, B and Granath, G},
title = {Climate niches structure a regional hybrid zone in Sphagnum (peatmoss, Bryophyta).},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e70143},
doi = {10.1002/ajb2.70143},
pmid = {41431142},
issn = {1537-2197},
abstract = {PREMISE: Hybridization is an important evolutionary process across all groups of embryophyte land plants, but relatively little is known about hybridization and introgression in plants with a dominant gametophyte life cycle stage. This paper focuses on hybridization between four closely related species of the moss genus Sphagnum.

METHODS: Analyses utilized three types of molecular data: restriction-site-associated DNA sequencing (RADseq), RADseq-like data derived from in silico digestion of genome sequences, and species-specific barcode markers developed previously for this group. Sampling included 582 gametophytes from 79 collecting sites from 27° to 56°N. A range of analytical methods were employed: phylogeny reconstruction, genetic analyses using the program structure, demographic modeling, and comparative genomics.

RESULTS: Gene flow was detected among all pairwise combinations of extant species and between ancestral lineages and those species. Hybridization between S. diabolicum and S. magniae was especially pronounced and plants in a regional zone from North Carolina to New Jersey were genetically admixed. Demographic analyses indicated that this admixture reflects hybridization. Introgressed SNPs were detected across all chromosomes, but introgressed SNPs fixed in genetically pure samples of the two species were concentrated on four autosomes: 2, 7, 14, and 19. Patterns of genomic admixture/introgression were significantly correlated with climate variation across collection sites within the hybrid zone.

CONCLUSIONS: The genomic structure of plants in a regional hybrid zone between S. magniae and S. diabolicum was structured by climate adaptation and strengthens the value of this group for learning more about speciation and climate adaptation.},
}

@article {pmid41428017,
year = {2025},
author = {Brehm, G and Böttger, D and Diniz, UM and Donoso, DA and Kortmann, M and Müller, J and Rabl, D and Keller, A and Laguerre, M},
title = {Illustrated Catalogue and Phylogenetic Relationships of 330 Species of Arctiinae Moth Species from the Chocó Rainforest in NW Ecuador: Most Species are Undescribed.},
journal = {Neotropical entomology},
volume = {54},
number = {1},
pages = {127},
pmid = {41428017},
issn = {1678-8052},
support = {FOR 5207//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Moths/classification/anatomy & histology/genetics ; Rainforest ; *Phylogeny ; Ecuador ; DNA Barcoding, Taxonomic ; Male ; Female ; },
abstract = {Tropical rain forests are the most species rich terrestrial habitats on Earth, but their insect diversity is understudied, and it is unclear how many species are already scientifically described. A model group to study description patterns are tiger moths (Erebidae: Arctiinae), a species-rich moth clade that comprises subtaxa that differ considerably in appearance. We inventoried Arctiinae moths in a lowland rainforest in the Canandé and Tesoro Escondido Reserves, NW Ecuador, and sorted 12,335 individuals into 330 species, of which 303 had DNA barcode (COI) data extracted. We found 52 species of Lithosiini, 4 species of Arctiina, 17 species of Pericopina, 132 species of Phaegopterina, 52 species of Euchromiina and 71 species of Ctenuchina. A total of 45% of the species can be assigned by us to known named species, but the numbers vary considerably within the subtaxa: while in the conspicuous butterfly-like Pericopina 82% are described, this figure is only 26% for the smaller and cryptic Lithosiini, indicating a strong description bias even within a relatively well-known group of macromoths. This may indicate that particularly small and inconspicuous moth species have so far been neglected and that museum collections might often not be representative archives of insect diversity. Therefore, more systematic and non-biased collection campaigns should be carried out for better estimates of insect diversity. All 330 Arctiinae species are listed in three electronic catalogues, which contain all barcoded individuals as well as corresponding type material from museums, allowing a transparent and straightforward verification of all identifications. We constructed a preliminary phylogeny using literature data as backbone in combination with our DNA COI sequence data which provides a unique and useful data base for future studies in the Chocó rainforest.},
}

Animals
*Moths/classification/anatomy & histology/genetics
Rainforest
*Phylogeny
Ecuador
DNA Barcoding, Taxonomic
Male
Female

@article {pmid41427923,
year = {2025},
author = {Mamani, MM and Catacora, L and Nina, N and Alarcon, WDT and Cai, FM and Rydén, J and Druzhinina, IS and Jensen, DF and Crespo, CF and Karlsson, M and Dubey, M},
title = {Diversity of Trichoderma in the unexplored Bolivian Amazon region and their potential for coffee diseases control.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf142},
pmid = {41427923},
issn = {1574-6968},
abstract = {Trichoderma fungi are colonizers of plant substrates and rhizosphere and are valued for their antagonism against phytopathogens and ability to promote plant health. We investigated Trichoderma diversity in coffee-growing soils in Caranavi region of Yungas-La Paz, Bolivia, where high humidity and fungal diseases threaten yield, and evaluated their potential as biocontrol agents against coffee pathogens. A total of 440 Trichoderma were isolated from coffee rhizosphere, fallow lands, and forest ecosystems across an altitudinal gradient in Caranavi. DNA barcode analyses using ITS, rpb2, and tef1 loci identified only four species. However, 47 taxa comprising 344 isolates were ambiguous, and 41 isolates were previously unrecognised species. The diversity of Trichoderma spp. was significantly affected by ecosystem type and altitude, with more species isolated from coffee rhizosphere than fallow lands and forest ecosystems, and from lower altitudes than higher ones. Evaluation of 100 isolates against a native coffee wilt pathogen Fusarium sp. C22 identified 70 potent antagonists, with 30 achieving 90-100% disease control. This is the first comprehensive study of Trichoderma diversity in Yungas, identifying indigenous Trichoderma for biocontrol applications against coffee diseases. It also emphasizes the need to refine the Trichoderma species concept and improve the taxonomic resolution within the genus.},
}

@article {pmid41427718,
year = {2026},
author = {Kanjo, K and Bhasin, M and Dey, C and Bakshi, N and Ashok, A and Singh, R and Kumar, S and Ringe, RP and Varadarajan, R},
title = {Charged scanning mutagenesis as a high-throughput approach for epitope mapping.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {1},
pages = {e70433},
pmid = {41427718},
issn = {1469-896X},
support = {JBR/2021/000033//JC Bose Fellow of the Department of Science and Technology, Ministry of Science and Technology, India/ ; BT/IN/EU-INF/15/RV/19-20//ENDFLU: the Department of Biotechnology, Ministry of Science and Technology, Government of India/ ; CRG/2022/004425//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Epitope Mapping/methods ; *SARS-CoV-2/immunology/genetics/chemistry ; Mice ; *Mutagenesis ; *Spike Glycoprotein, Coronavirus/genetics/immunology/chemistry ; *Epitopes/immunology/genetics/chemistry ; COVID-19/immunology/virology ; Humans ; },
abstract = {Identifying neutralizing epitopes is important for developing vaccines and inhibitors against viral pathogens. We describe a rapid method for epitope mapping, employing barcoded charged scanning mutagenesis libraries displayed on the yeast surface, and screening using flow cytometry coupled with deep sequencing. Prior scanning mutagenesis data suggest that mutations to a charged residue, such as Aspartic acid or Arginine, will be well tolerated at exposed positions of an antigen and minimally affect protein stability and expression. Yet such substitutions at epitope residues strongly perturb binding to a cognate partner. We constructed an Aspartate scanning library of SARS-CoV-2 receptor binding domain and linked every mutation in the library to a defined unique barcode. The approach was used to map epitopes targeted in polyclonal sera of mice immunized with different SARS-CoV-2 immunogens. In contrast to complete mutational scans, charged scanning mutagenesis with the introduced barcoding strategy employs libraries with >50-fold lower diversity, facilitating library construction, screening, and downstream analysis, and also allowing for further multiplexing of samples, thus accelerating interaction site identification, as well as vaccine and inhibitor development.},
}

Animals
*Epitope Mapping/methods
*SARS-CoV-2/immunology/genetics/chemistry
Mice
*Mutagenesis
*Spike Glycoprotein, Coronavirus/genetics/immunology/chemistry
*Epitopes/immunology/genetics/chemistry
COVID-19/immunology/virology
Humans

@article {pmid41426548,
year = {2025},
author = {Gerwin, S and Deng, X and He, F and Pauls, SU},
title = {Diversity of Rhyacophila (Trichoptera, Rhyacophilidae) in the Hengduan Mountains.},
journal = {ZooKeys},
volume = {1263},
number = {},
pages = {69-88},
pmid = {41426548},
issn = {1313-2989},
abstract = {Aquatic insects are particularly dependent on environmental conditions because their life cycles are directly linked to physico-chemical conditions in freshwater habitats. Here, we combine DNA barcoding and ecological analysis to determine general distributional patterns for an unknown fauna of Rhyacophila (Trichoptera, Rhyacophilidae) in the Hengduan Mountains in China. In total 415 larval and 109 adult specimens from four major Hengduan Mountain river basins (1022 m - 4381 m a.s.l.) were sequenced and analyzed. Molecular operational taxonomic units (MOTUs) were delimited as putative species analogs. MOTUs were derived from mitochondrial COI (mtCOI) and nuclear wingless (nuWG) data using the tree-based GMYC method. As expected, based on a higher mutation rate, mtCOI delimitation resulted in a much higher number of MOTUs (66) than in WG (27), but not all mtCOIMOTUs were nested within nuWGMOTUs. Many mtCOIMOTUs were geographically restricted and rare, often occurring in only one or two sampling sites. Multivariate GLM analyses confirmed the importance of basins as the primary factor for explaining the diversity of RhyacophilaMOTUs. The high level of geographical restriction of MOTUs among basins and along elevational gradients indicates that Rhyacophila in the Hengduan Mountains are largely range-restricted, dispersal limited and consequently vulnerable to local changes in environmental conditions.},
}

@article {pmid41426536,
year = {2025},
author = {Kučinić, M and Previšić, A and Ćukušić, A and Vučković, I and Žalac, S and Cerjanec, D and Ćuk, R and Stojanović, KZ and Akimbekova, N and Vuković, M and Skejo, J and Hlebec, D and Božić, A and Kutnjak, H},
title = {Fauna, distribution, and DNA barcoding data of caddisflies (Insecta, Trichoptera) in Croatia.},
journal = {ZooKeys},
volume = {1263},
number = {},
pages = {179-288},
pmid = {41426536},
issn = {1313-2989},
abstract = {This study presents a thorough overview of the diversity of the Trichoptera fauna in Croatia, encompassing several key aspects. First, it offers a historical overview of Trichoptera research conducted within the country, tracing the development and major milestones of this field. Second, it provides a detailed analysis of the distribution and species diversity of caddisflies across Croatia's three geographical regions, the Continental, Alpine, and Mediterranean, as well as within two ecoregions (ER5 - Dinaric Western Balkan and ER11 - Pannonian Lowlands) and two major river basins (AS - Adriatic Sea basin and BS - Black Sea basin). This biogeographic assessment is based on comprehensive records of adult specimens and, in certain cases, on DNA barcoding data obtained from larval stages. Third, the study includes a thorough examination of species synonyms and a critical review of the existing literature. Finally, it delivers a faunistic and taxonomic review of selected species and subspecies. A total of 225 species belonging to 18 families and 74 genera have been identified. Two of these species are represented by two and three subspecies, respectively, bringing the total number of recorded Trichoptera taxa in Croatia to 228. The presence of 223 species was confirmed in the adult stage. Only two species were identified by DNA barcoding as larvae. In the Continental region 170 species were recorded, in the Alpine region 155, and in the Mediterranean part 131 species. The Black Sea basin contains 203, and the Adriatic basin 141 species. In the Pannonian Lowland region (Ecoregion 11) we determined 152 and in the Dinaric Western Balkan (Ecoregion 5) 197 species. The BOLD Systems database currently contains about 593 DNA barcoded Trichoptera specimens from Croatia comprising 176 species, identifying 211 BINs, covering 78% of Croatian Trichoptera fauna.},
}

@article {pmid41424079,
year = {2025},
author = {Waki, T and Sekine, H and Aou, A and Nitta, M and Yamamoto, G and Toshino, S and Nakano, H and Okawa, T and Takano, K and Yamazaki, D and Hagihara, R},
title = {Metacercariae infecting seven cnidarian species with their life cycle information including their adult stages in Japan.},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e4},
doi = {10.1017/S0022149X25100989},
pmid = {41424079},
issn = {1475-2697},
mesh = {Animals ; Japan ; *Metacercariae/classification/genetics/isolation & purification/growth & development ; *Life Cycle Stages ; *Trematoda/classification/genetics/isolation & purification/growth & development/anatomy & histology ; Phylogeny ; *Cnidaria/parasitology/classification ; Fishes/parasitology ; DNA Barcoding, Taxonomic ; Fish Diseases/parasitology ; },
abstract = {This study examined the metacercariae of trematodes in cnidarian jellyfish around Japan to demonstrate the importance of the jellyfish as the second intermediate or paratenic hosts. Trematodes were sampled from cnidarian jellyfish in seven coastal regions of Japan between 2024 and 2025. Trematodes (adults and metacercariae) were also obtained from marine fish and arrow worms and included for data comparisons. DNA barcoding was used for the species identification of metacercariae in the jellyfish and for elucidating their partial life cycles. Eight cnidarian species (245 individuals) were sampled, with metacercarial infection detected in seven host species. Based on morphological and molecular analyses, the metacercariae were classified into nine species belonging to three families, Accacoeliidae, Hemiuridae, and Lepocreadiidae. Six of these species were identified as the same species of adults isolated from fish hosts around Japan, although species names of two of the six remained unclear. The remaining three trematode species were assumed to belong to Lepocreadiidae, a major group of fish trematodes. These findings indicate that cnidarian jellyfish are important intermediate or paratenic hosts of fish trematodes in Japanese waters, as has been reported in other areas in previous studies. Moreover, a metacercaria occasionally detected in an arrow worm was identified as the same species as those in jellyfish, suggesting predator-prey relationships between these hosts. The study also synonymised Tetrochetus hamadai Fukui and Ogata, 1935, T. aluterae (Hanson, 1955), and T. mitenevi Zubchenko, 1978, with T. coryphaenae Yamaguti, 1934, based on molecular and morphological data.},
}

Animals
Japan
*Metacercariae/classification/genetics/isolation & purification/growth & development
*Life Cycle Stages
*Trematoda/classification/genetics/isolation & purification/growth & development/anatomy & histology
Phylogeny
*Cnidaria/parasitology/classification
Fishes/parasitology
DNA Barcoding, Taxonomic
Fish Diseases/parasitology

@article {pmid41423517,
year = {2025},
author = {Chambwe, N and Kennedy, SR and Kohrn, BF and Lazarchuk, P and Leutert, M and Qin, G and Tercan, B and Sanchez-Contreras, M and Tang, W and Graber, JJ and Paddison, PJ and Villén, J and Shmulevich, I and Monnat, RJ},
title = {Cellular heterogeneity and therapeutic response profiling of human IDH + glioma stem cell cultures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33082-8},
pmid = {41423517},
issn = {2045-2322},
abstract = {Glioblastoma stem cell (GSC) cultures are initiated from glioblastoma (GBM) surgical resection tissue. When grown appropriately they can capture and propagate key GBM molecular and cellular features. We have characterized cellular, genomic and proteomic features of four isocitrate dehydrogenase (IDH)-expressing (IDH +) GSC cultures as cellular models for ~ 90% of adult GBMs. We demonstrate that GSC cultures can be continuously propagated in defined, serum-free media and 5% oxygen without specialized growth substrates; have culture-specific genomic and mtDNA variants together with gene/protein expression profiles; and display reproducible dose-survival curves for the GBM standard-of-care therapies ionizing radiation (IR) and temozolomide (TMZ). In order to better define GSC culture cellular heterogeneity and dynamics, we used lentiviral DNA barcoding, mtDNA variants and single cell gene expression profiling over 40 days after IR treatment. GSC cultures are versatile in their ability to support many in vitro protocols including high throughput screens as well as xenograft, organoid and other disease modeling protocols. They provide a simple cellular disease model for better understanding GBM biology, and for identifying new, potentially more effective GBM therapies and treatment regimens.},
}

@article {pmid41420443,
year = {2025},
author = {Torres, A and Lee, L and Srivathsan, A and Meier, R},
title = {UITOTO: a software for generating molecular diagnoses for species descriptions.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/cla.70023},
pmid = {41420443},
issn = {1096-0031},
abstract = {Millions of species remain undescribed, and each eventually will require a species description with a diagnosis. Yet, we lack software that can derive state-specific and contrastive molecular diagnoses and allows the user to validate them based on all available sequences for the taxon under study. Here we introduce UITOTO, which addresses this shortcoming by facilitating the identification, testing, and visualization of diagnostic molecular combinations (DMCs). The software uses a weighted random sampling algorithm based on the Jaccard Index for building candidate DMCs. It then selects DMCs with the highest specificity stability, meeting user-defined thresholds for exclusive character states. If multiple optimal DMCs are identified, UITOTO derives a majority-consensus DMC. To verify whether the generated DMCs are contrastive, UITOTO includes a validation module that tests DMCs against databases, efficiently handling thousands of aligned or unaligned sequences. We here, not only propose UITOTO, but also assess its performance relative to other software that can derive DMCs (e.g. MOLD). For this purpose, we analyse three large empirical datasets: (i) Megaselia (Diptera: Phoridae: 69 species, 2229 training and 30 289 testing barcodes); (ii) Mycetophilidae (Diptera: 118 species, 1456 training, 60 349 testing barcodes); and (iii) European Lepidoptera (49 species, 591 training, 21 483 testing barcodes). Based on classification metrics (e.g. F1 Score), UITOTO's DMCs outcompete DMCs from other software. We furthermore provide guidelines for generating molecular diagnoses and a user-friendly Shiny App-GUI that includes a module for obtaining publication-quality DMC visualizations. Overall, our study confirms that the biggest challenge for generating molecular and morphological diagnoses is similar: balancing specificity and length; short diagnoses often lack specificity, while excessively long DMCs are often so specific that they do not accommodate intraspecific variation.},
}

@article {pmid41419930,
year = {2025},
author = {Rodrigues, BL and Vasconcelos Dos Santos, T and Brilhante, AF and de Souza Pinto, I and Rocha, EG and Pereira Júnior, AM and da Silva Costa, G and de França, KP and de Souza Cavalcante, K and Shimabukuro, PHF and Medeiros, JF and Galati, EAB},
title = {On the integrative taxonomy of Trichophoromyia Barretto, 1962 and its relationship with Nyssomyia Barretto, 1962 (Diptera, Psychodidae, Phlebotominae): species delimitation, phylogeny, genus and subgenus description.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07155-6},
pmid = {41419930},
issn = {1756-3305},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2023/03715-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {BACKGROUND: The sand fly genus Trichophoromyia Barretto, 1962 is one of the most diverse inthe subfamily Phlebotominae. The taxonomy and systematics of this group is complex due toboth a high similarity among species and unclear relationships among other sand fly groupswithin the subtribe Psychodopygina Galati, 1995. Despite their great relevance as vectors of Leishmania spp., few studies have explored the usefulness of molecular markers in studyingthe diversity of this group.

METHODS: Here, we evaluated the use of barcode sequences of the cytochrome coxidasesubunit I gene (COI) for identifying several Trichophoromyia spp., by inferring intra- andinterspecific genetic distances, in addition to performing a set of several single-locus speciesdelimitation approaches using discovery methods. Moreover, we employed a multilocusdataset of four independent molecular markers (COI , ITS2 , 28S and PARA) to infer thephylogenetic species tree, estimate divergence times and delimit species under a validationmodel.

RESULTS: The phylogenetic inferences confirmed the paraphyly of Trichophoromyia and Nyssomy ia Barretto, 1962. Thus, two new genera, named Reburrus gen. nov. and Shawmyia gen. nov., were proposed to accommodate sand flyspecies that did not fit in the aforementioned groups. Additionally, a new subgenus wasproposed: Trichophoromyia (Dilermandomyia) subg. nov., containing most speciesof Trichophoromyia . A recent speciation history was also estimated, with most of the speciesstudied diversifying during the Pleistocene. However, our dataset was insufficient to fullyresolve relationships within Trichophoromyia (Dilermandomyia) subg. nov. Many speciesshowed paraphyletic patterns in the gene trees, and some could not be reliably identified anddelimited using both COI barcodes and multilocus tools.

CONCLUSIONS: The sand fly genus Trichophoromyia exhibits a complex diversification history.Our phylogenetic inference and morphological observations of Nyssomyia and Trichophoromy ia, allowed us to propose new groups for the Psychodopygina subtribe. However, theprevalence of species-level paraphyletic patterns for Trichophoromyia (Dilermandomyia) subg.nov., showed that further assessment of this group requires a broader locus sampling combined with detailed morphological analysis.},
}

@article {pmid41419813,
year = {2025},
author = {El-Demerdash, MM and El-Sayed, ASA and Yassin, MA and Elsehely, HH},
title = {Pyrene morphology and molecular identification of some garden ornamental palms of the family Arecaceae based on the plastid rbcL gene in Egypt morphological and molecular identification of ornamental palms (Arecaceae) in Egypt based on pyrene traits and rbcL gene sequence.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1715},
pmid = {41419813},
issn = {1471-2229},
mesh = {Egypt ; *Arecaceae/genetics/anatomy & histology/classification ; Phylogeny ; *Ribulose-Bisphosphate Carboxylase/genetics ; DNA Barcoding, Taxonomic ; *Pyrenes/analysis ; Fruit/anatomy & histology/genetics ; Plastids/genetics ; },
abstract = {The ornamental palms represent a diverse species in the national botanical gardens, and roadsides; however, the accurate identification of the palm trees (Arecaceae) is a problematic due to the numerous overlapped morphological traits, especially with the environmental conditions. So, the objective of this study was to implement the different morphological traits, especially based on the pyrene morphology, with the molecular barcoding markers of the plastid rbcL on delineation and revising the taxonomical identification of the most common Palm trees in Egypt in addition to their pharmacological and Ethnobotanical applications. An obvious variation on the surface of pyrenes among the studied Palm taxa ranged from ovoid to globose or discoid, with brown to pale brown, was recorded. The pyrene's fruit dimensions were ranged with S. yaba Becc. (5.65 × 6.85 mm), Washingtonia robusta (7.19 × 4.4 mm) and Sabal palmetto (Walter) Lodd. ex Schult. & Schult.f. (7.24 × 9.58 mm), while Syagrus romanzoffiana (Cham.) Glassman is (19.8 × 12.15 mm). The color of the pyrene of W. robusta, S. romanzoffiana, and Livistona decora (W.Bull) Dowe was brown, while was dark brown in Butia capitata (Mart.) Becc. Sabal yapa and S. palmetto. The SEM analysis of the pyrene surface microsculpture, the studied taxa of S. palmetto, S. yaba, Livistona, Brahea, and Sabal could be easily delimited at the generic level. The taxonomical identification of plant taxa based on their morphological characteristics, such as color, surface smoothness, and geometric shapes, was confirmed based on their molecular barcoding. The Principal Component Analysis (PCA) scatter plot based on the morphological traits distinguishes the taxa of tribe Cocoeae, subfamily Arecoideae and taxa of tribe Corypheae, subfamily Coryphoideae. From the UPGMA dendrogram based on the micromorphological characteristics, the studied taxa were grouped into two major clusters (I, II), the cluster I includes S. palmatto, S, yaba and W. robusta which belongs to subtribe Sabalinae, tribe corypheae, while cluster II includes L. decora, L. chinensis, (Jacq.) R.Br. ex Mart.and B. armata which belongs to subtribe Livistoninae and tribe Corypheae. Thus, the classification of the experimental plants based on the morphological traits of pyrene fruit microsculpturing was closely matched with the molecular barcoding based on the rbcL sequences.},
}

Egypt
*Arecaceae/genetics/anatomy & histology/classification
Phylogeny
*Ribulose-Bisphosphate Carboxylase/genetics
DNA Barcoding, Taxonomic
*Pyrenes/analysis
Fruit/anatomy & histology/genetics
Plastids/genetics

@article {pmid41418522,
year = {2025},
author = {Martel, C and Kreidt, J and Scott, J and Griffiths-Lee, J and Rázuri-Gonzales, E and Wright, GA and Stevenson, PC},
title = {Pollen and sterol content differentially affect solitary bee development.},
journal = {The Science of the total environment},
volume = {1012},
number = {},
pages = {181213},
doi = {10.1016/j.scitotenv.2025.181213},
pmid = {41418522},
issn = {1879-1026},
abstract = {Pollen sterols are essential micronutrients for bees, with roles as membrane components, hormone precursors and for regulating gene expression. It is historically accepted that bees are unable to produce sterols de novo or modify them and use them as they occur in pollen. This may require adaptation by bees to specific plants because pollen sterols vary dramatically across taxa. Here we investigated the effects of pollen with different sterol composition or supplementation on development of solitary red mason bees, Osmia bicornis, comparing bee provisioned pollen, with Castanea sativa pollen containing campesterol a key Osmia sterol, a sterol supplemented C. sativa pollen, a polyfloral pollen from which the key campesterol and cholesterol sterols were almost absent, and a combination of polyfloral and C. sativa pollen. DNA barcoding was used to characterise the Osmia pollen, which comprised at least 38 taxa but was mostly Quercus spp. Pollen diet significantly affected the larval final weight, larval development time and development over time. Larvae fed chestnut pollen supplemented with sterols developed significantly faster over time compared to those from the other treatments, including the chestnut pollen with no sterol supplementation. Despite sterol composition being distinctive among pollen diets, sterol profiles were more similar among bees from different pollen foods (i.e., different treatments) than between bees and their pollen foods. Moreover, bees fed on polyfloral pollen had much higher relative concentrations of campesterol (~8.5 %) and cholesterol (~26 %) than the pollen itself (~3 % and ~ 0.7 %, respectively), addressing the possibility that Osmia bees are highly efficient in sterol selective accumulation or possible transformation of sterols in Osmia bees. Our results suggest greater flexibility in sterol handling in bees than previously assumed.},
}

@article {pmid41413444,
year = {2025},
author = {Hookabe, N and Hiruta, SF and Yabuki, A and Yoshino, H and Hisasue, Y and Sawada, N and Ueshima, R and Kajihara, H},
title = {Unrecognized species-level diversity of terrestrial nemerteans in the UNESCO world heritage Ogasawara Islands revealed by mitogenomics.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {135},
pmid = {41413444},
issn = {2730-7182},
support = {23KJ2222//Japan Society for the Promotion of Science/ ; 25K09751//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; Japan ; Islands ; *Invertebrates/genetics/classification/anatomy & histology ; *Biodiversity ; Phylogeny ; *Genetic Variation ; },
abstract = {BACKGROUND: The terrestrial ribbon worm Geonemertes pelaensis Semper, 1863 (phylum Nemertea) is widely reported from tropical regions worldwide. In Japan, this species has been recorded from subtropical islands including the Ogasawara Islands, a UNESCO World Heritage Site south of Tokyo recognized for its unique biodiversity, where it has been implicated in the decline of native soil invertebrates. Here, we demonstrate that the nemerteans in the Ogasawara Islands are genetically and morphologically distinct from those found on Yonaguni Island (Okinawa, Japan), indicating the presence of at least two separate species in Japan.

RESULTS: We sequenced the complete mitochondrial genomes of both populations (18,755 bp for Ogasawara; 31,745 bp for Yonaguni), revealing substantial differences in genome size and gene arrangement. The mitochondrial genome of the Yonaguni population is unusually large, exceeding typical sizes reported for metazoans. Uncorrected p-distances in cytochrome c oxidase subunit I (COX1) sequences between the two populations ranged from 6.75 to 8.59%, which is above the widely used threshold for intraspecific variation in nemerteans. Morphological comparisons also support species-level distinction: live specimens from Yonaguni have a pale body with a prominent mid-dorsal stripe (body width-to-stripe ratio: 1:0.078-0.110), whereas individuals from Ogasawara are pale to light brown with a narrower and fading stripe (ratio: 1:0.042-0.050). Moreover, accessory-stylet pouches differ between populations: Yonaguni specimens possess four to five pouches, each containing 3-5 stylets, while Ogasawara specimens have two pouches, each with two stylets. Examination of museum specimens collected in the 1980s from Chichijima showed the extremely similar external morphology as our recent Ogasawara specimens, indicating that this form has been the only Geonemertes species in the Ogasawara Islands for nearly half a century.

CONCLUSIONS: Our results indicate the presence of species-level diversity in Japanese terrestrial nemerteans and demonstrate that accurate species identification using molecular barcodes is essential in insular ecosystems. Recognizing cryptic or pseudocryptic lineages is critical for effective biodiversity monitoring and for preventing mismanagement in ecologically sensitive regions such as the Ogasawara Islands.},
}

Animals
*Genome, Mitochondrial
Japan
Islands
*Invertebrates/genetics/classification/anatomy & histology
*Biodiversity
Phylogeny
*Genetic Variation

@article {pmid41411409,
year = {2025},
author = {Mazelis, I and Sun, H and Kulkarni, A and Torre, TL and Klein, AM},
title = {Multistep genomics on single cells and live cultures in subnanoliter capsules.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eady7209},
doi = {10.1126/science.ady7209},
pmid = {41411409},
issn = {1095-9203},
abstract = {Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multistep assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and their extension to live-cell assays.},
}