@article {pmid41599007,
year = {2025},
author = {Elshafie, NO and Kattoor, JJ and Kelly, J and Wilkes, RP},
title = {MinION Adapted tNGS Panel for Carnivore Pathogens Including SARS-CoV-2.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010023},
pmid = {41599007},
issn = {2076-0817},
support = {FAIN: AP23OA000000C008//United States Department of Agriculture/ ; },
mesh = {Animals ; *SARS-CoV-2/genetics/isolation & purification ; *COVID-19/diagnosis/virology/veterinary ; *High-Throughput Nucleotide Sequencing/methods ; Genome, Viral ; Whole Genome Sequencing/methods ; Animals, Wild/virology ; Sensitivity and Specificity ; Nucleic Acid Amplification Techniques/methods ; },
abstract = {Affordable, flexible surveillance tools are needed to detect SARS-CoV-2 and other pathogens in wildlife. Standard nucleic acid amplification tests (NAATs) are reliable but restricted to predefined targets, limiting their ability to detect co-infections or emerging pathogens. To address this, we adapted a targeted next-generation sequencing (tNGS) panel for mesocarnivores to the Oxford Nanopore Technologies (ONT) MinION platform and combined it with a SARS-CoV-2 whole-genome sequencing assay. Merging both assays before library preparation enables simultaneous SARS-CoV-2 detection, variant identification, and broader pathogen screening. The MinION platform also improves turnaround time because sequencing can begin immediately on small numbers of samples, reducing costs in low-volume workflows. We converted our validated carnivore tNGS panel from the Ion Torrent system to MinION, optimizing amplification conditions, primer pools, and barcoding for multiplexing. Analytical sensitivity was measured using contrived wildlife samples spiked with serial dilutions of SARS-CoV-2 and tested in parallel with a commercial NAAT. Diagnostic sensitivity was assessed using contrived positives, and specificity was evaluated using NAAT-negative wildlife samples and in silico analyses. All 161 wildlife samples were NAAT-negative. MinION tNGS detected SARS-CoV-2 down to Ct 34 and produced ≥ 99% genome coverage for Ct ≤ 24 while simultaneously identifying additional pathogens. Diagnostic sensitivity and specificity were 96.7% and 100%. This workflow offers a low-cost, scalable approach for comprehensive wildlife pathogen surveillance.},
}

Animals
*SARS-CoV-2/genetics/isolation & purification
*COVID-19/diagnosis/virology/veterinary
*High-Throughput Nucleotide Sequencing/methods
Genome, Viral
Whole Genome Sequencing/methods
Animals, Wild/virology
Sensitivity and Specificity
Nucleic Acid Amplification Techniques/methods

@article {pmid41598976,
year = {2026},
author = {Goglia, L and Formisano, G and Guastaferro, VM and Albano, L and Crispo, DG and Griffo, R and Di Prisco, G and Giorgini, M},
title = {The Invasive Nearctic Pest Platynota stultana Walsingham (Lepidoptera: Tortricidae) Is Established in Southern Italy.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010122},
pmid = {41598976},
issn = {2075-4450},
support = {CUP B73C24001270005//Vesuvius National Park Institution/ ; CUP B29I22001290009//Government of the Campania Region of Italy/ ; },
abstract = {Platynota stultana is a Nearctic moth of economic importance for many crops in North America. It is a quarantine pest in Europe, where Mediterranean regions, with warm climates similar to those of the moth's native range, are at risk of invasion. To date, the species is established only in Spain. It has been reported sporadically in Italy, but it is unknown whether these were transient findings or the result of an establishment. In this study, the presence of P. stultana in the Campania region, Southern Italy, was recorded. Adults of both sexes were found in different locations and in two consecutive years, suggesting that the species is established. Sequencing the COI gene identified three haplotypes of P. stultana, suggesting possible multiple introductions. The two most numerous haplotypes were identical to haplotypes from Florida. Phylogenetic analysis showed that the P. stultana clade splits into two subclades. The Italian haplotypes are all grouped into the same subclade. Our data suggest that P. stultana is expanding its range of invasion into Southern Italy, where, due to global warming, it may find increasingly favorable conditions and become an economic pest. A monitoring plan is required to allow timely implementation of control measures.},
}

@article {pmid41598975,
year = {2026},
author = {Wu, J and Yang, N and Ronkay, L and Han, HL},
title = {Unexpected Encounter: A New Genus of Orthosiini (Noctuidae: Hadeninae) Revealed by Tit Predation in Late-Winter Baihuashan National Nature Reserve, Beijing.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010121},
pmid = {41598975},
issn = {2075-4450},
support = {31872261//National Natural Science Foundation of China/ ; LBH-Z23059//Heilongjiang Postdoctoral Fund/ ; 415895//Full-Time Postdoctoral Support Program/ ; NABRI202303, 2572022DS09//Northeast Asia Biodiversity Research Center/ ; },
abstract = {During a late-winter field survey in Baihuashan National Nature Reserve, Beijing, several noctuid moths were observed flying during the daytime at low temperatures and being actively preyed upon by Marsh tits, which removed the heads and wings of captured individuals. These observations indicate that adults of this noctuid lineage are active in late winter, providing a critical nutritional resource for insectivorous birds during the ecologically constrained, food-limited winter period. Here, we formally describe this lineage as a new genus, Shoudus gen. nov., based on a new species, S. baihuashanus sp. nov., collected from Baihuashan reserve, including three specimens retrieved during active interception of tit predation, along with detached wings and heads recovered from the snow. The new genus is placed in the tribe Orthosiini Guenée, 1837, primarily based on adult external morphology, including large compound eyes with long interfacetal hairs and bipectinate male antennae, as well as forewing patterning similar to certain orthosiine genera such as Perigrapha and Clavipalpula. Notably, the dark reddish-brown forewings with sharply contrasting pale markings, as seen in the new genus and these related genera, appear well adapted for camouflage against bark, leaf litter, and exposed soil in their habitats-potentially functioning as both background matching and disruptive coloration. To further assess its phylogenetic placement, we conducted a molecular analysis based on mitochondrial COI sequences (13 newly generated and 6 retrieved from BOLD/NCBI). The resulting maximum likelihood and Bayesian trees consistently support the monophyly of the new genus and reveal a close phylogenetic relationship with Orthosia, the type genus of Orthosiini. This integrative evidence strongly supports the recognition of Shoudus as a distinct lineage within Orthosiini.},
}

@article {pmid41598974,
year = {2026},
author = {Ren, J and Xing, J and Liu, X and Zhang, R},
title = {Unveiling Weevil Diversity Drivers and Cryptic Species on the Qinghai-Xizang Plateau.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010120},
pmid = {41598974},
issn = {2075-4450},
support = {32470456//National Natural Science Foundation of China/ ; },
abstract = {Understanding patterns and mechanisms of species diversity is one fundamental issue in biogeography and ecology. As a critical region for biodiversity, the Qinghai-Xizang Plateau (QXP) still has unclear distribution patterns and drivers for cryptic, understudied taxa such as Curculionoidea. Here, we collected the distribution data of Curculionoidea on the QXP to analyze their diversity patterns and influencing factors, and compiled a DNA barcode dataset to uncover cryptic diversity. This comprehensive dataset encompasses 671 Curculionoidea species across 223 genera, demonstrating a level of diversity that surpasses that of certain vertebrate groups. We also observed an unbalanced biogeographic pattern of diversity, with a concentration of species in the eastern and southern regions and a scarcity in the northern and central areas of QXP. Further analysis showed that the elevation range is the most important factor influencing the diversity of Curculionoidea. In addition, based on 1147 COI-5' barcode sequences from 217 species, we found that 11 morphological species may contain cryptic species based on DNA barcode datadset. Our findings significantly enhance the current understanding of cryptic biodiversity patterns among understudied taxa in the QXP, while simultaneously highlighting persistent knowledge gaps in characterizing the plateau's full ecological complexity.},
}

@article {pmid41598946,
year = {2026},
author = {Russo, E and Melone, G and Pugliese, C and Laudonia, S},
title = {Integrative Taxonomy to Assess the Parasitoid Complex of the Jumping Plant-Louse Cacopsylla pulchella (Hemiptera: Psyllidae) on Cercis siliquastrum in Central and Southern Italy.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010092},
pmid = {41598946},
issn = {2075-4450},
support = {CUP B29I22001290009//U.R.Co.Fi (Regional Phytosanitary Coordination Unit) funded by the Government of the Campania Region of Italy/ ; },
abstract = {Urban green spaces host complex arthropod communities, in which natural insect antagonists play a key role in regulating pest populations. The jumping plant-louse Cacopsylla pulchella is a sap-sucking pest widespread across Europe that attacks Cercis siliquastrum L., which is commonly used as an ornamental tree. Heavy infestations may contribute to host tree decline and cause indirect damage in urban environments by reducing aesthetic value and by extensive deposition of honeydew secretions on surrounding surfaces. As with many phytophagous insects occurring in urban contexts, information on the natural enemies of this species remains limited, particularly in Italy, and requires further documentation. Here, we investigated the parasitoids associated with C. pulchella in central and southern Italy based on surveys conducted between 2022 and 2025. Specimens were obtained from infested plant material and identified using an integrative taxonomic approach combining detailed morphological examination with DNA barcoding. Prionomitus mitratus was confirmed as the primary parasitoid of C. pulchella, while two species, Pachyneuron muscarum and Pachyneuron aphidis, were identified as hyperparasitoids. In addition, a single specimen of Anastatus bifasciatus was also recorded emerging from the psyllid as a hyperparasitoid. Molecular analyses generated the first publicly available mitochondrial and nuclear sequences for P. mitratus. For Pachyneuron, molecular results showed variable correspondence with available reference sequences, reflecting the uneven representation of species-level data for Pteromalidae in public databases. By integrating morphological and molecular evidence, this study clarifies trophic relationships within the C. pulchella parasitoid complex. It provides vouchered molecular references to support future taxonomic and ecological research in urban ecosystems.},
}

@article {pmid41598914,
year = {2026},
author = {Qiao, YJ and Wang, ZP and Lv, MY and Su, PD and Wu, T and Xu, HF and Li, YF and Lin, XL and Zhang, CH},
title = {Decoding Biodiversity in Baiyangdian Lake: A DNA Barcode Reference Library for Aquatic Insects.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010060},
pmid = {41598914},
issn = {2075-4450},
abstract = {Freshwater ecosystems are among the most vulnerable habitats worldwide, and reliable biodiversity assessment is essential for their conservation. Baiyangdian Lake, the largest freshwater lake in northern China, has undergone severe ecological degradation but is now experiencing recovery through restoration efforts. To provide a molecular basis for monitoring biodiversity, we constructed a COI DNA barcode reference library of aquatic insects from Baiyangdian Lake. From January 2023 to May 2025, systematic sampling across representative habitats yielded 315 high-quality sequences covering 104 species, 74 genera, and 33 families within eight insect orders. Diptera, particularly Chironomidae, showed the highest diversity, followed by Odonata. Phylogenetic analysis using maximum likelihood resolved all orders and families as well-supported monophyletic groups, demonstrating strong congruence with morphological taxonomy. Genetic distance analysis revealed a pronounced barcode gap, with mean intraspecific divergence of 0.46% and nearest-neighbor divergence exceeding 15%, confirming the discriminatory power of COI for species identification. Accumulation curves indicated that genus-level diversity is largely captured, while species-level diversity, especially among Diptera, remains incompletely revealed. This study provides the first comprehensive DNA barcode reference library for Baiyangdian aquatic insects, supporting ecological restoration evaluation, eDNA applications, and regional biodiversity conservation strategies.},
}

@article {pmid41598890,
year = {2025},
author = {Zheng, C and Zhu, X and Zhang, Y and Wang, Y and Bu, W},
title = {Integrative Taxonomy Clarifies the Taxonomic Status of the Morphologically Intermediate Form Between Tropidothorax cruciger and T. sinensis (Hemiptera: Lygaeidae).},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010037},
pmid = {41598890},
issn = {2075-4450},
support = {32130014//National Natural Science Foundation of China/ ; 32100346//National Natural Science Foundation of China/ ; QNTJ202408//Youth Scholars Promotion Plan of North China University of Science and Technology/ ; },
abstract = {(1) Background: The identification of Tropidothorax cruciger and T. sinensis is often complicated by the presence of the "intermediate form". Due to the lack of molecular data, the taxonomic status of the "intermediate form" and the species boundaries between T. cruciger and T. sinensis remain uncertain; (2) Methods: In this study, we integrated morphological, molecular, and ecological data to delimit species boundaries of these two species using multiple species delimitation approaches; (3) Results: Most species delimitation analyses based on the cytochrome c oxidase subunit I (COI) fragment suggested that T. cruciger and the "intermediate form" comprised a single species, with T. sinensis representing a separate species. This delimitation result was also supported by the analyses of BFD* and genetic clustering based on genome-wide SNPs. Under this species delimitation scenario, a clear-cut barcode gap was discovered between the interspecific and intraspecific genetic distances. In addition, environmental-related analyses showed highly similar ecological requirements of T. cruciger and the "intermediate form", supporting their recognition as a single species; (4) Conclusions: This study clarifies the taxonomic status of the "intermediate form" and the species boundaries between T. cruciger and T. sinensis, which is essential for further studies of ecology and evolution of these species.},
}

@article {pmid41598858,
year = {2025},
author = {Huemer, P and Özden, Ö and Rennwald, E and Barton, I and Junnilainen, J and Hausmann, A and van Nieukerken, EJ and Hebert, PDN},
title = {Well-Known, Misidentified, or Unnamed? A DNA Barcode-Based Reassessment of the Lepidoptera Fauna of Cyprus Supported by Morphology.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010004},
pmid = {41598858},
issn = {2075-4450},
support = {Grant no.101059492//Genome Canada/ ; },
abstract = {This study presents the first comprehensive molecular analysis of the Lepidoptera fauna of Cyprus based on DNA barcoding. A total of 1859 DNA barcode sequences were generated, representing 701 Barcode Index Numbers (BINs) and thus putative species. Morphological examination enabled the assignment of 596 BINs to 580 Linnaean species. Based on this genetically validated species inventory-complemented by morphologically examined specimens and a critical review of the literature-a new checklist for the Lepidoptera of Cyprus is provided. In total, 1213 species are accepted as confirmed or considered likely based on published but unverified records. The checklist includes 57 genetically confirmed first records for Cyprus and 62 new records supported solely by morphology. Remarkably, 10 species are recorded as new to Europe: Alloclita deprinsi, Cochylimorpha diana, C. additana, Pammene avetianae, P. nannodes, Cydia alienana, Ephestia abnormalella, Hypsotropa paucipunctella, Dysauxes parvigutta, and Bryophilopsis roederi. In addition, 105 BINs could not be assigned to a species. Preliminary morphological assessment indicates that many of these represent cryptic taxa or belong to taxonomically unresolved species complexes. Furthermore, 35 morphology-based records could be identified at best to the genus level. The study also lists 158 previously published species that are now considered likely misidentifications and therefore excluded from the Cypriot fauna.},
}

@article {pmid41594906,
year = {2026},
author = {Qiao, Q and Chen, Y and Chen, J and Chen, T and Feng, H and Salum, YM and Wang, H and Tang, L and Zhang, H and Chen, Z and Lin, T and Wei, H and He, W},
title = {A Species-Specific COI PCR Approach for Discriminating Co-Occurring Thrips Species Using Crude DNA Extracts.},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020171},
pmid = {41594906},
issn = {2079-7737},
support = {2024NZ029029//Major Project of Science and Technology of Fujian Province/ ; },
abstract = {Thrips are cosmopolitan agricultural pests and important vectors of plant viruses, and the increasing coexistence of multiple morphologically similar species has intensified the demand for species-specific molecular identification. However, traditional morphological identification and PCR assays using universal primers are often inadequate for mixed-species samples and field-adaptable application. In this study, we developed a species-specific molecular identification framework targeting a polymorphism-rich region of the mitochondrial cytochrome c oxidase subunit I (COI) gene, which is more time-efficient than sequencing-based COI DNA barcoding, for four economically important thrips species in southern China, including the globally invasive Frankliniella occidentalis. By aligning COI sequences, polymorphism-rich regions were identified and used to design four species-specific primer pairs, each containing a diagnostic 3'-terminal nucleotide. These primers were combined with a PBS-based DNA extraction workflow optimized for single-insect samples that minimizes dependence on column-based purification. The assay achieved a practical detection limit of 1 ng per reaction, demonstrated species-specific amplification, and maintained reproducible amplification at DNA inputs of ≥1 ng per reaction. Notably, PCR inhibition caused by crude extracts was effectively alleviated by fivefold dilution. Although the chemical identities of the inhibitors remain unknown, interspecific variation in inhibition strength was observed, with T. hawaiiensis exhibiting the strongest suppression, possibly due to differences in lysate composition. This integrated framework balances target specificity, operational simplicity, and dilution-mitigated inhibition, providing a field-adaptable tool for thrips species identification and invasive species monitoring. Moreover, it provides a species-specific molecular foundation for downstream integration with visual nucleic acid detection platforms, such as the CRISPR/Cas12a system, thereby facilitating the future development of portable molecular identification workflows for small agricultural pests.},
}

@article {pmid41593779,
year = {2026},
author = {Lee, SH and Jin, BY and Lee, CR and Kim, DR and Shin, A and Park, SG and Kim, YJ and Kim, SH and Choi, M and Hwang, B},
title = {SCITO-seq2: ultra-high-throughput single-cell transcriptome and epitope sequencing.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03954-x},
pmid = {41593779},
issn = {1474-760X},
support = {SSTF-BA2301-01//Samsung Science and Technology Foundation/ ; RS-2023-00276271//National Research Foundation of Korea/ ; 6-2022-0181//Yonsei University College of Medicine/ ; },
abstract = {We introduce SCITO-seq2, an enhanced successor to SCITO-seq that integrates probe-based RNA detection with the established ultra-high-throughput protein profiling. SCITO-seq2 achieves robust quantification of transcripts and surface proteins across more than 100,000 cells, with a shared pool barcoding strategy ensuring precise matching of molecular profiles within multiplexed droplets. SCITO-seq2 is compatible with cell hashing technology, allowing efficient sample multiplexing. We demonstrate its utility in autoimmune diseases, including childhood systemic lupus erythematosus and CTLA4 haploinsufficiency with autoimmune infiltration, enabling the detection of minor immune clusters and disease-specific protein signatures. This platform establishes a scalable, streamlined, and cost-effective next-generation single-cell multi-omics workflow.},
}

@article {pmid41593459,
year = {2026},
author = {Ruckman, SN and Long, AD},
title = {Leveraging Low-Cost Short-Read Sequencing: Revolutionizing Complex Trait Genetics.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag025},
pmid = {41593459},
issn = {1537-1719},
abstract = {The genetics of complex traits has been fundamentally transformed by the dramatic reduction in short-read sequencing costs, leading to a dramatic reversal in the relative costs of genotyping versus phenotyping. We explore this new scientific landscape by examining key experimental strategies that leverage inexpensive sequencing, including low-coverage whole-genome sequencing with imputation (lcWGS+I) for genotyping large cohorts. Although somewhat limited in outbred populations, lcWGS+I can be extremely effective in multi-parent populations (MPPs) and in founder-unknown closed colonies, where imputation accuracy can exceed 98%. We further explore pooled-sequencing (Pool-seq) approaches for dissecting complex traits, such as Evolve and Resequence (E&R) for tracking adaptive changes in allele frequency over several generations, and Extreme QTL (X-QTL) mapping that identifies loci by contrasting pooled samples from phenotypic extremes. We show that X-QTL mapping in MPPs, by testing for shifts in founder haplotype frequencies across small genomic windows, can be extremely powerful and cost-effective. Finally, we discuss methods where sequencing reads serve as the phenotype itself. DNA barcoding enables massive-scale fitness assays, while the "*-seq" toolkit (e.g., RNA-seq, ATAC-seq) allows for mapping molecular QTLs, though this introduces a significant multiple testing burden. Systems leveraging certain breeding designs in concert with low cost sequencing can greatly accelerate progress towards a mechanistic understanding of the genotype-phenotype relationship.},
}

@article {pmid41590470,
year = {2026},
author = {Adotey, G and Quarcoo, A and Gedel, MA and Yerenkyi, P and Otu, P and Anang, AK and Okine, LKN and Gbewonyo, WSK and Holliday, JC and Lombardi, VC},
title = {The Medicinal Mushroom Ganoderma: A Review of Systematics, Phylogeny, and Metabolomic Insights.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/jof12010058},
pmid = {41590470},
issn = {2309-608X},
abstract = {Ganoderma is a genus of medically significant fungi, that is used in traditional medicine and is increasingly incorporated into modern nutraceuticals and pharmaceuticals. Accurate species identification and product standardization remain major challenges due to morphological plasticity and cryptic diversity. This review articulates current advances in Ganoderma systematics, phylogenetics, and metabolomics, with an emphasis on molecular identification strategies and chemical profiling. Internal transcribed spacer (ITS) sequencing has substantially improved species delineation compared with morphology alone, but its resolving power is limited in closely related species complexes, necessitating complementary multilocus approaches. Advances in metabolomics, and LC-MS- and HPLC-based profiling of triterpenes and polysaccharides, have enhanced species discrimination, chemotaxonomic resolution, and quality control of commercial products. Integrating molecular barcoding with metabolomic fingerprints provides a more robust framework for classification, pharmacological evaluation, and standardization. This review also highlights significant geographic knowledge gaps, particularly in Africa, where molecular and metabolomic data remain scarce despite high species diversity.},
}

@article {pmid41589108,
year = {2026},
author = {Rodriguez, A and Keel, K and Zapfe, G and Qiao, K and Liu, Y and Stallings, CD and Breitbart, M},
title = {Composition of fish egg assemblages varies with depth on the West Florida Shelf.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20498},
pmid = {41589108},
issn = {2167-8359},
mesh = {Animals ; Florida ; *Fishes/genetics/physiology/classification ; *Ovum ; DNA Barcoding, Taxonomic ; },
abstract = {Genetic barcoding of fish eggs has furthered our knowledge of fish spawning patterns and locations, providing valuable insights for conservation and management efforts. Since fish eggs tend to behave as buoyant, passive particles, most studies collect them from surface waters and assume that this method captures eggs from all the species that have recently spawned throughout the water column. To experimentally test this assumption, we used a Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS) to collect fish eggs from six depth bins within the upper 130 m of the water column at five stations on the West Florida Shelf. We used DNA barcoding to identify fish eggs collected within each depth bin to determine if the diversity of eggs recovered was consistent throughout the water column. Fish egg assemblage composition was heterogeneous throughout the water column, with most taxa only detected at one or two distinct depth bins per station, only a few taxa found at more than half the depth bins at any given station, and only a single taxon found at all depths within a single station. Disproving the hypothesis that all eggs present throughout the water column would be detected at the surface, only 19 of the 44 taxa identified in this study were observed in the samples collected from the upper 20 m. These findings suggest that exclusively sampling at the surface provides an incomplete picture of the fish assemblage spawning at a given station, which is difficult to predict due to variability in the rates of egg rise through the water column and further complicated by potential mismatches in the time of spawning relative to when collections are made, encounters with subsurface currents while rising to the surface, and the potential for denser eggs to reach neutral buoyancy at deeper isopycnals.},
}

Animals
Florida
*Fishes/genetics/physiology/classification
*Ovum
DNA Barcoding, Taxonomic

@article {pmid41589105,
year = {2026},
author = {Recuero, E and López-Estrada, EK and Harden, CW},
title = {Insights on the enigmatic millipede order Siphoniulida (Myriapoda, Diplopoda): a new species bearing ozopores and its phylogenetic implications.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20594},
pmid = {41589105},
issn = {2167-8359},
mesh = {*Phylogeny ; Animals ; Mexico ; *Arthropods/classification/genetics/ultrastructure/anatomy & histology ; Microscopy, Electron, Scanning ; Fossils ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; },
abstract = {The millipede order Siphoniulida is one of the most enigmatic and rare groups within Diplopoda, with fewer than 10 complete specimens known from two extant species and two amber fossils. This study presents the discovery of a new species, Siphoniulus porosus sp. nov., from a tropical montane cloud forest in Veracruz, Mexico, representing the highest elevation record for the order in the New World. We obtained the first molecular data for the order, a DNA barcode sequence of the Cytochrome C Oxidase I (COI). Detailed morphological analysis using scanning electron microscopy (SEM) showed that, unlike previously described species, Siphoniulus porosus sp. nov. exhibits ozopores, challenging the current understanding that Siphoniulida lack these structures. Phylogenetic analyses using both Maximum Parsimony and Bayesian methods were conducted, including a reassessment of existing morphological data considering the presence of ozopores in Siphoniulida as the ancestral state for this character. The results suggest a phylogentic position within the subterclass Eugnatha, though relationships in this group are not resolved. This discovery indicates a potentially greater diversity of Siphoniulida in the Neotropical Region and highlights the need for further exploration of montane cloud forests to discover additional species.},
}

*Phylogeny
Animals
Mexico
*Arthropods/classification/genetics/ultrastructure/anatomy & histology
Microscopy, Electron, Scanning
Fossils
DNA Barcoding, Taxonomic
Electron Transport Complex IV/genetics

@article {pmid41588237,
year = {2026},
author = {Yousefi, A and Mehregan, I and Hamedi, J and Asri, Y and Khan, G and Albach, DC},
title = {Belowground allies, aboveground threats: the vulnerability of the Persian oak (Quercus Brantii Lindl.)- arbuscular mycorrhizal fungi symbiosis in a changing climate.},
journal = {Mycorrhiza},
volume = {36},
number = {1},
pages = {4},
pmid = {41588237},
issn = {1432-1890},
mesh = {*Quercus/microbiology ; *Mycorrhizae/physiology/classification ; *Symbiosis ; *Climate Change ; Iran ; Soil Microbiology ; Plant Roots/microbiology ; Biodiversity ; Droughts ; Microbiota ; },
abstract = {Climate change poses a major threat to ecosystems worldwide, including Iran's ecologically important Zagros oak forests. These forests are experiencing accelerating decline due to climate-related stress and intensified human pressures, despite their key role in sustaining regional biodiversity. Soil health and the crucial symbiotic partnership between oak trees and arbuscular mycorrhizal fungi (AMF) are crucial for resilience in drought-prone Mediterranean environments. Due to a lack of comprehensive studies, this research aimed to analyze the root-associated microbiome of Persian oak (Quercus brantii) across western and southwestern Iran, specifically focusing on AMF diversity and their ecological role. Our study employed Illumina high-throughput sequencing of ITS and 18 S rRNA V4 markers of root-associated fungal communities to assess taxonomic composition and diversity of 160 trees across eight different sites. Analyses revealed dominant fungal groups, including key AMF taxa like Glomeraceae and Claroideoglomeraceae, with significant spatial variation in diversity and community structure, likely influenced by regional and abiotic factors. In addition, the findings highlight the important ecological function of the Persian oak canopy in creating a favorable microclimate and the essential symbiotic partnership with AMF for drought tolerance and nutrient uptake. However, our study ultimately concludes that despite this crucial symbiosis, the Zagros oak forests remain highly vulnerable to increasing pressures from agricultural expansion and the escalating impacts of climate change, seasonal wildfires, and declining groundwater levels, which pose significant threats to their long-term survival.},
}

*Quercus/microbiology
*Mycorrhizae/physiology/classification
*Symbiosis
*Climate Change
Iran
Soil Microbiology
Plant Roots/microbiology
Biodiversity
Droughts
Microbiota

@article {pmid41584927,
year = {2025},
author = {Sajjad, M and Kwon, SG},
title = {Reconstructing developmental lineages: a retrospective approach using somatic mutations and variant allele frequency.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1761810},
pmid = {41584927},
issn = {1664-8021},
abstract = {Somatic mutations accumulate during the first zygotic division and continue throughout an organism's lifespan. The characteristics and frequency of these mutations are contingent on developmental timing and tissue type, giving rise to somatic mosaicism, defined as the presence of unique genomic alterations across different cells. They serve as endogenous cellular barcodes, enabling detailed reconstruction of cell lineages and clonal dynamics. Although lineage tracing techniques have advanced from early microscopic observation and dye staining to the introduction of artificial barcodes via gene editing, owing to ethical considerations, such genetic manipulations in human developmental research are unavailable. Therefore, spontaneously arising somatic mutations are the most suitable strategy for tracing human lineages. Current approaches can be broadly categorized into two strategies: (i) high-resolution methods, including single-cell clonal expansion or laser-capture microdissection, which construct precise phylogenetic trees based on shared mutation profiles; and (ii) bulk sequencing methods, which infer lineage proximity by comparing variant allele frequencies across samples. As more lineage-tracing studies are being conducted focusing on a wider variety of organs, the integration of such data will make it possible to discover the general principles governing human development. This review highlights how the concept of somatic mutations has been applied across diverse biological contexts and discusses the insights and common principles that can be drawn from these findings.},
}

@article {pmid41584737,
year = {2026},
author = {Suh, H and Seo, CW and Park, KH and Yoo, S and Kim, D and Cho, Y and Lim, YW},
title = {Hidden diversity of crust-like Sebacinaceae (Sebacinales, Agaricomycetes) in Asia.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e168486},
pmid = {41584737},
issn = {2210-6340},
abstract = {Crust-like Sebacinaceae, comprising the genera Helvellosebacina, Sebacina, and Tremelloscypha, represent the only ectomycorrhizal lineage within the Sebacinaceae family. However, species delimitation within this group remains challenging because of their cryptic lifestyles, inconspicuous morphological traits, and limited taxonomic annotation. To address these limitations, we investigated crust-like Sebacinaceae in Asia by integrating two datasets: specimen-derived (barcoding) sequence data and root-associated metabarcoding data. A high diversity of crust-like Sebacinaceae species was uncovered, most of which did not match any previously described taxa. Multigene phylogenetic analyses (ITS, LSU, and rpb2) based on basidiomata identified eleven distinct species, of which six are proposed here as new to science. In parallel, metabarcoding data revealed additional crust-like Sebacinaceae species and confirmed their ectomycorrhizal association with Pinus and Quercus species. These findings advance our understanding of crust-like Sebacinaceae diversity and ecology in previously unexplored regions.},
}

@article {pmid41579861,
year = {2026},
author = {Wang, J and Suh, JM and Woo, BJ and Navickas, A and Garcia, K and Yin, K and Fish, L and Cavazos, T and Hänisch, B and Markett, D and Hirst, GL and Brown-Swigart, L and Esserman, LJ and van 't Veer, LJ and Goodarzi, H},
title = {Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102577},
doi = {10.1016/j.xcrm.2025.102577},
pmid = {41579861},
issn = {2666-3791},
abstract = {From extrachromosomal DNA to neo-peptides, reprogramming of cancer genomes leads to the emergence of cancer state-specific molecules. Here, we systematically identify and characterize a large repertoire of orphan non-coding RNAs (oncRNAs), a class of cancer-emergent small RNAs, across 32 tumor types. We show that oncRNA binary presence-absence patterns represent a digital molecular barcode that captures cancer type and subtype identities. Importantly, this barcode is partially accessible from the cell-free space as cancer cells secrete a subset of oncRNAs. Leveraging large-scale in vivo genetic screens in xenografted mice, we functionally identify driver oncRNAs in multiple tumor types. In a retrospective study across 192 breast cancer patients, we show that oncRNAs are reliably detected in blood and that changes in cell-free oncRNA burden predict both short-term and long-term clinical outcomes. Together, we establish that oncRNAs have potential roles in tumor progression and clinical utility in liquid biopsies for tumor-naive minimum residual disease monitoring.},
}

@article {pmid41578609,
year = {2026},
author = {Zhao, B and Andermann, T},
title = {Properties and Limitations of eDNA Substrates for Terrestrial Animal Monitoring.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70096},
pmid = {41578609},
issn = {1755-0998},
support = {2023-05366//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab & Wallenberg Data Driven Life Science Program/ ; },
mesh = {Animals ; *DNA, Environmental/genetics/isolation & purification ; *Environmental Monitoring/methods ; *Biodiversity ; },
abstract = {Environmental DNA (eDNA) constitutes a valuable tool for monitoring terrestrial animal diversity, but outcomes are affected by multiple factors. Among these factors, the choice of sampling substrate and method is especially important and must be aligned with research objectives. We reviewed 245 published studies that utilise eDNA for terrestrial animal monitoring and compiled an overview of the most frequently used environmental substrates. Based on the reviewed literature, we provide a key description of each substrate, as well as its particular properties and limitations related to the detection of animal species across different spatial and temporal scales. We categorise these substrates into three groups: abiotic substrates (soil, water, air, sediment), biotic substrates (invertebrate samples, plant tissues, spiderwebs) and direct-evidence substrates (scat, footprints, shelters, feeding sites). In addition, we identify several key challenges with the interpretation of eDNA-based biodiversity monitoring, including false negatives and false positives, as well as the dynamics of spatial and temporal deviations. The latter concepts, which we propose and define in this review, describe the temporal and spatial discrepancies between the DNA source and its detection in a given sample. We reflect on how these temporal and spatial deviations are expected to affect eDNA data extracted from the different types of substrates and how knowledge of these dynamics can inform effective and accurate biomonitoring. In summary, this review provides a decision basis for designing terrestrial eDNA monitoring studies by summarising the properties and limitations of different substrates and contextualising the interpretation of results in light of substrate-specific challenges.},
}

Animals
*DNA, Environmental/genetics/isolation & purification
*Environmental Monitoring/methods
*Biodiversity

@article {pmid41577483,
year = {2026},
author = {Betts, MM and Hultin, EA and Hallerman, EM and Maurakis, EG and Frimpong, EA},
title = {Embryonic selfish-herding blurs the line between brood parasitism and mutualism for communal-breeding stream fishes.},
journal = {Ecology},
volume = {107},
number = {1},
pages = {e70302},
doi = {10.1002/ecy.70302},
pmid = {41577483},
issn = {1939-9170},
support = {2039692//National Science Foundation/ ; //National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Symbiosis ; *Nesting Behavior/physiology ; Reproduction/physiology ; *Cyprinidae/physiology/embryology ; *Embryo, Nonmammalian/physiology ; Rivers ; Female ; Male ; },
abstract = {Mutualisms are complex, interspecific relationships, which sometimes create "selfish-herds" as individuals of each species compete to maximize their own fitness. Nest association, where individuals of different species spawn on a nest created by a host species, is a reproductive interaction characteristic of some minnows (Leuciscidae) and is considered mutualistic despite mimicking the behavior labeled "brood parasitism." We studied the spawning behaviors of bluehead chub (Nocomis leptocephalus) and its nest associates, testing the hypothesis that bluehead chub exploits the selfish-herd dynamic in a novel manner by arranging embryos within its nest to maximize the survival of its own offspring at the expense of the nest associates' offspring. Our results show that embryos were not uniformly distributed within a nest, as one section representing one-sixth of the nest's total volume contained a disproportionate percentage of embryos (x¯ = 40.0% ± 6.1% SE). We found three-quarters of host embryos within deeper nest sections safer from embryo predators, whereas only a third of all associate embryos were found in the same sections. These results support our hypothesis that male Nocomis leptocephalus create "embryonic selfish-herds" within their nests. This is the first study to document the existence of embryonic selfish-herds, a phenomenon that warrants the reexamination of some vertebrate reproductive interactions labeled as brood parasitism.},
}

Animals
*Symbiosis
*Nesting Behavior/physiology
Reproduction/physiology
*Cyprinidae/physiology/embryology
*Embryo, Nonmammalian/physiology
Rivers
Female
Male

@article {pmid41574122,
year = {2026},
author = {Asiri, MMA and Ali, MA and Alwahibi, MS and Ahmed, SS and Rahman, MO and Mahato, R and Faisal, M and Kim, SY and Lee, J},
title = {The First Complete Chloroplast Genome of Lycium shawii: Genomic Architecture, Molecular Phylogenetics and Evolutionary Insights.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72972},
pmid = {41574122},
issn = {2045-7758},
abstract = {Lycium shawii Roem. & Schult., a stress-resilient medicinal plant native to the deserts of Saudi Arabia, possesses notable bioactive compounds used in traditional medicine for treating inflammation, oxidative stress, and other ailments. However, its chloroplast (Cp) genome has not previously been sequenced or described, limiting accurate molecular identification and phylogenetic resolution. In this study, we present the first complete Cp genome of L. shawii. The plastome spans 155,936 bp and is organized into a large single-copy (LSC) region (86,608 bp), a small single-copy (SSC) region (18,430 bp), and two inverted repeats regions (IRA and IRB), each spanning 25,449 bp. A total of 128 genes were annotated, comprising 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Comparative genomic analyses revealed conservation of genome structure without major rearrangements across Solanaceae. Forty simple sequence repeats (SSRs) and 50 oligonucleotide repeats were identified, with mononucleotides (38) as the dominant SSR type, and forward repeats as the most common among longer repeats. RNA-editing sites were unevenly distributed, with the highest proportion in the LSC region (48%), followed by the SSC (29%) and IRs (23%). Nucleotide diversity analysis highlighted atpI, rbcL, and accD within the LSC region as hypervariable loci suitable for DNA barcoding. Plastome-wide phylogenetic reconstruction confirmed the placement of L. shawii within the tribe Lycieae of the subfamily Solanoideae. Molecular dating analysis suggested its emergence around 1.40 MYA, during the Calabrian stage of the Cenozoic era. This study provides the first Cp genome resource for L. shawii, offering new perspectives for evolutionary and comparative genomics within Solanaceae.},
}

@article {pmid41568947,
year = {2026},
author = {Robino, E and Perret, A and Noel, C and Haffner, P and Intertaglia, L and Richard, M and Descamps, N and Sellier, A and Onillon, L and Lebaron, P and Destoumieux-Garzón, D and Charrière, GM},
title = {Diversity and varying predation capacities of culturable Amoebozoae against opportunistic vibrios in contrasting Mediterranean coastal environments.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113825},
doi = {10.1128/spectrum.01138-25},
pmid = {41568947},
issn = {2165-0497},
abstract = {Free-living amoebae (FLA) are ubiquitous and can be found in many environments including soil, freshwater, and marine environments. They feed on various microorganisms and can play an important role in the food web and its dynamics. We previously described that FLA belonging to the Vannella genus isolated from oyster farms in the Thau lagoon in France are able to establish stable interactions with Vibrionaceae, suggesting they can play a role in pathogen dynamics. To further investigate the ecological interactions between FLA and Vibrionaceae in Mediterranean coastal waters, we conducted monthly sampling for 1 year at three contrasting sites. FLA populations were isolated from water and sediment samples on different bacterial lawns, including Escherichia coli or Vibrio tasmaniensis, Vibrio crassostreae, and Vibrio harveyi. Diversity analysis by v4-18S barcoding revealed distinct communities between fractions and sites. The Vannellidae were found significantly enriched in the water, whereas Paramoebidae were found enriched in the sediments. Additionally, uneven distribution of Vexilliferidae, Vermistellae, and, to a lesser extent, Acanthamoebidae and Subulatomonas contrasted between sampling sites. Selection of grazers on different bacterial lawns revealed that V. tasmaniensis inhibits the growth of most Vannellidae, whereas V. crassostreae inhibits the growth of Paramoebidae. These differences were further confirmed functionally using isolates belonging to each Amoebozoa taxonomic group. Overall, our results highlight the need for more comprehensive studies of the diversity and population dynamics of Amoebozoa in marine environments and indicate that the role of these diversified grazers in shaping Vibrio communities is complex and still poorly characterized.IMPORTANCEAlthough they can play an important role in shaping bacterial communities and as intracellular niches for potential pathogens, the diversity and ecology of free-living amoebae (FLA) in marine environments are still poorly characterized. Very few studies have used systematic approaches to unravel the population dynamics and ecological variations of FLA in different environments. Our study in marine coastal environments highlights that FLA taxonomic groups can harbor habitat preferences and have different predation capacities, suggesting that FLA-bacteria interactions need to be considered at different taxonomic levels to uncover generalist versus specialist adaptations.},
}

@article {pmid41568902,
year = {2026},
author = {Li, H and Dong, Q and Guo, J and Hu, E and Li, Y and Shan, R and Zhang, L and Zhao, D and Guo, H and Qian, G},
title = {A Smart-Perception Rare Earth MOF.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e21289},
doi = {10.1002/adma.202521289},
pmid = {41568902},
issn = {1521-4095},
support = {52302200//National Natural Science Foundation of China/ ; 52402206//National Natural Science Foundation of China/ ; 12574443//National Natural Science Foundation of China/ ; 52472173//National Natural Science Foundation of China/ ; LQ23E020004//Natural Science Foundation of Zhejiang Province/ ; LQN25E020013//Natural Science Foundation of Zhejiang Province/ ; 2024-3-029//Key Projects of Jinhua Science and Technology Burea/ ; },
abstract = {Smart responsive luminescent materials have attracted considerable scientific and technological interest owing to their broad optoelectronic applications. However, issues such as single responsive mode, inadequate spectral coverage, and poor environmental adaptability still hinder their diversified development. Herein, we propose the concept of smart multi-stimuli responsive scintillator (SMRS) and fabricate a new series of rare earth metal-organic frameworks (RE-MOFs) with active and passive perception capabilities. Such RE-MOFs exhibit excellent scintillation performances, including high relative light yield (max ∼ 42,200 photons MeV[-1]), low dose rate detection limit (min ∼ 128.2 nGyair s[-1]), and great photostability. Systematic modulation of RE[3+] contents endows MOFs with tunable broadband luminescence, thereby ensuring the passive perception. The distinct photo- and radio-luminescent mechanisms lead to significant spectral contrasts under UV and X-ray irradiation. Furthermore, RE-MOFs demonstrate thermal-stimuli responsive luminescent variation since heat will influence the energy transfer processing among the organic and inorganic units. As a result, RE-MOFs autonomously produce active luminescent perception toward both irradiation and thermal stimuli. These SMRSs exhibit great potential in in situ optical imaging and high-security photonic barcodes (the widest spectral range among MOFs for photonic encoding). This study establishes a new paradigm for smart MOF-based scintillators for an advanced intelligent perception system.},
}

@article {pmid41568360,
year = {2026},
author = {Hupało, K and Sassor, C and Fuhren, MM and Buchner, D and Grabner, D and Sures, B},
title = {Assessing whole-host homogenisation as a new tool for parasite detection and identification.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {9},
number = {},
pages = {100348},
pmid = {41568360},
issn = {2667-114X},
abstract = {Despite their importance in ecosystem functioning, parasites remain the most neglected components of biodiversity monitoring. This neglect is partly due to the methodological challenges associated with their detection and identification. Current traditional morphological and molecular approaches are time-consuming, labour-intensive, and require specialised expertise. Here, we explore a novel approach of deriving parasite information through whole-host homogenisation followed by DNA-based identification of its parasite biota. Our goal was to validate whether the approach is feasible and if it could become a complementary method for studying parasites, providing a time-efficient solution allowing for a holistic parasite scan with limited taxonomic expertise. To test the method's efficiency, we analysed five specimens of European eel as model hosts. Their parasites were identified morphologically, and then all the parasites and the entire host tissue were homogenised together using a commercial blender. Molecular identification of the morphologically detected parasites was conducted using DNA barcoding with parasite-specific primers. Following homogenisation and DNA-based identification, we successfully detected all parasite taxa identified during morphological analyses, even including instances where they had not been detected morphologically. A notable exception were acanthocephalans, which showed low levels of molecular detection. Despite certain limitations, the detection of parasites directly from the whole-host homogenate shows high potential for efficient and accurate parasite detection, in some cases even surpassing morphological identification. The further development of the method, particularly through exploration of DNA metabarcoding, could improve the reliability of parasite assessments and facilitate parasite detection, which could aid in proper parasite recognition.},
}

@article {pmid41568027,
year = {2026},
author = {Fusari, LM and Höcherl, A and Chimeno, C and Baranov, V},
title = {A new species and record of Xestochironomus Sublette & Wirth, 1972 (Diptera, Chironomidae) from the Dominican Republic, with males and females associated by DNA barcode.},
journal = {ZooKeys},
volume = {1266},
number = {},
pages = {219-230},
pmid = {41568027},
issn = {1313-2989},
abstract = {We describe a new species of Xestochironomus Sublette & Wirth, 1972 and provide notes on X. luteifurcatus Sublette & Wirth, 1972 from the Dominican Republic. The adult male and female of Xestochironomus digitulus sp. nov. are also described and illustrated. The male and female of X. luteifurcatus are redescribed. Males of the new species can be easily distinguished from congeners by the following combination of characters: the abdomen of both sexes bears cross bands; the anal point is long, slender; the male gonostylus has a slightly bifurcated apex; and there is a thumb-like lobe at the apex of the gonostylus.},
}

@article {pmid41566400,
year = {2026},
author = {Jiang, WJ and Cai, K and Sun, Y and Liu, A and Zhu, H and Gao, R and Zhong, C and Wei, N and Lai, F and Fei, T and Wang, YJ and Zheng, X and Xu, M and Wu, HJ},
title = {Harmonizing single-cell 3D genome data with STARK and scNucleome.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03938-x},
pmid = {41566400},
issn = {1474-760X},
abstract = {Single-cell three-dimensional genome sequencing (sc3DG-seq) reveals genome regulation and heterogeneity in various biological processes, but a universal analysis tool is lacking. Here we present STARK, a versatile toolkit for processing, quality control, and analysis of diverse sc3DG-seq data. Utilizing STARK, we benchmark 15 technologies, quantitatively comparing their strengths and limitations. We also develop EmptyCells to filter empty barcodes and introduce Spatial Structure Capture Efficiency (SSCE) to assess chromatin structure capture quality. Additionally, we establish scNucleome, a uniformly processed repository of sc3DG-seq datasets, to serve as a foundational resource for future 3D genome research.},
}

@article {pmid41565766,
year = {2026},
author = {Wu, B and Yang, X and Cai, Y and Wan, S and Liu, J and Xing, J and Chen, X and Zhang, J and Jin, Y and Yu, A and Yang, L},
title = {Proteomic profiling of single extracellular vesicles as a promising new approach for the diagnosis and treatment modality of advanced ovarian cancer.},
journal = {NPJ precision oncology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41698-026-01271-x},
pmid = {41565766},
issn = {2397-768X},
support = {82274266//National Natural Science Foundation of China/ ; 82505319//National Natural Science Foundation of China/ ; 2026ZL0202//The Traditional Chinese Medicine Science and Technology Project of Zhejiang Province/ ; },
abstract = {This study utilized a novel Proximity Barcoding Assay to perform high-resolution proteomic profiling of individual plasma extracellular vesicles from 85 patients with advanced high-grade serous ovarian carcinoma (OC) and 95 healthy controls (HC). Single-EV analysis identified 119 differentially expressed proteins and 17 distinct EV subpopulations. Cluster 7 (enriched in integrins ITGB3, ITGB1, and ITGA6) was significantly elevated in OC plasma (4.47% in HC vs. 14.79-15.82% in OC). Machine learning (SVM-RFE, LASSO, Random Forest) identified a diagnostic panel (ITGA6, ITGB2, ILK) achieving exceptional accuracy in distinguishing OC from HC (AUC = 0.999 training; 1.000 validation). Furthermore, risk models incorporating specific protein signatures effectively stratified patients by platinum sensitivity/resistance (9-protein panel: ILK, CDCP1, CD86, CLDN4, CLEC1B, CDHR5, CLDN11, JAM2, FOLH1), lymph node metastasis status (7-protein panel: APOE, CD28, CLDN4, FOLH1, ITGAL, JAML, ULBP3), and post-surgical residual disease burden (4-protein panel: CD44, CLMP, ITGA4, AMIGO1), with Cluster 13 (ITGB1-high) also significantly associated with residual disease. This work demonstrates the power of single-EV proteomics combined with machine learning for non-invasive diagnosis and clinical outcome assessment in advanced ovarian cancer, though the absence of early-stage patients limits its applicability for early detection.},
}

@article {pmid41563521,
year = {2026},
author = {Dela Cruz, JWR and Malit, EPB and Patanindagat, CY and Arevalo, CFL and Manalo, AJI and Boongaling, DDG and Ramos, JDA},
title = {Electron microscopy and molecular phylogenetic characterization of the allergenic dust mite species Suidasia pontifica (Acari: Suidasiidae).},
journal = {Experimental & applied acarology},
volume = {96},
number = {2},
pages = {12},
pmid = {41563521},
issn = {1572-9702},
mesh = {Animals ; Female ; Male ; Allergens ; Arthropod Proteins/genetics ; Electron Transport Complex IV/genetics ; *Microscopy, Electron ; Philippines ; *Phylogeny ; *Pyroglyphidae/classification/genetics ; },
abstract = {The clinical significance of house dust mites (HDMs) as sources of allergens for medical diagnostics, allergen-specific immunotherapy, and allergology research is dependent on accurate morphological and molecular data analysis for species identification and characterization. Here, we report the species identification and allergenicity of a tropical HDM, Suidasia pontifica (Sp), via morphological-molecular characterization tandem and IgE ELISA, respectively. Electron microscopy of monocultures of HDM samples collected from Laguna, Philippines, revealed different traits related to chaetotaxy, cuticle pattern, and body anatomy. Genus-specific characters such as the length of the scapular setae, cuticle patterns, vertical setae, ω1 setae, along with species-specific traits such as short dorsal setae, long h3 setae, average c1 to c1 verrucae count, presence of sclerotized bursa copulatrix (female), and c3 setae size, suggest that the sample identity is Sp. In addition, PCR amplification from the HDM monoculture genomic DNA and bidirectional sequencing of the 18S and COI gene markers were performed. Sequences were subjected to sequence assembly, consensus acquisition, sequence alignment, and phylogenetic inference. The COI gene showed an exact match and phylogenetic attachment of the sample assembly to Sp, confirming the species-level identification, corroborated with morphological data. Furthermore, 18S gene character analysis was able to prove phylogenetic demarcation of the Sp 18S gene from the sister species S. nesbitti and other allergenic sarcoptiform species. Our molecular phylogenetic analysis, which is strongly supported by electron microscopy data, indicates the identity of our monocultures as Sp. Interestingly, the Sp allergenicity profile of allergic patients and controls (n = 200) suggests 47% IgE-binding reactivity, confirming its allergenicity and clinical importance among atopic patients. This study emphasizes the resolving power of the morphological-molecular phylogenetic approach and IgE-reactivity to objectively verify Sp species identity and allergenicity for downstream immunological studies.},
}

Animals
Female
Male
Allergens
Arthropod Proteins/genetics
Electron Transport Complex IV/genetics
*Microscopy, Electron
Philippines
*Phylogeny
*Pyroglyphidae/classification/genetics

@article {pmid41562469,
year = {2026},
author = {Wan, Z and Xu, C and Wang, Y and Song, L and Yuan, W and Chen, M and Gong, R and Zhang, XE},
title = {An AND-Logic Gate-Based Biosensor for Simultaneous Detection of SARS-CoV-2 Nucleic Acids and Nucleocapsid Proteins.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c07321},
pmid = {41562469},
issn = {1520-6882},
abstract = {Nucleic acids and proteins are recognized as gold standard biomarkers for disease diagnosis and pathogen detection. However, conventional single-analyte detection methods remain susceptible to false positives caused by manual operational errors or sample contamination, thereby undermining diagnostic reliability and increasing the burden on healthcare systems. To address this limitation, we developed a one-pot isothermal amplification and CRISPR-Cas cooperative system (OIACS) that functions as an AND-logic gate biosensor for the simultaneous detection of SARS-CoV-2 RNA and nucleocapsid protein. Unlike conventional methods relying solely on CRISPR RNA (crRNA) recognition, the OIACS employs antibody-mediated target binding with blocker release for target recognition, offering increased flexibility in assay design for different targets. A universal Cas12a-targetable DNA barcode is generated via strand displacement isothermal amplification, enabling signal amplification upon dual-target recognition. The OIACS assay exhibited practical utility by reliably detecting SARS-CoV-2 transcription- and replication-competent virus-like-particles at 5000 copies/mL, and the limit of detection was determined to be as low as 1698 copies/mL, highlighting its robustness and potential for clinical diagnosis.},
}

@article {pmid41561880,
year = {2025},
author = {Zucco, Z and Cava, S and Bonacci, T and Scalercio, S},
title = {Effectiveness of DNA Barcoding Libraries Boosted through Taxonomy: the Case of a Neglected Taxon within an Underexplored Region.},
journal = {Zoological studies},
volume = {64},
number = {},
pages = {e49},
pmid = {41561880},
issn = {1810-522X},
abstract = {In recent decades, taxonomy has been significantly improved by integrating molecular techniques with classical morphological methods, leading to the discovery of cryptic species. On the other hand, molecular datasets by themselves are ineffective in several types of research without basic taxonomic studies, as the ecological and biological roles of a given species cannot be determined without an accurate name. DNA barcoding libraries are widely used as identification tools by non-specialists to overcome the taxonomic impediment, but they fail when basic taxonomic studies are insufficient and faunistic inventories are lacking. South European microlepidoptera are poorly studied, with the exception of a few families such as Depressariidae. We tested the effectiveness of the DNA barcoding library for this family to identify 174 specimens collected in southern Italy, where faunistic studies are very limited. All specimens were successfully barcoded, and 95% of them were assigned to 47 species, 43 of which correspond to a Barcode Index Number (BIN). Four additional species shared a BIN but were still clearly separated into different clusters at within-BIN resolution. Only seven specimens belonging to four BINs remain unnamed, and ad hoc studies are needed to clarify their status. The regional fauna was enriched by 37 species, three of which are new for the Italian mainland and 21 for peninsular Italy, demonstrating the usefulness of the DNA barcoding library in assessing local diversity and overcoming the taxonomic impediment. Improving taxonomic studies is crucial for utilizing molecular datasets to depict ongoing macroecological dynamics, highlight species richness trends, and identify changes in species assemblages.},
}

@article {pmid41560697,
year = {2026},
author = {Xue, Y and Su, J and Chao, Y and Liu, L and Lin, X and Xiang, Y and Ho, MK and Su, Z and Chen, J and Luo, Z and Lin, C and Luo, R and Aurich, T and Wu, J and Cheung, KSC and Huang, Y and Ho, JWK and Sugimura, R},
title = {Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18084},
doi = {10.1002/advs.202518084},
pmid = {41560697},
issn = {2198-3844},
support = {//Hong Kong Research Grant Council/ ; N_HKU731/21//NSFC/RGC Joint Research Scheme/ ; 2023A1515011265//Guangdong Natural Science Fund/ ; SGDX2021082310356025//Shenzhen-Hong Kong-Macau Technology Research Programme/ ; //InnoHK initiative of the Innovation and Technology Commission of the Hong Kong Special Administrative Region Government/ ; },
abstract = {Lineage tracing at single-cell resolution is vital for mapping cell fate decisions, yet synthetic barcoding faces limitations in precision, diversity, and toxicity-especially in human pluripotent stem cells (hPSCs). Here, we repurpose naturally occurring somatic mutations in mitochondrial transcripts from single-cell RNA sequencing as endogenous genetic barcodes. By enriching mitochondrial reads and applying a robust computational pipeline, we identified clonally informative variants to trace hematopoietic lineage emergence from hPSCs during early embryogenesis. Integrating mitochondrial barcoding with synthetic lineage tracing, we modeled embryonic tissue development and reconstructed the transcriptional logic and regulatory networks driving fate specification using a dynamical systems model. Extending this approach to spatial transcriptomics, we mapped the clonal architecture of human embryonic organoids, revealing spatial zonation orchestrated by NOTCH-mediated crosstalk between stromal cells and hematopoietic progenitors. This multimodal strategy links clonal dynamics with niche-driven fate decisions, offering a scalable, non-invasive method to dissect tissue organization in development and disease. Together, our work establishes a scalable, non-invasive multimodal framework that leverages endogenous mitochondrial DNA variants to reconstruct high-resolution spatiotemporal clonal dynamics and decode niche-driven fate decisions in a human stem cell-derived model. This approach provides a powerful strategy for dissecting tissue self-organization in development and disease.},
}

@article {pmid39113372,
year = {2025},
author = {Anbalagan, R and Srivastava, PK and Baruah, K and Krishnan, J},
title = {Insecticide resistance status and bar-coding of dengue vectors in three districts of Tamil Nadu, India.},
journal = {Journal of vector borne diseases},
volume = {62},
number = {1},
pages = {51-59},
doi = {10.4103/JVBD.JVBD_79_24},
pmid = {39113372},
issn = {0972-9062},
mesh = {India/epidemiology ; Animals ; *Insecticide Resistance ; *Aedes/drug effects/genetics/classification ; *Mosquito Vectors/genetics/drug effects/classification ; Phylogeny ; *Insecticides/pharmacology ; Dengue/transmission ; Female ; Malathion/pharmacology ; DDT/pharmacology ; },
abstract = {BACKGROUND OBJECTIVES: Occurrence and distribution of vector population are crucial for entomological study in context of prevention, control and elimination of vector-borne diseases. To update some entomological aspects the study was undertaken in three districts of Tamil Nadu state namely Kumbakonam, Nagapattinam and Thriuvarur. The objective of the study was to understand the prevalence of mosquitoes; to assess insecticide resistance and phylogenetic analysis of dengue vectors (Aedes aegypti and Ae. albopictus).

METHODS: The immature stages of mosquitoes were collected from different localities by standard WHO methods marking with GPS and mapping was done using ArcGIS 10.4 software for all three districts. Insecticide resistance test was conducted using WHO susceptibility test kits. The F1 generation of female adult mosquitoes of Ae. aegypti and Ae. albopictus were exposed to DDT 4% and malathion 5% with the control paper of Risella oil and olive oil, respectively. Further, genomic DNA of individual mosquito was isolated, and sequencing was done through Eurofins, Bangalore, India. The FASTA sequence was analyzed and phylogenic tree was constructed using the Maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software (version 10.0).

RESULTS: A total 5307 specimens were collected through expanded survey in all three study areas. The collection yielded 16 species from six genera of mosquitoes. In total collection, Ae. albopictus was the dominant species in Kumbakonam and Thiruvarur districts and Ae. aegypti was dominant in Nagapattinam. The predominant breeding sources were discarded tyres with rainwater, plastic cups, coconut shells, aluminum vessels, sliver containers, bottles, grinding stones and earthen pots. The study revealed high pupal indices in all three study areas. Insecticide resistance monitoring revealed possible resistance in Ae. aegypti against DDT in all three districts whereas against malathion, possible resistance was recorded in Kumbakonam and Nagapattinam and Thiruvarur district, the species was found to be susceptible. Ae. albopictus showed resistance against DDT in all three districts but susceptible to malathion. The sequences obtained for dengue vectors showed 99% similar with GenBank. The phylogenetic tree was constructed using COI region sequences. Certainly, we observed the different genetic relationship among Ae. aegypti and Ae. albopictus between the study areas.

INTERPRETATION CONCLUSION: The study confirmed the presence of Ae. aegypti and Ae. albopictus in all three districts. The study further revealed that these vectors are susceptible to malathion but resistant to DDT. The continued surveillance of dengue vector and monitoring of insecticide resistance will strengthen the control programme for appropriate vector control measurements.},
}

India/epidemiology
Animals
*Insecticide Resistance
*Aedes/drug effects/genetics/classification
*Mosquito Vectors/genetics/drug effects/classification
Phylogeny
*Insecticides/pharmacology
Dengue/transmission
Female
Malathion/pharmacology
DDT/pharmacology

@article {pmid41559823,
year = {2026},
author = {Harl, J and Himmel, T and Pacheco, MA and Weissenböck, H},
title = {New mitochondrial genomes of parasites belonging to the Leucocytozoon toddi and Haemoproteus nisi groups (Haemosporida, Apicomplexa).},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07244-0},
pmid = {41559823},
issn = {1756-3305},
support = {P37076//FWF Austrian Science Fund/ ; NSF-DEB 2146653//US National Science Foundation/ ; },
abstract = {BACKGROUND: Avian haemosporidians are single-celled eukaryotic parasites of vertebrates that require dipteran vectors for transmission. The genera Plasmodium, Haemoproteus and Leucocytozoon currently comprise over 5000 parasite lineages based on a 478-bp section of the mitochondrial cytochrome b gene, which is the standard DNA barcode for avian haemosporidians. The mitochondrial genomes of apicomplexan parasites are highly condensed, with a length of approximately 6000 bp, containing three coding genes (cytochrome c oxidase subunit I, cytochrome c oxidase subunit III and cytochrome b) and dispersed fragments of the small and large ribosomal RNA (rRNA) genes. Since the mitochondrial genomes are relatively conserved, they are valuable markers for studying the phylogenetic relationships between haemosporidian parasites. However, until recently, mitochondrial genomes were unavailable for parasites of the Haemoproteus nisi and Leucocytozoon toddi species groups, which are exclusive to accipitriform raptors and strongly diverged from other Haemoproteus and Leucocytozoon parasites.

METHODS: We screened 171 accipitriform raptors from Austria and Germany using new primers targeting the cytochrome b gene of a previously neglected L. toddi clade. We also developed a new primer assay that enables the amplification and sequencing of the complete mitochondrial genomes of haemosporidian parasites. This process involved long-range PCRs with lineage-specific primers placed within the cytochrome b gene, followed by five nested PCRs targeting conserved sequence regions.

RESULTS: Screening the accipitriform raptors revealed 10 new L. toddi group lineages. We sequenced 18 mitochondrial genomes belonging to five H. nisi group, nine L. toddi group, and two other Leucocytozoon lineages. Phylogenetic analyses based on mt genome sequences placed the L. toddi lineages within the genus Leucocytozoon, but the results did not support a monophyly of the genus Haemoproteus.

CONCLUSIONS: The new nested PCR approach with lineage-specific primers used for the long-range PCRs described herein successfully enabled the sequencing of the complete mitochondrial genomes, even in samples with mixed infections. The mitochondrial genomes of the H. nisi and L. toddi group lineages are highly valuable for resolving the phylogenetic relationships of the order Haemosporida since these parasites belong to clades distinct from other Haemoproteus and Leucocytozoon parasites.},
}

@article {pmid41555650,
year = {2026},
author = {Han, EL and Kim, D and Murray, AM and Mrksich, K and Hamilton, AG and Tang, S and Yoo, S and Zhu, AT and Tong, ER and Palanki, R and Hall, ML and Bedingfield, SK and Mitchell, MJ},
title = {High-Throughput In Vivo Screening Identifies Structural Factors Driving mRNA Lipid Nanoparticle Delivery to the Brain.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c19138},
pmid = {41555650},
issn = {1936-086X},
abstract = {Achieving systemic nonviral delivery of large nucleic acids such as mRNA to the brain is challenging due to high off-target delivery and the blood-brain barrier (BBB), a cellular barrier which prevents most nucleic acids in circulation from entering the brain. Ionizable lipid nanoparticles (LNPs) are a promising class of nanocarriers to facilitate the delivery of mRNA, as their highly modular nature enables fine-tuning of the LNP formulation for targeted delivery applications. In this work, we explore the role of ionizable lipid chemical structure and lipid molar ratios within the LNP formulation on mRNA delivery to and transfection of the brain. We utilize a high-throughput in vivo screening approach based on mRNA barcoding to study a large library of LNPs made with systematically varied ionizable lipid structures, amounts of ionizable lipid, and amounts of lipid-polyethylene glycol (PEG). We find that ionizable lipids with longer tail structures and linear amine cores can facilitate mRNA delivery to the mouse brain, and ultimately identify a specific ionizable lipid, C14-306, that facilitates brain transfection coupled with reduced liver transfection compared to an FDA-approved benchmark formulation. Furthermore, the lead LNP formulated with C14-306 is able to increase neuronal transfection and facilitate Cre-mediated recombination in the brain. Finally, safety analyses demonstrate that the lead LNP does not induce BBB leakage, increases in serum inflammatory cytokine levels, or increases in serum liver enzyme levels. Overall, our work highlights the utility of molecular barcoding for high-throughput screening of LNPs for delivery to the brain and suggests several design principles to guide the engineering of next-generation brain-tropic LNPs.},
}

@article {pmid41552826,
year = {2025},
author = {Kashuri, M and Ikrar, T and Sutriyo, and Mun'im, A and Yanuar, A},
title = {Evidence-based production framework for herbal medicine regulation in Indonesia.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1730273},
pmid = {41552826},
issn = {1663-9812},
abstract = {This narrative review synthesizes 2015-2025 evidence on evidence-based production (EBP) of herbal medicines with emphasis on advanced production technologies, omics-enabled authentication, quality by design (QbD), and regulatory harmonization relevant to Indonesia. We map how in vitro root culture, bioreactor scale-up, elicitation/metabolic engineering, and nanotechnology address supply variability and improve consistency; how DNA barcoding/metabarcoding and metabolomics with chemometrics underpin identity and chemical reproducibility; and how ASEAN/WHO initiatives enable 'loose harmonization' while preserving traditional diversity. We argue for a two-key batch-release specification (genomic × metabolite) and validated omics workflows within GLP to strengthen traceability, with real-world evidence and digital pharmacovigilance extending safety monitoring post-market. We translate these elements into an actionable framework for the Indonesian FDA (BPOM) to operationalize EBP through regulation, cross-sector training, and reliance pathways, positioning Indonesia as a regional hub for evidence-based herbal regulation.},
}

@article {pmid41551611,
year = {2025},
author = {Yu, S and Luo, Y and Dang, T and Peng, C and Gan, Q and Liang, Y and Yu, J and Long, P and Zhou, W and Dai, D},
title = {A single-sEV analysis identifies plasma EPCAM[+] sEVs as a biomarker for early diagnosis and monitoring postoperative remission of thyroid cancer.},
journal = {Extracellular vesicles and circulating nucleic acids},
volume = {6},
number = {4},
pages = {982-999},
pmid = {41551611},
issn = {2767-6641},
abstract = {Aim: Small extracellular vesicles (sEVs) are promising noninvasive biomarkers for several malignancies, including thyroid carcinoma (TC). However, their heterogeneity is frequently overlooked in bulk-level analyses. Methods: Plasma samples from TC and healthy controls (HC) were collected for a proximity-dependent barcoding assay (PBA) to identify plasma sEV biomarkers at the single-sEV level. We screened the potential biomarkers using the Panel260 (the panel that detects 260 proteins) of PBA in Cohort 1, and validated them using Panel550 (the panel that detects 550 proteins) in Cohort 2. Results: Plasma exosome counts were significantly elevated in TC compared with those in HC in both Cohort 1 and Cohort 2. Receiver operating characteristic curve analysis showed that sEV counts exhibited an area under the curve > 0.75 in both cohorts. The sEV proteomic analysis revealed that sEV epithelial cell adhesion molecule (EPCAM) levels were significantly increased, whereas claudin-11, integrin alpha X, and lymphocyte-activating 3 were significantly decreased in TC compared with HC. The increase in EPCAM in the plasma and tumor tissues was confirmed by enzyme-linked immunosorbent assay and immunohistochemistry analyses, respectively. The sEV subpopulation analysis further demonstrated that EPCAM[+] sEVs were significantly elevated in TC compared with HC in both cohorts. The reduction in sEV counts was observed in 18 out of 20 patients after the operation. The decrease in EPCAM[+] sEVs was observed in 20 patients with TC post-operatively, whereas the reduction in the conventional biomarker serum thyroglobulin (Tg) was observed in 14 patients. TC-derived plasma sEVs promoted TC cell proliferation, migration, invasion, and TC xenograft growth. Conclusion: EPCAM[+] sEVs could serve as a promising biomarker for the early diagnosis of TC and perform better in monitoring post-operative remission of TC than serum Tg.},
}

@article {pmid41551220,
year = {2025},
author = {Réblová, M and Nekvindová, J and Hernández-Restrepo, M and Hradilová, M and Kolařík, M},
title = {Phylogeny, taxonomy and geographic distribution of novel and known fungi with holoblastic-denticulate conidiogenesis in Rhamphoriales and Pleurotheciales (Sordariomycetes).},
journal = {Persoonia},
volume = {55},
number = {},
pages = {277-311},
pmid = {41551220},
issn = {0031-5850},
abstract = {As part of a broader survey of lignicolous saprobic fungi, we investigated fungal taxa from the class Sordariomycetes displaying holoblastic-denticulate conidiogenesis, a distinct developmental process and phylogenetically informative trait. Although these fungi appear morphologically similar in culture, they represent distinct evolutionary lineages. This taxonomic study integrates comparative morphological analyses, phylogenetic reconstruction of five nuclear markers, and analysis of biogeographical patterns through environmental DNA data to introduce novel taxa in the Pleurotheciales and Rhamphoriales. A new genus and species Echinodenticula allantospora and three new species, Phaeoisaria parallela, Rhamphoriopsis cuprea and Rh. denticulata, are described. A rarely encountered species Rhamphoria separata is reported, along with its previously undocumented asexual morph. Furthermore, we successfully demonstrate the utility of two protein-coding genes, rpb2 and tef1, as complementary barcodes for distinguishing closely related Phaeoisaria species. Our findings highlight the significance of holoblastic-denticulate conidiogenesis as a diagnostic feature of the Rhamphoriales and a prevalent trait in the Pleurotheciales. An unknown ascomycete that produced only sterile mycelium in culture is described here as Melanocrypta curvata and placed at an incertae sedis position within the Sordariomycetes. Additionally, we present short-read whole-genome sequencing data for the ex-type strains of the newly described species, providing a valuable genomic resource for future taxonomic, phylogenetic, and functional studies. Environmental DNA data from the GlobalFungi database bring new perspective into the biogeographical patterns of Phaeoisaria, Rhamphoria, and Rhamphoriopsis. The distribution of E. allantospora and M. curvata remains poorly understood, as no records for these species were found in GlobalFungi. This study provides new insights into the molecular systematics, taxonomy, and biogeography of the Rhamphoriales and Pleurotheciales, and highlights the role of environmental DNA metabarcoding in uncovering fungal diversity and distribution patterns. Citation: Réblová M, Nekvindová J, Hernández-Restrepo M, Hradilová M, Kolařík M (2025). Phylogeny, taxonomy and geographic distribution of novel and known fungi with holoblastic-denticulate conidiogenesis in Rhamphoriales and Pleurotheciales (Sordariomycetes). Persoonia 55: 277-311. doi: 10.3114/persoonia.2025.55.08.},
}

@article {pmid41550687,
year = {2026},
author = {Back, J and Bang, HW},
title = {A new genus of Orthopsyllidae Huys, 1990 (Copepoda, Harpacticoida) from the Pacific Ocean.},
journal = {ZooKeys},
volume = {1266},
number = {},
pages = {137-192},
pmid = {41550687},
issn = {1313-2989},
abstract = {This study reports the discovery of four new benthic harpacticoids from Korean waters in the Pacific Ocean. The harpacticoids were collected using SCUBA or a grab sampler and sorted using a stereomicroscope for both molecular and morphological analysis. The study employed standard DNA sequencing methods (COI and 18S rRNA) and detailed morphological characterization through microscopy and scanning electron microscopy. As a result, three new species belonging to the family Orthopsyllidae and classified as a new genus were discovered. Although the new genus lacks brush setae on leg 1, a diagnostic feature of Orthopsyllidae, it shares similarities with other orthopsyllids in characters such as the large thorn-like process on the antennule, leg 5, and sexual dimorphism. This finding necessitates an expanded diagnosis of Orthopsyllidae to reflect the characters of the new genus based on the three new species. In addition, a new species belonging to the genus Orthopsyllus was discovered. This study is the first to describe a new species of Orthopsyllus from Korea, where the genus has not been previously reported at the species level. This study provides a key for classifying genera and species within the Orthopsyllidae family.},
}

@article {pmid41546775,
year = {2026},
author = {Debnath, R and Rajmohana, K and Dinesh, KP},
title = {A new species of Telenomus Haliday (Hymenoptera: Scelionidae) and a novel host association with Creatonotos transiens (Walker) (Lepidoptera: Erebidae) in India.},
journal = {Systematic parasitology},
volume = {103},
number = {1},
pages = {5},
pmid = {41546775},
issn = {1573-5192},
support = {CRG/2021/005047//DST-SERB, Govt. of India/ ; },
mesh = {Animals ; India ; *Moths/parasitology ; Species Specificity ; *Wasps/classification/anatomy & histology/genetics ; DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; Phylogeny ; Female ; *Hymenoptera/classification/anatomy & histology/genetics ; Male ; },
abstract = {Telenomus hexodon Debnath & Rajmohana sp. nov. (Hymenoptera: Scelionidae), is described as new to science. The species was reared from eggs of the polyphagous pest Clouded Tiger moth, Creatonotos transiens (Walker) (Lepidoptera: Erebidae). This represents the first record of an insect parasitoid association with C. transiens. Host identity was confirmed through DNA barcoding, while the parasitoid was characterized using an integrative taxonomic approach combining morphological and molecular data. Further, a checklist of Telenomus species reported from India is provided.},
}

Animals
India
*Moths/parasitology
Species Specificity
*Wasps/classification/anatomy & histology/genetics
DNA Barcoding, Taxonomic
Host-Parasite Interactions
Phylogeny
Female
*Hymenoptera/classification/anatomy & histology/genetics
Male

@article {pmid41546422,
year = {2026},
author = {Tang, Q and Yu, H and Hou, J and Jiang, M and Zhang, Z and Wang, J and Zhang, M and Han, D and Guo, P},
title = {Spatial Mapping of Membrane Protein Interactions Using a DNA Origami Rubbing.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e13795},
doi = {10.1002/anie.202513795},
pmid = {41546422},
issn = {1521-3773},
support = {XDB1020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 22304176//National Natural Science Foundation of China/ ; 32341017//National Natural Science Foundation of China/ ; 22225402//National Natural Science Foundation of China/ ; 22374132//National Natural Science Foundation of China/ ; 2024R01005//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang Province/ ; KF2101//State Key Laboratory of Fine Chemicals, Dalian University of Technology/ ; },
abstract = {Revealing the protein-protein interactions (PPIs) of membrane proteins is as challenging as their structural reconstruction, primarily because the molecular structures and related PPIs of membrane proteins are highly dependent on the bio-membrane where they are situated. DNA origami offers a platform for manipulating molecules with nanoscale precision. Herein, we used a square-like DNA origami, refer to as DNA origami rubbing, to map the two-dimensional distribution of membrane proteins in situ. Through artificial models and cell studies, we correlated the efficiency of barcode recording of DNA origami rubbings with the distance between adjacent proteins, and we observed that the frequency of adjacent proteins mapped by DNA origami rubbings was correlated to the abundance of the bait protein. We demonstrated that the DNA origami rubbing was able to reflect the distribution change of adjacent proteins caused by adding the ligand of bait protein. Our results suggested that the DNA origami rubbing can serve as a powerful tool in the field of protein interactomics.},
}

@article {pmid41544931,
year = {2026},
author = {Romariz, APPL and da Silva, DT and Benassi, JC and Leonel, JAF and Spada, JCP and Rodrigues, CMF and Pérez, HAG and de Almeida Paula, NF and Teixeira, MMG and de Sousa Oliveira, TMF and Buzetti, WAS},
title = {Water buffaloes (Bubalus bubalis): potential reservoirs of trypanosomatids in endemic areas.},
journal = {Parasitology international},
volume = {},
number = {},
pages = {103242},
doi = {10.1016/j.parint.2026.103242},
pmid = {41544931},
issn = {1873-0329},
abstract = {Trypanosomatids are protozoan parasites that include the genera Trypanosoma and Leishmania, which infect a wide range of mammalian species, including humans and ruminants. This study aimed to assess the presence of Trypanosomatid parasites in water buffaloes (Bubalus bubalis) using molecular techniques. Blood samples and conjunctival swabs from the right and left eyes were collected from 100 buffaloes (44 females and 56 males). PCR analysis detected Trypanosomatids in 32% (32/100) of the buffaloes: 29% (29/100) tested positive for DNA extracted from blood, and 4% (4/100) tested positive from conjunctival swab samples. Using the Fluorescent Fragment Length Barcoding (FFLB) technique, 38% (38/100) of blood samples were positive for Trypanosomatids, with 35% (35/100) identified as Trypanosoma theileri and 3% (3/100) as Trypanosoma vivax. Direct sequencing and analysis of PCR amplicons from four buffaloes revealed that three samples matched 100% with Trypanosoma theileri, while one matched 100% with Leishmania infantum. Our findings confirm that buffaloes can serve as hosts for Trypanosomatids and support previous observations that these parasites are often underdiagnosed. This is the first report of Leishmania infantum DNA in buffalo conjunctival swabs in Brazil and the first detection of Trypanosoma vivax DNA in buffaloes in the city of Andradina and in São Paulo state. These findings underscore the need for further studies to clarify the role of buffaloes in the epidemiology and dissemination of trypanosomatids in livestock populations.},
}

@article {pmid41542514,
year = {2026},
author = {Hornick, AC and Walters, LC and Dobson, CS and Gaglione, SA and Birnbaum, ME},
title = {Interrogating antiviral antibody responses with multiplexed, high-throughput serum assays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.03.697501},
pmid = {41542514},
issn = {2692-8205},
abstract = {The COVID-19 pandemic underscored the importance of rapidly analyzing antibody responses against emerging viruses. Existing techniques, however, are limited in their ability to probe antibodies' recognition of multiple native-conformation antigens simultaneously. To increase the throughput and multiplexability of antibody profiling, we developed A ntibody R eactivity C haracterization by A ntibody- D ependent E nhancement (ARCADE). This assay employs an antigen-agnostic Fc receptor-expressing cell line and a library of antigen-displaying, genetically barcoded lentiviruses that, when mixed with serum, infect cells and integrate their barcodes at rates reflecting the relative abundances and affinities of the antigen-specific antibodies present. Verified using sera from COVID-19-convalescent and - vaccinated donors, ARCADE delivers insights that align with and expand upon those offered by established immunoassays, highlighting, for example, how an mRNA-based vaccine elicits broader and stronger antibody responses than an adenovirus vector-based vaccine. ARCADE can comprehensively assess how infection and vaccination impact antiviral antibody repertoires over time and across patient populations.},
}

@article {pmid41542380,
year = {2026},
author = {Vallin, H and Fraser, M and Pakeman, RJ and Hipperson, H},
title = {Evaluating the Quantitative Accuracy and Application of DNA Metabarcoding for Dietary Reconstruction in Ruminants.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72878},
pmid = {41542380},
issn = {2045-7758},
abstract = {DNA metabarcoding offers a powerful, non-invasive tool to identify dietary composition with high taxonomic resolution, yet its quantitative accuracy and bias remain a well-recognised limitation across taxa and sample types. This universal challenge is particularly evident in herbivores, where plant material introduces additional amplification constraints. This study evaluates the accuracy of DNA metabarcoding in reconstructing the diets of sheep under controlled feeding trials involving high and low digestibility forage, using two widely used plant DNA barcodes (ITS2 and trnL). A secondary trial tested the detectability and proportional representation of a target species, Medicago sativa, when added to the diet in varying amounts (1%, 5%, 10%). ITS2 provided greater species-level resolution, while trnL showed broader taxonomic coverage but reduced precision. Both markers distinguished diet treatments effectively; however, faecal DNA showed proportional discrepancies from vegetation input, particularly under low-digestibility conditions. M. sativa was reliably detected even at 1% inclusion but was consistently overrepresented in sequence reads. Our findings highlight the strengths and limitations of DNA metabarcoding for herbivore diet studies and underscore the importance of marker choice and the effects of differential digestion biases. These findings demonstrate the need for multi-marker approaches and calibration controls in dietary studies, especially when quantitative interpretation is required. Despite limitations in quantitative accuracy, faecal DNA metabarcoding provides valuable insights into herbivore diet composition and preferences, with future refinements expected to improve its resolution and reliability for ecological monitoring and grazing management.},
}

@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.},
}