@article {pmid41052572,
year = {2025},
author = {Krücken, J and Diekmann, I and Andreotti, S and Bredtmann, CM and Mbedi, S and Sparmann, S and Schmidt, JS and de Almeida Borges, F and de Freitas, MG and Sallé, G and Hofer, H and Matthews, JB and Tzelos, T and Nielsen, MK and Kuzmina, TA and Samson Himmelstjerna, GV},
title = {Cytochrome c oxidase I deep amplicon sequencing for metabarcoding of equine strongyle communities: unexpectedly high Strongylus spp. prevalence in treated horses.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.09.007},
pmid = {41052572},
issn = {1879-0135},
abstract = {Equines are parasitized by complex communities of Strongylidae (Nematoda) comprising multi-species infections. Currently, Cyathostominae are most prevalent, while Strongylus species are only rarely detected. Since eggs and, in most cases, infective larvae cannot be differentiated to species level, except for Strongylus spp., species-specific knowledge of the pathology, epidemiology and ecology of these parasitic nematodes is limited. Reference sequence data for several cyathostomin species are limited or missing. Deep amplicon sequencing of internal transcribed spacer 2 (ITS-2) regions of nematodes has been used in equines previously, although barcoding studies demonstrated a better species resolution for the cytochrome c oxidase subunit I (COI) region. The present study introduces a nemabiome method based on sequencing of COI fragments. This method was applied to compare third stage larvae, representing strongyle communities, derived from regularly treated (RT) and never treated (NT) equine populations from Brazil, France (only RT), Germany, Ukraine, the UK, and the USA. Samples were predominantly from horses, but some were obtained from Przewalski's horses (Ukraine), donkeys (Germany, Ukraine) and kulans (Ukraine). Most sequence reads (87.7%) were identified to species level, but unclassified reads occurred more frequently in donkeys and kulans than horses. No obvious difference in species diversity and richness was observed between RT and NT equines. However, there were significant differences in species composition between the RT and NT groups. Strongylus spp. were more common in NT groups but also showed unexpectedly high abundances in RT horses. Cylicocyclus nassatus, Cylicostephanus longibursatus, and Cyathostomum catinatum were more abundant in RT groups, suggesting that strongyle communities in domestic equines may have been shaped by anthelmintic treatments during last decades. The decreased classification success for reads from non-caballine equines suggests that there are more strongyle species specific for this rarely-investigated group which requires additional efforts to improve the sequence database, particularly for these hosts.},
}

@article {pmid41052227,
year = {2025},
author = {Shi, PQ and Feng, L and Huang, KC and Hu, JC and Feng, F and Xu, J},
title = {Two hymenopteran parasitoid species of the jackfruit borer Diaphania caesalis (Lepidoptera: Pyralidae) in China.},
journal = {Journal of insect science (Online)},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/jisesa/ieaf079},
pmid = {41052227},
issn = {1536-2442},
support = {R19029//Guangdong Ocean University/ ; A24403//Guangdong Science and Technology Department/ ; 202305AF150146//Yunnan Province Science and Technology Talents and Platform Plan/ ; //Feng Feng Expert Workstation in Yunnan Province/ ; //Jackfruit Germplasm Resource Nursery of Guangdong province (Guangdong Ocean University)/ ; //Jackfruit Science and Technology Backyard in Yunnan's Hekou/ ; },
mesh = {Animals ; China ; *Moths/parasitology/growth & development ; Pest Control, Biological ; *Wasps/physiology/classification/genetics/anatomy & histology ; Host-Parasite Interactions ; Larva/parasitology/growth & development ; DNA Barcoding, Taxonomic ; Artocarpus/growth & development ; Female ; *Hymenoptera/physiology/classification ; },
abstract = {Jackfruit borer, Diaphania caesalis (Walker), is a major boring pest of Artocarpus plants (Moraceae). Biological control is considered an environmentally sustainable means of managing pests. However, parasitoids of D. caesalis in China are unknown. Here, we investigated the parasitoids of D. caesalis through field monitoring and surveys and identified them through morphological observation and DNA barcoding technology. Two hymenopteran parasitoid species, Dolichogenidea sp. and Eulophidae undet. sp., were identified on D. caesalis. The parasitism rate of Dolichogenidea sp. (21.0 ± 1.8%) was significantly higher than that of Eulophidae undet. sp. (3.8 ± 2.2%). The field incidence of Dolichogenidea sp. in the Artocarpus integer and Artocarpus heterophyllus orchards was 30.8 ± 2.5% and 22.3 ± 7.6%, respectively, but there was no significant difference. Overall, Dolichogenidea sp. was the dominant parasitoid of D. caesalis in China. Further research is needed to determine the species' identity, and their biological characteristics should be evaluated to determine their potential applications in biocontrol programs.},
}

Animals
China
*Moths/parasitology/growth & development
Pest Control, Biological
*Wasps/physiology/classification/genetics/anatomy & histology
Host-Parasite Interactions
Larva/parasitology/growth & development
DNA Barcoding, Taxonomic
Artocarpus/growth & development
Female
*Hymenoptera/physiology/classification

@article {pmid41051286,
year = {2025},
author = {Paladini, A and Carvalho, GS and Cabral-de-Mello, DC and Mariguela, TC and Domahovski, AC and Barão, KR},
title = {Shades of red: several lines of evidence reveal a pest of sugarcane as new species of Mahanarva (Hemiptera: Auchenorrhyncha: Cercopidae).},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-17},
doi = {10.1017/S0007485325100503},
pmid = {41051286},
issn = {1475-2670},
abstract = {Many species of spittlebugs (Auchenorrhyncha: Cercopidae) use sugarcane and other grasses as host plants, and when damage is extensive they are considered pests leading tom economic losses. Mahanarva fimbriolata and Mahanarva spectabilis are the most common in sugarcane and can be distinguished mainly by genital morphology. Recently, another morphotype of Mahanarva occurring in sugarcane fields that did not match the morphologies of either of these Mahanarva species mentioned above has been widely collected in Brazil, raising doubts on the identification of Mahanarva species using sugarcane. Accurate specimen identification is critical for sugarcane pest management, because misidentifications can lead to economic losses and inefficient control strategies. Thus, we combined morphology, geometric morphometrics, and molecular techniques to investigate the hypothesis that this morphotype could be considered a new species of Mahanarva. Morphological analyses included examination of male genitalia and tegminal colouration patterns. We also quantified hindwing shapes using geometric morphometrics; and performed a phylogenetic analysis using the mitochondrial COI gene. Morphological evidence distinguished the new morphotype through unique traits in male genitalia. Geometric morphometrics reliably separated species, with over 89% classification accuracy. Molecular analyses confirmed the morphotype as a distinct lineage closely related to M. fimbriolata and M. spectabilis. Thus, we describe M. diakantha sp. n., demonstrating the effectiveness of an integrative approach in resolving taxonomic challenges. Additionally, we provide formal diagnoses for M. fimbriolata and M. spectabilis. This work underscores the importance of precise taxonomy in agroecosystems, supporting sustainable pest management practices.},
}

@article {pmid41051238,
year = {2025},
author = {Gencel, M and Gagné-Leroux, D and Serohijos, AWR},
title = {Doblin: Inferring dominant clonal lineages from high-resolution DNA barcoding time series.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf555},
pmid = {41051238},
issn = {1367-4811},
abstract = {MOTIVATION: The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population's ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms.

RESULTS: In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin's accuracy using lineage data from evolutionary simulations, showing that it recovers the clones' identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of E. coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin's versatility allows it to be applied to lineage time-series data across different experimental setups.

Doblin is available on CRAN (https://CRAN.R-project.org/package=doblin) and Github (https://github.com/dagagf/doblin).},
}

@article {pmid41049183,
year = {2025},
author = {Fussy, A and Austoni, S and Winkelmann, T and Papenbrock, J},
title = {Comparative assessment of species identification methods for European Salicornia sources: a multifaceted approach employing morphology, nuclear DNA content, phylogenetic markers, RNA topology, and SSR fingerprinting.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1666009},
pmid = {41049183},
issn = {1664-462X},
abstract = {Accurate identification of Salicornia species is a fundamental prerequisite for their potential usability and domestication. This study utilized a multifaceted methodological approach integrating morphological, cytogenetic, and molecular techniques to identify species from available European Salicornia sources. The following methods were compared: nuclear DNA content analysis; application of marker-based DNA barcoding via four common Salicornia markers; investigations of RNA topologies of these marker sequences by predicting theoretical secondary structures; utilization of diagnostic single-nucleotide polymorphism (SNP) positions within the external transcribed spacer (ETS) marker sequences for European Salicornia taxa; comparison of three promising microsatellite (SSR) markers regarding their ability to differentiate Salicornia subspecies; and evaluation of morphological data on habitus and flower characteristics utilizing a Salicornia identification key. The results demonstrate that ETS marker analysis offers reliable and cost-effective species determination, with SNP comparisons being more user friendly than phylogenetic trees are, and microsatellite markers can be differentiated down to the subspecies level via fragment length differences. However, microsatellite analysis alone is not suitable for primary species identification. DNA content can provide a rough estimation of potential species and is already more reliable than morphological methods. The differentiation among species is crucial for creating transparency for farmers and consumers and for initiating breeding processes, particularly within the context of frequent misidentification.},
}

@article {pmid41047867,
year = {2025},
author = {Fontes, JT and Mokhtar-Jamaï, K and Nchioua, Z and Durand, JD and Landi, M and Meira, J and Machado, L and Baali, A and Sobrino, I and Barri, I and Kouamé, E and Adepo-Gourène, BA and Diop, M and Kidé, NG and Wehye, AS and Sohou, Z and Carneiro, M and Martins, R and Soares, P and Costa, FO},
title = {Phylogeography of the widely distributed John Dory (Zeus faber, Actinopterygii: Zeiformes) reaffirms the prevalence of at least two deeply divergent clades.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70245},
pmid = {41047867},
issn = {1095-8649},
abstract = {The John Dory Zeus faber is a commercially exploited demersal fish species with a known distribution ranging from the Northeast Atlantic to parts of the Indian and Pacific oceans. A previous genetic survey using cytochrome c oxidase subunit I (COI) DNA barcodes suggested the presence of two geographically segregated taxonomic units within Z. faber. We revisit this hypothesis by expanding the number and geographic coverage of DNA barcodes, addressing a major data gap along parts of the Atlantic coast of Africa and conducting a comprehensive phylogeographic analysis. Our findings consolidated the existence of two highly divergent mitochondrial clades, Clade A and Clade B (mean K2P distance: 7.4%), with the transition zone between them located along the Atlantic coast of Morocco. Clade A exhibited no phylogeographic structure, with haplotypes shared between Northeast Atlantic and Mediterranean populations. Conversely, four geographically structured subclades (mean K2P distance: 0.9%) were detected within Clade B, extending south and eastward from Morocco to Japan and New Zealand. Historical demographic events driving allopatric divergence, along with oceanographic and environmental factors, likely shaped the current geographic distribution of the two clades. These findings not only prompt the need to re-evaluate the taxonomic status of Z. faber but also highlight the probable existence of multiple evolutionarily significant units (ESUs) that must be considered in the scope of stock assessment, fisheries management and conservation purposes.},
}

@article {pmid41045070,
year = {2025},
author = {Stenbäck, JB and Schmidt, D and Noborg, U and Gustafsson, J and Norberg, P and Andersson, ME and Fu, MX and Harvala, H and Ringlander, J},
title = {Accurate and Cost-Efficient Whole Genome Sequencing of Hepatitis B Virus Using Nanopore.},
journal = {Journal of medical virology},
volume = {97},
number = {10},
pages = {e70630},
doi = {10.1002/jmv.70630},
pmid = {41045070},
issn = {1096-9071},
support = {//This study was funded by the Gothenburg Society of Medicine and the Sahlgrenska University Hospital./ ; },
mesh = {*Hepatitis B virus/genetics/isolation & purification ; Humans ; *Whole Genome Sequencing/methods/economics ; *Genome, Viral ; DNA, Viral/genetics ; *Nanopores ; *High-Throughput Nucleotide Sequencing/methods/economics ; Hepatitis B/virology ; *Nanopore Sequencing/methods/economics ; Genotype ; },
abstract = {Deep sequencing of the whole hepatitis B virus genome increases the analytical resolution and has the potential to improve molecular epidemiology investigations. The aim of this study was to develop and evaluate the performance of such deep sequencing using the Nanopore technology. The method includes an initial PCR step to generate two overlapping amplicons that cover the whole relaxed circular HBV genome found in circulating viral particles and covalently closed circular DNA in infected hepatocytes, followed by sequencing using the Nanopore rapid barcoding kit that allows parallel analysis of several samples in one reaction. The libraries can be sequenced with the standard Nanopore flow cell on MiniIon or GridIon devices, as well as the Flongle. The performance of the method was evaluated by comparing Nanopore and Sanger sequences or qPCR results from 64 clinical samples. The Nanopore-derived consensus sequences were, on average, 99.9% similar to those from Sanger sequencing, and the full HBV genome was determined in samples with HBV DNA levels of approximately 3 log10 IU/mL with MagNA pure 96 extraction and < 2 log10 IU/mL using a high-volume manual extraction protocol on a subset of samples from patients with very low viral load (1.62-3.74 IU/mL). A perfect agreement with Sanger/qPCR-derived genotype was seen. The cost of sequencing per genome using the Nanopore method is low, ranging from 6 to 37 euros. We conclude that whole genome sequencing of HBV with Nanopore is well suited for genomic characterization, antiviral resistance mutation analysis, and genotyping of HBV in a routine laboratory setting.},
}

*Hepatitis B virus/genetics/isolation & purification
Humans
*Whole Genome Sequencing/methods/economics
*Genome, Viral
DNA, Viral/genetics
*Nanopores
*High-Throughput Nucleotide Sequencing/methods/economics
Hepatitis B/virology
*Nanopore Sequencing/methods/economics
Genotype

@article {pmid41044471,
year = {2025},
author = {Afshan, NU and Ahmad, MA and Jabeen, M and Binyameen, S and Khalid, AN},
title = {New species and new records of genus Melampsora (Melampsoraceae) from Pakistan using electron microscopy and DNA barcoding techniques.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1310},
pmid = {41044471},
issn = {1471-2229},
abstract = {The genus Melampsora, known for its significant role as a plant pathogen, exhibits a rich species diversity. Current study reports Melampsora himalayensis sp. nov. as new species with M. ferrinii and M. populnea as new records from different regions (Fairy Meadows, Gilgit Baltistan; Khanspur, Khyber Pakhtunkhwa) of Pakistan, contributing to the knowledge of rust fungi diversity and distribution. Their placement within genus Melampsora was validated by comparative morpho-anatomical investigation. Detailed morphological characterization was employed using Scanning electron microscopy which provided features of spore morphology including their surface ornamentation. Additionally, molecular analysis was performed for species delimitation and to resolve phylogenetic relationships within genus Melampsora. Combined morpho-anatomical and phylogenetic data led to the discovery of previously unrecorded species, Melampsora ferrinii and M. populnea from Pakistan, including a novel taxon, Melampsora himalayensis sp. nov. This study provides information about taxonomy, host range and distribution of Melampsora in Pakistan.},
}

@article {pmid41044180,
year = {2025},
author = {Warguła, J and Dmuchowska, W and Stec, D and Kaczmarek, Ł},
title = {Integrative taxonomy elucidates phylogenetic position of a clawless African eutardigrade (Tardigrada) supporting the erection of a new genus.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34511},
pmid = {41044180},
issn = {2045-2322},
abstract = {In the presented study, we re-investigated the soil-dwelling clawless tardigrade species Apodibius nuntius (Binda, 1984) using an integrative taxonomic approach. Our analysis is based on detailed morphological comparisons between three populations from three different countries: Mozambique (type population), Australia and Uganda. The first two populations comprise historical specimens deposited in museum collections, whereas the third one is newly found and reported for the first time in this study. In addition to morphological analysis, we constructed a phylogenetic tree of Isohypsibioidea using two ribosomal gene fragments (18S rRNA and 28S rRNA). The obtained results enabled us to establish a new genus, Sinunguibius gen. nov., which is assigned to the family Hexapodibiidae. The new genus constitutes the second known genus within Eutardigrada characterized by a complete absence of claws. The main morphological chacter that differentiates the new genus from the also clawless genus Apodibius is the number of placoids in the pharynx. Our results suggest that the complete loss of claws is a convergent trait that occurs in at least two families: Doryphoribiidae and Hexapodibiidae. The inclusion of the new genus within the family Hexapodibiidae required a corresponding amendment to its family diagnosis.},
}

@article {pmid41042067,
year = {2025},
author = {Lam, L and Watson, S and Ramaswamy, Y and Singh, G},
title = {High-Throughput Strategies for Streamlining Lipid Nanoparticle Development Pipeline.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e11551},
doi = {10.1002/advs.202511551},
pmid = {41042067},
issn = {2198-3844},
abstract = {Lipid nanoparticles (LNPs) have become clinically validated nanocarriers for nucleic acid delivery, enabling applications in mRNA vaccines and therapies for cancer, ocular, and infectious diseases. Identifying LNPs formulations with optimal physicochemical and pharmacokinetic properties using traditional low-throughput methods is resource-intensive and impractical for evaluating large libraries. Recent advances in automation, high-throughput platforms for lipid synthesis, characterization, and screening tools are transforming the landscape of LNP formulation. These strategies enable rapid multi-parametric generation and evaluation of hundreds to thousands of formulations across key properties such as size, charge, stability, biodistribution, cellular uptake, and intracellular trafficking. In parallel, advanced biomimetic models and in vivo multiplexed barcoding screening strategies provide deeper insights into tissue targeting and therapeutic delivery outcomes. This review provides an integrated framework that combines automation with high-throughput combinatorial synthesis, characterization, and in vitro/in vivo screening tools. In this development pipeline, performance benchmarks applied at each step systematically exclude suboptimal candidates, ensuring that only clinically viable LNP candidates advance. Future directions, including automation, high-throughput, and closed-loop machine learning guided design strategies, are further discussed to advance the development of next-generation LNP therapeutics and accelerate their translation from bench to bedside.},
}

@article {pmid41041654,
year = {2025},
author = {Nakahama, N and Hirasawa, K and Kato, M and Watanabe, K and Kurata, S and Hayashi, M},
title = {Mitochondrial DNA 16S region and voucher specimen collection of Japanese aquatic Coleoptera and Hemiptera for environmental DNA metabarcoding analyses.},
journal = {ZooKeys},
volume = {1253},
number = {},
pages = {103-119},
pmid = {41041654},
issn = {1313-2989},
abstract = {Aquatic coleopteran and hemipteran insects primarily inhabit lentic waters, many of which are at risk of extinction due to development, agriculture, and invasive alien species. Environmental DNA (eDNA) analysis has recently emerged as a powerful tool for conducting comprehensive distribution surveys. The cytochrome c oxidase subunit I (COI) universal primers are conventionally used for DNA barcoding but they often result in non-specific amplification and frequent amplication failures. Primers in the mitochondrial DNA (mtDNA) 16S rRNA region that alleviate these issues have been developed and are considered helpful for eDNA analysis. It is necessary to accumulate reference sequences of the mtDNA 16S rRNA region in aquatic coleopteran and hemipteran insects. However, molecular identification at the genus or species level remains challenging, as only a few of these insect groups in Japan have registered reference DNA sequences for both the mtDNACOI and 16S rRNA. Therefore, we constructed a comprehensive dataset of the mtDNA 16S rRNA region for these insects distributed in Japan. As a result of this study, we were able to obtain partial sequences of the mtDNA 16S rRNA region from 140 coleopteran taxa (35.5% of Japanese aquatic species or subspecies) and 58 hemipteran taxa (45.3% of Japanese aquatic species or subspecies). These voucher specimens were deposited in four research institutions. The DNA sequence datasets are expected to significantly contribute as an essential database for eDNA analysis and other DNA metabarcoding studies.},
}

@article {pmid41041551,
year = {2025},
author = {Zhang, N and Fu, Y and Mathew, D and Wang, M and Chen, X and Lin, K and Schaff, D and Shaffer, S and Pardoll, D and Jackson, C},
title = {Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7510946/v1},
pmid = {41041551},
issn = {2693-5015},
abstract = {Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.},
}

@article {pmid41041396,
year = {2025},
author = {Irawan, AD and Eguchi, K},
title = {Application of Invertebrate-Derived DNA Barcoding (iDNA) in Blood Sucking Leeches From West Sumatra: A Discovery of Blue-Eyed Litter Frog Leptobrachium waysapuntiense.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72235},
pmid = {41041396},
issn = {2045-7758},
abstract = {Indonesia is one of the world's most biodiversity-rich countries, including a wide variety of vertebrate and plant species. However, assessing biodiversity in tropical rainforests remains challenging itself. The use of conventional tools has commonly been employed for monitoring and research purposes. Invertebrate-derived DNA (iDNA), a subdiscipline of environmental DNA (eDNA), has emerged as a noninvasive tool that complements traditional methods for biodiversity assessment. It enables the detection of vertebrate species and the monitoring of their populations through molecular approaches. Utilizing abundant haematophagous leeches provides a promising approach to sample a broader range of host species within an area, as these leeches retain high-quality host DNA in their guts for extended periods. Using Sanger sequencing with five primer sets (16Scp, 16Sed, 12S, ND2, and RepCOI) designed to target broad taxonomic groups, 272 Haemadipsa spp. samples were successfully amplified, resulting in the identification of 17 unique vertebrate hosts, including mammals, amphibians, and reptiles. Within our 16Sed results, we noted that the primer sets could capture a broader range of taxa than originally targeted, encompassing both mammals and reptiles, thereby enhancing species richness detection. Notably, we present evidence of the first iDNA-based detection of the rare blue-eyed litter frog, Leptobrachium waysepuntiense, from western Sumatra. Therefore, this study suggests that the use of haematophagous leeches represents a promising approach for biodiversity monitoring in Indonesia. This method offers a complementary strategy that can be integrated with existing practices to strengthen conservation efforts.},
}

@article {pmid41040332,
year = {2025},
author = {Ashok, Y and Bubb, KL and Oi, 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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.21.677650},
pmid = {41040332},
issn = {2692-8205},
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 growth, as proxy for protein activity. Here, we covalently link variant proteins in vivo to an RNA barcode by fusing them to E. coli tRNA (m 5 U 54) methyltransferase TrmA (E358Q), which forms a covalent bond with a tRNA stem-loop. Following cell lysis, variant proteins are separated in vitro according to their biochemical properties and identified by their barcodes. We use this method, Dosa, to analyze a large pool of FLAG epitope variants for binding to an anti-FLAG antibody, to profile the cleavage preferences of variants of 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.},
}

@article {pmid41040279,
year = {2025},
author = {Park, SY and Sheridan, A and An, B and Jarvis, E and Lyudchik, J and Patton, W and Axup, JY and Chan, SW and Damstra, HGJ and Leible, D and Leung, KS and Magno, CA and Meeran, A and Michalska, JM and Rieger, F and Wang, C and Wu, M and Church, GM and Funke, J and Huffman, T and Leeper, KGC and Truckenbrodt, S and Winnubst, J and Kornfeld, JMR and Boyden, ES and Rodriques, SG and Payne, AC},
title = {Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.26.678648},
pmid = {41040279},
issn = {2692-8205},
abstract = {Mapping nanoscale neuronal morphology with molecular annotations is critical for understanding healthy and dysfunctional brain circuits. Current methods are constrained by image segmentation errors and by sample defects (e.g., signal gaps, section loss). Genetic strategies promise to overcome these challenges by using easily distinguishable cell identity labels. However, multicolor approaches are spectrally limited in diversity, whereas nucleic acid barcoding lacks a cell-filling morphology signal for segmentation. Here, we introduce PRISM (Protein-barcode Reconstruction via Iterative Staining with Molecular annotations), a platform that integrates combinatorial delivery of antigenically distinct, cell-filling proteins with tissue expansion, multi-cycle imaging, barcode-augmented reconstruction, and molecular annotation. Protein barcodes increase label diversity by >750-fold over multicolor labeling and enable morphology reconstruction with intrinsic error correction. We acquired a ∼10 million μm [3] volume of mouse hippocampal area CA2/3, multiplexed across 23 barcode antigen and synaptic marker channels. By combining barcodes with shape information we achieve an 8x increase in automatic tracing accuracy of genetically labelled neurons. We demonstrate PRISM supports automatic proofreading across micron-scale spatial gaps and reconnects neurites across discontinuities spanning hundreds of microns. Using PRISM's molecular annotation capability, we map the distribution of synapses onto traced neural morphology, characterizing challenging synaptic structures such as thorny excrescences (TEs), and discovering a size correlation among spatially proximal TEs on the same dendrite. PRISM thus supports self-correcting neuron reconstruction with molecular context.},
}

@article {pmid41039089,
year = {2025},
author = {Liu, Y and Vukic, M and Hannon, E and Mei, H and Walker, E and Sinke, L and , and Mill, J and Daxinger, L and Heijmans, BT},
title = {Identification of SENP7 and UTF1/VENTX as new loci influencing clustered protocadherin methylation across blood and brain using a genome-wide association study.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {41039089},
issn = {1476-5578},
support = {K013807//RCUK | Medical Research Council (MRC)/ ; W004984//RCUK | Medical Research Council (MRC)/ ; M008924//RCUK | Medical Research Council (MRC)/ ; },
abstract = {The epigenetic regulation of clustered protocadherin (cPCDH) genes is tightly linked to their function as specific cell surface barcodes for neural self-nonself discrimination. Differential cPCDH DNA methylation has been implicated in diverse neurological diseases as well as body weight, cancer and aging. However, the unique regulation of cPCDH methylation remains poorly understood. Therefore, we performed a genome-wide association study to evaluate the association of >7 million genetic variants with DNA methylation at 607 cPCDH CpGs measured in whole blood of 3777 individuals and validated findings in prefrontal cortex samples obtained from 523 brain donors. We observed concordant cPCDH methylation patterns in blood and prefrontal cortex, which switched between hypo-, intermediate and hypermethylation over short distances with the former overlapping with the promoter regions of each cPCDH member. Through methylation quantitative trait locus (meQTL) analysis in trans, we first confirmed the broad effect of the candidate gene SMCHD1 on cPCDH methylation in blood and then validated this effect in prefrontal cortex. Through a genome-wide analysis, we next identified the SENP7 and UTF1/VENTX loci to have widespread, subcluster-specific effects on cPCDH methylation in blood and brain. While SENP7 can indirectly affect DNA methylation through the deSUMOylation of the chromatin repressor KAP1, UTF1 and VENTX are two genes involved in embryonic development not previously implicated in epigenetic regulation. Our findings shed new light on the processes involved in cPCDH methylation that may underlie associations with neurological disease.},
}

@article {pmid41034732,
year = {2025},
author = {Khezri, A and Branders, S and Bellankimath, AB and Ali, J and Chapagain, C and Asadi, F and Grabherr, MG and Ahmad, R},
title = {MysteryMaster: scraping the bottom of the barrel of barcoded Oxford nanopore reads.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {235},
pmid = {41034732},
issn = {1471-2105},
abstract = {BACKGROUND: The high error rate associated with Oxford Nanopore sequencing technology adversely affects demultiplexing. To improve demultiplexing and reduce unclassified reads from nanopore sequencing data, we developed MysteryMaster, a demultiplexer that utilizes the optimal sequence aligner, Cola.

RESULTS: When compared to Oxford Nanopore´s Dorado and Guppy demultiplexing tools across three datasets of 37 diverse samples with established ground truth, we found that MysteryMaster accurately identifies a similar or greater percentage of reads among the different basecalling models: Fast, HAC, and SUP. MysteryMaster performs slightly better than the other tools on data that was basecalled using the Fast basecalled model, while its performance in HAC and SUP data is similar to Dorado's. MysteryMaster has a false positive rate of just 0.41% with default settings.

CONCLUSIONS: While MysteryMaster can function as a standalone demultiplexer tool, the sequential application of Dorado and MysteryMaster produced the best overall performance.},
}

@article {pmid41034246,
year = {2025},
author = {Sánchez-Vendizú, P and Erkenswick, G and Reyes, J and Clinton, SL and Espejo, TS and Cáceres, G and Libke, Z and Arana, A and Mendoza-Silva, J and Tirapelle, C and Williams, S and Swamy, V and Martínez-Altamirano, J and Esteves, J and Barnuevo-Bullón, JP and Hernández-Mejía, J and Caffo, X and Mendevil Malpica, A and Salazar-Aragón, R and Gutiérrez-Jiménez, L and Stabile, J and Cuzmar, N and Paine, TD and Peralta-Aguilar, P and Inga-Díaz, G and Lescano, J and Viñas-Martínez, A and McElroy, ME and Coayla, D and Linares R, LM and Pilfold, NW and Sacco, AJ and Arakaki, M and Mena, JL and Tobler, MW and Salinas, L and Arana, C and Pacheco, V and Prost, S and Watsa, M},
title = {Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1545},
pmid = {41034246},
issn = {2052-4463},
support = {9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9772//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9772//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
mesh = {*DNA Barcoding, Taxonomic ; Peru ; Animals ; *Birds/genetics/classification ; *Mammals/genetics/classification ; *Vertebrates/genetics/classification ; *Plants/genetics/classification ; },
abstract = {Species extinctions in the tropics are accelerating, outpacing documentation efforts. Meanwhile, DNA barcoding is flourishing in the Global North, backed by extensive infrastructure, allowing non-taxonomic experts to identify species from nonlethal, minimally invasive, and environmental samples. However, hyper-diverse regions like Peru make up only 0.52% (n = 93,246) of the Barcode of Life Database (BOLD). To address this, we established three decentralized laboratories with low-cost, portable nanopore sequencers. From 2018-2023, we generated 1,858 barcodes in situ using six genetic markers for 1,097 vertebrates and 76 plants from existing and new biobanks. We present the first genetic barcodes for 30 mammal and 196 bird species from Peruvian specimens, increasing the number of Peruvian mammal and bird species in BOLD by 110% and 36.5% respectively. We also report the first records of the marsupial Marmosops ocellatus and the bat Sturnira lilium for Peru. This dataset represents an effort to go from fresh or museum-preserved samples to barcodes entirely in situ, avoiding the export of samples outside the country, and facilitating local capacity in molecular biodiversity research.},
}

*DNA Barcoding, Taxonomic
Peru
Animals
*Birds/genetics/classification
*Mammals/genetics/classification
*Vertebrates/genetics/classification
*Plants/genetics/classification

@article {pmid41033544,
year = {2025},
author = {Świątek, P and Gajda, Ł and Urbisz, AZ},
title = {Ovary organization and oogenesis in two species of cave-living clitellate annelids from the genus Delaya (Clitellata, Pelodrilidae).},
journal = {Developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ydbio.2025.09.021},
pmid = {41033544},
issn = {1095-564X},
abstract = {Clitellate annelids (Clitellata) are hermaphrodites with gonads localized in specific segments in the anterior body part. Localization of gonads and the structure of the reproductive systems are considered conservative traits of clitellate evolution and are used as crucial features in their taxonomy and in phylogenetic considerations. The study aimed to present the ovary morphology, histology, and ultrastructure in two Delaya species. The genus Delaya groups poorly known cave-living clitellate annelids, and their ovary organization and oogenesis are entirely unknown. Moreover, their taxonomic status is under debate. According to recent molecular analyses, Delaya and two other genera form the family Pelodrilidae, closely related to earthworms. To enhance our understanding of these cave-living animals' reproductive biology and provide new characters that may aid in phylogenetic considerations, the light and electron microscopic techniques were used to study the organization of the ovaries and the course of oogenesis in two species: one from a cave in Greece (Delaya sp. GR) and the other from a cave in France (Delaya sp. FR). In both species studied, two pairs of ovaries are located in two consecutive segments - XII and XIII. Each ovary consists of 3-5 functional units. The ovarian units are polarized: their apical parts (attached to the septum) contain oogonia and early meiotic cells, while the broader distal ends contain growing oocytes and nurse cells. Initially, germline cells (oogonia and early meiotic cells) develop synchronously, forming syncytial cysts in which each cell is connected via a single ring canal to the central cytoplasm (cytophore). Then, during meiotic prophase (in diplotene), synchrony is lost, and it is likely that one cell per cyst begins accumulating nutrients and differentiating into an oocyte. As oocytes detach from the cyst and continue oogenesis as individual cells, the remaining cells stay interconnected, do not grow, and are regarded as nurse cells. Yolk absorption is not completed in the ovary; vitellogenic oocytes are transferred to the ovisacs, where they continue to accumulate nutrients. Ovisacs are paired, long, sac-like structures, extending through several body segments (XII-XV). Delaya produces mesolecithic eggs with prominent yolk spheres, lipid droplets, and glycogen granules. Only some minor differences were observed between the two studied species. The most notable difference concerns the cytophore shape and volume in cysts connecting nurse cells. In Delaya sp. FR, the cytophore is reticular and inconspicuous, whereas in Delaya sp. GR, the cytophore is more prominent and may contain nurse cell nuclei. The obtained results confirm that the formation of the germline cysts equipped with the cytophore is a conservative phase of oogenesis in clitellates. Morphological observations suggest that in Delaya, the clustering cells differentiate into two subpopulations: oocyte and nurse cells, which aligns with the reports presenting oogenesis in other clitellates. Considering the differences in ovary organization between Delaya and other clitellates, we propose to refer to these as "Delaya-type" ovaries. The main similarities and differences between "Delaya" ovaries and other clitellate annelids are discussed. It is suggested that the presence of cysts equipped with the reticular cytophore could be an apomorphy of Pelodrilidae, earthworms, and allied taxa. We also provide DNA barcode sequences for Delaya sp. FR to shed light on its taxonomic identity. Furthermore, the phylogenetic analysis that was conducted indicates that Delaya sp. FR occupies a basal position among its congeners for which molecular data are available.},
}

@article {pmid41030982,
year = {2025},
author = {Chen, D and Isakova, A and Wan, ZJ and Wagner, MJ and Wu, Y and Zhao, BS},
title = {Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.13.638129},
pmid = {41030982},
issn = {2692-8205},
abstract = {Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods particularly limited in mapping long-distance circuits and preserving cell type information. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and parallel single-nucleus and single-synaptosome sequencing to map neuronal connectivity at single-synapse resolution. This AAV-based approach enables simultaneous capture of both synaptic connections and molecular identities of connected neurons. We validated this approach in the mouse pontocerebellar circuit, identifying both established projections and potentially novel synaptic partnerships. Through integrated analysis of connectivity and gene expression, we identified molecular markers enriched in connected neurons, suggesting potential determinants of circuit organization. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision and gene expression information, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.},
}

@article {pmid41030583,
year = {2025},
author = {Maroni, PJ and Weston, JNJ and Kitazato, H and Jamieson, AJ},
title = {Hadal Snailfishes (Teleostei: Liparidae) Extend Across Multiple Trenches: Molecular Insights and Implications for Taxonomic Nomenclature.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e71779},
pmid = {41030583},
issn = {2045-7758},
abstract = {The hadal zone, Earth's deepest oceanic region, is defined by distinct geological features and hosts a variety of endemic species, including the Liparidae Gill, 1861 (snailfishes). Ecological understanding of snailfishes dwelling at depths greater than 6000 m remains limited due to challenges in physical specimen collection and preservation. This study employs molecular tools to assess the phylogenetic relationships and distribution patterns of hadal snailfishes by analyzing three mitochondrial DNA markers (16S, Cyt-B, COI) and incorporates 20 new specimens from the Japan and Tonga trenches (Pacific Ocean) and the Diamantina Fracture Zone (Indian Ocean). The phylogenetic hypotheses and species delimitation assessments were tested among a framework of six taxonomic units -Pseudoliparis swirei Gerringer and Linley, 2017, Pseudoliparis belyaevi Andriashev and Pitruk, 1993, Notoliparis kermadecensis Nielsen, 1964, Notoliparis stewarti Stein, 2016, and Paraliparis selti Linley, Gerringer, and Canto-Hernández, 2022. The results revealed wider geographic distributions than previously thought, particularly for Notoliparis c.f. stewarti. Further, the molecular data support the hypothesis that Notoliparis Andriashev, 1975 should be treated as a subjective junior synonym of Pseudoliparis Andriashev, 1955. Our findings do emphasize the challenges and limitations of using DNA barcoding solely to distinguish closely related or recently diverged species. Together, this study advances the biogeographic understanding of hadal snailfishes and highlights the importance of expanding sampling efforts.},
}

@article {pmid41029546,
year = {2025},
author = {Ma, D and Tian, Q and Wang, Y and Duan, H and Zhang, Y and Luo, Y and Li, L},
title = {Comparative chloroplast genome of six species in Hypoxidaceae from China: insights into phylogenetic relationships and molecular marker development.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1232},
pmid = {41029546},
issn = {1471-2229},
support = {NSFC 32060049//National Natural Science Foundation of China/ ; NSFC 32270225//National Natural Science Foundation of China,China/ ; },
mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; Genetic Markers ; China ; },
abstract = {BACKGROUND: The family Hypoxidaceae (order Asparagales) is a predominantly Southern Hemisphere lineage comprising approximately 11 genera and 200 species, many of which possess significant medicinal and ornamental value. Despite their economic importance, Hypoxidaceae has received limited research attention, leading to problematic identification of species and misuse of wild resources in traditional medicine markets. Taxonomically, the phylogenetic position of Hypoxidaceae and the intergeneric relationships within this family remain controversial and unresolved, particularly concerning the delimitation of Curculigo and Molineria. Previous studies based on morphological traits and molecular markers have yielded inconsistent results, highlighting the need for more robust genomic evidence. In angiosperms, complete chloroplast genomes have proven highly effective in resolving systematic uncertainties considering their conserved structure and high informational content. However, such genomic data remain scarce for Hypoxidaceae, limiting phylogenetic clarity. In this research, the complete chloroplast genomes of six species representing three key genera (Curculigo, Molineria, and Hypoxis) were sequenced and characterized for a comparative and phylogenetic analysis.

RESULTS: The chloroplast genomes of six species exhibited conserved quadripartite structures, measured 157,472 bp to 158,550 bp in length. The overall GC content of these genomes ranged between 37.3 and 37.5%. Gene annotations identified 132 genes, 19 duplicated in the inverted repeat regions, and had complete ndh gene. Comparative analysis of six complete chloroplast genomes revealed highly similarity, but they were varied in repeats sequence, codon usage bias, contractions and expansions in the IR region. Five molecular markers showed the highest degree of variability between the six cp genomes. Phylgenetic analysis based on cp genomic data confirmed that Hypoxidaceae was a monophyly, being a sister to Asteliaceae with higher supports than the previous research. Three main clades were recognized in Hypoxidaceae, including Curculigo clade, Hypoxis clade, and Pauridia-Empodium clade. And what's more, Curculigo clade could be divided into three subclades, containing Molineria subclade, Curculigo subclade, and Seychellean subclade, indicating significantly phylogenetic insights.

CONCLUSIONS: The complete cp genomes of six species of three representative genera from Hypoxidaceae were sequenced and analyzed in detail, including the general data on the genome length, repeat sequence, codon usage, IR expansion and contraction, structural comparison and divergence hotspot identification analyses, and phylogenetic analysis. A comparative analysis revealed that the cp genome was highly consistent of four Molineria species, but varied greatly at the generic level between Hypoxis, Curculigo, and Molineria, which could be used for generic delimitation. Five DNA barcodes (psbK-psbI, rpoB-trnC, ndhF-rpl32, ycf1, and trnE-trnT) were selected for authentication of Hypoxidaceae medicinal materials. Hypoxidaceae was a monophyletic lineage, containing three major clades, being a sister to Asteliaceae with stronger supports than before. The three main clades in Hypboxidaceae were re-confirmed as the three stable lineages for this family. In the Curculigo Clade, three subclades were identified with significant phylogenetic insights. The phylogenetic evidence presented here, combined with distinct chloroplast genome features, supports Molineria Subclade separated from Curuculigo Subclade, being a monophyletic group by transferring Sinocurculigo taishanica and two Borneo Curculigo species into Molineria. Further research should provide a better understanding of the intergeneric relationships among Hypoxidaceae, adding more genomic data with extensive samplings across the center distribution of Southern Hemisphere.},
}

*Genome, Chloroplast/genetics
*Phylogeny
Genetic Markers
China

@article {pmid41028562,
year = {2025},
author = {Ren, J and Zeng, H and Huang, J and Tian, J and Wu, M and Shi, H and Sui, X and Wang, CK and Zhou, H and Tang, Z and Luo, S and Wang, X},
title = {Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {41028562},
issn = {1750-2799},
support = {Stanley center gift//Broad Institute | Stanley Center for Psychiatric Research, Broad Institute (Stanley Center)/ ; },
abstract = {Controlled gene expression programs have a crucial role in shaping cellular functions and activities. At the core of this process lies the RNA life cycle, ensuring protein products are synthesized in the right place at the right time. Here we detail an integrated protocol for imaging-based highly multiplexed in situ profiling of spatial transcriptome using antibody-based protein comapping (STARmap PLUS), spatial translatome mapping (RIBOmap) and spatiotemporal transcriptome mapping (TEMPOmap). These methods selectively convert targeted RNAs, ribosome-bound mRNAs or metabolically labeled RNAs to DNA amplicons with gene-unique barcodes, which are read out through in situ sequencing under a confocal microscope. Compared with other methods, they provide the analytical capacity to track the spatial and temporal dynamics of thousands of RNA species in intact cells and tissues. Our protocol can be readily performed in laboratories experienced in working with RNA and equipped with confocal microscopy instruments. The wet lab experiments in preparing the amplicon library take 2-3 d, followed by variable sequencing times depending on the sample size and target gene number. The spatially resolved single-cell profiles enable downstream analysis, including cell type classification, cell cycle identification and determination of RNA life cycle kinetic parameters through computational analysis guided by the established tutorials. This spatial omics toolkit will help users to better understand spatial and temporal RNA dynamics in heterogeneous cells and tissues.},
}

@article {pmid41028292,
year = {2025},
author = {Sahu, A and Singh, M},
title = {First report of aberrant Mystus vittatus (Bloch, 1794) from wild population in the Gomti River, Uttar Pradesh, India, based on integrative approach: a new conservation concern.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1163},
pmid = {41028292},
issn = {1573-2959},
support = {FISHNBFGRSIL 2023001300260//ICAR-NBFGR, Lucknow, India/ ; },
mesh = {India ; Animals ; Rivers/chemistry ; *Environmental Monitoring ; *Conservation of Natural Resources ; Water Pollutants, Chemical/analysis ; },
abstract = {This present study documents first recorded abnormality in Mystus vittatus (Bloch 1794) from the Gomti River near Thauri, Sultanpur District, Uttar Pradesh, India. Collected fish specimens were identified using integrative taxonomy, combining morphological and molecular data (Sanger or dideoxy sequencing). Interestingly, both the morphologically abnormal M. vittatus (MYAB1) and normal (NKG44N) exhibited 0% genetic divergence based on analysis of COI datasets. Molecular result indicates that the reported deformity is not associated with mitochondrial genetic variation and may instead be attributed to environmental factors. Comparative assessment of normal and abnormal individuals revealed no significant differences in morphological characters, except for the complete absence of caudal fin in abnormal fish. The total weight and length of the abnormal specimen were recorded as 9.59 g and 7.17 cm, respectively. Radiographic (X-ray) imaging further exposed underlying vertebral fusion at the hypural region from the 23rd to 27th vertebrae. Recorded water parameters included temperature (28.2 ± 7.2 °C), dissolved oxygen (5.1 ± 0.4 mg/L), pH (7.7 ± 0.7), ammonia (0.39 ± 0.05 mg/L), salinity (0.41 ± 0.20 ppt), TDS (264 ± 31 mg/L), conductivity (930 ± 40 µS/cm), and transparency (22 ± 3 cm). These values indicate potential environmental stress that may have contributed to the reported abnormality. Potential etiological and environmental factors include chemical contaminants, microplastics (MPs), heavy metals, essential nutrient deficiencies, and genetic mutations during larval development. In riverine habitats and other water bodies, documented exposure to agricultural and urban pollutants could also be responsible, emerging as plausible drivers of observed abnormalities. Malformation of the caudal fin may be referred to as "saddleback syndrome," which is often attributed to physical injury or developmental disruption during early life stages. Additionally, any predatory attack on its caudal region during its early development stages could have resulted in physical and traumatic injury. Despite such predatory attack, suspected individual might have escaped, survived, and healed, albeit with severe and permanent deformity. This study underscores the utility of radiology as critical diagnostic tool for detecting sub-surface anatomical abnormalities in wild fish populations. Our findings highlight the urgent action for targeted water quality monitoring in the Gomti River to mitigate anthropogenic impacts on native aquatic genetic resources (AGR). Future research should include both temporal and spatial assessments of water quality with fish health, particularly focusing on skeletal and soft tissue abnormalities.},
}

India
Animals
Rivers/chemistry
*Environmental Monitoring
*Conservation of Natural Resources
Water Pollutants, Chemical/analysis

@article {pmid41028017,
year = {2025},
author = {Gutiérrez-Rodríguez, J and Zaldívar-Riverón, A and López-Estrada, EK and Barranco, P and García-París, M},
title = {DNA barcode reference library of bush-crickets (Orthoptera, Tettigoniidae) from the Iberian Peninsula.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33883},
pmid = {41028017},
issn = {2045-2322},
support = {FJC2018-035899-I//Juan de la Cierva-Formación, Ministerio de Ciencia e Innovación, Spain/ ; DOC_00668//Doctores Junta de Andalucía (FEDER EU/Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía)/ ; 58548//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; PID2019-110243GB-100/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación, Spain/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Spain ; *Gryllidae/genetics/classification ; *Gene Library ; Phylogeny ; *Orthoptera/genetics/classification ; Biodiversity ; },
abstract = {Curated DNA barcode reference libraries are crucial for advancing environmental DNA (eDNA) studies, monitoring biological invasions, reliable biodiversity assessments, accurate species identification, etc. However, DNA barcode databases remain highly incomplete for most invertebrate taxa. In this study, we present the most comprehensive reference library to date for the family Tettigoniidae (Orthoptera) from the Iberian Peninsula-the most species-rich orthopteran family globally, with over 8,000 valid species. We generated 402 new DNA barcodes from at least 121 tettigoniid species from the Iberian Peninsula and integrated these with 169 previously published sequences. The resulting dataset comprises 571 barcoded specimens, representing 49 genera and 123 species, including many recently described taxa. Notably, we provide DNA barcodes for at least 68 described species that previously lacked them. Our dataset covers 85% of the tettigoniid species in the Iberian Peninsula and approximately 25% of European bush-cricket species. Furthermore, our analyses show that most tettigoniid species (95%) can be reliably identified using DNA barcoding. However, mitochondrial introgression events were detected in several species of the subfamilies Bradyporinae and Tettigoniinae, highlighting the need for cautious application of this molecular identification tool.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Spain
*Gryllidae/genetics/classification
*Gene Library
Phylogeny
*Orthoptera/genetics/classification
Biodiversity

@article {pmid41026659,
year = {2025},
author = {, },
title = {Correction: Pot-pollen DNA barcoding as a tool to determine the diversity of plant species visited by Ecuadorian stingless bees.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0333633},
pmid = {41026659},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323306.].},
}

@article {pmid41024994,
year = {2025},
author = {Ross, EG and Piertney, SB and Sigwart, JD and Crook, NF and Moreau, A and Layton, KKS},
title = {A Comprehensive DNA Barcode Reference Library for the Macroinvertebrates of Scottish Seagrass Beds Using Oxford Nanopore Flongle Flowcells.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72219},
pmid = {41024994},
issn = {2045-7758},
abstract = {Oxford Nanopore Sequencing Technology (ONT) has emerged as a scalable method for generating DNA barcode reference libraries, capable of sequencing hundreds of DNA barcodes simultaneously using the portable, benchtop MinION sequencing device. In this study, we use ONT Flongle flowcells to produce DNA barcodes for 146 seagrass-associated marine invertebrate OTUs collected from four seagrass beds in Scotland, targeting COI and 18S V4 regions. We make use of degenerate and group-specific primer pairs to improve recovery and demonstrate how mapping ONT reads to pre-existing DNA barcodes can be used to reduce ambiguous basecalls and improve recovery of sequences from contaminated specimens. Overall, this study informs prospective users intending to carry out multimarker DNA barcoding projects using Oxford Nanopore Sequencing. Furthermore, we generated the first DNA barcode reference library for seagrass beds in Scotland to support future biomonitoring of these priority habitats.},
}

@article {pmid41024993,
year = {2025},
author = {Nhlengethwa, N and Stewart, RD and Emami-Khoyi, A and Teske, PR and Csányi, S and Heltai, M and van der Bank, M},
title = {An eDNA Survey of Plant Biodiversity in a Local Dam Within South Africa's Largest City.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72196},
pmid = {41024993},
issn = {2045-7758},
abstract = {Ecosystems within cities can play a crucial role in conserving local biodiversity amid rapidly expanding urban sprawl, but they face significant threats from anthropogenic activities and the introduction of alien invasive species (AIS). A comprehensive management plan is required to effectively preserve the biodiversity supported by urban ecosystems. However, the ecological information needed to establish, implement and monitor such plans is often incomplete. In this study, we assessed the application of eDNA metabarcoding in surveying plant biodiversity in an aquatic habitat by collecting water samples at five sites in an urban dam in the City of Johannesburg. Out of 1001 reconstructed Amplicon Sample Variants (ASVs), plant taxa were assigned to 47 unique taxonomic ranks at the family level, 42 unique ranks at the generic level and only 13 unique ranks at the species level (including three AIS). The remaining ASVs could only be identified at higher taxonomic ranks, indicating that no DNA barcodes have yet been generated for the putative species in question. Although this study provides a good overview of plant community structure, it also highlights a gap in the taxonomic coverage of South African plants on public DNA databases. To address this shortcoming, increased national DNA barcoding efforts are needed to expand current reference databases. This will be indispensable for the effective application of eDNA metabarcoding in studying South Africa's unique biodiversity.},
}

@article {pmid41023109,
year = {2025},
author = {Macrina, L and Terraneo, TI and McFadden, CS and Chimienti, G and Marchese, F and Vimercati, S and Vicario, S and Reimer, JD and Purkis, SJ and Eweida, AA and Pieribone, V and Qurban, M and Duarte, CM and Rodrigue, M and van der Zwan, FM and Augustin, N and Westphal, H and Benzoni, F},
title = {The hidden diversity of Saudi Arabian Red Sea octocorals revealed through a morpho-molecular assessment across bathymetric and latitudinal gradients.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33651},
pmid = {41023109},
issn = {2045-2322},
mesh = {Saudi Arabia ; Indian Ocean ; *Biodiversity ; *Anthozoa/genetics/classification/anatomy & histology ; Animals ; Phylogeny ; Genetic Variation ; Ecosystem ; DNA Barcoding, Taxonomic ; },
abstract = {Octocorals, a globally distributed class of Cnidaria, inhabit a wide range of environments, from cold to tropical waters and from shallow to deep-sea ecosystems. In the Red Sea, studies on octocoral diversity have mostly been focused on the Gulf of Aqaba and selected families or genera. While these studies have revealed a remarkable richness and diversity of shallow-water species, mesophotic and deep-sea octocoral research remains limited in the region, in particular along the Saudi Arabian coast. Here, we provide a first comprehensive assessment of this group's genetic diversity across the basin's bathymetric and latitudinal gradients. Following six Red Sea oceanographic expeditions and various biodiversity surveys conducted between 2020 to 2023, we analysed a collection of 728 octocoral specimens sampled along 13 degrees of latitude in the Saudi Arabian Red Sea, from shallow-water reefs to deep-sea habitats. We combined morphological identification and sequencing of mitochondrial barcode markers (mtMutS and COI) to delimit lineages. Our integrated results revealed the occurrence of 26 families and 56 genera in the basin from 3 to 859 m of depth. While the description of new species was beyond the scope of this work, here we provide a reference dataset for octocoral diversity from a biodiversity hotspot, as well as essential insights to inform biodiversity management and planning of conservation measures, particularly relevant for the rapidly developing Saudi Arabian Red Sea coast.},
}

Saudi Arabia
Indian Ocean
*Biodiversity
*Anthozoa/genetics/classification/anatomy & histology
Animals
Phylogeny
Genetic Variation
Ecosystem
DNA Barcoding, Taxonomic

@article {pmid41023068,
year = {2025},
author = {Flitcroft, RL and Penaluna, BE and Hauck, LL and Munyon, JW and Capurso, JM},
title = {Multi-species eDNA as a screening tool to facilitate early detection and eradication of aquatic invasive species in large water bodies.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33615},
pmid = {41023068},
issn = {2045-2322},
mesh = {*Introduced Species ; *DNA, Environmental/analysis/genetics ; Animals ; *Aquatic Organisms/genetics ; *Environmental Monitoring/methods ; Biodiversity ; Fishes/genetics ; Plants/genetics ; },
abstract = {Aquatic invasive species can devastate native biodiversity and human water infrastructure. Effective eradication relies on early detection. However, commonly used visual surveys are ineffective for detection of small populations of submerged invasive species in large water bodies. Here, we explored detection of invasive aquatic plants, animals (vertebrate and invertebrate), and pathogens using 10 environmental DNA (eDNA) water sampling events every two weeks between June and October, 2018, informing ideal sampling times for long-term early-detection monitoring. The highest number of species detections across taxa were found using 6 replicates in late August and early September. Detections varied by taxon, with the most detections for fishes, followed by invertebrates, amphibians, and submerged plants. All expected species were detected with eDNA except for three terrestrial and emergent riparian plants. Reservoirs had the most consistent presence of AIS, suggesting that those systems and aquatic communities may be susceptible to new invasions. AIS detections occurred across more sites and water bodies than had been previously documented which provided evidence of silent invasions by species such as crayfishes, mollusks, and plants. We offer a framework for interpreting management response to low-read counts from multispecies eDNA sampling that balances interpretation of results with the cost of management responses.},
}

*Introduced Species
*DNA, Environmental/analysis/genetics
Animals
*Aquatic Organisms/genetics
*Environmental Monitoring/methods
Biodiversity
Fishes/genetics
Plants/genetics

@article {pmid41022899,
year = {2025},
author = {Ceballos-Escalera, A and Llewellyn, T and Richards, J and Inward, D and Vogler, A},
title = {A Reference DNA Barcode Library for UK Fungi associated with Bark and Ambrosia Beetles.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1580},
pmid = {41022899},
issn = {2052-4463},
support = {Leverhulme Centre for the Holobiont//Leverhulme Trust/ ; Leverhulme Centre for the Holobiont//Leverhulme Trust/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic ; United Kingdom ; *Weevils/microbiology ; *Fungi/genetics/classification ; Biodiversity ; Gene Library ; *Coleoptera/microbiology ; Plant Bark ; Forests ; },
abstract = {Bark and ambrosia beetles are ecologically important and widespread forest organisms. While flying between host plants and tunnelling into bark, they vector a high diversity of plant and insect-associated fungi within and between forests. These fungal communities live under the bark and rarely produce visible spore-bearing structures, making them difficult to sample and identify at scale. By combining passive insect trapping across the United Kingdom with individual beetle metabarcoding, we generated a reference DNA barcode library for fungi associated with over 1000 beetles, representing 25 native weevil species in the subfamily Scolytinae (Curculionidae). Sampling sites span longitudinal and latitudinal gradients, multiple forest types, and both natural and plantation forests. We use state-of-the-art fungal ITS2 OTU clustering and identification, resulting in 5274 identified fungal OTUs. This fungal diversity data can be used alongside extensive site and sample metadata to explore geographic and ecological biodiversity patterns. As these associations can be highly invasive and damaging, this resource provides a baseline to understand current fungal communities and monitor future changes.},
}

Animals
*DNA Barcoding, Taxonomic
United Kingdom
*Weevils/microbiology
*Fungi/genetics/classification
Biodiversity
Gene Library
*Coleoptera/microbiology
Plant Bark
Forests

@article {pmid41021029,
year = {2025},
author = {He, Q and Sun, J and Huang, S},
title = {GPCR Phospho-Barcodes and Biased Signaling.},
journal = {Handbook of experimental pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41021029},
issn = {0171-2004},
abstract = {G protein-coupled receptors (GPCRs), the largest family of membrane receptors in humans, primarily regulate diverse physiological and pathological processes through G protein- and arrestin-mediated signaling pathways, making them important drug targets. Notably, arrestins not only mediate GPCR desensitization and internalization but also regulate G protein-independent signal transduction. However, the mechanisms underlying arrestin-mediated biased signaling remain incompletely understood, posing significant challenges for developing targeted GPCR drugs with signaling bias. To address this knowledge gap, researchers have conducted systematic investigations and proposed innovative models, including the flute model, the polyproline sorting dock model, and the time order effects of GPCR phospho-barcodes to elucidate the dynamic processes driving biased signaling in arrestin activations. These key findings not only refine the theoretical framework of GPCR phosphorylation in biased signaling but also provide a solid foundation for developing biased drugs targeting the GPCR-arrestin pathway, offering new opportunities for precision therapeutics in diverse diseases.},
}

@article {pmid41020297,
year = {2025},
author = {Chen, C and Zhan, T and Hu, L and Ding, M and Wu, X and Wang, H and Xu, B},
title = {Barcode-integrated cellulose based microfluidic system for intelligent point-of-care blood typing.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5lc00688k},
pmid = {41020297},
issn = {1473-0189},
abstract = {Accurate and rapid blood typing plays a critical role in life-saving clinical procedures such as blood transfusions and organ transplantation. Herein, we proposed a novel blood typing system (BloodStrips) that combines cellulose based microfluidics with universal barcode technology, achieving intelligent, rapid, and user-friendly blood type detection. The BloodStrips system employed heat transfer printing to create barcode patterns on hydrophobic cotton substrates and integrated cotton threads to construct hydrophilic channels. Meanwhile, the swinging elution method was harnessed to remove free red blood cells (RBCs) while retaining aggregated RBCs on the cotton threads, thereby resulting in creating a distinct white/red contrast at the macro level (white represents cotton thread, red represents bloodstain). The white/red barcodes with different combinations were used to represent various blood types. Based on this principle, we further developed a portable and automated blood tying chip called the BloodBar chip. It is worth noting that this device leverages a simple and straightforward smartphone scanning technique to decipher blood types, avoiding reading errors caused by ambient light intensity and personal bias. This work provides a universal and intelligent visual diagnostic platform for simple, rapid, and accurate blood typing, which may find wide applications in developing countries or resource-limited areas.},
}

@article {pmid41019179,
year = {2025},
author = {Yıldırım, N and Gerçek, YC},
title = {Preliminary Characterization of Monofloral Helianthus annuus L. Bee Pollen Using Advanced Analytical Techniques: A Comparative Study With Polyfloral Pollen.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e71016},
pmid = {41019179},
issn = {2048-7177},
abstract = {In recent years, there has been an increased interest in the characterization of monofloral bee pollen of different botanical origins as it offers a more homogeneous and traceable component profile compared to polyfloral bee pollen. In this study, we aimed to verify the botanical origin of monofloral Helianthus annuus (sunflower) pollen and polyfloral bee pollen samples collected from the same geographical region and to evaluate their metabolomic profiles comparatively. The botanical origins of the pollen samples were confirmed by palynological analysis and DNA barcoding. Then, physicochemical, phytochemical, and advanced chromatographic analyses (LC-MS/MS) were performed to reveal the bioactive compound contents and nutrient profiles of the samples in detail. When the polyphenol profile was analyzed, the highest level of hyperoside (11,071.28 mg/kg) was detected in monofloral sunflower pollen and rutin (1287.16 mg/kg) in the polyfloral sample. The most dominant amino acid in both pollen types was proline, which was measured as 4652.08 mg/kg (monofloral) and 12,476.82 mg/kg (polyfloral), respectively. Moreover, both samples contained remarkable levels of folic acid (vitamin B9; 20.80 and 20.77 mg/kg). The results obtained from this study reveal that bee pollen derived from the widely cultivated sunflower plant also possesses remarkable potential for the development of functional foods and nutraceutical products. However, as the study was conducted solely with monofloral and polyfloral bee pollen samples collected from a single geographical region, it can be stated that the findings should be considered as part of a preliminary evaluation. Despite this limitation, the data obtained through comprehensive analytical methods provide a scientific basis for the functional applications of monofloral sunflower pollen with its biologically valuable components.},
}

@article {pmid41018503,
year = {2025},
author = {Alqurashi, SI and Alqahtani, SM and Alghamdi, KMS and Sharawi, SE and Al-Solami, HM and Alghamdi, AG and Alyahya, HS and Al-Rashidi, HS and Mahyoub, JA},
title = {Molecular insights into Aedes aegypti (L.) populations and vector surveillance in the urban areas of Jeddah and Jizan, Saudi Arabia.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1638582},
pmid = {41018503},
issn = {2673-8600},
abstract = {INTRODUCTION: The Aedes aegypti constitutes the primary vector for dengue fever, yellow fever, chikungunya, Zika, West Nile, and encephalitis viruses, all of which have impacted One Health (human, animal, and environmental health) significantly. It has been distributed widely in urban settings in Saudi Arabia, particularly in cities like Jeddah and Jizan, a situation that underscores the urgent need for innovative and sustainable vector control strategies. Molecular tools, such as DNA barcoding using mitochondrial markers, have become essential for identifying mosquito species accurately and understanding their role in disease transmission. Such knowledge is vital for informing effective, climate-resilient public health interventions.

METHODS: This research focuses on identifying Aedes species in various regions of Saudi Arabia using polymerase chain reaction (PCR) and sequencing techniques, in order to evaluate the molecular diversity of these dengue vectors in Jeddah and Jizan. The study utilizes the cytochrome one oxidase (COI) gene as a molecular marker for phylogenetic analysis to compare the populations of Aedes species.

RESULTS: The findings reveal the presence of significant genetic variation among mosquito populations. In the Jeddah region, the Ae. aegypti types MN299016.1 and KU495081.1 match completely (100%) the respective populations found in Argentina and Australia, with 93.1% (27/29) and 6.9% (2/29) respectively. Meanwhile, the samples from the Jizan region are 100% and 99.6% similar to the Ae. aegypti types MN298998.1, MK300226.1, PP892777.1, and MF043259.1 found in Canada, Kenya, India, and England.

CONCLUSION: This study underscores the necessity of using molecular techniques in vector surveillance to mitigate the spread of Zoonotic and vector borne diseases in Saudi Arabia. Moreover, these efforts align with the objectives of the Saudi Vision 2030 by promoting environmentally responsive vector surveillance in Jeddah and Jizan, thereby supporting integrated approaches to public health and ecological sustainability.},
}

@article {pmid41017704,
year = {2025},
author = {Methou, P and Johnson, SB and Sherrin, J and Shank, TM and Chen, C and Tunnicliffe, V},
title = {A Tale of Two Shrimps-Speciation and Demography of Two Sympatric Shrimp Species From Hydrothermal Vents.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70119},
doi = {10.1111/mec.70119},
pmid = {41017704},
issn = {1365-294X},
support = {ANR-22-POCE-0007//ANR LIFEDEEPER/ ; ANR-17-EURE-0015//ANR ISBLUE/ ; //David and Lucile Packard Foundation/ ; },
abstract = {Hydrothermal vents can serve as natural laboratories to study speciation processes due to their fragmented distribution, often with geographic barriers between habitats. Two sympatric species of Rimicaris shrimps occur at vents on the Izu-Bonin-Mariana volcanic arc: Rimicaris loihi also occurs near Hawai'i and R. cambonae is present on the Tonga Arc. These two species biogeographically co-occur and are genetically similar, raising questions about their speciation mechanisms, how they maintain distinct species, and whether interbreeding occurs. Here, we used barcoding and shotgun sequencing to test their genetic isolation and investigate their speciation process. We also evaluated population demography over 10 years to assess population densities and sex ratios at vents. Our results supported R. cambonae and R. loihi as two distinct species despite sympatry throughout part of their range. We also observed regional-scale genetic structure among R. loihi populations from the Izu-Bonin-Mariana volcanic arc, despite high dispersal potential. Finally, we found concomitant variations of shrimp densities and genetic diversity following fluctuations in geological and venting activities over a decade. A combination of geological instability, ocean currents dynamics and sea-level changes might drive temporary isolation among these local populations. We suggest that similar factors, with longer isolation periods, may also have promoted speciation between the two Rimicaris species, whereas distinct life-history traits could strengthen and maintain reproductive barriers. Overall, we found that the two species with large geographic distributions had significant patterns of genetic partitioning on a volcanic arc; this scenario contrasts with those observed previously at vents from mid-ocean ridges or back-arc basin systems.},
}

@article {pmid41013878,
year = {2025},
author = {Dopheide, A and Buckley, T},
title = {Optimising Extraction of DNA From Museum Insect Specimens.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70048},
doi = {10.1111/1755-0998.70048},
pmid = {41013878},
issn = {1755-0998},
abstract = {DNA technologies have many advantages for biomonitoring and biodiversity analyses, but these depend on the availability of relevant reference DNA barcodes. To be most useful, a DNA barcode should be linked to a taxonomic name, which can in turn be connected to ecological information. This linking can be achieved by DNA barcoding of taxonomically identified specimens. Museums are a promising source of such specimens, but the DNA in museum specimens is often degraded, necessitating carefully optimised DNA extraction methods. In this issue of Molecular Ecology Resources, Holmquist et al. (2025) present a DNA extraction protocol for museum insect specimens, using in-house formulated Solid Phase Reversible Immobilisation (SPRI) beads. The authors carried out several experiments with statistical evaluation to determine optimal DNA extraction parameters, before testing the protocol on a large and diverse pool of museum-held insect specimens. The result is a low-cost and effective DNA extraction protocol for diverse museum insect specimens.},
}

@article {pmid41013580,
year = {2025},
author = {Licheri, M and Mwanga, M and Licheri, MF and Graaf-Rau, A and Sägesser, C and Bittel, P and Harder, T and Suter-Riniker, F and Kelly, JN and Dijkman, R},
title = {Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {103},
pmid = {41013580},
issn = {1756-994X},
support = {IZCOZ0_220329//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; IZCOZ0_220329//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; IZCOZ0_220329//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 2821ERA24//ICRAD/ ; 2821ERA24//ICRAD/ ; },
mesh = {*Influenza A virus/genetics ; Humans ; Animals ; *Whole Genome Sequencing/methods ; Workflow ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Swine ; Influenza, Human/virology ; Birds ; },
abstract = {Whole-genome sequencing (WGS) is essential for monitoring the genetic diversity of influenza A virus (IAV) across host species. We optimized a multisegment RT-PCR (mRT-PCR) protocol to enhance amplification of all eight IAV segments using modified RT and PCR conditions. Additionally, we introduced a dual-barcoding approach for the Oxford Nanopore platform, enabling high-throughput multiplexing without compromising sensitivity. The resulting workflow is robust, scalable, and effective for avian, swine, and human IAV samples, even at low viral loads. This approach strengthens genomic surveillance at the human-animal interface, supporting early detection, evolutionary monitoring, and rapid identification of IAV spillover events.},
}

*Influenza A virus/genetics
Humans
Animals
*Whole Genome Sequencing/methods
Workflow
*Genome, Viral
*High-Throughput Nucleotide Sequencing/methods
Swine
Influenza, Human/virology
Birds

@article {pmid41012048,
year = {2025},
author = {Yin, W and Du, C and Zhang, X and Zhang, W and Wu, W and Fang, C and Xiao, X and Zhu, J and Yang, F and Zhang, M},
title = {DNA Barcoding Provides Taxonomic Clues for Identifying Five Endangered Phoebe Species in Southern China.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/plants14182895},
pmid = {41012048},
issn = {2223-7747},
support = {2024C03258//the Key Research and Development Program of Zhejiang Province/ ; 2022HK124//Research projects of the General Administration of Customs the People's Republic of China/ ; LTGC23C160001//Zhejiang Provincial Natural Science Foundation of China/ ; 2017YFF0210304//the National Key Research and Development Program of China/ ; 2022SJ052//the Zhejiang Provincial Science and Technology Program/ ; },
abstract = {Trees in the genus Phoebe of the Lauraceae family are commonly known as "Nanmu" in traditional Chinese culture. As they have offered highly valued timbers for construction, furniture, and coffins since the pre-Qin Dynasty, it is crucial to identify and protect these Phoebe species. However, the accuracy of Phoebe species identification is frequently hampered due to the limitations of traditional morphological and wood anatomy methods as the marker characteristics are very similar between the species, alongside the requirement for specialized expertise. Here, we use DNA barcoding technology for the rapid and accurate identification of five endangered Phoebe species in China, including Phoebe bournei, P. chekiangensis, P. hui, P. sheareri and P. zhennan. Four highly divergent regions (petA-psbJ-psbL-psbF-psbE, Ψycf1-ndhF, rpl32-trnL[UAG] and ycf1) were identified from a comparison of the 20 Phoebe plastomes downloaded from the database. Furthermore, phylogenetic analysis on 20 Phoebe species showed that rpl32-trnL[UAG] + ycf1, as well as rpl32-trnL[UAG] + ycf1 + Ψycf1-ndhF, effectively distinguished the fifteen Phoebe species. We further validated the usefulness of the core 2-locus barcode using wood and leaf samples from multiple sites for five target species. The study confirms the reliability of molecular diagnostics for five Phoebe species. It also establishes critical taxonomic protocols for conserving these endangered Nanmu species in southern China.},
}

@article {pmid41011285,
year = {2025},
author = {Song, JH and Seo, YS and Kim, Y and Jeong, S and Yang, S and Choi, G and Kim, JS and Park, I},
title = {Integrative Study of Dipsaci Radix and Phlomidis Radix: Nomenclature, Morphology, DNA-Based Authentication, and Comparative Effects on Osteoclastogenesis.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/ph18091418},
pmid = {41011285},
issn = {1424-8247},
support = {RS-2023-00208589//National Research Foundation of Korea/ ; RS-2024-00445180//National Research Foundation of Korea/ ; RS2024-00444460//National Research Foundation of Korea/ ; KSN2511030//Korea Institute of Oriental Medicine/ ; },
abstract = {Background/Objectives: Dipsaci Radix (Dipsacus asper) and Phlomidis Radix (Phlomoides umbrosa) are both traditional medicines used in Korea and China for various bone-associated diseases. However, the two are misused due to similarities in name and appearance. Additionally, D. japonicus root frequently contaminates Dipsaci Radix in Korean herbal markets. Methods: We examined morphological plant traits and performed a DNA barcoding analysis using ITS2 and matK sequences to differentiate between these three species. The effects of root extracts on bone resorption and osteoclast differentiation, measured as tartrate-resistant acid phosphatase (TRAP)-positive cell formation, were evaluated using mouse (5 weeks male ICR mice) bone marrow-derived macrophages. Cytotoxicity assays were conducted to assess extract safety. Results: Phlomoides umbrosa is easily distinguished by its verticillaster inflorescences and 2-labiate corollas. Dipsacus asper and D. japonicus, which share globose inflorescences, are distinguishable by flower color and leaf lobation. The ITS2 and matK sequences clearly differentiated the three species, with haplotype analysis supporting their genetic distinctiveness, enabling robust species discrimination. All three extracts decreased osteoclastic bone resorption and inhibited TRAP-positive cell formations in a dose-dependent manner. Only the D. japonicus extract demonstrated toxicity. Conclusions: This integrative study provides the current scientific names of the original species and proposes their use in the Korean Herbal Pharmacopoeia. Moreover, a reasonable molecular method for authenticating medicinal materials is suggested. Dipsacus japonicus shows promise as an additional origin species in the Korean Pharmacopoeia. However, processing methods that reduce toxicity must be discovered.},
}

@article {pmid41009963,
year = {2025},
author = {Chen, H and Zhang, J},
title = {Chloroplast Genome Evolution and Codon Usage In the Medicinal Plant Pothos chinensis (Araceae).},
journal = {Genes},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/genes16091017},
pmid = {41009963},
issn = {2073-4425},
support = {sszx077//Funding of Special Project for Applying for Master's Degree during the 14th Five-Year Plan of Anshan Normal University/ ; },
mesh = {*Genome, Chloroplast/genetics ; *Codon Usage/genetics ; *Plants, Medicinal/genetics ; *Evolution, Molecular ; Phylogeny ; *Araceae/genetics/classification ; Codon/genetics ; Chloroplasts/genetics ; },
abstract = {BACKGROUND/OBJECTIVES: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants' evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis.

METHODS: In this study, the chloroplast genome of the medicinal plant P. chinensis was newly obtained. Comparative analyses, DNA barcoding investigation, codon usage bias, and phylogenetic reconstruction were conducted to reveal the chloroplast genome characteristics of P. chinensis.

RESULTS: The length of the chloroplast genome of P. chinensis was 165,165 bp. A total of 134 genes were annotated, i.e., 90 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Compared to its sister group Anthurium andraeanum, the length of the large single-copy region (LSC) had been expanded, while the small single-copy region (SSC) had been contracted. Within P. chinensis and P. scandens there were no obvious differences in the length of LSC, SSC, and two inverted repeat regions. Based on Pi values, seven hypervariable regions of whole plastomes were identified. The analysis of codons showed that an average frequency of the 50 candidate genes was 35.30%, and these genes preferred A/U-ending codons. The average effective number of codon (ENC) value was 45.49, which indicated weak codon usage bias. ENCs had a highly significant positive correlation with GC3. Fourteen optimal codons had been identified, 11 of which ended with A/U. The results of the neutrality plot, ENC-plot, and PR2-plot analysis indicated that natural selection might have a significant impact on codon usage patterns.

CONCLUSIONS: Taken together, our study unraveled the codon usage patterns in P. chinensis and provided valuable genetic information for the genus Pothos.},
}

*Genome, Chloroplast/genetics
*Codon Usage/genetics
*Plants, Medicinal/genetics
*Evolution, Molecular
Phylogeny
*Araceae/genetics/classification
Codon/genetics
Chloroplasts/genetics

@article {pmid41009161,
year = {2025},
author = {Rizzo, D and Downes, A and Zubieta, CG and Moriconi, M and Ranaldi, C and Palmigiano, B and Aronadio, A and Bartolini, L and Bolige, E and Garonna, AP and Russo, E},
title = {Development of an LNA-Based qPCR Assay for Detecting Toumeyella parvicornis (Cockerell, 1897) (Hemiptera: Coccidae) from Insect and Honeydew DNA.},
journal = {Insects},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/insects16090982},
pmid = {41009161},
issn = {2075-4450},
support = {000001--ALTRO_R-2022-F-PENNACCHIO_001_001//Campania Region-funded URCOFI project/ ; },
abstract = {The invasive sap-feeding pest Toumeyella parvicornis (pine tortoise scale) is rapidly spreading across Europe, threatening pine ecosystems, particularly in forest-urban areas of Italy. In this scenario, early detection and monitoring strategies are critical to prevent new outbreaks and mitigate impacts in infested regions. Current surveillance is challenged by the lack of rapid, sensitive tools for indirect detection of this cryptic, canopy-dwelling pest, despite advancements in molecular diagnostics and environmental DNA (eDNA). Here, we established a highly specific qPCR assay using LNA probe chemistry for detecting T. parvicornis DNA from both adult insects and their excreted honeydew. DNA was successfully isolated/quantified from all tested matrices. We recorded average Cq values of 20.9 for insect specimens and 30.3 for collected honeydew samples. Targeting the COI barcoding region, the assay demonstrated excellent specificity in both in silico and in vitro tests, showing no cross-reactivity to other pine-associated taxa. The limit of detection for DNA isolated from insect was 64 fg/µL. This is the first diagnostic protocol to use honeydew as a matrix for indirect detection of T. parvicornis. Optimized for routine application by Plant Health Services, this eDNA-based tool offers a valuable approach for future monitoring of sap-sucking hemipterans in multiple environments.},
}

@article {pmid41009156,
year = {2025},
author = {Podeniene, V and Podenas, S and Butkauskas, D and Sneideris, D and Yum, JW and Ahn, NH and Kim, SY and Kim, J and Starkevich, P},
title = {Integrative Study of the Crane Fly Genus Brithura Edwards, 1916 (Diptera: Tipulidae) in East Asia: First Larval Descriptions of the Genus and Insights from Adult Morphology and DNA Barcoding.},
journal = {Insects},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/insects16090978},
pmid = {41009156},
issn = {2075-4450},
abstract = {Brithura Edwards, 1916 (Diptera: Tipulidae) is a small genus of crane flies currently comprising 16 described species distributed across the East Palaearctic and Oriental regions. Although the adults of this genus rank among the largest representatives of the family Tipulidae, their immature stages have remained undocumented until now. In this study, mitochondrial cytochrome c oxidase subunit I (COI) gene fragment sequences (DNA barcodes) of Brithura sancta Alexander, 1929 were analyzed using both recently collected adult specimens from the Republic of Korea and historical museum specimens from China (collected in 1933). These sequences were compared with COI data obtained from larvae collected in Republic of Korea. We present the first description, with detailed illustrations and ecological information, of the previously unknown final instar larva of Brithura, specifically for the East Palaearctic species B. sancta. Diagnostic larval characters for the genus are discussed. Additionally, a redescription and comprehensive morphological documentation of the adult male and female B. sancta, including habitus and genitalia, are provided. This study represents the first phylogenetic contribution to the taxonomy of Brithura larvae based on mitochondrial COI sequence data.},
}

@article {pmid41009153,
year = {2025},
author = {Qian, X and Fu, Y and Ma, Y},
title = {A Review of the Genus Homidia (Collembola, Entomobryidae) in China Informed by COI DNA Barcoding, with the Description of Three New Species.},
journal = {Insects},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/insects16090974},
pmid = {41009153},
issn = {2075-4450},
abstract = {The genus Homidia contains 84 species of which 60 have been reported from China. The sequence of COI for ten Homidia species are provided and a neighbour-joining tree is presented. Three new species of Homidia are described from Chongqing Municipality, China. Homidia wuxiensis sp. nov. is characterised by its colour pattern and chaetotaxy of Abd. IV; Homidia pseudochroma sp. nov. by some expanded post-labial chaetae and chaetotaxy of dorsal head and Abd. II-IV and Homidia yangi sp. nov. by its colour pattern. Based on similarities in COI sequences and morphology, we designate Homidia linhaiensis (Shi, Pan & Qi), as a junior synonym of Homidia tiantaiensis (Chen & Li).},
}

@article {pmid41008247,
year = {2025},
author = {Biltes, R and Villa, C and Costa, J and Mafra, I},
title = {Exploiting Marker Genes for Reliable Botanical Authentication of Bacopa monnieri Products.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/foods14183275},
pmid = {41008247},
issn = {2304-8158},
support = {PTDC/SAU-PUB/3803/2021//Fundação para a Ciência e Tecnologia/ ; UIDB/50006/2020//Fundação para a Ciência e Tecnologia/ ; 2023.07644.CEECIND/CP2842/CT0011//Fundação para a Ciência e Tecnologia/ ; 2021.03583.CEECIND/CP1662/CT0012//Fundação para a Ciência e Tecnologia/ ; 2021.03670.CEECIND/CP1662/CT0011//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Bacopa monnieri, commonly known as Brahmi, is a perennial herbaceous plant used in Ayurvedic medicine owing to its nootropic properties. The increased demand for bacopa-derived herbal/food products has motivated adulteration practices through plant substitution. This work is aimed at developing a new method for B. monnieri detection and quantification in herbal products. The chloroplast gene encoding the Ycf1 photosystem I assembly protein (Ycf1) and the nuclear gene coding for the flavonoid glucosyltransferase (Flag) were selected as candidate markers to develop a real-time PCR assay with EvaGreen dye for B. monnieri detection. Both markers were specific to the target species, with Ycf1 providing the best real-time PCR kinetics and highest sensitivity. Therefore, a new method targeting the Ycf1 barcode was developed, exhibiting high specificity and a sensitivity of 1 pg of bacopa DNA. Additionally, a calibration model was proposed using reference mixtures of B. monnieri in Ginkgo biloba with a linear dynamic range of 25-0.1% (w/w). The curve parameters of slope, PCR efficiency and correlation coefficient met the acceptance criteria. The method was successfully validated with blind mixtures and further applied to commercial herbal products, revealing an important level of adulteration in bacopa/Brahmi-labelled products (60%) due to absence of or reduction in bacopa content. In this work, the first quantitative real-time PCR method for the botanical authentication of B. monnieri in herbal products is proposed as a powerful tool, which can be used by quality control laboratories and regulatory authorities to ensure labelling compliance.},
}

@article {pmid41008229,
year = {2025},
author = {Tsolakidou, MD and Nikoloudakis, N and Tisseyre, C and Knez, M and Barilli, E and Mattas, K and Katsiotis, A},
title = {DNA Barcoding for Tracing Biodiversity in Mixed Crop Food Products: A Proof of Concept Within the BioValue Project.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/foods14183256},
pmid = {41008229},
issn = {2304-8158},
support = {101000499//European Union's Horizon 2020 research and innovation program/ ; },
abstract = {In a world of rapidly globalizing food markets, biodiversity, authenticity, and the safety of food products have become a universal concern. DNA barcoding is a widely used molecular-based method that can identify biological material and is used for the traceability of both raw materials and ingredients in processed food. In the present study, contacted within the framework of the BioValue Horizon Project, which promotes the role of agrobiodiversity in sustainable food systems, DNA barcoding using the ITS and rbcL markers was employed as a proof-of-concept approach to reveal the biodiversity and authenticity of ten commercial plant-based products. Following successful DNA amplification and sequencing using six products as a proof-of-concept, a diverse range of plant genera and species were identified, verifying biodiversity. A strong correlation between ITS and rbcL-based markers was demonstrated, supporting their combined use for reliable species-level biodiversity assessment. Finally, heat map analysis of label contents and sequencing-based genera identification confirmed high concordance between label claims and sequencing results in most cases, though undeclared species and absent labeled taxa were also detected, highlighting potential mislabeling or cross-contamination.},
}

@article {pmid41007952,
year = {2025},
author = {Gál, J and Kovács, G and Vincze, Z and Keve, G and Páll-Gergely, B and Bagyó, R and Fehér, E and Bali, K and Kaszab, E},
title = {The Red-Colored Oddball-A New Ladybird Spider with Unusual Coloring from Morocco, Eresus rubrocephalus sp. nov. (Araneae: Eresidae).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/ani15182707},
pmid = {41007952},
issn = {2076-2615},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; },
abstract = {According to our current knowledge, the prothorax of male spiders belonging to the genus Eresus is covered with black hairs. However, during our collection activities in Morocco, we found male specimens showing habitus that can be clearly distinguished from the previously known species based on their pars cephalica of prosoma covered with distinct red hairs. Diagnostic drawings and digital photographs of male copulatory organs, alongside DNA and COI barcoding results, are also presented.},
}

@article {pmid41007276,
year = {2025},
author = {Iacovelli, MV and Bellia, E and Caruso, M and Zaffuto, E and Crobe, V and Marrone, F and Mazzotti, S and Tinti, F},
title = {Integrated Taxonomy and Species Diversity of the Historical Chondrichthyan Collection of the Zoology Museum "Pietro Doderlein" at the University of Palermo (Italy).},
journal = {Biology},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biology14091129},
pmid = {41007276},
issn = {2079-7737},
abstract = {In the context of the progressive tendency to perceive a degraded environmental state as normal, due to the loss of memory of past ecological conditions (i.e., the Shifting Baseline Syndrome), natural history museum collections represent invaluable resources for studying long-term biodiversity shifts. This study deals with the taxonomic validation of the chondrichthyan species from the historical ichthyological collection assembled by Pietro Doderlein from 1863 to 1922 at the Museum of Zoology of the University of Palermo. The chondrichthyan specimens were digitally catalogued to meet current standards of museum documental identification. Biometric measurements were taken for each specimen, and an integrated analytical approach-combining morphology and ancient DNA analysis-was applied to assign species identities. The collection comprises 342 specimens associated with 76 valid codes. Of these, 288 specimens were identified to species level by morphology, revealing 58 discrepancies with the historical identifications. Sixteen specimens that could not be morphologically assigned were analyzed by DNA barcoding, resulting in eight additional species-level identifications. In total, 62 valid species belonging to 27 families were digitally catalogued according to ministerial guidelines. This taxonomic validation and cataloguing of the "P. Doderlein" chondrichthyan collection represent the first successful effort to bridge the gap in available data and tissue resources from Italian historical natural museums.},
}

@article {pmid41006299,
year = {2025},
author = {Dimaquibo, AC and Jhuang, WC and Huang, WC and Encarnacion, AB and Villarao, MC and Yutuc, RV and Liao, TY},
title = {DNA Barcoding of Teleost Fishes from North Luzon, Philippines: A Dataset for Ichthyofaunal Diversity Assessment.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1571},
pmid = {41006299},
issn = {2052-4463},
mesh = {Philippines ; *DNA Barcoding, Taxonomic ; Animals ; *Fishes/genetics/classification ; *Biodiversity ; RNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; },
abstract = {Reliable identification of teleost fishes is essential for understanding their biology and conserving biodiversity. To support this, a comprehensive DNA barcode reference library was developed for Aurora, Cagayan, and Zambales, Luzon, Philippines. A total of 1,513 specimens were collected from 27 sampling sites, including fish markets, landing areas, and freshwater habitats, and analyzed using COI (707 sequences) and 12S rRNA gene (343 sequences) markers. The dataset identified 323 fish species across 187 genera, 83 families, and 37 orders, including nine newly recorded species for the Philippines and nine deep-sea species (>200 meters). Additionally, 29 newly barcoded taxa were deposited in GenBank, with sequences available for COI, 12S rRNA gene, or both. The expansion of the 12S rRNA gene sequence library enhances its utility as an alternative genetic tool, particularly for environmental DNA (eDNA) studies. This reference database serves as a valuable resource for species identification, biodiversity assessments, and sustainable fisheries management in North Luzon, Philippines.},
}

Philippines
*DNA Barcoding, Taxonomic
Animals
*Fishes/genetics/classification
*Biodiversity
RNA, Ribosomal/genetics
Electron Transport Complex IV/genetics

@article {pmid41005946,
year = {2025},
author = {Gao, K and Chen, B},
title = {The application of advanced analytical techniques in ensuring quality, nutrition, and safety of cereal-based food.},
journal = {Advances in food and nutrition research},
volume = {117},
number = {},
pages = {265-302},
doi = {10.1016/bs.afnr.2025.07.005},
pmid = {41005946},
issn = {1043-4526},
mesh = {*Edible Grain/chemistry ; *Food Safety/methods ; *Nutritive Value ; *Food Analysis/methods ; Food Contamination/analysis ; Humans ; Food Quality ; },
abstract = {Cereals and cereal-based foods are fundamental to global nutrition, providing essential macronutrients and micronutrients that support food security. Ensuring their quality, nutrition, and safety is impacted by factors such as contamination, adulteration, and nutrient degradation during processing and storage. Advanced analytical techniques have emerged as powerful tools to address these challenges, offering innovative solutions for detecting contaminants, optimizing nutritional value, and ensuring food safety. This chapter explores the application of these techniques, including spectroscopy, chromatography, molecular biology, and omics technologies, in the cereal-based food systems. Spectroscopy and chromatography enable rapid and precise detection of chemical contaminants and adulterants, while molecular biology methods like PCR and DNA barcoding ensure product authenticity. Omics approaches, such as lipidomics, proteomics, and flavoromics, provide comprehensive insights into the molecular composition and functional properties of cereals, facilitating the development of high-quality, nutritious products. Emerging technologies, including nanotechnology and artificial intelligence, further enhance the efficiency and accuracy of cereal safety monitoring. By integrating these advanced methods, the cereal research field can address existing challenges, ensuring the production of safe, high-quality, and nutritious cereal-based foods to meet global dietary needs.},
}

*Edible Grain/chemistry
*Food Safety/methods
*Nutritive Value
*Food Analysis/methods
Food Contamination/analysis
Humans
Food Quality

@article {pmid41002353,
year = {2025},
author = {Chen, Q and Xu, Y and Wu, JW and Yang, JM and Huang, CH},
title = {Decoding Molecular Network Dynamics in Cells: Advances in Multiplexed Live Imaging of Fluorescent Biosensors.},
journal = {Biosensors},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/bios15090614},
pmid = {41002353},
issn = {2079-6374},
support = {R01GM136711/GF/NIH HHS/United States ; P50CA098252/GF/NIH HHS/United States ; NA//Sol Goldman Pancreatic Cancer Research Center/ ; },
mesh = {*Biosensing Techniques/methods ; Humans ; Luminescent Proteins ; Signal Transduction ; },
abstract = {Genetically encoded fluorescent protein (FP)-based biosensors have revolutionized cell biology research by enabling real-time monitoring of molecular activities in live cells with exceptional spatial and temporal resolution. Multiplexed biosensing advances this capability by allowing the simultaneous tracking of multiple signaling pathways to uncover network interactions and dynamic coordination. However, challenges in spectral overlap limit broader implementation. Innovative strategies have been devised to address these challenges, including spectral separation through FP palette expansion and novel biosensor designs, temporal differentiation using photochromic or reversibly switching FPs, and spatial segregation of biosensors to specific subcellular regions or through cell barcoding techniques. Combining multiplexed biosensors with artificial intelligence-driven analysis holds great potential for uncovering cellular decision-making processes. Continued innovation in this field will deepen our understanding of molecular networks in cells, with implications for both fundamental biology and therapeutic development.},
}

*Biosensing Techniques/methods
Humans
Luminescent Proteins
Signal Transduction

@article {pmid41001831,
year = {2025},
author = {de Jager, ML and Reiter, N and Wicks, M and Bohman, B and Holmes, GD and Phillips, RD},
title = {Sexually deceptive orchids with distinct flower morphologies elicit different behaviours from a shared pollinator.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcaf234},
pmid = {41001831},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Pollination by sexual deception is one of the most specialised pollination strategies among angiosperms, with co-occurring plant species often exploiting males of different insect species. We test if the morphologically divergent orchids Caladenia cardiochila and its sympatric Endangered congener C. lowanensis are dependent on the same thynnine wasp pollinator. We further investigate the role of floral traits on pollinator behaviour and evaluate potential hybridisation risk.

METHODS: Pollinator sharing was tested for with DNA barcoding. Pollinator behaviour was quantified and experimental floral dissections used to determine the site of sexual attractant release. We employed GC-MS to test for the presence of sugar on orchid labella, hand crosses to assess the impact of interspecific pollen transfer on seed viability, and population monitoring to quantify natural pollination success.

KEY RESULTS: We found that C. cardiochila and C. lowanensis both employ sexual deception of Phymatothynnus aff. nitidus wasps as pollination strategy. However, the behaviour they elicit differs with wasps attempting to mate with the insectiform labellum in C. cardiochila and the glandular sepal tips in C. lowanensis, which are the respective sources of sexual attractant. Unlike most sexually deceptive orchids, C. lowanensis secretes minute amounts of sugar from its labellum. While wasps interacted more frequently with the labellum in C. cardiochila, placing them closer to its reproductive structures, both species exhibited comparable pollination success and pollen transfer efficiency. Experimental crosses revealed that hybrid seed has high viability.

CONCLUSIONS: Sexual deception of the same pollinator by orchids varying in the location of sexual attractant and flower morphology highlights the considerable flexibility of this pollination strategy. Given their overlapping distributions and the viability of hybrid seed, pollinator sharing poses a hybridisation risk that needs to be considered in the management of wild C. lowanensis populations and future conservation translocations.},
}

@article {pmid41001662,
year = {2025},
author = {Lekuti, AA and Li, VYC and Malekjahani, A and Ahmed, S and Mladjenovic, SM and Macduff, MGG and Chan, WCW},
title = {Designing Nanoparticle Surfaces with DNA Barcodes for Accurate In Vivo Quantification.},
journal = {JACS Au},
volume = {5},
number = {9},
pages = {4211-4223},
pmid = {41001662},
issn = {2691-3704},
abstract = {DNA barcoding is a common method for identifying the biodistribution of nanoparticles. DNA barcodes are typically encapsulated within nanoparticles to ensure accurate measurements by next-generation sequencing. This method limits the types of nanoparticles that can be screened. DNA can also be coated on nanoparticle surfaces. However, it is unclear whether surface-coated DNA can be used as barcodes because they can degrade, making the identification and quantification of nanoparticle designs challenging. Here, we developed strategies to reduce DNA degradation on nanoparticle surfaces, allowing surface-based DNA barcodes for biodistribution applications. We demonstrate that nanoparticle size, DNA density, and polymer length and density are essential design parameters for accurately identifying and quantifying nanoparticles in vivo. We found that chemical modification of DNA and shielding using neutral polymers reduce DNA degradation. We validated that surface barcoding can determine the in vivo distribution of nanoparticles. Our findings pave the way for the use of surface-based DNA barcodes for in vivo screening of nanoparticle formulations for targeted applications.},
}

@article {pmid41001006,
year = {2025},
author = {Zhang, X and Zhang, L and Wang, E and Benton, S and Modolo, E and Maksimov, M and Shleizer-Burko, S and Gong, Q and Wang, C and Lamkin, M and Mendenhall, E and Gymrek, M and Goren, A},
title = {Systematic evaluation of the impact of promoter proximal short tandem repeats on expression.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.14.676153},
pmid = {41001006},
issn = {2692-8205},
abstract = {Genetic variation at thousands of short tandem repeats (STRs), which consist of consecutive repeated sequences of 1-6bp, has been statistically associated with gene expression and other molecular phenotypes in humans. However, the causality and regulatory mechanisms for most of these STRs remains unknown. Massively parallel reporter assays (MPRA) enable testing the regulatory activity of a large number of synthesized variants, but have not been applied to STRs due to experimental and computational challenges. Here, we optimized an MPRA framework based on random barcoding to study the impact of variation in repeat copy number on expression. We first performed an MPRA on sequences derived from 30,516 promoter-proximal STR loci along with up to 152bp of genomic context, testing 3-4 variants with differing repeat copy numbers for each locus in HEK293T cells. We identified 1,366 loci with significant associations between repeat copy number and expression, which were enriched for positive effect sizes (P=2.08e-110). We then designed a second MPRA in which we performed deeper perturbations, including systematic manipulation of the repeat unit sequence, orientation, and copy number, with 200-300 perturbations for each of the 300 loci with the strongest signals. Our results revealed that the repeat unit sequence is the primary driver of differences in the relationship between copy number and expression across loci, whereas orientation and flanking sequence have weaker effects, primarily for AT-rich repeat units. The high resolution of these perturbations enabled us to detect non-linear effects, most notably for AAAC/GTTT repeats, which emerge only beyond a certain copy number threshold. Finally, we observed that a subset of STRs in our library show expression levels that are tightly linked with predicted DNA secondary structure formation. We repeated our perturbation MPRA in HeLa S3 cells under wildtype and RNase H1 knockdown conditions, which, via reduction in RNase H1 activity, are expected to hinder resolution of R-loops. This demonstrated that associations between copy number and expression at G-quadruplex-forming CCCCG/CGGGG repeats are particularly sensitive to loss of RNase H1, providing support for an R-loop mediated mechanism for these repeats. Altogether, we establish STRs as a critical component of the non-coding regulatory grammar and provide a framework for understanding how this dynamic form of genetic variation shapes gene expression.},
}

@article {pmid41000875,
year = {2025},
author = {Li, H and Chen, Y and Kaster, J and Dunne, M and Xiao, M and Li, L and Thomas, M and Promi, N and Fingerman, D and Brown, GS and Zheng, Q and Zhu, X and Reale, M and Patterson, A and Gao, L and Zhang, X and Jiang, S and Hu, T and Fang, H and Ren, J and Qi, C and Wang, L and Mou, H and Thacker, G and Salazar, ER and Villanueva, J and Raj, A and Hoon, DS and Bin, T and Madzo, J and Wei, Z and Auslander, N and Herlyn, M},
title = {Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.16.676608},
pmid = {41000875},
issn = {2692-8205},
abstract = {Most advanced melanomas initially respond to targeted therapy but eventually relapse. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells that enter a reversible drug-refractory state. We developed MeRLin, a high-resolution lineage tracing platform integrating cellular barcoding, single-cell transcriptomics, RNA fluorescence in situ hybridization (FISH), and computational analyses to track clonal and transcriptional dynamics in patient-derived melanoma models during prolonged therapy. Clonal dynamics revealed that persister subpopulations first responded to treatment but persisted and expanded during minimal residual disease, ultimately leading to tumor recurrence. Pre-treatment melanoma populations diversified into four conserved persister states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics showed the organization of these adaptive programs and a complex signaling network of autocrine and paracrine interactions among persister subpopulations. Barcoded RNA-FISH enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone with SLC2A1 expression. MeRLin provides a robust framework for dissecting cancer heterogeneity and identifying vulnerabilities in persister populations.},
}

@article {pmid41000852,
year = {2025},
author = {Salla, M and Obermayer, B and Cotta, M and Friebel, E and Campo-Garcia, J and Charalambous, G and Bueno, RJ and Lieu, D and Dabek, P and Helmuth, A and Tellides, G and Assi, R and Bankov, K and Lodrini, M and Deubzer, H and Beule, D and Chung, H and Radbruch, H and Capper, D and Heppner, F and Starossom, SC and Lareau, CA and Liu, I and Ludwig, LS},
title = {Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.17.675534},
pmid = {41000852},
issn = {2692-8205},
abstract = {High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fresh-frozen clinical specimens preserve tissue architecture but compromise cell integrity, thereby precluding their use in multi- omic approaches such as mitochondrial genotyping at single-cell resolution. Here, we introduce Cryo-mtscATAC-seq, a broadly applicable method for diverse pathophysiological contexts to isolate nuclei with their associated mitochondria ("CryoCells") from frozen samples for high-throughput clonal analysis. We applied Cryo-mtscATAC-seq to the neurodegenerated human brain, glioblastoma (GBM), pediatric neuroblastoma, and human aorta, and implemented mitobender, a computational tool to reduce ambient mtDNA in single-cell assays. Our approach revealed regional clonal gliogenesis and microglial expansions in amyotrophic lateral sclerosis (ALS), persistence of oligodendrocyte progenitor cell (OPC)-like clones in GBM recurrence, mtDNA depth heterogeneity after neuroblastoma chemotherapy, and oligoclonal proliferation of smooth muscle cells in human aorta. In conclusion, Cryo-mtscATAC-seq broadly extends mtDNA genotyping to archival frozen specimens across tissue types, opening new avenues for investigation of cell state- informed clonality in human health and disease.},
}

@article {pmid40997258,
year = {2025},
author = {Prati, S and Reyes Camargo, AC and Jamonneau, T and Halima, IB and Sures, B},
title = {Seasonal exchange of microsporidian parasites between native and non-native pet-traded freshwater crustaceans: Is parasite spillover favored over spillback?.},
journal = {Parasite (Paris, France)},
volume = {32},
number = {},
pages = {61},
doi = {10.1051/parasite/2025053},
pmid = {40997258},
issn = {1776-1042},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Seasons ; *Microsporidia/isolation & purification/physiology/classification ; France ; Fresh Water ; *Introduced Species ; *Decapoda/microbiology/parasitology ; Ecosystem ; Pets/parasitology ; *Crustacea/microbiology/parasitology ; Rivers ; *Microsporidiosis/epidemiology/veterinary/transmission ; Biodiversity ; },
abstract = {The introduction of non-native pet-traded species poses potential threats to global biodiversity, particularly in freshwater ecosystems. This study investigated the seasonal dynamics of microsporidian infections in an established feral population of cherry shrimp (Neocaridina davidi) and the coexisting populations of crustaceans, comprising both native and non-native species, inhabiting the thermal waters of the Fontcaude Park and the nearby Mosson River in southern France. Our aim was to assess the potential occurrence of spillover and/or spillback events between N. davidi and co-occurring crustaceans, as well as the influence of seasonal dynamics on these interactions. The prevalence and diversity of microsporidian parasites exhibited strong seasonal variations. Although parasites associated with the pet trade were not detected, we highlight the acquisition of native parasites by feral N. davidi, which seems to be a suitable alternative host for native host-generalist microsporidians. Our findings indicate that all prerogatives for spillback events to occur are met. Feral N. davidi may establish and survive year-round in European rivers with natural thermal regimes. Thus, human-mediated introductions can potentially alter parasite transmission dynamics in these ecosystems.},
}

Animals
*Seasons
*Microsporidia/isolation & purification/physiology/classification
France
Fresh Water
*Introduced Species
*Decapoda/microbiology/parasitology
Ecosystem
Pets/parasitology
*Crustacea/microbiology/parasitology
Rivers
*Microsporidiosis/epidemiology/veterinary/transmission
Biodiversity

@article {pmid40995013,
year = {2025},
author = {D'Agostino, N and Fruggiero, I and Maisto, A and Taranto, F and Al-Kilani, MA and Al-Abdallat, AM},
title = {Exploring the plastome diversity of fifteen centuries-old olive trees (Oleae europaea L.) from Jordan: insights and implications for conservation.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1647776},
pmid = {40995013},
issn = {1664-462X},
abstract = {The olive tree (Olea europaea L.) holds exceptional ecological, cultural, and economic significance in the Mediterranean Basin. Understanding its genetic diversity is critical for conservation, breeding, and authentication of olive cultivars. While nuclear genome analyses have elucidated much of the species' genetic structure, chloroplast genome sequencing provides complementary insights, particularly in tracing maternal lineages, uncovering domestication pathways, and identifying cryptic genetic variation. In this study, we investigated the plastome diversity of fifteen centuries-old olive trees from Jordan through reference-guided assembly and comparative analysis using the FARGA cultivar plastome as a reference. Despite overall genomic conservation, nucleotide diversity analyses revealed several polymorphic hotspots-most notably within the psbM and ycf1 genes and the atpB-rbcL intergenic spacer. Structural variation, including simple sequence repeats and tandem repeats, highlighted intra-population diversity. One sample (TF - 3) exhibited heteroplasmy, suggesting a biological origin that warrants further investigation. Phylogenetic reconstruction grouped most samples within the Mediterranean E1 lineage, with TF - 3 and a few others forming distinct clusters. Comparisons with nuclear genotyping data demonstrated both congruence and divergence, emphasizing the value of a dual-genome approach. This study reinforces the utility of plastome sequencing in varietal identification, conservation genetics, and evolutionary studies, and contributes novel genomic resources for Jordanian olive germplasm.},
}

@article {pmid40994301,
year = {2025},
author = {Sherwood, AR and Allsopp, KR and Alvarado, EA and Kosaki, RK and Paiano, MO and Rentsch, P and Spalding, HL and Wade, RM},
title = {Systematics and taxonomy of Codium (Bryopsidales, Chlorophyta) in the Hawaiian Islands: Description of six new species.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70091},
pmid = {40994301},
issn = {1529-8817},
support = {NFWF 0810.20.068602//National Fish & Wildlife Foundation/ ; DEB-1754117//NSF Division of Environmental Biology (DEB)/ ; DEB-2242142//NSF Division of Environmental Biology (DEB)/ ; //National Oceanic and Atmospheric Administration (NOAA) Papahānaumokuākea National Marine Sanctuary/ ; },
abstract = {The well-known Bryopsidalean genus Codium has a worldwide distribution and contains almost 150 species, with cryptic diversity confusing the actual number. In the Hawaiian Islands, 15 species have been previously recorded, with several of these described in the past several decades, largely from specimens collected from mesophotic coral ecosystems. We assessed the diversity of Codium in Hawai'i from both shallow and mesophotic habitats by employing DNA barcoding and phylogenetic analyses of partial rbcL and tufA gen plastid markers and morphological characterization. DNA sequence analyses supported 18 species of Hawaiian Codium (eight of which are considered endemic), which is a 20% increase in recognized species richness for this genus in Hawai'i. Ten previously reported species were confirmed or provisionally confirmed, six new species have been described (C. pikoii sp. nov., C. upohoae sp. nov., C. hakakaupilii sp. nov., C. kanepohihiae sp. nov., C. torulosum sp. nov., and C. iolekaae sp. nov.), and two new records have been reported (C. "geppiorium4" and C. taylorii). Twenty-eight percent of Hawaiian Codium clades were mesophotic only, and 22% were shallow only, while 50% of clades were known from both shallow and mesophotic depths. Recent emphasis on the systematics of Hawaiian mesophotic algae has sufficiently increased specimen numbers from this habitat to allow a more complete assessment of the genus in this location, making it one of the most thoroughly collected and studied marine algal genera from Hawai'i and an excellent model for future examination of both horizontal (i.e., spatial) and vertical (i.e., depth) distributional trends.},
}

@article {pmid40985397,
year = {2025},
author = {McPherson, VJ and Gillings, MR and Ghaly, TM},
title = {Diverse, Cryptic, and Undescribed: Club and Coral Fungi in a Temperate Australian Forest.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/jof11070502},
pmid = {40985397},
issn = {2309-608X},
abstract = {Fungi are the most poorly described kingdom of Eukarya. Fundamental questions about their species diversity, their distributions, and their biotic interactions remain largely unanswered, despite fungi playing important roles in the ecology and biogeochemistry of terrestrial ecosystems. To assess some of these data gaps, we intensively surveyed club and coral fungi in a temperate Australian forest in the Upper Lane Cove Valley, Sydney, Australia, over a period of two years. Specimens identified as Clavulinopsis, Ramaria, or Ramariopsis based on morphology were then assigned to operational taxonomic units (OTUs) using the criterion of 97% identity across the entire rDNA internal transcribed spacer (ITS) region. Based on this criterion and ITS-based phylogenies, we identified 80 OTUs in these genera of club and coral fungi within the survey area. Of these OTUs, only 11.25% could be assigned a species name based on BLASTn matches to full-length ITS sequences, suggesting that almost 90% of OTUs were novel taxa, or are yet to be represented in DNA databases. Specimens that were morphologically similar to well-known Northern Hemisphere species were shown to be distinct upon DNA sequencing. Accumulation curves suggest that our surveys only recovered about half of the species in the target genera, and seven times the effort would be required to sample to exhaustion. In summary, even in a small area of less than 100 km[2], there is evidence for multiple undescribed, cryptic, and undiscovered species. This highlights the fundamental work that remains to be completed in fungal taxonomy and biology.},
}

@article {pmid40984528,
year = {2025},
author = {Li, B and Liu, L and Xu, L},
title = {Ultra-sensitive and wide-range temperature sensing utilizing a microbottle resonator coupled with fiber Mach-Zehnder interferometer.},
journal = {Optics express},
volume = {33},
number = {16},
pages = {33704-33714},
doi = {10.1364/OE.566867},
pmid = {40984528},
issn = {1094-4087},
abstract = {An ultra-sensitive and wide-range temperature detection method has been proposed based on coupling a microbottle resonator with a fiber Mach-Zehnder Interferometer (FMZI), which can change the small mode shift into a large intensity variation. We theoretically and experimentally investigated the sensing performance of this method. Through appropriately adjusting the length difference of FMZI, the microbottle resonant peaks and the FMZI peak move in opposite directions. Measuring the Fano dip depth gives a temperature sensitivity of up to 307.5 dB/°C and a temperature resolution of 4 × 10[-3] °C. Theoretical calculations demonstrate that the temperature detection limit can reach 4 × 10[-6] °C under an 80 dB Signal-to-Noise Ratio (SNR). Moreover, experiments have confirmed that by using the encoding method of universal commercial barcodes to record the changes in the resonant frequencies and intensities of the modes and by matching the proposed barcodes with the Bit Error Rate, temperature sensing with an almost unlimited range can be achieved. The proposed method makes it possible to achieve high sensitivity and a wide range of temperature sensing applications.},
}

@article {pmid40980947,
year = {2025},
author = {Harms, D and McRae, J and Curran, M and Harvey, MS},
title = {Identifying refugia for invertebrate conservation in biodiversity hotspots: examples from a new genus of dragon pseudoscorpions (Pseudotyrannochthoniidae: Karrichthonius).},
journal = {Invertebrate systematics},
volume = {39},
number = {},
pages = {},
doi = {10.1071/IS25028},
pmid = {40980947},
issn = {1447-2600},
mesh = {Animals ; *Biodiversity ; Western Australia ; *Conservation of Natural Resources ; *Refugium ; *Odonata/classification/anatomy & histology/genetics ; Species Specificity ; Phylogeny ; DNA Barcoding, Taxonomic ; },
abstract = {Conservation management in ancient landscapes has shifted in recent years from the protection of single species to the broader management of areas of high biodiversity. One of the landscapes that has most benefited from this shift is the south-west of Western Australia, an internationally recognised biodiversity hotspot and one of the oldest and most stable landscapes on Earth. Significant progress has been made in recent years to identify refugia in the south-west and prioritise them for invertebrate protection but more studies are still needed to assist practical conservation management. Here, we describe a new genus of pseudoscorpions from south-western Australia (Pseudoscorpiones: Pseudotyrannochthoniidae: Karrichthonius gen. nov.) that has speciated extensively within mesic refugia. Karrichthonius is endemic to the High Rainfall Province of the biodiversity hotspot and features often-localised populations in spatially isolated mesic habitats. Through a combination of DNA barcoding, morphological features and spatial mapping, we infer 12 species: Karrichthonius giganteus (Beier, 1971) comb. nov. , K. booraraensis , sp. nov. , K. buzattoi , sp. nov. , K. dalei , sp. nov. , K. farquhari , sp. nov. , K. heatherae , sp. nov. , K. leniae , sp. nov. , K. porongurupensis , sp. nov. , K. pyungurupensis , sp. nov ., K. rixi , sp. nov. , K. talyuberlupensis , sp. nov. and K. toolbrunupensis , sp. nov . All species are short-range endemics and occur in landforms that are either known refugia for invertebrate conservation or inferred here as potential refugia to be recognised and analysed further. By mapping species distributions and providing species diagnoses, we contribute to an understanding of invertebrate biodiversity in the south-west, and strengthen the concepts that are underlying conservation management practices in biodiversity hotspots. ZooBank: urn:lsid:zoobank.org:pub:EC51BFC7-0C8E-49D6-A704-DA59648B2325.},
}

Animals
*Biodiversity
Western Australia
*Conservation of Natural Resources
*Refugium
*Odonata/classification/anatomy & histology/genetics
Species Specificity
Phylogeny
DNA Barcoding, Taxonomic

@article {pmid40979753,
year = {2025},
author = {Jeong, JH and Heo, UH and Lee, JY and Oh, JI and Song, YG and Kim, SY and Park, Y and Byun, BK},
title = {Two new species of the genus Acrolepiopsis Gaedike, 1970 (Lepidoptera, Glyphipterigidae) from Korea.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e163874},
pmid = {40979753},
issn = {1314-2828},
abstract = {BACKGROUND: The family Glyphipterigidae comprises small-sized moths with a wingspan ranging from 8 to 14 mm. This family is mainly distributed in the Palaearctic and Oriental Regions. In Korea, five species of the genus Acrolepiopsis Gaedike, 1970 have been recorded. However, species-level identification within this genus is often challenging due to high morphological similarity amongst species.

NEW INFORMATION: In this study, two new species of the genus Acrolepiopsis, A. quinquelobatae sp. nov. and A. koreana sp. nov., are described from Korea. Species delimitation is supported by COI gene analysis and morphological characteristics of genitalia, both of which reveal clear genetic divergence from other Acrolepiopsis species previously recorded in Korea. Photographs of adults and genitalia, along with information on host plants, are also provided.},
}

@article {pmid40978795,
year = {2025},
author = {Qazi, IH and Yuan, T and Liu, X and Liu, J},
title = {Identification of Pseudocercospora mori as the causal agent of grey leaf spot disease in mulberry (Morus atropurpurea) from various localities in Guangdong Province, China.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1648690},
pmid = {40978795},
issn = {1664-462X},
abstract = {During periods of high temperature and humidity, mulberry trees become susceptible to fungal leaf spot disease, which can significantly reduce both the yield and quality of their leaves. In this study, we collected samples of mulberry leaf spot disease from six regions of Guangdong province of China. The disease samples were studied using traditional morphological methods, high-throughput sequencing technology, molecular phylogenetic analysis, and pathogenicity tests. The observed morphological features of the pathogen were consistent with those of Pseudocercospora. High-throughput sequencing results revealed the presence of multiple fungal species in the samples, with Pseudocercospora spp. comprising the highest proportion. The complete rDNA and mitochondrial genome sequences of Pseudocercospora spp. were assembled. Based on the sequencing data, primers were designed to amplify and sequence barcode gene regions, including ITS, Cyt b, and COI. Phylogenetic analyses consistently placed the pathogen within the family Mycosphaerellaceae. ITS-based identification confirmed the pathogen as a member of the genus Pseudocercospora, while the Cyt b and COI sequences indicated a relatively distant relationship with the closely related genus Cercospora, thereby supporting the morphological classification of the pathogen at the molecular level. In addition, pathogenicity validation identified Pseudocercospora mori as a primary causal pathogen of leaf spot disease in mulberry. PCR primers specifically designed based on the rDNA sequence of Pseudocercospora mori achieved a detection sensitivity as low as 3 × 10[-2] ng/μL. In conclusion, based on morphological and molecular phylogenetic evidence, we identified Pseudocercospora mori as the causal pathogen of mulberry leaf spot disease. This study provides useful data for practical management of mulberry leaf spot disease at the field level, aiding in the sustainable development of sericulture.},
}

@article {pmid40977149,
year = {2025},
author = {Schneider, T and Vierstraete, A and Kosterin, OE and Ikemeyer, D and Hu, FS and Kompier, T and Dumont, HJ},
title = {Molecular phylogenetic analysis of the family Chlorogomphidae (Odonata, Anisoptera).},
journal = {Invertebrate systematics},
volume = {39},
number = {},
pages = {},
doi = {10.1071/IS25016},
pmid = {40977149},
issn = {1447-2600},
mesh = {*Phylogeny ; Animals ; *Odonata/classification/genetics ; Species Specificity ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; },
abstract = {Phylogenetic analysis of the family Chlorogomphidae was carried out using two nuclear markers, the ITS and histone H3-H4 regions, and a barcoding fragment of the mitochondrial COI gene, using sequences obtained in this study and adopted from GenBank. Their joint analysis was performed using StarBEAST software. In total, 36 (64%) of 56 species of all three genera currently recognised in this family were analysed. Our analysis showed Chlorogomphidae as a monotypic family containing the single speciose genus Chlorogomphus Selys, 1854. Chlorogomphus montanus Chao, 1999, syn. nov., is synonymised to Chlorogomphus nasutus Needham, 1930, Chlorogomphus urolobatus Chen, 1950, syn. nov., is synonymised to Chlorogomphus infuscatus Needham, 1930. The synonymy of Chlorogomphus suzukii Oguma, 1926 and Chlorogomphus tunti Needham, 1930 is confirmed. Some other potential synonyms are discussed. The phylogenetic trees reconstructed here showed that the species name C. nasutus Needham, 1930 actually refers to two (not three) different taxa. Thus, we suggest considering these two taxa as separate species, C. nasutus and C. satoi Asahina, 1995. ZooBank: urn:lsid:zoobank.org:pub:5188C826-AD51-4605-8B06-3C63DE80F1F0.},
}

*Phylogeny
Animals
*Odonata/classification/genetics
Species Specificity
DNA Barcoding, Taxonomic
Electron Transport Complex IV/genetics

@article {pmid40976471,
year = {2025},
author = {Hornok, S and Keskin, A and Uspensky, I and Kontschán, J and Takács, N and Lesiczka, P and Warbroek, T and van den Bosch, TJM and Keve, G and Pitó, A and Sándor, AD},
title = {Updates on subgenus Ixodes in the Mediterranean region: validity of Ixodes festai Rondelli, 1926, reinstatement of Ixodes tatei , and a new species closely related to Ixodes gibbosus.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.09.002},
pmid = {40976471},
issn = {1879-0135},
abstract = {The southern part of Europe is one of the most species-rich regions from the point of view of the genus and subgenus Ixodes. However, numerous unresolved or questionably interpreted issues exist in the context of tick species indigenous to Mediterranean countries, such as the validity of Ixodes festai, synonymy of Ixodes tatei with Ixodes eldaricus (never tested molecularly) or the haplotype heterogeneity of Ixodes gibbosus. In this study, 21 specimens of six tick species from the subgenus Ixodes were compared morphologically with high resolution digital microscopy and also analyzed with molecular-phylogenetic methods based on two mitochondrial genetic markers. The nymphs of I. eldaricus and I. tatei showed differences in the morphology of the scutum and basis capituli. Both the nymph and the females of I. festai could be distinguished from those of I. eldaricus, I. ventalloi and I. acuminatus. A female tick resembled I. gibbosus but was also different from this species, based on its descriptions. Analysis of phylogenetic relationships confirmed with moderate to strong support that all six species examined in this study represent different taxa of the subgenus Ixodes, including a previously unknown sister species to I. gibbosus. The latter is recognized and described here as a new species, Ixodes paragibbosus Hornok and Kontschán, sp. nov. Based on findings of this study, the tick species I. tatei Arthur, 1959 should be resurrected and reestablished. Morphological and phylogenetic comparisons performed here (including the first barcoding sequences of I. eldaricus and I. festai) confirm that the latter is a valid species, distinct from both I. eldaricus and I. ventalloi. For the differential diagnosis of the above species, the results highlight the importance of observing (among other structures) the auriculae, the internal spur of coxa I and the hypostome.},
}

@article {pmid40970423,
year = {2025},
author = {Castanon, CP and Hernandez, D and Khetrapal, AN and Hellberg, RS},
title = {Comparison of PCR-Based Methods for the Detection of Canned Tuna Species.},
journal = {Journal of food science},
volume = {90},
number = {9},
pages = {e70424},
doi = {10.1111/1750-3841.70424},
pmid = {40970423},
issn = {1750-3841},
support = {//Chapman University/ ; //National Science Foundation/ ; },
mesh = {Animals ; *Tuna/genetics/classification ; *Real-Time Polymerase Chain Reaction/methods ; *Food, Preserved/analysis ; *DNA Barcoding, Taxonomic/methods ; Multiplex Polymerase Chain Reaction/methods ; Species Specificity ; Food Contamination/analysis ; *Seafood/analysis ; DNA ; *Polymerase Chain Reaction/methods ; Food Labeling ; },
abstract = {Canned tuna is susceptible to mislabeling due to its high consumer demand, complex global supply chains, and range of prices. DNA barcoding of a short fragment of the mitochondrial control region (CR), termed the CR mini-barcode, has been established as an effective method for tuna species identification. However, the high level of DNA degradation in canned tuna products reduces the effectiveness of this method. Therefore, this study aimed to compare CR mini-barcoding to targeted (i.e., real-time or multiplex) PCR-based methods to determine the most effective approach for canned tuna species identification. DNA was extracted in duplicate from 24 canned tuna products labeled as albacore, skipjack, yellowfin, and light tuna. Each sample was analyzed with CR mini-barcoding, real-time PCR, and multiplex PCR. The top-performing targeted method also underwent sensitivity testing using binary species mixtures. Real-time PCR showed the highest species identification rate, with 100% of products detected, followed by CR mini-barcoding (33%) and multiplex PCR (29%). Real-time PCR also showed excellent sensitivity, detecting 0.1%-1% of the target species in fresh and heat-treated binary species mixtures. Multiplex PCR and real-time PCR showed similar effectiveness in terms of cost and time, with a price of US$6 per sample and a total time of 3-6 h when testing all targeted species. Although CR mini-barcoding required greater costs and time, it allowed for sequencing-based detection of a range of species in the products. In conclusion, a combination of real-time PCR and CR mini-barcoding is recommended to allow for rapid screening of target species along with sequencing-based confirmation. PRACTICAL APPLICATIONS: This research provides a practical recommendation regarding the use of genetic methods for detecting species in canned tuna. Implementation of the recommended methodology is expected to enhance consumer protection and help regulatory agencies enforce accurate labeling.},
}

Animals
*Tuna/genetics/classification
*Real-Time Polymerase Chain Reaction/methods
*Food, Preserved/analysis
*DNA Barcoding, Taxonomic/methods
Multiplex Polymerase Chain Reaction/methods
Species Specificity
Food Contamination/analysis
*Seafood/analysis
DNA
*Polymerase Chain Reaction/methods
Food Labeling

@article {pmid40967690,
year = {2025},
author = {Nagarajan, G and Kanagarajadurai, K and Pachaiyappan, K and Yadav, G},
title = {Identification and DNA barcoding of Tabanid flies in the pasture area of sheep at Mannavanur, Palani Hills, Tamil Nadu, India.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {64},
number = {},
pages = {101326},
doi = {10.1016/j.vprsr.2025.101326},
pmid = {40967690},
issn = {2405-9390},
mesh = {Animals ; *DNA Barcoding, Taxonomic/veterinary ; India ; *Diptera/genetics/classification/anatomy & histology ; Sheep ; Electron Transport Complex IV/genetics ; *Sheep Diseases/parasitology ; Phylogeny ; },
abstract = {The present study was carried out to identify the tabanid flies creating annoyance to sheep in the grazing area of SRRC, Mannavanur by means of morphological keys and DNA barcoding targeting mitochondrial cytochrome c oxidase subunit I (COI) gene. Two different kinds of tabanid flies were caught from the pasture area by graziers during the months of May & June 2021. With the help of Dept. of Agricultural Entomology, Centre for Plant Protection studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India and Zoological Survey of India, Kolkata, West Bengal, India, it was identified that Haematopota nathani (Cleg fly) and Tabanus subcinerascens (Horse fly) were the two dipteran tabanid flies causing annoyance and aching bite in sheep and shepherds. The total genomic DNA isolated from the flies were subjected to COI gene based PCR assay using the universal primer set and the resultant PCR amplified DNA fragments were cloned into E.coli based vector. The confirmed recombinant plasmids were subjected for gene sequencing protocol through outsourcing. Upon the BLAST analysis, the nucleotide sequences obtained from the flies identified by TNAU and ZSI, were having the highest identity with COI gene of Haematopota sp and Tabanus sp., respectively. The obtained nucleotide sequences were analysed using the standard bioinformatics tools. Small number of fly specimens and the analysis based on the partial nucleotide sequences of COI gene are the limitations. It was concluded that the documentation of H. nathani and T. subcinerascens as well as barcoding of both tabanid flies from Palani hills, Tamil Nadu, India, based on mitochondrial COI DNA marker had been carried out for the first time.},
}

Animals
*DNA Barcoding, Taxonomic/veterinary
India
*Diptera/genetics/classification/anatomy & histology
Sheep
Electron Transport Complex IV/genetics
*Sheep Diseases/parasitology
Phylogeny

@article {pmid40967208,
year = {2025},
author = {Tai, H and Li, Q and Wang, J and Tan, J and Zhao, B and Lang, R and Petrof, BJ and Ding, J},
title = {Computational tracking of cell origins using CellSexID from single-cell transcriptomes.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101181},
doi = {10.1016/j.crmeth.2025.101181},
pmid = {40967208},
issn = {2667-2375},
abstract = {Cell tracking in chimeric models is essential yet challenging in developmental biology, regenerative medicine, and transplantation research. Current methods like fluorescent labeling and genetic barcoding are technically demanding, costly, and often impractical for dynamic tissues. We present CellSexID, a computational framework that uses sex as a surrogate marker for cell-origin inference. By training machine-learning models on single-cell transcriptomic data, CellSexID accurately predicts individual cell sex, enabling in silico distinction between donor and recipient cells in sex-mismatched settings. The model identifies minimal sex-linked gene sets through ensemble feature selection and has been validated using public datasets and experimental flow sorting, confirming biological relevance. We demonstrate CellSexID's applicability beyond chimeric models, including organ transplantation and sample demultiplexing. As a practical alternative to physical labeling, CellSexID facilitates precise cell tracking and supports diverse biomedical applications where mixed cellular populations need to be distinguished.},
}

@article {pmid40963787,
year = {2025},
author = {Rossouw, L and Ngcobo, N and Clouse, K and Nattey, C and Technau, KG and Maskew, M},
title = {Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study.},
journal = {Discover health systems},
volume = {4},
number = {1},
pages = {115},
pmid = {40963787},
issn = {2731-7501},
abstract = {BACKGROUND: The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information.

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

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

CONCLUSIONS: The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective deterministic linkage tool that enable creation of large linked datasets without compromising confidentiality.},
}

@article {pmid40963001,
year = {2025},
author = {Liu, S and Huang, J and Qu, L and Li, B and Yang, J},
title = {NAP-seq for full-length noncapped RNA sequencing.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40963001},
issn = {1750-2799},
support = {32225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32430019//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370588//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The majority of the mammalian genome is transcribed into RNAs, most of which are noncapped RNAs (napRNAs) that not only regulate diverse biological processes through their functions as noncoding RNAs but also serve as processing products to delineate specific RNA biogenesis pathways. However, due to their heterogeneous lengths, diverse terminal modifications and complex secondary structures, identifying these napRNAs poses substantial challenges. Recently, we developed a napRNA sequencing technique (NAP-seq) to identify full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution. Here we describe the experimental design principles and detailed step-by-step procedures for discovering napRNAs across multiple cell types. The procedure includes T4 polynucleotide kinase pretreatment to standardize RNA termini, enabling comprehensive capture of modified napRNAs; size-selection followed by depletion of known high-abundance RNAs via RNase H to enrich long and low-abundance RNAs; and use of custom-designed adapters with random barcodes, permitting identification of full-length napRNAs at single-nucleotide resolution while minimizing PCR biases and adapter ligation inefficiencies. The use of thermally stable reverse transcriptase enzymes and nested reverse transcriptase primers ensures full-length cDNA synthesis across structured or modified RNA regions while minimizing mispriming artifacts. Libraries are sequenced in parallel using Oxford Nanopore (long-read) and Illumina (short-read) platforms, synergizing advantages of third-generation and next-generation sequencing technologies. The entire experimental procedure, from library preparation to deep sequencing and computational analysis, can be completed within 8 d. The NAP-seq approach enables researchers to discover novel classes of noncoding RNAs with regulatory functions and to investigate RNA biogenesis in various tissues and cell lines.},
}

@article {pmid40956667,
year = {2025},
author = {Plaza, DF},
title = {Protocol for genomic surveillance of Plasmodium falciparum antigens using amplicon-based PacBio long-read sequencing.},
journal = {STAR protocols},
volume = {6},
number = {4},
pages = {104093},
doi = {10.1016/j.xpro.2025.104093},
pmid = {40956667},
issn = {2666-1667},
abstract = {Here, we present a protocol that identifies and classifies structurally diverse variants of msp1, msp2, glurp, and csp in Plasmodium falciparum using an amplicon-based long-read sequencing platform. We describe steps for PCR barcoding, PacBio circular consensus sequencing (CCS), in silico PCR-based size variant calling, and advanced data analysis in Galaxy. By resolving full-length sequences for each antigenic clone, this approach measures infection complexity, constructs isolate phylogenies, and supports vaccine design. For complete details on the use and execution of this protocol, please refer to Plaza et al.[1].},
}

@article {pmid40955360,
year = {2025},
author = {Wacira, TN and Makonde, HM and Kamau, JN and Kibiti, CM},
title = {Identification and Antimicrobial Potential of Marine Sponges (Carteriospongia foliascens, Callyspongia fallax, and Paratetilla arcifera) from Kenyan Marine Waters.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {4208163},
pmid = {40955360},
issn = {1687-918X},
abstract = {Emerging and re-emerging infectious diseases and pathogens present a significant global public health threat that has led researchers to focus on discovering new antimicrobial agents in order to address the challenge. Sponges are a promising source of marine natural products, which can be used as lead molecules for drug discovery. This study was aimed at identifying marine sponges through morphological and molecular techniques and evaluate the bioactivity potential of their organic crude extracts against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. Deoxyribonucleic acid (DNA) barcoding of the cytochrome c oxidase subunit I (COI) gene identified three genera of sponges (Carteriospongia, Callyspongia, and Paratetilla). Disk diffusion assay was used to determine the inhibition zone diameter (IZD) of the sponges' extracts. Minimum inhibitory concentrations (MICs) and the minimum bactericidal/fungicidal concentrations (MBCs/MFCs) of the most active sponge extracts were determined. The bioactive compounds were analyzed using gas chromatography-mass spectrometry (GC-MS). The dichloromethane extracts of Carteriospongia foliascens demonstrated the highest antifungal activity against C. albicans (31.33 ± 1.2 mg mL[-1]), surpassing the standard drug fluconazole (29.33 ± 1.5 mg mL[-1]). The MIC values for the sponge extracts ranged from 3.86 to 5.89 mg mL[-1], and the ethyl acetate extract of Callyspongia fallax had an MBC of 4.03 mg mL[-1] against S. aureus. GC-MS chromatogram identified 98 compounds across 41 classes in three sponge extracts. Notably, 9.2% of these compounds have been reported to exhibit antimicrobial activity against human pathogens. This study confirms that sponges are a source of useful biochemicals, which have potential for drug discovery. To the best of our knowledge, this is the first comprehensive study to report on the characterization of marine sponges from the Kenyan waters. Further research work to structurally elucidate and identify the most active bioactive compounds from the extracts of C. foliascens and C. fallax is recommended.},
}

@article {pmid40951674,
year = {2025},
author = {Gan, J and Mi, X and Wang, C and Fan, L},
title = {Three new species of Theridiidae Sundevall, 1833 (Araneae) from Xizang, China.},
journal = {ZooKeys},
volume = {1251},
number = {},
pages = {1-15},
pmid = {40951674},
issn = {1313-2989},
abstract = {Three new species belonging to the spider family Theridiidae are described based on materials collected from Xizang Autonomous Region, Southwestern China: Moneta linzhi Gan, Mi & Wang, sp. nov. (♀♂), M. yinae Gan, Mi & Wang, sp. nov. (♀♂) and Phoroncidia cibagou Gan, Mi & Wang, sp. nov. (♀♂). Diagnostic photos of the habitus and copulatory organs, and a distribution map are provided.},
}

@article {pmid40950469,
year = {2025},
author = {Rueda, M and Gut, IG},
title = {ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.05.25335150},
pmid = {40950469},
abstract = {BACKGROUND: In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making integration, cohort selection, and downstream analysis cumbersome. While structured barcoding systems exist in large consortia (e.g., TCGA, GTEx) or domain-specific contexts (e.g., SPREC, GOLD), no unified, extensible framework currently spans both subjects and biosamples in a human- and machine-readable way.

METHODS: We developed ClarID, a domain-agnostic specification that supports two identifier formats: (i) a human-readable form (e.g., 'CNAG_Test-HomSap-00001-LIV-TUM-RNA-C22.0-TRT-P1W' that encodes key metadata such as project, species, subject_id, tissue, assay, disease, timepoint and duration (from that event); and (ii) a compact version named 'stub' (e.g., 'CT01001LTR0N401T1W') optimized for filenames, pipelines, and labeling.ClarID is implemented through an open-source command-line tool, ClarID-Tools, which processes tabular metadata files (CSV/TSV) and uses a YAML-based codebook to generate, decode, and validate identifiers, as well as to create and read QR codes. The tool supports bulk and single-sample processing and allows easy integration with institutional workflows.

RESULTS: To demonstrate ClarID's utility, we applied it to datasets from the Genomic Data Commons (GDC), generating interpretable identifiers for more than 113,000 clinical records (subjects) and 4,255 biospecimen records. All materials, including pre-processing scripts, input and encoded data, are publicly available and fully reproducible via the accompanying GitHub repository and Google Colab.

CONCLUSIONS: ClarID fills a critical gap between opaque accession numbers and rich metadata schemas by embedding key context directly into structured identifiers. It enhances traceability, facilitates downstream analysis, and remains adaptable to project-specific needs through a configurable codebook. The accompanying ClarID-Tools software is freely available, together with full documentation and reproducible pipelines, at https://github.com/CNAG-Biomedical-Informatics/clarid-tools .},
}

@article {pmid40950163,
year = {2025},
author = {Fu, Y and Mathew, D and Wang, M and Chen, XE and Lin, KZ and Schaff, D and Shaffer, SM and Pardoll, DM and Jackson, C and Zhang, NR},
title = {Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.01.673503},
pmid = {40950163},
issn = {2692-8205},
abstract = {Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.},
}

@article {pmid40947820,
year = {2025},
author = {Prosser, SWJ and Floyd, RM and Thompson, KA and Monckton, SK and Hebert, PDN},
title = {BOLDistilled: Automated Construction of Comprehensive but Compact DNA Barcode Reference Libraries.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70043},
doi = {10.1111/1755-0998.70043},
pmid = {40947820},
issn = {1755-0998},
support = {MSI 42450//Canada Foundation for Innovation/ ; OGI-233//Genome Canada and Ontario Genomics/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; },
abstract = {Advances in DNA sequencing technology have stimulated the rapid uptake of protocols-such as eDNA analysis and metabarcoding-that infer the species composition of environmental samples from DNA sequences. DNA barcode reference libraries play a critical role in the interpretation of sequences gathered through such protocols, but many of these libraries lack a taxonomic consensus, include redundant records, do not support end-user analytical pipelines, and are not permanently archived. Furthermore, because DNA sequencers are outpacing Moore's Law and reference libraries are growing, the computational power required to assign sequences to source taxa is rapidly increasing. This paper introduces an algorithmic approach to construct DNA barcode reference libraries that addresses these issues. Hosted online, 'BOLDistilled' libraries are comprehensive but compact, because the algorithm distills genetic variation into a minimal set of records. We provide a BOLDistilled library for the barcode region of the cytochrome c oxidase 1 gene (COI) based on data in the Barcode of Life Data System (BOLD). It contains 1.7 M records versus the 15.7 M in the complete library, a compression that reduced the time required for sequence analysis of metabarcoded samples by ≥ 98% with no reduction in the accuracy of taxonomic placements. BOLDistilled libraries will be updated regularly, with current and previous versions available at https://boldsystems.org/data/boldistilled. By providing access to persistent, comprehensive, and high-quality reference data, these libraries strengthen the capacity of DNA-based identification systems to advance biodiversity science.},
}

@article {pmid40946051,
year = {2025},
author = {Guo, Z and Fan, L and Ma, Y and Tian, K and Qiu, W and Wei, A and Fu, W and Chen, Y and Cui, Z and Wang, S and Zhan, C},
title = {Vascular endothelial cell-targeted mRNA delivery via synthetic lipid nanoparticles for venous thrombosis prevention.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114147},
doi = {10.1016/j.jconrel.2025.114147},
pmid = {40946051},
issn = {1873-4995},
abstract = {Venous thromboembolism significantly contributes to the global disease burden. Anticoagulant and antiplatelet therapies are currently the treatment strategies. However, challenges remain due to hemorrhagic complications and the inability to resolve established thrombi. There is an urgent need for a new generation of antithrombotic agents. Given the fibrin specificity and rapid thrombus dissolution capacity of recombinant tissue plasminogen activator (TPA) protein, along with the significant advantages of mRNA therapeutics in protein replacement, we aim to develop an antithrombotic strategy through the targeted delivery of TPA mRNA to vascular endothelial cells using synthetic lipid nanoparticles (LNPs). A series of amino ionizable lipids were synthesized to create an LNP library, from which the LNP selectively targeting vascular endothelial cells (vtLNP) was selected by a DNA barcode labeling high-throughput screening method. The antithrombotic efficacy and safety of vtLNP loaded with TPA mRNA (vtLNP@TPA) were evaluated in a deep vein thrombosis (DVT) mouse model and normal ICR mice, respectively. The results revealed that vtLNP@TPA significantly prevented the occurrence and development of venous thrombosis. This study provides relevant experimental evidence for a novel antithrombotic therapy strategy for venous thrombosis using mRNA therapeutics.},
}

@article {pmid40945162,
year = {2025},
author = {Koppala Narayana, SK and Kaira, P and Karthikeyan, M and Shanmugam, M and Sundharamoorthy, S and Andalil, R and Kallingil Gopi, D and Prakasam, R and Ramachandran, S and Arumugam, K},
title = {Integrating macro-microscopy, DNA barcoding and HPTLC for quality assessment of berberine containing botanicals traded as Maramanjal/Daruharidra.},
journal = {Journal of Ayurveda and integrative medicine},
volume = {16},
number = {5},
pages = {101192},
doi = {10.1016/j.jaim.2025.101192},
pmid = {40945162},
issn = {0975-9476},
abstract = {BACKGROUND: Daruharidra/Maramanjal is one of the most popular shrub used in Ayurveda, Siddha and other Indian medicinal systems. More than one botanical source is traded under this name, predominantly Berberis aristata and Coscinium fenestratum with an annual trade of 1000-2000 metric tonnes. The herbal drug trade is often reported with misidentification, adulteration and/or substitution issues due to morphological resemblance and confusion in vernacular names. This work aimed to integrate macro-microscopic, DNA marker strategies and phytochemical assay to differentiate Berberis aristata from its traded sources.

MATERIAL AND METHODS: Thirteen marketed samples and one authentic field sample from natural habitat were collected from various regions of the Indian market under the trade name Maramanjal/Daruharidra. The traditional identification methods included macro-microscopic and phytochemical screening by High-Performance Thin Layer Chromatography (HPTLC). Additionally, DNA barcode-based molecular identification and phylogenetic analysis were done using the ITS2 (Internal Transcribed Spacer 2) marker.

RESULTS: The macroscopic observations revealed 80 % ad-mixing of various allied botanicals in addition to accepted north Indian and south Indian sources such as B. aristata and C. fenestratum respectively. DNA barcoding enabled the identification of genuine and adulterated raw drugs from the collected samples. The HPTLC quantification revealed the presence of berberine in all 14 samples varying from 1.12 % to 26.33 %.

CONCLUSIONS: The macro-micro, HPTLC, and DNA barcoding helped in the identification of adulteration and substitution practices in this highly traded botanical drug. DNA barcoding can prove an effective tool for discovering the adulteration and substitution of Maramanjal/Daruharidra and this is its first report on the application of morphology, microscopy, phytochemical analysis, and DNA markers in differentiating these traded species.},
}

@article {pmid40944710,
year = {2025},
author = {Dutta, N and Svensson, J and Saad, GA and Mello, M and Eklund, EA and Altinönder, I and Torstensson, P and Sayin, VI and Rohlin, A and Luche, H and Hallqvist, A and Raghavan, S},
title = {High baseline PD-1+ CD8 T Cells and TIGIT+ CD8 T Cells in circulation associated with response to PD-1 blockade in patients with non-small cell lung cancer.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {10},
pages = {309},
pmid = {40944710},
issn = {1432-0851},
support = {21/1721//Cancerfonden/ ; },
abstract = {Blockade of PD-1 or its ligand PD-L1 with antibodies revolutionized treatment for stage III and IV non-small cell lung cancer (NSCLC) since FDA approval in 2015. However, resistance to PD-1/PD-L1 blockade remains a challenge, highlighting the need for biomarkers. This study analyzed 36 stage III and IV NSCLC patients, classified as responders or non-responders by iRECIST criteria. Peripheral blood mononuclear cells collected at baseline and post-treatment were examined for surface and intracellular markers via flow cytometry. CITE sequencing of CD8 T cells from three patients and plasma ctDNA analysis from 13 patients was performed using an ultrasensitive barcoding and next-generation sequencing method. Phenotypic analysis of CD8 T cells revealed higher TIGIT and PD-1 expression at baseline in responders compared to non-responders. Long-term responders (> 21 months) exhibited increased TCF-1[+]PD-1[+] CD8 T cell frequencies relative to shorter-term responders (> 15 months) and non-responders. CITE sequencing revealed intrinsic differences in immune regulation pathways between responders and non-responders. Finally, non-responders showed elevated and increasing ctDNA levels post-treatment, correlating with declining TCF-1[+]PD-1[+] CD8 T cells. Our data suggests combining CD8 T cell analysis with ctDNA dynamics could identify promising biomarkers for monitoring clinical response and treatment efficacy to PD-1/PD-L1 blockade in NSCLC.},
}

@article {pmid40944309,
year = {2025},
author = {Parmar, DR and Johnston, NP and Dinka, MD and Szpila, K},
title = {Species delimitation of the Afrotropical and Palaearctic Calliphora Robineau-Desvoidy and discovery of two new species in Afrotropics.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70011},
pmid = {40944309},
issn = {1365-2915},
support = {2018/31/B/NZ8/02113//Polish National Science Centre/ ; 4-G046X5I//Australian Biological Resources Study/ ; },
abstract = {The blowflies (Calliphoridae) represent a significant portion of schizophoran fly diversity, comprising approximately 2000 known species. Among them, the genus Calliphora Robineau-Desvoidy is one of the largest, with over 100 species primarily distributed in the Holarctic Region and Australasia. Blowflies include several ubiquitous species and are primarily recognised for their medical and veterinary importance. In the Afrotropics, Calliphora was previously known from only two species: the native Calliphora croceipalpis Jaennicke and the introduced Calliphora vicina Robineau-Desvoidy. Two new distinctive species of Calliphora collected during recent fieldwork in Ethiopia are described using methods of integrative taxonomy. Calliphora teraramma sp. n. is characterised by peculiar male genitalia, with large cerci and a minute phallus. Calliphora mesay sp. n. is characterised by morphological and molecular traits, a close relative of the cosmopolitan C. vicina. In addition, we developed a cytochrome c oxidase subunit I (COI) barcode reference library for Palaearctic and Afrotropical Calliphora species, including 33 newly generated barcodes. Molecular species delimitation analyses using the software Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), implemented through the recently developed integrative platform Spart Explorer, largely support morphological species concepts.},
}

@article {pmid40943390,
year = {2025},
author = {Baig, A and Akram, A and Lin, MK},
title = {Agarwood in the Modern Era: Integrating Biotechnology and Pharmacology for Sustainable Use.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178468},
pmid = {40943390},
issn = {1422-0067},
support = {MOST 111-2320-B-039-023-MY3//National Science Council/ ; },
abstract = {Agarwood, valued for its resin, has long been used in perfumery, incense, and traditional medicine. Its resin is primarily derived from species of Aquilaria and is produced through a still-unknown process in response to biotic or abiotic stress. Concerns regarding agarwood's sustainability and conservation have emerged because of the substantial loss of natural resources due to overharvesting and illegal trade. To address these concerns, artificial techniques are being used to produce agarwood. The mechanism underlying agarwood production must be elucidated to enhance yield. The authentication of agarwood species is challenging because of morphological similarities between pure and hybrid Aquilaria species. Techniques such as DNA barcoding, molecular marker assessment, and metabolomics can ensure accurate identification, facilitating conservation. Artificial intelligence and machine learning can support this process by enabling rapid, automated identification on the basis of genetic and phytochemical data. Advances in resin induction methods (e.g., fungal inoculation) and chemical induction treatments are improving yield and quality. Endophytic fungi and bacteria promote resin production at minimal harm to the tree. Agarwood's pharmacological potential-antimicrobial, anti-inflammatory, and anticancer effects-has driven research into bioactive compounds such as sesquiterpenes and flavonoids for the development of novel drugs. This systematic review synthesized current evidence on species authentication, induction techniques, and pharmacological properties. The findings may guide future research aimed at ensuring sustainable use and enhancing the medicinal value of agarwood.},
}

@article {pmid40941119,
year = {2025},
author = {Kim, KR and Kim, HJ and Bang, IC},
title = {Development of a Rapid and Cost-Effective Multiplex PCR Assay for the Simultaneous Identification of Three Commercially Important Sea Squirt Species (Halocynthia spp.).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173003},
pmid = {40941119},
issn = {2304-8158},
support = {20200425-03//Ministry of Oceans and Fisheries Korea/ ; 2025//Soonchunhyang University Research Fund, Korea/ ; R2025046//National Institute of Fisheries Science, Korea/ ; },
abstract = {We developed and validated a rapid, cost-effective multiplex PCR assay targeting mitochondrial cytochrome c oxidase subunit I (COX1) to discriminate three commercially important sea-squirt species, Halocynthia roretzi, H. aurantium and H. hilgendorfi ritteri. Species-specific forward primers were designed from interspecific single-nucleotide polymorphisms within the barcode region and combined with a common reverse primer in a single reaction. Specificity was confirmed in all tested individuals (n = 7 per species) without cross-amplification. Sensitivity tests demonstrated consistent amplification down to 0.1 ng of template DNA, matching or surpassing detection limits reported for other food-authentication markers. Because the entire reaction including DNA extraction can be completed within three hours and requires only basic laboratory equipment, the method is well suited for quality control laboratories, border inspections and routine monitoring of processed products. The COX1 multiplex PCR set proposed here provides a reliable tool to enhance traceability, protect consumer choice, and support regulatory enforcement in the sea-squirt supply chain.},
}

@article {pmid40940606,
year = {2025},
author = {Waghmode, MS and Sahoo, DK and Patil, NN and Abhyankar, PS and Gaikwad, DD and Shekh, S},
title = {Pseudomonas sp. MSW2-Mediated Biodegradation of Pharmaceutical Micropollutants: Experimental and In Silico Investigations.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {499},
pmid = {40940606},
issn = {1432-0991},
abstract = {Environmental contamination from pharmaceutical and personal care products is a growing concern due to their widespread use. This study was aimed to investigate the biodegradation of acetaminophen and hydroxychloroquine alongside computational analysis (DFT calculations and molecular docking). The acetaminophen and hydroxychloroquine-tolerant strain was isolated from pharma industrial wastewater and identified as Pseudomonas sp. MSW 2 (GenBank: PP800223.1) based on morphological, biochemical, as well as DNA barcoding method. Based on the UV-VIS spectroscopy and HPLC data it was confirmed that Pseudomonas sp. MSW 2 degrades 1000 ppm of acetaminophen by 95% within 3 days and 50 ppm of hydroxychloroquine by 95% within 5 days, following first-order degradation kinetic models with rate constants of 0.65 d[-1] and 0.457 d[-1], respectively. Based on HRMS and [1]H NMR spectroscopy data, 1,4-benzoquinone and 7-chloro-4-quinolinamine were identified as degradative product of acetaminophen and hydroxychloroquine, respectively. The HOMO-LUMO energy gap (ΔEg) for acetaminophen,1,4 benzoquinone, hydroxychloroquine and 7-chloro-4-quinolinamine is 5.35 eV, 2.38 eV, 4.45 eV, and 4.55 eV, respectively. Data suggests that 1,4 benzoquinone has lower stability and higher reactivity compared to the acetaminophen. Whereas in case of hydroxychloroquine degradative product (7-chloro-4-quinolinamine), negligible changes were observed in the reactivity. Molecular docking simulations predicted a strong binding affinity (-26 kcal/mol) between acetaminophen and the amidase (PDB ID 2UXY) enzyme from P. aeruginosa, facilitated by hydrogen bonding. This study gives new insights in the bioremediation process, using the DFT calculations to theoretically document the reactivity and stability of pollutant as well as their biodegradative metabolites.},
}

@article {pmid40938793,
year = {2025},
author = {Brock, AA and Duraivel, S and Jiang, J and Fischer, J and Greenberg, ZF and He, M and Angelini, TE and Schmittgen, TD},
title = {RNA Sequencing at Single Vesicle Resolution via 3D Printed Embedded Droplet Arrays.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c09959},
pmid = {40938793},
issn = {1944-8252},
abstract = {Single-cell RNA sequencing has transformed our understanding of cellular heterogeneity; however, comparable methods for studying individual extracellular vesicles (EVs) remain scarce. To address the heterogeneity of RNA cargo contained within EVs, we developed a platform that 3D prints droplet arrays that generate cDNA for sequencing single EVs. The printing method leverages the interfacial instability between a hydrocarbon-based support material and printed aqueous solutions, driving printed features to break up into controllable, homogeneous droplets of a desired size that become stably trapped in 3D space. We printed picoliter aqueous droplets of EVs, DNA barcoded oligonucleotide beads, and biochemicals and performed a variety of reactions within the organogel support medium including PCR and synthesis of poly(A)[+] RNA sequencing compatible cDNA. Printing conditions were optimized to ensure ideal droplet loading of individual barcoded beads and single EVs within each droplet. Following collection of aqueous cDNA material from the organogel, additional biochemical reactions were performed in tubes in order to generate sequencable RNA libraries. Individual CD9, CD63, and CD81 positive EVs contained a wide variety of poly(A)[+] RNAs including mRNA, mitochondrial RNA, and noncoding RNAs. Poly(A)[+] RNAs of individual 100 nm immunopurified THP-1 EVs were sequenced using the 3D printing method and identified 3689 unique barcodes with at least two corresponding reads of poly(A)[+] RNA per EV, and the average amount of poly(A)[+] RNA per EV was 3.32. The developed platform resolves EV poly(A)[+] RNA heterogeneity with potential implications for biomarker discovery and other clinical applications.},
}

@article {pmid40937516,
year = {2025},
author = {Stefani, F and Laterrière, M and Abdellatif, L and Banchini, C and Mader Stevens, G and Séguin, S and Dadej, K and Koziol, L and Findlay, W and Dalpé, Y},
title = {The pitfalls of rDNA-based AMF identification: a comparative analysis of rDNA and protein-coding genes.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70557},
pmid = {40937516},
issn = {1469-8137},
support = {J-001012//Agriculture and Agri-Food Canada/ ; J-001315//Agriculture and Agri-Food Canada/ ; J-002272//Agriculture and Agri-Food Canada/ ; J-0161867//Agriculture and Agri-Food Canada/ ; J-002295//Agriculture and Agri-Food Canada/ ; },
abstract = {Intragenomic polymorphism of rDNA in arbuscular mycorrhizal fungi (AMF) has been largely overlooked in ecological and taxonomic studies, and the reliability of nuclear rDNA regions for species identification has not been comprehensively evaluated and compared with protein-coding genes. Analysis of rDNA copies from Rhizophagus irregularis strains revealed average intragenomic distances ranging from 0.08% (small subunit) to 6.9% (internal transcribed spacer 2 (ITS2)), with a maximum of 21.1% in ITS1 within strain DAOM 197198. Intragenomic rDNA polymorphisms are widespread throughout the AM fungal phylogeny, as confirmed by single nucleotide polymorphism density analysis and PacBio sequencing of 148 AM fungal cultures representing 44 species. All commonly targeted rDNA loci in ecological and taxonomic studies are polymorphic, with ITS and large subunit being the most variable, leading to paraphyletic clades and misleading phylogenetic interpretations among closely related species. No unique genetic distance threshold can be applied to identify AMF, because none of the examined protein-coding genes or partial rDNA had a barcode gap. However, indicative distance thresholds of 1% for glomalin, 1.1% for RPB1, and 1.7% for H[+]-ATPase provide guidance for species delimitation. This study characterizes the extent of intragenomic rDNA polymorphism in AMF, underscores the taxonomic challenges posed by highly variable loci, and describes a bioinformatics pipeline for recovering rDNA copies.},
}

@article {pmid40936965,
year = {2025},
author = {Chen, HP and Huang, CL and Shiao, SF},
title = {A taxonomic revision of the genus Alexeter Förster (Hymenoptera, Ichneumonidae, Ctenopelmatinae, Mesoleiini) from Taiwan, with descriptions of six new species.},
journal = {ZooKeys},
volume = {1250},
number = {},
pages = {315-358},
pmid = {40936965},
issn = {1313-2989},
abstract = {The genus Alexeter Förster, 1869 is first recorded from Taiwan. One previously described species, A. shakojiensis Uchida, 1930, is newly recorded from Taiwan. Six new species, A. flavomaculatus sp. nov., A. hsiaoae sp. nov., A. mediolobus sp. nov., A. monticola sp. nov., A. pseudozangicus sp. nov., and A. rufispeculus sp. nov., are described and can be distinguished from their congeners primarily based on color pattern, mandibular teeth, propodeal carinae, fore wing length and venation, ocellar and first metasomal tergite measurements, and flagellomere counts. Illustrations of the male genitalia and a diagnostic key to the Taiwanese Alexeter species are provided. DNA-based species delimitations are provided as supporting evidence for four new species. In a COI-based phylogeny sampling 31 operative taxonomic units of Alexeter and similar genera, the genus Alexeter was not resolved as a monophyletic group. Additionally, the COI barcode showed limitations in distinguishing some Alexeter morphospecies, indicating the need for further evaluation of COI-based species delimitation in this genus.},
}

@article {pmid40934910,
year = {2025},
author = {Guo, W and Chen, Z and Li, X and Huang, J and Hu, Q and Gu, J},
title = {scTrace+: Enhancing cell fate inference by integrating the lineage-tracing and multi-faceted transcriptomic similarity information.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101398},
doi = {10.1016/j.cels.2025.101398},
pmid = {40934910},
issn = {2405-4720},
abstract = {Deciphering the cell state dynamics is crucial for understanding biological processes. Single-cell lineage-tracing technologies provide an effective way to track single-cell lineages by heritable DNA barcodes, but the high missing rates of lineage barcodes and the intra-clonal heterogeneity bring great challenges to dissecting the mechanisms of cell fate decision. Here, we systematically evaluate the features of single-cell lineage-tracing data and then develop an algorithm, scTrace+, to enhance the cell dynamic traces by incorporating multi-faceted transcriptomic similarities into lineage relationships via a kernelized probabilistic matrix factorization model. We assess its feasibility and performance by conducting ablation and benchmarking experiments on multiple real datasets and show that scTrace+ can accurately predict the fates of cells. Further, scTrace+ effectively identifies some important driver genes implicated in cellular fate decisions of diverse biological processes, such as cell differentiation or tumor drug responses. A record of this paper's transparent peer review process is included in the supplemental information.},
}

@article {pmid40933667,
year = {2024},
author = {Cheng, HJ and Bellini, BC and Janssens, F and Nakamori, T and Chang, CH},
title = {The Cryptic Diversity of the Terrestrial Microarthropods, Ptenothrix Börner (Collembola: Dicyrtomidae) from Taiwan: New Species Plus the Lectotype Designation for Ptenothrix denticulata (Folsom, 1899).},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e42},
doi = {10.6620/ZS.2024.63-42},
pmid = {40933667},
issn = {1810-522X},
abstract = {This is the first taxonomic study of Collembola in Taiwan integrating morphological and molecular evidence to investigate the Taiwanese species in the genus Ptenothrix Börner. We discovered that specimens previously identified as Ptenothrix denticulata (Folsom, 1899) actually consist of several cryptic species, of which we described two species new to science. Our data revealed that, although these species are remarkably similar to each other, they can be distinguished by color patterns, chaetotaxic characters and DNA barcoding (COI). We also designated one of the syntypes of Ptenothrix denticulata (Folsom, 1899) as its lectotype, and treated Dicyrtoma denticulata (Salmon 1964) as a synonym of Ptenothrix denticulata (Salmon 1964) (syn. nov.). Lastly, our study suggests that the diversity of Collembola in Taiwan is still poorly understood, with a high potential for new studies focusing on these microarthropods.},
}

@article {pmid40933665,
year = {2024},
author = {Jiang, GC and Yang, CH and Wakabayashi, K and Chan, TY},
title = {An Integrated Taxonomy Approach Identified the Final Stage of Giant Phyllosoma of Parribacus antarcticus (Lund, 1793) (Crustacea: Decapoda: Scyllaridae) from Taiwan Waters.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e56},
doi = {10.6620/ZS.2024.63-56},
pmid = {40933665},
issn = {1810-522X},
abstract = {A bizarre marine planktonic organism giant phyllosoma with a body length of 79 mm was collected off Taiwanese waters for the first time. The specimen is positively identified as Parribacus antarcticus (Lund, 1793) by DNA barcoding, representing the largest and the first final stage giant phyllosoma with identification confirmed. The characteristics of the phyllosoma from Taiwan is described and illustrated in detail. As morphometric ratios previously proposed for identifying phyllosomae of Parribacus failed to assign correctly the species of the Taiwanese specimen, there is still no reliable morphological character for separating these giant phyllosomae. A key to the different phyllosoma stages of P. antarcticus is provided.},
}

@article {pmid40933664,
year = {2024},
author = {Fuke, Y},
title = {Commentary: Integrative Taxonomy Reveals Freshwater Shrimp Diversity (Decapoda: Atyidae: Neocaridina) from Kyushu and Southern Honshu of Japan, with a Discussion on Introduced Species.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e53},
doi = {10.6620/ZS.2024.63-53.},
pmid = {40933664},
issn = {1810-522X},
abstract = {Shih et al. (2024) reported on the detection of Neocaridina species in Japan and their morphological characteristics in Zoological Studies. Eleven taxa were identified based on mitochondrial DNA (mtDNA) analysis and morphological examination. Among these, they identified two taxa that formed sister groups: N. denticulata and N. davidi, which are primarily found in Japan and China. In this commentary, I argue that both species are actually N. davidi. This conclusion was previously drawn by Onuki and Fuke (2022) based on their examination of genome-wide SNPs, mtDNA, and morphological data. The doubts raised about this identification represent a serious issue in terms of conservation, as N. denticulata is a native species, whereas N. davidi is considered an invasive alien species in Japan. Two likely reasons for this misidentification are the oversight of previous studies and the inability to account for the effects of interspecific and intraspecific hybridization. Inaccurate or unsubstantiated identifications pose significant challenges to taxonomy and conservation, underscoring the need for research grounded in reliable methods and well-characterized specimens.},
}

@article {pmid40932095,
year = {2025},
author = {Del Sambro, L and Ali, A and Normanno, G and Capozzi, L and Castellana, S and Di Taranto, P and Petruzzi, F and Belluscio, D and Parisi, A and Bianco, A},
title = {A retail market survey on fish fraud from Southern Italy using DNA barcoding.},
journal = {Italian journal of food safety},
volume = {},
number = {},
pages = {},
doi = {10.4081/ijfs.2025.13376},
pmid = {40932095},
issn = {2239-7132},
abstract = {Consumption of seafood, which includes both wild and aquaculture products, has increased several-fold during the last 50 years. Species substitution, in which low-value fish are replaced with high-value fish, is one of the prominent phenomena happening in the international seafood trade and the leading cause of fraud in the fishery sector, leading to both economic and health concerns. In this study, DNA barcoding was employed to identify 78 fishery product samples collected from markets and supermarkets located in the Apulia region (Southern Italy) at the genus or species level. Non-compliance between the species detected and the species declared in the label was detected in 5 (6.41%) samples. This study highlights the need for further investigations regarding the traceability and assessment of food product authentication. Indeed, accurate taxonomic assignment and a robust traceability system are essential tools for tackling food adulteration problems, providing transparency, and protecting food safety.},
}

@article {pmid40931279,
year = {2025},
author = {Sarmento, FRP and Duarte, T and Teixeira, ACP and Salles, FF},
title = {Decoding Tupiperla illiesi Froehlich 1998 (Plecoptera: Gripopterygidae): Insights into Morphological Variation and Molecular Species Delimitation.},
journal = {Neotropical entomology},
volume = {54},
number = {1},
pages = {96},
pmid = {40931279},
issn = {1678-8052},
support = {309666/2019-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ 05461-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-01591-23//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; RESOL-2022-788-APN-DIR#CONICET//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; },
abstract = {This study addresses historical uncertainties regarding morphological variation in the paraprocts of Tupiperla illiesi, a stonefly with a complex taxonomic history. We tested whether these variations represent phenotypic plasticity or distinct species using integrative taxonomy. Adult gripopterygids were collected from Estação Biológica de Boracéia utilizing Malaise and light traps. The morphology of the specimens was analyzed in accordance with existing literature, and selected individuals underwent DNA extraction, amplification, and sequencing of the cytochrome c oxidase subunit I (COI) barcode region. Molecular distances were estimated using the Kimura 2-parameter model, and clustering was determined using Neighbor-Joining and Bayesian methods. Species delimitation was further refined using the SPdel pipeline. The combined analysis of COI sequence and morphological differences in the paraprocts led to the identification of distinct morphotypes within T. illiesi, resulting in the description of a new species, Tupiperla tucum sp. nov.},
}

@article {pmid40931062,
year = {2025},
author = {Gabbutt, C and Duran-Ferrer, M and Grant, HE and Mallo, D and Nadeu, F and Househam, J and Villamor, N and Müller, M and Heath, S and Raineri, E and Krali, O and Nordlund, J and Zenz, T and Gut, IG and Campo, E and Lopez-Guillermo, A and Fitzgibbon, J and Barnes, CP and Shibata, D and Martin-Subero, JI and Graham, TA},
title = {Fluctuating DNA methylation tracks cancer evolution at clinical scale.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40931062},
issn = {1476-4687},
abstract = {Cancer development and response to treatment are evolutionary processes[1,2], but characterizing evolutionary dynamics at a clinically meaningful scale has remained challenging[3]. Here we develop a new methodology called EVOFLUx, based on natural DNA methylation barcodes fluctuating over time[4], that quantitatively infers evolutionary dynamics using only a bulk tumour methylation profile as input. We apply EVOFLUx to 1,976 well-characterized lymphoid cancer samples spanning a broad spectrum of diseases and show that initial tumour growth rate, malignancy age and epimutation rates vary by orders of magnitude across disease types. We measure that subclonal selection occurs only infrequently within bulk samples and detect occasional examples of multiple independent primary tumours. Clinically, we observe faster initial tumour growth in more aggressive disease subtypes, and that evolutionary histories are strong independent prognostic factors in two series of chronic lymphocytic leukaemia. Using EVOFLUx for phylogenetic analyses of aggressive Richter-transformed chronic lymphocytic leukaemia samples detected that the seed of the transformed clone existed decades before presentation. Orthogonal verification of EVOFLUx inferences is provided using additional genetic data, including long-read nanopore sequencing, and clinical variables. Collectively, we show how widely available, low-cost bulk DNA methylation data precisely measure cancer evolutionary dynamics, and provides new insights into cancer biology and clinical behaviour.},
}

@article {pmid40930527,
year = {2025},
author = {van der Toorn, W and Naarmann-de Vries, IS and Liu-Wei, W and Dieterich, C and von Kleist, M},
title = {WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing.},
journal = {Nucleic acids research},
volume = {53},
number = {17},
pages = {},
doi = {10.1093/nar/gkaf873},
pmid = {40930527},
issn = {1362-4962},
support = {//European Union's Horizon 2020/ ; 955974//MarieSklowska-Curie Actions Innovative Training Networks/ ; 01KI2016//German Ministry for Science and Education/ ; 390685689//Deutsche Forschungsgemeinschaft/ ; 439669440 TRR319 RMaP TP B01//German RMaP consortium/ ; //Robert Koch Institute/ ; },
mesh = {*RNA, Transfer/genetics/chemistry ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopores ; *Software ; },
abstract = {Transfer RNA (tRNA) plays an essential role in protein translation, and tRNA modifications are important to their function. Recently, nanopore direct RNA sequencing (dRNA-seq) has shown promising results in the detection of complex tRNA modifications. However, its wider adoption in the tRNA field has been limited by a lack of (de)multiplexing solutions. Here, we present WarpDemuX-tRNA: an extension to the WarpDemuX method specifically optimized for multiplexed nanopore tRNA sequencing. Using consensus-based signal analysis using (soft) dynamic time warping and barycenter averaging, our approach improves barcode feature generation and achieves more robust barcode identification. WarpDemuX-tRNA outperforms the original method and achieves 99% precision and 95% recovery for four barcodes, while reducing computational complexity and runtime to 6 min per one million reads. WarpDemuX-tRNA is an open-source and free-to-use solution to high-throughput nanopore tRNA sequencing, facilitating more accessible, cost-effective, and high-throughput studies of tRNA modifications and their regulatory mechanisms.},
}

*RNA, Transfer/genetics/chemistry
*Nanopore Sequencing/methods
*Sequence Analysis, RNA/methods
High-Throughput Nucleotide Sequencing/methods
Nanopores
*Software

@article {pmid40927319,
year = {2025},
author = {Sadyrova, M and Martin, E and Ramsey, P and Bullington, L},
title = {Mock Plant Communities and a Large Mammal Case Study Reveal ITS2 Primer Bias Against Graminoids.},
journal = {Ecology and evolution},
volume = {15},
number = {9},
pages = {e72102},
pmid = {40927319},
issn = {2045-7758},
abstract = {DNA fecal metabarcoding has revolutionized the field of herbivore diet analyses, offering deeper insight into plant-herbivore interactions and more reliable ecological inferences. However, due to PCR amplification bias, primer selection has a major impact on the validity of these inferences and insights. Using two pooling approaches on four mock communities and a case study examining diets of four large mammalian herbivores (LMH), we evaluated the efficacy of two primer pairs targeting the internal transcribed spacer 2 (ITS2) region: the widely used ITS-S2F/ITS4 pair and the UniPlant F/R pair, designed specifically for DNA metabarcoding. Both primer pairs consistently underrepresented graminoids, where > 40% of graminoid species did not amplify in vitro. However, the UniPlant F/R primer pair more accurately amplified mock plant communities, whereas the ITS-S2F/ITS4 pair underestimated graminoid relative abundance by at least twofold more than UniPlant F/R primers. Furthermore, in the LMH case study, UniPlant F/R primers identified graminoids as the dominant plant group for at least one LMH, indicating diet niche partitioning, while ITS-S2F/ITS4 primers largely failed to amplify graminoid DNA, potentially overestimating LMH diet overlap. Our findings underscore the importance of incorporating mock community analyses into DNA metabarcoding protocols to identify and mitigate primer bias, thereby enhancing the accuracy of ecological conclusions and supporting more effective conservation and management decisions.},
}

@article {pmid40926684,
year = {2025},
author = {Tian, S and Li, Y and Yao, J and Huan, C and Zhang, W and Li, S and Zhang, Z and Guo, Z and Yang, Q and Li, C and Li, C and Li, J and Zhou, L},
title = {A barcode-specific immobilization interface for microfluidics-assisted uniform spatially barcoded microarray analysis.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5an00534e},
pmid = {40926684},
issn = {1364-5528},
abstract = {Microfluidics-assisted spatially barcoded microarray technology offers a high-throughput, low-cost approach towards spatial transcriptomic profiling. A uniform barcoded microarray is crucial for spatially unbiased mRNA analysis. However, non-specific adsorption of barcoding reagents in microchannels occurs during liquid transport, causing non-uniform barcoding in the chip's functional regions. The uneven microarray further leads to biased transcriptome capture. Herein, we develop a barcode-specific immobilization (BarSI) interface with both anti-adsorption properties and biological activity for the development of uniform spatially barcoded microarray chips. We immobilize DNA probes in straight and serpentine microchannels with coefficients of variation (CV) of 2.3% and 3.2%. Based on the orthogonal barcoding system, we developed spatially barcoded microarray chips with an overall fluorescence intensity CV of 8.47 ± 1.26%, compared with the CV of 20.91 ± 2.84% of microarrays developed on conventional amino glass slides. Using the uniform spatially barcoded microarray chip, we achieved spatially unbiased detection of mouse liver mRNA with an absolute value of Moran's I below 0.05. We present an economical and accessible method for manufacturing uniform spatially barcoded microarray chips, introducing a novel strategy for unbiased transcriptome analysis.},
}

@article {pmid40926494,
year = {2025},
author = {Lee, M and Kanturski, M and Lee, S},
title = {Unveiling host plant associations and cryptic genetic diversity of Miyalachnus sorini (Aphididae: Lachninae) on cherry trees in South Korea.},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S0007485325100400},
pmid = {40926494},
issn = {1475-2670},
abstract = {This study presents the first record of Miyalachnus sorini Kanturski & Lee, 2024 (Aphididae: Lachninae) in South Korea, thereby extending its known distribution beyond Japan and identifying a new host plant, Prunus sargentii (Rosaceae). We describe diagnostic morphological traits across multiple life stages and compare them with those of Japanese populations. Comparative analyses with Japanese populations demonstrated consistent morphological differentiation, notably elevated ratios of the ultimate rostral segment to antennal segments across multiple morphs in the Korean population, indicating potential ecological adaptation. DNA barcoding using the mitochondrial cytochrome c oxidase I gene revealed low intraspecific divergence (average 0.2%) and interspecific divergence (average 10.5%) between Miyalachnus sp. and M. sorini. Haplotype analysis was performed to investigate the relationship between host plants and cryptic genetic diversity. These findings enhance our understanding of the morphological and genetic diversity of M. sorini and underscore the importance of monitoring its spread for informed pest management strategies.},
}

@article {pmid40925998,
year = {2025},
author = {Qi, Z and Xue, S and Chen, J and Zhao, W and Johnson, K and Wen, X and Charles Richard, JL and Lin, P and Zhong, S},
title = {Genome-wide mapping of RNA-protein associations through sequencing.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40925998},
issn = {1546-1696},
support = {R01GM138852//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UH3CA256960//Center for Strategic Scientific Initiatives, National Cancer Institute (NCI Center for Strategic Scientific Initiatives)/ ; R01HD107206//U.S. Department of Health & Human Services | NIH | NICHD | National Center for Medical Rehabilitation Research (NCMRR)/ ; DP1DK126138//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
abstract = {RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing. We apply PRIM-seq to two human cell lines and construct a human RNA-protein association network (HuRPA), encompassing >350,000 associations involving ~7,000 RNAs and ~11,000 proteins, including 2,610 proteins that each interact with at least 10 distinct RNAs. We experimentally validate the tumorigenesis-associated lincRNA LINC00339, the RNA with the highest number of protein associations in HuRPA, as a protein-associated RNA. We further validate the RNA-associating abilities of chromatin-conformation regulators SMC1A, SMC3 and RAD21, as well as the metabolic enzyme PHGDH. PRIM-seq enables systematic discovery and prioritization of RNA-binding proteins and their targets without gene- or protein-specific reagents.},
}

@article {pmid40923893,
year = {2025},
author = {Reyes Gamas, K and Seamons, TR and Dysart, MJ and Fang, L and Chappell, J and Stadler, LB and Silberg, JJ},
title = {Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00313},
pmid = {40923893},
issn = {2161-5063},
abstract = {Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNAs (rRNAs) and perform a trans-splicing reaction that adds a barcode to the rRNAs. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida, the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNAs that store information within user-defined sets of microbes in environmental communities for gene transfer studies.},
}