@article {pmid41931230,
year = {2026},
author = {Sweileh, MW},
title = {Global scientific growth and thematic development of spatial transcriptomics in oncology research.},
journal = {Discover oncology},
volume = {17},
number = {1},
pages = {},
pmid = {41931230},
issn = {2730-6011},
abstract = {BACKGROUND: Spatial transcriptomics (ST) is a rapidly transforming cancer research by enabling spatially resolved gene expression profiling within intact tissues. However, the growth, structure, and thematic evolution of research on ST research in oncology have not been comprehensively mapped.

OBJECTIVE: This study aims to map and analyze global research trends of ST in oncology, identifying key contributors, collaborations, thematic focus areas, and technological evolutions in the field.

METHOD: A bibliometric analysis was conducted using data extracted from Scopus database. VOSviewer tool was used to construct knowledge maps reflecting thematic clusters and intellectual clusters in ST-oncology research. Quantitative indicators were evaluated to identify historical evolution, key players, and research hotspots.

RESULTS: The study identified 987 publications on ST in oncology. The annual growth of publications showed a significant surge over the past five years. China and the United States emerged as leading contributors with high levels of intra- and inter-national collaboration. Key journals included Nature Communications and Frontiers in Immunology. Academic and research institutions based in China dominated the field. Co-occurrence mapping identified the following high-frequency keywords: “tumor microenvironment”, “single-cell RNA sequencing”, and spatial resolution suggesting strong emphasis on integrating spatial biology with precision oncology. Bibliographic coupling illustrated a clustering around barcoding technologies and immune-oncology interfaces. The overlay visualization suggested a shift toward high resolution imaging, multi-omics integration, and AI-supported analytics.

CONCLUSION: ST-oncology research is expanding rapidly with clear shifts toward higher resolution and integrative analytical frameworks. These findings provide a structured overview of the field’s knowledge base and can inform researchers, funders, and stakeholders about leading about leading contributors and emerging directions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12672-026-04937-x.},
}

@article {pmid42124710,
year = {2026},
author = {Fazzari, E and Azizad, DJ and Li, MX and Ge, W and Baisiwala, S and Cadet, D and Nano, PR and Kan, RL and Perryman, T and Tum, HA and Tse, C and Wick, B and Arguelles, CV and Patel, KS and Liau, LM and Prins, RM and Nathanson, DA and Bhaduri, A},
title = {Predictable clonal hierarchies from restricted progenitors provide a framework for cell type-specific therapies in glioblastoma.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.21.707071},
pmid = {42124710},
issn = {2692-8205},
abstract = {Extensive molecular profiling has revealed profound heterogeneity in glioblastoma (GBM), yet how cellular lineages organize over time to govern tumor propagation and therapeutic response remains poorly understood. Existing single-cell approaches define transcriptional states but provide limited insight into how clonal dynamics shape functional tumor behavior. Here, we integrate high-complexity combinatorial DNA barcoding with single-cell transcriptomics in direct-from-patient IDH1-wild-type GBM, enabling lineage-resolved mapping of progenitor organization in a human microenvironmental context. Across 235,155 malignant cells from nine tumors, clonal relationships form reproducible lineage tracks in which distinct progenitor populations give rise to specific differentiated cell types, revealing that tumor growth is sustained by multiple non-redundant progenitors rather than a single dominant population. These progenitors exhibit distinct propensities for self-renewal, fate restriction, and cross-compartment interactions, collectively accounting for the full spectrum of tumor states. Using this lineage-resolved framework, we identify complementary drug targets in distinct progenitor compartments and demonstrate that hierarchy-informed combination therapies disrupt progenitor-progenitor interactions and reshape lineage output. These findings move beyond descriptive heterogeneity to define functional logic underlying GBM propagation and establish a generalizable framework for rational, cell type-specific combinatorial therapies.},
}

@article {pmid42124945,
year = {2026},
author = {Zhao, W and Jiang, Q and Zhou, X and Ye, Z and Bao, W and Wu, J and Zhang, Y},
title = {Optimization of a magnetic bead-based DNA extraction method combined with 12S rRNA barcoding for species traceability in fish oil products.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100408},
pmid = {42124945},
issn = {2666-5662},
abstract = {Fish oil is a widely consumed nutritional supplement rich in ω-3 polyunsaturated fatty acids (PUFAs) and of high economic value, but it is susceptible to economically motivated adulteration, including the incorporation of lower-value fish species. Reliable methods for species authentication are therefore needed. In this study, we established and systematically optimized a magnetic bead-based DNA extraction protocol tailored for fish oil matrices. The method incorporates an exogenous DNA fragment as an internal control to quantitatively assess extraction efficiency, and key parameters-including bead surface chemistry, particle size and dosage, binding buffer composition, wash conditions, and elution temperature and duration-were evaluated and optimized. The final optimized protocol (500 nm hydroxyl-functionalized beads, 3 mol/L guanidine thiocyanate binding system, 70% ethanol wash, and 56 °C elution) achieved significantly higher DNA yield and purity than multiple commercial extraction kits. When coupled with 12S rRNA metabarcoding, the method enabled the recovery of amplifiable DNA from all ten commercial fish oil products tested and allowed species-level identification. The results revealed discrepancies between labeled claims and actual biological composition in several products, including indications of substitution of high-value deep-sea fish with lower-value species. Taken together, this workflow provides a practical technical basis for species traceability and authenticity evaluation of fish oil, and it may be further applicable to quality monitoring in other high-lipid food matrices.},
}

@article {pmid42125613,
year = {2026},
author = {Wariss, HM and Yang, L and Gu, J and Liu, D and Li, W},
title = {Phylogenomic and metabolomic approaches to provide insight for species delimitation of cultivated Ferula species in Xinjiang, China.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1754844},
pmid = {42125613},
issn = {1664-462X},
abstract = {The genus Ferula is an important medicinal group within the Apiaceae family, valued globally for its health and culinary uses. Recently, it has gained significant attention because of its cultivation and use to meet growing demands for food and medicine. However, in the Xinjiang production region, farmers often cultivate multiple Ferula species together. In the market, leaves from different species are frequently bundled and sold, leading to inconsistent product quality. This issue greatly reduces the economic value of Ferula as a food resource and affects the efficacy and safety of its clinical applications. Correctly identifying species is essential for the sustainable use and conservation of these plants. Traditional methods mainly rely on floral and fruit traits, but the monocarpic or polycarpic nature of these plants makes species identification difficult, especially since flowering or fruiting specimens are hard to obtain in cultivated conditions. In this study, leaf samples from 30 Ferula specimens collected from ten cultivated locations in Xinjiang were analyzed using phylogenetic methods and ultraperformance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) to provide insight for species identification and discrimination. Phylogenomic analysis based on the complete plastome was used to clarify relationships among species. The plastome super-barcoding results showed that cultivated Ferula species clustered into three distinct clades: F. sinkiangensis, F. teterrima, and F. fukanensis. Untargeted metabolomic profiling detected 7,169 metabolites, and multivariate analyses (PCA, PLS-DA and HCA) revealed clear chemotaxonomic separation among the three species, with clustering patterns consistent with the phylogenetic tree. Our findings demonstrate that the integration of plastome super-barcoding with metabolomic fingerprinting offers a robust strategy to species discrimination in cultivated Ferula. This combined approach provides complementary chemotaxonomic evidence for differentiating species, with direct implications for ensuring appropriate use in distinct culinary, medicinal, and pharmaceutical applications.},
}

@article {pmid42125748,
year = {2026},
author = {Liu, A and Yang, X and Lu, J and Qu, K and Chen, J and Su, X and Ren, G and Hu, H},
title = {Genomic Insights Into Species Divergence and Adaptive Evolution in the Grass Genus Orinus on the Qinghai-Tibet Plateau.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73641},
pmid = {42125748},
issn = {2045-7758},
abstract = {The grass genus Orinus, endemic to the Qinghai-Tibet Plateau (QTP), has long been taxonomically controversial. Recent integrative studies combining morphological and DNA barcoding proposed revising the genus from six to three species; however, this hypothesis lacks validation from genome-wide data, and the evolutionary history of the putative species remains poorly resolved. Here, we conducted whole-genome resequencing of 126 individuals from 40 populations representing three putative species of Orinus-Orinus thoroldii, Orinus kokonorica, and Orinus intermedius-and performed population genomic and demographic analyzes. Genome-wide evidence robustly supports the three-species delimitation and reveals pronounced genetic differentiation among lineages. We further detected both historical and recent hybridization between O. kokonorica and O. intermedius , indicating incomplete reproductive isolation. Demographic inference suggests that divergence among lineages occurred during Quaternary climatic oscillations, when repeated climate fluctuations, together with the complex topography of the QTP, likely promoted lineage divergence while allowing persistent and asymmetric gene flow, particularly during early stages of divergence. Across species pairs, we consistently identified genomic islands of divergence characterized by elevated absolute nucleotide divergence (D xy). Genes located within these regions show signatures of positive selection and are enriched in functions related to environmental adaptation, suggesting a role of natural selection in maintaining species boundaries. Together, our results provide robust genomic support for the revised taxonomy of Orinus and offer new insights into how Quaternary environmental dynamics have shaped speciation and genomic divergence in a montane grass lineage.},
}

@article {pmid41776501,
year = {2026},
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 = {Molecular cancer},
volume = {25},
number = {1},
pages = {},
pmid = {41776501},
issn = {1476-4598},
support = {P01 CA114046-15, R01 CA238237-05, R01 CA240362-05, R01 CA241148-05, P50 CA261608-03, U54 CA224070-05//NIH/NCI grants/ ; R-202206-00540//Sheldon G. Adelson Medical Research Grant/ ; },
abstract = {BACKGROUND: Most advanced melanomas initially respond to targeted therapy but eventually relapse. Increasing evidence suggests that drug-tolerant persister cells can adopt a reversible drug-refractory state and represent a key driver of therapeutic resistance.

METHODS: We developed MeRLin, a lineage tracing platform that integrates cellular barcoding, single-cell transcriptomic profiling, RNA fluorescence in situ hybridization, and computational analyses to track clonal and transcriptional dynamics in a patient-derived melanoma model during prolonged targeted therapy. Longitudinal analyses enabled the characterization of clonal fates, transcriptional states, and spatial organization of persister populations.

RESULTS: Clonal dynamics showed that persister subpopulations initially responded to therapy, persisted through minimal residual disease, and expanded during tumor recurrence. Four persister-associated transcriptional states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs were associated with persister populations arising from minor pre-treatment subpopulations under sustained drug pressure. Spatial transcriptomic analyses revealed structured spatial organization of these programs and suggested coordinated autocrine and paracrine interactions among persister states. Targeted barcode RNA fluorescence in situ hybridization enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone marked by SLC2A1 expression.

CONCLUSIONS: Together, MeRLin provides a robust framework for dissecting cancer heterogeneity and characterizing persister subpopulations. Our findings demonstrate that melanoma recurrence is associated with diverse, spatially organized persister states linked to adaptive transcriptional programs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12943-026-02622-9.},
}

@article {pmid42111707,
year = {2026},
author = {Gao, F and Liu, X and Sun, F and Xiao, Y and Xiao, G and Qu, Z},
title = {An Advanced Single-Cell RNA Sequencing (scRNA-seq) Protocol Utilizing Custom-Designed Multiplexing.},
journal = {Bio-protocol},
volume = {16},
number = {9},
pages = {e5678},
pmid = {42111707},
issn = {2331-8325},
abstract = {While cell hashing enhances single-cell RNA sequencing (scRNA-seq) efficiency and minimizes batch effects, commercial mouse hashtags often fail in FVB/N and several other strains due to antibody-epitope incompatibility. We describe a robust alternative utilizing biotinylated antibody cocktails and streptavidin-conjugated oligos to enable reliable sample multiplexing. This approach was validated in FVB/N lung tissues, yielding high-quality single-cell libraries. Our protocol offers a practical solution for researchers requiring strain-specific or custom-designed multiplexing strategies for single-cell transcriptomics. Key features • Strain-specific compatibility: Resolves the known H-2[q] haplotype mismatch in FVB/N mice that fails standard commercial MHC-I hashtag antibodies in cell hashing. • Multi-omic 5' workflow integration: Enables simultaneous sample multiplexing with 10× Genomics 5 chemistry, facilitating joint gene expression and V(D)J repertoire (TCR/BCR) profiling. • Enhanced non-immune cell labeling: Incorporates anti-CD326 (Ep-CAM) to ensure robust hashing of epithelial and tumor cells that may exhibit MHC-I downregulation or lack CD45. • Customizable biotin-streptavidin framework: Provides a modular system using biotinylated antibody cocktails and streptavidin-barcodes, adaptable for any mouse strain or tissue-specific cell markers.},
}

@article {pmid42112774,
year = {2026},
author = {Jourdain, L and Rossi, P and Charpagne, A and Chevalier, E and Praz, V and Marquis, J and Weber, J and Gu, W},
title = {A Scalable and Cost-Effective In-Line Barcoding Strategy for Standardized 16S rRNA Gene Amplicon Sequencing: Performance Evaluation and Bias Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70138},
pmid = {42112774},
issn = {1755-0998},
support = {200021_219222//Swiss National Science Fundation (SNF)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic/methods/economics ; *Bacteria/genetics/classification ; *Archaea/genetics/classification ; DNA Primers/genetics ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA/methods ; },
abstract = {In-line barcoding offers a streamlined and scalable alternative to two-step PCR library preparation for 16S rRNA gene amplicon sequencing, enabling cost-effective, high-throughput profiling of microbial communities. Here, we tested 136 and 156 in-line barcoded primer pairs for bacterial and archaeal communities for their performance across environmental samples and a mock standard community. The primers were designed by combining widely used universal 16S rRNA gene primers with existing barcode sets from Illumina kits. The designed primer pairs produced efficient and consistent amplification with minimal dropout and no systematic taxonomic bias. Through clustering and performance-based filtering, we selected final sets of 96 pairs for both bacterial and archaeal communities that work efficiently and well together for direct further use. This in-line tagging strategy is easy to adopt with fewer processing steps and PCR-associated artefacts, allows straightforward sample tracking, and supports reliable large-scale microbiome studies. We also present a framework for evaluating barcode- or primer-induced biases. More broadly, the proposed in-line barcoding strategy can be adapted to any amplicon-sequencing application, as well as targeted sequencing, highlighting its relevance beyond 16S rRNA gene surveys. All validation datasets, open-source processing scripts, and barcode design resources are provided to promote reproducibility and community-wide adoption.},
}

*RNA, Ribosomal, 16S/genetics
*DNA Barcoding, Taxonomic/methods/economics
*Bacteria/genetics/classification
*Archaea/genetics/classification
DNA Primers/genetics
Cost-Benefit Analysis
High-Throughput Nucleotide Sequencing/methods
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA/methods

@article {pmid42113811,
year = {2026},
author = {Mussa, AJ and Ruboha, JO and Kabota, SA and Martin, MJ and Mwatawala, MW},
title = {Elevation and land use shape soil entomopathogenic fungal communities in the Uluguru mountains, Tanzania: Insights from metagenomic and culture-based approaches.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0348781},
pmid = {42113811},
issn = {1932-6203},
mesh = {Tanzania ; *Soil Microbiology ; Animals ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Biodiversity ; Soil/chemistry ; Metagenomics/methods ; *Mycobiome ; },
abstract = {BACKGROUND: Soil-borne entomopathogenic fungi (EPFs) support ecological regulation of pests, yet their distribution across tropical mountain agroecosystems is poorly characterized. The study conducted between April and December 2024, evaluated diversity and distribution of soil EPF along the Uluguru Mountains slopes in Morogoro, Tanzania.

METHODS: Twenty-four soil samples were collected from cultivated and fallow soils at low (518 m), medium (1100 m), and high (1700 m) elevations on the Uluguru slopes (Morogoro, Tanzania). Amplicon sequencing of the ITS region profiled fungal communities, and selective isolation with ITS barcoding confirmed cultivable taxa. Diversity indices, Bray-Curtis dissimilarity, Principal Coordinate Analysis (PCoA), and PERMANOVA evaluated patterns across elevation and land use.

RESULTS: Fourteen EPF species in 12 genera were detected, dominated by Ophiocordycipitaceae (56.1%) and Clavicipitaceae (37.8%). Purpureocillium lilacinum, Metarhizium anisopliae, Clonostachys rosea, and Pochonia chlamydosporia were widespread. Cultivated soils at medium- and high elevations showed greater richness and diversity (1.37 and 1.57) than fallows (0.64 and 0.48) respectively, while high-altitude fallows were strongly dominated by Metapochonia suchlasporia. Community composition clustered by land use, with elevation as a secondary driver (PERMANOVA p = 0.06). Selected P. lilacinum and C. rosea species caused 10-50% mortality of Spodoptera frugiperda larvae in preliminary laboratory assays.

CONCLUSIONS: Elevation and land use jointly structure EPF communities in the Uluguru Mountains. Some taxa showed preliminary pathogenicity in laboratory assays, indicating potential for future evaluation as biological control agents in smallholder farming systems. Public deposition of sequencing reads will facilitate reuse and benchmarking.},
}

Tanzania
*Soil Microbiology
Animals
*Fungi/genetics/classification/isolation & purification
*Altitude
Biodiversity
Soil/chemistry
Metagenomics/methods
*Mycobiome

@article {pmid42116196,
year = {2026},
author = {Abreu, FVS and Mosmann, LB and Martins, CB and da Silva Xavier, A and da Rocha Corpas Maciel, IM and Nascimento-Pereira, AC and Ribeiro, PS and Alencar, J and Tubaki, RM and Motta, MA and Lourenço-de-Oliveira, R and Pavan, MG},
title = {Mitochondrial introgression hampers the DNA barcoding of cryptic yellow fever vectors Haemagogus capricornii Lutz and Hg. janthinomys in the Atlantic Forest, Brazil.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07343-y},
pmid = {42116196},
issn = {1756-3305},
support = {309577/2013-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {BACKGROUND: Yellow fever is a major public health concern in Brazil, transmitted in sylvatic cycles by Haemagogus and Sabethes mosquitoes. Among them, Haemagogus janthinomys and Hg. capricornii occur in sympatry in the Atlantic Forest and females are morphologically indistinguishable, complicating vector identification during outbreaks. Here, we aimed to investigate their taxonomic status and evolutionary history using an integrative approach including morphological and phylogenetic analyses.

METHODS: Mosquitoes were collected in 17 municipalities across nine Brazilian states, including simultaneous captures of both species in sympatric areas. Males were identified by genitalia morphology and molecular analyses were performed using three mitochondrial and two nuclear genes. Diversity analyses and neutrality tests were performed, and phylogenies were reconstructed with Maximum Likelihood and Bayesian inferences. Divergence times were estimated using strict molecular clock, and population history was assessed through mismatch distribution analysis and Bayesian Skyline Plots.

RESULTS: A total of 79 specimens were morphologically identified, with Hg. janthinomys showing a broader geographic and altitudinal distribution than Hg. capricornii, which was usually restricted to higher elevations. Phylogenetic analyses based on mitochondrial markers revealed two clades, but did not recover clear reciprocal monophyly, thus evidencing that these markers alone cannot separate the two species. The inclusion of nuclear markers evidenced introgression events of Hg. janthinomys mitochondria in Hg. capricornii specimens in the Paraíba River Valley and Espírito Santo State, and successive breeding of Hg. capricornii on few samples morphologically identified as Hg. janthinomys in São Paulo State. Molecular clock and population history analyses evidenced that these species have probably speciated in peripatry or parapatry during the Pleistocene era at approximately 1.2 million years ago, and a recent sudden expansion of Hg. capricornii in the last 10 thousand years ago has tripled its population and likely led to a secondary contact between the two species.

CONCLUSIONS: Haemagogus janthinomys and Hg. capricornii are valid and closely related species with evolutionary histories shaped by divergence during the Pleistocene era and subsequent introgression events. The use of cytochrome c oxidase subunit I gene (COI) DNA barcoding alone could not reliably distinguish them, and integrating morphology with multiple molecular markers is essential for accurate identification. Future work is needed for a finer resolution of hybridization patterns to help clarify if the observed mito-nuclear discordance reflects historical introgression or active genetic exchange between species.},
}

@article {pmid42119158,
year = {2026},
author = {Liu, DD and Qian, C and Loh, WT and Xu, C and Ng, J and Cheow, LF},
title = {CUBED: Universal combinatorial barcoding platform for highly multiplexed digital PCR.},
journal = {Biosensors & bioelectronics},
volume = {308},
number = {},
pages = {118793},
doi = {10.1016/j.bios.2026.118793},
pmid = {42119158},
issn = {1873-4235},
abstract = {Highly multiplexed molecular assays are essential for applications ranging from pathogen detection to genetic and copy number analysis. Here, we introduce CUBED (Combinatorial Universal Barcode End-point Digital PCR), a platform that enables simultaneous detection and quantification of numerous nucleic acid targets in a single reaction using standard endpoint digital PCR instruments. CUBED combines combinatorial color barcoding with multi-amplitude probe labeling to expand multiplexing capacity beyond the limits imposed by fluorescence channel count. An integrated error-detection scheme minimizes misclassification from signal dropout, ensuring robust decoding of complex barcodes. We demonstrate accurate quantitative detection and discrimination of 26 ternary barcodes using only three fluorescence channels, and separately resolve 20 binary barcodes on a six-channel system. We further apply CUBED to pooled SARS-CoV-2 RNA detection across 20 uniquely barcoded samples, confirming its quantitative accuracy and scalability. This framework provides a high-throughput, error-tolerant solution for multiplexed nucleic acid detection in research and clinical diagnostics.},
}

@article {pmid42121708,
year = {2026},
author = {Huang, M and Li, S and Yu, S},
title = {One New Species and Four New Records of the Genus Amaloxestis Gozmány (Lepidoptera: Lecithoceridae) from China: Integrative Taxonomic Evidence.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091288},
pmid = {42121708},
issn = {2076-2615},
support = {ZR2022QD130//Natural Science Foundation of Shandong Province, China/ ; },
abstract = {The family Lecithoceridae represents one of the most diverse yet understudied groups within Lepidoptera, with numerous unresolved taxonomic problems that require urgent attention. This study reports one new species and four newly recorded species of the genus Amaloxestis Gozmány, 1973 from China. Amaloxestis similinepalensis Yu is described as new to science, while A. astringens Gozmány, 1973, A. callitricha (Meyrick, 1910), A. chiloptila (Meyrick, 1921) and A. nepalensis Gozmány, 1973 are newly recorded from China. All treated species were identified based on morphological characters and molecular phylogenetic evidence. Additionally, the females of A. chiloptila and A. nepalensis are described for the first time.},
}

@article {pmid42121788,
year = {2026},
author = {Gao, F and Zuo, Z and Wu, Q and Xiao, H and Peng, Z and Zou, L and Jiang, G and Tian, X and Feng, Z and Xie, X and Tian, L},
title = {Analysis of Ochetobibus elongatus (Kner) Dietary Habits Based on Digestive System Morphology, Histology, and Intestinal Content Sequencing Technology.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {9},
pages = {},
doi = {10.3390/ani16091369},
pmid = {42121788},
issn = {2076-2615},
support = {HARS-07//Hunan Provincial Modern Agriculture (Aquaculture) Industry Technology System Project/ ; },
abstract = {Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.},
}

@article {pmid42122866,
year = {2026},
author = {Samartza, I and Kriemadi, E and Pappas, D and Karagianni, AG and Kofinas, I and Matsi, T and Adamakis, ID and Tsoktouridis, G and Bareka, P and Krigas, N},
title = {Taxonomic Reassessment and Rediscovery of Tulipa scardica Bornm. in Greece: Insights from Integrated Analyses Compared to T. undulatifolia Boiss.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/plants15091374},
pmid = {42122866},
issn = {2223-7747},
abstract = {Tulipa scardica (Balkan endemic) was last recorded in Greece in 1896, possibly attributed to longstanding taxonomic ambiguity, as it has frequently been considered as conspecific with T. gesneriana or T. undulatifolia. In the present study we aimed to investigate the historical Greek locality of T. scardica and to reassess its taxonomic status in comparison with the closely related T. undulatifolia (also native to Greece and member of T. scardica complex). Targeted field surveys were conducted to verify the presence of T. scardica in Greece. The newly identified tulip population was subjected to an integrated analytic approach, including qualitative and quantitative morphological assessment, seed micromorphology, DNA barcoding, karyological investigation, and habitat/soil properties analyses. These datasets were comparatively evaluated against four reference populations of T. undulatifolia. Molecular data did not provide consistent species-level resolution, whereas morphological and karyological evidence statistically supported their distinction. Mitotic metaphase chromosomes of T. scardica were documented herein for the first time, while first-time scanning electron microscopy (SEM) analysis revealed the presence of different types of stomatal complexes in seed coats of both taxa. In addition, soil parameters differed between the examined taxa, and those of the rediscovered population were consistent with habitat preferences of T. scardica. Although both taxa exhibited considerable variability, the combined evidence derived from the present study strongly supported the rediscovery of T. scardica in Greece after approximately 130 years, unless proven otherwise in a wider context across its Balkan range.},
}

@article {pmid42124703,
year = {2026},
author = {Gaszek, IK and Yildiz, MS and Sari, L and Ahmed, A and Toprak, E and Lin, MM},
title = {Saturation mutagenesis map of generalist versus specialist adaptations of β-lactamase to novel antibiotics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.14.682469},
pmid = {42124703},
issn = {2692-8205},
abstract = {The evolution of β-lactamase proteins is shaped by the need to maintain enzymatic activity against previously prevalent β-lactam antibiotics while expanding substrate range against new classes of antibiotics. Using saturation mutagenesis and sequence-barcoding-based quantification, we comprehensively mapped the response of the fitness landscape of TEM-1 β-lactamase, which evolved against penicillin-class antibiotics, to mutational perturbations against six diverse β-lactam antibiotics. This systematic panel of antibiotic substrates, including representatives from penicillin, cephalosporin, and monobactam classes, allowed us to classify resistance mutations into two categories. Generalist mutations conferred resistance to multiple antibiotics and were consistently restricted to three positions critical for substrate recognition and catalytic function R164, G238, and E240. These substitutions produced broad spectrum resistance through mechanisms such as expansion of the active site and improved substrate accommodation. In contrast, specialist mutations conferred resistance to only a single antibiotic and exhibited much wider positional diversity. Ceftazidime selection yielded the greatest number of distinct specialist mutations, which were frequently found in flexible or peripheral regions including the omega loop. One especially unexpected finding was the identification of the E166P variant. E166 is a catalytic residue required for deacylation during hydrolysis, and substitutions at this site are generally assumed to abolish function. However, E166P conferred a significant increase in ceftazidime resistance despite eliminating activity against penicillins. Molecular dynamics simulations and mutational analysis revealed that the E166P mutant employs an alternative catalytic mechanism, involving residue N132, rather than the canonical pathway. Together, our findings reveal, at the molecular level, how specialist mutations open up a wide range of diverse and idiosyncratic solutions at the expense of generalizability. These insights may inform strategic design of antibiotic administration protocols to systematically lower pathogenic evolvability.},
}

@article {pmid42124708,
year = {2026},
author = {Urke, A and Dolan, MJ and Silverman, J and Kim, M and Pineda, J and Garcia, S and Luu, J and Buckley, A and Kumar, V and Zhao, B and Chan, K and Nadaf, N and Balderrama, KS and Arnold, DB and Stevens, B and Deverman, BE and Macosko, EZ},
title = {Protein-guided RNA barcoding links transcriptomes to synaptic architecture.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.26.705527},
pmid = {42124708},
issn = {2692-8205},
abstract = {Mammalian brain function relies on the precise synaptic architecture of diverse cell types, yet scalable methods for linking a neuron's transcriptomic profile to its neuroanatomy remain limited. We present Synapse-seq, an in vivo strategy in which cell-identifying barcoded mRNAs are routed to subcellular compartments via targeting proteins and detected by single-cell and spatial genomics. Using AAV delivery for minimal perturbation of gene expression, we directed barcodes to presynaptic terminals (via synaptophysin) in four distinct circuits, or to postsynaptic sites (via nanobodies to endogenous PSD95) of hippocampal excitatory neurons. In the mouse primary visual cortex, presynaptic Synapse-seq recovered known long-range projections and discovered cortical layer subtypes with distinct thalamic innervation. In the anterior cortex, we elucidated simple topographic rules of corticostriatal innervation: intratelencephalic neurons followed a continuous depth-to-target gradient, while extratelencephalic neurons exhibited striatal collaterals that spatially correlated with medullary innervation. Finally, postsynaptic barcoding of excitatory neurons revealed cell type-specific variation in dendritic architectures across and within hippocampal subfields. These data establish Synapse-seq as a versatile, genomics-based approach for the integrated definition of molecular identity and synaptic organization across mammalian brains.},
}

@article {pmid42109179,
year = {2026},
author = {Untergasser, A and Fritz, MH and Benes, V and Rausch, T},
title = {GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag445},
pmid = {42109179},
issn = {1362-4962},
abstract = {Many routine genomics tasks in molecular biology still depend on heterogeneous and proprietary software tools that hinder accessibility, reproducibility, and seamless laboratory use. We present GEAR (https://www.gear-genomics.com/), a unified, web-based genomics framework that provides a collection of lightweight, interactive applications for common molecular biology and genomics analyses directly in the browser. GEAR requires no software installation, user registration, or licensing and is designed for rapid, intuitive use without prior bioinformatics expertise. The platform integrates robust, well-established backend algorithms with modern web technologies to support a diverse set of tasks, including Sanger chromatogram visualization, alignment and variant detection, primer and padlock probe design, in-silico PCR, qPCR analysis, barcode generation and inspection, sequencing quality control, DNA manipulation, and sequence alignment visualization. In summary, GEAR serves as an integrated, open, extendible, and user-friendly genomics web server that consolidates a diverse set of tools within a single coherent framework with all code free and open-source (https://github.com/gear-genomics). By emphasizing interactivity, reproducibility, and ease of use, GEAR aims to support both routine laboratory tasks and exploratory genomic analyses across a broad range of research applications.},
}

@article {pmid42111143,
year = {2026},
author = {Yan, M and Li, M and Ballarin, F and Yao, Z},
title = {Morphological and molecular data reveal a new spider species of the little-known Pholcus nagasakiensis species group (Araneae, Pholcidae) from the Ryukyu Archipelago.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e193642},
pmid = {42111143},
issn = {1314-2828},
abstract = {BACKGROUND: The Pholcus nagasakiensis species group is a relatively small group, comprising only five species. Of these, four species inhabit Kyushu Island in mainland Japan, the Ryukyu Archipelago and the Diaoyu Islands of China, while one additional species has been documented from Wuyishan Mountain in mainland China.

NEW INFORMATION: Three morphologically similar species from the Ryukyu Archipelago, belonging to the Pholcus nagasakiensis species group were identified, based on an integrative approach combining morphology and molecular species-delimitation methods. These comprise one new species, namely Pholcus yajiyagama Yan, Ballarin & Yao, sp. nov., herein described, based on both sexes and two previously described species, P. nagasakiensis Strand, 1918 and P. otomi Huber, 2011. DNA barcodes were obtained for all three species to estimate p-distances and K2P distances and confirm their identifications. New diagnoses and detailed photomicroscopy images of the two previously described species, as well as a distribution map of all the species discussed, are also provided.},
}

@article {pmid42096627,
year = {2026},
author = {Cruz-Campuzano, EA and Avila Muñoz, M and Silva-Tostado, CE and Estrada Avendaño, A and Salas-Lizana, R and Hernández-Navarro, E and Kennedy, P and Smith, ME and Miller, KO and Franck, AR and Alvarez-Manjarrez, J},
title = {Species delimitation in a cryptic Neotropical Thelephora species complex, with insights into the phylogenetic informativeness of loci.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/00275514.2026.2651040},
pmid = {42096627},
issn = {1557-2536},
abstract = {Thelephora is a genus of ectomycorrhizal fungi with a global distribution. Recent taxonomic efforts have revealed new species and species complexes, often distinguished by subtle morphological differences. Here, we describe Thelephora renispora, a new species resembling T. versatilis and T. pseudoversatilis, and support its recognition as a distinct taxon based on morphological traits, phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and D1-D2 domains of nuc 28S rDNA (28S), and statistical comparisons of its micromophology against closely related allies. New distribution records for T. pseudoversatilis are also provided. Additionally, we present phylogenetic informativeness analyses to assess the utility of ITS, 28S, and other markers previously used for the order Thelephorales. Our results identify the DNA-directed RNA polymerase II second-largest subunit (RPB2) as the most informative locus for delimiting species-level relationships in the Thelephorales order, whereas ITS contributes to solving interspecific relations within the Thelephora-Tomentella clade.},
}

@article {pmid42098235,
year = {2026},
author = {Anwar, AR and Kralj, S and Humar, M},
title = {Edible optical microcavities for optical barcoding, authentication, and sensing.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51128-3},
pmid = {42098235},
issn = {2045-2322},
support = {851143 and 101188166/ERC_/European Research Council/International ; 956265//Horizon 2020 Framework Programme/ ; P1-0099 and N1-0362//The Slovenian Research and Innovation Agency/ ; RGY0068/2020//Human Frontier Science Program/ ; },
abstract = {The safety, authenticity, and traceability of food and pharmaceutical products are critical challenges, especially in the context of widespread counterfeiting. Most existing anti-counterfeiting and sensing technologies are applied externally to packaging, making them vulnerable to tampering. A more robust approach is to incorporate them directly into edible products. Whispering-gallery modes (WGMs), highly sensitive optical resonances supported by spherical microcavities, provide a promising platform due to their environmental responsiveness and spectral uniqueness. Here, we demonstrate edible WGM microcavities based on chlorophyll-coated silica microspheres. Monodisperse microspheres exhibit stable WGM resonances under continuous-wave laser excitation, with quality factors ranging from 2,000 to 10,000. Individual microsphere diameters are determined with a precision of approximately 40 nm. When embedded in low-refractive-index agarose matrices, the microspheres generate size-specific spectral signatures that function as optical barcodes and remain stable for at least six months. Based on intrinsic size variations, we further demonstrate edible physical unclonable functions (PUFs) with stable and unique optical identifiers. In addition, the microcavities enable sugar concentration measurements with uncertainties as low as 0.23 percentage points and pH sensing with an accuracy of approximately 0.3 pH units, when embedded in a pH-responsive hydrogel. These results establish edible WGM microcavities as a multifunctional platform for secure labeling, sensing, and anti-counterfeiting in consumable products.},
}

@article {pmid42100831,
year = {2026},
author = {Burris-Otero, B and Achatz, TJ and Marcogliese, DJ and Reyda, FB and Colston, TJ and Locke, SA},
title = {On misidentification of metacercariae of Posthodiplostomum minimum (MacCallum, 1921) Dubois, 1936, in Nearctic minnows.},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e46},
doi = {10.1017/S0022149X26101485},
pmid = {42100831},
issn = {1475-2697},
support = {1845021//National Science Foundation/ ; null//Clark Foundation/ ; },
mesh = {Animals ; *Trematoda/classification/genetics/isolation & purification/anatomy & histology ; *Metacercariae/classification/genetics/isolation & purification/anatomy & histology ; *Trematode Infections/parasitology/veterinary ; Phylogeny ; Electron Transport Complex IV/genetics ; North America ; },
abstract = {Posthodiplostomum minimum (MacCallum, 1921) Dubois, 1936 (Digenea, Diplostomidae) was described from adult worms from a great blue heron (Ardea herodias; Ardeidae) in New York. Metacercariae have been widely reported from diverse freshwater fishes, despite early experimental work and recent molecular data indicating exclusive infection of minnows (Leuciscidae) in North America. We compared the type specimens of P. minimum to adults taken from domestic chicks (Gallus gallus domesticus) fed metacercariae from fathead minnow (Pimephales promelas; Leuciscidae), as well as adults in naturally infected ardeid hosts. Sequences of cytochrome c oxidase I (CO1) showed these specimens were conspecific with worms from leuciscids and ardeids sampled across North America. However, adult morphology of the species with metacercariae in North American leuciscids differed markedly from the type specimens of P. minimum. Consequently, we resurrect and transfer to Posthodiplostomum Dubois, 1936, the earliest name for the lineage infecting leuciscids in North America: Posthodiplostomum vancleavei (Agersborg, 1926) n. comb. In North America, the four most likely junior synonyms of P. minimum are Posthodiplostomum aztlanensis González-García, López-Jiménez, Ortega-Olivares, Sereno-Uribe, Pérez-Ponce de León et García-Varela, 2024, Posthodiplostomum dawnsherryae Achatz, Von Holten, Pritchard et Keel, 2025, Posthodiplostomum nanum Dubois, 1937, and Posthodiplostomum seminolense Achatz, Von Holten, Pritchard et Keel, 2025. Sequences of CO1 indicate P. vancleavei n. comb. has been introduced in Japan and we discuss the high likelihood of its establishment in Europe. The complete rDNA operon and near-complete mitochondrial genome sequence of P. vancleavei show expected phylogenetic affiliation with Posthodiplostomum centrarchi Hoffman, 1958.},
}

Animals
*Trematoda/classification/genetics/isolation & purification/anatomy & histology
*Metacercariae/classification/genetics/isolation & purification/anatomy & histology
*Trematode Infections/parasitology/veterinary
Phylogeny
Electron Transport Complex IV/genetics
North America

@article {pmid42102049,
year = {2026},
author = {Yehia, N and Ibrahim, M and Shady, RM and Mohamed, AAE and Said, D and Taha, ME and Arafa, A and Eid, S and Shalaby, MA and Truyen, U and Kobialka, RM and Abd El Wahed, A and Ceruti, A},
title = {Concurrent circulation of avian influenza viruses H5N1 and H9N2 enhances the genetic evolution of reassortant viruses in Egyptian poultry populations.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0348609},
pmid = {42102049},
issn = {1932-6203},
mesh = {Animals ; *Influenza A Virus, H9N2 Subtype/genetics/isolation & purification ; Egypt/epidemiology ; *Influenza in Birds/virology/epidemiology ; *Reassortant Viruses/genetics ; *Influenza A Virus, H5N1 Subtype/genetics/isolation & purification ; Chickens/virology ; *Poultry Diseases/virology/epidemiology ; Phylogeny ; *Evolution, Molecular ; Poultry/virology ; Genome, Viral ; },
abstract = {The co-circulation of the recently emerged H5N1 clade 2.3.4.4b and the endemic H9N2 avian influenza viruses (AIV) in poultry farms has led to significant economic losses and increased the likelihood of viral reassortment. Continuous and extensive surveillance with full genome sequencing is highly recommended. The objective of this study was to monitor AIV circulating in Egyptian poultry populations throughout 2024 using molecular surveillance and to detect genetic reassortment events. A total of 50 chicken flocks that exhibited respiratory symptoms from seven governorates in Egypt were tested for avian influenza H5, H9, Infectious Bronchitis virus (IBV), and Newcastle Disease Virus (NDV) using real-time RT-PCR. Four flocks that tested positive for H5 (AN1, AN6, AN7, and AN8) and three flocks that tested positive for H9N2 (AN2, AN3, and AN4) were selected for isolation and full-genome sequencing. They were subjected to virus isolation in specific-pathogen-free (SPF) embryonated chicken eggs, and identification was done using real-time RT-PCR assay. The full-genome sequencing was performed using rapid barcoding from Oxford Nanopore Technologies. The genome analysis revealed a H5N2 reassortant virus, comprising the HA, PB2, PB1, and PA gene segments from H5N1 clade 2.3.4.4b (EA-2021-AB), while the NA, NP, NS, and M genes were from H9N2 (G5.6). Additionally, two reassorted H9N2 viruses were identified, containing HA, NA, NP, M, and NS genes from H9N2 (G5.6), and PB1, PB2, and PA genes from Highly Pathogenic Avian Influenza H5N1 virus Clade 2.3.4.4b (EA-2021-AB). Interestingly, both reassortant H9N2 viruses have specific adaptive mutations in some of their internal genes that were not present in any other Egyptian H9N2 viruses. Several mutations, potentially associated with increased virulence and mammalian adaptation, were also detected in the internal genes. This study highlights the emergence of novel reassortant AIV viruses and underscores the need for continuous molecular surveillance, as well as further studies on the pathogenicity and vaccine efficacy against these newly emerged viruses.},
}

Animals
*Influenza A Virus, H9N2 Subtype/genetics/isolation & purification
Egypt/epidemiology
*Influenza in Birds/virology/epidemiology
*Reassortant Viruses/genetics
*Influenza A Virus, H5N1 Subtype/genetics/isolation & purification
Chickens/virology
*Poultry Diseases/virology/epidemiology
Phylogeny
*Evolution, Molecular
Poultry/virology
Genome, Viral

@article {pmid42102585,
year = {2026},
author = {Hornok, S and Takács, N and Lesiczka, P and Warbroek, T and van den Bosch, TJM and Keve, G and Kontschán, J and Péteri, O},
title = {DNA of Ehrlichia muris, hyperendemicity of Babesia microti in Ixodes ricinus and age-related detection of nuclear mitochondrial DNA (NUMTs) in Dermacentor reticulatus from an urban, marshy biotope of South-central Europe.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {3},
pages = {102648},
doi = {10.1016/j.ttbdis.2026.102648},
pmid = {42102585},
issn = {1877-9603},
abstract = {The present study was initiated to analyze ticks collected periodically from the vegetation in an urban marshy biotope of central Europe. During the one-year-long study period, 1960 ticks were found, including Ixodes ricinus (n = 1037), Dermacentor reticulatus (n = 610) and Haemaphysalis concinna (n = 313). DNA was extracted from 199 Dermacentor reticulatus and 47 Ixodes ricinus, selected from the beginning of their questing period. Molecular analysis of the cytochrome c oxidase subunit I (cox1) barcoding gene with the classical Folmer primers revealed that among 37 D. reticulatus all except two ticks had serial mutations along a 129-bp-long part of the gene. The majority of these ticks were young, freshly molted adults. However, when the complete mitogenome was sequenced from two such "aberrant" ticks, these serial mutations were absent. In D. reticulatus, host DNA was detected from four synanthropic bird species, the dog, the red fox, the bank vole, the Eurasian shrew and the wild boar. Besides long-known endemic tick-borne pathogens, specimens of D. reticulatus and I. ricinus were shown to contain the DNA of Ehrlichia muris. Babesia microti had very high, 36% prevalence in I. ricinus. In conclusion, mutations in the cox1 fragment amplified with the Folmer primers were not present in the complete mitochondrial genome of D. reticulatus, indicating that probably nuclear mitochondrial DNA (NUMT) was amplified with the first method. To our knowledge, similarly high local prevalence of B. microti was only reported in ticks in North America, where this piroplasm is responsible for most cases of human babesiosis (unlike in Europe).},
}

@article {pmid42092807,
year = {2026},
author = {Wu, ZH and Zhang, Q and Zhu, BY and Mou, LR and Yang, J and Gao, H and Shi, ZP and Shi, C},
title = {Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships in Styrax (Styracaceae).},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08747-9},
pmid = {42092807},
issn = {1471-2229},
abstract = {Styrax is the most species-rich and economically important genus within Styracaceae, valued for its medicinal, ornamental, and bioactive properties. Chloroplast genomic resources for this genus remain limited. Here, we conducted comparative genomic analyses of 23 newly assembled chloroplast genomes of Styrax to characterize genome architecture and evolutionary patterns, and performed phylogenetic analyses using broader sampling across the genus to resolve infrageneric relationships. All genomes exhibited a typical quadripartite structure with highly conserved IR/SC boundaries and core genes involved in photosynthesis and replication. Six tandem repeat sequences were identified. Codon usage bias indicated a preference for A/U endings, reflecting the interplay of mutation bias and moderate selection. Phylogenetic analyses recovered two well-supported monophyletic clades and revealed that the two sections (Sect. Valvatae and Sect. Styrax) are not monophyletic, whereas all four series recognized by Fritsch (Ser. Styrax, Ser. Valvatae, Ser. Cyrta, and Ser. Benzoin) were recovered as monophyletic. These findings enrich Styracaceae genomic resources, clarify infrageneric relationships, and provide a foundation for DNA barcoding and adaptive evolution studies in Styrax.},
}

@article {pmid42093938,
year = {2026},
author = {Botha, I and Maduna, SN and Hagen, SB and Lall, N and Berger, DK},
title = {3RAD-Guided SNP Discovery for Species Identification and Conservation of the Medicinal Southern African Tree Genus Greyia Hook. & Harv.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73412},
pmid = {42093938},
issn = {2045-7758},
abstract = {Accurate species identification is essential for conserving and managing plants that provide important ecosystem services and have ethnobotanical value. The Greyia tree genus (G. sutherlandii, G. radlkoferi and G. flanaganii) is endemic to South Africa and Eswatini, and certain genotypes have medicinal value for treating skin hyper-pigmentation. However, distinguishing among species is difficult because of overlapping phenotypes and the limited resolution of standard DNA barcodes. To overcome these limitations, a robust molecular identification assay was developed using a two-phase strategy. First, de novo SNP discovery using 3RAD sequencing identified 47,726 genome-wide SNPs from two to three plants sampled from each species' core geographic range: G. radlkoferi in northern Limpopo, G. sutherlandii in eastern KwaZulu-Natal, and G. flanaganii in the south-eastern Eastern Cape. Principal component analysis and coancestry matrices revealed three discrete genetic clusters, supporting the recognition of the three species. Selecting a set of 200 SNPs with intermediate Fst values (0.2-0.5) resulted in optimal separation of the three clusters. This led to the final selection of a 23-SNP panel that included five informative barcoding loci (ITS, trnL-F, matK). Second, the 23 SNPs were converted into allele-specific fluorescent PCR assays (SNP Type) for genotyping on the BioMark HD platform. The panel was validated using genomic DNA from 17 individuals from the 3RAD population groups and successfully differentiated all three species. It was then applied to 73 trees sampled across a 1000-km transect from the Eastern Cape to Limpopo. Genetic clustering (PCA, UPGMA and ADMIXTURE) assigned each tree to one of three species-level groups matching their expected ranges. In a practical case study, the assay also identified the species origin of 33 Greyia trees of unknown provenance from production orchards. This study provides an efficient SNP-based tool for accurate species identification, supporting conservation planning and the sustainable management of Greyia populations.},
}

@article {pmid42094362,
year = {2026},
author = {Keer, FR and Al'Khafaji, AM and Blainey, PC},
title = {Stitch-seq: Scalable CRISPR gene expression response profiling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.27.719216},
pmid = {42094362},
issn = {2692-8205},
abstract = {Single-cell profiling of genetic perturbations has expanded our ability to map causal links between genes and phenotypes; however, the high cost and technical complexity of current methods restrict systematic interrogation of dynamic cellular programs. Here, we present Stitch-seq, a high-throughput pooled functional genomics sequencing method enabling simultaneous capture of CRISPR perturbations and targeted gene and protein expression across millions of cells. Stitch-seq utilizes single-cell droplet-based overlap-extension reverse-transcription PCR reactions to physically link gene expression features of interest to perturbation identifiers without cell barcoding or extensive sequencing. We validated Stitch-seq's high fidelity using simplified models, benchmarked multi-omic Stitch-seq against single-cell RNA-sequencing in the MCF10A Epithelial-Mesenchymal Transition (EMT) model, and applied Stitch-seq to map transcriptional responses of MCF10A cells undergoing TGF-β-induced EMT to perturbations across five time points. By efficiently delivering large-scale multi-omic gene expression readouts, Stitch-seq provides a powerful and accessible modality for the routine dissection of complex biological pathways.},
}

@article {pmid42085517,
year = {2026},
author = {Islam, M and Sajjad, S and Hazzazi, Y and Sumayli, M and Alruzayza, S and Muhammad, K and Ghafoor, SU and Muhammad, T and Ullah, I and El-Shabasy, A},
title = {Molecular identification and DNA barcoding of Chaenomeles japonica in Pakistan.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0348503},
pmid = {42085517},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic/methods ; Pakistan ; Phylogeny ; *Rosaceae/genetics/classification ; DNA, Chloroplast/genetics ; DNA, Plant/genetics ; },
abstract = {Chaenomeles japonica (Thunb.) Lindl., an ornamental species belonging to the family Rosaceae, was molecularly identified from a cultivated population in the Hazara region, Khyber Pakhtunkhwa (KP), Pakistan. Fresh leaf samples were collected from a cultivated garden, and genomic DNA was extracted for molecular analysis. Four chloroplast DNA markers (matK, rbcLa, trnA, and ycf3) were amplified and sequenced. PCR amplification showed a 100% success rate, generating sequence lengths ranging from 400-1600 bp depending on the marker. BLAST analysis revealed 99-100% sequence identity, 100% query coverage, and E-values of 0.0 when compared with reference sequences available in GenBank, primarily from China, Japan, and the United States. Phylogenetic analysis using Neighbour Joining method demonstrated that the obtained sequences clustered with authenticated Chaenomeles japonica accessions, supported by bootstrap values. The results confirm the molecular identity of cultivated C. japonica in Pakistan and highlight the utility of chloroplast DNA barcoding markers for accurate species identification of ornamental plants.},
}

*DNA Barcoding, Taxonomic/methods
Pakistan
Phylogeny
*Rosaceae/genetics/classification
DNA, Chloroplast/genetics
DNA, Plant/genetics

@article {pmid42086644,
year = {2026},
author = {Park, HJ and Byeon, SY and Park, SR and Son, YB and Kang, JH and Lee, HJ},
title = {Molecular identification of major green tide-forming Ulva species and their spatiotemporal patterns on the Korean coast.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50151-8},
pmid = {42086644},
issn = {2045-2322},
support = {RS-2025-02304432//Korea Institute of Marine Science and Technology promotion/ ; 2026-RISE-10-005//Regional Innovation System & Education (RISE) program through the Gangwon RISE Center, funded by the Ministry of Education (MOE) and the Gangwon State (G.S.), Republic of Korea/ ; },
abstract = {Green tides - massive proliferations of green macroalgae (Ulva spp.) - have increasingly occurred worldwide in recent years, driven by accelerating climate change and anthropogenic nutrient inputs. These blooms disrupt coastal ecosystems, leading to biodiversity loss and economic damage. In Korea, green tides have persisted on Jeju Island since the 2000s, and have also been sporadically reported on the southern mainland coasts. However, the specific Ulva species responsible for these blooms and their spatiotemporal dynamics remain largely unknown. Here, we investigated Ulva community structure and relative frequencies from 46 sites (966 specimens) on Jeju Island and the southern coasts, using chloroplast tufA gene-based phylogenetic analysis, complemented by additional nuclear 5S rDNA marker. We found considerable differences in Ulva community composition between Jeju Island and the southern coasts, along with pronounced seasonal variation. A total of 11 Ulva species were identified from both regions, with Ulva ohnoi and U. australis being dominant on Jeju Island and U. australis and U. linza prevailed on the southern coasts. Our results provide essential genetic insights into major bloom-forming Ulva species and their spatiotemporal dynamics in order to support effective management of green tide events in Korean coastal ecosystems.},
}

@article {pmid42086709,
year = {2026},
author = {Mohammad Nejad Havestin, M and Sabahi, Q and Amiri, A and Sheikhi Garjan, A and Bandani, AR},
title = {Life-stage-specific resistance to imidacloprid and thiamethoxam in COI-confirmed Bemisia tabaci MEAM1 and adult detoxification enzyme activity.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51780-9},
pmid = {42086709},
issn = {2045-2322},
abstract = {Neonicotinoids such as imidacloprid and thiamethoxam remain widely used for managing the whitefly, Bemisia tabaci, yet intensive applications have selected for resistance in many production systems. Here, we quantified stage-resolved susceptibility to imidacloprid and thiamethoxam across eggs, second-instar nymphs, and adults in five field populations of B. tabaci molecularly confirmed as MEAM1 by COI sequencing and phylogenetic analysis. The study further examined whether population-level resistance patterns were associated with detoxification enzyme activity measured in adults. Standardized leaf-dip bioassays on colonies reared on eggplant under controlled conditions were analyzed by probit methods to estimate LC50 values and resistance ratios (RRs) relative to a field-derived reference population (Marand). Across life stages, among-population differences were consistent, with Jiroft showing the highest LC50 and RR values. In adults, imidacloprid resistance in Jiroft approached ~ 60-fold, whereas thiamethoxam resistance reached ~ 24-fold. Second-instar nymphs showed lower RRs than adults but still exhibited meaningful resistance (imidacloprid RR ≈ 15-fold in Jiroft), and eggs also displayed elevated tolerance relative to the reference population. In adult biochemical assays, resistant populations showed increased cytochrome P450 monooxygenase and glutathione S-transferase activities and/or elevated carboxylesterase activity, consistent with a metabolic component to resistance. These results delineate a life-stage-resolved resistance profile within a single MEAM1 lineage and under the present assay framework, second-instar nymphs appeared to be the most operationally responsive stage for potential intervention, but are no longer fully susceptible in highly selected populations, underscoring the value of stage-explicit monitoring in intensive vegetable systems.},
}

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48529-9},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

@article {pmid42092186,
year = {2026},
author = {Saliba, D and Osman, EA and Elmanzalawy, A and Saab, C and Bui, S and Hirka, S and Anderson, S and Toader, V and Dore, MD and Rizzuto, FJ and de Rochambeau, D and McKeague, M and Sleiman, HF},
title = {Unlocking chemical diversity in aptamers with DNA orthogonal barcodes.},
journal = {Nature chemistry},
volume = {},
number = {},
pages = {},
pmid = {42092186},
issn = {1755-4349},
abstract = {Aptamers are a versatile alternative to antibodies as they are smaller, easier to synthesize and less immunogenic. However, while antibodies are composed of 20 chemically diverse amino acids and are established therapeutics, aptamers are composed of only 4 similar nucleobases, thereby limiting their therapeutic potential. Aptamer chemical modifications are restricted to maintain compatibility with enzymatic selection. Here we introduce aptamer-like encoded oligomers (alenomers), highly chemically modified aptamers that are read and sequenced using a DNA code branching from and corresponding to the target-binding oligomer. We build ~300,000-member DNA-encoded libraries using an automated DNA synthesizer and split-and-pool methods, and screen them for protein binding via next-generation sequencing. In contrast to aptamers, alenomers are not restricted by the need for conservative enzyme-compatible modifications. They can thus explore an almost limitless chemical space, enabling the discovery of highly stable, high-affinity protein-binding aptamers, while offering structural insights into their interactions with target molecules.},
}

@article {pmid42081452,
year = {2026},
author = {Brewster, C and Mann, FG and Benham-Pyle, B and Sánchez Alvarado, A},
title = {Syrah: a pipeline to maximize spatial transcriptomics data output.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag107},
pmid = {42081452},
issn = {2160-1836},
abstract = {Spatial analysis of gene expression patterns has been a key technique for revealing the potential functions of genes. Traditionally, these analyses conducted using in-situ hybridizations and other labor-intensive protocols were constrained to examining only a few candidate genes per sample. However, the advent of spatial transcriptomic techniques like Slide-seqV2 has transformed this field, enabling massively parallel exploration of gene expression patterns within their tissue contexts by pairing spatial locations with RNA sequencing. Despite its potential, Slide-seqV2 datasets often produce fewer usable reads than expected. We have identified that a significant source of errors in the technology stems from the chemical synthesis of barcodes used in Slide-seqV2. These errors are systematic, and in many cases, they can be bioinformatically identified and corrected. We have developed "Syrah, " an analysis pipeline that identifies and corrects barcode errors in Slide-SeqV2 and Curio seeker datasets. Syrah can dramatically enhance read numbers in Slide-seqV2 datasets, recovering up to 35% more reads, reassigning erroneous barcode matches, and removing improperly formed reads. Unlike other dataset improvement methods that rely on data driven imputation, Syrah uses a biochemical model and the barcode sequence data and does not, require additional datasets or intricate calculations. This innovative technique promises to transform the utility of Slide-seqV2 and Curio Seeker datasets by identifying usable reads that were discarded during previous analysis that required exact matching of barcode sequences.},
}

@article {pmid42083652,
year = {2026},
author = {Ghotbi, FS and Soorni, A},
title = {Chloroplast Phylogenomics and Barcode Discovery in Medicinal Stachys Species Reveal Evolutionary Relationships and Adaptive Signatures.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73618},
pmid = {42083652},
issn = {2045-7758},
abstract = {The genus Stachys, a large and taxonomically intricate group within the Lamiaceae family, includes numerous species valued in traditional medicine, yet their evolutionary relationships are often obscured by morphological complexity. To resolve these persistent difficulties, we sequenced and assembled the complete chloroplast genomes of two medicinally important Iranian species, Stachys persica and Stachys germanica, and compared them against seven congeneric genomes. Despite an overall picture of strong structural conservation across the genus, we discovered that evolutionary variation concentrates in specific genomic hotspots. Several non-coding intergenic spacers, most notably trnL-trnF, along with the matK and ycf1 genes emerged as exceptionally variable regions, making them promising candidates for species-level DNA barcoding. In a more surprising finding, we detected clear signatures of positive selection acting on the photosynthetic gene petB, suggesting that even core energy pathways have experienced adaptive refinement within this lineage. Phylogenetically, whole-plastome data placed S. germanica as sister to S. byzantina, with S. persica as their closest relative, a relationship that individual barcode loci failed to recover reliably. Taken together, this study provides a robust evolutionary framework for Stachys, identifies practical molecular tools for authenticating medicinal materials, and demonstrates the power of whole-plastome sequencing to untangle taxonomically intricate plant groups.},
}

@article {pmid42078674,
year = {2026},
author = {Li, H and Zhang, S and Abdullah, and Shah, SA and Huang, Y and Jia, J and Guo, L and Cui, Y and Sun, J and Heidari, P and Tian, X},
title = {Complete Chloroplast Genomes of Ranunculus arvensis and Ranunculus laetus: Comparative Analysis and Phylogenetic Insights.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73559},
pmid = {42078674},
issn = {2045-7758},
abstract = {Ranunculus L., the largest genus of Ranunculaceae, exhibits remarkable ecological diversity, yet genomic resources for this genus remain limited. Here we report the complete chloroplast (cp) genomes of Ranunculus arvensis L. and Ranunculus laetus Wall. ex Hook.f. & Thomson. The R. laetus assembly is the first cp genome reported for this species, whereas the R. arvensis assembly, generated from a Pakistani population, provides an independent accession that complements the recently released GenBank record PV621859 from China. Both genomes were analyzed comparatively against 22 previously published Ranunculus cp genomes. The cp genomes ranged from 154,474 to 158,314 bp in length and displayed a typical quadripartite structure. All analyzed species harbored 112 unique genes, comprising 78 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. The cp genomes were highly conserved in terms of gene order, guanine-cytosine content, codon usage, amino acid composition, and simple sequence repeats. Phylogeny-aware selection analysis models (BUSTED, MEME, FUBAR) revealed that, despite overall purifying selection at the gene level, codon-based FUBAR detected pervasive positive selection across ~34.6% of plastid genes; matK and ycf1 emerged as the most prominent hotspots for both episodic and pervasive adaptation. Nucleotide diversity analyses revealed several highly variable regions, notably rpl32-ndhF, ycf1, and ndhF. Phylogenetic analyses based on complete cp genome sequences and complementary single-gene trees resolved two major clades corresponding to biogeographic patterns: Clade I comprised predominantly Eurasian and East Asian taxa, whereas Clade II comprised a transcontinental assemblage of East Asian, North American, and Himalayan species. The R. laetus and R. arvensis were grouped in Clade II. Overall, these results elucidate the conserved genomic architecture, evolutionary dynamics, and phylogenetic relationships of Ranunculus cp genomes and provide valuable genomic resources for future studies on phylogeny, taxonomy, DNA barcoding, and population genetics within Ranunculaceae.},
}

@article {pmid42080206,
year = {2026},
author = {Sibaja-Cordero, JA and Miranda-García, W},
title = {Sthenelais onca sp. nov. (Phyllodocida, Sigalionidae) from a sandy beach on the North Pacific coast of Costa Rica.},
journal = {ZooKeys},
volume = {1278},
number = {},
pages = {73-93},
pmid = {42080206},
issn = {1313-2989},
abstract = {Errant polychaetes of the family Sigalionidae are active, scale-covered predators inhabiting sandy marine bottoms. Knowledge of this family in tropical America is scarce, with only a few species reported from Costa Rica. In this study, seven specimens of Sthenelais were collected from the intertidal zone of Playa Naranjo, Área de Conservación Guanacaste, on the North Pacific coast of Costa Rica. Morphological examinations and Bayesian phylogenetic analyses based on DNA barcoding (COI) were conducted to determine their taxonomic identity. The specimens were recovered within the Sthenelais clade, forming a distinct and well-supported subclade that includes S. limicola from Europe and representatives from Asia, and that differs from western Pacific congeners. Morphologically, the new species Sthenelais onca sp. nov. differs from other Eastern Tropical Pacific congeners by the absence of serrations on the shafts of neurochaetae throughout the body, stylodes without papillae, and anterior elytra bearing a notch on the supra-interior margin that diminishes posteriorly. The species inhabits saturated sand in the intertidal zone and exhibits a unique elytral coloration pattern reminiscent of a jaguar's coat. This study describes a new species of Sthenelais from sandy beaches of the Pacific coast of Costa Rica and provides an updated identification key for the genus in the region, expanding the known diversity and distribution of Sigalionidae in the Tropical Eastern Pacific.},
}

@article {pmid42080207,
year = {2026},
author = {Martínez, L and Eyes-Escalante, M and Cabra-García, J},
title = {Morphological and molecular evidence support a new species of the genus Ilocomba Brescovit, 1997 (Araneae, Anyphaenidae, Anyphaeninae) from the Andes of Colombia.},
journal = {ZooKeys},
volume = {1278},
number = {},
pages = {19-51},
pmid = {42080207},
issn = {1313-2989},
abstract = {We describe a new species of the genus Ilocomba Brescovit, 1997 from the Andean region of Colombia using an integrative taxonomic approach that combines morphological and molecular data. We assess the phylogenetic position of the new species using four molecular markers: COI, 16S, 28S, and H3. The distinctiveness of the new species, Ilocomba yotoco sp. nov., is supported by its placement in the phylogenetic tree, unique morphological characteristics, and uncorrected pairwise genetic distances. We also provide new morphological data and geographic records for Ilocomba marta Brescovit, 1997. Additionally, we present a distribution map of the genus and an updated identification key for all known species of Ilocomba.},
}

@article {pmid42080279,
year = {2026},
author = {Abato, J and Along, A and Aspe, N and Awa, CK and Burias, NA and Calagui, L and Calagui, SI and Demetillo, M and Jovita, AJ and Leones, JA and Niez, AM and Seronay, R and Kajihara, H},
title = {Morphology and Phylogeny of Notospermus psittacinus comb. nov. (Nemertea: Pilidiophora: Lineidae) from Mindanao, Philippines.},
journal = {Zoological science},
volume = {43},
number = {2},
pages = {202-211},
doi = {10.2108/zs250101},
pmid = {42080279},
issn = {0289-0003},
mesh = {Animals ; *Phylogeny ; Philippines ; Species Specificity ; },
abstract = {This study provides a redescription of the lineid heteronemertean Notospermus psittacinus (Bürger, 1890) comb. nov. based on specimens collected from Mindanao, Philippines. The species was previously assigned to the genus Lineus Sowerby, 1805, and has not been reported since its original description from Ambon, Indonesia. No DNA barcode sequences based on reliably identified material from the type locality are currently available. Notospermus psittacinus comb. nov. differs from the other six named species of the genus in body coloration, but can be distinguished from N. annulatus (Grube, 1840) only by molecular and biogeographic evidence. Despite the observed morphological variations in our specimens, genetic distance analyses indicated that all represent a single species (cytochrome c oxidase subunit I [COI] p-distance = 0%-2.12% [n = 7], 16S ribosomal RNA [16S] p-distance = 0%-1.57% [n = 6]). Genetic divergence between N. annulatus and N. psittacinus comb. nov. was 11.39%-12.18% for the 16S gene and 5.79% for the histone H3 (H3) gene, supporting their status as distinct species. A multigene phylogenetic analysis based on 16S, 18S ribosomal RNA, 28S ribosomal RNA, COI, and H3 sequences showed that all N. psittacinus comb. nov. specimens formed a well-supported clade within the genus Notospermus Huschke, 1830. Although intra-generic relationships remain poorly resolved, this result corroborates the generic reassignment of the species from Lineus to Notospermus.},
}

Animals
*Phylogeny
Philippines
Species Specificity

@article {pmid42064442,
year = {2026},
author = {Siew, ZY and Zariman, NF and Sa'idi, WSMW and Lui, ZY and Coomarhesan, HSM and Seow, I and Shafie, NJ and Wong, ST and Razak, MFAA and Gani, M and Sindang, SW and Voon, K},
title = {Surveillance of Zoonotic Pathogens and Taxonomic Identification of Non-volant Small Mammals in Peninsular Malaysia.},
journal = {Tropical life sciences research},
volume = {37},
number = {1},
pages = {293-313},
pmid = {42064442},
issn = {1985-3718},
abstract = {Malaysia's tropical rainforests host a rich biodiversity, including various non-volant small mammals. Among these, murid rodents (family Muridae) are ecologically significant and frequently associated with zoonotic pathogens, making them important subjects for public health research. In recent years, treeshrews (family Tupaiidae), small omnivorous mammals once grouped with primates, have also gained increasing scientific attention due to their unique evolutionary position and emerging role in disease ecology. Rapid species identification is vital for effective surveillance, particularly in the context of emerging infectious diseases. In this study, PCR amplification targeting mitochondrial and nuclear DNA regions was performed using a range of primers, followed by Sanger sequencing to validate the amplicons. Among the primers tested, mcb398 and mcb869, targeting the mitochondrial cytochrome b gene, proved most effective, yielding consistent amplification and high-quality sequences for both rodents and treeshrews. Besides, 22 animals were captured and screened for selected zoonotic pathogens. Paramyxoviruses, coronaviruses, picornaviruses, orthoreoviruses and Dengue viruses were not detected in the faecal samples of rats, Asian house shrews and palm civets. However, mammalian orthoreovirus type 3 and Dengue virus serotype 2 were detected in one and three faecal samples from treeshrews, respectively. Notably, Tupaia sp. m ZYS-2025, detected in this study, may represent a novel species that has not known to science previously.},
}

@article {pmid42064967,
year = {2026},
author = {Lai, M and Duan, P and He, Z and Zhang, P and Chen, Z},
title = {Development of Loop-Mediated Isothermal Amplification (LAMP) Methods for Rapid Identification of Nephrotoxic Amanita Species.},
journal = {Mycobiology},
volume = {54},
number = {2},
pages = {293-302},
pmid = {42064967},
issn = {1229-8093},
abstract = {Mushroom poisoning remains the leading cause of foodborne morbidity and mortality in China. The mushrooms that cause acute kidney injury (AKI) belong to the species of Amanita genus section Roanokenses. These species exhibit highly similar morphological characteristics, which is a challenge for their identification for non-specialists. Although conventional DNA barcoding identification is reliable, it is time-consuming for rapid diagnosis. In this study, we developed a loop-mediated isothermal amplification (LAMP) method based on the internal transcribed spacer (ITS) region to enable rapid identification of five species within A. sect. Roanokenses which can cause AKI. The optimized LAMP system was rigorously evaluated for specificity and sensitivity, with comparative analysis performed against conventional PCR. The results demonstrated that the established LAMP method achieved visual detection without specialized equipment, exhibiting high specificity and a detection limit of 10 pg per reaction. Critically, this approach can reduce identification time to approximately 1 h and provides sensitivity 100 times greater than that of the conventional PCR protocol.},
}

@article {pmid42065640,
year = {2026},
author = {Xue, H and Qin, Y and Han, Y and Xu, S and Willner, I and Xia, F and Huang, F},
title = {Photoactivated Signaling Networks using DNA-Based Synthetic Organelles as Biomimetic Protocells.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e4889049},
doi = {10.1002/anie.4889049},
pmid = {42065640},
issn = {1521-3773},
support = {22377112//National Natural Science Foundation of China/ ; 22090050//National Natural Science Foundation of China/ ; U24A20502//National Natural Science Foundation of China/ ; 2021YFA1200403//National Key R&D Program of China/ ; JCYJ20220530162406014//Natural Science Foundation of Shenzhen/ ; },
abstract = {Membraneless organelles formed by phase-separated nucleic acid or protein condensates play vital roles in regulating cellular functions. Integrating such synthetic organelles into protocell carriers remains a key challenge. Here, we introduce a method to assemble functional phase-separated organelles within liposome protocells. Pre-engineered nucleic acids are encapsulated with ligase in locked-DNA-nanopore modified protocells. Upon nanopore unlocking and Mg[2+] influx, the nucleic acid constituents ligate into programmable polymer chains that crosslink into barcode-modified condensates. Photoresponsive, caged nucleic acids hybridize with barcode tethers on two distinct organelles, forming a functional two-organelle system in the protocells. Light-induced uncaging releases an information-transfer strand from one organelle, triggering intercommunication and reconfiguration of the partner organelle. By predesigning organelle compositions and transfer strands, the emergence of catalytic DNAzymes or transcriptional machinery in the organelle/protocell assemblies is demonstrated, resulting in dynamic structural reconfiguration of the organelles.},
}

@article {pmid42067223,
year = {2026},
author = {Andres-Lopez, Y and Santambrogio, A and Kafetzopoulos, I and Todd, CD and El Khouri-Gonzalez, C and Gonzalez-Alvarez, JE and Alda-Catalinas, C and Clark, SJ and Reik, W and Hernando-Herraez, I},
title = {Using CRISPR barcoding as a molecular clock to capture dynamic processes at single-cell resolution.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280915.125},
pmid = {42067223},
issn = {1549-5469},
abstract = {Biological processes are inherently dynamic, yet current methods for capturing temporal changes remain limited. Here, we present scDynaBar, a novel approach that combines CRISPR-Cas9 dynamic barcoding with single-cell sequencing. In this system, genetic barcodes gradually accumulate mutations over time; these barcodes are sequenced alongside the transcriptome of individual cells. We propose that the divergence of these barcodes from the original sequence can serve as a record of the timing of cellular events. To demonstrate the potential of this method, we track the transition from a pluripotent state to a two-cell (2C)-like state in mouse embryonic stem cells (mESCs), providing evidence for the transient nature of the 2C-like state. Additionally, our system shows consistent mutation rates across diverse cell types in a mouse gastruloid model, highlighting its applicability to other biological systems. This approach not only improves our ability to study single-cell dynamics but also opens up new possibilities for recording other temporal signals-in other words, using dynamic barcoding as a molecular clock in individual cells.},
}

@article {pmid42068669,
year = {2026},
author = {Kang, TM and Jung, JB and Park, KL and Kwak, NJ and Oh, DG and Lee, HJ and Lee, KM and Ko, KS and Park, SH},
title = {Necrophagous fly occurrence and primary colonizing species in forensic entomology cases from the Yeongnam Region, South Korea.},
journal = {Forensic science international},
volume = {386},
number = {},
pages = {112984},
doi = {10.1016/j.forsciint.2026.112984},
pmid = {42068669},
issn = {1872-6283},
abstract = {Forensic entomology is widely used in death investigations to estimate the minimum postmortem interval (mPMI). In South Korea, however, casework-based ecological data remain limited, particularly for indoor scenes. We established a collaborative framework with investigating officers in the Yeongnam region (Gyeongsangbuk-do, Daegu, and Busan) and compiled forensic entomology cases from 2019 to 2022 to summarize the occurrence patterns of necrophagous flies. Scene information and specimens were collected using a standardized field record form, and species were identified by morphological examination and confirmed by COI DNA barcoding. Occurrence patterns were summarized by month, region, and scene type. The primary colonizing species was operationally defined as the species with the longest estimated developmental time in each case. Among the 73 cases analyzed, 66 (90.4%) were indoor and 7 (9.6%) were outdoor, yielding 17 identified species. Lucilia sericata was the most frequently detected species (n = 55, 75.3%) across most months, followed by Sarcophaga peregrina (n = 16, 21.9%), Chrysomya pinguis (n = 13, 17.8%), and Chrysomya megacephala (n = 13, 17.8%). Regarding primary colonizing species, L. sericata predominated in indoor cases (n = 41, 62.1%), whereas Calliphora calliphoroides (n = 3, 42.9%) and Calliphora nigribarbis (n = 2, 28.6%) were the most frequent in outdoor cases. Overall, the observed patterns were broadly consistent with previous Korean surveys. These findings provide a casework-based regional reference for mPMI interpretation in Korea.},
}

@article {pmid42075420,
year = {2026},
author = {Zegeye, W and Burridge, A and Siluveru, A and Orford, S and Sayers, L and Goram, R and Horler, R and Barker, G and Chayut, N},
title = {Molecular Labelling Tool for Cereal Genetic Resources Management Derived from Barley and Tetraploid Wheat Genebank-Genomics Projects.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081219},
pmid = {42075420},
issn = {2223-7747},
support = {BBS/E/JI/23NB0001/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; QZA-20/0154//Norwegian Agency for Development Cooperation/ ; },
abstract = {Globally, 5.94 million accessions are conserved across 867 genebanks, of which 41.5% (2.47 million) are cereal crop accessions. Only a small portion of global germplasm diversity has been marker-genotyped or genome-sequenced. Accurate identification of genebank accessions is essential to improve the efficiency and effectiveness of global genebanking. It is crucial for preserving the legacy knowledge associated with the germplasm and for maintaining its value to current plant science and breeding efforts. Existing practices generally fall into two categories: either expensive and complex, or inefficient, labour-intensive, and inaccurate. The first relies on high-resolution genomic sequences or saturated markers, while the second relies on morphological comparisons of regenerated plants with historical records. We propose a genotyping method based on a minimal set of Single Nucleotide Polymorphism (SNP) markers and exemplify its use on a genebank scale. We identified a small, effective set of SNPs that can differentiate between the global diversity of genebank accessions of barley (Hordeum vulgare and Hordeum spontaneum) and tetraploid wheat collections (Triticum turgidum) maintained at the Germplasm Resources National Capability at the John Innes Centre, UK. This approach offers a straightforward, automatable, and inexpensive alternative to traditional genebank crop descriptors used during seed regeneration and distribution. By establishing the minimal genomic resolution needed to distinguish genetically distinct accessions, we show that as few as 24 and 25 carefully chosen SNP markers for barley and durum wheat, respectively, can effectively differentiate individual accessions. Unlike morphology-based identification, which can detect mislabelling or contamination but often cannot prevent or correct such errors, our SNP-based molecular labelling enables error correction and the retrieval of lost germplasm identity. This study highlights how accuracy and reliability in germplasm management can be improved without costly whole-genome sequencing or resource-intensive analysis. We discuss the impact of this method on enhancing quality assurance in genebanks and its broader usefulness for the user community.},
}

@article {pmid42075733,
year = {2026},
author = {Ward, HM and Lunders, JJ and Ocegueda, C},
title = {From RAMP to Triplex RT-qPCR: Modernizing Arbovirus Surveillance and Confirming the First Aedes aegypti in Idaho.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040406},
pmid = {42075733},
issn = {2076-0817},
support = {Mosquito Abatement District contracts (MADS)//The Idaho Department of Health and Welfare Division of Public Health/ ; },
mesh = {Animals ; *Aedes/virology ; Idaho/epidemiology ; *Arboviruses/genetics/isolation & purification ; *Mosquito Vectors/virology ; *Arbovirus Infections/epidemiology/virology/transmission ; West Nile virus/genetics/isolation & purification ; Real-Time Polymerase Chain Reaction/methods ; Epidemiological Monitoring ; },
abstract = {West Nile virus (WNV) remains the most frequently reported locally acquired arboviral infection in the United States, yet many small and mid-sized mosquito abatement districts lack the diagnostic capacity and integrated data systems needed for rapid detection and response. The Canyon County Mosquito Abatement District (CCMAD) in southwestern Idaho undertook a multi-year capacity-building effort to expand arbovirus surveillance, standardize mosquito identification and pooling procedures, and implement triplex RT-qPCR testing for WNV, Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Historical trapping datasets (2021-2025) were consolidated, geospatially harmonized, and grouped into biologically meaningful sampling units to enable multi-year spatial comparisons. Surveillance revealed recurrent WNV activity annually, with peak transmission occurring between epidemiological weeks 31 and 37. The highest WNV activity occurred in 2023 and 2025, with 192 and 92 positive pools, respectively, while no WEEV or SLEV detections were observed. Enhanced laboratory capacity reduced sample-processing times, decreased the reliance on external confirmatory testing, lowered per-pool testing costs, and enabled same-day reporting to operational staff. In 2025, routine gravid trap surveillance detected a single Aedes aegypti, which was identified morphologically and subsequently confirmed by DNA barcoding, prompting targeted follow-up trapping. CCMAD's integrated approach provides a scalable model for strengthening local surveillance and response capabilities in resource-limited settings.},
}

Animals
*Aedes/virology
Idaho/epidemiology
*Arboviruses/genetics/isolation & purification
*Mosquito Vectors/virology
*Arbovirus Infections/epidemiology/virology/transmission
West Nile virus/genetics/isolation & purification
Real-Time Polymerase Chain Reaction/methods
Epidemiological Monitoring

@article {pmid42075742,
year = {2026},
author = {Vetri, A and Basso, A and D'Onofrio, C and Pretto, T and Turolla, E and Marcer, F and Fiocchi, E and Arcangeli, G and Cortinovis, L and Bilska-Zając, E and Menconi, V},
title = {First Report of Haplosporidium edule Infection in the Olive-Green Cockle (Cerastoderma glaucum) from the Northern Adriatic Sea: Expanding Host Range and Geographic Distribution.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040415},
pmid = {42075742},
issn = {2076-0817},
mesh = {Animals ; *Cardiidae/parasitology ; *Haplosporida/genetics/isolation & purification/physiology/classification ; *Host Specificity ; Italy ; Cross-Sectional Studies ; Phylogeny ; },
abstract = {Haplosporidium edule is a haplosporidian parasite originally described in the common edible cockle (Cerastoderma edule) along the European Atlantic coast. In this study, we report the first detection of H. edule in the olive-green cockle (Cerastoderma glaucum) from the northern Adriatic Sea, representing both a novel host record and a new geographic occurrence. During a cross-sectional study conducted in May 2019, 90 C. glaucum specimens were collected from three lagoon sites in northeastern Italy. Histological examination of soft tissues revealed haplosporidian developmental stages, including plasmodia, sporoblasts and mature spores, within connective tissues of the mantle, digestive gland, gills and between gonadal tubules in eight individuals from the Goro Lagoon. Molecular characterization based on a fragment of the small subunit ribosomal DNA showed high similarity with the previously published H. edule sequence. Host identification was confirmed through cytochrome c oxidase subunit I barcoding together with morphological and histological analyses. These findings indicate that H. edule has a broader host range than previously recognized. Although prevalence was relatively low, the detection of this parasite in a new host species and geographic area highlights the importance of continued surveillance, particularly in the context of climate change, shellfish translocations and the expansion of aquaculture activities.},
}

Animals
*Cardiidae/parasitology
*Haplosporida/genetics/isolation & purification/physiology/classification
*Host Specificity
Italy
Cross-Sectional Studies
Phylogeny

@article {pmid42078670,
year = {2026},
author = {Gielings, RL and Foulon, V and Renema, W and Macher, JN},
title = {Phloxine B Staining is Compatible With High-Throughput DNA Barcoding of Meiofauna.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73597},
pmid = {42078670},
issn = {2045-7758},
abstract = {Modern, integrative biodiversity research requires methods capable of bridging the gap between detailed morphological observations and the scalability of DNA sequencing. Integrative approaches like megabarcoding generate DNA sequences, while morphological functional data and abundance data are retained. For small, transparent, and highly abundant animals like meiofauna, the necessity to sort the specimens from organic matter and sediment forms a major bottleneck, as the use of stains required for enhanced manual or automated specimen detection can inhibit downstream molecular workflows. To address this, we tested the compatibility of phloxine B staining with DNA sequencing to facilitate simultaneous morphological and molecular specimen processing. Meiofauna preserved in ethanol, propylene glycol, or a DMSO/EDTA/saturated NaCl solution (DESS) was incubated with phloxine B for 30 min or 24 h. Specimens were manually isolated, the V1-V2 region of the 18S rDNA gene was sequenced, and success was quantified across major meiofaunal phyla. Nematodes, copepods, and annelids consistently showed high sequencing success irrespective of the preservative or staining incubation time. Platyhelminths showed lower success, likely due to misidentification or primer limitations rather than dye inhibition. Overall, these findings demonstrate that phloxine B is compatible with downstream DNA amplification and sequencing, enabling efficient integration of morphological and molecular data. The approach offers high potential for broader application in other microscopic taxa, supporting the way to comprehensive, high-throughput biodiversity assessments or ecological monitoring.},
}

@article {pmid42064429,
year = {2026},
author = {Aristya, GR and Halim, TA and Judith, TP and Kasiamdari, RS and Damaiyani, J and Prabowo, H},
title = {Genetic Variation and Phylogenetic Analysis of Indonesian Sugarcane (Saccharum officinarum L.) based on Internal Transcribed Spacer (ITS-nrDNA).},
journal = {Tropical life sciences research},
volume = {37},
number = {1},
pages = {49-65},
pmid = {42064429},
issn = {1985-3718},
abstract = {Sugarcane (Saccharum officinarum L.) is a crucial agricultural crop in global sugar production. Over the past decade (2010-2019), sugarcane production in Indonesia has experienced annual fluctuations, reaching its peak in 2013 with 35.5 million tons and declining to 27.7 million tons in 2019. Concurrently, Indonesia's sugar production only met 38% of domestic demand, necessitating the development of superior sugarcane cultivars with high sucrose content and resistance to pests and diseases. The aim of this study was to identify and determine the relationship among three sugarcane cultivars in Indonesia using DNA barcoding and constructing a phylogenetic tree based on ITS nuclear ribosomal DNA sequences. The ITS region was amplified using the primers ITS1 and ITS4, yielding a final base pair length of 531 bp. The sequences were then analysed to construct a phylogenetic tree using Maximum-Likelihood (ML) and Bayesian Inference (BI) methods. Sequence analysis was also conducted to determine genetic distances, polymorphic sites, haplotype distributions, and Principal Coordinate Analysis (PCoA). Phylogenetic tree construction grouped all cultivars into three distinct clades for both methods, with all three cultivars placed in the same clade with a bootstrap value of 94 for ML and a posterior probability of 1 for BI. Haplotype distribution showed that cultivars POJ and Pringu belonged to the same group, and PCoA analysis indicated no separation based on geographic origin, with some compositions similar to those of other countries such as Mexico, Taiwan and China.},
}

@article {pmid42050585,
year = {2026},
author = {Rueda, M and Gut, IG},
title = {ClarID: a human-readable and compact identifier specification for biomedical metadata integration.},
journal = {Journal of biomedical semantics},
volume = {17},
number = {1},
pages = {},
pmid = {42050585},
issn = {2041-1480},
support = {831434//Innovative Medicines Initiative 2 Joint Undertaking (JU)/ ; PI19/01772//Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias and cofunded with ERDF funds/ ; MINECO/FEDER, BIO2015-71792-P//Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the 2014-2020 Smart Growth Operating Program, and institutional co-financing with the European Regional Development Fund/ ; },
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 (relative to that event); and (ii) a compact version named ‘stub’ (e.g., ‘CT01001LTR0N401T1W’) optimized for filenames, pipelines, and labeling. ClarID is supported by an open-source reference implementation, ClarID-Tools, a command-line tool that 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 is designed to complement, not replace, persistent identifiers such as UUIDs, by providing a human-readable layer that enhances interpretability and facilitates metadata curation. 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.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13326-026-00349-6.},
}

@article {pmid42053442,
year = {2026},
author = {Maridakis, C and Freire, VP and Marani, G and Sancho, MT and Le Gall, L and Rousseau, F},
title = {Are integrative systematic tools efficient toward unraveling species diversity with the genus Jania (Corallinaceae, Rhodophyta)?.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70167},
pmid = {42053442},
issn = {1529-8817},
abstract = {The articulated genus Jania currently comprises 54 accepted species, making it the fourth most speciose genus among corallines, following Lithophyllum, Amphiroa, and Lithothamnion. Unlike these other genera, Jania is relatively easy to identify at a generic rank. However, morpho-anatomical characters are insufficiently discriminant for species identification, making DNA sequences essential for reliable species delimitation. We evaluated species diversity within Jania using the most comprehensive sampling to date, spanning a broad geographic range with a focus on the Mediterranean and Caribbean regions. Our data set comprised 186 specimens from the National Herbarium of the Muséum national d'Histoire naturelle (PC), including four type specimens with the basionyms Jania micrarthrodia, Corallina polydactyla, Corallina mauritiana, and Jania digitata. We also incorporated publicly available sequences from GenBank and Barcode of Life Data System (BOLD) to delimit species and infer their phylogenetic relationships using the psbA and COI genes. Through an integrative taxonomic approach, combining morpho-anatomical traits, molecular systematics, and biogeography, we delineated 39 putative species-28% fewer than the currently accepted number. Most of the putative species had a restricted distribution, whereas five were widely distributed. We determined seven species from the European Atlantic and Mediterranean seas and six from the Caribbean. Furthermore, we demonstrated that intergenicular morphometry is an unreliable trait for species identification, highlighting the morphological plasticity of Jania. Many putative species remained unidentified (67%), while some of those putative species included specimens with different identifications. Additional sequences of type specimens would be crucial for further resolving taxonomy and bridging the gap between type-bearing name and putative species delineated based on molecular data.},
}

@article {pmid42058642,
year = {2026},
author = {Into, T and Petcharad, B and Boonyuen, N and Chanklan, R and Pannanusorn, S and Mongkolsamrit, S and Kobmoo, N and Nuankaew, S and Kwanthong, P},
title = {Spider webs as reservoirs of culturable fungal diversity: evidence from orb-weaving Cyclosa mulmeinensis spider in Thai rice agroecosystems.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e187035},
pmid = {42058642},
issn = {1314-2828},
abstract = {Spider webs are increasingly recognised as passive environmental collectors; however, fungi remain amongst the least explored biological components associated with spider silk, particularly when examined using culture-based and taxonomically resolved approaches. In this study, we present a proof-of-concept investigation of culturable fungal diversity associated with two-dimensional, debris-decorated orb webs, constructed by the orb-weaving spider Cyclosa mulmeinensis in rice agroecosystems in Thailand. Using a standardised field-to-laboratory isolation workflow combined with genus-appropriate multilocus phylogenetic analyses, decorated orb webs were sampled as individual units from rice agroecosystems in Thailand and fungi were isolated via dilution plating on potato dextrose agar supplemented with chloramphenicol. A total of 112 fungal isolates were recovered, grouped into 45 colony morphotypes and resolved into 23 taxa across six genera: Alternaria, Aspergillus, Cladosporium, Fusarium, Penicillium and Talaromyces. Taxonomic placement was inferred primarily from multilocus phylogenetic analyses, with morphological characteristics used as supporting evidence. Notably, several isolates formed well-supported lineages within Cladosporium and Talaromyces that could not be assigned to any described species, indicating the presence of potentially undescribed taxa. These findings demonstrate that spider webs can serve as a low-impact, non-destructive substrate for accessing viable fungal diversity in agricultural ecosystems. This approach enables reproducible culture-based recovery of taxonomically informative fungal lineages and highlights the potential of spider web sampling as a complementary tool for biodiversity assessment and environmental monitoring.},
}

@article {pmid42059966,
year = {2026},
author = {Saikia, A and Manu, M and Tewari, G and Tyagi, A and Datta, SN and Kaur, S},
title = {Development of a modified protocol for extraction of environmental DNA from water samples to assess the presence of fish species in wetland ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {42059966},
issn = {1573-2959},
support = {F. No. 82-7/2022(SA-III).//University Grants Commission (UGC)/ ; },
mesh = {*Wetlands ; *DNA, Environmental/analysis ; Animals ; *Environmental Monitoring/methods ; *Fishes/classification ; India ; Biodiversity ; },
abstract = {Accurate fisheries assessment is challenged by limitations in traditional catch estimation methods, suggesting the need for advanced molecular tools such as environmental DNA (eDNA) analysis. This approach has transformed non-invasive biodiversity monitoring worldwide, yet standardized protocols remain underdeveloped in India, limiting practical application. The absence of validated, field-applicable eDNA extraction protocols optimized for complex aquatic environment like wetlands hinders reliable fish diversity assessment. This study validates a modified eDNA extraction protocol using mesocosm and field experiments. Water samples (300 mL) were filtered through glass fiber filters (1.5 μm), preserved in Longmire's and phosphate-buffered saline (PBS) lysis buffers, and processed using a modified phenol-chloroform isoamyl alcohol (PCI) extraction method. eDNA yield was quantified over 0, 10, and 20-day storage intervals and log transformed for analyses, eDNA degradation, and inhibitor modeling was performed. Amplification efficiency was compared for Ward barcode (COI) and Ac12S (12S rRNA) primers. The modified protocol outperformed the conventional protocol. PBS-preserved samples showed initial high yields (log10 mean ± SD, 3.06 ± 0.02 at Day 0) but degraded rapidly (λ = 0.102 day[-][1], half‑life = 6.8 days), falling to 2.18 ± 0.42 by Day 20. Longmire's buffer maintained statistically stable yields across storage (p > 0.05 for all pairwise comparisons), with no significant degradation. Ward barcode consistently amplified Longmire's preserved samples at 50 to 400 ng/μL; PBS samples showed no amplification. Ac12S showed limited amplification in both buffers. Application of the modified protocol in Harike wetland field samples confirmed its sensitivity and practical utility, detecting fish eDNA of Cyprinus carpio, Pethia conchonius, and Lepidocephalichthys thermalis. The findings suggest that buffer selection and standardized extraction are critical for reliable eDNA-based diversity surveys. The optimized workflow enhances flexibility for sampling in resource-limited areas, facilitating non-invasive surveys in protected wetlands.},
}

*Wetlands
*DNA, Environmental/analysis
Animals
*Environmental Monitoring/methods
*Fishes/classification
India
Biodiversity

@article {pmid42062685,
year = {2026},
author = {Xiao, L and Guo, J},
title = {Highly Multiplexed Single-Cell In Situ RNA and DNA Analysis by Consecutive Hybridization.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2995},
number = {},
pages = {219-226},
pmid = {42062685},
issn = {1940-6029},
mesh = {*In Situ Hybridization, Fluorescence/methods ; *Single-Cell Analysis/methods ; Humans ; *RNA/genetics/analysis ; *DNA/genetics/analysis ; Fluorescent Dyes/chemistry ; Gene Expression Profiling/methods ; *Nucleic Acid Hybridization/methods ; },
abstract = {Knowledge of the copy numbers of transcripts and genomic loci in their natural spatial contexts plays an important role in our understanding of biology and medicine. Fluorescent hybridization probes have emerged as a powerful tool to profile transcripts and genomic loci in single cells in situ. However, the number of different nucleic acid species that can be quantified by fluorescence imaging-based methods is limited. Here, we report a highly multiplexed in situ hybridization approach for spatial transcriptomics and genomics analysis. In this approach, each nucleic acid molecule is visualized as a fluorescent spot at its natural cellular context throughout the consecutive cycles of fluorescence in situ hybridization. In each analysis cycle, fluorescent oligonucleotide probes stain the nucleic acid targets by hybridizing to the probes applied in the previous cycle. And these probes also introduce the binding sites for the next cycle probes. Through reiterative cycles of hybridization, imaging, and photobleaching, unique color sequences are generated as barcodes for varied nucleic acids. With multi-color staining and reiterative cycles, tens of thousands of different transcripts or genomic loci could be precisely profiled in individual cells in situ.},
}

*In Situ Hybridization, Fluorescence/methods
*Single-Cell Analysis/methods
Humans
*RNA/genetics/analysis
*DNA/genetics/analysis
Fluorescent Dyes/chemistry
Gene Expression Profiling/methods
*Nucleic Acid Hybridization/methods

@article {pmid42044152,
year = {2026},
author = {Bradley, NJ and Pendyala, S and Partington, K and Fowler, DM},
title = {STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.},
journal = {PLoS computational biology},
volume = {22},
number = {4},
pages = {e1013689},
doi = {10.1371/journal.pcbi.1013689},
pmid = {42044152},
issn = {1553-7358},
abstract = {Fluorescent in situ sequencing involves imaging-based sequencing by synthesis in intact cells or tissues to reveal target nucleotide sequences inside each cell. Often, the target sequences are barcodes that indicate a perturbation (e.g., CRISPR guide or genetic variant) delivered to the cell. However, processing in situ sequencing data presents a considerable challenge, requiring stitching and aligning tens of thousands of images with millions of cells, detecting small amplicon colonies across sequencing cycles, and calling reads. To address these challenges, we introduce STARCall: STitching, Alignment and Read Calling for in situ sequencing, a software package that analyzes raw in situ sequencing images to produce a genotype-to-phenotype mapping for each cell. STARCall improves upon previous solutions by combining stitching and alignment of images into a single step that minimizes both inter-cycle and intra-cycle alignment error. STARCall also improves detection and extraction of sequencing reads, incorporating filters and normalization to combat background fluorophore signal. We compare STARCall to other methods using a diverse set of images that include commonly encountered imaging problems such as variable intensity across channels and cycles and high levels of background. Specifically, this comprises ~250,000 images from a pooled screen of ~3,500 barcoded LMNA variants expressed in U2OS cells and ~1,200 barcoded PTEN variants in induced pluripotent stem cells (iPSC) and iPSC-derived neurons. Overall, STARCall aligned more than 50% of tiles with <1 pixel residual misalignment on all nine image sets, outperforming alternative packages by 14-35%. STARCall also yielded an 8-40% increase in genotyped cells due to improved filtering and normalization methods that address background fluorescence. STARCall can call tools like CellPose to segment cells and CellProfiler to compute cell features from the phenotyping images. STARcall is open-source and freely available, providing a robust solution for the analysis of in situ sequencing data.},
}

@article {pmid42046693,
year = {2026},
author = {de Souza, NF and Shing, TF and Souto, LG and Vieira, FFA and Nishihara, JKLF and Santos, NYYD and Rostirolla, BP and Gomes, MDC and de Moura, FBC and Rocha, NS},
title = {Biobanks in veterinary forensic medicine: A systematic review on Advances, challenges, and applications in combating wildlife trafficking.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {933-947},
pmid = {42046693},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Biobanks represent organized repositories of biological samples linked to associated data, designed for long-term scientific, clinical, and forensic utilization. In veterinary medicine, animal biobanks facilitate biomedical research, genetic resource preservation, species conservation, and forensic investigations. The present systematic review aimed to synthesize advances, persistent challenges, and practical applications of biobanks in veterinary forensic medicine, with particular emphasis on their contribution to detection, investigation, and suppression of wildlife trafficking.

MATERIALS AND METHODS: A systematic literature search was conducted across Periódicos Capes, PubMed, SciELO, and ScienceDirect databases, covering publications from 2013 to 2023. Search strings combined terms such as "animal biobank", "animal biorepository", "wildlife forensic", "wildlife trafficking", and "forensic veterinary" (English), together with Portuguese equivalents. Only peer-reviewed articles published in English or Portuguese that explicitly addressed biobanks in veterinary forensic contexts or wildlife crime were included. The review adhered to PRISMA 2020 guidelines. Screening involved title/abstract evaluation followed by full-text assessment. Data were narratively synthesized.

RESULTS: Of 1,495 records identified, 15 studies fulfilled all inclusion criteria after exclusion of 1,460 irrelevant or non-qualifying publications. No eligible articles appeared between 2013 and 2014. From 2015 onward, publications demonstrated progressive refinement, transitioning from molecular barcoding for species identification toward integrated applications in geographic origin assignment, chain-of-custody documentation, and evidentiary support in judicial proceedings. Key materials included DNA from muscle, scales, claws, and feathers; cryopreserved gonadal tissues; and somatic cells derived from minimally invasive sources (e.g., feather follicles) or roadkill specimens. Studies highlighted particular utility in identifying fraudulently labeled fishery products, counterfeit mammalian derivatives (e.g., fake tiger claws), and confiscated pangolin scales, as well as in tracing trafficking routes in high biodiversity regions.

CONCLUSION: Veterinary forensic biobanks offer substantial potential for accurate species and geographic provenance determination, thereby strengthening enforcement against illegal wildlife trade. Nevertheless, implementation remains constrained by absent standardized operating procedures, limited practitioner awareness, fragmented reference databases, inadequate inter-institutional connectivity, and elevated logistic/financial demands. Regionalized biobanks integrated with wildlife screening centers (CETAS), harmonized chain-of-custody protocols, and artificial intelligence-supported data curation are proposed as priority strategies to translate existing scientific advances into routine forensic and conservation practice.},
}

@article {pmid42049714,
year = {2026},
author = {Özil, E and Gombkoto, P and Apostolelli, A and Yasar, TB and Vavladeli, AD and Marks, M and Rohr-Fukuma, M and von der Behrens, W and Yanik, MF},
title = {Magnetic resonance identification tags for ultra-flexible electrodes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71887-x},
pmid = {42049714},
issn = {2041-1723},
support = {818179//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Ultra-flexible electrodes, due to their superior biocompatibility, are likely to lead the future of neuroprosthetics. However, identifying the precise positions of implanted high-density ultra-flexible electrodes in the brain for accurately assigning neural signals to specific structures remains a major challenge. To address this, we developed magnetic resonance identification (MRID)-tags. Each ultra-flexible electrode bundle carries an MRID-tag with unique barcode patterns visible in MRI (MRI-barcodes) for identification of the bundle. Individual bars in MRI-barcodes allow an accurate 3D reconstruction of the ultra-flexible electrode bundle's trajectory in the brain and determine the anatomical positions of individual electrodes. We generate the MRI-barcodes by patterning superparamagnetic iron-oxide nanoparticles into electrode fibers (10 µm[2]) with dot-matrix nanoparticle coating technique. We chronically tested MRID-tagged ultra-flexible electrodes in vivo in the dorsal hippocampus of freely-moving rats, where distinct electrophysiological landmarks validated our electrode localization results. We were able to localize individual electrodes with a mean accuracy of 95 μm. MRID-tagged ultra-flexible electrodes demonstrated high long-term recording stability with mean single-unit signal-to-noise ratios as high as 20.},
}

@article {pmid42041883,
year = {2026},
author = {Wu, Y and Xu, H and Li, H and Chen, H and Zhang, L and Ali, S and Che, J and Bao, B},
title = {Seasonal Dynamics of the Gut Microbiota of Ayu (Plecoglossus altivelis) Revealed by a Cross-Sectional Seasonal Survey in the Dajing Stream, Zhejiang Province, China.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041883},
issn = {2079-7737},
support = {25FW044//Special Survey on River- and Lake-Migratory Fish Resources in Yueqing City/ ; },
abstract = {Ayu (Plecoglossus altivelis) is an East Asian amphidromous river fish, yet seasonal microbiota dynamics remain unclear. We investigated ayu in the Dajing Stream (Zhejiang Province, China) by synchronously sampling water microbiota (H), gut content microbiota (N), and gut tissue-associated microbiota (C) across four seasons. Each season, four fish were collected, and an overlapping pooling strategy (abc/abd/bcd) generated three composite replicates for C and N (n = 3 composites/season); water was collected as three field replicates (n = 3/season), yielding 36 samples (12 per niche). Using 16S rRNA amplicon sequencing and COI barcoding of stomach contents, we observed the clearest seasonal differentiation in H and seasonal variation in N consistent with diet shifts, whereas C was comparatively stable. COI signals indicated a diet dominated by aquatic insects in spring/summer, which shifted toward smaller prey (e.g., rotifers) in winter. Together, these results highlight strong niche partitioning and season-linked shifts in water and gut content communities relative to the more stable tissue-associated microbiota. These findings should be interpreted as exploratory and require validation in larger individual-level studies.},
}

@article {pmid42043355,
year = {2026},
author = {Çalişir, B and Erdi, B and Hunutlu, FÇ and Kazak, E and Özkalemkaş, F and Akalin, EH and Ener, B},
title = {[Rasamsonia argillacea in Patient with Immunodeficiency: First Suspected Case in Türkiye].},
journal = {Mikrobiyoloji bulteni},
volume = {60},
number = {2},
pages = {237-244},
doi = {10.5578/mb.202602102},
pmid = {42043355},
issn = {0374-9096},
mesh = {Humans ; Female ; Aged ; Antifungal Agents/therapeutic use ; *Leukemia, Myeloid, Acute/complications/drug therapy/immunology ; *Immunocompromised Host ; Amphotericin B/therapeutic use ; Fatal Outcome ; },
abstract = {Rasamsonia species are thermophilic fungi that primarily cause infection in immunocompromised patients. R.argillacea species complex is frequently misidentified as a pathogen due to its morphological similarity to the genera Penicillium and Paecilomyces and its incidence remains undetermined. This situation further complicates the process of timely diagnosis and treatment. Rasamsonia species can be identified using internal transcribed spacer (ITS) sequence analysis, which is considered the primary fungal barcode. Accurate species identification is imperative for the administration of appropriate antifungal treatment. In this report, a case of acute myeloid leukaemia (AML) with R.argillacea growth was presented. A 69-year-old female patient diagnosed with AML who was undergoing chemotherapy was admitted to the hospital due to febrile neutropenia. Despite the administration of appropriate antibiotic therapy, the patient's fever did not respond and her respiratory distress worsened. A subsequent chest computerized tomography scan revealed the presence of bilateral nodular lesions and halo findings in some nodules. The empirical liposomal amphotericin B was initiated at a dosage of 3 mg/kg/day. Following a 17-day course of empirical amphotericin B therapy, the patient exhibited an escalation in respiratory distress and an increase in her blood galactomannan (GM) level (Platelia™ Aspergillus Ag; Bio-Rad, France). Consequently, intravenous (IV) voriconazole was administered at a loading dose of 2x6 mg/kg followed by a maintenance dose of 2x4 mg/kg. Notwithstanding the administration of voriconazole therapy, the patient's blood GM levels persisted at elevated levels on three separate occasions. Consequently, a bronchoalveolar lavage (BAL) sample was obtained for further analysis. However, no growth was detected in the bronchoalveolar lavage (BAL) culture. The BAL GM level was found to be elevated (optic indices: 4.38). The patient developed increasing respiratory distress and confusion and was intubated. A deep tracheal aspirate (DTA) sample was collected. The patient died shortly thereafter. Velvety, beige-colored colonies were observed in the culture media to which the DTA sample inoculated. Microscopic examination of the culture using a lactophenol cotton blue stain revealed cylindrical conidia, rough-walled conidiophores and long, pointed phialides. The isolate was identified as R.argillacea using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (Bruker, Bremen, Germany). This isolate could not be identified based on colony morphology and microscopic appearance; however, it was identified as R. argillacea using the ribosomal DNA ITS region. Its antifungal susceptibility was then assessed using the microdilution method according to the Clinical and Laboratory Standards Institute M38-A2 guidelines. The minimum inhibitory concentrations (MICs) for the antifungal drugs were as follows: fluconazole >64 μg/mL, itraconazole 0.5 μg/mL, voriconazole >16 μg/mL, posaconazole 0.5 μg/ mL, anidulafungin ≤0.015 μg/mL, micafungin 0.03 μg/mL and amphotericin B 1 μg/mL. In this case, the patient died without the causative agent being identified. Although it cannot be definitively stated that R. argillacea was the cause of the patient's mortality due to the lack of an autopsy, this case was presented because it is the first suspected case of R. argillacea isolated and confirmed by molecular methods in Türkiye and to highlight the importance of not neglecting Rasamsonia species which are rare mold fungi.},
}

Humans
Female
Aged
Antifungal Agents/therapeutic use
*Leukemia, Myeloid, Acute/complications/drug therapy/immunology
*Immunocompromised Host
Amphotericin B/therapeutic use
Fatal Outcome

@article {pmid42040836,
year = {2026},
author = {Marín-Villa, J and Rincón-Flórez, JC and Úsuga-Monroy, C and López-Herrera, A},
title = {Mitochondrial Markers COI and 16S rRNA for the Molecular Identification of Parrots and Macaws Recovered From Illegal Trafficking in Three Areas of Colombia.},
journal = {Ecology and evolution},
volume = {16},
number = {4},
pages = {e73335},
pmid = {42040836},
issn = {2045-7758},
abstract = {Illegal wildlife trafficking is a major threat to biodiversity, severely affecting many species, including Psittacidae. In this context, molecular tools such as DNA barcoding provide an effective alternative for taxonomic identification, complementing traditional morphological methods. This study aimed to molecularly characterize parrots (Amazona spp.) and macaws (Ara spp.) recovered from illegal trafficking in Colombia using two mitochondrial markers (COI and 16S rRNA). Eighty-eight DNA samples from whole blood of Psittacidae individuals from three regions (Antioquia, Valle del Cauca, and Cesar) were analyzed. The COI gene provided higher resolution for species identification, generating 65 new sequences and 35 haplotypes (20 Amazona spp. and 15 Ara spp.). Unique haplotypes were found for each species, with clear differentiation in phylogenetic and PCoA analyses. High intraspecific diversity was detected in Amazona amazonica, Ara severus, and Ara ararauna, relevant for future population studies. In contrast, 16S rRNA yielded 77 new sequences clustered into 28 haplotypes (19 Amazona spp. and 9 Ara spp.). However, its low variability limited taxonomic resolution, with poorly defined clusters in haplotype networks and PCoA. Phylogenetic inference supported species-level grouping under mitochondrial data, except within the yellow-headed parrot complex. Overall, the COI gene demonstrated greater utility for species identification and genetic characterization in Amazona and Ara species, while the 16S rRNA gene showed limited discriminatory power due to its conserved nature. These findings highlight the value of COI as a reliable molecular tool for wildlife forensic applications and strengthen molecular identification frameworks to combat illegal wildlife trafficking.},
}

@article {pmid42040977,
year = {2026},
author = {Luo, XX and Qiu, MY and Cai, TT and Wang, ZQ and Che, YL},
title = {Taxonomic update on the genus Unihamus Luo & Wang, 2025 (Blattidae, Blattinae), with three new species described.},
journal = {ZooKeys},
volume = {1277},
number = {},
pages = {175-197},
pmid = {42040977},
issn = {1313-2989},
abstract = {Unihamus Luo & Wang, 2025 was recently split from Periplaneta sensu lato, yet its diversity and morphology remain poorly documented. Here we redescribe the type, Unihamus elegans (Hanitsch, 1927) and describe three new species, U. flavus Luo & Che, sp. nov., U. concavus Luo & Che, sp. nov., and U. longispinus Luo & Che, sp. nov. Males and females are associated by using DNA barcoding. We present high-resolution photographs and detailed diagnoses for each species. Finally, the future research directions of the distinctive sclerite L3 were prospected.},
}

@article {pmid42027772,
year = {2026},
author = {Yongsa, M and Nguyen, NTT and Nguyen, LTN and Sy, TD and Tu, TQ and Chu, MH},
title = {Dataset of chloroplast intergenic spacer sequences and candidate DNA markers for species identification in Hoya (Apocynaceae) based on the plastome of Hoya lockii V.T. Pham & Aver. from Vietnam.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112757},
pmid = {42027772},
issn = {2352-3409},
abstract = {Hoya lockii V.T. Pham & Aver. is an epiphytic species that exhibits strong morphological similarity to several closely related congeners, which may hinder accurate species identification, especially when specimens are incomplete or degraded. This article presents a curated dataset of chloroplast intergenic spacer sequences to support molecular identification and phylogenetic assessment of H. lockii. The dataset includes six plastid intergenic spacer regions (trnK-rps16, psbI-atpA, trnH-psbA, psbK-psbI, ndhC-trnV, and rbcL-accD) extracted from complete chloroplast genomes. Phylogenetic analyses based on individual loci revealed variation in topological resolution and bootstrap support among regions. Among them, the markers psbI-atpA and ndhC-trnV showed relatively strong phylogenetic signals. In the ndhC-trnV tree, H. lockii formed a well-supported clade with Hoya exilis (bootstrap = 99%). In the psbI-atpA tree, H. lockii was recovered as the sister of Hoya lanceolata, with strong bootstrap support (99%). Multilocus phylogenetic reconstruction based on concatenated alignments of six intergenic spacers further improved tree stability and resolution, recovering H. lockii as the sister taxon of H. exilis with strong bootstrap support (100%). These results indicate that psbK-psbI, psbI-atpA, and ndhC-trnV, together with the concatenated dataset, represent potential DNA marker candidates to support species identification within the genus Hoya. The dataset provides a reproducible molecular resource that may facilitate phylogenetic analysis, DNA barcoding, and taxonomic studies of Hoya and related taxa in Apocynaceae.},
}

@article {pmid42027885,
year = {2026},
author = {Barman, S and Pathour Rajendra, S and Diksha, D and Sharma, SK and Gupta, N and Hadpad, G and Dhillon, MK and Ray, S},
title = {Simple, rapid and cost-effective DNA extraction techniques for detection of economically important fruit flies in India.},
journal = {MethodsX},
volume = {16},
number = {},
pages = {103900},
pmid = {42027885},
issn = {2215-0161},
abstract = {Fruit flies (Diptera: Tephritidae) include nearly 200 economically important species, many of which are quarantine pests. Accurate identification is vital for pest management, but morphological diagnosis is often difficult for non-specialists due to similarities in diagnostic traits. DNA barcoding has become the gold standard, providing precise species identification using molecular markers. However, conventional DNA extraction methods, though reliable, are time-consuming and require advanced laboratory facilities, while commercial kits are costly and unsuitable for large-scale use and resource-limited settings. To address this, we established four new rapid and inexpensive DNA extraction methods using Tween 20 + NaOH solution (RDI) buffer, Phosphate Buffer Saline (PBS), Tris-EDTA (TE) buffer and Chelex + Proteinase K solution (Chelex buffer). These methods consistently yielded DNA of sufficient quality and concentration across five major tephritid pests: Zeugodacus cucurbitae, Z. tau, Bactrocera dorsalis, B. divenderi and B. zonata. DNA integrity was confirmed through fluorometric and spectrophotometric analysis and successful amplification of the mitochondrial COI gene.•Here, we developed rapid and inexpensive DNA extraction protocols capable of producing DNA from five major fruit fly pests..•Requires only 20-45 min, without special equipment and produces DNA of sufficient quality for PCR-based barcoding.•Provides a practical alternative for resource-poor laboratories.},
}

@article {pmid42030163,
year = {2026},
author = {Fernandez Bonet, D and Blumenthal, J and Lang, S and Dahlberg, S and Hoffecker, IT},
title = {Computational protocol to assess the quality of sequencing-based microscopy networks using spatial coherence metrics.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104521},
doi = {10.1016/j.xpro.2026.104521},
pmid = {42030163},
issn = {2666-1667},
abstract = {Sequencing-based microscopy captures spatial information as DNA barcode networks. Here, we present a protocol for measuring the spatial quality of such networks by estimating the intrinsic network dimension and Gram-matrix spectral scores from the network's shortest-path distances. We describe steps for installing the software, inputting the edge list of the network, and computing spatial coherence. We then detail procedures for transforming the network into an image. The pipeline handles fast strategies for large graphs and optionally reconstructs spatial layouts for visualization. For complete details on the use and execution of this protocol, please refer to Fernandez Bonet et al.[1].},
}

@article {pmid42031935,
year = {2026},
author = {Hao, D and Xu, X and Li, P and Liu, Y and Liu, G and Deng, S},
title = {A method for CRISPR/Cas9-induced genetic barcoding and lineage tracing in sheep.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49093-y},
pmid = {42031935},
issn = {2045-2322},
support = {2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; },
}

@article {pmid42034633,
year = {2026},
author = {Armbrust, N and Grosshauser, M and Geilenkeuser, J and Stroppel, L and Jozinovic, M and Levermann, H and Panne, T and Wißmann, J and Goelitz, L and Schmidt, S and Orschmann, T and Rusha, E and Steinmaßl, E and Widenmeyer, F and Warsing, N and Sabry, M and Sultanbai, A and Santl, T and Geerlof, A and Berezin, O and Bodea, SV and Moretti, A and Schneider, S and Theis, F and Gagneur, J and Truong, DJ and Westmeyer, GG},
title = {Non-destructive transcriptomics via vesicular export.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42034633},
issn = {2041-1723},
support = {Proof of Concept 101138939//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Animals ; Humans ; Mice ; *Transcriptome ; *Gene Expression Profiling/methods ; Cell Differentiation/genetics ; Induced Pluripotent Stem Cells/metabolism/cytology ; Cell Line ; RNA, Messenger/metabolism/genetics ; Coculture Techniques ; },
abstract = {Transcriptomics enables comprehensive, multiplexed characterization of cellular states, yet prevailing methods typically require cell fixation or lysis, precluding longitudinal analysis of RNA expression in living cells. Here, we present non-destructive transcriptomics by vesicular export (NTVE), a platform for multi-time-point monitoring of RNA expression dynamics in living cells. Stabilized RNA reporter barcodes can be selectively packaged and exported from cells via virus-like particles (VLPs) bearing bioorthogonal affinity handles for convenient multichannel tracking of co-cultured cells. Using an engineered poly(A)-binding protein adapter, NTVE exports endogenous transcripts from inducible human and murine cell lines with high concordance to conventional lysate-derived RNA-seq. NTVE captures transcriptome changes in response to genetic and chemical perturbations within the same cells over time using standard sequencing workflows. NTVE can further be equipped with fusogens to deliver mRNA-encoded effectors or ribonucleoprotein gene editors from sender cells, activating gene reporters in co-cultured recipient cells. We demonstrate the utility of NTVE for monitoring hiPSC differentiation through daily non-destructive transcriptomic profiling of lineage-specific marker dynamics.},
}

Animals
Humans
Mice
*Transcriptome
*Gene Expression Profiling/methods
Cell Differentiation/genetics
Induced Pluripotent Stem Cells/metabolism/cytology
Cell Line
RNA, Messenger/metabolism/genetics
Coculture Techniques

@article {pmid42039104,
year = {2026},
author = {Shah, HK and Fathima, PA and Rahi, M and Saini, P},
title = {Sergentomyia (Neophlebotomus) chattiensis n. sp.: morphological and molecular description of a new sand fly species from Himachal Pradesh, India.},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1814368},
pmid = {42039104},
issn = {2673-8600},
abstract = {INTRODUCTION: Himachal Pradesh, an ecologically diverse state in northern India, has recently emerged as a focus of atypical cutaneous leishmaniasis. As part of a molecular xenomonitoring, systematic entomological surveillance of sand flies resulted in the reporting of a novel species, Sergentomyia (Neophlebotomus) chattiensis n. sp. (Diptera: Psychodidae), from Chatti village in Kullu district, Himachal Pradesh, India.

METHODS: A systematic cross-sectional entomological survey was carried out in the districts of Kinnaur, Kullu, Shimla, and Mandi during August 2022, employing standard sand-fly collection techniques. Molecular characterization was performed using mitochondrial cytochrome c oxidase subunit I (COI) gene-based DNA barcoding, followed by phylogenetic analysis of the generated sequences.

RESULTS: The study reports Sergentomyia (Neo.) chattiensis as a newly recorded sand fly species and discusses its taxonomic association with other members of the subgenus Neophlebotomus. COI-based phylogenetic assessment confirmed that the collected specimens form a single taxonomic unit with negligible intraspecific genetic variation, while a genetic divergence of 12.3% from its closest congener supports its designation as a distinct species.

DISCUSSION: Despite its diverse physiography, rich biodiversity, and ecological suitability for sand fly breeding, Himachal Pradesh has lacked systematic entomological surveillance. The present study contributes to bridging this gap by expanding the existing knowledge of sand fly fauna in the state and providing comprehensive morphological and molecular characterization of this newly described species.},
}

@article {pmid42039444,
year = {2026},
author = {Hayford, CE and Baleami, B and Stauffer, PE and Paudel, BB and Al'Khafaji, A and Brock, A and Quaranta, V and Tyson, DR and Harris, LA},
title = {Heterogeneous, population-level drug-tolerant persisters exhibit ion-channel remodeling and ferroptosis susceptibility.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2022.02.03.479045},
pmid = {42039444},
issn = {2692-8205},
abstract = {Drug-tolerant persisters (DTPs) represent a major obstacle to durable responses in targeted cancer therapy. DTPs are commonly described as distinct single-cell states that survive drug treatment via reversible, non-genetic mechanisms and drive tumor recurrence. Recent work demonstrates that multiple DTPs can coexist, reflecting diversity in lineage, signaling programs, or stress responses. However, each DTP is still generally viewed as a uniform cellular phenotype. Building on our prior work describing a population-level DTP termed "idling" [Paudel et al., Biophys. J. (2018) 114, 1499-1511], here we present evidence supporting a fundamentally different view: that DTPs are not single-cell states, but rather heterogeneous populations composed of multiple sub-states with distinct division and death rates that balance to produce near-zero net population growth. Using single-cell transcriptomics and lineage barcoding, we identify multiple phenotypic states within idling DTP populations, with reduced heterogeneity compared to untreated populations, and find that idling DTP cells emerge from nearly all lineages. Transcriptomic and functional analyses further reveal altered ion-channel activity in idling DTPs, which we confirm experimentally. Moreover, drug-response assays reveal increased susceptibility of idling DTPs to ferroptosis, a non-apoptotic form of regulated cell death, indicating the emergence of vulnerabilities associated with drug tolerance. Altogether, our results support a population-level view of tumor drug tolerance in which DTPs comprise stable collections of phenotypic states, shaped by treatment-defined phenotypic landscapes, which are potentially vulnerable to subsequent interventions. This perspective implies that eradicating DTPs will require a fundamental shift away from cell-type-centric strategies toward sequential treatments that progressively reduce phenotypic heterogeneity by modulating the molecular and cellular processes that establish the DTP landscape, an approach previously termed "targeted landscaping."},
}

@article {pmid42039491,
year = {2026},
author = {Aydin, Y and Zhuo, Y and Yen, YC and Chen, CL and Klug, CS and Marchese, A and Chen, Q},
title = {Cooperative Control of Arrestin Activation By Membrane Lipids And Phosphorylation Barcodes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.13.718317},
pmid = {42039491},
issn = {2692-8205},
abstract = {Arrestins regulate G protein-coupled receptor (GPCR) signaling by binding phosphorylated receptors embedded in lipid bilayers, yet how receptor phosphorylation and membrane composition cooperate to control arrestin activation remains unclear. Here, we reconstitute this interplay using N-terminally palmitoylated phosphopeptides tethered to nanodiscs of defined lipid composition and quantitatively measure arrestin-2 (Arr2) activation and membrane engagement. We find that both receptor phosphorylation and the lipid environment are essential for robust Arr2 activation, with phosphoinositides (PIPs) and other anionic lipids facilitating Arr2 activation and membrane association through distinct mechanisms. Systematic profiling of phosphorylation barcodes derived from atypical chemokine receptor 3 (ACKR3) and vasopressin receptor 2 (V 2 R) identifies phospho-motifs that potently activate Arr2. Moreover, the position of these motifs relative to the membrane determines Arr2 engagement, supporting a model of regional phosphorylation barcodes. Genome-wide motif analysis further links the phosphorylation barcode to predicted arrestin coupling strength and classification into Class A or Class B GPCRs. Finally, lipidated phosphopeptides inhibit GPCR-Arr2 interactions in live cells and enable structural characterization of Arr2-phosphopeptide complexes by cryo-electron microscopy, establishing a membrane-integrated framework for decoding arrestin response.},
}

@article {pmid42039607,
year = {2026},
author = {Luo, C and Liu, YH and Liu, H and Zhang, Z and Zhang, L and Peters, BA and Zhou, XM},
title = {A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.31.646392},
pmid = {42039607},
issn = {2692-8205},
abstract = {Accurate detection of genetic variants, including single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), and structural variants (SVs), is essential for comprehensive genomic analysis. While short-read sequencing performs well for SNP and INDEL detection, it remains limited in resolving SVs, particularly in complex genomic regions, due to its short read length. Linked-read sequencing technologies, such as single-tube Long Fragment Read (stLFR), partially address this limitation by incorporating molecular barcodes to provide long-range information. In this study, we evaluate conventional paired-end linked reads (PE100_stLFR) and explore a conceptual extension: long single-end barcoded reads of 500 bp (SE500_stLFR) and 1000 bp (SE1000_stLFR). We developed_stLFR-sim, a Python-based simulator that reproduces the_stLFR workflow and enables realistic benchmarking. Using a high-quality T2T assembly of HG002, we generated multiple datasets across 12 sequencing configurations. SVs were called using Aquila_stLFR (v2) and benchmarked against the Genome in a Bottle (GIAB) HG002 SV truth set with Truvari. We show that simulated PE100_stLFR closely matches real data, validating the simulation framework. Increasing read length consistently improves SV detection accuracy, with SE1000_stLFR achieving the best performance and approaching long-read methods while outperforming short-read and pangenome-based approaches. Collectively, our results highlight the strong potential of long single-end barcoded reads for improving SV detection, and suggest that even modest increases in read length, when combined with barcode information, can provide a cost-effective and practical strategy for enhancing future sequencing technologies and SV discovery.},
}

@article {pmid42027143,
year = {2026},
author = {Huang, Z and Lun, XK and Liu, R and Lv, Y},
title = {Elemental Barcoding Beyond Optics: Metal-Isotopic Suspension Array for Emerging High-Throughput Diagnostics.},
journal = {Accounts of chemical research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.accounts.6c00101},
pmid = {42027143},
issn = {1520-4898},
abstract = {ConspectusPrecision medicine is transforming healthcare by enabling stratified and personalized treatments driven by our growing ability to comprehensively characterize molecular features in diseased tissues and liquid biopsies. Advances in genomic, transcriptomic, proteomic, and metabolomic profiling have increasingly reshaped disease diagnostics, shifting monitoring paradigms from a small number of single-analyte biomarkers toward highly multiplexed platforms capable of capturing biological complexity at the systems level. For liquid biopsy profiling in particular, suspension arrays have emerged as a powerful approach for broad biomarker coverage, leveraging "barcode"-based identification to achieve exponentially scalable multiplexing from a limited set of barcoding units. Since the early 1980s, suspension array technologies have evolved within flow cytometry frameworks, accompanied by continuous innovation in optical barcoding architectures. However, optical barcoding remains fundamentally challenged by constrained color palettes and spectral cross-talk, imposing a multiplexing ceiling that restricts barcoding scalability.The multiplexing challenge imposed by optical barcoding has been substantially alleviated by the emergence of metal-isotopic barcoding strategies coupled with inductively coupled plasma mass spectrometry (ICP-MS). Rather than encoding analytes using spectrally overlapping fluorophores, metal barcoding encodes sample identities using combinatorial patterns of multiple nonradioactive metal isotopes with distinct atomic masses, enabling intrinsically orthogonal detection with minimal crosstalk and allowing a far greater number of analytes to be quantified simultaneously within a single assay. Within this class of technologies, mass cytometry, a specialized ICP-MS platform optimized for single-cell (single-particle) analysis, can resolve up to 135 mass channels with high precision, more than 60 of which can be technically used as molecular tags or barcoding channels. Such capability has paved the way for highly scalable suspension array technologies. Despite these advances, two critical challenges still remain: (1) the absence of templated and scalable barcode frameworks that enable rapid and reproducible construction of high-capacity barcode libraries and (2) the need to amplify the biomarker reporter signals to maximize assay sensitivity without compromising barcoding fidelity.To address these challenges, our group has pursued long-term research since 2010 on metal nanoparticle tagging to enhance both the sensitivity and multiplexing capability in pooled-sample bioassays. We began this effort with an early demonstration of metal nanoparticles as "signal amplifiers" in ICP-based mass spectrometry. Beyond sustained efforts in signal enhancement using metal nanotags, our more recent work on a barcoding strategy by controllable nanoparticle accumulation and self-assembly has notably rekindled interest in facile and scalable barcode designs for customizable mass cytometric suspension platforms. Herein, we provide an evolution account of cytometric suspension array and highlight key breakthroughs in scalability by metal-isotopic barcoding. We summarize the mechanism, design considerations, and emerging applications of these barcoding strategies in high-throughput bioassays. Particular emphasis is placed on our conceptual framework, recent advances, and ongoing progress in metal nanoparticle tagging to break through a sensitive bioassay and programmable barcoding for new suspension arrays. We envision that the barcoding strategies iterating from optical to mass cytometry could profoundly reshape biological discovery, multiplexing capacity, and clinical diagnostics, further opening the postfluorescence era for ultrasensitive and high-throughput precision medicine.},
}

@article {pmid42014735,
year = {2026},
author = {Orsholm, J and Quinto, J and Autto, H and Banelyte, G and Chazot, N and deWaard, J and deWaard, S and Farrell, A and Furneaux, B and Hardwick, B and Ito, N and Kar, A and Kalttopää, O and Kerdraon, D and Kristensen, E and McKeown, J and Mononen, T and Nein, E and Rogers, H and Roslin, T and Schmitz, P and Sones, J and Sujala, M and Thompson, A and Zakharov, EV and Zarubiieva, I and Gupta, A and Lowe, SC and Taylor, GW},
title = {A multi-modal dataset for insect biodiversity with imagery and DNA at the trap and individual level.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42014735},
issn = {2052-4463},
support = {856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 856506//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 2330423//National Science Foundation (NSF)/ ; 2330423//National Science Foundation (NSF)/ ; 2330423//National Science Foundation (NSF)/ ; 585136//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; 585136//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; 585136//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; 225-20-002//Naturvårdsverket (Swedish Environmental Protection Agency)/ ; NFRFT-2020-00073//Government of Canada (Gouvernement du Canada)/ ; },
mesh = {Animals ; *Biodiversity ; DNA Barcoding, Taxonomic ; *Insecta/classification/genetics ; DNA ; },
abstract = {Insects comprise millions of species, many experiencing severe population declines under environmental and habitat changes. High-throughput approaches are crucial for accelerating our understanding of insect diversity, with DNA barcoding and high-resolution imaging showing strong potential for automatic taxonomic classification. However, most image-based approaches rely on individual specimen data, unlike the unsorted bulk samples collected in large-scale ecological surveys. We present the Mixed Arthropod Sample Segmentation and Identification (MassID45) dataset for training automatic classifiers of bulk insect samples. It uniquely combines molecular and imaging data at both the unsorted sample level and the full set of individual specimens. Human annotators, supported by an AI-assisted tool, performed two tasks on bulk images: creating segmentation masks around each individual arthropod and assigning taxonomic labels to over 17000 specimens. Combining the taxonomic resolution of DNA barcodes with precise abundance estimates of bulk images holds great potential for rapid, large-scale characterization of insect communities. This dataset pushes the boundaries of tiny object detection and instance segmentation, fostering innovation in both ecological and machine learning research.},
}

Animals
*Biodiversity
DNA Barcoding, Taxonomic
*Insecta/classification/genetics
DNA

@article {pmid42016216,
year = {2026},
author = {Munusamy, S and Jahani, R and Chen, J and Zhou, S and Kong, J and Zheng, H and Guan, X},
title = {A CRISPR-Cas12a amplified RNase activity sensor powered by gold nanoparticle-barcode DNA multipliers.},
journal = {Materials advances},
volume = {},
number = {},
pages = {},
pmid = {42016216},
issn = {2633-5409},
abstract = {Ribonuclease A (RNase A) is a clinically relevant biomarker whose aberrant activity compromises RNA stability and interferes with RNA-based therapeutics, highlighting the need for rapid and ultrasensitive detection tools. In this work, we developed a CRISPR/Cas12a-assisted biosensing platform integrated with a substrate-bridged magnetic bead-gold nanoparticle assembly (SB-MAC) for highly sensitive and selective RNase A detection. By optimizing AuNP loading density, RNA substrate/barcode DNA molar ratio, and enzymatic incubation conditions, the prepared dual-functionalized SB-MAC architecture enabled efficient substrate/RNase A cleavage interaction and significant signal amplification, yielding a limit of detection (LOD) of 0.16 pg mL[-1] for RNase A. The sensor exhibited excellent specificity against structurally and functionally related biomolecules and demonstrated strong analytical performance when tested on serum and water samples, with recoveries obtained ranging from 104 to 110%. Owing to its modular substrate design and robust signal amplification, this DNA-assisted platform offers a versatile and clinically relevant tool for monitoring RNase A activity and can be readily adapted for detecting other nuclease-based biomarkers.},
}

@article {pmid42016944,
year = {2026},
author = {Sukupayo, PR and Khadka, D and Maharjan, J and Poudel, RC and Ghimire, TR},
title = {Genetic Diversity and Phylogenetic Relationships of Mosquitoes (Diptera: Culicidae) in Central Nepal.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73249},
pmid = {42016944},
issn = {2045-7758},
abstract = {Mosquitoes (family: Culicidae) include several species that act as vectors of major human diseases by transmitting pathogens such as Plasmodium spp. (malaria), dengue virus (dengue), filarial worms (filariasis), and various other arboviruses. Species from the subfamilies Anophelinae and Culicinae are key transmitters of pathogens. This research aimed to assess genetic diversity and phylogenetic relationships among different species of mosquitoes collected from five districts of central Nepal. The mitochondrial cytochrome c oxidase I (COI) and Internal Transcribed Spacer 2 (ITS2) genes were employed for genetic diversity. A total of 7223 mosquitoes were gathered, encompassing 18 species from eight genera across an altitudinal range from 62 to 3840 m above sea level. From the collected mosquitoes, 114 high-quality sequences were obtained. Ae. aegypti exhibited lower diversity, with a haplotype diversity (Hd) of 0.46 ± 0.20 and a nucleotide diversity (π) of 0.006. The significantly negative Tajima's D value (-1.76, p < 0.05) suggests the possibility of a recent population expansion or the effect of purifying selection on this species. Phylogenetic analysis revealed distinct clades for most genera, while Aedes exhibited paraphyly. Intraspecific genetic divergence (K2P distances) was below 2.39%, while interspecific divergence exceeded 8%. The highest interspecific divergence was observed between Tx. splendens and An. subpictus (25.28%), and the lowest between Cx. pipiens and Cx. quinquefasciatus (0.43%). Haplotype network analysis revealed that Ae. aegypti exhibited a star-like pattern with a widely shared central haplotype and low-frequency variants, whereas Ae. albopictus showed a more structured network with two main clusters. These findings provide valuable information on the genetic diversity and evolutionary relationships among mosquito species in Nepal.},
}

@article {pmid42016980,
year = {2026},
author = {De Panis, D and Priotto, O and Padró, J},
title = {Mitogenomic and Metabarcoding Resources for the Study and Conservation of Keystone Neotropical Raptors.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73262},
pmid = {42016980},
issn = {2045-7758},
abstract = {Neotropical raptors are among the most threatened birds, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the mitochondrial genomes of nine high-priority raptors from the Neotropics, including the threatened Chaco Eagle (Buteogallus coronatus), Black-and-Chestnut Eagle (Spizaetus isidori), Rufous-tailed Hawk (Buteo ventralis), and Harpy Eagle (Harpia harpyja), as well as the Near Threatened Orange-breasted Falcon (Falco deiroleucus), Crested Eagle (Morphnus guianensis), Ornate Hawk-Eagle (Spizaetus ornatus), Plumbeous Hawk (Cryptoleucopteryx plumbea), and Solitary Eagle (Buteogallus solitarius). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagle's Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. Our study provides essential molecular tools for monitoring and protecting these ecologically vital yet threatened raptors across the Americas.},
}

@article {pmid42018598,
year = {2026},
author = {Chugá-Puetate, KP and Peñaranda-Valla, M and Escobar-Camacho, D and Valdiviezo-Rivera, J and Rivadeneira, JF},
title = {Cryptic diversity in Astroblepus (Siluriformes: Astroblepidae): Integrative taxonomy reveals evolutionary complexity in the Esmeraldas River Basin, Ecuador.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0343879},
pmid = {42018598},
issn = {1932-6203},
mesh = {Animals ; *Catfishes/genetics/classification/anatomy & histology ; Ecuador ; Phylogeny ; Rivers ; DNA Barcoding, Taxonomic ; *Biodiversity ; *Biological Evolution ; },
abstract = {Astroblepus is a genus of endemic Andean catfishes with problematic taxonomy because of cryptic diversity, ambiguous historical descriptions, and morphological plasticity. This study applied an integrative taxonomy approach-combining DNA barcoding (COI gene), geometric morphometrics, and traditional morphological characters-to assess the species diversity within the genus Astroblepus in the Esmeraldas River basin (Ecuador), where five species are currently recognized. A total of 395 specimens were analyzed (386 for morphometrics, 33 for genetics), integrating both new and publicly available sequences. The molecular analysis delimited seven evolutionary lineages, exceeding previously known diversity. The validity of A. eigenmanni and A. fissidens was confirmed; a possible synonym between A. mindoensis and A. theresiae was suggested, and A. aff. mindoensis was recovered as their sister group. Within A. cyclopus we identified two cryptic lineages (5.6% divergence), and two new lineages (Astroblepus sp. and A. aff. mindoensis) were discovered, characterized by distinct morphometric autapomorphies. Geometric morphometrics revealed four morphological clusters, with significant segregation between A. cyclopus and Astroblepus sp., but overlap within more complex groups. Altitudinal distribution and isolation among sub-basins may be drivers of divergence. These results reveal an underestimated diversity in the basin, highlighting the need for formal taxonomic revisions, sampling in unexplored areas, and urgent conservation strategies considering habitat fragmentation.},
}

Animals
*Catfishes/genetics/classification/anatomy & histology
Ecuador
Phylogeny
Rivers
DNA Barcoding, Taxonomic
*Biodiversity
*Biological Evolution

@article {pmid41807586,
year = {2026},
author = {Phoungphosop, J and Arpornsuwan, T and Jaresitthikunchai, J and Phaonakrop, N and Thaisakul, S and Thongngao, P and Thiplakorn, P and Roytrakul, S and Krasao, P},
title = {Rapid peptide analysis in dried bloodspots to identify novel markers for newborn screening for congenital hypothyroidism.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807586},
issn = {2045-2322},
support = {Grant number: 2239918//Thailand Science Research and Innovation (TSRI) Fundamental Fund fiscal year 2022/ ; },
abstract = {Early diagnosis of Congenital Hypothyroidism (CH) is critical to prevent irreversible neurodevelopmental damage. However, current TSH-based newborn screening using Dried Blood Spots (DBS) is limited by factors that lead to false-positive and false-negative results, necessitating the development of alternative methods. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a high-throughput solution was investigated. This study presents a novel diagnostic approach utilizing DBS peptide barcoding, which was supported by comprehensive LC-MS/MS and network analysis. Peptide profiles showed a marked and reproducible difference between groups. MALDI-TOF MS identified a unique signature, including six dominant peptides specific to the CH-positive group. Subsequent analysis identified 37 candidate peptides, with network analysis linking 12 key proteins to established CH-related agents (e.g., thyroxine, TSHR). The MALDI-TOF MS peptidomic approach is validated as a robust, rapid, and cost-effective alternative for CH screening. This methodology represents a significant advance toward overcoming the limitations of current TSH assays and establishing a clinically translatable biomarker panel for improved personalized diagnosis of CH.},
}

@article {pmid42005800,
year = {2026},
author = {Knorrn, AH and Sonnewald, M and Moctar, SMM and Dia, M and Beibou, E and Freiwald, A},
title = {Annotated checklist of the invertebrate macrozoobenthos from Mauritanian marine shallow-water habitats.},
journal = {ZooKeys},
volume = {1277},
number = {},
pages = {1-55},
pmid = {42005800},
issn = {1313-2989},
abstract = {From 2020 to 2024, The Institut Mauritanien de Recherches Océanographiques et des Pêche (IMROP) and the Senckenberg Research Institute conducted five joint expeditions, exploring the marine biodiversity of the North-Mauritanian coastal habitats, primarily focusing on the Baie de l'Étoile north of Nouadhibou and to the Banc d'Arguin National Park. In order to establish a Mauritanian scientific reference collection of the marine fauna and to build up a DNA barcode library, macrozoobenthic invertebrates from all major groups were collected using various methods and gear. A total of 103 living marine macrozoobenthic invertebrate species were found and their key morphological features were described herein. This checklist gives an overview on the most common species of the Mauritanian coastal macroinvertebrates and provides a baseline for future biodiversity assessments along the Mauritanian coast.},
}

@article {pmid42007506,
year = {2026},
author = {Chen, W and Demirci, R and Xie, M and Walther, A},
title = {DNA Condensates Enable Crosstalk-Free Operation of Identical DNA Computing Cascades.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e5954994},
doi = {10.1002/anie.5954994},
pmid = {42007506},
issn = {1521-3773},
support = {//Max Planck Graduate Center with the Johannes Gutenberg University of Mainz/ ; 405552959//German Research Foundation/ ; WA3084/19-1//German Research Foundation/ ; //Alexander von Humboldt Foundation/ ; //Gutenberg Research Council/ ; //Max-Planck Fellowship/ ; },
abstract = {DNA strand displacement reactions (SDR) have enabled the development of biosensing devices, molecular machines, and molecular computing. However, the need for high sequence orthogonality poses a major challenge to the modular integration and scaling of DNA SDR networks into more complex systems capable of advanced or parallel functions. Here, we propose the use of liquid-like DNA condensates with addressable barcodes for confining DNA SDR networks for parallel and selective operation of near-identical circuits that would otherwise show undesired crosstalk in a homogeneous solution. By introducing Transducer modules, specific inputs can be recognized by corresponding condensates and converted to a unified Messenger for triggering downstream DNA processing locally. This allows orthogonal execution of DNA SDRs of the same sequence design in different compartments in parallel without crosstalk and interference. Our strategy contributes a facile approach to enhance modularity and scalability in DNA SDR network design, paving the way for more sophisticated and complex functionalities.},
}

@article {pmid42013141,
year = {2026},
author = {Kgatla, MM and Barker, C and Baxter, JR and Bester-van der Merwe, AE and Chaisi, M and Chakona, A and Cherry, MI and Daniels, SR and Du Preez, LH and Haddad, CR and Hawkes, PG and Ho, C and Hoareau, TB and Jacobs, A and Jacobs, K and Janion-Scheepers, C and Jansen van Vuuren, B and Kabongo, RM and Khoza, TT and Khumalo, NL and Mahlanza, T and Makapela, L and Makhubo, BG and Maneveldt, GW and Mashego, K and Matcher, G and Matthee, CA and Mavhunga, M and Midgley, JM and Mlambo, M and Monsanto, DM and Mthombeni, R and Murray, SL and Mynhardt, S and Nang-Mba, BJ and Ndlovu, M and Parbhu, SP and Phetla, V and Phukuntsi, M and Pitcher, TR and Samaai, T and Simon, CA and Sink, K and Sole, CL and Theron, GL and van Asch, B and van der Bank, M and van Steenderen, CJM and Villet, MH and Visagie, CM and Williams, KA and Willows-Munro, S and Sethusa, MT and Da Silva, JM and Mwale, M},
title = {An overview of DNA barcoding of biodiversity in South Africa.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0345173},
pmid = {42013141},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic/methods ; South Africa ; *Biodiversity ; Animals ; Conservation of Natural Resources ; Plants/genetics/classification ; Ecosystem ; Fungi/genetics ; },
abstract = {The global decline in biodiversity, driven by habitat loss, overexploitation, climate change, biological invasions, and illegal trade, poses significant challenges for conservation management. Although many South African ecosystems and species are under threat, effective conservation efforts are hindered by incomplete foundational biodiversity data and assessments, caused by taxonomic gaps and unverified distributions. DNA barcoding has emerged as an invaluable tool for species identification and classification of biodiversity. While substantial barcoding progress has been made, for many taxa, others remain underrepresented in sequence databases. This study evaluates the status and progress of DNA barcoding in South Africa through a gap analysis, comparing verified species checklists with barcoded sequences from the Barcode of Life Database (BOLD) and GenBank to assess taxonomic and geographic representation. A literature review (2003-2023) highlights applications across terrestrial, freshwater, and marine habitats. Of the 931,476 South African species barcode records, 52% were publicly available. Although the insects dominated with the highest number of records and BINs, reptiles had the highest taxonomic representation. Plants and fungi were underrepresented (16.1% and 2.8%, respectively). Regionally, Mpumalanga and Limpopo provinces showed the highest BIN counts, while North-West and Free State provinces had the lowest. The majority of barcode records were for mtDNA genes such as cytochrome c oxidase subunit I (COI) and were contributed by both local and international institutions. Discrepancies between GenBank records and those mined by BOLD indicated that many GenBank sequences for South Africa have poor quality metadata, including geographic sampling locality information. While significant progress has been made across taxa, further efforts are needed to expand species and geographic coverage, enhance sequence quality, improve species metadata, and resolve inconsistencies in BIN assignments, particularly for underrepresented groups such as plants and fungi. These advances would strengthen biodiversity assessments and support conservation efforts in South Africa.},
}

*DNA Barcoding, Taxonomic/methods
South Africa
*Biodiversity
Animals
Conservation of Natural Resources
Plants/genetics/classification
Ecosystem
Fungi/genetics

@article {pmid42013531,
year = {2026},
author = {Zhu, Y and Li, X and Maknitikul, S and Bileckaja, N and Peng, Q and Gracie, J and Drabwell, O and Li, S and Glidle, A and Dobson, P and Yuan, X and Yang, Z and Jimenez, M and Peveler, WJ and Yin, H},
title = {A surface enhanced Raman scattering nanotag library based on cucurbit[7]uril controlled nanoparticle aggregates for fast cell imaging.},
journal = {Journal of colloid and interface science},
volume = {718},
number = {},
pages = {140538},
doi = {10.1016/j.jcis.2026.140538},
pmid = {42013531},
issn = {1095-7103},
abstract = {Surface Enhanced Raman Spectroscopy (SERS) nanotags offer ultrahigh sensitivity and multiplexing capability over and above traditional fluorescence dyes for bioimaging but suffer from more drawbacks of more complex synthesis and measurement. Here we report a facile method to create libraries of nanotags with diverse Raman reporters for sensitive SERS labelling, whilst addressing complexity and reproducibility of synthesis that many nanotags suffer from. We create and demonstrate a library of SERS nanotags synthesized via incorporation of different thiolated and non-thiolated Raman reporters (including barcoded combinations) into silver nanoparticle (Ag NP) aggregates, mediated by water soluble cucurbit[7]uril (CB7) as a molecular glue. These controlled aggregates achieve significant SERS enhancement regardless of whether the Raman reporter possesses functional groups for metal adsorption, greatly increasing the choice of potential Raman reporters for creating libraries of SERS nanotags with massive barcoding and multiplexing depth. Further coating of the SERS nanotag aggregates with functional polyethylene glycols results in long-term stability, excellent biocompatibility, and versatile functionality to attach biomolecules. We demonstrate the utility of our SERS nanotags in fast imaging of cell-particle interactions and multiplexed ('multicolor') surface biomarker mapping at 10 ms per point using a 1.5 mW laser or less. Our method is not only simple to implement but offers flexible and reproducible libraries of SERS nanotags with great potential for a broad range of biological labelling challenges requiring sensitivity, speed and multiplexing.},
}

@article {pmid42003721,
year = {2026},
author = {Pfeiler, E},
title = {DNA barcodes reveal population structure in a widely-distributed agricultural pest, the Hawaiian beet webworm Spoladea recurvalis (Lepidoptera: Crambidae).},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S0007485326100996},
pmid = {42003721},
issn = {1475-2670},
abstract = {Population genetic analysis of mitochondrial DNA barcodes, comprised of a standard segment of the cytochrome c oxidase subunit I gene (COI or cox1), was conducted on Spoladea recurvalis (Fabricius), an important agricultural pest commonly referred to as the Hawaiian beet webworm. Results of genetic diversity analyses indicate significant population structure between samples mainly from Australia and nearby regions and those from North America, Africa, Europe, and Asia. Adults of the two groups are morphologically indistinguishable but are characterised by diagnostic barcode nucleotides and genetic diversity values. Factors possibly involved in driving genetic divergence in S. recurvalis in the Australian region are briefly discussed.},
}

@article {pmid42003807,
year = {2026},
author = {Menchetti, M and Schifani, E and García, F and Schär, S and Sbrega, E and Balević, N and Blaimer, BB and Borowiec, L and Cioppa, D and Corbella, C and Dincă, V and Gentile, V and Giotis, I and Gómez, K and Gómez Durán, JM and Kalaentzis, K and Lapeva-Gjonova, A and Mori, E and Talavera, G and Tinaut, A and Ruano, F and Salata, S and Sequeira, E and Serracanta, M and Suchan, T and Hebert, PDN and Dapporto, L and Vila, R},
title = {DNA Barcode Reference Library for European Ants: A Roadmap for Phylogeography and Species Discovery.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70135},
doi = {10.1111/1755-0998.70135},
pmid = {42003807},
issn = {1755-0998},
support = {LCF/BQ/DR20/11790020//'la Caixa' Foundation/ ; 101206623//H2020 Marie Skłodowska-Curie Actions/ ; PID2022-139689NB-I00//Ministerio de Ciencia, Innovación y Universidades AEI/10.13039/501100011033/ ; PID2023-152239NB-I00//Ministerio de Ciencia, Innovación y Universidades AEI/10.13039/501100011033/ ; 2021-SGR-00420//Departament de Recerca i Universitats, Generalitat de Catalunya/ ; 101059492//HORIZON EUROPE Framework Programme/ ; CN_00000033//National Biodiversity Future Center (NBFC), National Recovery and Resilience Plan (NRRP), Palermo, Italy/ ; KP-06-N-51/6//National Science Fund of the Republic of Bulgaria/ ; NFRFT-2020-00073//New Frontiers In Research Fund/ ; MSI 42450//Canada Foundation for Innovation/ ; JDC2024-054485-I//MICIU/AEI/10.13039/501100011033 and FSE+/ ; //Research Council of Finland/ ; //European Social Fund; European Regional Development Fund/ ; },
mesh = {Animals ; *Ants/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Europe ; Phylogeography/methods ; Genetic Variation ; DNA, Mitochondrial/genetics/chemistry ; *Gene Library ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {DNA barcode reference libraries provide useful tools for specimen identification, highlighting potential new species and detecting introduced ones. Here, we present a comprehensive DNA barcode library for European ants and, in order to tackle the Linnean, Wallacean and Darwinian shortfalls of this group, we provide an updated checklist, distribution data, mitochondrial genetic diversity maps and mitochondrial gene trees. The European ant fauna is here established to include 55 genera and 650 species (587 of which are native), including one species newly recorded for Europe and novel citations for 26 species from 11 countries. Our genetic dataset includes 6530 georeferenced COI sequences (62.1% de novo) for 506 species (77.8%) across all genera. On average, 12.9 sequences were obtained per species, and 209 species were sequenced for the first time. We generated intra- and interspecific genetic distance estimates, 52 genus-level trees, mitochondrial genetic diversity and specimen maps for 384 species, as well as haplotype networks for 289 species, available in the Atlas V1.0 'The Mitochondrial Genetic Diversity Maps of European Ants'. We estimate that 56.3% of European ants are monophyletic with respect to the COI gene and can be unambiguously identified by DNA barcoding, though performance varies widely among genera. We observed moderate levels of barcode sharing (19.3%) and of barcode gap presence (47.6%), as well as high levels of intraspecific divergences (up to 17.9%). These findings likely reflect both biological and operational factors and highlight the existence of potential cryptic taxa and the need for taxonomic revisions. The framework presented here aims to facilitate future research, species discovery and conservation of European ants.},
}

Animals
*Ants/genetics/classification
*DNA Barcoding, Taxonomic/methods
Europe
Phylogeography/methods
Genetic Variation
DNA, Mitochondrial/genetics/chemistry
*Gene Library
Phylogeny
Sequence Analysis, DNA

@article {pmid42005385,
year = {2026},
author = {Liu, Z and Jiang, S and Hu, T and Xue, Z and Chen, Y and Ruan, D and Xia, H and Feng, Y and Hao, J and Li, W and Zhou, JT and Fang, B and Wu, J and Liu, W},
title = {DestinyNet: A deep-learning framework for cell-fate analysis from lineage-tracing single-cell RNA sequencing data.},
journal = {Patterns (New York, N.Y.)},
volume = {7},
number = {4},
pages = {101471},
pmid = {42005385},
issn = {2666-3899},
abstract = {Unraveling cell-development dynamics, including lineage commitment, differentiation, and disease progression, is fundamental to biology. Despite advances in single-cell omics and barcoding technologies, comprehensive frameworks for accurate, robust, and scalable cell-fate analysis using lineage-tracing single-cell RNA sequencing (LT-scSeq) data remain limited. We introduce DestinyNet, a multi-task deep-learning framework addressing three key challenges: (1) fate clustering, integrating fate and cell-type information; (2) fate flow, depicting dynamic pseudotime trajectories with fate information; and (3) fate prediction, identifying early-stage cell-fate biases. DestinyNet enables end-to-end cell representation learning through cell-relation triplets and is robust across various LT-scSeq data types, including static, cumulative, and dynamic barcoding with single or multiple time points. Experiments on diverse datasets, including hematopoiesis differentiation and fibroblast reprogramming (in vitro and in vivo), demonstrate DestinyNet's effectiveness in multiple fate-analysis tasks.},
}

@article {pmid41982339,
year = {2026},
author = {Kim, H and Xu, C and Washington, C and Shi, C and Lowman, M and Kebschull, JM},
title = {Cell type-specific barcoding reveals the single-neuron projectional architecture of the mouse midbrain dopaminergic system.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.25.661405},
pmid = {41982339},
issn = {2692-8205},
abstract = {UNLABELLED: Brain-wide neural circuits are formed by the diverse axonal branching patterns of neurons of different cell types. Here we introduce POINTseq (projections of interest by sequencing), a cell type-specific barcoded connectomics method that uses selective barcoding and sequencing to rapidly map single-cell projections of a cell type of interest for thousands of neurons per animal. POINTseq leverages pseudotyping of Sindbis virus and a specific alphavirus-cellular receptor pair to make Sindbis infections cell type specific. It thus integrates MAPseq-style high-throughput barcoded projection mapping with the established viral-genetic neural circuit analysis toolbox. We validated POINTseq by mapping genetically and projection-defined cell populations in the mouse motor cortex. We then applied POINTseq to midbrain dopaminergic neurons and reconstructed the brain-wide single-cell projections of 5,902 dopaminergic neurons in ventral tegmental area (VTA) and substantia nigra pars compacta (SNc). These neurons cluster into over 25 connectomic cell types, vastly exceeding the known diversity of dopaminergic cells, and form stereotyped projection motifs that may mediate parallel dopamine signaling. This data constitutes the anatomical substrate on which the diverse functions of dopamine in the brain are built.

HIGHLIGHTS: We develop POINTseq, which uses pseudotyped Sindbis virus and cell type-specific expression of a viral receptor for cell type-specific barcoding.POINTseq enables massively multiplexed single-cell projection mapping of cell types of interest.We map the brain-wide projections of 5,902 individual VTA and SNc dopaminergic neurons.VTA and SNc dopaminergic neurons form over 25 connectomic cell types.Projections are organized into stereotyped motifs that may mediate the distinct functions of dopamine.},
}

@article {pmid41986505,
year = {2026},
author = {Ahn, JY and Park, JY and Park, HS and Lee, JH and Kim, SK and Kim, YJ and Lee, YS and Yang, TJ},
title = {Development of plastome-based HRM markers for the authentication of 12 major medicinal herbs in the Apiaceae family.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47346-4},
pmid = {41986505},
issn = {2045-2322},
support = {HI23C1420//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {Medicinal plants of the Apiaceae family often exhibit high morphological similarity, making accurate species identification challenging and leading to frequent cases of adulteration or substitution. To establish a systematic barcoding framework, we simultaneously assembled the chloroplast genomes (plastomes) and 45 S nuclear ribosomal DNA (nrDNA) sequences of 12 major medicinal herb species and performed comparative genomic analyses to identify interspecific variations in single-nucleotide polymorphisms (SNPs), insertions/deletions, nucleotide diversity (π), and simple sequence repeats (SSRs). Based on these genomic insights, seven high-resolution melting (HRM) markers were developed, which generated species-specific melting curve profiles and enabled unambiguous identification and discrimination of all 12 taxa. Compared with conventional DNA barcoding, HRM demonstrated advantages in cost-effectiveness, speed, and suitability for high-throughput analysis. Collectively, our study provides genomic resources and molecular tools that establish a comprehensive barcoding system for 12 medicinal herbs in the Apiaceae family, facilitating reliable species identification, genetic diversity assessment, and phylogenetic research, while contributing to the conservation and safe utilization of these plants.},
}

@article {pmid41993258,
year = {2026},
author = {Blattman, SB and Maslah, N and Varela, AA and Kumpaitis, K and Nalbant, B and Snopkowski, C and Mariani, M and Kida, LC and Takizawa, M and Ratnayeke, N and Yu, KKH and Fernandes, S and Mousavi, N and Borgstrom, E and Vallejo, D and Boghospor, L and Xin, R and Mignardi, M and Wu, S and Scarlott, N and Delgado-Rivera, L and Kumar, P and Krishnan, S and Giraudier, S and Kiladjian, JJ and Howitt, BE and Kohlway, A and Lund, P and Pe'er, D and Chaligne, R and Lareau, CA},
title = {Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.11.717967},
pmid = {41993258},
issn = {2692-8205},
abstract = {Single-cell transcriptomics has revolutionized our understanding of heterogeneous cell populations. However, technical limitations of widely-used platforms have limited our ability to link transcriptional states to somatic mutations within the same cells at scale. Here, we introduce Genotyping in Fixed Transcriptomes (GIFT), a novel assay for simultaneous detection of hundreds of targeted genetic variants and whole transcriptome profiles in single cells. The core innovation of GIFT is a rationally designed gapfilling reaction between adjacent single-stranded DNA (ssDNA) probes that barcodes native transcript sequence to enable highly-specific targeted mutation detection. GIFT achieves >99% genotyping accuracy and flexible capture of hundreds of mutations per cell, including in FFPE (Formalin-Fixed Paraffin-Embedded) tissue, enabling clonal lineage tracing in heterogeneous settings. We demonstrate the unique scalability of GIFT by profiling >700,000 cells from 35 donors with myeloproliferative neoplasms (MPN), revealing mutation-dependent hematopoietic responses to systemic inflammation associated with the characteristic JAK2V617 mutation, including an allelic dose gradient of interferon-associated transcriptional programs and transcriptional priming of hematopoietic stem cells that develop into divergent disease states. Together, the unique technical advantages of GIFT enable direct resolution of genotype-to-phenotype relationships via clonal lineage tracing with comprehensive cell state measurements at single-cell resolution.},
}

@article {pmid41993269,
year = {2026},
author = {Liu, Z and Cordero, A and Kinney, JB},
title = {PoolParty: streamlined design of DNA sequence libraries in Python.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.716802},
pmid = {41993269},
issn = {2692-8205},
abstract = {Computationally designed DNA sequence libraries are essential components of many high-throughput assays. They are also increasingly used in silico to analyze genomic AI models. Designing these libraries, however, remains tedious and error-prone. Here we describe PoolParty, a Python package that streamlines the design of complex oligo pools using a simple but flexible API. In PoolParty, each library is represented by a computational graph that can be specified in just a few lines of code. Over 50 built-in operations cover nucleotide- and codon-level mutagenesis, motif insertion, barcode generation, and more. PoolParty also provides "design cards" detailing how each sequence was generated.},
}

@article {pmid41994344,
year = {2026},
author = {Salden, T and Schneider, JA and Mikó, I and S Peters, R},
title = {Update on the enigmatic Pteroceraphron mirabilipennis Dessart, 1981 (Hymenoptera, Ceraphronidae): description of male and first record from the Neotropics, including first DNA barcodes.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e189669},
pmid = {41994344},
issn = {1314-2828},
abstract = {BACKGROUND: Pteroceraphron is a morphologically distinct genus of ceraphronid wasps known only from few female specimens of two species, Pteroceraphron mirabilipennis Dessart, 1981 from the Nearctic Region and P. apoorva Bijoy & Rajmohana, 2021 from the Oriental Region.

NEW INFORMATION: Our study provides the first report and description of male specimens of the genus Pteroceraphron, the first record of Pteroceraphron mirabilipennis Dessart, 1981 from the Neotropics (Costa Rica), including the first DNA barcode data, as well as an updated diagnosis for the genus.},
}

@article {pmid42002606,
year = {2026},
author = {Alajmi, R and Alosaimi, J and Alzahrani, F and Alotaibi, F and AlKuriji, M and Abdel-Gaber, R and Hashem, A},
title = {Morphological and molecular identification of Oryctes species and their potential role in transmitting pathogenic fungi to date palms in Al-Kharj and Al-Qassim regions, Saudi Arabia.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag086},
pmid = {42002606},
issn = {1938-291X},
support = {//King Saud University/ ; },
abstract = {Oryctes sp. is a key pest of date palms, where larval and adult feeding on different plant parts reduces tree vigor and yield. Although insects are recognized as potential vectors of plant pathogenic fungi, the role of Oryctes beetles in transmitting fungal pathogens to date palms remains unclear. This study aimed to identify Oryctes species in two major date-producing regions of Saudi Arabia-Al Kharj and Al Qassim-and to characterize the fungal communities associated with beetles, infested roots, and rhizosphere soils. Adult beetles were collected from date palms and identified using morphological characters and DNA barcoding of the mitochondrial cytochrome c oxidase I gene. Fungi were isolated from beetle exoskeletons, root tissues of infested palms, and rhizosphere soils; cultured on Czapek Dox Agar; grouped by colony and microscopic features; and identified using standard morphological keys. Morphological and molecular analyses of collected specimens revealed two species-Oryctes elegans and Oryctes agamemnon-in Al Kharj, while only O. agamemnon occurred in Al Qassim. In total, 72 fungal isolates representing 13 genera were recovered. From beetles, 27 isolates included common taxa such as Phytophthora parasitica, Fusarium sp., Aspergillus niger, Aspergillus flavus, Penicillium sp., Alternaria alternata, Helminthosporium sp., and Stemphylium verruculosum, with additional species unique to each Oryctes species and region. Similar overlapping and region-specific assemblages occurred in roots and rhizosphere soils. The frequent detection of phytopathogenic fungi on beetle exoskeletons, together with their presence in roots and rhizosphere soils, supports a role for Oryctes species as mechanical vectors that facilitate fungal entry through feeding wounds.},
}

@article {pmid41975273,
year = {2026},
author = {Li, D and Mo, ZQ and Cheng, S and Wang, J and Fu, CN and Möller, M and Thomas, P and Yan, J and Gao, LM},
title = {DNA barcodes analyses provide insights into species delineation and possible cryptic species in Amentotaxus (Taxaceae).},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08719-z},
pmid = {41975273},
issn = {1471-2229},
support = {2023YFA0915800//National Key Research and Development Program of China/ ; 202101BC070003//Key Basic & Applied Research Program of Yunnan Province, China/ ; },
}

@article {pmid41977662,
year = {2026},
author = {Anantaworasakul, P and Arunotayanun, W and Chaichit, S and Khamnuan, S and Ngernsaengsaruay, C and Chittasupho, C and Leksungnoen, N and Na Takuathung, M and Yubolphan, R and Jiso, A and Techarang, T and Intharuksa, A},
title = {DNA Barcoding and Chemical Profile Using UHPLC, GC-MS and LC-MS/QTOF of Mitragyna speciosa Variation and Allied Species for Quality Control of Kratom Materials.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41977662},
issn = {2223-7747},
abstract = {Kratom (Mitragyna speciosa Korth.) has gained increasing global attention due to its traditional use, psychoactive properties, and emerging therapeutic potential; however, concerns regarding adulteration, substitution, and inconsistent quality of commercial products necessitate robust authentication strategies. This study aimed to integrate DNA barcoding and comprehensive chemical profiling to authenticate kratom variants and discriminate them from closely allied Mitragyna species for quality control and forensic applications. Nine DNA barcoding regions were analyzed, alongside chemical characterization using UHPLC, GC-MS, and LC-MS/QTOF. Among the tested loci, the internal transcribed spacer (ITS) and ITS2 regions exhibited the highest interspecific variation and effectively distinguished kratom from allied species. UHPLC and GC-MS analyses confirmed that mitragynine was exclusively detected in kratom variants, with Kan Khiao exhibiting the highest content (94.33 ± 0.14 mg/g) when quantified against the mitragynine standard using UHPLC analysis. LC-MS/QTOF profiling revealed an alkaloid-rich chemotype in kratom dominated by mitragynine and 7-hydroxymitragynine, whereas M. diversifolia, M. hirsuta, and M. rotundifolia showed distinct profiles enriched in phenolic acids and flavonoid glycosides. Multivariate analyses further identified procyanidin B1, datiscetin-3-O-rutinoside, mitragynine, and 7-hydroxymitragynine as key discriminatory markers. Overall, the combined molecular and chemical workflow provides a robust framework for kratom authentication, supporting regulatory monitoring, quality assurance, and forensic identification of kratom materials.},
}

@article {pmid41978880,
year = {2026},
author = {Elías-Gutiérrez, M and Suárez-Morales, E and Garcia-Morales, AE and Cohuo-Colli, JA},
title = {DNA barcoding of North American freshwater copepods (Diaptomidae and Cyclopoida): an overview after 20 years with emphasis in the Mexican fauna, the transition between the Nearctic and Neotropics.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20989},
pmid = {41978880},
issn = {2167-8359},
mesh = {Animals ; *Copepoda/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Mexico ; Fresh Water ; Electron Transport Complex IV/genetics ; Phylogeny ; Biodiversity ; },
abstract = {BACKGROUND: In 2003, Paul Hebert proposed DNA barcoding, based on the first half of a standardized gene, the Cytochrome c Oxidase subunit I (COI), to identify animals. Subsequently, two large-scale projects enabled the sequencing of more than 1.3 million putative species worldwide. Two decades ago, we decided to adopt this approach as a tool to investigate the freshwater zooplankton diversity of Mexican aquatic systems. Several copepod species have been described by us with the aid of this marker, mainly of the family Diaptomidae, particularly of the species-rich genera Leptodiaptomus and Mastigodiaptomus. We also re-described topotypes of the widespread M. albuquerquensis and documented the invasion of exotic cyclopid species.

METHODS: In Mexico, we have sequenced the COI of 1,725 free-living freshwater copepods, including 925 diaptomid calanoids and 811 cyclopid cyclopoids, representing up to 43.7% of the total specimens sequenced for North America. To delineate the putative species diversity, we used the Barcode Index Number (BIN) and the Assemble Species by Automatic Partitioning method and compared both. For Leptodiaptomus we prepared a Maximum Likelihood (ML) tree, for a detailed analysis.

RESULTS: Our results suggest that central-southeastern Mexico may represent a potential radiation center for speciose diaptomid genera like Mastigodiaptomus (15 species), Leptodiaptomus (eight species), and Arctodiaptomus, which likely constitutes a regional species complex yet to be described. A comparison of Mexican data with that from North America (NA) showed that the only truly widespread copepod species, distributed from Arctic latitudes to the central Mexican plateau, is Leptodiaptomus sicilis, while all others have more restricted distributions. From the total specimens sequenced in NA, the BIN count revealed 89 Molecular Operational Taxonomic Units (MOTUs), but only 47 of them have been identified to species level. In some cases, diaptomid haplotype variants have received different BINs for a single specimen. The taxonomic impediment appears to be more pronounced in Cyclopoida, with only 32% of the total 235 BINs identified to species level. Despite these limitations, the use of MOTUs from these baselines is valuable for biomonitoring changes in freshwater ecosystems. We found that in some cases, mostly where singletons represented a BIN, the Assemble Species by Automatic Partitioning (ASAP) method provided a better representation of MOTUs. Conversely, when haplotypes of different species, such as those found in the Leptodiaptomus novamexicanus complex, are closely similar, ASAP fails, but ML can distinguish them. Therefore, it is urgent to apply an integrative taxonomy approach to propose the most convincing hypotheses regarding these issues. This publicly available online copepod baseline represents a useful tool for exploring and understanding species distributions, detecting possible new species and translocations, and revealing centers of speciation in NA.},
}

Animals
*Copepoda/genetics/classification
*DNA Barcoding, Taxonomic/methods
Mexico
Fresh Water
Electron Transport Complex IV/genetics
Phylogeny
Biodiversity

@article {pmid41975113,
year = {2026},
author = {Liu, Y and Ma, L and Zhu, T and Wu, D and Liu, Y},
title = {Extracellular vesicle-derived CDCP1 promotes chemoresistance and macrophage polarization in breast cancer.},
journal = {Human cell},
volume = {39},
number = {4},
pages = {},
pmid = {41975113},
issn = {1749-0774},
mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; *Breast Neoplasms/pathology/genetics/drug therapy ; Female ; *Drug Resistance, Neoplasm/genetics ; *Antigens, CD/metabolism/genetics/physiology ; *Macrophages/physiology ; *Cell Adhesion Molecules/physiology/genetics/metabolism ; *Antigens, Neoplasm/physiology/genetics/metabolism ; Tumor Microenvironment/genetics ; Carcinogenesis/genetics ; Disease Progression ; },
abstract = {Breast cancer derived extracellular vesicles (EVs) mediate tumor progression through surface protein-dependent intercellular communication; however, their molecular heterogeneity remains poorly characterized. In this study, we employed a proximity-dependent barcoding assay (PBA) together with patient-derived organoid (PDO) models and identified CDCP1 as a key driver of EV-mediated oncogenesis. PBA-based surface proteomics revealed CDCP1 as the most upregulated protein in breast cancer-derived EVs compared with EVs from normal tissues. Clinical validation confirmed elevated CDCP1 expression in tumor tissues and matched EVs. PDOs generated from fresh clinical specimens recapitulated CDCP1 expression levels of the parental tumors and secreted CDCP1-enriched EVs. Functional experiments showed that CDCP1-knockdown EVs suppressed PDO proliferation and sensitized tumors to chemotherapy. Mechanistically, CDCP1-positive EVs promoted macrophage polarization toward an M2 phenotype, accompanied by upregulation of IL-10 and TGF-β and CCL22. Multiplex immunofluorescence confirmed that CDCP1-high tumors exhibited increased co-localization of CD68[+] and CD163[+] macrophages. These results establish CDCP1 as a master regulator of EV driven breast cancer progression, linking surface proteome remodeling to chemo-resistance and immunosuppressive microenvironment reprogramming. The integration of single-EV profiling and PDO modeling establishes a translational framework for targeting CDCP1 as a promising therapeutic target and a candidate biomarker for future liquid biopsy development in aggressive breast cancer subtypes.},
}

Humans
*Extracellular Vesicles/metabolism/genetics
*Breast Neoplasms/pathology/genetics/drug therapy
Female
*Drug Resistance, Neoplasm/genetics
*Antigens, CD/metabolism/genetics/physiology
*Macrophages/physiology
*Cell Adhesion Molecules/physiology/genetics/metabolism
*Antigens, Neoplasm/physiology/genetics/metabolism
Tumor Microenvironment/genetics
Carcinogenesis/genetics
Disease Progression

@article {pmid41975122,
year = {2026},
author = {Xia, FN and Liu, K and Wang, J and Liu, Z and Li, A and Hu, Z and Li, JF and He, X},
title = {Mapping the zygote-to-adult developmental cell phylogeny in Arabidopsis thaliana reveals a three-cell rule of branching.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {41975122},
issn = {2055-0278},
support = {32293191//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32200494//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Similar to the evolutionary history of all species on Earth, the developmental lineage history of all cells in a multicellular organism is stored in a phylogenetic tree. Mapping the zygote-to-adult developmental cell phylogeny of a complex organism is of tremendous value but technically challenging. We here developed e-SMALT, a powerful cell lineage tracing system integrated with single-cell RNA sequencing, in Arabidopsis thaliana to record the zygote-to-adult developmental lineages of two plant individuals. The system performed efficiently in A. thaliana, with an average of ~50 barcoding mutations accumulated on the 1-kb barcode sequence of each cell in 3-month-old plants. Using the barcoding mutations, we reconstructed the phylogenetic tree for thousands of cells sampled from various shoot branches of each plant, with high statistical confidence and at single-cell resolution. The cell phylogenies show that cells of every shoot branch are derived from exactly three founder cells, each belonging to one of three early-determined lineages. The three-cell pattern holds for primary, secondary and tertiary branches, and even for single flowers/siliques. Incorporating single-cell RNA sequencing data revealed the three founder cells responsible for establishing the three germ layers of each branch/organ, which in turn updates our understanding of plant germ layers to single-cell resolution. We further showed that the three-cell rule reflects an adaptive strategy for an indeterminate plant to manage its stem cell pool, suggesting an analytical framework to unify the distinct strategies between plants and animals in organogenesis.},
}

@article {pmid41972092,
year = {2026},
author = {Nakai, M and Yamaguchi, A and Suga, H and Shirayama, H and Kobayashi, T and Suzuki, T and Koizumi, J and Abe, T and Funatsu, Y and Sugiyama, Y},
title = {Re-examination of the morphological and molecular features of Amanita clarisquamosa and Amanita avellaneosquamosa based on specimens collected in Hokkaido.},
journal = {Mycoscience},
volume = {67},
number = {1},
pages = {10-19},
pmid = {41972092},
issn = {1618-2545},
abstract = {Amanita clarisquamosa and A. avellaneosquamosa, both of which belong to the section Amidella, were described in 1933 in Nopporo, Hokkaido, Japan. Owing to large intraspecific variation and high interspecific resemblance in morphology, species delimitation and identification of section Amidella members is difficult. This also applies to the two focal species. Furthermore, the minimality of the original descriptions of A. clarisquamosa and A. avellaneosquamosa exacerbates this problem. For reliable identification, detailed morphological and molecular information of reliably identified specimens, hopefully type specimens is required. However, further morphological and molecular information cannot be obtained from the degraded type specimens. In this study, new specimens that showed morphological and molecular matches with A. clarisquamosa and A. avellaneosquamosa were obtained from Nopporo and the surrounding areas of Hokkaido. Detailed morphology and barcoding region sequences of these specimens were recorded. Importantly, the newly collected specimens showed morphological and molecular mismatches with previously reported A. clarisquamosa or A. avellaneosquamosa specimens. This indicated that specimens previously identified as these two species might have included misidentifications. Overall, the study results suggest a need for reconfirmation of species within the section Amidella.},
}

@article {pmid41972329,
year = {2026},
author = {Dello Russo, JJ and Logan, JM and Austin, R and Whitener, ZT and Sée, I and Hurley, BM and Kerr, LA and Quattro, JM and Golet, WJ},
title = {Diet composition of data-limited marlins (Istiophoridae) in the Northwest Atlantic.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70431},
pmid = {41972329},
issn = {1095-8649},
support = {#NSN866//Mid-Atlantic Fishery Management Council/ ; #NA17NMF4540140//National Oceanic and Atmospheric Administration/ ; },
abstract = {Knowledge of the dietary composition of Atlantic marlins, especially for recently acknowledged species such as roundscale spearfish (Tetrapturus georgii), is limited, as sample access is constrained by international quotas and intermittent landing rates. A series of annual offshore recreational fishing tournaments target Atlantic blue marlin (Makaira nigricans), white marlin (Kajikia albida) and roundscale spearfish on their seasonal foraging grounds in the South and Mid-Atlantic Bight. Through this network of tournaments and recreational anglers, we collected stomachs from Atlantic blue marlin (n = 32), white marlin (n = 35) and roundscale spearfish (n = 44) from 2018 to 2020 to investigate general diet composition. Stomach content analysis and DNA barcoding identified a total of 16 prey families across the three focal species, but the majority of prey weight (%W) was from two families (Scombridae and Ommastrephidae). Blue marlin and roundscale spearfish were predominantly piscivorous (99.0 and 80.6%W fishes, respectively), whereas white marlin mainly consumed cephalopods (80%W). The contribution of Scombridae was highest for blue marlin (94.6%W), intermediate for roundscale spearfish (51.7%W) and lowest for white marlin (11%W), with an inverse pattern of relative contribution for Ommastrephidae (0.9, 16.1 and 73.9%W, respectively). Roundscale spearfish and white marlin, despite having a near identical morphology, had diets composed of different prey types in our sample. These dietary data, from three epipelagic apex predators, provide important information for wider ecosystem-based studies, including in relation to the Mackerel, Squid and Butterfish Fishery Management Plan overseen by the Mid-Atlantic Fishery Management Council.},
}

@article {pmid41959175,
year = {2026},
author = {Chen, HM and Kao, JC and Yang, CP and Tan, C and Lee, T and Sugino, K},
title = {ESPeR-seq: Extremely Sensitive and Pure, End-to-end, RNA-seq library preparation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.12.711386},
pmid = {41959175},
issn = {2692-8205},
abstract = {The Smart-seq family of methods represents the gold standard for high-sensitivity, full-length single-cell RNA sequencing. Despite iterative improvements, fundamental challenges remain: the generation of non-specific PCR products that limit sensitivity, the inability to capture precise Transcription End Sites (TES), and the insidious generation of "phantom UMIs"-artificial molecular barcodes created during PCR that systematically inflate molecular counts. Here, we present ESPeR-seq, a novel architecture that resolves these barriers. To enable precise, stranded TES capture, we developed an "Omega-dT" primer that bypasses synthetic poly-T tracts, restoring high-quality sequencing directly at transcript termini. To eliminate both PCR background and phantom UMIs, we implemented a biochemical "multi-lock" mechanism utilizing uracil-containing TSOs and a uracil-intolerant DNA polymerase. We validate this approach using the logQ-slope, a novel metric that sensitively diagnoses UMI fidelity. Benchmarking reveals that while state-of-the-art methods still exhibit signs of UMI inflation, ESPeR-seq strictly prevents it. Furthermore, the strandedness and precise end-delineation provided by TSO and dT reads support robust de novo gene model reconstruction, enabling the discovery of novel multi-exon genes, unannotated 3' UTR extensions, and candidate eRNAs across aggregated single-cell populations. Thus, ESPeR-seq establishes a robust framework for absolute quantitative accuracy and full-length isoform resolution.},
}

@article {pmid41959368,
year = {2026},
author = {Andrews, B and Ranganathan, R},
title = {BCAR: A fast and general barcode-sequence mapper for correcting sequencing errors.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.27.714882},
pmid = {41959368},
issn = {2692-8205},
abstract = {MOTIVATION: DNA barcodes are commonly used as a tool to distinguish genuine mutations from sequencing errors in sequencing-based assays. In the presence of indel errors, utilizing barcodes requires accurate alignment of the raw reads to distinguish genuine indels from indel errors. Existing strategies to do this generally rely on aligners built for homology comparison and do not fully utilize quality scores. We reasoned that developing an aligner purpose-built for error correction could yield higher quality barcode-sequence maps.

RESULTS: Here, we present BCAR, a fast barcode-sequence mapper for correcting sequencing errors. BCAR considers all of the evidence for each base call at each position both during alignment and during final consensus generation. BCAR creates high-accuracy barcode-sequence maps from simulated reads across a broad range of error rates and read lengths, outperforming existing methods. We apply BCAR to two experimental datasets, where it generates high-quality barcode-sequence maps.

BCAR source code, documentation and test data are available from: https://github.com/dry-brews/BCAR.},
}

@article {pmid41963347,
year = {2026},
author = {Mata, JM and Liu, J and McKenna, SM and van der Nol, E and Havermans, M and Delwel, R and Filius, M and Joo, C and Vallaro, M and Caron, G and Pomplun, SJ},
title = {Massive barcode-free chemical screenings enable the discovery of bioactive macrocycles with passive membrane permeability.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71641-3},
pmid = {41963347},
issn = {2041-1723},
support = {OCENW.M.21.157//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 101039354//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Synthetic macrocycles offer exceptional potential as therapeutics. However, most high-throughput discovery platforms rely on genetically encoded libraries of large peptide macrocycles, which typically are not optimized for drug like properties. Fully synthetic libraries offer greater flexibility in accessing broader chemical space. Leveraging recent advances in mass spectrometry based library techniques, here we report CycloSEL (Cyclic Self-Encoded Libraries), an end-to-end workflow, that screens synthetic macrocycle libraries enriched in drug-like 'beyond rule of five' features. The workflow relies on affinity selections and hit identification by tandem mass spectrometry, eliminating the need for genetic barcodes. We construct a 16 million-member library and validate the approach against the oncology target carbonic anhydrase IX, achieving robust enrichment and accurate identification of true binders. Applying CycloSEL to the acute myeloid leukemia target WD repeat-containing protein 5 (WDR5) yields a macrocycle with subnamolar affinity, and potent inhibition of the WDR5-Mixed-Lineage Leukemia 1 (MLL1) interaction. Subsequent modifications produce a chameleonic macrocycle with passive membrane permeability, serum stability, and anti-proliferative activity in leukemia cells. Together, these results demonstrate that CycloSEL enables discovery of drug-like macrocycles from fully synthetic libraries for intracellular targets.},
}

@article {pmid41963749,
year = {2026},
author = {Rastegarpanah, M and Kafi, ZZ and Negahdari, B},
title = {In Vivo Tracking Modalities for Oncolytic Reovirus: Principles, Clinical Applications, and Translational Integration.},
journal = {Molecular imaging and biology},
volume = {},
number = {},
pages = {},
pmid = {41963749},
issn = {1860-2002},
abstract = {OBJECTIVES: Oncolytic reovirus, particularly Pelareorep, is a promising cancer therapeutic due to selective replication in Ras-activated tumor cells and immunomodulatory effects. This review aims to critically evaluate current and emerging in vivo tracking strategies, emphasizing translational relevance and clinical implementation.

EVIDENCE ACQUISITION: We systematically analyzed preclinical and clinical studies employing optical imaging, nuclear imaging, magnetic resonance imaging, ultrasound/photoacoustic techniques, molecular reporters, and nanoparticle-based platforms. Special focus was placed on integrating functional imaging and molecular assays in Pelareorep trials to monitor viral distribution and therapeutic response.

RESULTS: Optical imaging offers high sensitivity for preclinical investigations; however, it is limited by shallow tissue penetration. Nuclear imaging provides quantitative, whole-body monitoring that is suitable for clinical translation, whereas MRI and ultrasound/photoacoustic modalities enable real-time visualization of both structural and functional aspects. Nanotechnology-based platforms facilitate multimodal imaging and targeted delivery, while molecular tools such as reporter genes, CRISPR-driven circuits, and viral barcoding further enhance spatiotemporal resolution. Clinical trials with Pelareorep demonstrate the feasibility of integrating imaging with molecular assays to evaluate safety, delivery efficiency, and antitumor activity. Persisting challenges include limited genome capacity, immune-mediated clearance, and suboptimal signal penetration.

CONCLUSION: Emerging strategies, including synthetic biology reporters, AI-driven image analysis, biosensors, and liquid biopsies, provide scalable, patient-specific tracking solutions. This integrative framework bridges preclinical insights with clinical translation, supporting optimized design, monitoring, and personalization of oncolytic reovirus therapy.},
}

@article {pmid41967853,
year = {2026},
author = {Wragg, D and Kang, E and Morgan, MD},
title = {Harvesting more reads from single-cell combinatorial barcoding data with scarecrow.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag182},
pmid = {41967853},
issn = {1367-4811},
abstract = {SUMMARY: Combinatorial barcoding technologies for single-cell nucleotide sequencing, such as split-pool ligation protocols, involve sequential rounds of cell barcoding to uniquely tag individual cells. The rapid adoption of combinatorial barcoding in recent years is due in part to its scalability across cells and samples. However, small shifts in barcode positions within sequencing reads caused by technical artifacts, e.g. during barcode incorporation or synthesis, can impact the accurate assignment of reads to cell barcodes. Existing processing tools typically assume barcodes contain fixed-length nucleotide sequences located at fixed positions within reads, overlooking any positional variability. Consequently, reads containing truncated or mispositioned barcodes are discarded during initial data processing steps leading to significant data loss. To solve this limitation and maximise the retention of sequencing reads from single-cell combinatorial barcoding experiments, we introduce scarecrow. This tool screens a subsample of reads to generate position-specific barcode profiles, which are then used to flexibly identify barcode sequences in each read whilst accounting for positional errors, a phenomenon we refer to as "jitter". Barcode matches are then prioritised to minimise nucleotide mismatches and the degree of jitter. These initial profiles are subsequently used to extract and error correct barcode combinations in high throughput sequencing libraries. By incorporating jitter into barcode error correction, scarecrow enables greater data recovery and improved downstream single-cell analyses. Scarecrow is fully open access, implemented in Python, and generates output files using standardised sequence file formats for maximal interoperability. A detailed explanation of the scarecrow workflow can be found in the supplementary materials.

AVAILABILITY: Scarecrow is freely available on GitHub https://github.com/MorganResearchLab/scarecrow and Zenodo https://doi.org/10.5281/zenodo.18621784.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}