@article {pmid41714417,
year = {2026},
author = {Wei, X and Xu, Y and Yang, D and Kim, K and Yi, L and Luo, W and Lin, X and Xiang, Y and Williams, AB and Wang, X and Srivas, S and Tan, C and Zhang, K and Li, W and Li, YE and Yue, F and Huang, ZJ and Jung, I and Diao, Y},
title = {Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41714417},
issn = {1546-1696},
abstract = {The three-dimensional (3D) organization of cis-regulatory elements (CREs) is critical in transcription control. However, capturing transcriptome, epigenome and 3D genome from the same single cells remains challenging. Here we present scHiCAR (single-cell Hi-C with assay for transposase-accessible chromatin and RNA sequencing), a plate-based combinatorial barcoding method that simultaneously profiles mRNA, open chromatin and chromosome conformation capture from the same cells. Compared to existing single-cell 3D genome methods, scHiCAR more efficiently enriches long-range cis-interactions anchored at candidate CREs (cCREs). Applied to 1.62 million mouse brain cells and complemented with a deep-learning-based loop caller, scHiCAR accurately defines cell-type-specific transcriptomes, accessible cCREs and 5-kb-resolution enhancer-promoter pairs across 22 brain cell types. scHiCAR also performs robustly in challenging tissues such as skeletal muscle, enabling trimodal single-cell-level analysis of gene regulation dynamics during muscle stem cell regeneration. By providing a scalable and cost-effective system for single-cell trimodal analysis of gene-regulatory landscapes in complex tissues, scHiCAR reveals gene-locus-specific regulatory roles of 3D genome reorganization in transcriptional control.},
}

@article {pmid41712450,
year = {2026},
author = {Fisher, H and de Lussy Kubisa, L and Jakhmola, A and Walker, E and Kirk, JA and Oatley, P and Chaudhuri, RR and Douce, GR and Ormsby, MJ and Fagan, RP},
title = {A set of genetic tools for use in Clostridioides difficile and related species.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {2},
pages = {},
doi = {10.1099/mic.0.001665},
pmid = {41712450},
issn = {1465-2080},
mesh = {*Clostridioides difficile/genetics ; Plasmids/genetics ; Promoter Regions, Genetic ; *Clostridium/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The Clostridia are a phylogenetically diverse group of anaerobic, spore-forming bacteria that include species of medical, veterinary and industrial importance. The last two decades have seen major advances in our understanding of Clostridial biology despite the difficulties of anaerobic microbiology and the challenges associated with limited genetic tools. Effort has largely focused on the human pathogen Clostridioides difficile, but many of the methods developed have also proven useful in other species. Here, we present a collection of new genetic tools, including an array of promoters of varying strength, that we have characterized in C. difficile, the food spoilage bacterium Clostridium sporogenes and industrially important Clostridium saccharoperbutylacetonicum. We also present a set of modular plasmids that allow expression of proteins with a variety of tags, including for protein purification and fluorescence microscopy and a method for genetic barcoding of C. difficile to facilitate competitive index experiments. We make these tools available in the hope that they will prove useful to the community in support of our growing understanding of these important bacteria.},
}

*Clostridioides difficile/genetics
Plasmids/genetics
Promoter Regions, Genetic
*Clostridium/genetics
Bacterial Proteins/genetics/metabolism

@article {pmid41711885,
year = {2026},
author = {Habila, S and Wahyuni, DK},
title = {DNA barcoding confirms the identity of the invasive Sonchus arvensis in Java, Indonesia.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e296844},
doi = {10.1590/1519-6984.296844},
pmid = {41711885},
issn = {1678-4375},
mesh = {*DNA Barcoding, Taxonomic/methods ; Indonesia ; *Introduced Species ; Phylogeny ; *Sonchus/genetics/classification ; *DNA, Plant/genetics ; },
abstract = {Sonchus arvensissubsp.arvensisis a perennial plant that serves both as a traditional medicinal herb and a prolific invasive weed. Its recent introduction to Southeast Asia, including Java, Indonesia, poses a potential threat to native biodiversity, yet its genetic provenance and invasion history in the region are uncharacterized. To provide a reliable species-level identification, we employed DNA barcoding of the chloroplast genesrbcLandmatK. Phylogenetic analysis revealed that samples from the four geographically distinct areas were genetically uniform based on these markers and were placed within a clade containing EurasianS. arvensisaccessions. The invader was distinct from the native AustralasianSonchusspecies. This work represents the first molecular confirmation ofS. arvensisin Java using DNA barcodes. While it establishes species identity, further genomic studies are required to resolve the population history, introduction pathway, and ecological impact of this invasive species.},
}

*DNA Barcoding, Taxonomic/methods
Indonesia
*Introduced Species
Phylogeny
*Sonchus/genetics/classification
*DNA, Plant/genetics

@article {pmid41710425,
year = {2026},
author = {Mirzaee, Z and Wiemers, M and Schmitt, T and Govorov, V and Shcherbakov, E},
title = {Review of the genus Hierodula Burmeister (Mantodea: Mantidae) in Iran.},
journal = {Frontiers in insect science},
volume = {6},
number = {},
pages = {1757219},
pmid = {41710425},
issn = {2673-8600},
abstract = {INTRODUCTION: Hierodula is a morphologically conservative mantid genus with a complex taxonomic history and several problematic species-level concepts across its native and invaded ranges. In Iran, four nominal Hierodula species have historically been reported (H. macrostigmata, H. tenuidentata, H. transcaucasica, and "H. trimacula"), but their validity and distributions have remained uncertain due to overlapping diagnostic characters and limited molecular data. This study addresses these issues by reassessing all available Iranian material within an integrative framework.

METHODS: The revision combines: Morphological examination of type and non-type material from Iran, India, Pakistan, and Oman, including detailed study of external characters and male genitalia. Mitochondrial COI barcoding of Hierodula specimens from multiple Iranian provinces and Pakistan, analyzed with Bayesian inference, maximum likelihood, and model-based genetic distance estimation. Compilation and critical validation of distributional data from museum collections, literature, and iNaturalist records, followed by mapping in QGIS.

RESULTS: Morphological comparisons show that the holotype of H. macrostigmata and recently collected southern Iranian specimens are indistinguishable from H. coarctata in forewing stigma, pronotal shape, and male genitalia, supporting their synonymy. COI phylogenies and TN93 genetic distances recover two deeply divergent, well-supported clades corresponding to H. coarctata and the H. tenuidentata complex, with minimal intraspecific divergence and no separation between Iranian "H. macrostigmata" and Indian/Pakistani H. coarctata. Re-examination of specimens and literature demonstrates that records of "Hierodula/Sphodromantis trimacula" from Iran lack verifiable material, while male genital characters place the species unambiguously in Sphodromantis and confirm its absence from the Iranian fauna.

DISCUSSION: The integrative evidence indicates that only H. coarctata and H. tenuidentata are currently valid Hierodula species in Iran, with H. macrostigmata as a junior synonym of H. coarctata and previous Iranian reports of S. trimacula rejected. The clear molecular separation between H. coarctata and the H. tenuidentata complex, combined with broad morphological variability in traits such as forefemoral spine coloration, underscores the need to abandon historically overemphasized colour characters and highlights the utility of COI barcoding in resolving conservative mantid lineages. Remaining uncertainty regarding the status of H. transcaucasica versus H. tenuidentata at a broader Eurasian scale calls for a forthcoming multi-locus, range-wide revision to formally resolve their taxonomy.},
}

@article {pmid41709109,
year = {2026},
author = {Cutrim, CHG and Vicente, MM and de Amorim, TP and Soares, KDA},
title = {New data on maximum size and geographic distribution of the Brazilian stingray Hypanus berthalutzae Petean, Naylor & Lima, 2020 (Batoidea: Myliobatiformes).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70365},
pmid = {41709109},
issn = {1095-8649},
support = {E-26/204.488/2024//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; },
abstract = {This study reports the first record of the endemic Lutz's stingray, Hypanus berthalutzae, from Brazil, at the upwelling ecosystem of Cabo Frio, southeastern Brazil. A mature female (2.44 m of total length) was incidentally captured by artisanal fisheries at 7 m depth in January 2025. Molecular identification (COI, Cytb), based on DNA barcoding and maximum likelihood phylogenetic analyses, confirmed similarity with H. berthalutzae sequences deposited in GenBank and supported its monophyly. Although the species is distributed from the mouth of the Amazon River to São Paulo, the large size of the specimen documented in this study suggests marked growth associated with highly productive upwelling zones. This record represents the first occurrence for the area, including Cabo Frio, and extends the genetic analysis of the species in southeastern Brazil. These results highlight the importance of integrating morphological analyses with molecular tools to accurately identify species and support conservation actions for endemic species in regions where their populations are vulnerable, enabling a more precise evaluation of species threats and conservation status.},
}

@article {pmid41707607,
year = {2026},
author = {Kiefer, L and Maniatis, T and Canzio, D},
title = {The role of cohesin and DNA loop extrusion in the generation of single neuron identity.},
journal = {Current opinion in genetics & development},
volume = {97},
number = {},
pages = {102445},
doi = {10.1016/j.gde.2026.102445},
pmid = {41707607},
issn = {1879-0380},
abstract = {Stochastic and combinatorial expression of clustered Protocadherin (Pcdh) genes generates extraordinary cell-surface protein diversity, which provides individual neurons with a unique cell surface 'barcode' that functions in neuronal self/non-self discrimination. Recent advances in understanding the mechanisms by which individual neurons randomly express Pcdh genes have revealed critical insights into the function of the cohesin complex, its unloader WAPL, and the insulator protein CTCF in neural self/non-self discrimination. The unique genomic architecture of the Pcdh locus - where nearly 60 tandemly organized promoters compete for a handful of shared enhancers over nearly 1 million base pairs of DNA - have provided novel insights into how enhancers and promoters communicate, and how these interactions vary with genomic distances and between distinct cell-types. These studies highlight the importance of investigating cohesin and its DNA loop extrusion activity in mice, where the relative stoichiometries of the cohesin complex and its regulators, and thus their activities, differ among neural cell-types, and where molecular mechanisms can be directly linked to cellular physiology and brain development. Here, we review recent findings and discuss how the Pcdh gene cluster has become a new paradigm for the study of the molecular functions of cohesin, its role in the regulation of gene expression, and the implications regarding neuropsychiatric and neurodevelopmental diseases.},
}

@article {pmid41707113,
year = {2026},
author = {Zhu, T and Sato, Y and Fukunaga, T and Miya, M and Iwasaki, W and Yoshizawa, S},
title = {MitoNGS: an online platform to analyze fish metabarcoding data in high-resolution.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag046},
pmid = {41707113},
issn = {1537-1719},
abstract = {Environmental DNA (eDNA) metabarcoding has become a powerful tool for assessing fish biodiversity in aquatic ecosystems. However, accurate species-level identification remains challenging due to incomplete and contaminated reference databases, as well as ambiguous taxa sharing identical barcode sequences. Here, we present MitoNGS, a next-generation platform that succeeds the widely used MiFish pipeline, designed for high-resolution analysis of fish metabarcoding data. MitoNGS addresses these challenges by incorporating more comprehensive references including non-fish species and detailed annotations of heterospecific regions. Additionally, it introduces the "species complex" strategy in conjunction with environmental habitat and geographic occurrence data to resolve ambiguous taxa. Furthermore, MitoNGS expands the functionalities of the legacy MiFish pipeline. It can analyze data from any mitochondrial markers and from Nanopore sequencing platforms. MitoNGS demonstrated excellent performance on our testing datasets from diverse locations, markers, and sequencing platforms. MitoNGS offers a user-friendly, web-based solution for fish detection, biodiversity monitoring, conservation research, and bioresource management. MitoNGS is freely available via https://mitofish.aori.u-tokyo.ac.jp/mito-ngs.},
}

@article {pmid41705258,
year = {2026},
author = {Khalil, A and Dinh, T and Parks, M and Obeng, RC and Gryder, B and Kresak, A and Wang, Y and Maltas, J and Bedrock, M and Wei, X and Faber, Z and Rahm, M and Scott, J and LaFramboise, T and Wang, Z and McFarland, C},
title = {In vivo multiplexed modeling reveals diverse roles of the TBX2 subfamily and Egr1 in Kr as-driven lung adenocarcinoma.},
journal = {Genes & diseases},
volume = {13},
number = {3},
pages = {101840},
pmid = {41705258},
issn = {2352-3042},
abstract = {The TBX2 subfamily of T-box transcription factors (e.g., Tbx2, Tbx3, Tbx4, Tbx5) plays an essential role in lung development. Down-regulation of these genes in human lung adenocarcinoma suggests that these genes may be tumor-suppressive; however, because down-regulation appears to occur primarily via epigenetic change, it remains unclear if these changes causally drive tumor progression or are merely the consequence of upstream events. Herein, we developed the first multiplexed mouse model to study the impact of TBX2 subfamily loss, alongside associated signaling genes (Egr1, Chd2, Tnfaip3a, and Atf3) in Ras-driven lung cancer. Using tumor-barcoding with high-throughput barcode sequencing (TuBa-seq), a high-throughput tumor-barcoding system, we quantified the growth effects of these knockouts during early and late tumorigenesis. Chd2 knockout suppressed both tumor initiation and progression, whereas Tnfaip3 knockout enhanced tumor initiation and overall tumor growth. Tbx2 loss showed stage-specific effects on tumor development. Notably, Egr1 emerged as a strong tumor suppressor and its knockout resulted in approximately a fivefold increase in tumor size at 20 weeks (two-sample t-test, p < 0.05), exceeding the impact observed with Rb1 loss. Transcriptomic analyses of Egr1-deficient tumors suggested immune dysregulation, including heightened inflammation and potential markers of T cell exhaustion in the tumor microenvironment. These findings indicate that Egr1 may play a role in suppressing tumor growth through modulating immune dynamics, offering new insights into the interplay between tumor progression and immune regulation in lung adenocarcinoma.},
}

@article {pmid41704917,
year = {2026},
author = {Han, W and Chan, TY and Zhang, CM and Lin, XL and Cranston, PS and Nimalrathna, TS and Lin, BA and Tang, HQ and Seymour, M},
title = {Integrative Assessment of Hong Kong Chironomidae (Diptera) Shows High Species Richness Linked to Spatial and Environmental Factors.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73110},
pmid = {41704917},
issn = {2045-7758},
abstract = {Inland waters face escalating anthropogenic pressures, driving an unprecedented collapse in freshwater biodiversity. Enhanced knowledge of aquatic taxa is essential to reverse this decline. Chironomidae (non-biting midges), often the dominant zoobenthic group in freshwater ecosystems, remain poorly documented globally. Here, we provide the first integrative assessment of Chironomidae biodiversity in Hong Kong through a year-long survey of five streams. Integrative taxonomy expanded the known species in Hong Kong from 17 to 243, and yielded a reference library of 827 cytochrome c oxidase subunit I (COI) barcodes representing 225 species. Beta-diversity partitioning revealed that community dissimilarity was primarily driven by species turnover, which was strongly associated with environmental gradients but only weakly related to geographic distance. Variation partitioning revealed that environmental factors explained slightly more variation in community composition (9.0%) than spatial factors (6.7%). These patterns indicate that environmental filtering and mass effects play key roles in structuring Chironomidae metacommunities in Hong Kong, with dispersal limitation exerting little influence. Cross-database barcode matching analysis suggested that Hong Kong fauna is predominantly tropical-to-subtropical, with the strongest affinities to coastal East and Southeast Asia (e.g., eastern China, Thailand, Malaysia). Many species displayed wide geographic ranges, likely facilitated by high passive dispersal and broad ecological tolerances. This study delivers the first robust biodiversity baseline for Hong Kong Chironomidae and a well-curated DNA barcode library. These resources will benefit taxonomic refinement and eDNA-based biomonitoring, strengthening conservation of human-impacted freshwater ecosystems.},
}

@article {pmid41617809,
year = {2026},
author = {Seo, S and Erol, Ö and Kim, HK and van Mil, HGJ and Jung, J and Jang, YP and Lee, DY and Wang, M and Sheridan, H and Han, SB and Choi, YH},
title = {Leveraging metabolic similarity in a [1]H NMR database of medicinal plants to advance pharmacognostic insights.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6691},
pmid = {41617809},
issn = {2045-2322},
support = {DOJProject209825//The Department of Justice, Ireland/ ; KSN2312021//The Korea Institute of Oriental Medicine/ ; 203876//Programma EFROWEST-Netherland 2021-2027/ ; GanCao 025009//Hangzhou Ganzhicao Technology Co. Ltd/ ; },
abstract = {UNLABELLED: Natural products remain a central resource for drug discovery, and increasing evidence suggests that therapeutic effects often arise from the combined action of multiple constituents rather than single compounds. In this context, metabolomic profiling is essential for comparing complex plant chemical phenotypes, and [1]H NMR provides robust whole-profile fingerprints that support cross-species metabolic barcoding and systematic comparison. In this study, we establish and apply a standardized large-scale [1]H NMR database to enable macroscopic metabolomic similarity profiling of medicinal plants. Specifically, using [1]H NMR profiles from 656 traditional medicinal herbs, we demonstrate how this standardized large-scale metabolomic framework can be applied to key challenges in medicinal plant research, including quality control across different locations and time periods, identification of metabolically similar alternative species, and compositional analysis of multi-herb formulations. Our findings demonstrate the utility of this NMR-based strategy as a scalable approach for standardization, authentication, and holistic characterization of medicinal plants, advancing the field beyond reductionist paradigms. This study establishes a standardized large-scale [1]H NMR database of medicinal plants and introduces a macroscopic framework for large-scale metabolomic similarity profiling that enables chemotaxonomic contextualization, quality surveillance, and identification of metabolically similar candidate substitutes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-37725-2.},
}

@article {pmid41704508,
year = {2026},
author = {Sidiq, Y and Rahayu, T and Indrayudha, P and Tyastuti, EM and Althaf, AZW and Sari, BK},
title = {Metabarcoding data: Full-length 16S rRNA sequence of endophytic bacteria in the root of asymptomatic and blast-symptomatic rice plants (Oryza sativa, L.).},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112522},
pmid = {41704508},
issn = {2352-3409},
abstract = {There is a sustained demand for biofertilizers to enhance crop productivity. Endophytic bacteria associated with disease-tolerant rice varieties offer significant potential as biofertilizers; however, the bacteriome diversity within these plants remains underexplored. This dataset presents full-length 16S metagenomic sequences of endophytic bacteria isolated from the roots of blast-infected and uninfected rice plants. Root samples were processed and subjected to surface sterilisation. Following total genomic DNA extraction, sequencing was performed using 16S ribosomal RNA primers via the high-throughput Oxford Nanopore Technologies platform. The raw sequence data were filtered for quality control using NanoFilt. Subsequently, the sequences were aligned against the National Center for Biotechnology Information (NCBI) 16S RefSeq database to identify the species of the endophytic root bacteria. The data associated with this project have been registered in the NCBI BioProject database under accession number PRJNA992961. The dataset comprises two distinct sample groups, each analysed in duplicate, with sequencing yields ranging from 17.7 to 20.3 Mb. Consequently, this dataset provides valuable insights regarding the comparative composition of endophytic bacteria inhabiting healthy roots versus those found in blast-infected rice. Characterizing this diversity, particularly within healthy rice plants, is essential for foundational research underpinning the future development of biofertilizers.},
}

@article {pmid41702708,
year = {2026},
author = {Elgood Hunt, E and Vivori, C and Mitter, R and Agnadottir, V and van Werven, FJ},
title = {Mapping and quantifying nascent transcript start sites using TT-TSS-seq.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.280726.125},
pmid = {41702708},
issn = {1549-5469},
abstract = {Transcription initiation is a highly dynamic and tightly regulated process involving the coordinated action of transcription factors, chromatin remodelers, and RNA polymerase, which determine where and when transcription begins. Accurately mapping and quantifying transcription start sites (TSSs) from nascently transcribed RNAs remains a key area of interest, as it provides critical insights into transcription dynamics. Here, we combine transient transcriptome sequencing with transcription start site sequencing (TT-TSS-seq) to accurately map and quantify transcription initiation sites from nascent transcripts. Because transient metabolic labeling yields low-input RNA, we optimize the TSS-seq protocol to enhance sensitivity and accuracy. Specifically, we refine enzymatic reactions for decapping and RNA ligation and incorporate 5' oligonucleotides containing unique molecular identifiers (UMIs) and barcodes to enable accurate quantification and sample multiplexing. The TT-TSS-seq approach detects transcription initiation of unstable transcripts, such as enhancer RNAs. Moreover, we show that a large fraction of genes use multiple transcription initiation sites, yet often produce only a single stable transcript. Overall, TT-TSS-seq provides precise mapping and quantification of transcription initiation sites, offering new insights into transcriptional dynamics and expanding the toolkit for studying gene regulation.},
}

@article {pmid41701208,
year = {2026},
author = {Feng, C and Li, W and Wang, Y and Sun, L and Wang, X and Bian, F},
title = {Wettable Porous Arrays with Structural Color Barcodes Integration for Multiplex Urinary Tract Infection Bacteria Screening.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c07570},
pmid = {41701208},
issn = {1520-6882},
abstract = {Urinary tract infection (UTI) is one of the most common bacterial infections in clinical practice and is a potentially life-threatening infection with high morbidity, recurrence, and mortality rates. High-sensitivity multiplexed biomarker detection is crucial for the early diagnosis and treatment of UTI. Digital nucleic acid amplification technologies (dNAATs) offer highly sensitive molecular characterization by isolating individual template molecules and amplifying them separately. However, multiplex analysis with dNAATs often requires parallel amplification, which is time-consuming and labor-intensive. Here, we present a novel multiplex detection method that integrates structural color barcodes into superhydrophilic porous arrays. This method enables the sensitive detection of multiple targets simultaneously in a highly efficient manner. The excellent hydrophilicity of the microwells allows the reaction solution to fill each well, ensuring random and complete isolation of the nucleic acid molecules. The amplification reactions occur independently in each unit, enabling the absolute quantification of nucleic acids. The structural color barcodes fixed in the microwells have stable reflection peaks and large surface areas, serving as encoding carriers based on their distinct reflection wavelengths. This enables the screening of multiplexed UTI bacteria to be performed quickly, accurately, and reproducibly. By using different probes on the color barcodes, we were able to detect single and multiple UTI pathogens with high sensitivity. The results demonstrate that the integrated porous array platform with structural color barcodes realized the highly sensitive detection and screening of UTI bacteria, which has great potential in multiplex biomolecule detection and early diagnosis of infections.},
}

@article {pmid41700630,
year = {2026},
author = {Huang, X and Tian, X and Chen, K and Wu, Y and Xue, C and Quek, Y and Low, J and Kumar, A and Tay, A},
title = {High-Throughput In Vivo Subcellular Analysis of Gold Nanoparticles for Tumor Mitochondrial Targeting.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e17706},
doi = {10.1002/adma.202517706},
pmid = {41700630},
issn = {1521-4095},
support = {//NUS Presidential Young Professorship/ ; DEGAP200//Ministry of Education Tier 1/ ; GAP2002023-03-14//Ministry of Education Tier 1/ ; MOH-001746-00//National Medical Research Council/ ; T2EP30224-0021//Ministry of Education - Singapore/ ; },
abstract = {Mitochondrial targeting is a powerful strategy for cancer precision therapy. This study presents a subcellular DNA barcoding system for high-throughput in vivo screening of mitochondrial-targeting gold nanoparticles (NPs). After validating the robustness of the barcode system with six PEG/TPP‑modified NPs in vitro, the materials library expands to 30 NP species differing in shape, size, and ligand. Their biodistributions are systematically evaluated across subcutaneous, orthotopic, and contralateral tumor models at organ, cell-subtype, and mitochondrial levels. This multiplexed approach yields more than 1000 data points on in vivo nanoparticle uptake and targeting behaviors, while requiring 30-fold fewer mice than conventional approaches. The data reveal a strong correlation between tumor accumulation and mitochondrial delivery, indicating that effective tumor accumulation is a prerequisite for mitochondrial targeting. 80 nm cube (CL‑FA) and sphere (PL‑FA) nanoparticles tagged with folic acid (FA) emerge as top performers, with CL‑FA achieving 99% tumor regression when combined with mild photothermal therapy and mitochondria-targeted siRNA delivery. Underlying mechanisms are attributed to geometry-dependent protein corona formation patterns and cellular uptake via clathrin‑mediated endocytosis and specific curvature‑sensing protein interactions. Overall, this subcellular high-throughput barcoding platform offers a rational framework to select inorganic nanomaterials for precision subcellular drug delivery.},
}

@article {pmid41699392,
year = {2026},
author = {Moracho, E and Arroyo, JM and Arroyo-Correa, B and Calvo, G and Homet, P and Isla, J and Jácome-Flores, M and Mendoza, I and Quintero, E and Rodríguez-Sánchez, F and Villalva, P and Jordano, P},
title = {A comprehensive, multi-method dataset of plant-frugivore interactions in a Mediterranean hotspot.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06835-x},
pmid = {41699392},
issn = {2052-4463},
support = {PID2020-115129RJ-I00//Ministerio de Ciencia e Innovación/ ; no. 798269//European Union's Horizon 2020, Marie Sklodowska-Curie grant/ ; LIFEWATCH-2019-09-CSIC-13//LifeWatch ERIC-SUMHAL CSIC/ ; PID2022-136812NB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; Plan Propio de Investigación y Transferencia, University of Sevilla (2021-2025)//Universidad de Sevilla/ ; },
abstract = {Mutualistic plant-animal interactions for seed dispersal are crucial for vegetation dynamics, benefiting over half of the world's plant species. Beyond the tropics, the Mediterranean biome harbors the highest proportion of species adapted to endozoochory, yet major gaps remain in quantifying interaction diversity in these biodiversity-rich areas and their links to ecosystem functioning. High-resolution, quantitative interaction data are essential not only to fill these gaps but also to enable large-scale ecological modeling of species interactions across biomes. Here, we present the FRUGivory INTegration (FRUGINT) dataset - an extensive collection of quantitative frugivory interactions and associated species traits from a Mediterranean biodiversity hotspot in southwestern Spain. By integrating six complementary sampling methods (camera trapping, continuous-monitoring cameras, DNA-barcoding, mist-netting, direct observation and track records) across multiple years, the dataset overcomes limitations of sampling biases, variable effort and spatio-temporal heterogeneity, providing a comprehensive picture of plant-frugivore interactions across the region. Based on a total of 37,923 interaction records and 481 unique pairwise interactions, involving 26 fleshy-fruited plant species present in Doñana and 78 frugivorous vertebrate species, FRUGINT yields estimates of regional-scale plant-frugivore networks based on pairwise interaction probabilities. The dataset encompasses both common and numerous rare interactions, offering a valuable resource for advancing research on plant-animal interactions, network ecology, and biodiversity conservation.},
}

@article {pmid41698997,
year = {2026},
author = {Kang, Y and Lee, H and Park, DK and Akimoto, S and Hong, KJ and Lee, W},
title = {High utility of DNA barcoding for species identification and cryptic diversity in Korean aphids (Hemiptera: Aphididae).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38901-0},
pmid = {41698997},
issn = {2045-2322},
support = {RS-2025-02216505//Research Program for Agriculture Science and Technology Development/ ; RS-2025-02216505//Research Program for Agriculture Science and Technology Development/ ; RS-2025-02216505//Research Program for Agriculture Science and Technology Development/ ; HNIBR202501211//Honam National Institute of Biological Resources/ ; HNIBR202501211//Honam National Institute of Biological Resources/ ; HNIBR202501211//Honam National Institute of Biological Resources/ ; },
}

@article {pmid41698531,
year = {2026},
author = {Pingault, CG and Richard, C and Murison, G and Sylvoz, N and Py, P and Salomez-Ihl, C and Bedouch, P},
title = {INSTRUMENT TRACEABILITY: OPTIMISATION OF DATAMATRIX READERS BY AN EXPERIMENTAL DESIGN.},
journal = {Annales pharmaceutiques francaises},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pharma.2026.02.002},
pmid = {41698531},
issn = {2772-803X},
abstract = {Implementing traceability at instrument's individual level showed that Datamatrix readers were unable to read the Data Matrix barcodes effectively. This led to slow down medical procedure trays repackaging's stage and a great reluctance from operators to continue the Datamatrix process deployment. To improve reader performance, an experimental design was developed using the Taguchi method. This experimental design made possible, in a limited number of trials, to identify influencing parameters and their optimal settings. The reading time of instruments was reduced by 81% while using the leanest possible production resources. Thanks to this improvement, the Sterilisation department team has been able to continue ramping up Individual Level Instrument traceability with greater efficiency and increased satisfaction of the medical staff.},
}

@article {pmid41696484,
year = {2026},
author = {Martinez, JI and Homziak, NT and Pierson, TL and Campo, RJL and Plotkin, DM and Castillo-Argaez, RJ},
title = {Revision of the comose flame moths of the genus Sosxetra Walker (Noctuidae, Dyopsinae), with descriptions of a new genus and three new species.},
journal = {ZooKeys},
volume = {1268},
number = {},
pages = {227-248},
pmid = {41696484},
issn = {1313-2989},
abstract = {As part of our Neotropical Dyopsinae Project, a revision of the Neotropical genus Sosxetra Walker is proposed. Morphological and molecular evidence challenge its previous monotypic classification. The genus is redescribed and a neotype is designated for Sosxetra grata Walker, previously considered the only species in the genus. Two new species are described: Sosxetra mamanina Martinez, Homziak, & Castillo-Argaez, sp. nov. and Sosxetra thutakanay Martinez, Homziak, & Castillo-Argaez, sp. nov. Finally, Covellana Martinez, Homziak, Plotkin & Castillo-Argaez, gen. nov., is established based on Covellana niomalan Martinez, Homziak, Plotkin & Castillo-Argaez, sp. nov., previously misidentified as Sosxetra grata.},
}

@article {pmid41696483,
year = {2026},
author = {Guiguet, A and van Nieukerken, EJ and Giron, D and Gravendeel, B and Lopez-Vaamonde, C and Ohshima, I},
title = {Two new species of Caloptilia (Lepidoptera, Gracillariidae) from New Caledonia inducing galls on Glochidion billardierei (Phyllanthaceae) and redescription of C. xanthopharella (Meyrick, 1880).},
journal = {ZooKeys},
volume = {1268},
number = {},
pages = {113-137},
pmid = {41696483},
issn = {1313-2989},
abstract = {New Caledonia is a biodiversity hotspot with high levels of micro-endemism, yet its gracillariid fauna remains poorly documented. Here, two new species of Caloptilia Hübner, 1825 (Gracillariidae) are described from Glochidion J.R.Forst. & G.Forst. (Phyllanthaceae) host plants in Parc des Grandes Fougères, New Caledonia: Caloptilia augeas Guiguet, Lopez-Vaamonde, van Nieukerken & Ohshima, sp. nov., and Caloptilia ceryneia Guiguet, Lopez-Vaamonde, van Nieukerken & Ohshima, sp. nov. Both species induce leaf galls on Glochidion billardierei Baill., co-occurring on the same host species, sometimes even on the same leaf. They exhibit distinct wing patterns, but very similar male and female genitalia, and DNA barcoding supports their status as separate species. These findings provide evidence for potential within-host sympatric speciation, as documented in other gall-inducing insects. The larval biology of C. augeas and C. ceryneia reveals a unique frass disposal behaviour, whereby waste is excreted through a hole and the aperture is subsequently sealed-an adaptation not previously reported in gall-inducing Lepidoptera. Our findings double the known number of gall-inducing species in Gracillariidae, highlighting that this life history strategy may be more common than currently appreciated. We also provide new information on distribution and host plants of Caloptilia xanthopharella (Meyrick, 1880), a leaf roller found on the same host plant, G. billardierei. These findings mark the first records of the subfamily Gracillariinae in New Caledonia. This study underscores the underexplored diversity of New Caledonian gracillariids and emphasises the conservation value of Parc des Grandes Fougères. Further surveys in the Indo-Pacific region may reveal additional yet undescribed Caloptilia species associated with Phyllanthaceae and help clarify the evolutionary mechanisms underpinning their diversification.},
}

@article {pmid41689801,
year = {2026},
author = {Strauss, SK and Golomb, R and Khoury, D and Aharon-Hefetz, N and Meyer, H and Sheykhkarimli, D and Liti, G and Dahan, O and Pilpel, Y},
title = {Quantitative genetics of natural S. cerevisiae strains upon mating reveal heritable determinants of fitness and differential mating affinities.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116972},
doi = {10.1016/j.celrep.2026.116972},
pmid = {41689801},
issn = {2211-1247},
abstract = {Among the fundamental questions in sexual reproduction are how fitness is inherited and whether parents exhibit differential mating affinities. Addressing these questions requires quantitative genetic tools and large phenotyped and genotyped strain collections from a single species. We leverage sexual mating among nearly 100 natural isolates of Saccharomyces cerevisiae, generating thousands of offspring across several growth conditions. Using genomic barcodes and a barcode-recombination method to track mating events, we measure fitness for all parents and offspring. In fermentable carbon (glucose), offspring fitness correlates positively, though modestly, with parental fitness. In contrast, in non-fermentable carbon (glycerol), no such correlation is detectable. Instead, offspring fitness in glycerol increases sharply with genetic distance between parents, indicating that outbreeding maximizes fitness independently of parental fitness. Finally, mate affinity varies among parental pairs, with some combinations enriched and others avoided. This work reveals factors shaping fitness inheritance and provides resources for quantitative genetics.},
}

@article {pmid41689291,
year = {2026},
author = {Feng, V and Høegh-Guldberg, C and Meier, R and Buček, A},
title = {Balancing Barcoding and Genomics: gDNA Quality in Insect Vouchers After HotSHOT DNA Extraction.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70103},
pmid = {41689291},
issn = {1755-0998},
support = {23-08010M//Grantová Agentura České Republiky/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Insecta/genetics/classification ; *DNA/isolation & purification/genetics ; *Genomics/methods ; *Specimen Handling/methods ; },
abstract = {DNA extraction with an alkaline buffer system called 'HotSHOT' is widely used for barcoding because it is rapid, inexpensive, and voucher preserving, but it remains unclear whether sufficient genomic DNA (gDNA) remains in small vouchers for downstream use in genomics. We here evaluate gDNA quality and quantity before and after HotSHOT treatment of 11 insect families representing six orders. Some specimens were flash frozen immediately after collection, while others were kept for 1 week at tropical temperatures in ethanol to mimic Malaise trap conditions. Encouragingly, we show that gDNA of sufficiently high quality and quantity for genomic sequencing remained in specimens treated with HotSHOT. We also show that DNA integrity was strongly influenced by field storage, with specimens exposed to Malaise trap conditions showing such pronounced degradation that the standard HotSHOT treatment no longer significantly altered DNA quality. For control material, HotSHOT treatments involving longer exposure to high temperature led to smaller fragment lengths, with the effect apparently being influenced by the degree of specimen sclerotization. Our results thus suggest that optimised HotSHOT treatments, together with carefully controlled pre-extraction storage, preserve voucher gDNA of sufficient quality for downstream genomic analyses with both short-read and possibly even some long-read sequencing technologies. We provide protocol selection guidelines that improve voucher gDNA preservation in HotSHOT-treated samples. This is particularly important for many species which are only known from one or few specimens discovered during barcoding projects.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Insecta/genetics/classification
*DNA/isolation & purification/genetics
*Genomics/methods
*Specimen Handling/methods

@article {pmid41687792,
year = {2026},
author = {Hassanin, A and Jullemier, E and Chardonnet, B and Robinson, TJ},
title = {Species delimitation based on phylogenetic analyses of males: A case study revealing the complex evolutionary history of giraffes.},
journal = {Molecular phylogenetics and evolution},
volume = {218},
number = {},
pages = {108571},
doi = {10.1016/j.ympev.2026.108571},
pmid = {41687792},
issn = {1095-9513},
abstract = {Male mammals are of particular interest for molecular systematics as their cells contain two non-recombinant markers, the mitochondrial genome and the male-specific Y chromosome (MSY), which provide information on maternal and paternal evolutionary histories, respectively. Here, we assembled four single-copy MSY genes (AMELY, DDX3Y, SRY and ZFY), three homologs on the X chromosome, the mitogenome, and 21 autosomal introns from whole genome sequencing (WGS) data available for 123 male giraffes. We detected several instances of introgression between giraffe subspecies involving the mitogenome, MSY, and X-linked genes. The analysis of MSY haplotypes supports a deep separation in Africa between northern giraffes (subspecies antiquorum, peralta, rothschildi, and reticulata) and southern giraffes, with a large gap between intragroup and intergroup DNA distances (referred to as the 'MSY barcoding gap'). At a finer scale, southern giraffes can be divided into two geographic MSY groups that are distributed in East Africa (comprising the subspecies tippelskirchi and thornicrofti) and southern Africa (comprising the subspecies giraffa and wardi). These relationships are all supported by several exclusive synapomorphies in most DNA datasets. Our results provide strong support for two species of Giraffa, i.e., G. camelopardalis (northern giraffes) and G. giraffa (southern giraffes), but with ZFX alleles showing evidence of ancient introgression between the two taxa. The delimitation of Giraffa in two species is consistent with skull morphology and the evolution of highly distinctive phenotypes (reticulated versus Masai) in the hybrid zone between northern and southern species in southern Kenya which may have promoted the reinforcement of prezygotic isolation, thus limiting gene flow between them.},
}

@article {pmid41686737,
year = {2026},
author = {Lee, JJ and Kang, JS and Kim, YJ and Lee, YS and Park, JY and Jang, W and Moon, BC and Kim, Y and Kim, TY and Yang, TJ},
title = {Super-barcoding of four Agrimonia species distributed in Korea based on complete plastid genomes and nuclear ribosomal DNAs.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0341151},
pmid = {41686737},
issn = {1932-6203},
mesh = {*Genome, Plastid/genetics ; *DNA Barcoding, Taxonomic/methods ; Phylogeny ; Republic of Korea ; *Agrimonia/genetics/classification ; *DNA, Ribosomal/genetics ; Genetic Variation ; Cell Nucleus/genetics ; DNA, Plant/genetics ; },
abstract = {The genus Agrimonia is widely distributed throughout temperate regions and includes species used in traditional medicine in Asia and Europe. However, their accurate identification is often challenging because the vegetative parts used, such as leaves and roots, are morphologically highly similar across species. To investigate the genetic diversity of Agrimonia species commonly distributed and traded in Korea and to develop reliable molecular tools for species authentication, we collected 36 samples primarily representing four Agrimonia species (A. pilosa, A. coreana, A. nipponica, and A. eupatoria). We sequenced and assembled complete plastid genomes (plastomes) and 45S nuclear ribosomal DNA (nrDNA) sequences from these four species. The assembled plastomes ranged from 155,128-155,313 bp, while the nrDNA sequences spanned 5,860-5,873 bp. Phylogenetic analyses based on both plastome and nrDNA datasets revealed that each species formed a distinct clade, demonstrating clear genetic differentiation among taxa. Based on plastome sequence variations, we developed eight plastome-based super-barcoding markers and validated their reliability using 36 Agrimonia accessions, including an additional closely related congeneric accession, A. gorovoii. The markers successfully classified samples into species-specific haplotype groups. This plastome-based super-barcoding approach provides a practical molecular authentication method for major Agrimonia species used as medicinal resources in Korea, thereby facilitating quality control and accurate utilization of Agrimonia materials.},
}

*Genome, Plastid/genetics
*DNA Barcoding, Taxonomic/methods
Phylogeny
Republic of Korea
*Agrimonia/genetics/classification
*DNA, Ribosomal/genetics
Genetic Variation
Cell Nucleus/genetics
DNA, Plant/genetics

@article {pmid41685734,
year = {2026},
author = {Lu, H and Wu, B and Liu, YX and Li, YY and Gu, LF and Yuan, XL and Ding, XY and Chen, D and Chen, SQ and Zhang, KQ and Zhuo, MP},
title = {Supramolecular Self-Assembly of Organic Topological Structures from Charge-Transfer Cocrystal Alloys to Triblock Microrods.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c21313},
pmid = {41685734},
issn = {1520-5126},
abstract = {The organic charge-transfer (CT) cocrystal alloys integrating the charming CT feature and the unique structure-property of alloys have attracted intensive attention in organic semiconductors. Finely modulating the CT interaction is critical in rationally designing the desired organic cocrystal alloys with novel topological configurations. Herein, we purposely selected 7,12-dimethylbenz[a]anthracene (DBA) and 9,10-dicyanoanthracene (DCA) to coassemble and ensured the formation of organic cocrystal alloys rather than pure cocrystals via tuning the CT interaction between them. Owing to the CT characteristics between DCA and DBA, the prepared cocrystal alloy microrods present red emission, in contrast with the green-emissive DCA microrods and the blue-emissive DBA microplates. Furthermore, the prepared cocrystal alloy demonstrates perfect lattice matching with the DCA crystal, which is conducive to forming their triblock microrods through an epitaxial-growth process for advanced optoelectronics, such as spatially resolved photonic barcodes. This work provides further insights into cocrystal alloys and their topological heterostructures.},
}

@article {pmid41683418,
year = {2026},
author = {Wang, M and Li, W and Zuo, Y and Jiang, Q and Li, J and Zhang, W and Meng, X},
title = {Rapid Authentication of Flowers of Panax ginseng and Panax notoginseng Using High-Resolution Melting (HRM) Analysis.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {3},
pages = {},
pmid = {41683418},
issn = {1420-3049},
support = {YQYB2024085//Anhui Provincial Outstanding Young Teacher Cultivation Project (General)/ ; GXXT-2023-073//University Synergy Innovation Program of Anhui Province/ ; 2020SX//Bozhou City Chief Expert Studio/ ; },
mesh = {*Panax/genetics/classification ; *Flowers/genetics/classification ; *Panax notoginseng/genetics/classification ; Phylogeny ; DNA, Plant/genetics ; Transition Temperature ; },
abstract = {The flowers of Panax ginseng C. A. Mey. (PG) and Panax notoginseng (Burkill) F. H. Chen ex C. H. Chow (PN) are morphologically indistinguishable after drying, leading to prevalent adulteration that compromises product quality and consumer safety. To address this issue, we developed a rapid, closed-tube molecular authentication method based on high-resolution melting (HRM) analysis. Species-specific primer pairs were designed to target the conserved ITS and rbcL-accD regions, with PNG-2 selected as the optimal candidate owing to its stable genotyping performance and moderate GC content. Our results established GC content, rather than amplicon length, as the primary determinant of the melting temperature (Tm). Notably, the experimentally measured Tm values were consistently 0.7-1.5 °C higher than theoretical predictions, a discrepancy attributable to the stabilizing effect of the saturated fluorescent dye. To ensure maximum diagnostic reliability, the HRM results were cross-validated through a three-tier system comprising ITS2 phylogenetic analysis, agarose gel electrophoresis, and Sanger sequencing. The practical utility and matrix robustness of the assay were further verified using a diversified validation cohort of 30 commercial samples, including 24 floral batches and 6 root-derived products (root slices and ultramicro powders). The HRM profiles demonstrated 100% concordance with DNA barcoding results, effectively identifying mislabeled products across different botanical matrices and processing forms. This methodology, which can be completed within 3 h, provides a significantly more cost-effective and rapid alternative to traditional sequencing-based methods for large-scale market surveillance and industrial quality control.},
}

*Panax/genetics/classification
*Flowers/genetics/classification
*Panax notoginseng/genetics/classification
Phylogeny
DNA, Plant/genetics
Transition Temperature

@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}

@article {pmid41677694,
year = {2026},
author = {Alharbi, SA},
title = {First Plastome Sequences of Two Endemic Taxa of Orbea Haw. from the Arabian Peninsula: Comparative Genomics and Phylogenetic Relationships Within the Tribe Ceropegieae (Asclepiadoideae, Apocynaceae).},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677694},
issn = {2079-7737},
abstract = {Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG-ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM-trnD, and rpl32-trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus.},
}

@article {pmid41677260,
year = {2026},
author = {Leyson, CM and Vargas-Maldonado, N and Gaddy, M and Raghunathan, V and Ferreri, LM and Sethi, M and Patatanian, K and Carnaccini, S and Ganti, K and VanInsberghe, D and Lowen, AC},
title = {Viral lineage and mode of exposure modulate within-host spatial dynamics of influenza A viruses in a guinea pig model.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0188925},
doi = {10.1128/jvi.01889-25},
pmid = {41677260},
issn = {1098-5514},
abstract = {The upper and lower respiratory tracts (URT and LRT) present distinct environments for influenza A virus (IAV) replication. Their differential features have major implications for viral evolutionary dynamics, transmission potential, and pathogenesis. To investigate the implications of differential viral replication in the URT and LRT, we assessed dispersal of IAVs throughout the guinea pig respiratory system. Guinea pigs were inoculated intranasally with a 300 μL volume to deliver inoculum to both the URT and LRT. Two strains were used to represent the circulating seasonal IAV lineages: influenza A/TX/50/2012 (H3N2) and influenza A/CA/07/2009 (H1N1). For the H1N1 virus, a genetically diverse barcode library enabled high-resolution tracking of viral dispersal. Infectious virus was consistently detected in the URT for both strains; however, only the H1N1 virus was detected in the LRT. To determine whether replication of the H1N1 virus in the LRT extends to other routes of infection, virus distribution was evaluated following infection via aerosol exposure or transmission. Infectious virus in lung homogenates was observed in both cases, confirming the LRT tropism of the H1N1 virus. Sequencing genetic barcodes revealed that diversity was largely maintained in nasal samples and trachea but was reduced upon dispersal to the lungs. This contraction of diversity was associated with increased distance and branching from the major airways, suggesting long-distance dispersal through the respiratory tract imposes within-host population bottlenecks. Together, these findings highlight how the distinct environments of the URT and LRT shape within-host IAV population dynamics.IMPORTANCEThe upper (URT) and lower (LRT) respiratory tracts create different conditions for influenza A virus (IAV) spread and evolution. We studied how the virus moves through guinea pigs' airways after infection with H3N2 or H1N1 strains of IAV. Whether delivered intranasally, by aerosol or by transmission, the H1N1 virus replicated in the nasal cavity, trachea, and lungs. By contrast, the H3N2 virus stayed mostly in the nasal cavity. Genetic barcodes were used to track how the H1N1 virus moved and changed. The populations replicating in the nasal cavity and trachea maintained high diversity, but those sampled from the lungs showed low diversity. This bottlenecking effect was stronger for viral populations present deeper in the lungs. These findings show that the different environments of the URT and LRT strongly shape how influenza spreads and evolves inside a host.},
}

@article {pmid41676703,
year = {2026},
author = {Ng, CF and Krishnamurthy, D and Dextre, A and Chorlay, A and Ott, M and Fletcher, DA},
title = {LUCas: Light-Uncaged Cas13a using photocleavable interfering guide RNAs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.700737},
pmid = {41676703},
issn = {2692-8205},
abstract = {CRISPR diagnostics have emerged as powerful tools for detecting infectious diseases, with the RNA endonuclease Cas13a enabling sensitive and specific, amplification-free RNA detection through collateral trans -cleavage of fluorescent reporters. However, background cleavage from unbound enzyme, contaminating nucleases, and unsynchronized initiation of reactions limits assay sensitivity and interpretability. A strategy to precisely control the onset of Cas13a catalytic activity, essentially a molecular "starting gun", would address these challenges and expand assay design space. Here, we introduce Light-Uncaged Cas13a (LUCas), a light controllable system that directly gates Cas13a using a photocleavable interfering guide RNA (pc-igRNA) that suppresses trans -cleavage activity even in the presence of target RNA. Brief UV illumination releases this suppression, restoring full activity. Quantitative kinetic analysis reveals an approximately 100-fold suppression of trans -cleavage activity prior to photo-activation. Importantly, LUCas also suppresses target-independent background activity, enabling a predictive, background-limited determination of assay sensitivity. Using measured kinetic parameters, we predict and experimentally validate the limit-of-detection of the LUCas system. Finally, we demonstrate a multiplexed detection strategy termed "temporal barcoding," which enables quantitative detection of viral co-infections in a single bulk reaction. Together, these results establish LUCas as a general framework for mechanistically informed, light-based control of Cas13a activity.},
}

@article {pmid41676323,
year = {2026},
author = {Li, S and Wang, K and Wang, X and Hu, Z},
title = {Single-cell mitochondrial lineage tracing: Opportunities and challenges.},
journal = {Quantitative biology (Beijing, China)},
volume = {14},
number = {1},
pages = {e70018},
pmid = {41676323},
issn = {2095-4697},
abstract = {Lineage tracing using endogenous mitochondrial DNA (mtDNA) variants holds great promise for reconstructing the lineage histories of individual cells, with broad applications in oncology, developmental biology, and regenerative medicine. Unlike synthetic DNA barcoding techniques, mitochondrial lineage tracing does not require genetic engineering of exogenous genetic markers, and thus is particularly suitable for human clinical samples. Various experimental and computational methods have been developed to profile mtDNA variants from single-cell genomic, transcriptomic, and epigenomic sequencing data. Despite the technical advances, several challenges still limit the robustness of single-cell mitochondrial lineage tracing, such as random genetic drift, genetic bottlenecks, informative variant identification, and low mtDNA coverage. In this review, we systematically examine current experimental and computational approaches for analyzing mtDNA variants in single cells and discuss current challenges and future technical developments aimed at enhancing the robustness and applicability of single-cell mitochondrial lineage tracing.},
}

@article {pmid41674713,
year = {2025},
author = {Mao, S and Zhang, C and Chen, R and Tang, S and Fan, X and Hu, J},
title = {Cell lineage tracing: Methods, applications, and challenges.},
journal = {Quantitative biology (Beijing, China)},
volume = {13},
number = {4},
pages = {e70006},
pmid = {41674713},
issn = {2095-4697},
abstract = {Cell lineage tracing is a crucial technique for understanding cell fate and lineage relationships, with wide applications in developmental biology, tissue regeneration, and disease progression studies. Over the years, experimental cell lineage tracing methods have advanced from early labeling techniques to modern genetic tools such as CRISPR-Cas9-based barcoding, whereas computational methods have emerged to analyze high-dimensional data from single-cell sequencing and other omics technologies. This paper reviews both experimental and computational methods, highlighting their respective strengths, limitations, and synergies. Experimental techniques focus on labeling and tracking cells, whereas computational approaches reconstruct lineage relationships and model cellular dynamics. Despite significant progress, challenges remain, including issues with accuracy, resolution, multi-omics integration, and scalability. Future directions involve improvements in experimental techniques and the development of computational methods enhanced by advancements in artificial intelligence. These innovations are expected to drive the field forward, offering potential applications in uncovering the mysteries of life.},
}

@article {pmid41674080,
year = {2026},
author = {Cui, M and Hu, C and Dong, J and Cheng, Y and Sun, B and Fan, C and Wang, L and Chao, J},
title = {Multimodal DNA Nanostructure Barcodes for Single-Cell Protein Profiling and Tumor Subtyping.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c18968},
pmid = {41674080},
issn = {1936-086X},
abstract = {Molecular classification of diseases that accurately reflects clinical behavior is fundamental to the realization of precision medicine. Single-cell protein analysis combined with coding technology offers a promising approach for constructing robust molecular classifiers. However, the low abundance of disease-related cells and the technical challenges in parallel profiling of multiple proteins remain major obstacles. Herein, we present a DNA nanostructure-based multicomponent coding strategy that enables multiprotein analysis at the single-cell level by precisely controlling the stoichiometry, orientation, and modularity of the magnetized tags and multicolor fluorescent tags. Compared with conventional linear DNA barcoding methods, our approach allows for the simultaneous magnetic separation of heterogeneous cell populations and multicolor fluorescence-based phenotypic encoding. By integrating single-cell trapping techniques, we demonstrate the accurate molecular subtyping of breast cancer based on fluorescence-encoded phenotypic features. This strategy expands the scope of applications in cell sorting, proteomic profiling, and genomic analysis, thus advancing the frontiers of precision medicine.},
}

@article {pmid41674072,
year = {2026},
author = {Kim, KR and Choi, C and Kim, JS and Kim, MH and Jung, HJ and Jeon, D and Kim, JH},
title = {Complete chloroplast genome of Triticum aestivum cultivar 'Keumkang' from Korea (Poaceae) and comparative chloroplast genomes of the members of the Triticum genus.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70489},
pmid = {41674072},
issn = {1097-0010},
support = {//Rural Development Administration/ ; PJ017444//Cooperative Research Program for Agriculture Science and Technology Development/ ; },
abstract = {BACKGROUND: Bread wheat (Triticum aestivum L.) is a major global food crop, and understanding its maternal lineage and genetic diversity is essential for breeding, authentication, and evolutionary studies. Chloroplast genomes provide valuable markers for phylogenetic inference and cultivar discrimination; however, conventional plant DNA barcodes often lack sufficient resolution within the genus Triticum. This study aimed to characterize the complete chloroplast genome of the Korean wheat cultivar 'Keumkang' and to develop effective chloroplast-based barcode markers for improved identification of Triticum species and cultivars.

RESULTS: The complete chloroplast genome of T. aestivum cv. Keumkang was assembled using PacBio HiFi reads and determined to be 135 909 bp in length, exhibiting a typical quadripartite structure. Comparative analyses of 44 Triticum and related Aegilops chloroplast genomes revealed that Keumkang shared an identical chloroplast genome structure with several Korean cultivars, indicating a common maternal origin. Phylogenomic analysis placed T. aestivum in close association with T. turgidum subsp. durum, supporting its maternal derivation from the AABB genome lineage. Nucleotide diversity analysis identified six coding sequences and 11 intergenic regions with relatively high polymorphism. Based on these regions, 17 chloroplast-specific barcode markers were developed and experimentally validated. While conventional barcodes (matK, rbcL, trnL-F) achieved only approximately 18% cultivar discrimination, the combined use of the 17 newly developed markers improved identification accuracy to 50% among the examined accessions.

CONCLUSION: The complete chloroplast genome of T. aestivum cv. Keumkang provides new insights into the maternal lineage and chloroplast diversity of wheat. The newly developed set of 17 chloroplast barcode markers substantially enhances cultivar-level discrimination within the genus Triticum and represents a useful molecular tool for wheat breeding, germplasm authentication, and evolutionary studies. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid41673461,
year = {2026},
author = {Serrano, A and Weber, TS and Berthelet, J and Ftouni, S and El-Saafin, F and Lee, S and Lim, E and Charafe-Jauffret, E and Ginestier, C and Williams, D and Hollande, F and Yeo, B and Dawson, SJ and Naik, SH and Merino, D},
title = {Genetic barcoding uncovers the clonal makeup of solid and liquid biopsies and their ability to capture intra-tumoral heterogeneity.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {41673461},
issn = {1744-4292},
support = {N/A//Love Your Sister (LYS)/ ; MCRF21011//VicGovAu | Victorian Cancer Agency (VCA)/ ; GNT2012196 and GNT2027459//DHAC | National Health and Medical Research Council (NHMRC)/ ; IIRS0049//National Breast Cancer Foundation (NBCF)/ ; Melbourne Research Scholarship//University of Melbourne (UNIMELB)/ ; },
abstract = {Intratumoral heterogeneity (ITH) is fueling tumor progression in breast cancer, as specific clones present within a tumor may have a selective advantage to colonize distant organs and escape therapy. Accurate sampling of ITH is therefore a pressing challenge in clinical oncology to adequately predict recurrence and inform rational and personalized therapies. Here, we used genetic barcoding to track the spatiotemporal composition of human breast cancer clones in six preclinical models-across two cell lines and four patient-derived xenografts (PDXs). This allowed a direct side-by-side quantitative comparison of both intra-tumor clonal composition and how that composition was reflected in needle biopsies and cell-free DNA (cfDNA). These analyses highlighted several biologically and clinically relevant findings. First, the use of barcoding revealed that clonal diversity in the center of non-necrotic primary tumors was significantly higher than in the periphery. Second, cfDNA barcode analysis suggested that DNA 'shedding' in the vasculature varied widely, not only depending on necrosis and tumor burden but also across models. Third, combining information captured in both solid and liquid biopsies can provide a more robust assessment of tumor clonal composition. Taken together, these results showcase the utility of these barcoded models to optimize the use of solid and liquid biopsies as surrogates of tumor heterogeneity.},
}

@article {pmid41673033,
year = {2026},
author = {Chudinov, IK and Krinitsina, AA and Petukhova, DA and Lukina-Gronskaya, AV and Korneenko, EV and Gremyacheva, VD and Kovalenko, AV and Fedorov, OV and Kozhemyakin, GL and Mironov, KS and Antipin, MI and Butenko, IO and Logacheva, MD and Speranskaya, AS},
title = {Proteogenomic investigation of plant constituents in herbal beverages.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00747-1},
pmid = {41673033},
issn = {2396-8370},
support = {124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; 124021600055-6//State Project/ ; },
abstract = {Manufacturing adulteration is the major cause of discrepancies between the declared and actual composition of food products. While high-throughput sequencing (HTS) of DNA barcodes is a promising method to identify adulterants, its practical application is hampered by technical challenges. Food pre-processing and differences in GC composition can lead to unequal amplification or complete loss of DNA barcode components. Consequently, HTS results require independent confirmation using an orthogonal method based on very different physical principles than DNA sequencing. To address this, we evaluated the suitability of a multi-omic approach that coupled DNA barcode HTS analysis with proteomic analysis, to enhance the detection of food fraud in herbal beverages. To resolve discrepancies between genomic and proteomic findings, we employed traditional botanical morphology as an arbiter. Among the samples studied, the combined approach revealed two main adulterations of Epilobium with Lythrum - a substitution potentially hazardous to consumers - as well as several minor substitutions, all confirmed by orthogonal methods. Our findings demonstrate that proteomic analysis provides enhanced confidence for verifying the presence or absence of plant components identified by HTS. However, its effective application is guided by prior sequencing to define specific targets for subsequent proteomic verification. This study established that a multimodal analytical approach is not only beneficial, but essential for the reliable and comprehensive characterization of components in complex plant mixtures.},
}

@article {pmid41672066,
year = {2026},
author = {Kim, PG and Hergott, CB and Miller, AP and Deik, A and Boileau, M and Bullock, K and Pierce, KA and Choy, AH and Shin, W and McConkey, M and Loke, J and Ryback, BA and Trinh, MN and Rutter, JC and Yue, H and Yoon, H and Park, P and Roy Burman, SS and Vander Heiden, MG and Fischer, ES and Armstrong, SA and Clish, C and Ebert, BL},
title = {Metabolic control of innate immune activation in TET2-mutant clonal hematopoiesis.},
journal = {Cell chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chembiol.2026.01.006},
pmid = {41672066},
issn = {2451-9448},
abstract = {Somatic mutations in TET2 drive hyper-inflammation in clonal hematopoiesis of indeterminate potential (CHIP), but the molecular link between TET2 inactivation and myeloid immune activation remains unclear. We used in vivo genome-wide genetic perturbations enabled by ultra-diverse barcoding in primary wild-type (WT) or Tet2 knockout (KO) Cas9[+] hematopoietic stem-progenitor cells (HSPCs) to elucidate the basis of Tet2 KO inflammation. We uncover a metabolic circuit by which Tet2 restrains O-linked N-acetylglucosamine (O-GlcNAc) glycosyltransferase (Ogt), a Tet2 binding partner and metabolic sensor. Tet2 loss disrupts this inhibitory Tet2-Ogt interaction, and dysregulated Ogt facilitates widespread H3K4 trimethylation including lipid-related gene loci and inflammatory lipid droplet formation. We identified that ATP citrate lyase (Acly) is decorated with O-GlcNAc and is a critical node for lipid accumulation and inflammation in Tet2 KO. These findings reveal that Tet2 suppresses inflammation by gating nutrient-responsive chromatin remodeling and nominate metabolic interventions to restrain inflammatory disease in TET2-mutant clonal hematopoiesis.},
}

@article {pmid41671394,
year = {2026},
author = {Wagner, M and Resl, P and Klar, N and Huie, JM and Bista, I and McCarthy, S and Smith, M and Durbin, R and Koblmüller, S and Svardal, H},
title = {The genomics of convergent adaptation to intertidal gravel beaches in Mediterranean clingfishes.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evag031},
pmid = {41671394},
issn = {1759-6653},
abstract = {Understanding the genetic basis of widespread phenotypic convergence, particularly for complex morphological traits, remains a major challenge in evolutionary biology. The Mediterranean gravel beach clingfishes of the genus Gouania provide an excellent system to study this phenomenon. Within this genus, two distinct morphotypes, "slender" and "stout", have repeatedly evolved, adapting to different microhabitats. These morphotypes differ in multiple complex traits, including body elongation, head compression, vertebral number, eye size, and the structure of the adhesive disc. First, to scrutinize phylogenetic convergence, we combined 3D morphometrics of the pelvic girdle and skull, with molecular species delimitation based on >660 DNA barcodes, and a phylogenomic framework based on more than 3,400 single-copy orthologs. Second, by employing whole-genome resequencing and a novel "convergence score" statistic, we examined genomic convergence across multiple levels: nucleotides, sequences, genes, and functional pathways. While we found no evidence of large-scale genomic or protein-level convergence, we identified promising candidate regions at the level of single variants, genes, and biological pathways. Notably, a longer shared (but interrupted) haplotype around the candidate gene adam12 was associated with convergent traits. The lack of simple genomic patterns may reflect the radiation's age and the complex genetic basis of the underlying morphological traits (e.g., eye size, neurocranium shape). Altogether, our findings highlight the importance of assessing genomic convergence at multiple molecular levels to uncover diagnostic signals across varying evolutionary processes and timescales.},
}

@article {pmid41671286,
year = {2026},
author = {Jann, J and Gagnon-Arsenault, I and Pageau, A and Dubé, AK and Fijarczyk, A and Durand, R and Landry, CR},
title = {A cost-effective and scalable barcoded library construction method for deep mutational scanning studies.},
journal = {PLoS biology},
volume = {24},
number = {2},
pages = {e3003645},
doi = {10.1371/journal.pbio.3003645},
pmid = {41671286},
issn = {1545-7885},
abstract = {Recent developments in DNA synthesis and sequencing allowed the construction of comprehensive gene variant libraries and their functional analysis. Achieving high-replication and thorough mutation characterization remains technically and financially challenging for long genes. Here, we developed an efficient, affordable, and scalable library construction approach that relies on low-cost DNA synthesis and standard cloning technologies, which will increase accessibility to mutational studies and help advance the field of protein science. Each degenerate codon variant is physically associated with multiple DNA barcodes during synthesis, which overcomes the need for long-read sequencing for linking variants to barcodes. We demonstrate the scalability of our approach by constructing a complete library for PDR1, a 3.2 kb multidrug resistance gene encoding a pleiotropic transcription factor in the yeast Saccharomyces cerevisiae. We demonstrate a near-perfect correspondence in the measurement of amino acid variants impact when assessed by barcode sequencing and direct sequencing of the mutated coding sequence.},
}

@article {pmid41667686,
year = {2026},
author = {Seddaiu, S and Morittu, C and Franceschini, A and Iotti, M and Scali, E and Lancellotti, E},
title = {Dynamics of ectomycorrhizal communities in Sardinian cork oak forests: influence of management system, lithological substrate and season.},
journal = {Mycorrhiza},
volume = {36},
number = {1},
pages = {7},
pmid = {41667686},
issn = {1432-1890},
abstract = {UNLABELLED: Ectomycorrhizal fungi represent a key component of forest ecosystems, contributing significantly to tree nutrition, stress tolerance, and overall ecosystem resilience. In the Mediterranean region, cork oak (Quercus suber L.) forests, have significant ecological and economic value, and their vitality strongly depends on these belowground mutualistic relationships. Although previous studies have investigated the diversity and function of ectomycorrhizal fungi, several aspects concerning their ecological dynamics remain inadequately understood, particularly in cork oak forests. This study investigates the structural and dynamics of ectomycorrhizal fungal communities in cork oak forests of Sardinia located on granitic, basaltic, and trachytic substrates and subjected to different management practices (natural, grazed, and ploughed). We assess how forest management and seasonal variability interact with lithological conditions to shape community structure and diversity. Three cork oak stands for each lithological substrate (nine in total) were selected in areas where all the three forestry managements were present. Two transects were established in each stand, and soil samples were collected during spring and autumn to assess seasonal variations in the ectomycorrhizal community. In total, 82,345 ectomycorrhizal root tips were morphologically characterized and classified in 167 morphotypes based on morpho-anatomical characteristics. From these, 120 were successfully assigned to distinct Operational Taxonomic Units (OTUs) through internal transcribed spacer (ITS) barcoding. Our results indicate that lithological substrate, management system, and sampling season significantly influence the structure and composition of ectomycorrhizal communities. Notably, ploughing caused a marked reduction in fungal richness, highlighting the sensitivity of these communities to soil disturbance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00572-026-01252-9.},
}

@article {pmid41675242,
year = {2023},
author = {Yan, Y and Yang, L and Meng, L and Su, H and Zhou, C and Yu, L and Li, Z and Zhang, X and Cai, H and Gao, J},
title = {Introduction to bioimaging-based spatial multi-omic novel methods.},
journal = {Quantitative biology (Beijing, China)},
volume = {11},
number = {3},
pages = {231-245},
pmid = {41675242},
issn = {2095-4697},
abstract = {UNLABELLED: In this review, we introduced five different multiplex FISH methods used for image-based spatial multi-omics: seqFISH+, merFISH, DNA seqFISH+, DNA merFISH, and MINA. We provided a systematic collective perspective to review these FISH methods that could significantly benefit researchers on conducting their studies in the field. Our study provided an informative survey on these multiplex FISH methods. Therefore, this review would provide better understanding for researchers in the community to help them select the proper method, in order to understand the molecular mechanism in life sciences.

BACKGROUND: Spatial multi-omics are demonstrated to be a powerful method to assist researchers on genetic studies. In this review, bioimaging-based spatial multi-omics techniques such as seqFISH+, merFISH, integrated DNA seqFISH+, DNA merFISH, and MINA are introduced along with each technique's probe design, development, and imaging processes.

RESULTS: seqFISH employed 4-5 fluorophores to barcode and conducted multiple rounds of hybridization, in order that mRNA can be identified through color-coding. seqFISH+ added 60 pseudo-color and distributed them equally into three channels to enhance imaging power, in order that i.e., 24,000 genes can be imaged in total. merFISH utilized 4 out 16 Hamming distance to innovatively provide a robust error-detecting method. MINA, a methodology combining merFISH (multiplexed error-robust fluorescence in situ hybridization) and chromosomal tracing, enabled multiplexed genomic architecture imaged in mammalian single cells. Optical reconstruction of chromatin architecture (ORCA) a method that could conduct DNA path tracing in nanoscale manner with kilobase resolution, an FISH variation that improved genetic resolution, enable high-precision fiducial registration and sequential imaging, and utilized Oligopaint probe to hybridize the short genomic region ranging from 2 to 10 kilobase. ORCA then prescribes these short section primary probes with individual barcodes to attach fluorophore and to be imaged.

CONCLUSION: This review concentrated on providing a comprehensive overview for these spatial-multi-omics techniques with the intention on helping researchers on selecting appropriate technique for their research.},
}

@article {pmid41669637,
year = {2025},
author = {Lei, R and Cao, Y and Yang, Y and Cong, H and Li, L and Li, X and Shi, J},
title = {Rapid authentication of endangered Cistanche Herba (Rou Cong Rong) using a high-throughput multi-SNP panel and MALDI-TOF MS platform.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1677826},
pmid = {41669637},
issn = {1664-462X},
abstract = {Cistanche Herba (Rou Cong Rong), a critically endangered edible tonic and medicinal plant, is traditionally valued for its nephroprotective and kidney-yang tonifying properties. However, wild populations are declining due to habitat loss, overharvesting, and increasing market demand, leading to widespread adulteration in commercial supplies. Conventional authentication methods, such as morphological examination, photochemical profiling, and ITS/ITS2 barcoding, often fail with processed materials due to DNA degradation. To overcome these limitations, we developed a high-throughput single-nucleotide polymorphism (SNP) genotyping platform that integrates multiplex PCR with MALDI-TOF mass spectrometry, targeting validated nuclear ITS and chloroplast-encoded ribosomal protein large subunit 16 (rpl16) loci. The assay utilizes four diagnostic SNPs specific to C. deserticola, allowing unambiguous differentiation from six adulterants. It demonstrates high sensitivity, detecting 0.07% genomic DNA (6.8 pg/μL) in mixed samples and 1% C. deserticola powder in dried tissue mixture. When validated on 27 dried specimens, the method showed 100% concordance with Sanger sequencing while reducing the total analysis time to approximately 10 hours. By overcoming the resolution limitations of traditional techniques, this approach provides a rapid and scalable solution to combat herbal substitution, support CITES compliance, ensure the integrity of functional foods and traditional medicines.},
}

@article {pmid41667612,
year = {2026},
author = {Inoue, F},
title = {Massively parallel reporter assays: from barcodes to biology.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {41667612},
issn = {1471-0064},
}

@article {pmid41666622,
year = {2026},
author = {Mei, J and Liu, S and Tao, H and Xia, S and Wang, Y},
title = {Transcriptomics in forensic entomology: Research progress and prospects.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {81},
number = {},
pages = {102801},
doi = {10.1016/j.legalmed.2026.102801},
pmid = {41666622},
issn = {1873-4162},
abstract = {The rapid development of transcriptomics technology has brought revolutionary breakthroughs to the field of forensic entomology, demonstrating significant potential in addressing critical issues such as postmortem interval (PMI) estimation. This review summarizes the research progress and future prospects of transcriptomics in forensic entomology. In species identification, traditional morphological methods and DNA barcoding techniques have limitations, while molecular markers such as SSRs and SNPs developed from transcriptomic data demonstrate significant potential for enhancing the differentiation of closely related species, thereby providing new tools for accurate identification. For PMImin estimation, transcriptomics enables high-precision quantification of insect age by analyzing stage-specific gene expression patterns and integrating bioinformatics approaches, thereby overcoming the subjectivity of traditional morphological methods. Additionally, transcriptomics facilitates the discovery of olfactory and resistance genes in necrophagous insects, offering molecular insights into pre-colonization intervals and developmental regulation under extreme environmental conditions. In the future, combining transcriptomics with multi-omics technologies and optimizing data analysis methods will provide comprehensive theoretical support and practical guidance for forensic entomology, significantly driving its advancement.},
}

@article {pmid41660357,
year = {2026},
author = {Villaescusa-González, L and Cardiel, JM and Montero-Muñoz, I and Muñoz-Rodríguez, P},
title = {Revisiting Acalypha medicinal interest: ethnobotany, experimental studies, and the implications of taxonomic misuse pitfalls.},
journal = {PhytoKeys},
volume = {270},
number = {},
pages = {119-142},
pmid = {41660357},
issn = {1314-2011},
abstract = {Acalypha L. (Euphorbiaceae) is a pantropical genus comprising approximately 470 species, many of which have been traditionally used to treat human and animal ailments. Despite its widespread use, the interpretation of ethnobotanical information has been hindered by misidentifications, outdated or incorrect names, and the lack of studies for many species - factors that limit its value for pharmacological research and conservation. Previous efforts to synthesise medicinal knowledge in Acalypha have been constrained by limited taxonomic coverage, inconsistent methodologies, and narrow geographic scope. In this study, a comprehensive global review of medicinal uses in Acalypha was conducted, based on data retrieved from peer-reviewed literature, scientific databases, historical sources, and other publications. A total of 62 species with reported uses across 55 countries were identified. Uses include applications in human and veterinary medicine, rituals, and as pesticides, while experimental studies reported antibacterial, antifungal, antioxidant, and anti-inflammatory effects. Reported uses were classified as ethnobotanical and/or experimental (in vitro, in vivo, and ex vivo) and standardised following WHO and national disease classification systems, and all scientific names were taxonomically verified. The phylogenetic distribution of medicinal species was assessed using DNA barcode phylogenies. Nearly 25% of the studies reviewed were found to contain at least one taxonomic error, rendering the associated information unreliable and underscoring the need for improved taxonomic rigour and standardisation. This review provides the first standardised, taxonomically validated global synthesis of Acalypha's medicinal knowledge, identifies major knowledge gaps, and offers a foundation for future phytochemical and pharmacological research on this diverse genus.},
}

@article {pmid41659619,
year = {2026},
author = {Melhuish, TA and Adair, SJ and Pemberton, OS and Bauer, TW and Wotton, D},
title = {A simple method for analyzing competitive growth of multiple cell types in xenograft tumors.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.23.701386},
pmid = {41659619},
issn = {2692-8205},
abstract = {Low take rates and inter-tumor variability in growth rates can limit the effectiveness of mouse xenograft models when comparing between groups. To address this problem we developed a simple method to compare multiple cell types within a single mixed xenograft. Individual cell lines or clones were transduced with a lentiviral vector that includes a unique PCR tag, allowing the use of qPCR to determine the proportion of each tagged cell type within a mixed xenograft tumor. We generated vectors with six distinct PCR tags, and two different selectable markers, and have optimized the approach for determining their relative proportions within a mix. An initial pre-amplification step is used to increase the amount of material for subsequent qPCR reactions. This also removes the bulk of the genomic DNA, increasing the specificity of the qPCR step. Samples are then used for qPCR with specific pairs of primers that distinguish between each of the individual PCR tags, and the relative proportion of each tag is determined relative to that in the starting mix. We have tested this approach for in vitro growth of mixed cell cultures and in an orthotopic cecal xenograft model using a human colon cancer cell line. Since each individual tumor is initiated with a mix of cells, multiple tumors within a single animal can be analyzed separately, and overall tumor size is not important. Similarly, multiple metastatic lesions from the same animal can be analyzed individually. Thus, each tumor provides a direct comparison between individually tagged cell lines or clones. This low throughput "bar-coding" approach is simple and cost effective and has the potential to reduce the number of animals needed for xenograft experiments.},
}

@article {pmid41659616,
year = {2026},
author = {Vander Velde, RJ and Ng, RWS and Coté, C and Shaffer, SM},
title = {Multiplexed enrichment and tracking of lineages with CloneSweeper.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.30.700779},
pmid = {41659616},
issn = {2692-8205},
abstract = {A fundamental challenge in studying therapy resistance is understanding whether it results from pre-existing cellular states ("priming") or drug-induced changes ("adaptation"). While lineage barcoding enables retrospective analysis of cells before and after treatment, current methods struggle to efficiently capture rare lineages in single-cell RNA sequencing (scRNA-seq) or isolate multiple specific lineages simultaneously for functional study. To overcome these limitations, we developed CloneSweeper, a multiplexed lineage tracking platform that pools enrichment libraries to isolate or enrich multiple rare lineages. CloneSweeper utilizes a dual-function barcode expressed as both a Cas9 gRNA for live-cell sorting and a 3' UTR transcript for high-recovery detection in 10x Genomics scRNA-seq. We applied CloneSweeper to a model of BRAF V600E melanoma, where we identified that resistance to targeted therapy emerges from a polyclonal population of rare, pre-existing lineages. By simultaneously targeting and enriching 21 distinct rare lineages prior to treatment, we defined a heritable, primed state characterized by de-differentiation and elevated mesenchymal markers. We demonstrate that these primed cells are not quiescent but instead exhibit upregulated inflammatory and stress response signaling, specifically via the AP-1 and NF-κB1 pathways. CloneSweeper thus provides a robust framework for dissecting the molecular mechanisms of rare biological phenomena through simultaneous, multiplexed lineage isolation.},
}

@article {pmid41659213,
year = {2026},
author = {Uphoff, RC and Schüler, S and Grosse, I and Müller-Hannemann, M},
title = {Fast barcode calling based on k-mer distances.},
journal = {PNAS nexus},
volume = {5},
number = {2},
pages = {pgag001},
pmid = {41659213},
issn = {2752-6542},
abstract = {DNA barcodes, which are short DNA strings, are regularly used as tags in pooled sequencing experiments to enable the identification of reads originating from the same sample. A crucial task in the subsequent analysis of pooled sequences is barcode calling, where one must identify the corresponding barcode for each read. This task is computationally challenging when the probability of synthesis and sequencing errors is high, like in photolithographic microarray synthesis. Identifying the most similar barcode for each read is a theoretically attractive solution for barcode calling. However, an all-to-all exact similarity calculation is practically infeasible for applications with millions of barcodes and billions of reads. Hence, several computational approaches for barcode calling have been proposed, but the challenge of developing an efficient and precise computational approach remains. Here, we propose a simple, yet highly effective new barcode calling approach that uses a filtering technique based on precomputed k-mer lists. We find that this approach has a slightly higher accuracy than the state-of-the-art approach, is more than 500 times faster than that, and allows barcode calling for one million barcodes and one billion reads per day on a server GPU. The same throughput can even be realized using a CPU-parallel implementation.},
}

@article {pmid41655994,
year = {2026},
author = {Butcher, RG and Ng, B and Hyndman, TH and Wesson, JP and Jones, E and Williams, M and Brown, D and Kay, E and Gillett, A and Valenza, L and Grogan, LF},
title = {Emergence of Ophidiomyces ophidiicola, Nannizziopsis barbatae and Paranannizziopsis in free-ranging Australian reptiles.},
journal = {Australian veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/avj.70060},
pmid = {41655994},
issn = {1751-0813},
support = {//Wildlife Health Australia National Significant Disease Investigation Program/ ; },
abstract = {Emerging fungal diseases pose a threat to reptiles globally. Increasing detections of onygenalean fungi, particularly Ophidiomyces ophidiicola, Nannizziopsis spp. and Paranannizziopsis spp. in clinically diseased free-ranging reptiles, indicate likely ongoing spread within wild reptile populations. These fungal pathogens have not previously been reported in free-ranging Australian reptiles, except for N. barbatae in select lizard species. We present 10 cases of onygenalean dermatomycoses in five free-ranging native Australian squamate species that presented to the Australia Zoo Wildlife Hospital between 2023 and 2024. Coastal carpet pythons (Morelia spilota mcdowelli) represented five of the cases, with O. ophidiicola, N. barbatae and P. australasiensis detected in this snake species. In addition, we confirmed O. ophidiicola in an eastern bandy-bandy (Vermicella annulata) and white-crowned snake (Cacophis harriettae), Nannizziopsis barbatae in an eastern water dragon (Intellagama lesueurii lesueurii), and Paranannizziopsis spp. in two eastern bearded dragons (Pogona barbata). Clinical presentations ranged from mild to severe dermatitis, with secondary outcomes of dysecdysis, stomatitis, emaciation and moribundity. Diagnoses were confirmed using a combination of histopathology, PCR, DNA sequencing and/or culture and barcoding. Our study reports the first known cases of Ophidiomyces ophidiicola and Paranannizziopsis in free-ranging Australian reptiles, and the first case of N. barbatae in a snake species globally. These cases represent an expansion of the known host and geographic range of onygenalean fungi into free-ranging Australian reptiles. Importantly, these fungi were associated with debilitating disease that could threaten native reptile populations if not promptly addressed.},
}

@article {pmid41654607,
year = {2026},
author = {Vinay, CM and Ware, AP and Sanjay, KU and Samantray, D and Krishnan, RR and Raval, K and Sekar, M and Ramachandra, YL and Paul, B and Rai, PS},
title = {CDMMM: a comprehensive platform of traditional Indian medicinal plant DNA barcodes and metabolite fingerprints database.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37812-4},
pmid = {41654607},
issn = {2045-2322},
abstract = {Herbal medicines, derived from medicinal plants, are in high demand due to global population growth and the increasing prevalence of chronic diseases; however, the use of substitutes or adulterants can compromise the quality of these medicines. DNA barcoding and metabolite fingerprinting are used to identify plants and ensure the safety of drugs. The effectiveness of authentication methods depends on the availability and coverage of the reference library. However, reference DNA barcodes and metabolite fingerprint libraries for traditional Indian medicinal plants are lacking, which hinders the authentication of herbal drugs and the elucidation of the therapeutic effects of secondary metabolites. In the present study, we developed a user-friendly 'Comprehensive Database of Medicinal Plants, Molecular Markers, and Metabolite Fingerprinting (CDMMM)' that provides extensive details on traditional Indian medicinal plants used in drug formulations, DNA barcode sequences, metabolites, and their therapeutic targets associated with diseases. CDMMM is an expandable data resource comprising 89 experimentally obtained DNA barcode accessions from 67 plant species, 3033 annotated plant metabolites, and 1414 therapeutic targets associated with 441 diseases from 20 plant species. The ever-expanding CDMMM resource is available at https://slsdb.manipal.edu/cdmmm/. Overall, it is a powerful platform for taxonomy, systematics, species identification, and drug discovery, promoting knowledge and addressing taxonomic uncertainties.},
}

@article {pmid41648248,
year = {2026},
author = {Pan, X and Chen, Y and Zhang, X},
title = {Integrative Inference of Spatially Resolved Cell Lineage Trees using LineageMap.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.19.700383},
pmid = {41648248},
issn = {2692-8205},
abstract = {Understanding the spatio-temporal processes of tissue growth, including how new cell types emerge and how cells form the tissue architecture, is a fundamental problem in biology. The emerging spatially resolved lineage tracing data, where three modalities, lineage barcodes, gene expression profiles, and spatial locations, are measured for each single cell, provides an unprecedented opportunity to understand these processes. Computational methods that take advantage of all three modalities to reconstruct cell lineage tree and ancestral cell states and locations are needed. We introduce LineageMap, a hybrid lineage inference algorithm that integrates the scalability of distance-based tree reconstruction methods with the flexibility of likelihood-based methods under a unified probabilistic framework. The input to LineageMap is spatially resolved lineage tracing data, where for each single cell, the gene expression, lineage barcode and spatial locations are available. LineageMap enables accurate, interpretable, and scalable inference of high-resolution lineage trees as well as locations of ancestral cells from the tri-modality single-cell data. Across simulated and experimental datasets, LineageMap consistently outperforms existing methods in the accuracy of reconstructed cell lineage trees, while revealing biologically coherent spatiotemporal trajectories. Our framework bridges molecular lineage tracing with spatial and transcriptomic information, advancing computational reconstruction of dynamic cellular ancestries in both time and space. LineageMap is available at: https://github.com/ZhangLabGT/LineageMap .},
}

@article {pmid41647252,
year = {2026},
author = {Schaub, D and Lessing, A and von Haugwitz, G and Meyer, F and Scheuermann, J and Buller, R},
title = {Toward the Chemoenzymatic Synthesis of DNA-Encoded Libraries.},
journal = {ACS central science},
volume = {12},
number = {1},
pages = {28-39},
pmid = {41647252},
issn = {2374-7943},
abstract = {DNA-encoded libraries (DELs) have become a powerful platform in drug discovery, practiced both by the pharmaceutical industry and academia. Each small molecule contained in a DEL is covalently linked to a DNA tag which serves as an amplifiable barcode facilitating binder identification. However, the chemical diversity accessible in DELs remains limited by the need to perform reactions under conditions that preserve the integrity of the DNA tag. Additionally, chemical reactions must proceed with high efficiency and selectivity to minimize side products and unreacted starting materials, which cannot be removed and may hamper hit identification. Consequently, expanding the DEL chemical space requires the development of methods that combine high reaction performance with DNA compatibility. In this outlook, we highlight the potential of enzymatic catalysis for on-DNA synthesis, which offers a promising route to expand DEL-accessible chemical space.},
}

@article {pmid41646351,
year = {2026},
author = {Luo, C and Liu, Y and Liu, H and Zhang, Z and Zhang, L and Peters, B and Zhou, XM},
title = {Enhancing variant detection in complex genomes: leveraging linked reads for robust SNP, Indel, and structural variant analysis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8408441/v1},
pmid = {41646351},
issn = {2693-5015},
abstract = {Background: Accurate detection of genetic variants, including single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), and structural variants (SVs), is critical for comprehensive genomic analysis. While traditional short-read sequencing performs well for SNP and INDEL detection, it struggles to resolve SVs, especially in complex genomic regions, due to inherent read length limitations. Linked-read sequencing technologies, such as single-tube Long Fragment Read sequencing (stLFR), overcome these challenges by employing molecular barcodes, providing crucial long-range information. Methods: This study investigates traditional pair-end linked-reads and a conceptual extension of linked-read technology: barcoded single-end reads of 500 bp (SE500 stLFR) and 1000 bp (SE1000 stLFR), generated using the single-tube Long Fragment Read (stLFR) platform. Unlike conventional paired-end (PE100 stLFR) linked reads, these longer single-end reads could offer improved resolution for variant detection by leveraging extended read lengths per barcode. To explore the potential of stLFR reads, we developed stLFR-sim, a Python-based simulator that reproduces the stLFR linked-read sequencing workflow to enable realistic simulation and benchmarking of linked-read sequencing data. Using stLFR-sim, we simulated a diverse set of datasets for the HG002 sample using T2T-based realistic genome simulation. Variant detection performance was then systematically assessed across three stLFR configurations: standard PE100 stLFR, SE500 stLFR, and SE1000 stLFR. Results: Benchmarking against the Genome in a Bottle (GIAB) gold standard reveals distinct strengths of each configuration. Extended single-end reads (SE500 stLFR and SE1000 stLFR) significantly enhance SV detection, with SE1000 stLFR providing the best balance between precision and recall. In contrast, the shorter PE100 stLFR reads exhibit higher precision for SNP and INDEL calling, particularly within high-confidence regions, though with reduced performance in low-mappability contexts. To explore optimization strategies, we constructed hybrid libraries combining paired-end and single-end barcoded reads. These hybrid approaches integrate the complementary advantages of different read types, consistently outperforming single libraries across small variant types and genomic contexts. Conclusion: Collectively, our findings offer a robust comparative framework for evaluating stLFR sequencing strategies, highlight the promise of barcoded single-end reads for improving SV detection, and provide practical guidance for tailoring sequencing designs to the complexities of the genome.},
}

@article {pmid41646200,
year = {2026},
author = {Badano, D and Zheng, Y and Aspöck, U and Aspöck, H and Dobosz, R and Funari, R and Pantaleoni, RA and Ábrahám, L and Liu, X},
title = {Integrative revision of the Palaearctic owlfly genus Deleproctophylla Lefèbvre (Neuroptera, Myrmeleontidae, Ascalaphinae).},
journal = {ZooKeys},
volume = {1267},
number = {},
pages = {197-254},
pmid = {41646200},
issn = {1313-2989},
abstract = {The ascalaphid genus Deleproctophylla Lefèbvre is a characteristic element of insects from dry, warm grasslands across the Palaearctic, currently comprising five described species distributed in northern Africa, southern Europe, and western Asia. As with other colorful owlfly genera, species of Deleproctophylla have traditionally been differentiated based on wing pattern, a trait prone to high variability and misidentification. The genus currently includes five species: D. australis (Fabricius), D. variegata (Klug), D. dusmeti (Navás), D. gelini Navás, and D. bleusei Kimmins; however, the taxonomic identity of some populations, particularly from Anatolia, has remained uncertain. Even western European species have been affected by taxonomic confusion, as exemplified by D. bleusei, whose presence in southern Spain was only recently detected. A comprehensive revision of all species in the genus demonstrated that the shape of the male ectoproct is the most reliable diagnostic character for species identification. This study also led to the discovery of two new species, D. dandizenor Badano, Zheng, U. Aspöck & Dobosz, sp. nov. from Afghanistan and Pakistan, and D. tengri Zheng, Badano, H. Aspöck & Liu, sp. nov. from Turkmenistan, Kyrgyzstan, and China, significantly expanding the known range of the genus. Morphological findings were further supported by species delimitation analyses of COI sequences, which helped identify specimens with atypical pigmentation patterns and confirmed the validity of both European species and the newly described D. tengri sp. nov.},
}

@article {pmid41644517,
year = {2026},
author = {Pan, Y and Yan, H and Han, J and Wu, R and Xu, C and Lei, G and Ma, X and Guan, Y and Li, Z and Deng, J and Li, K and Wei, Q and Zhang, G and Liu, L and Goel, A and Yang, Z and Jiao, S and Zhang, Y and Tian, C},
title = {Integrating single-nucleus barcoding with spatial transcriptomics via Stamp-seq to reveal immunotherapy response-enhancing functional modules in NSCLC.},
journal = {Cell discovery},
volume = {12},
number = {1},
pages = {10},
pmid = {41644517},
issn = {2056-5968},
support = {82372937//National Natural Science Foundation of China (National Science Foundation of China)/ ; L234035//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
abstract = {Deciphering the spatial organization of cell states is fundamental for understanding development, tissue homeostasis and disease. Emerging advances in spatial transcriptomic profiling techniques allow transcript localization but face limitations in unambiguous cell state assignments due to cellular boundary inference, low gene detection and prohibitive cost. Here, a method, Stamp-seq, is developed that leverages custom-fabricated high-density DNA sequencing chips to label single nuclei with restriction enzyme-cleavable spatial barcodes. Stamp-seq spatial barcodes are distributed at a density of 1.6 μm on the chip, allowing for single physical cell resolution with precise subtype classification and spatial mapping (with an average 4 μm localization error) and reduced cost. We utilize Stamp-seq to delineate chemoimmunotherapy-responsive cellular ecosystems in non-small cell lung carcinoma, including a distinct IGHG1[+] plasma cell-enriched community. Through a novel application of Stamp-seq to spatially resolve BCR clonotypes, we elucidate the spatiotemporal trajectory of treatment-potentiating IGHG1[+] plasma cells, which originate from tertiary lymphoid structures (TLSs) or the vasculature, migrate through antigen-presenting CAF (apCAF)-enriched survival niches, and ultimately contact tumor cells. We highlight the power of spatial cellular subtyping and molecular tracking using Stamp-seq and suggest that the IGHG1[+] plasma cell niche is a better prognostic biomarker for the chemoimmunotherapy response.},
}

@article {pmid41643680,
year = {2026},
author = {Culp, JM and Ashby, DM and George, AG and Teskey, GC and Nicola, W and McGirr, A},
title = {Neural barcoding representing cortical spatiotemporal dynamics based on continuous-time Markov chains.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101294},
doi = {10.1016/j.crmeth.2025.101294},
pmid = {41643680},
issn = {2667-2375},
abstract = {Populations of neurons form assemblies at many scales and display recurring spatiotemporal patterns of activity. In the cerebral cortex, these patterns of activity involve coordinated activity spanning large distances and anatomical regions subserving distinct functions. The constraints governing how these activity motifs transition over time is not known because conventional computational modeling and analyses collapse either the spatial or the temporal properties of the dynamics. Here, we use a continuous-time Markov chain (CTMC) modeling framework to probabilistically describe the temporal sequences elicited in large-scale complex cortical activity recorded with mesoscale imaging. This reveals a conserved dynamical structure across animals, with modular transitions serving as pseudo-"absorbing states." The parameters of the CTMC model are readily analyzed and used as a "neural barcode," a low-dimensional description of neural dynamics that is sensitive to cortical imaging applications, including pathological brain dynamics. This neural barcode provides a powerful computational tool to characterize cortical dynamics.},
}

@article {pmid41639717,
year = {2026},
author = {Mitrea, IB and Iani, AD and Gherman, CM and Cazan, CD and Ionică, AM and Rabei, ȘO and Deak, G and Cernea, MS and Alexe, V and Chișamera, GB and Marinov, M and Mihalca, AD},
title = {Ancylostomatidae in wild canids and felids from Romania: new host associations and haplotype diversity.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07219-7},
pmid = {41639717},
issn = {1756-3305},
support = {PCE 84/2025//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; RO1567-IBB09/2025//the Institute of Biology Bucharest of Romanian Academy/ ; },
abstract = {BACKGROUND: Hookworms (Ancylostomatidae) significantly impact on the health of both domestic animals and humans worldwide, with some species capable of causing zoonotic diseases. While hookworm infections in pets are frequently reported in Europe primarily through coproscopic studies, there are limited data regarding their presence in wild carnivores. To address this, this study aimed to assess the diversity, prevalence, and distribution of hookworms in wild canids and felids from Romania through both morphological and molecular analyses.

METHODS: From November 2011 to February 2025, 319 carcasses belonging to six species of wild canids and felids from Romania [23 gray wolves (Canis lupus), 137 golden jackals (Canis aureus), 79 red foxes (Vulpes vulpes), 2 raccoon dogs (Nyctereutes procyonoides), 70 European wildcats (Felis silvestris), and 8 Eurasian lynxes (Lynx lynx)] were collected as road kills or legally hunted. Hookworms were recovered from the intestinal tract during necropsy and preserved in formalin for morphological examination and in absolute ethanol for genetic analysis. Genomic DNA was extracted and analyzed using a PCR targeting a barcode region of the second nuclear ribosomal internal transcribed spacer (ITS-2), followed by sequencing. Sequencing results were compared with other entries from GenBank™.

RESULTS: The overall hookworm infection rate was 14.1%, with hookworms detected in 4 wolves (17.4%), 23 golden jackals (16.8%), 11 European wildcats (15.7%), 4 red foxes (5.1%), 2 raccoon dogs (100%), and 1 lynx (12.5%). Three hookworm species were identified: Uncinaria stenocephala, Ancylostoma caninum, and A. tubaeforme. Molecular analysis revealed 14 unique sequences, comprising nine haplotypes of U. stenocephala, three of A. caninum, and two of A. tubaeforme. We report for the first time the Eurasian lynx as a host for A. caninum, expanding the known host range of this species.

CONCLUSIONS: This study provides the first comprehensive molecular assessment of hookworm diversity in European wild carnivores, showing new host-parasite associations and highlighting the importance of these hosts as reservoirs for domestic pets and, potentially, humans. The detected haplotypes showed high similarity to isolates from Europe, Asia, and the Americas, indicating a broad global connectivity of hookworm populations.},
}

@article {pmid41639126,
year = {2026},
author = {Molino, RJEJ and Van Weerd, M and Torreno, VPM and Rellin, KFB and Mondragon, MV and Parungao, L and Manila-Fajardo, AC and Santos, DMC and Junio, HA},
title = {Multi-omics and palynology of selected Philippine forest honey.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-024-71385-4},
pmid = {41639126},
issn = {2045-2322},
support = {ORG 2021-0013//Forest Foundation Philippines/ ; },
abstract = {The Sierra Madre Mountains, which happen to be the longest mountain range in the Philippines, is home to lush floral and faunal species as well as forest-based indigenous communities actively involved in preserving local biodiversity. With active reforestation efforts ongoing for decades, the locals are further encouraged to continue their long-standing practice of honey gathering as a form of cultural manifestation and as an important source of livelihood. To further inspire ongoing conservation efforts, we aim to show that the small molecule diversity in Sierra Madre forest honey reflects the local floral composition and is reflective of the positive impact of previous reforestation initiatives. In order to do this, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to profile and compare metabolite diversity in honey produced by Apis cerana, Apis breviligula Maa. and Tetragonula biroi (Friese) honey from Palaui Island and Laiban in Northern and Southern Sierra Madre, respectively. Surprisingly, the Philippine National Tree and unfortunately endangered Pterocarpus indicus Willd (loc. Narra) proved to be important, especially in Palaui Island where honey from A. cerana is close to being monofloral. Aside from P. indicus and its small molecule marker hypaphorine, caffeine was detected in Palaui honey beautifully reflecting the way of life of native Agtas who manage a small coffee plantation. The abundance of caffeine, however, is higher in stingless honey samples from Tanay, Rizal where Coffea trees have been extensively included in restoration activities over the past few decades. Our results imply the possibility of using honey as an ecological monitoring tool while generating baseline chemical information that reflects the state of Philippine forests. Furthermore, the identification of unique chemical components in forest honey can be further used in programs that assist indigenous communities in safeguarding the ownership and origin of forest honey sources.},
}

@article {pmid41638687,
year = {2026},
author = {Samimi-Namin, K and Benayahu, Y and Abadiano, AJ and Durkin, K and Ekins, M and Quattrini, A and McFadden, C},
title = {Phylogenomics-guided revision of the genus <italic>Rhytisma</italic> Alderslade, 2000 (Octocorallia: Malacalcyonacea: Lemnaliidae), with descriptions of six new species.},
journal = {Invertebrate systematics},
volume = {},
number = {},
pages = {},
doi = {10.1071/IS25068},
pmid = {41638687},
issn = {1447-2600},
abstract = {The genus Rhytisma Alderslade, 2000 (Octocorallia: Malacalcyonacea: Lemnaliidae), formerly comprising four nominal species ( R. fulvum , R. fuscum , R. monticulum , and R. rubiginosum ), is revised using an integrative approach. We combine morphological and phylogenomic data for newly-collected and historical specimens. A neotype is designated for R. fulvum and a lectotype for R. fuscum to stabilize the application of these names. Six new species are described from the Indo-Pacific: R. acoronatum sp. nov., R. calyaceum sp. nov., R. oblongum sp. nov., R. inaequale sp. nov., R. karibu sp. nov., and R. sperkolae sp. nov. Species delimitation is supported by discrete combinations of morphological characters-particularly those of the tentacle and polyp sclerites-as well as multi-locus DNA barcoding and phylogenomic analyses of conserved elements (UCE and exon loci). Our findings highlight the diagnostic value of tentacle sclerites and reveal extensive species-level diversity that was previously obscured by insufficient morphological examination. The revised genus currently comprises ten valid species, many of which display restricted geographic distributions, reflecting patterns of regional endemism in Indo-Pacific octocoral assemblages. These results underscore the importance of integrative taxonomy in uncovering hidden biodiversity.},
}

@article {pmid41635750,
year = {2025},
author = {Laojun, S and Changbunjong, T and Kaewthamasorn, M and Charnwichai, P and Kaewmee, S and Wichit, S and Hamel, R and Chaiphongpachara, T},
title = {Accurate identification of medically important Aedes mosquitoes (Diptera: Culicidae) in Thailand through DNA barcoding, wing geometric morphometrics, and machine learning.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100334},
pmid = {41635750},
issn = {2667-114X},
abstract = {Mosquito-borne diseases remain a significant public health concern, underscoring the need for accurate species-level identification of vector species, including Aedes mosquitoes. Identification based solely on morphology is often limited by interspecific overlap, environmentally induced phenotypic plasticity, and physical damage to field-collected specimens. This study evaluated nine Aedes species (Ae. aegypti, Ae. albopictus, Ae. chrysolineatus, Ae. lineatopennis, Ae. macfarlanei, Ae. poicilius, Ae. vexans, Ae. vigilax, and Ae. vittatus) and a related taxon (Aedeomyia catasticta) in Thailand, using DNA barcoding, wing geometric morphometric (WGM) analysis, and the Random Forests (RF) machine learning algorithm. DNA barcoding of the cytochrome c oxidase subunit 1 (cox1) gene showed strong concordance with morphological classifications, confirming its reliability for species-level identification. Across all 10 species, sequence similarity with GenBank and the Barcode of Life Data System ranged from 96% to 100%, highlighting reliable identification when robust references are available. WGM analysis revealed significant wing shape differences among species (P < 0.05), with 91.05% classification accuracy. The Mahalanobis distance and RF algorithms, applied to newly field-collected specimens assigned as unknown species, demonstrated strong discriminatory power, both achieving 100% accuracy for seven species based on wing shape. Slightly lower accuracy was observed for three species, with Mahalanobis distance achieving 90% (one misclassified individual) and the RF algorithm 80% (two misclassified individuals). These findings present a practical guideline for identifying Aedes mosquitoes and a related taxon in Thailand by integrating approaches. Accurate species identification is essential for selecting targeted vector control strategies and enhancing the effectiveness of Aedes-borne disease surveillance and management.},
}

@article {pmid41634731,
year = {2026},
author = {Schwabl, P and Amaya-Romero, JE and Kelley, KA and Manrique, P and Murphy, SC and Crompton, PD and Neafsey, DE},
title = {SIMPLseq: a high-sensitivity Plasmodium falciparum genotyping and PCR contamination tracking tool.},
journal = {Malaria journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12936-026-05796-1},
pmid = {41634731},
issn = {1475-2875},
support = {INV-052365//Bill and Melinda Gates Foundation/ ; },
abstract = {BACKGROUND: Pathogen genotyping via polymerase chain reaction (PCR) amplicon sequencing (AmpSeq) is an informative disease surveillance tool. Several large AmpSeq panels containing > 100 multiplexed PCR amplicons have been developed as alternatives to whole-genome sequencing (WGS) methods for the Plasmodium spp. parasites that cause malaria, especially for parasite drug resistance tracking and relatedness analysis. However, these large multiplexes typically yield sparse data for samples with parasitemia below 10 parasites/μl. Smaller multiplexes optimized for low-parasitemia genotyping have received insufficient methodological work but have the potential to serve multiple important use cases. Managing contamination risk during PCR steps represents another key methodological gap that requires attention in the AmpSeq field.

METHODS: Here we describe a new 6-locus Plasmodium falciparum AmpSeq 'miniplex' (SIMPLseq) optimized for high-sensitivity analyses that also integrates a contamination detection system based on well-specific inline barcodes applied during first-round PCR (PCR1; in addition to conventional indexing steps during second-round PCR). We assess panel diversity using publicly available WGS and use mock samples to estimate sensitivity and precision relative to 4CAST, a previously described miniplex. We also create deliberate contamination events to assess contamination detection rigor and estimate unintentional contamination rates during assay application to malaria-infected dried blood spots collected in Mali.

RESULTS: SIMPLseq shows high haplotypic diversity in silico, distinguishing 96.0% of sample pairs drawn randomly from 12 subnational sample sets. SIMPLseq outperforms 4CAST in sensitivity analyses, achieving 100% average locus detection at ≥ 0.5 parasites/μl and ≥ 50% average locus detection at 0.25 and 0.125 parasites/μl, with zero false-positive haplotypes at a 1% detection limit across 25 replicates. Inline barcoding does not significantly affect yield when using a 'sentinel' design, whereby one of the six multiplexed PCR1 primer pairs contains the well-specific sequence pair. Sentinel barcoding correctly identified all 24 contaminations introduced deliberately during PCR1 product handling and identified 39 unintentional contaminations in the 1420-sample Malian run.

CONCLUSIONS: SIMPLseq significantly extends the malaria genomic epidemiology toolkit, coupling high-sensitivity P. falciparum genotyping with PCR contamination detection in a simple laboratory protocol that uses only open-source reagents and does not require a costly pre-amplification step. Key prospective use cases for SIMPLseq include recurrent infection classification, polyclonality estimation, and genotypic infection endpoint application to intervention efficacy trials.},
}

@article {pmid41632583,
year = {2026},
author = {Crockford, SK and Satta, E and Severino, I and Fiacchino, D and Vitale, A and Bertelsen, N and Busuoli, EM and Mandelli, V and Lombardo, MV},
title = {Detection of Idiosyncratic Gaze-Fingerprint Signatures in Humans.},
journal = {Psychological science},
volume = {},
number = {},
pages = {9567976251415352},
doi = {10.1177/09567976251415352},
pmid = {41632583},
issn = {1467-9280},
abstract = {Do individuals possess a "gaze fingerprint" that reveals how they uniquely look at the world? We tested this question by examining intra- and intersubject gaze similarity across 700 static pictures of complex natural scenes. Independent discovery (n = 105) and replication data sets (n = 46) of adults aged 18 to 50 years (sampled from Italy and Germany) revealed that gaze fingerprinting is possible at relatively high rates (e.g., 52%-63%) compared with chance (e.g., 1%-2%). We also identify gaze-fingerprint barcodes, which reveal a unique individualized code describing which stimuli an individual can be gaze-fingerprinted on. Preregistered longitudinal follow-up experiments have shown that gaze-fingerprint barcodes are nonrandom within an individual over short and long time fraframmes. Finally, we find that increased gaze fingerprintability for social stimuli is associated with decreased levels of autistic traits. To summarize, this work showcases the potential of gaze fingerprinting for isolating traitlike factors that may be of high neurodevelopmental and biological significance.},
}

@article {pmid41631484,
year = {2026},
author = {Kubala, A and Warren, K and Meiswinkel, R and Cranfield, M and Robertson, I and Yeap, L and Vaughan-Higgins, R and Nishuli, R and Syaluha, EK and Lukusa, JK and Balyananzi, MK and Linton, YM},
title = {An updated checklist of Culicoides Latreille, 1809 biting midges from the highlands of eastern Democratic Republic of the Congo.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70049},
pmid = {41631484},
issn = {1365-2915},
support = {//Murdoch University/ ; //Cleveland Metroparks Zoo/ ; //Chester Zoo/ ; //Private Donations to the Smithsonian Institution/ ; },
abstract = {The highlands of the eastern Democratic Republic of the Congo (DRC) are home to critically endangered eastern gorillas (Gorilla beringei). Concerns have been raised that the increased temperatures and extreme weather conditions associated with climate change will lead to an increase in the abundance and distribution of Culicoides-borne diseases. Here, we utilized an integrated morphological and molecular approach to identify Culicoides species in a small but significant collection of Culicoides captured from highland eastern gorilla habitat and surrounding areas and updated the Culicoides spp. reported from the highlands of the eastern DRC. A review of the literature related to Culicoides collections in the DRC was conducted in French and English. Recent worldwide checklists were consulted to rectify synonyms and other discrepancies found in the literature for the region. Fresh Culicoides specimens were collected, wings slide-mounted and remaining carcasses subjected to DNA extraction. A total of 82 Culicoides specimens were collected. From these, 75 high-quality DNA barcodes (658-bp of the mtDNA COI gene) were obtained, belonging to 14 distinct taxa, 11 of which were new records for the DRC, including C. bolitinos Meiswinkel, 1989, C. hortenis Khamala & Kettle, 1971, C. citroneus Carter, Ingram & Macfie, 1920, and C. radiomaculatus Khamala & Kettle, 1971, and seven species new to science (C. sp. nr. citroneus, C. sp. nr. glabripennis 1, C. sp. nr. glabripennis 2, C. sp. nr. kibatiensis 1, C. sp. nr. kibatiensis 2, C. sp. nr. neavei 1 and C. sp. nr. neavei 2), increasing the known Culicoides fauna of the DRC from 20 to 31. The presence of C. imicola Kieffer, 1913, C. enderleini Cornet & Brunhes, 1994 and C. neavei Austin, 1912, was confirmed. The potential health impact of the association of known Culicoides pathogen vectors with endangered gorillas is discussed.},
}

@article {pmid41625959,
year = {2026},
author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR},
title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100344},
pmid = {41625959},
issn = {2666-5662},
abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.},
}

@article {pmid41625082,
year = {2026},
author = {Kane, TL and Sikes, DS and Schiff, N},
title = {A taxonomic review of Boreus (Mecoptera, Boreidae) with descriptions of two new Alaskan species.},
journal = {ZooKeys},
volume = {1267},
number = {},
pages = {119-178},
pmid = {41625082},
issn = {1313-2989},
abstract = {Boreus (Mecoptera, Boreidae) species are reviewed. Two new Alaskan species are described (Boreus tananaensis Kane, sp. nov., Boreus timaryi Kane, sp. nov.), a previously synonymized species is resurrected (Boreus gracilis Carpenter, 1935, stat. res.), and morphological descriptions are provided for all five Alaskan species. A key to male and female Alaskan Boreus species is provided. An estimate of the mitochondrial gene tree, based on COI DNA barcodes, is used to infer relationships, and morphological species are tested using five molecular species delimitation methods. What is known about the subgeneric classification of Boreus, and how Alaskan species are classified, is discussed. A checklist of all 33 currently valid species of the family Boreidae is provided.},
}

@article {pmid41625016,
year = {2026},
author = {Thomas, C and Wilken, PM and Coetzee, MPA and Visagie, CM},
title = {Advancing the taxonomy of Sclerotinia (Helotiales, Sclerotiniaceae): a review and recommendations for an important plant-pathogenic genus.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e175737},
pmid = {41625016},
issn = {2210-6340},
abstract = {Sclerotinia is a fungal genus of significant agricultural and scientific importance, as it includes multiple plant pathogens and provides an informative case study for mechanisms of host generalism. However, the taxonomy of this group remains unsettled, which hinders research on these pathogens. The last monographic treatment of Sclerotinia was published more than 40 years ago and was centered on the morphological data available at that time. Here, we examine that revision alongside other pivotal publications to trace the taxonomic history of Sclerotinia and to evaluate the morphological traits used to identify Sclerotinia species. We also briefly assess the composition of genera in the family Sclerotiniaceae, emphasising the need for a modern taxonomic investigation of the broader group. Thirteen new Sclerotinia species have been described since the last taxonomic revision, including Sclerotinia antarctica, S. asari, S. atrostipitata, S. cirsii-spinosissimi, S. ginseng, S. glacialis, S. himalayensis, S. nivalis, S. pseudoplatani, S. subarctica, S. tetraspora, S. trillii, and S. verrucispora. These species are evaluated here. Finally, several recommendations are made regarding how future taxonomic research on Sclerotinia should incorporate molecular data. We highlight potential obstacles and opportunities for this research, including the limitations of the internal transcribed spacer rDNA region (ITS) as a DNA barcode and the untapped potential of genomic data for the genus. By outlining the gaps that need to be addressed, this review charts a course toward a clearer understanding of taxonomic relationships among Sclerotinia species. This understanding will facilitate research into other aspects, such as pathogenicity and host generalism, and may ultimately contribute to improved management of the devastating diseases caused by these pathogens.},
}

@article {pmid41624517,
year = {2026},
author = {Navid Talemi, M and Ramezani Farani, M and Alipour Eskandani, N and Mirzaee, D and Alipourfard, I and Huh, YS},
title = {Programmable lipid nanoparticles for RNA therapeutics: Design principles and clinical translation.},
journal = {Materials today. Bio},
volume = {37},
number = {},
pages = {102774},
pmid = {41624517},
issn = {2590-0064},
abstract = {RNA therapeutics have come of age as clinically validated modalities including mRNA, siRNA, antisense oligonucleotides (ASOs), and in vivo genome editing, with lipid nanoparticles (LNPs) as the main non-viral delivery system. This review defines programmable LNPs as systems whose composition and interfacial chemistry are tuned to control organ tropism, cell specificity, intracellular trafficking, and immune interactions. We summarize design rules across four core components (ionizable lipid, phospholipid, cholesterol, PEG-lipid) and highlight levers like apparent pKa optimization (∼6-7 for hepatic delivery), biodegradable linkers, PEG-anchor-dependent shedding, ligands (e.g., GalNAc), and selective organ-targeting (SORT) lipids that redirect biodistribution beyond the liver. We survey advances in data-guided formulation, including DNA-barcoded in vivo libraries, machine learning, and physics-based prediction, plus scalable manufacturing (microfluidics, confined impinging-jet mixing, tangential-flow filtration) and Quality-by-Design with process-analytical technologies. A comprehensive characterization toolkit (size/ζ-potential, cryo-EM/SAXS, RNA encapsulation and integrity, apparent pKa, in vivo barcoding) maps to critical quality attributes. Applications span vaccines, protein replacement, siRNA/ASO delivery, and CRISPR platforms, with clinical examples like patisiran, COVID-19 and RSV mRNA vaccines, in-human transthyretin (TTR) editing, and individualized melanoma vaccination. We analyze translational constraints like endosomal escape, reactogenicity and anti-PEG immunity, complement activation, and lot-to-lot control, plus success factors: corona-aware design, dose-efficient potency at low lipid burden, redosing strategies, and fit-for-purpose biomarkers. Together, programmable LNPs offer a generalizable path to extrahepatic, cell-aware RNA medicine when coupled to rigorous analytics and platform manufacturing.},
}

@article {pmid41624439,
year = {2026},
author = {Cheng, D and Zhu, F and Zhao, L and Qiao, Y and Dang, E and Chen, X},
title = {The complete mitochondrial genome data of Ylistrum balloti (Bernardi 1861) (Bivalvia: Pectinidae) from China.},
journal = {Data in brief},
volume = {64},
number = {},
pages = {112437},
pmid = {41624439},
issn = {2352-3409},
abstract = {The marine bivalve Ylistrum balloti, an economically important species found in the South China Sea, remains largely unexplored in terms of its genetic background. In this study, we have determined the complete mitochondrial genome of Y. balloti. The entire mitogenome of Y. balloti spans 19484 bp, with a base composition of 21.94% A, 13.12% C, 29% G and 35.94% T. The genome contains 13 protein-coding genes (PCGs), 3 ribosomal RNA (rRNA) genes, 23 transfer RNA (tRNA) genes, and a major non-coding region (MNR). A phylogenetic analysis, based on 12 protein-coding genes (PCGs) from 15 species within related taxa, supported the grouping of Y. balloti with Y. japonicum and their clustering within the Pectinidae family. This dataset presents the complete mitochondrial genome of Y. balloti, providing insights for studies in evolution, taxonomy, DNA barcoding, and population genetics of Ylistrum.},
}

@article {pmid41624091,
year = {2026},
author = {Dong, H and Feng, B and Yang, S and Jia, Y and Qin, M and Bai, W},
title = {Diet Switching and Interspecific Competition in Sympatric Steppe Ungulates Under Seasonal Resource Variability.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e72971},
pmid = {41624091},
issn = {2045-7758},
abstract = {Understanding the mechanisms of competition and coexistence among sympatric species is crucial for deepening our understanding of interspecific interactions and informing the conservation of rare and endangered wildlife. In this study, we utilized DNA macro-barcoding technology to analyze the seasonal dietary habits of Kiang (Equus kiang) and Tibetan Gazelle (Procapra picticaudata) in Shiqu County, Sichuan Province, aiming to investigate their resource partitioning strategies and potential competition for limited forage resources. The results showed that Kiang mainly consumed Cyperaceae and Polygonaceae in both seasons, while Tibetan Gazelle fed on Polygonaceae and Rosaceae in the warm season and shifted to Ephedraceae in the cold season. Both species exhibited significant seasonal differences in dietary composition, with Tibetan Gazelle showing greater individual variation and seasonal shifts. In addition, their dietary niche was broader in the warm season, and overlap remained high, with indices of 0.89 and 0.87 in the warm and cold seasons, respectively. The results indicate that although Kiang and Tibetan Gazelle exhibit partial dietary overlap, they mitigate interspecific competition and achieve sympatric coexistence through differential use of dominant forage species, adjustments in dietary proportions, and individual dietary flexibility; notably, Tibetan gazelles exhibit stronger ecological adaptability. This study highlights a competition-coexistence dynamic along the trophic niche axis in typical plateau ungulates, providing insights for effective conservation strategies and biodiversity conservation in plateau regions.},
}

@article {pmid41622702,
year = {2026},
author = {},
title = {Correction to "Advancing Yeast Identification Using High-Throughput DNA Barcode Data From a Curated Culture Collection".},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70106},
doi = {10.1111/1755-0998.70106},
pmid = {41622702},
issn = {1755-0998},
}

@article {pmid41622237,
year = {2026},
author = {Samadi, S and Moazzeni, H and Pirani, A and Sharghi, HR and Bahadori, S and Esser, HJ and Zare, G and Turdiboyev, O and Balandari, A},
title = {Limited resolution of DNA barcodes and environmental influence on phytochemical diversity in Berberis integerrima (Berberidaceae).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37409-x},
pmid = {41622237},
issn = {2045-2322},
support = {97003448//Iran National Science Foundation/ ; },
}

@article {pmid41621553,
year = {2026},
author = {Ling, JA and He, JX and Lin, CH and Sheu, SC and Cheng, JH and Lee, MS},
title = {Species-specific Isothermal Nucleic Acid Amplification Assay Targeting Internal Transcribed Spacer (ITS) for Rapid Authentication of the Medicinal Crop Cirsium japonicum and Cirsium setosum in Herbal Markets.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116063},
doi = {10.1016/j.ab.2026.116063},
pmid = {41621553},
issn = {1096-0309},
abstract = {BACKGROUND: Cirsium japonicum (CJ) and Cirsium setosum (CS) are two widely recognized medicinal crops in Chinese herbal medicine (CHM) that are listed as authentic herbal plants in the herbal pharmacopeia. Given their strikingly similar morphological characteristics, CJ and CS are particularly susceptible to adulteration in the herbal marketplace, raising significant concerns about product integrity and consumer safety.

PURPOSE: To ensure the safety and efficacy of CHM, proper authentication of these herbs is a critical step in maintaining high-quality pharmaceutical production.

METHODS: In this study, we developed a species-specific loop-mediated isothermal amplification (LAMP) method for the authentication of CS and CJ.

RESULTS: We designed specific LAMP primer sets for both species using the selected DNA barcode, the internal transcribed spacer (ITS) sequence, through in silico analysis. After validating the specificity of the primers, we successfully authenticated CS and CJ using the LAMP primer sets and visualized the detection results through gel electrophoresis. The sensitivity of the LAMP method for CJ and CS authentication was established, with a limit of detection (LOD) of 100 pg for CJ and 50 pg for CS, using direct SYBR Green staining. When we applied the LAMP method to commercial Cirsium products, we found that only 25% (5 out of 20) of the samples contained CJ, while none contained CS.

CONCLUSION: In conclusion, we successfully established a species-specific LAMP assay for authenticating CJ and CS. This method can be used for species verification and is applicable to commercial Cirsium products for authenticity testing, contributing to quality control in pharmaceutical manufacturing.},
}

@article {pmid41620282,
year = {2026},
author = {Pantsulaia, G and Brody, J},
title = {High-parameter T-cell spectral phospho-flow-cytometry.},
journal = {Methods in cell biology},
volume = {201},
number = {},
pages = {39-53},
doi = {10.1016/bs.mcb.2025.03.011},
pmid = {41620282},
issn = {0091-679X},
mesh = {Humans ; Animals ; *Flow Cytometry/methods ; *T-Lymphocytes/immunology/cytology/metabolism ; Mice ; Lymphocyte Activation ; Staining and Labeling/methods ; },
abstract = {Phospho-flow is an invaluable tool for investigation into immunological signaling, enabling concurrent staining of cell lineage markers alongside sensitive intracellular phospho-proteins. Phospho-flow holds promise as a powerful diagnostic and therapeutic tool that can enable signal profiling, cell phenotyping, drug screening, pharmacodynamic profiling and assessment of drug efficacy across multiple cell types. When combining phospho-flow with fluorescent cell barcoding (FCB) multiplexing technique, high throughput flow cytometry can be achieved. FCB enhances experiment robustness while reducing variability in staining and decreasing antibody usage. Despite its utility, inter-operator technique variability persists, highlighting the need for protocol and analysis standardization. Here we describe an experimental mechanism for stimulating mouse and human T cells that demonstrates robust activation that can be adapted for various experimental designs.},
}

Humans
Animals
*Flow Cytometry/methods
*T-Lymphocytes/immunology/cytology/metabolism
Mice
Lymphocyte Activation
Staining and Labeling/methods

@article {pmid41620165,
year = {2026},
author = {Loc, DH and Șuleşco, T and Sauer, FG and Schmidt-Chanasit, J and Velavan, TP and Lühken, R},
title = {Host-feeding patterns of mosquitoes across land use types and regions in Vietnam and its implications for mosquito-borne disease transmission.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108001},
doi = {10.1016/j.actatropica.2026.108001},
pmid = {41620165},
issn = {1873-6254},
abstract = {Understanding mosquito host-feeding patterns is essential for elucidating the transmission dynamics of mosquito-borne pathogens and informing targeted control strategies. In this study, we investigated the host-feeding patterns of mosquitoes collected in 2022 and 2023 across three land use types (urban, rural, and forest) in four geographical regions of Vietnam (North, South, Central Coast, and Central Highlands). Mosquitoes were sampled using BG-Pro traps, and host identification was performed via DNA barcoding of the cytochrome b and 16S rRNA genes. A total of 349 blood-fed mosquito specimens, representing 13 species and three undifferentiated taxa, were analyzed. The dominant species were Culex tritaeniorhynchus, Cx. quinquefasciatus, and Cx. vishnui. Host-DNA was successfully identified in 267 specimens (77%), revealing blood meals from 18 mammal and 4 bird species. Chickens (45%), humans (28%), and dogs (12%) were the most frequent hosts. Mixed blood meals were detected in 23% of successfully analyzed specimens, indicating potential for bridge vector transmission between host groups. No statistically significant effect of land use on host-feeding patterns was observed for the three dominant mosquito species. These findings highlight the diverse feeding behaviour of mosquitoes in Vietnam, characterize by broad host species and frequent mixed blood meals, and emphasize the need for continued research to better understand mosquito-host interactions and their implications for vector-borne pathogen transmission.},
}

@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}

Humans
Malaysia/epidemiology
*Pediculus/genetics/classification
Animals
*Microbiota
Male
*Lice Infestations/epidemiology/parasitology
Female
Child
Child, Preschool
*Genetic Variation
RNA, Ribosomal, 16S/genetics
Vulnerable Populations
Infant
Bacteria/classification/genetics/isolation & purification

@article {pmid41617893,
year = {2026},
author = {Keele, BF and Okoye, AA and Immonen, TT and Varco-Merth, B and Duell, D and Nkoy, C and Goodwin, W and Hoffmeister, S and Hughes, CM and Kose, E and Conchas, A and Goodman, CA and Fennessey, CM and Macairan, A and Bosche, WJ and Fast, R and Homick, CM and Hull, M and Oswald, K and Shoemaker, R and Silipino, L and Welker, JL and Smedley, J and Labriola, CS and Axthelm, MK and Hansen, SG and Estes, JD and Barouch, DH and Lifson, JD and Picker, LJ},
title = {Initial sites of SIV rebound after antiretroviral treatment cessation in rhesus macaques.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41617893},
issn = {2058-5276},
support = {INV-002377/GATES/Gates Foundation/United States ; INV-002704/GATES/Gates Foundation/United States ; INV-002377/GATES/Gates Foundation/United States ; UM1AI164560//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; 75N91019D00024/CA/NCI NIH HHS/United States ; 75N91019D00024/CA/NCI NIH HHS/United States ; },
abstract = {The tissue origin(s) and the earliest viral dynamics of HIV rebound after antiretroviral therapy (ART) remain unclear. Here, using barcoded SIVmac239 in rhesus macaques (n = 24), we defined the distribution of barcode-specific viral RNA expression in tissues during ART (n = 6) and then assessed initial clonal rebound 5 and 7 days after ART cessation by identifying barcodes in individual tissues that exceeded the 99th percentile of the on-ART distribution ('outliers'). In 4 of 11 aviraemic and 6 of 7 viraemic animals, 32 such outlier barcodes were identified. Sixteen of these barcodes were also identified in rebound viraemia, confirming specific tissues as rebound origin and early amplification sites. Overall, 27 of the 32 outlier barcodes were determined to reflect rebound origins, of which 96% were in the gastrointestinal tract (26%) or gastrointestinal tract-associated lymphoid tissues (70%). These results indicate that distinct tissue sites differentially support post-ART viral rebound, with potential therapeutic implications for interventions designed to prevent or control these events.},
}

@article {pmid41616745,
year = {2026},
author = {Henderson, Z and Holzmann, M and Gooday, AJ},
title = {Scottish nearshore monothalamid Foraminifera (Rhizaria): Description of five new species and one new genus.},
journal = {European journal of protistology},
volume = {102},
number = {},
pages = {126181},
doi = {10.1016/j.ejop.2026.126181},
pmid = {41616745},
issn = {1618-0429},
abstract = {Henderson (2023) gave informal descriptions of several soft-walled, monothalamid foraminifera from intertidal zones in the Lorne area of northwest Scotland based on morphology. In the present study, we use a combination of morphological and molecular data to formally establish one new genus and five new monothalamid species from the same area. Lorneia sphaerica gen. & sp. nov. (monothalamid Clade D) has a spherical, coarsely agglutinated test containing magnetic particles and minute aperture-like openings distributed around the test. Lorneia ovalis gen. & sp. nov. (Clade D) has similar characteristics, but the test is oval, and there is a terminal aperture situated at each end. Psammophaga owensi sp. nov. (Clade E) has an oval, finely agglutinated test with a simple terminal aperture and intracellular magnetic particles. In Hilla brevis sp. nov. (Clade Y), the test is broadly oval and finely agglutinated with a reflective sheen and a large terminal aperture with a pronounced collar. Flaviatella zaninettiae sp. nov. (Clade Y) has an elongate, finely agglutinated test with a reflective sheen, a tubular terminal apertural structure, and distinctive yellow cytoplasm. Two species, Flexammina islandica Voltski and Pawlowski, 2015 and Ovammina opaca Dahlgren, 1962, are reported for the first time in Scottish coastal waters. This study underlines the importance and diversity of monothalamid foraminifera in coastal settings.},
}

@article {pmid41614453,
year = {2026},
author = {Wan, N and Xue, Y and Chen, S and Yu, H and Ma, X and Cheng, R and Jiang, X and Zhang, ZS and Yang, W and Li, J and Chen, Y},
title = {Development of a unified mass cytometry assay integrating activation-induced markers (AIMs) and cytokine profiling for high-throughput assessment of antigen-specific T cell responses.},
journal = {Human vaccines & immunotherapeutics},
volume = {22},
number = {1},
pages = {2610068},
doi = {10.1080/21645515.2025.2610068},
pmid = {41614453},
issn = {2164-554X},
mesh = {Humans ; *Cytokines/analysis/metabolism ; *Lymphocyte Activation/immunology ; *High-Throughput Screening Assays/methods ; *Flow Cytometry/methods ; *CD8-Positive T-Lymphocytes/immunology ; Biomarkers/analysis ; Reproducibility of Results ; *CD4-Positive T-Lymphocytes/immunology ; *T-Lymphocytes/immunology ; },
abstract = {Accurate profiling of antigen-specific T cells by measuring T cell activation markers and cytokine production has been limited by inconsistent marker usage across studies and substantial methodological variability. To overcome these challenges, we established a unified mass cytometry (CyTOF) platform that integrates optimized activation-induced marker (AIM) panels, intracellular cytokine staining (ICS), and a cadmium-based barcoding system for high-throughput, multiplexed analysis of T cell responses. We optimized stimulation conditions (18-24 h) and validated highly sensitive dual AIM combinations, including CD25[+]CD134[+] and CD25[+]CD69[+] in CD4[+] T cells, as well as CD25[+]CD137[+] and CD25[+]CD69[+] in CD8[+] T cells. These combinations were stable under protein transport inhibition and closely paralleled cytokine-producing populations. In addition, we developed a cadmium-tagged β2 M/CD298 barcoding strategy that supports 21-plex sample processing without signal distortion. Validation in two independent cohorts confirmed the platform's high sensitivity, reproducibility, and its ability to simultaneously detect AIM[+] T cells and cytokine-producing subsets. Together, this integrated workflow provides a robust and scalable framework for comprehensive immune monitoring in vaccine development and infectious disease research.},
}

Humans
*Cytokines/analysis/metabolism
*Lymphocyte Activation/immunology
*High-Throughput Screening Assays/methods
*Flow Cytometry/methods
*CD8-Positive T-Lymphocytes/immunology
Biomarkers/analysis
Reproducibility of Results
*CD4-Positive T-Lymphocytes/immunology
*T-Lymphocytes/immunology

@article {pmid41607585,
year = {2025},
author = {Huang, SP and Chen, YH and Wang, TY},
title = {Museum Fish Collections and DNA Barcoding Reveal the Invasion History of the Zoonotic Yellow Grub Parasite (Clinostomum sinensis) in Taiwan's Rivers.},
journal = {Zoological studies},
volume = {64},
number = {},
pages = {e62},
pmid = {41607585},
issn = {1810-522X},
abstract = {Clinostomum species are typical trematodes (or flatworms) and zoonotic parasites of humans, fish, and birds. These parasites require at least two definitive hosts, fish and birds, to complete their life cycle. Previous studies indicated that the yellow grub, identified as C. complanatum, first appeared in northern Taiwan around the 1990s, with uncertain origins. This study identified 65 of 2,181 museum fish specimens with leech-like metacercariae across four main river systems (Tamshui, Houlong, Tzengwen, and Xiuguluan Rivers) and documented new infection records in fishes from Beigang, Puzih, Kaoping, and Bie Rivers during subsequent field work. The parasite appears to have established in the Houlong and Tamshui Rivers before dispersing to southern and eastern waterways. COI barcode analysis revealed that most metacercariae belong to C. sinensis with low nucleotide diversity (π = 0.00314353). The closely related haplotypes with insignificant Tajima's D (-1.89473 with p-value = 0.981839) suggest a gentle population expansion after their colonization to Taiwan. Additionally, yellow grub infections were more prevalent in carnivorous fishes (> 60%) compared to omnivorous and algal-feeding fishes. The high infection rates documented in literature and museum specimens suggest that Jhonggang and Houlong rivers represent the primary (or earlier) infection areas from which the parasite subsequently spread throughout Taiwan, highlighting the need for enhanced regulations to protect endangered or cultivated species.},
}

@article {pmid41604161,
year = {2026},
author = {Jang, W and Song, CW and Hong, J and Lim, SY and Moon, DGRM and Roh, HY and Park, KH and Han, CS and Bong, KW},
title = {Amplification-Free and Label-Free Multiplexed Profiling of Extracellular Vesicle-Derived MicroRNA via Micropore Sensing Based on PNA-Functionalized Hydrogel Barcodes.},
journal = {ACS sensors},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssensors.5c03052},
pmid = {41604161},
issn = {2379-3694},
abstract = {Extracellular vesicle (EV)-derived microRNA (miRNA) is a promising biomarker for various diseases, including cancer. However, the current EV-miRNA detection technologies, such as RT-qPCR and microarray, have depended on the complex amplification and labeling processes, which are not preferred for constructing an on-site diagnosis system. Herein, we present an EV-miRNA detection platform utilizing micropore sensing based on peptide nucleic acid (PNA)-functionalized hydrogel barcodes. Based on the low background signal and high affinity to the miRNA of the PNA probes, the breast cancer-related miRNAs (miR-21 and let-7a) can be detected with femtomolar sensitivities (481 and 551 fM) without any amplification and labeling steps by penetrating the target-captured barcodes into the pore and analyzing the electrical signal. By designing the geometrical codes of the particles, the multiplexed detection of miR-21 and let-7a can be implemented with high specificity and practically applicable recovery rates. Finally, we validate the clinical potential of the presented assay by differentiating the expression patterns of the plasma EV-derived miR-21 and let-7a between the breast cancer patients and healthy donors.},
}

@article {pmid41466218,
year = {2025},
author = {Gálvez-Galván, A and Aguilar, M and Prieto, P},
title = {Role of chromosome ends in meiotic stability, recombination and wheat evolution in the context of breeding.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {187},
pmid = {41466218},
issn = {1471-2229},
abstract = {UNLABELLED: Wheat is one of the most important crops worldwide, and understanding its genome organisation is crucial for geneticists and breeders. In this study, we examined the dynamic roles of telomeric and subtelomeric regions in wheat, focusing on their influence on homologous chromosome pairing during meiosis, the process that produces gametes. We analysed various Triticum species and modern cultivars, uncovering a complex “barcode” at chromosome ends that rules homologous recognition. Phylogenetic analysis of the ZIP4-5B gene highlighted the evolutionary relationships among wheat species, emphasising the contribution of wild relatives to genetic diversity, especially in terminal chromosomal regions. Our findings suggest that telomeric regions, although traditionally seen as conserved, display significant variability and structural complexity influenced by genetic background and chromosomal context. We observed a strong link between telomere position and variant accumulation, with subtelomeric regions acting as hot spots for instability and chromatin remodelling. G-quadruplex (G4) structures were found to be distributed unevenly, with their density affected by telomere distance and genomic context. Subtelomeric regions were identified as key sites for genetic improvement, harbouring rapidly evolving sequences and transposable elements that may impact meiotic pairing accuracy. Our results indicate that telomeres and subtelomeres serve as dynamic genomic centres, encoding chromosomal identity and regulating homologous pairing through a balance of sequence diversity and structural motifs. This research enhances our understanding of wheat genome stability and provides insights for breeding strategies aimed at increasing genetic diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-08020-5.},
}

@article {pmid41603601,
year = {2026},
author = {Stairs, B and Johnson, H and Mondron, K and Syring, KC and Guerrero, A and Ballou, ER and King, JS and Pawlowska, TE and Adeleke, R and Stevens, DA and Uehling, JK},
title = {Genomic analyses of globally distributed Rhizopus microsporus populations indicate clinical isolates derived from environmental diversity reservoirs.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/00275514.2025.2594974},
pmid = {41603601},
issn = {1557-2536},
abstract = {Mucormycosis is a group of diseases that is increasing in frequency. A common opportunistic human fungal pathogen in this group is Rhizopus microsporus, which is a globally distributed species present in soil-associated environments. A subset of isolates in this species host endobacteria that are hypothesized to influence fungal pathogenicity in both clinical and environmental settings. We have limited understanding of how clinically and environmentally derived isolates are related or how physiological attributes, including thermotolerance and endosymbiosis, are correlated with population structure. Traditional molecular barcodes used to assess intraspecific relationships, such as ribosomal DNA internal transcribed spacer (ITS-rDNA)-based markers, do not provide species-level resolution, necessitating analyses of whole genome data. In this study, we generated novel whole genome sequencing data for six R. microsporus isolates and combined these data with publicly available whole genome sequences of 46 R. microsporus isolates. We evaluated these sequences to understand the evolutionary relationships among clinical and environmental isolates using phylogenomic and single nucleotide polymorphism (SNP)-based population genomics methods. We further studied their relationships by quantifying and comparing potential physiological differences and endosymbiont presence in a subset of 16 isolates with live cultures. We found that clinical isolates that originate from environmental settings contain higher molecular diversity than subpopulations isolated from clinical settings. We observed that environmental isolates grow faster than clinical isolates at temperatures between 22 and 37 C and that 7 of 16 (44%) contain endobacteria in the genus Mycetohabitans (Burkholderiales). Lastly, we observed that genome assembly size in R. microsporus is variable and that long-read sequencing technologies greatly enhance our ability to investigate the underlying genomic features. Our study provides a valuable backdrop for probing the basic biology and applied biomedical importance of Rhizopus and related fungi that cause mucormycosis.},
}

@article {pmid41603298,
year = {2026},
author = {Shen, Q and Deng, E and Luo, L and Zhang, J and Yang, Q and Su, D and Fan, X},
title = {High-throughput single-cell DNA methylation and chromatin accessibility co-profiling with SpliCOOL-seq.},
journal = {Clinical and translational medicine},
volume = {16},
number = {2},
pages = {e70584},
pmid = {41603298},
issn = {2001-1326},
support = {GZNL2024A03001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A02003//Major Project of Guangzhou National Laboratory/ ; 2021QN02Y747//the Guangdong Provincial Pearl River Talents Program/ ; SL2024A04J01788//Guangzhou science and technology elite "pilot" project/ ; },
mesh = {Humans ; *DNA Methylation/genetics ; *Single-Cell Analysis/methods ; *Chromatin/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Lung Neoplasms/genetics ; Epigenesis, Genetic ; },
abstract = {BACKGROUND: DNA methylation and chromatin accessibility are pivotal epigenetic regulators of gene expression and cellular identity, with significant implications in tumorigenesis and progression. Current single-cell multi-omics methods are limited in throughput and sensitivity, hindering comprehensive biomarker discovery.

METHODS: We developed single-cell split-pool ligation-based multi-omics sequencing technology (SpliCOOL-seq), a high-throughput single-cell sequencing technology that simultaneously profiles whole-genome DNA methylation and chromatin accessibility in thousands of cells. By integrating in situ GpC methylation, universal Tn5 tagmentation, and split-pool combinatorial barcoding, SpliCOOL-seq achieves enhanced sensitivity and scalability.

RESULTS: SpliCOOL-seq accurately distinguished lung cancer cell types based on genetic and multiple epigenetic modalities and revealed that the two DNA methyltransferase (DNMT) inhibitors, 5-Azacitidine and Decitabine, both cause large-scale demethylation but in distinct patterns. Applied to primary lung adenocarcinoma, SpliCOOL-seq identified tumour subclones within the tumour lesion and uncovered novel DNA methylation biomarkers (e.g., FAM124B, SFN, OR7E47P) associated with patient survival. Additionally, we demonstrated accelerated epigenetic ageing and mitotic activity in tumour subclones, providing new insights into tumorigenesis.

CONCLUSION: SpliCOOL-seq achieves parallel profiling of whole-genome DNA methylation and chromatin accessibility in the same individual cells in a high-throughput manner and is hopefully used to illustrate regulatory interactions under different cell states. SpliCOOL-seq enables high-resolution, multi-modal epigenetic profiling at single-cell resolution, offering a powerful platform for discovering cancer biomarkers. Its application reveals novel therapeutic targets and early-diagnostic markers, underscoring its potential in precision oncology.

KEY POINTS: SpliCOOL-seq achieves high-throughput single-cell co-profiling of DNA methylation and chromatin accessibility. DNMT inhibitors caused cancer cell demethylation with divergent patterns. SpliCOOL-seq enables the discovery of genes related to LUAD tumorigenesis. Ageing and LUAD tumorigenesis may share similar epigenetic alterations.},
}

Humans
*DNA Methylation/genetics
*Single-Cell Analysis/methods
*Chromatin/genetics
*High-Throughput Nucleotide Sequencing/methods
Lung Neoplasms/genetics
Epigenesis, Genetic

@article {pmid41602288,
year = {2025},
author = {Warguła, J and Kayastha, P and Cygert, K and Nawrot, K and Dmuchowska, W and Polishchuk, A and Gawlak, M and Krakowiak, M and Stec, D and Kaczmarek, Ł},
title = {Integrative Descriptions of Two New Species of the Genus Mesobiotus (Tardigrada: Eutardigrada: Macrobiotidae) from Kibale National Park in Uganda.},
journal = {Zoological studies},
volume = {64},
number = {},
pages = {e65},
pmid = {41602288},
issn = {1810-522X},
abstract = {In this study, we present descriptions of two new species of the genus Mesobiotus discovered in the tropical rainforest of Kibale National Park in Uganda, the first new tardigrade species from this location. Our research utilized morphological data obtained with phase-contrast and scanning electron microscopes and DNA sequences of four genetic markers (28S rRNA, 18S rRNA, CO1 and ITS-2). The main character distinguishing the new species, Mesobiotus ugandicus sp. nov., is the presence of egg processes in the shape of wide cones without filaments. The second new species Mesobiotus krystynae sp. nov. is distinguished mainly by having egg processes with long, slender endings with short filaments. However, both new species are properly differentiated from phenotypically similar species of the Mesobiotus harmsworthi morpho-group by morphological and morphometric details of animals and eggs. The genetic data allowed us also to conduct a phylogenetic analysis, which elucidated positions of the new taxa and extended our understanding of the relationships within the genus.},
}

@article {pmid41600102,
year = {2026},
author = {Al Shaye, NA},
title = {Chemical and Molecular Insights into the Arid Wild Plant Diversity of Saudi Arabia.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41600102},
issn = {2223-7747},
support = {PNURSP2025R187//Princess Nourah bint Abdulrahman University/ ; },
abstract = {Arid and semi-arid ecosystems harbor a wealth of underexplored plant biodiversity with untapped ecological and pharmacological potential. This study integrates morphological and molecular barcoding (ITS and rbcL) to confirm the identity of eight wild plant species native to the Saudi Arabian desert: Calligonum crinitum, Tribulus terrestris, Cornulaca monacantha, Cleome pallida, Leptadenia pyrotechnica, Cyperus conglomeratus, Indigofera argentea, and Artemisia monosperma. High-resolution GC-MS analysis identified over 25 bioactive compounds across these taxa, grouped into functional classes including hydrocarbons, esters, fatty acids, quinones, terpenoids, and phenolics. Notable compounds such as n-hexadecanoic acid, 2,4-di-tert-butylphenol, lupeol, and D-limonene were linked to antioxidant activity, desiccation tolerance, and membrane protection under stress. L. pyrotechnica and A. monosperma emerged as chemical outliers with unique metabolite profiles, suggesting divergent strategies for climate resilience. Our results highlight the ecological and bioeconomic value of desert flora, positioning them as candidates for future research in metabolic engineering, dryland restoration, and plant-based pharmaceuticals. This integrative approach underscores the relevance of desert plants for sustainable development in the face of climate change.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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