@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 {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.<br><br>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.<br><br>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.<br><br>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 {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.<br><br>RESULTS: The complete chloroplast genome of T. aestivum cv. Keumkang was assembled using PacBio HiFi reads and determined to be 135&#x2009;909&#x2009;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.<br><br>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. &#xa9; 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; 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.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00572-026-01252-9.}, }
@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 &amp; Dobosz, sp. nov. from Afghanistan and Pakistan, and D. tengri Zheng, Badano, H. Aspöck &amp; 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, &#x218;O 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 &amp; 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.<br><br>METHODS: From November 2011 to February 2025, 319 carcasses belonging to six species of wild canids and felids from Romania [23&#xa0;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&#x2122;.<br><br>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.<br><br>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 &lt;italic&gt;Rhytisma&lt;/italic&gt; 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 <italic> Rhytisma </italic> Alderslade, 2000 (Octocorallia: Malacalcyonacea: Lemnaliidae), formerly comprising four nominal species (<italic> R. fulvum </italic>, <italic> R. fuscum </italic>, <italic> R. monticulum </italic>, and <italic> R. rubiginosum </italic>), is revised using an integrative approach. We combine morphological and phylogenomic data for newly-collected and historical specimens. A neotype is designated for <italic> R. fulvum </italic> and a lectotype for <italic> R. fuscum </italic> to stabilize the application of these names. Six new species are described from the Indo-Pacific: <italic> R. acoronatum </italic> sp. nov., <italic> R. calyaceum </italic> sp. nov., <italic> R. oblongum </italic> sp. nov., <italic> R. inaequale </italic> sp. nov., <italic> R. karibu </italic> sp. nov., and <italic> R. sperkolae </italic> 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 &amp; 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.<br><br>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.<br><br>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&#x2009;&#x2265;&#x2009;0.5 parasites/&#x3bc;l and&#x2009;&#x2265;&#x2009;50% average locus detection at 0.25 and 0.125 parasites/&#x3bc;l, 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.<br><br>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 &amp; Kettle, 1971, C. citroneus Carter, Ingram &amp; Macfie, 1920, and C. radiomaculatus Khamala &amp; 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 &amp; 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.<br><br>PURPOSE: To ensure the safety and efficacy of CHM, proper authentication of these herbs is a critical step in maintaining high-quality pharmaceutical production.<br><br>METHODS: In this study, we developed a species-specific loop-mediated isothermal amplification (LAMP) method for the authentication of CS and CJ.<br><br>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.<br><br>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.}, }
@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 &amp; 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.}, }
@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. &amp; 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. &amp; 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 &amp; 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.}, }
@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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.}, }
@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, &#x141;}, 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 &amp; 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.}, }
@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, &#xd6; 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&amp;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.}, }
@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 &amp; 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.}, }
@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.}, }
@article {pmid41584927, year = {2025}, author = {Sajjad, M and Kwon, SG}, title = {Reconstructing developmental lineages: a retrospective approach using somatic mutations and variant allele frequency.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1761810}, pmid = {41584927}, issn = {1664-8021}, abstract = {Somatic mutations accumulate during the first zygotic division and continue throughout an organism's lifespan. The characteristics and frequency of these mutations are contingent on developmental timing and tissue type, giving rise to somatic mosaicism, defined as the presence of unique genomic alterations across different cells. They serve as endogenous cellular barcodes, enabling detailed reconstruction of cell lineages and clonal dynamics. Although lineage tracing techniques have advanced from early microscopic observation and dye staining to the introduction of artificial barcodes via gene editing, owing to ethical considerations, such genetic manipulations in human developmental research are unavailable. Therefore, spontaneously arising somatic mutations are the most suitable strategy for tracing human lineages. Current approaches can be broadly categorized into two strategies: (i) high-resolution methods, including single-cell clonal expansion or laser-capture microdissection, which construct precise phylogenetic trees based on shared mutation profiles; and (ii) bulk sequencing methods, which infer lineage proximity by comparing variant allele frequencies across samples. As more lineage-tracing studies are being conducted focusing on a wider variety of organs, the integration of such data will make it possible to discover the general principles governing human development. This review highlights how the concept of somatic mutations has been applied across diverse biological contexts and discusses the insights and common principles that can be drawn from these findings.}, }
@article {pmid41584737, year = {2026}, author = {Suh, H and Seo, CW and Park, KH and Yoo, S and Kim, D and Cho, Y and Lim, YW}, title = {Hidden diversity of crust-like Sebacinaceae (Sebacinales, Agaricomycetes) in Asia.}, journal = {IMA fungus}, volume = {17}, number = {}, pages = {e168486}, pmid = {41584737}, issn = {2210-6340}, abstract = {Crust-like Sebacinaceae, comprising the genera Helvellosebacina, Sebacina, and Tremelloscypha, represent the only ectomycorrhizal lineage within the Sebacinaceae family. However, species delimitation within this group remains challenging because of their cryptic lifestyles, inconspicuous morphological traits, and limited taxonomic annotation. To address these limitations, we investigated crust-like Sebacinaceae in Asia by integrating two datasets: specimen-derived (barcoding) sequence data and root-associated metabarcoding data. A high diversity of crust-like Sebacinaceae species was uncovered, most of which did not match any previously described taxa. Multigene phylogenetic analyses (ITS, LSU, and rpb2) based on basidiomata identified eleven distinct species, of which six are proposed here as new to science. In parallel, metabarcoding data revealed additional crust-like Sebacinaceae species and confirmed their ectomycorrhizal association with Pinus and Quercus species. These findings advance our understanding of crust-like Sebacinaceae diversity and ecology in previously unexplored regions.}, }
@article {pmid41579861, year = {2026}, author = {Wang, J and Suh, JM and Woo, BJ and Navickas, A and Garcia, K and Yin, K and Fish, L and Cavazos, T and Hänisch, B and Markett, D and Hirst, GL and Brown-Swigart, L and Esserman, LJ and van 't Veer, LJ and Goodarzi, H}, title = {Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102577}, doi = {10.1016/j.xcrm.2025.102577}, pmid = {41579861}, issn = {2666-3791}, abstract = {From extrachromosomal DNA to neo-peptides, reprogramming of cancer genomes leads to the emergence of cancer state-specific molecules. Here, we systematically identify and characterize a large repertoire of orphan non-coding RNAs (oncRNAs), a class of cancer-emergent small RNAs, across 32 tumor types. We show that oncRNA binary presence-absence patterns represent a digital molecular barcode that captures cancer type and subtype identities. Importantly, this barcode is partially accessible from the cell-free space as cancer cells secrete a subset of oncRNAs. Leveraging large-scale in vivo genetic screens in xenografted mice, we functionally identify driver oncRNAs in multiple tumor types. In a retrospective study across 192 breast cancer patients, we show that oncRNAs are reliably detected in blood and that changes in cell-free oncRNA burden predict both short-term and long-term clinical outcomes. Together, we establish that oncRNAs have potential roles in tumor progression and clinical utility in liquid biopsies for tumor-naive minimum residual disease monitoring.}, }
@article {pmid41578609, year = {2026}, author = {Zhao, B and Andermann, T}, title = {Properties and Limitations of eDNA Substrates for Terrestrial Animal Monitoring.}, journal = {Molecular ecology resources}, volume = {26}, number = {2}, pages = {e70096}, pmid = {41578609}, issn = {1755-0998}, support = {2023-05366//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab &amp; Wallenberg Data Driven Life Science Program/ ; }, mesh = {Animals ; *DNA, Environmental/genetics/isolation &amp; purification ; *Environmental Monitoring/methods ; *Biodiversity ; }, abstract = {Environmental DNA (eDNA) constitutes a valuable tool for monitoring terrestrial animal diversity, but outcomes are affected by multiple factors. Among these factors, the choice of sampling substrate and method is especially important and must be aligned with research objectives. We reviewed 245 published studies that utilise eDNA for terrestrial animal monitoring and compiled an overview of the most frequently used environmental substrates. Based on the reviewed literature, we provide a key description of each substrate, as well as its particular properties and limitations related to the detection of animal species across different spatial and temporal scales. We categorise these substrates into three groups: abiotic substrates (soil, water, air, sediment), biotic substrates (invertebrate samples, plant tissues, spiderwebs) and direct-evidence substrates (scat, footprints, shelters, feeding sites). In addition, we identify several key challenges with the interpretation of eDNA-based biodiversity monitoring, including false negatives and false positives, as well as the dynamics of spatial and temporal deviations. The latter concepts, which we propose and define in this review, describe the temporal and spatial discrepancies between the DNA source and its detection in a given sample. We reflect on how these temporal and spatial deviations are expected to affect eDNA data extracted from the different types of substrates and how knowledge of these dynamics can inform effective and accurate biomonitoring. In summary, this review provides a decision basis for designing terrestrial eDNA monitoring studies by summarising the properties and limitations of different substrates and contextualising the interpretation of results in light of substrate-specific challenges.}, }
@article {pmid41577483, year = {2026}, author = {Betts, MM and Hultin, EA and Hallerman, EM and Maurakis, EG and Frimpong, EA}, title = {Embryonic selfish-herding blurs the line between brood parasitism and mutualism for communal-breeding stream fishes.}, journal = {Ecology}, volume = {107}, number = {1}, pages = {e70302}, doi = {10.1002/ecy.70302}, pmid = {41577483}, issn = {1939-9170}, support = {2039692//National Science Foundation/ ; //National Institute of Food and Agriculture/ ; }, mesh = {Animals ; *Symbiosis ; *Nesting Behavior/physiology ; Reproduction/physiology ; *Cyprinidae/physiology/embryology ; *Embryo, Nonmammalian/physiology ; Rivers ; Female ; Male ; }, abstract = {Mutualisms are complex, interspecific relationships, which sometimes create "selfish-herds" as individuals of each species compete to maximize their own fitness. Nest association, where individuals of different species spawn on a nest created by a host species, is a reproductive interaction characteristic of some minnows (Leuciscidae) and is considered mutualistic despite mimicking the behavior labeled "brood parasitism." We studied the spawning behaviors of bluehead chub (Nocomis leptocephalus) and its nest associates, testing the hypothesis that bluehead chub exploits the selfish-herd dynamic in a novel manner by arranging embryos within its nest to maximize the survival of its own offspring at the expense of the nest associates' offspring. Our results show that embryos were not uniformly distributed within a nest, as one section representing one-sixth of the nest's total volume contained a disproportionate percentage of embryos (x¯ = 40.0% ± 6.1% SE). We found three-quarters of host embryos within deeper nest sections safer from embryo predators, whereas only a third of all associate embryos were found in the same sections. These results support our hypothesis that male Nocomis leptocephalus create "embryonic selfish-herds" within their nests. This is the first study to document the existence of embryonic selfish-herds, a phenomenon that warrants the reexamination of some vertebrate reproductive interactions labeled as brood parasitism.}, }
@article {pmid41574122, year = {2026}, author = {Asiri, MMA and Ali, MA and Alwahibi, MS and Ahmed, SS and Rahman, MO and Mahato, R and Faisal, M and Kim, SY and Lee, J}, title = {The First Complete Chloroplast Genome of Lycium shawii: Genomic Architecture, Molecular Phylogenetics and Evolutionary Insights.}, journal = {Ecology and evolution}, volume = {16}, number = {1}, pages = {e72972}, pmid = {41574122}, issn = {2045-7758}, abstract = {Lycium shawii Roem. &amp; Schult., a stress-resilient medicinal plant native to the deserts of Saudi Arabia, possesses notable bioactive compounds used in traditional medicine for treating inflammation, oxidative stress, and other ailments. However, its chloroplast (Cp) genome has not previously been sequenced or described, limiting accurate molecular identification and phylogenetic resolution. In this study, we present the first complete Cp genome of L. shawii. The plastome spans 155,936 bp and is organized into a large single-copy (LSC) region (86,608 bp), a small single-copy (SSC) region (18,430 bp), and two inverted repeats regions (IRA and IRB), each spanning 25,449 bp. A total of 128 genes were annotated, comprising 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Comparative genomic analyses revealed conservation of genome structure without major rearrangements across Solanaceae. Forty simple sequence repeats (SSRs) and 50 oligonucleotide repeats were identified, with mononucleotides (38) as the dominant SSR type, and forward repeats as the most common among longer repeats. RNA-editing sites were unevenly distributed, with the highest proportion in the LSC region (48%), followed by the SSC (29%) and IRs (23%). Nucleotide diversity analysis highlighted atpI, rbcL, and accD within the LSC region as hypervariable loci suitable for DNA barcoding. Plastome-wide phylogenetic reconstruction confirmed the placement of L. shawii within the tribe Lycieae of the subfamily Solanoideae. Molecular dating analysis suggested its emergence around 1.40 MYA, during the Calabrian stage of the Cenozoic era. This study provides the first Cp genome resource for L. shawii, offering new perspectives for evolutionary and comparative genomics within Solanaceae.}, }
@article {pmid41568947, year = {2026}, author = {Robino, E and Perret, A and Noel, C and Haffner, P and Intertaglia, L and Richard, M and Descamps, N and Sellier, A and Onillon, L and Lebaron, P and Destoumieux-Garzón, D and Charrière, GM}, title = {Diversity and varying predation capacities of culturable Amoebozoae against opportunistic vibrios in contrasting Mediterranean coastal environments.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0113825}, doi = {10.1128/spectrum.01138-25}, pmid = {41568947}, issn = {2165-0497}, abstract = {Free-living amoebae (FLA) are ubiquitous and can be found in many environments including soil, freshwater, and marine environments. They feed on various microorganisms and can play an important role in the food web and its dynamics. We previously described that FLA belonging to the Vannella genus isolated from oyster farms in the Thau lagoon in France are able to establish stable interactions with Vibrionaceae, suggesting they can play a role in pathogen dynamics. To further investigate the ecological interactions between FLA and Vibrionaceae in Mediterranean coastal waters, we conducted monthly sampling for 1 year at three contrasting sites. FLA populations were isolated from water and sediment samples on different bacterial lawns, including Escherichia coli or Vibrio tasmaniensis, Vibrio crassostreae, and Vibrio harveyi. Diversity analysis by v4-18S barcoding revealed distinct communities between fractions and sites. The Vannellidae were found significantly enriched in the water, whereas Paramoebidae were found enriched in the sediments. Additionally, uneven distribution of Vexilliferidae, Vermistellae, and, to a lesser extent, Acanthamoebidae and Subulatomonas contrasted between sampling sites. Selection of grazers on different bacterial lawns revealed that V. tasmaniensis inhibits the growth of most Vannellidae, whereas V. crassostreae inhibits the growth of Paramoebidae. These differences were further confirmed functionally using isolates belonging to each Amoebozoa taxonomic group. Overall, our results highlight the need for more comprehensive studies of the diversity and population dynamics of Amoebozoa in marine environments and indicate that the role of these diversified grazers in shaping Vibrio communities is complex and still poorly characterized.IMPORTANCEAlthough they can play an important role in shaping bacterial communities and as intracellular niches for potential pathogens, the diversity and ecology of free-living amoebae (FLA) in marine environments are still poorly characterized. Very few studies have used systematic approaches to unravel the population dynamics and ecological variations of FLA in different environments. Our study in marine coastal environments highlights that FLA taxonomic groups can harbor habitat preferences and have different predation capacities, suggesting that FLA-bacteria interactions need to be considered at different taxonomic levels to uncover generalist versus specialist adaptations.}, }
@article {pmid41568902, year = {2026}, author = {Li, H and Dong, Q and Guo, J and Hu, E and Li, Y and Shan, R and Zhang, L and Zhao, D and Guo, H and Qian, G}, title = {A Smart-Perception Rare Earth MOF.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e21289}, doi = {10.1002/adma.202521289}, pmid = {41568902}, issn = {1521-4095}, support = {52302200//National Natural Science Foundation of China/ ; 52402206//National Natural Science Foundation of China/ ; 12574443//National Natural Science Foundation of China/ ; 52472173//National Natural Science Foundation of China/ ; LQ23E020004//Natural Science Foundation of Zhejiang Province/ ; LQN25E020013//Natural Science Foundation of Zhejiang Province/ ; 2024-3-029//Key Projects of Jinhua Science and Technology Burea/ ; }, abstract = {Smart responsive luminescent materials have attracted considerable scientific and technological interest owing to their broad optoelectronic applications. However, issues such as single responsive mode, inadequate spectral coverage, and poor environmental adaptability still hinder their diversified development. Herein, we propose the concept of smart multi-stimuli responsive scintillator (SMRS) and fabricate a new series of rare earth metal-organic frameworks (RE-MOFs) with active and passive perception capabilities. Such RE-MOFs exhibit excellent scintillation performances, including high relative light yield (max ∼ 42,200 photons MeV[-1]), low dose rate detection limit (min ∼ 128.2 nGyair s[-1]), and great photostability. Systematic modulation of RE[3+] contents endows MOFs with tunable broadband luminescence, thereby ensuring the passive perception. The distinct photo- and radio-luminescent mechanisms lead to significant spectral contrasts under UV and X-ray irradiation. Furthermore, RE-MOFs demonstrate thermal-stimuli responsive luminescent variation since heat will influence the energy transfer processing among the organic and inorganic units. As a result, RE-MOFs autonomously produce active luminescent perception toward both irradiation and thermal stimuli. These SMRSs exhibit great potential in in situ optical imaging and high-security photonic barcodes (the widest spectral range among MOFs for photonic encoding). This study establishes a new paradigm for smart MOF-based scintillators for an advanced intelligent perception system.}, }
@article {pmid41568360, year = {2026}, author = {Hupało, K and Sassor, C and Fuhren, MM and Buchner, D and Grabner, D and Sures, B}, title = {Assessing whole-host homogenisation as a new tool for parasite detection and identification.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {9}, number = {}, pages = {100348}, pmid = {41568360}, issn = {2667-114X}, abstract = {Despite their importance in ecosystem functioning, parasites remain the most neglected components of biodiversity monitoring. This neglect is partly due to the methodological challenges associated with their detection and identification. Current traditional morphological and molecular approaches are time-consuming, labour-intensive, and require specialised expertise. Here, we explore a novel approach of deriving parasite information through whole-host homogenisation followed by DNA-based identification of its parasite biota. Our goal was to validate whether the approach is feasible and if it could become a complementary method for studying parasites, providing a time-efficient solution allowing for a holistic parasite scan with limited taxonomic expertise. To test the method's efficiency, we analysed five specimens of European eel as model hosts. Their parasites were identified morphologically, and then all the parasites and the entire host tissue were homogenised together using a commercial blender. Molecular identification of the morphologically detected parasites was conducted using DNA barcoding with parasite-specific primers. Following homogenisation and DNA-based identification, we successfully detected all parasite taxa identified during morphological analyses, even including instances where they had not been detected morphologically. A notable exception were acanthocephalans, which showed low levels of molecular detection. Despite certain limitations, the detection of parasites directly from the whole-host homogenate shows high potential for efficient and accurate parasite detection, in some cases even surpassing morphological identification. The further development of the method, particularly through exploration of DNA metabarcoding, could improve the reliability of parasite assessments and facilitate parasite detection, which could aid in proper parasite recognition.}, }
@article {pmid41568027, year = {2026}, author = {Fusari, LM and Höcherl, A and Chimeno, C and Baranov, V}, title = {A new species and record of Xestochironomus Sublette &amp; Wirth, 1972 (Diptera, Chironomidae) from the Dominican Republic, with males and females associated by DNA barcode.}, journal = {ZooKeys}, volume = {1266}, number = {}, pages = {219-230}, pmid = {41568027}, issn = {1313-2989}, abstract = {We describe a new species of Xestochironomus Sublette &amp; Wirth, 1972 and provide notes on X. luteifurcatus Sublette &amp; Wirth, 1972 from the Dominican Republic. The adult male and female of Xestochironomus digitulus sp. nov. are also described and illustrated. The male and female of X. luteifurcatus are redescribed. Males of the new species can be easily distinguished from congeners by the following combination of characters: the abdomen of both sexes bears cross bands; the anal point is long, slender; the male gonostylus has a slightly bifurcated apex; and there is a thumb-like lobe at the apex of the gonostylus.}, }
@article {pmid41566400, year = {2026}, author = {Jiang, WJ and Cai, K and Sun, Y and Liu, A and Zhu, H and Gao, R and Zhong, C and Wei, N and Lai, F and Fei, T and Wang, YJ and Zheng, X and Xu, M and Wu, HJ}, title = {Harmonizing single-cell 3D genome data with STARK and scNucleome.}, journal = {Genome biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13059-026-03938-x}, pmid = {41566400}, issn = {1474-760X}, abstract = {Single-cell three-dimensional genome sequencing (sc3DG-seq) reveals genome regulation and heterogeneity in various biological processes, but a universal analysis tool is lacking. Here we present STARK, a versatile toolkit for processing, quality control, and analysis of diverse sc3DG-seq data. Utilizing STARK, we benchmark 15 technologies, quantitatively comparing their strengths and limitations. We also develop EmptyCells to filter empty barcodes and introduce Spatial Structure Capture Efficiency (SSCE) to assess chromatin structure capture quality. Additionally, we establish scNucleome, a uniformly processed repository of sc3DG-seq datasets, to serve as a foundational resource for future 3D genome research.}, }
@article {pmid41565766, year = {2026}, author = {Wu, B and Yang, X and Cai, Y and Wan, S and Liu, J and Xing, J and Chen, X and Zhang, J and Jin, Y and Yu, A and Yang, L}, title = {Proteomic profiling of single extracellular vesicles as a promising new approach for the diagnosis and treatment modality of advanced ovarian cancer.}, journal = {NPJ precision oncology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41698-026-01271-x}, pmid = {41565766}, issn = {2397-768X}, support = {82274266//National Natural Science Foundation of China/ ; 82505319//National Natural Science Foundation of China/ ; 2026ZL0202//The Traditional Chinese Medicine Science and Technology Project of Zhejiang Province/ ; }, abstract = {This study utilized a novel Proximity Barcoding Assay to perform high-resolution proteomic profiling of individual plasma extracellular vesicles from 85 patients with advanced high-grade serous ovarian carcinoma (OC) and 95 healthy controls (HC). Single-EV analysis identified 119 differentially expressed proteins and 17 distinct EV subpopulations. Cluster 7 (enriched in integrins ITGB3, ITGB1, and ITGA6) was significantly elevated in OC plasma (4.47% in HC vs. 14.79-15.82% in OC). Machine learning (SVM-RFE, LASSO, Random Forest) identified a diagnostic panel (ITGA6, ITGB2, ILK) achieving exceptional accuracy in distinguishing OC from HC (AUC = 0.999 training; 1.000 validation). Furthermore, risk models incorporating specific protein signatures effectively stratified patients by platinum sensitivity/resistance (9-protein panel: ILK, CDCP1, CD86, CLDN4, CLEC1B, CDHR5, CLDN11, JAM2, FOLH1), lymph node metastasis status (7-protein panel: APOE, CD28, CLDN4, FOLH1, ITGAL, JAML, ULBP3), and post-surgical residual disease burden (4-protein panel: CD44, CLMP, ITGA4, AMIGO1), with Cluster 13 (ITGB1-high) also significantly associated with residual disease. This work demonstrates the power of single-EV proteomics combined with machine learning for non-invasive diagnosis and clinical outcome assessment in advanced ovarian cancer, though the absence of early-stage patients limits its applicability for early detection.}, }
@article {pmid41563521, year = {2026}, author = {Dela Cruz, JWR and Malit, EPB and Patanindagat, CY and Arevalo, CFL and Manalo, AJI and Boongaling, DDG and Ramos, JDA}, title = {Electron microscopy and molecular phylogenetic characterization of the allergenic dust mite species Suidasia pontifica (Acari: Suidasiidae).}, journal = {Experimental &amp; applied acarology}, volume = {96}, number = {2}, pages = {12}, pmid = {41563521}, issn = {1572-9702}, mesh = {Animals ; Female ; Male ; Allergens ; Arthropod Proteins/genetics ; Electron Transport Complex IV/genetics ; *Microscopy, Electron ; Philippines ; *Phylogeny ; *Pyroglyphidae/classification/genetics ; }, abstract = {The clinical significance of house dust mites (HDMs) as sources of allergens for medical diagnostics, allergen-specific immunotherapy, and allergology research is dependent on accurate morphological and molecular data analysis for species identification and characterization. Here, we report the species identification and allergenicity of a tropical HDM, Suidasia pontifica (Sp), via morphological-molecular characterization tandem and IgE ELISA, respectively. Electron microscopy of monocultures of HDM samples collected from Laguna, Philippines, revealed different traits related to chaetotaxy, cuticle pattern, and body anatomy. Genus-specific characters such as the length of the scapular setae, cuticle patterns, vertical setae, ω1 setae, along with species-specific traits such as short dorsal setae, long h3 setae, average c1 to c1 verrucae count, presence of sclerotized bursa copulatrix (female), and c3 setae size, suggest that the sample identity is Sp. In addition, PCR amplification from the HDM monoculture genomic DNA and bidirectional sequencing of the 18S and COI gene markers were performed. Sequences were subjected to sequence assembly, consensus acquisition, sequence alignment, and phylogenetic inference. The COI gene showed an exact match and phylogenetic attachment of the sample assembly to Sp, confirming the species-level identification, corroborated with morphological data. Furthermore, 18S gene character analysis was able to prove phylogenetic demarcation of the Sp 18S gene from the sister species S. nesbitti and other allergenic sarcoptiform species. Our molecular phylogenetic analysis, which is strongly supported by electron microscopy data, indicates the identity of our monocultures as Sp. Interestingly, the Sp allergenicity profile of allergic patients and controls (n = 200) suggests 47% IgE-binding reactivity, confirming its allergenicity and clinical importance among atopic patients. This study emphasizes the resolving power of the morphological-molecular phylogenetic approach and IgE-reactivity to objectively verify Sp species identity and allergenicity for downstream immunological studies.}, }
@article {pmid41562469, year = {2026}, author = {Wan, Z and Xu, C and Wang, Y and Song, L and Yuan, W and Chen, M and Gong, R and Zhang, XE}, title = {An AND-Logic Gate-Based Biosensor for Simultaneous Detection of SARS-CoV-2 Nucleic Acids and Nucleocapsid Proteins.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c07321}, pmid = {41562469}, issn = {1520-6882}, abstract = {Nucleic acids and proteins are recognized as gold standard biomarkers for disease diagnosis and pathogen detection. However, conventional single-analyte detection methods remain susceptible to false positives caused by manual operational errors or sample contamination, thereby undermining diagnostic reliability and increasing the burden on healthcare systems. To address this limitation, we developed a one-pot isothermal amplification and CRISPR-Cas cooperative system (OIACS) that functions as an AND-logic gate biosensor for the simultaneous detection of SARS-CoV-2 RNA and nucleocapsid protein. Unlike conventional methods relying solely on CRISPR RNA (crRNA) recognition, the OIACS employs antibody-mediated target binding with blocker release for target recognition, offering increased flexibility in assay design for different targets. A universal Cas12a-targetable DNA barcode is generated via strand displacement isothermal amplification, enabling signal amplification upon dual-target recognition. The OIACS assay exhibited practical utility by reliably detecting SARS-CoV-2 transcription- and replication-competent virus-like-particles at 5000 copies/mL, and the limit of detection was determined to be as low as 1698 copies/mL, highlighting its robustness and potential for clinical diagnosis.}, }
@article {pmid41561880, year = {2025}, author = {Zucco, Z and Cava, S and Bonacci, T and Scalercio, S}, title = {Effectiveness of DNA Barcoding Libraries Boosted through Taxonomy: the Case of a Neglected Taxon within an Underexplored Region.}, journal = {Zoological studies}, volume = {64}, number = {}, pages = {e49}, pmid = {41561880}, issn = {1810-522X}, abstract = {In recent decades, taxonomy has been significantly improved by integrating molecular techniques with classical morphological methods, leading to the discovery of cryptic species. On the other hand, molecular datasets by themselves are ineffective in several types of research without basic taxonomic studies, as the ecological and biological roles of a given species cannot be determined without an accurate name. DNA barcoding libraries are widely used as identification tools by non-specialists to overcome the taxonomic impediment, but they fail when basic taxonomic studies are insufficient and faunistic inventories are lacking. South European microlepidoptera are poorly studied, with the exception of a few families such as Depressariidae. We tested the effectiveness of the DNA barcoding library for this family to identify 174 specimens collected in southern Italy, where faunistic studies are very limited. All specimens were successfully barcoded, and 95% of them were assigned to 47 species, 43 of which correspond to a Barcode Index Number (BIN). Four additional species shared a BIN but were still clearly separated into different clusters at within-BIN resolution. Only seven specimens belonging to four BINs remain unnamed, and ad hoc studies are needed to clarify their status. The regional fauna was enriched by 37 species, three of which are new for the Italian mainland and 21 for peninsular Italy, demonstrating the usefulness of the DNA barcoding library in assessing local diversity and overcoming the taxonomic impediment. Improving taxonomic studies is crucial for utilizing molecular datasets to depict ongoing macroecological dynamics, highlight species richness trends, and identify changes in species assemblages.}, }
@article {pmid41560697, year = {2026}, author = {Xue, Y and Su, J and Chao, Y and Liu, L and Lin, X and Xiang, Y and Ho, MK and Su, Z and Chen, J and Luo, Z and Lin, C and Luo, R and Aurich, T and Wu, J and Cheung, KSC and Huang, Y and Ho, JWK and Sugimura, R}, title = {Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e18084}, doi = {10.1002/advs.202518084}, pmid = {41560697}, issn = {2198-3844}, support = {//Hong Kong Research Grant Council/ ; N_HKU731/21//NSFC/RGC Joint Research Scheme/ ; 2023A1515011265//Guangdong Natural Science Fund/ ; SGDX2021082310356025//Shenzhen-Hong Kong-Macau Technology Research Programme/ ; //InnoHK initiative of the Innovation and Technology Commission of the Hong Kong Special Administrative Region Government/ ; }, abstract = {Lineage tracing at single-cell resolution is vital for mapping cell fate decisions, yet synthetic barcoding faces limitations in precision, diversity, and toxicity-especially in human pluripotent stem cells (hPSCs). Here, we repurpose naturally occurring somatic mutations in mitochondrial transcripts from single-cell RNA sequencing as endogenous genetic barcodes. By enriching mitochondrial reads and applying a robust computational pipeline, we identified clonally informative variants to trace hematopoietic lineage emergence from hPSCs during early embryogenesis. Integrating mitochondrial barcoding with synthetic lineage tracing, we modeled embryonic tissue development and reconstructed the transcriptional logic and regulatory networks driving fate specification using a dynamical systems model. Extending this approach to spatial transcriptomics, we mapped the clonal architecture of human embryonic organoids, revealing spatial zonation orchestrated by NOTCH-mediated crosstalk between stromal cells and hematopoietic progenitors. This multimodal strategy links clonal dynamics with niche-driven fate decisions, offering a scalable, non-invasive method to dissect tissue organization in development and disease. Together, our work establishes a scalable, non-invasive multimodal framework that leverages endogenous mitochondrial DNA variants to reconstruct high-resolution spatiotemporal clonal dynamics and decode niche-driven fate decisions in a human stem cell-derived model. This approach provides a powerful strategy for dissecting tissue self-organization in development and disease.}, }
@article {pmid39113372, year = {2025}, author = {Anbalagan, R and Srivastava, PK and Baruah, K and Krishnan, J}, title = {Insecticide resistance status and bar-coding of dengue vectors in three districts of Tamil Nadu, India.}, journal = {Journal of vector borne diseases}, volume = {62}, number = {1}, pages = {51-59}, doi = {10.4103/JVBD.JVBD_79_24}, pmid = {39113372}, issn = {0972-9062}, mesh = {India/epidemiology ; Animals ; *Insecticide Resistance ; *Aedes/drug effects/genetics/classification ; *Mosquito Vectors/genetics/drug effects/classification ; Phylogeny ; *Insecticides/pharmacology ; Dengue/transmission ; Female ; Malathion/pharmacology ; DDT/pharmacology ; }, abstract = {BACKGROUND OBJECTIVES: Occurrence and distribution of vector population are crucial for entomological study in context of prevention, control and elimination of vector-borne diseases. To update some entomological aspects the study was undertaken in three districts of Tamil Nadu state namely Kumbakonam, Nagapattinam and Thriuvarur. The objective of the study was to understand the prevalence of mosquitoes; to assess insecticide resistance and phylogenetic analysis of dengue vectors (Aedes aegypti and Ae. albopictus).<br><br>METHODS: The immature stages of mosquitoes were collected from different localities by standard WHO methods marking with GPS and mapping was done using ArcGIS 10.4 software for all three districts. Insecticide resistance test was conducted using WHO susceptibility test kits. The F1 generation of female adult mosquitoes of Ae. aegypti and Ae. albopictus were exposed to DDT 4% and malathion 5% with the control paper of Risella oil and olive oil, respectively. Further, genomic DNA of individual mosquito was isolated, and sequencing was done through Eurofins, Bangalore, India. The FASTA sequence was analyzed and phylogenic tree was constructed using the Maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software (version 10.0).<br><br>RESULTS: A total 5307 specimens were collected through expanded survey in all three study areas. The collection yielded 16 species from six genera of mosquitoes. In total collection, Ae. albopictus was the dominant species in Kumbakonam and Thiruvarur districts and Ae. aegypti was dominant in Nagapattinam. The predominant breeding sources were discarded tyres with rainwater, plastic cups, coconut shells, aluminum vessels, sliver containers, bottles, grinding stones and earthen pots. The study revealed high pupal indices in all three study areas. Insecticide resistance monitoring revealed possible resistance in Ae. aegypti against DDT in all three districts whereas against malathion, possible resistance was recorded in Kumbakonam and Nagapattinam and Thiruvarur district, the species was found to be susceptible. Ae. albopictus showed resistance against DDT in all three districts but susceptible to malathion. The sequences obtained for dengue vectors showed 99% similar with GenBank. The phylogenetic tree was constructed using COI region sequences. Certainly, we observed the different genetic relationship among Ae. aegypti and Ae. albopictus between the study areas.<br><br>INTERPRETATION CONCLUSION: The study confirmed the presence of Ae. aegypti and Ae. albopictus in all three districts. The study further revealed that these vectors are susceptible to malathion but resistant to DDT. The continued surveillance of dengue vector and monitoring of insecticide resistance will strengthen the control programme for appropriate vector control measurements.}, }
@article {pmid41559823, year = {2026}, author = {Harl, J and Himmel, T and Pacheco, MA and Weissenböck, H}, title = {New mitochondrial genomes of parasites belonging to the Leucocytozoon toddi and Haemoproteus nisi groups (Haemosporida, Apicomplexa).}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07244-0}, pmid = {41559823}, issn = {1756-3305}, support = {P37076//FWF Austrian Science Fund/ ; NSF-DEB 2146653//US National Science Foundation/ ; }, abstract = {BACKGROUND: Avian haemosporidians are single-celled eukaryotic parasites of vertebrates that require dipteran vectors for transmission. The genera Plasmodium, Haemoproteus and Leucocytozoon currently comprise over 5000 parasite lineages based on a 478-bp section of the mitochondrial cytochrome b gene, which is the standard DNA barcode for avian haemosporidians. The mitochondrial genomes of apicomplexan parasites are highly condensed, with a length of approximately 6000 bp, containing three coding genes (cytochrome c oxidase subunit I, cytochrome c oxidase subunit III and cytochrome b) and dispersed fragments of the small and large ribosomal RNA (rRNA) genes. Since the mitochondrial genomes are relatively conserved, they are valuable markers for studying the phylogenetic relationships between haemosporidian parasites. However, until recently, mitochondrial genomes were unavailable for parasites of the Haemoproteus nisi and Leucocytozoon toddi species groups, which are exclusive to accipitriform raptors and strongly diverged from other Haemoproteus and Leucocytozoon parasites.<br><br>METHODS: We screened 171 accipitriform raptors from Austria and Germany using new primers targeting the cytochrome b gene of a previously neglected L. toddi clade. We also developed a new primer assay that enables the amplification and sequencing of the complete mitochondrial genomes of haemosporidian parasites. This process involved long-range PCRs with lineage-specific primers placed within the cytochrome b gene, followed by five nested PCRs targeting conserved sequence regions.<br><br>RESULTS: Screening the accipitriform raptors revealed 10 new L. toddi group lineages. We sequenced 18 mitochondrial genomes belonging to five H. nisi group, nine L. toddi group, and two other Leucocytozoon lineages. Phylogenetic analyses based on mt genome sequences placed the L. toddi lineages within the genus Leucocytozoon, but the results did not support a monophyly of the genus Haemoproteus.<br><br>CONCLUSIONS: The new nested PCR approach with lineage-specific primers used for the long-range PCRs described herein successfully enabled the sequencing of the complete mitochondrial genomes, even in samples with mixed infections. The mitochondrial genomes of the H. nisi and L. toddi group lineages are highly valuable for resolving the phylogenetic relationships of the order Haemosporida since these parasites belong to clades distinct from other Haemoproteus and Leucocytozoon parasites.}, }
@article {pmid41555650, year = {2026}, author = {Han, EL and Kim, D and Murray, AM and Mrksich, K and Hamilton, AG and Tang, S and Yoo, S and Zhu, AT and Tong, ER and Palanki, R and Hall, ML and Bedingfield, SK and Mitchell, MJ}, title = {High-Throughput In Vivo Screening Identifies Structural Factors Driving mRNA Lipid Nanoparticle Delivery to the Brain.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.5c19138}, pmid = {41555650}, issn = {1936-086X}, abstract = {Achieving systemic nonviral delivery of large nucleic acids such as mRNA to the brain is challenging due to high off-target delivery and the blood-brain barrier (BBB), a cellular barrier which prevents most nucleic acids in circulation from entering the brain. Ionizable lipid nanoparticles (LNPs) are a promising class of nanocarriers to facilitate the delivery of mRNA, as their highly modular nature enables fine-tuning of the LNP formulation for targeted delivery applications. In this work, we explore the role of ionizable lipid chemical structure and lipid molar ratios within the LNP formulation on mRNA delivery to and transfection of the brain. We utilize a high-throughput in vivo screening approach based on mRNA barcoding to study a large library of LNPs made with systematically varied ionizable lipid structures, amounts of ionizable lipid, and amounts of lipid-polyethylene glycol (PEG). We find that ionizable lipids with longer tail structures and linear amine cores can facilitate mRNA delivery to the mouse brain, and ultimately identify a specific ionizable lipid, C14-306, that facilitates brain transfection coupled with reduced liver transfection compared to an FDA-approved benchmark formulation. Furthermore, the lead LNP formulated with C14-306 is able to increase neuronal transfection and facilitate Cre-mediated recombination in the brain. Finally, safety analyses demonstrate that the lead LNP does not induce BBB leakage, increases in serum inflammatory cytokine levels, or increases in serum liver enzyme levels. Overall, our work highlights the utility of molecular barcoding for high-throughput screening of LNPs for delivery to the brain and suggests several design principles to guide the engineering of next-generation brain-tropic LNPs.}, }
@article {pmid41552826, year = {2025}, author = {Kashuri, M and Ikrar, T and Sutriyo,  and Mun'im, A and Yanuar, A}, title = {Evidence-based production framework for herbal medicine regulation in Indonesia.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1730273}, pmid = {41552826}, issn = {1663-9812}, abstract = {This narrative review synthesizes 2015-2025 evidence on evidence-based production (EBP) of herbal medicines with emphasis on advanced production technologies, omics-enabled authentication, quality by design (QbD), and regulatory harmonization relevant to Indonesia. We map how in vitro root culture, bioreactor scale-up, elicitation/metabolic engineering, and nanotechnology address supply variability and improve consistency; how DNA barcoding/metabarcoding and metabolomics with chemometrics underpin identity and chemical reproducibility; and how ASEAN/WHO initiatives enable 'loose harmonization' while preserving traditional diversity. We argue for a two-key batch-release specification (genomic × metabolite) and validated omics workflows within GLP to strengthen traceability, with real-world evidence and digital pharmacovigilance extending safety monitoring post-market. We translate these elements into an actionable framework for the Indonesian FDA (BPOM) to operationalize EBP through regulation, cross-sector training, and reliance pathways, positioning Indonesia as a regional hub for evidence-based herbal regulation.}, }
@article {pmid41551611, year = {2025}, author = {Yu, S and Luo, Y and Dang, T and Peng, C and Gan, Q and Liang, Y and Yu, J and Long, P and Zhou, W and Dai, D}, title = {A single-sEV analysis identifies plasma EPCAM[+] sEVs as a biomarker for early diagnosis and monitoring postoperative remission of thyroid cancer.}, journal = {Extracellular vesicles and circulating nucleic acids}, volume = {6}, number = {4}, pages = {982-999}, pmid = {41551611}, issn = {2767-6641}, abstract = {Aim: Small extracellular vesicles (sEVs) are promising noninvasive biomarkers for several malignancies, including thyroid carcinoma (TC). However, their heterogeneity is frequently overlooked in bulk-level analyses. Methods: Plasma samples from TC and healthy controls (HC) were collected for a proximity-dependent barcoding assay (PBA) to identify plasma sEV biomarkers at the single-sEV level. We screened the potential biomarkers using the Panel260 (the panel that detects 260 proteins) of PBA in Cohort 1, and validated them using Panel550 (the panel that detects 550 proteins) in Cohort 2. Results: Plasma exosome counts were significantly elevated in TC compared with those in HC in both Cohort 1 and Cohort 2. Receiver operating characteristic curve analysis showed that sEV counts exhibited an area under the curve > 0.75 in both cohorts. The sEV proteomic analysis revealed that sEV epithelial cell adhesion molecule (EPCAM) levels were significantly increased, whereas claudin-11, integrin alpha X, and lymphocyte-activating 3 were significantly decreased in TC compared with HC. The increase in EPCAM in the plasma and tumor tissues was confirmed by enzyme-linked immunosorbent assay and immunohistochemistry analyses, respectively. The sEV subpopulation analysis further demonstrated that EPCAM[+] sEVs were significantly elevated in TC compared with HC in both cohorts. The reduction in sEV counts was observed in 18 out of 20 patients after the operation. The decrease in EPCAM[+] sEVs was observed in 20 patients with TC post-operatively, whereas the reduction in the conventional biomarker serum thyroglobulin (Tg) was observed in 14 patients. TC-derived plasma sEVs promoted TC cell proliferation, migration, invasion, and TC xenograft growth. Conclusion: EPCAM[+] sEVs could serve as a promising biomarker for the early diagnosis of TC and perform better in monitoring post-operative remission of TC than serum Tg.}, }
@article {pmid41551220, year = {2025}, author = {Réblová, M and Nekvindová, J and Hernández-Restrepo, M and Hradilová, M and Kolařík, M}, title = {Phylogeny, taxonomy and geographic distribution of novel and known fungi with holoblastic-denticulate conidiogenesis in Rhamphoriales and Pleurotheciales (Sordariomycetes).}, journal = {Persoonia}, volume = {55}, number = {}, pages = {277-311}, pmid = {41551220}, issn = {0031-5850}, abstract = {As part of a broader survey of lignicolous saprobic fungi, we investigated fungal taxa from the class Sordariomycetes displaying holoblastic-denticulate conidiogenesis, a distinct developmental process and phylogenetically informative trait. Although these fungi appear morphologically similar in culture, they represent distinct evolutionary lineages. This taxonomic study integrates comparative morphological analyses, phylogenetic reconstruction of five nuclear markers, and analysis of biogeographical patterns through environmental DNA data to introduce novel taxa in the Pleurotheciales and Rhamphoriales. A new genus and species Echinodenticula allantospora and three new species, Phaeoisaria parallela, Rhamphoriopsis cuprea and Rh. denticulata, are described. A rarely encountered species Rhamphoria separata is reported, along with its previously undocumented asexual morph. Furthermore, we successfully demonstrate the utility of two protein-coding genes, rpb2 and tef1, as complementary barcodes for distinguishing closely related Phaeoisaria species. Our findings highlight the significance of holoblastic-denticulate conidiogenesis as a diagnostic feature of the Rhamphoriales and a prevalent trait in the Pleurotheciales. An unknown ascomycete that produced only sterile mycelium in culture is described here as Melanocrypta curvata and placed at an incertae sedis position within the Sordariomycetes. Additionally, we present short-read whole-genome sequencing data for the ex-type strains of the newly described species, providing a valuable genomic resource for future taxonomic, phylogenetic, and functional studies. Environmental DNA data from the GlobalFungi database bring new perspective into the biogeographical patterns of Phaeoisaria, Rhamphoria, and Rhamphoriopsis. The distribution of E. allantospora and M. curvata remains poorly understood, as no records for these species were found in GlobalFungi. This study provides new insights into the molecular systematics, taxonomy, and biogeography of the Rhamphoriales and Pleurotheciales, and highlights the role of environmental DNA metabarcoding in uncovering fungal diversity and distribution patterns. Citation: Réblová M, Nekvindová J, Hernández-Restrepo M, Hradilová M, Kolařík M (2025). Phylogeny, taxonomy and geographic distribution of novel and known fungi with holoblastic-denticulate conidiogenesis in Rhamphoriales and Pleurotheciales (Sordariomycetes). Persoonia 55: 277-311. doi: 10.3114/persoonia.2025.55.08.}, }
@article {pmid41550687, year = {2026}, author = {Back, J and Bang, HW}, title = {A new genus of Orthopsyllidae Huys, 1990 (Copepoda, Harpacticoida) from the Pacific Ocean.}, journal = {ZooKeys}, volume = {1266}, number = {}, pages = {137-192}, pmid = {41550687}, issn = {1313-2989}, abstract = {This study reports the discovery of four new benthic harpacticoids from Korean waters in the Pacific Ocean. The harpacticoids were collected using SCUBA or a grab sampler and sorted using a stereomicroscope for both molecular and morphological analysis. The study employed standard DNA sequencing methods (COI and 18S rRNA) and detailed morphological characterization through microscopy and scanning electron microscopy. As a result, three new species belonging to the family Orthopsyllidae and classified as a new genus were discovered. Although the new genus lacks brush setae on leg 1, a diagnostic feature of Orthopsyllidae, it shares similarities with other orthopsyllids in characters such as the large thorn-like process on the antennule, leg 5, and sexual dimorphism. This finding necessitates an expanded diagnosis of Orthopsyllidae to reflect the characters of the new genus based on the three new species. In addition, a new species belonging to the genus Orthopsyllus was discovered. This study is the first to describe a new species of Orthopsyllus from Korea, where the genus has not been previously reported at the species level. This study provides a key for classifying genera and species within the Orthopsyllidae family.}, }
@article {pmid41546775, year = {2026}, author = {Debnath, R and Rajmohana, K and Dinesh, KP}, title = {A new species of Telenomus Haliday (Hymenoptera: Scelionidae) and a novel host association with Creatonotos transiens (Walker) (Lepidoptera: Erebidae) in India.}, journal = {Systematic parasitology}, volume = {103}, number = {1}, pages = {5}, pmid = {41546775}, issn = {1573-5192}, support = {CRG/2021/005047//DST-SERB, Govt. of India/ ; }, mesh = {Animals ; India ; *Moths/parasitology ; Species Specificity ; *Wasps/classification/anatomy &amp; histology/genetics ; DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; Phylogeny ; Female ; *Hymenoptera/classification/anatomy &amp; histology/genetics ; Male ; }, abstract = {Telenomus hexodon Debnath &amp; Rajmohana sp. nov. (Hymenoptera: Scelionidae), is described as new to science. The species was reared from eggs of the polyphagous pest Clouded Tiger moth, Creatonotos transiens (Walker) (Lepidoptera: Erebidae). This represents the first record of an insect parasitoid association with C. transiens. Host identity was confirmed through DNA barcoding, while the parasitoid was characterized using an integrative taxonomic approach combining morphological and molecular data. Further, a checklist of Telenomus species reported from India is provided.}, }
@article {pmid41546422, year = {2026}, author = {Tang, Q and Yu, H and Hou, J and Jiang, M and Zhang, Z and Wang, J and Zhang, M and Han, D and Guo, P}, title = {Spatial Mapping of Membrane Protein Interactions Using a DNA Origami Rubbing.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e13795}, doi = {10.1002/anie.202513795}, pmid = {41546422}, issn = {1521-3773}, support = {XDB1020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 22304176//National Natural Science Foundation of China/ ; 32341017//National Natural Science Foundation of China/ ; 22225402//National Natural Science Foundation of China/ ; 22374132//National Natural Science Foundation of China/ ; 2024R01005//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang Province/ ; KF2101//State Key Laboratory of Fine Chemicals, Dalian University of Technology/ ; }, abstract = {Revealing the protein-protein interactions (PPIs) of membrane proteins is as challenging as their structural reconstruction, primarily because the molecular structures and related PPIs of membrane proteins are highly dependent on the bio-membrane where they are situated. DNA origami offers a platform for manipulating molecules with nanoscale precision. Herein, we used a square-like DNA origami, refer to as DNA origami rubbing, to map the two-dimensional distribution of membrane proteins in situ. Through artificial models and cell studies, we correlated the efficiency of barcode recording of DNA origami rubbings with the distance between adjacent proteins, and we observed that the frequency of adjacent proteins mapped by DNA origami rubbings was correlated to the abundance of the bait protein. We demonstrated that the DNA origami rubbing was able to reflect the distribution change of adjacent proteins caused by adding the ligand of bait protein. Our results suggested that the DNA origami rubbing can serve as a powerful tool in the field of protein interactomics.}, }
@article {pmid41544931, year = {2026}, author = {Romariz, APPL and da Silva, DT and Benassi, JC and Leonel, JAF and Spada, JCP and Rodrigues, CMF and Pérez, HAG and de Almeida Paula, NF and Teixeira, MMG and de Sousa Oliveira, TMF and Buzetti, WAS}, title = {Water buffaloes (Bubalus bubalis): potential reservoirs of trypanosomatids in endemic areas.}, journal = {Parasitology international}, volume = {}, number = {}, pages = {103242}, doi = {10.1016/j.parint.2026.103242}, pmid = {41544931}, issn = {1873-0329}, abstract = {Trypanosomatids are protozoan parasites that include the genera Trypanosoma and Leishmania, which infect a wide range of mammalian species, including humans and ruminants. This study aimed to assess the presence of Trypanosomatid parasites in water buffaloes (Bubalus bubalis) using molecular techniques. Blood samples and conjunctival swabs from the right and left eyes were collected from 100 buffaloes (44 females and 56 males). PCR analysis detected Trypanosomatids in 32% (32/100) of the buffaloes: 29% (29/100) tested positive for DNA extracted from blood, and 4% (4/100) tested positive from conjunctival swab samples. Using the Fluorescent Fragment Length Barcoding (FFLB) technique, 38% (38/100) of blood samples were positive for Trypanosomatids, with 35% (35/100) identified as Trypanosoma theileri and 3% (3/100) as Trypanosoma vivax. Direct sequencing and analysis of PCR amplicons from four buffaloes revealed that three samples matched 100% with Trypanosoma theileri, while one matched 100% with Leishmania infantum. Our findings confirm that buffaloes can serve as hosts for Trypanosomatids and support previous observations that these parasites are often underdiagnosed. This is the first report of Leishmania infantum DNA in buffalo conjunctival swabs in Brazil and the first detection of Trypanosoma vivax DNA in buffaloes in the city of Andradina and in São Paulo state. These findings underscore the need for further studies to clarify the role of buffaloes in the epidemiology and dissemination of trypanosomatids in livestock populations.}, }
@article {pmid41542514, year = {2026}, author = {Hornick, AC and Walters, LC and Dobson, CS and Gaglione, SA and Birnbaum, ME}, title = {Interrogating antiviral antibody responses with multiplexed, high-throughput serum assays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.03.697501}, pmid = {41542514}, issn = {2692-8205}, abstract = {The COVID-19 pandemic underscored the importance of rapidly analyzing antibody responses against emerging viruses. Existing techniques, however, are limited in their ability to probe antibodies' recognition of multiple native-conformation antigens simultaneously. To increase the throughput and multiplexability of antibody profiling, we developed A ntibody R eactivity C haracterization by A ntibody- D ependent E nhancement (ARCADE). This assay employs an antigen-agnostic Fc receptor-expressing cell line and a library of antigen-displaying, genetically barcoded lentiviruses that, when mixed with serum, infect cells and integrate their barcodes at rates reflecting the relative abundances and affinities of the antigen-specific antibodies present. Verified using sera from COVID-19-convalescent and - vaccinated donors, ARCADE delivers insights that align with and expand upon those offered by established immunoassays, highlighting, for example, how an mRNA-based vaccine elicits broader and stronger antibody responses than an adenovirus vector-based vaccine. ARCADE can comprehensively assess how infection and vaccination impact antiviral antibody repertoires over time and across patient populations.}, }
@article {pmid41542380, year = {2026}, author = {Vallin, H and Fraser, M and Pakeman, RJ and Hipperson, H}, title = {Evaluating the Quantitative Accuracy and Application of DNA Metabarcoding for Dietary Reconstruction in Ruminants.}, journal = {Ecology and evolution}, volume = {16}, number = {1}, pages = {e72878}, pmid = {41542380}, issn = {2045-7758}, abstract = {DNA metabarcoding offers a powerful, non-invasive tool to identify dietary composition with high taxonomic resolution, yet its quantitative accuracy and bias remain a well-recognised limitation across taxa and sample types. This universal challenge is particularly evident in herbivores, where plant material introduces additional amplification constraints. This study evaluates the accuracy of DNA metabarcoding in reconstructing the diets of sheep under controlled feeding trials involving high and low digestibility forage, using two widely used plant DNA barcodes (ITS2 and trnL). A secondary trial tested the detectability and proportional representation of a target species, Medicago sativa, when added to the diet in varying amounts (1%, 5%, 10%). ITS2 provided greater species-level resolution, while trnL showed broader taxonomic coverage but reduced precision. Both markers distinguished diet treatments effectively; however, faecal DNA showed proportional discrepancies from vegetation input, particularly under low-digestibility conditions. M. sativa was reliably detected even at 1% inclusion but was consistently overrepresented in sequence reads. Our findings highlight the strengths and limitations of DNA metabarcoding for herbivore diet studies and underscore the importance of marker choice and the effects of differential digestion biases. These findings demonstrate the need for multi-marker approaches and calibration controls in dietary studies, especially when quantitative interpretation is required. Despite limitations in quantitative accuracy, faecal DNA metabarcoding provides valuable insights into herbivore diet composition and preferences, with future refinements expected to improve its resolution and reliability for ecological monitoring and grazing management.}, }
@article {pmid41541251, year = {2025}, author = {Wu, Y and Liu, R and Wang, WJ and Li, DZ and Burgess, KS and Yu, WB and Wang, H}, title = {High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites.}, journal = {Plant diversity}, volume = {47}, number = {6}, pages = {920-930}, pmid = {41541251}, issn = {2468-2659}, abstract = {Complete plastid genomes have been proposed as potential "super-barcodes" for plant identification and delineation, particularly in cases where standard DNA barcodes may be insufficient. However, few studies have systematically addressed how taxonomic complexity, especially in rapidly radiating lineages with intricate evolutionary histories, might influence the efficacy of plastome-scale barcodes. Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains, and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus. Therefore, Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity. In this study, we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes. Our results revealed that the traditional standard barcode combination (nrITS + matK + rbcL + trnH-psbA) achieved the highest discrimination rates (81.25%), closely followed by the plastid large single copy (LSC) region (80.21%), then by full plastome, the supermatrix of protein-coding genes, and hypervariable regions (79.17%). Notably, the matK and ycf1 gene alone could discriminate 78.13% of species. Key determinants of species discrimination by integrating alignment length (AL) and the proportion of parsimony-informative sites (PPIS), as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity. Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes, this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis' specific biological habits and potentially reflecting unique evolutionary patterns in the plastid genome.}, }
@article {pmid41540123, year = {2026}, author = {Enninful, A and Zhang, Z and Klymyshyn, D and Ingalls, M and Yang, M and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Lu, Y and Bao, S and Deng, S and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R}, title = {Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {41540123}, issn = {1548-7105}, support = {U54CA274509//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA245313//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; U54CA268083//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; UH3CA257393//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1MH128876//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54AG079759//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54AG076043//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RM1MH132648//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01CA294514//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 2245575//Center for Selective C-H Functionalization, National Science Foundation/ ; 2245575//Center for Selective C-H Functionalization, National Science Foundation/ ; 2345215//National Science Foundation (NSF)/ ; 2245575//National Science Foundation (NSF)/ ; }, abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can profoundly advance our understanding of cellular heterogeneity and function. Here we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multimodal spatial omics approach combining sequencing-based spatial transcriptomics and multiplexed protein imaging on the same section, enabling both single-cell-resolution cell typing and transcriptome-wide interrogation of biological pathways. DBiTplus utilizes spatial barcoding and RNase H-mediated cDNA retrieval, preserving tissue architecture for multiplexed protein imaging. We developed computational pipelines to integrate these modalities, allowing imaging-guided deconvolution to generate single-cell-resolved spatial transcriptome atlases. We demonstrate DBiTplus across diverse samples including frozen mouse embryos, and formalin-fixed paraffin-embedded human lymph nodes and lymphoma tissues, highlighting its compatibility with challenging clinical specimens. DBiTplus uncovered mechanisms of lymphomagenesis, progression and transformation in human lymphomas. Thus, DBiTplus is a unified workflow for spatially resolved single-cell atlasing and unbiased exploration of biological mechanisms in a cell-by-cell manner at transcriptome scale.}, }
@article {pmid41539929, year = {2026}, author = {Li, X and Zheng, J and Fang, X and Gao, W and Chen, H and Liu, Z and Li, C and Zhang, R}, title = {Multiple microRNAs analysis based on DNAzyme cascade DNA fiber barcodes for cell typing.}, journal = {Biosensors &amp; bioelectronics}, volume = {}, number = {}, pages = {118383}, doi = {10.1016/j.bios.2026.118383}, pmid = {41539929}, issn = {1873-4235}, abstract = {Accurate tumor subtyping through multiplex miRNA profiling is critical for precision medicine but remains challenging due to limitations in current methods, including cross-reactivity, cost, and stability. Herein, we present a DNAzyme-powered DNA fiber barcode platform that combines G-quadruplex (G4)/hemin catalysis, miRNA-responsive displacement, and polydopamine (PDA)-mediated fluorescence modulation for sensitive and specific miRNA detection. The system operates via a target-dependent "switch": in the absence of target miRNAs, G4/hemin DNAzymes catalyze dopamine (DA) oxidation into PDA that efficiently quench fluorescence through Förster resonance energy transfer (FRET); when target miRNAs are present, they competitively binding to the capture strands on DNA fibers with higher affinity, displacing the G4 structures, inhibiting DNAzyme formation and preserving the fluorescence signal, with fluorescence intensity showing a positive correlation with target concentration. This mechanism enables dual qualitative and quantitative analysis with a broad linear range (50 pM-100 nM) and low detection limits (5.50 pM). Key advantages include stable, tunable G4/hemin transduction, enhanced kinetics and signal-to-noise through synergistic displacement-quenching, and multicolor barcoding for one-pot multiplex miRNA detection. Validated against qPCR with high concordance, this platform overcomes existing technical barriers to enable robust miRNA-based cell typing classification and precision diagnostics.}, }
@article {pmid41539305, year = {2026}, author = {Kurochkin, I and Altman, AR and Caiado, I and Pértiga-Cabral, D and Halitzki, E and Minaeva, M and Zimmermannová, O and Henriques-Oliveira, L and Klein, D and Nair, M and Oliveira, D and Cajal, LR and Knittel, R and Feick, C and Ringnér, M and Martin, M and Cirovic, B and Pires, CF and Rosa, FF and Sitnicka, E and Theis, FJ and Pereira, CF}, title = {A combinatorial transcription factor screening platform for immune cell reprogramming.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101457}, doi = {10.1016/j.cels.2025.101457}, pmid = {41539305}, issn = {2405-4720}, abstract = {Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode's discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.}, }
@article {pmid41538080, year = {2026}, author = {Juhász, A and Makaula, P and Cunningham, LJ and Nkolokosa, C and Archer, J and Jones, S and Namacha, G and Chammudzi, P and Mainga, B and Lally, D and Kayuni, SA and LaCourse, EJ and O'Ferrall, AM and Musaya, J and Stothard, JR}, title = {One Health insights into local transmission of zoonotic Schistosoma mattheei in southern Malawi.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1941}, pages = {}, doi = {10.1098/rstb.2024.0519}, pmid = {41538080}, issn = {1471-2970}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Malawi/epidemiology ; *Schistosoma/genetics/physiology ; *Schistosomiasis/transmission/veterinary/parasitology/epidemiology ; Cattle ; Humans ; *Zoonoses/transmission/parasitology/epidemiology ; *Cattle Diseases/parasitology/transmission/epidemiology ; Snails/parasitology ; Goats ; *One Health ; *Goat Diseases/parasitology/transmission/epidemiology ; Praziquantel/therapeutic use ; Prevalence ; Haplotypes ; }, abstract = {Schistosoma mattheei is a zoonotic schistosome species in central and southern Africa and is of increasing public health concern in southern Malawi. To gain insight into its local transmission, we investigated the biology of Schistosoma mattheei in southern Malawi, integrating epidemiological, environmental and genetic data within a One Health framework. Cattle, goats, humans and snails were surveyed, with DNA barcoding revealing nine mitochondrial S. mattheei haplotypes. Two haplotypes were shared across species, indicating cross-host transmission. Infected snails were detected year-round, with seasonal variation linked to vegetation cover (Normalized Difference Vegetation Index (NDVI)). Praziquantel (40 mg kg-1) treatment in selected cattle herds reduced infection prevalence over 12 weeks. These findings highlight the zoonotic potential of S. mattheei and the need for integrated control strategies. This article is part of the Royal Society Science+ meeting issue 'Parasite evolution and impact in action: exploring the importance and control of hybrid schistosomes in Africa and beyond'.}, }
@article {pmid41538056, year = {2026}, author = {Rehman, U and Sarfraz, M and Bibi, F and Noor, A and Ullah, M and Tarafder, E and Shinwari, ZK}, title = {DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {2}, pages = {40}, pmid = {41538056}, issn = {1572-9699}, mesh = {*DNA Barcoding, Taxonomic/methods/trends ; *Phylogeny ; *Agaricales/genetics/classification ; Genomics/methods ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Metabolomics ; }, abstract = {Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.}, }
@article {pmid41536623, year = {2026}, author = {Noenrimnong, C and Suttinun, C and Tungpairojwong, N and Boonsoong, B}, title = {Taxonomic insights into the diversity of Cloeon Leach, 1815 (Ephemeroptera, Baetidae) in Thailand.}, journal = {ZooKeys}, volume = {1266}, number = {}, pages = {1-39}, pmid = {41536623}, issn = {1313-2989}, abstract = {Four species of the genus Cloeon have previously been reported in Thailand: C. bicolor Kimmins, 1947, C. bimaculatum Eaton, 1885, C. harveyi (Kimmins, 1947) and C. marginale Hagen, 1858. However, since 1961, no systematic studies or investigations of this genus have been conducted in that country. This study reviews Cloeon Leach, 1815 in Thailand and investigates five species-C. bengalense, C. bicolor, C. harveyi, C. rubellum, and C. viridulum-based on morphological, molecular, and taxonomic analyses. Three species (C. bengalense, C. rubellum, and C. viridulum) are recorded for the first time in Thailand, and C. rubellum is described for the first time as a mature nymph and adult female. Additionally, the egg chorionic surface of all five species is described for the first time, and its use is demonstrated for species identification in Thailand. A key to the species of Cloeon in Thailand is provided based on the egg structure, mature nymph, and adult female and male.}, }
@article {pmid41536601, year = {2025}, author = {Schmidt-Stohn, G and Bellanger, JM and Brandrud, TE and Bidaud, A and Oertel, B and Saar, G and Ballarà, J and Carteret, X and Reyes García, JDD and Dondl, M and Ploch, S and Thines, M and Dima, B}, title = {The big brown Telamonia unlocked: four new species in Cortinarius section Bovini (Agaricales, Basidiomycota) and a revised taxonomy of bovinoid Cortinarii.}, journal = {Persoonia}, volume = {55}, number = {}, pages = {1-57}, pmid = {41536601}, issn = {0031-5850}, abstract = {In this study, we describe four species of Cortinarius subgen. Telamonia sect. Bovini as new to science: Cortinarius acutipes, C. cepiformis, C. schistaceus and C. sericeovelatus. We also provide updated descriptions and synonymies for several known species in the section, including C. pachypus (formerly C. terribilis and C. pseudobulbosus), C. sordescens (neotypified here), C. turgidulus and C. urbis-veteris, as well as for C. hillieri, here supported as a genuine Bovini member. In addition, through DNA sequencing of its holotype, we fix here the interpretation of C. aprinus, the iconic member of a difficult group of large, fleshy, grey brown Telamonia species often referred to as Aprini or Sordescentes. We also update the taxonomy of C. diffractosuavis (sect. Sordescentes) and C. testaceomicaceus (sect. Exsulares), to yield a most comprehensive overview of phylogenetically supported "bovinoid" species from deciduous forests on calcareous soils of Europe. The habitat and distribution of all treated species are presented, and a tentative identification key is also proposed. Citation: Schmidt-Stohn G, Bellanger J-M, Brandrud TE, Bidaud A, Oertel B, Saar G, Ballarà J, Carteret X, Reyes García JdD, Dondl B, Ploch S, Thines M, Dima B (2025). The big brown Telamonia unlocked: four new species in Cortinarius section Bovini (Agaricales, Basidiomycota) and a revised taxonomy of bovinoid Cortinarii. Persoonia 55: 1-57. doi: 10.3114/persoonia.2025.55.01.}, }
@article {pmid41535733, year = {2026}, author = {Wang, Y and Liu, H and Zhao, D and Wang, S and Wang, J and Chi, X and Zhang, C and Wang, T and Lyu, C and Kang, C and Sun, J and Guo, L and Huang, L}, title = {Assessment of suitable cultivation area for Paris polyphylla var. chinensis and var. yunnanensis under anthropogenic disturbance based on ensemble modeling and germplasm identification.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-025-08010-7}, pmid = {41535733}, issn = {1471-2229}, support = {2023YFC3503801//National Key Research and Development Program of China/ ; }, }
@article {pmid41534951, year = {2026}, author = {Lichtner, V and Irnazarow, A and Bush, S and Dowding, D and Elphick, P and Franklin, BD and Jani, YH and Songhurst, M}, title = {Complexities and capabilities of Scan4Safety in NHS hospitals: a qualitative study of a national demonstrator site.}, journal = {BMJ health &amp; care informatics}, volume = {33}, number = {1}, pages = {}, doi = {10.1136/bmjhci-2024-101366}, pmid = {41534951}, issn = {2632-1009}, mesh = {Qualitative Research ; Humans ; *State Medicine ; Interviews as Topic ; United Kingdom ; *Hospitals ; Patient Safety ; }, abstract = {OBJECTIVES: Data standards and barcoding technologies are implemented in hospitals to uniquely identify objects, people and locations; streamline the management of supplies and inventories; improve efficiency; reduce waste and improve patient safety and quality of care. This study examined the implementation of the Scan4Safety programme at one NHS demonstrator site to understand the hospital experience of adopting these standards, barcoding and related technologies.<br><br>METHODS: Exploratory case study design, informed by information infrastructure theory, at one Scan4Safety demonstrator site. Semi-structured interviews were conducted with internal and external stakeholders (n=19), and 67 documents related to the Scan4Safety programme were identified. Interview transcripts and documents underwent thematic analysis.<br><br>RESULTS: Key enablers for Scan4Safety included allocated funding, government role/regulation, executive buy-in/wide stakeholder involvement, patient focus, agile/adaptive approach and data linkage. Challenges were both internal and external, mainly pertaining to data quality, work-as-done and trade-offs. Mechanisms of anticipated positive outcomes and potential risks were also identified.<br><br>DISCUSSION: Scan4Safety benefits are delivered through tracking and tracing capabilities, and automating data capture, alerts and data linkages. For traceability of devices, the benefits depend on the extent to which items are tracked in inventory and consistent barcode scanning at the point of care.<br><br>CONCLUSIONS: Linked standards for identification of patients, products, places and procedures, across supplies and hospital processes, constitute a wide-ranging information infrastructure with the potential for significant value to patients and the whole health system.}, }
@article {pmid41532186, year = {2026}, author = {Mur, M and Kavčič, A and Jagodič, U and Podlipec, R and Humar, M}, title = {Two-Photon 3D Printing of Functional Microstructures Inside Living Cells.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e19286}, doi = {10.1002/adma.202519286}, pmid = {41532186}, issn = {1521-4095}, support = {851143//HORIZON EUROPE European Research Council/ ; N1-0362//The Slovenian Research and Innovation Agency/ ; P1-0099//The Slovenian Research and Innovation Agency/ ; }, abstract = {3D printing is transforming manufacturing and biomedicine, yet it has not been demonstrated inside living cells. Additionally, there is no method to deliver micron-scale, free-standing solid microstructures directly into the cytosol of non-phagocytic cells. Here, both of these challenges are addressed by fabricating custom-shaped polymeric microstructures directly inside living cells using two-photon polymerization. A bio-compatible photoresist is injected into cells and selectively polymerized with a femtosecond laser, creating intracellular structures with submicron resolution. Structures of various shapes are printed in live cells, including a 10 μ m $\umu {\rm m}$ elephant, barcodes for cell tracking, diffraction gratings for remote readout, and microlasers. The printed structures in cells can affect the cell biology. The demonstrated top-down intracellular biofabrication approach, combined with functional photoresists, may enable new applications in intracellular sensing, biomechanical manipulation, bioelectronics, and targeted drug delivery. These embedded structures could provide novel control over the intracellular environment, allowing engineering of cellular properties beyond natural limits and genetic engineering.}, }
@article {pmid41366305, year = {2025}, author = {Tsafack, DT and Monamele, CG and Koro Koro, F and Essengue, LLM and Mounchili-Njifon, A and Esso, L and Njankouo Ripa, M and Touoyem, PI and Mouliem, JLM and Tamoufe, U and Moumbeket-Yifomnjou, MH and Njouom, R}, title = {Whole-genome analysis of influenza A(H1N1)pdm09 viruses in Cameroon (2019-2024) using nanopore sequencing.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {53}, pmid = {41366305}, issn = {1471-2334}, abstract = {BACKGROUND: Since 2019, Cameroon has reported a high number of seasonal influenza cases caused by the A(H1N1)pdm09 subtype, which remained the predominant global strain as of 2024.<br><br>METHODS: To characterize the evolutionary dynamics of circulating A(H1N1)pdm09 viruses, whole-genome sequencing was conducted using Oxford Nanopore Technologies, with multiplexing native barcode expansion kits. DNA repair and end preparation were performed using the NEBNext Ultra II End-Repair/dA-tailing kit. Phylogenetic trees for HA genes segments were inferred using the maximum likelihood (ML) method implemented in IQ-TREE v3.0.1under the LG&#x2009;+&#x2009;F&#x2009;+&#x2009;G4 substitution model. Additionally, Mutation analysis was performed across all eight gene segments using MEGA with A/Wisconsin/67/2022 (A/H1N1pdm09) serving as the reference strain. Identified amino acid substitutions were annotated and their potential phenotypic effects were evaluated using FluSurver.<br><br>RESULTS: All Cameroonian A(H1N1)pdm09 strains from 2019 to 2024 belonged to subclade 6B.1A.5a.2a. Phylogenetic analysis revealed annual divergence from Northern Hemisphere vaccine strains, suggesting a mismatch with locally circulating variants. Several functionally relevant mutations were identified in the viral genes, including A3L, A214T, and F12V in HA; R159K and A267V in PA; A241E and T137A in M2; I42L and V7I in NS1; and I84V and I33V in PB1. Many of these mutations have been associated with increased virulence. In addition, amino acid substitutions were observed in the NA protein at V13I, S200N, L339S, S37T, V80M, and I163V, relative to the 2024 vaccine strain A/Wisconsin/67/2022.Overall, the number of amino acid mutations between circulating strains and the vaccine strain was notably high, indicating that local viruses may be evolving away from the vaccine strain selected for the 2023&#x2013;2024 season.<br><br>CONCLUSIONS: These findings underscore the ongoing genetic evolution of the influenza A(H1N1)pdm09 virus in Cameroon and highlight the importance of local genomic data into the selection of WHO vaccine candidate strains for the Northern Hemisphere.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-12284-5.}, }
@article {pmid41531910, year = {2026}, author = {Muirberry, J and Lancaster, LT}, title = {Global Changes in Lepidopteran Phylogenetic Diversity Across Space and Time.}, journal = {Ecology and evolution}, volume = {16}, number = {1}, pages = {e72557}, doi = {10.1002/ece3.72557}, pmid = {41531910}, issn = {2045-7758}, abstract = {Amidst increasing reports of insect declines, it is ever more important to understand spatial and temporal insect diversity patterns and processes. Phylogenetic diversity (PD) is an important biodiversity metric in that it relates strongly to ecosystem processes, and it can be estimated more accurately from opportunistic occurrence data than other elements of biodiversity. Here, we assess recent changes across global variation in Lepidopteran PD, to discover overall patterns, their repeatability across regions and environmental drivers. We assess global, spatiotemporal variation in PD, as compared to null expectations given sampling effort, determining how such variation relates to region, space, time and environment. Our analysis is based on 374,749 gene sequence accessions from the barcode of life database (BOLD), representing 3158 species assemblages, spanning 62 years. We find that global variation in PD of Lepidopteran species assemblages has significantly increased over time at high latitudes while remaining relatively unchanged near the equator. This pattern exhibits parallelism across global regions, with the strongest increases in PD towards the present observed in high-latitude communities in North America and Asia, in lowland sites in Europe, and across the African continent. In contrast, PD has declined through time in wetter portions of Australasia and in Africa and South America. Our reported patterns likely reflect changes in Lepidopteran responses to tropical habitat loss and widespread range expansions to higher latitudes. However, changing clines in DNA barcoding strategies could also play a role. Detecting spatiotemporal patterns of change in PD at the global scale is enabled by the increasing use of genetic markers in taxonomy. Our replicated findings provide confidence in biogeographic interpretation, yet increased metadata on sub-sampling decisions would aid future interpretation of biodiversity trends using ecological genomics synthesis.}, }
@article {pmid41531273, year = {2026}, author = {Lim, VC and Kanthaswamy, S and Malaivijitnond, S}, title = {DNA Barcoding Supports Mitochondrial Lineage Structure in the Genus Macaca With Implications for Biomedical Research and Laboratory Colony Management.}, journal = {Journal of medical primatology}, volume = {55}, number = {1}, pages = {e70054}, doi = {10.1111/jmp.70054}, pmid = {41531273}, issn = {1600-0684}, support = {//Second Century Fund (C2F), Chulalongkorn University/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Biomedical Research ; *Macaca/genetics/classification ; *DNA, Mitochondrial/genetics ; *Macaca fascicularis/genetics/classification ; }, abstract = {BACKGROUND: Cynomolgus macaques are widely used in biomedical research, yet the hybridisation between the subspecies M. f. fascicularis (Mff) and M. f. aurea (Mfa), and introgression from another species M. mulatta (Mm) may affect the research outcomes.<br><br>METHODS: DNA barcoding targeting COI mtDNA, as well as phylogenetic, pairwise distance and statistical analyses were employed to examine the relationships between Mff, Mfa and Mm using 52 newly sequenced and 59 public DNA barcodes representing 17 Macaca taxa and seven species groups.<br><br>RESULTS: DNA barcoding delineated the Macaca taxa, revealing genetic distinctions between Mff and Mfa greater than between Mff and Mm, as well as delineating geographical populations. This underscores the need for verification of laboratory individuals, besides genetic management of breeding colonies, as genetic differences can influence disease susceptibility and drug trial outcomes.<br><br>CONCLUSIONS: DNA barcoding offers a rapid, cost-effective tool to ensure appropriate selection and genetic management of laboratory individuals used in biomedical research.}, }
@article {pmid41530905, year = {2026}, author = {Kindree, K and Chochinov, CA and Bhachu, K and Cheng, Y and Caron, A and McDonald, M and Mamai, Z and Nguyen Ba, AN}, title = {Deep-mutational scanning libraries using tiled-region exchange mutagenesis.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkag006}, pmid = {41530905}, issn = {2160-1836}, abstract = {The analysis of gene function frequently requires the generation of mutants. Deep-mutational scanning (DMS) has emerged as a powerful tool to decipher important functional residues within genes and proteins. However, methods for performing DMS tend to be complex or laborious. Here, we introduce Tiled-Region Exchange (T-REx) Mutagenesis, which is a multiplexed modification of the EMPIRIC mutagenesis approach. Self-encoded removal fragments are cloned in parallel in non-overlapping gene locations and pooled. In a one-pot reaction, oligonucleotides are then swapped with their corresponding self-encoded removal fragments in bulk using a single Golden Gate reaction. To aid in downstream phenotyping, the library is then fused with unique DNA barcodes using the Bxb1 recombinase. We demonstrate this approach and its optimizations, to show that it is both easy to perform and efficient. This method offers simple and expedient means to create comprehensive mutagenesis libraries.}, }
@article {pmid41528854, year = {2026}, author = {Wang, J and Wang, B and Zhou, S and Cao, B and Li, W and Zheng, P}, title = {DNACSE: Enhancing Genomic LLMs with Contrastive Learning for DNA Barcode Identification.}, journal = {Journal of chemical information and modeling}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jcim.5c02747}, pmid = {41528854}, issn = {1549-960X}, abstract = {DNA barcoding is a powerful tool for exploring biodiversity, and DNA language models have significantly facilitated its construction and identification. However, since DNA barcodes come from a specific region of mitochondrial DNA and there are structural differences between DNA barcodes and reference genomes used to train existing DNA language models, it is difficult to directly apply the existing DNA language models to the DNA barcoding task. To address this, this paper introduces DNACSE (DNA Contrastive Learning for Sequence Embeddings), an unsupervised noise-contrastive learning framework designed to fine-tune the DNA language foundation model while enhancing the distribution of the embedding space. The results demonstrate that DNACSE outperforms the direct usage of DNA language models in DNA barcoding-related tasks. Specifically, in fine-tuning and linear probe tasks, it achieves accuracy rates of 99.17 and 98.31%, respectively, surpassing the current state-of-the-art BarcodeBERT by 6.44 and 6.44%. In zero-shot clustering tasks, it raises the adjusted mutual information (AMI) score to 92.25%, an improvement of 8.36%. In addition, zero-shot benchmarking and genomic benchmarking tests are evaluated, indicating that DNACSE enhances the performance of DNA language models in generalized genomic tasks. In summary, DNACSE has demonstrated excellent performance in DNA barcode species classification by making full use of multispecies information and DNA barcode information, providing a feasible way to further explore and protect biodiversity. The code repository is available at https://github.com/Kavicy/DNACSE.}, }
@article {pmid41528393, year = {2026}, author = {McPhail, BA and Veinot, HES and Podruzny, A and Shen, N and Tomusiak, S and Dodds, N and Hanington, PC}, title = {Integrating eDNA, molecular cercariometry, and snail surveys enhances characterization of digenetic trematode diversity.}, journal = {Parasitology research}, volume = {125}, number = {1}, pages = {8}, pmid = {41528393}, issn = {1432-1955}, support = {2018-05209 and 2018-522661//Natural Sciences and Engineering Research Council of Canada/ ; 2078//Alberta Innovates/ ; }, mesh = {*Trematoda/genetics/classification/isolation &amp; purification ; Animals ; *Snails/parasitology ; *DNA Barcoding, Taxonomic/methods ; Alberta ; *Biodiversity ; *DNA, Environmental/genetics ; Cercaria/genetics ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; }, abstract = {Traditional methods for studying digenetic trematode populations involve collecting the snail first intermediate hosts and either shedding larval cercariae or dissecting the snails. Because larval trematodes can be difficult to identify based on morphology alone, these methods are often supplemented with DNA sequencing. This approach can be labour-intensive, and environmentally disruptive. Metabarcoding of environmental DNA (eDNA) or cercariometry (counting of cercariae in water) samples offers an alternative method to simplify this process without negatively affecting the trematode community through the removal of parasites and hosts from the environment. Through ongoing trematode research in central Alberta, Canada, we have documented 102 trematode species infecting multiple snail species and have developed a database of sequences using several DNA barcoding genes. To understand how the trematode community composition derived from metabarcoding compares to a snail infection baseline, we examined the trematode species richness detected by each method. We also established a 16 S rDNA database using representative sequences to align our metabarcoding datasets with others in the field. We found no significant difference between eDNA and cercariometry samples regarding the ability of either method to estimate pooled trematode species richness, but cercariometry detected more species than eDNA when trematode richness was compared between sites. However, snail collections predicted lower species richness than both molecular methods. These findings indicate that the combination of these methods result in enhanced characterization of the trematode community. As more researchers adopt 16 S rDNA for digenetic trematode studies, metabarcoding will become an increasingly valuable tool for trematode surveillance and diversity assessments.}, }
@article {pmid41526574, year = {2026}, author = {Luo, P and Ma, Z and Wu, Q and Zhao, T and Shen, X}, title = {Efficient adaptive rotated object detection for 1D and QR barcodes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-34854-y}, pmid = {41526574}, issn = {2045-2322}, support = {GDRC202415//Natural Science Foundation of Top Talent of SZTU/ ; 20231128141501001//Shenzhen Science and Technology Program/ ; }, abstract = {This study introduces EA-OBB, a lightweight rotated object detection framework designed for detecting one-dimensional (1D) and Quick Response barcodes. Built upon the YOLO11 architecture, EA-OBB integrates several innovative modules-KWConv, ORPNCSPELAN, and LADH-OBB-to enhance both accuracy and computational efficiency in rotated object detection. The KWConv module utilizes a dynamic convolution kernel mechanism to improve rotational barcode feature extraction. The ORPNCSPELAN module enhances computational efficiency through multi-path feature aggregation and online re-parameterization. The LADH-OBB module decouples classification and regression tasks, improving the precision of rotation angle regression. To further adapt to resource-constrained environments, this study incorporates the Taylor Pruning algorithm, significantly reducing model parameters and computational costs. Experimental results on the RotBar dataset demonstrate the superior performance of EA-OBB, achieving an optimal balance of precision, recall, and computational complexity compared to existing methods.}, }
@article {pmid41526492, year = {2026}, author = {Xu, W and Hu, Y and Zhang, Y and Schnepp, PM and Lo, LM and Zhang, Q and Cheng, SM and Chen, X}, title = {Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {41526492}, issn = {1750-2799}, abstract = {Multimodal profiling of different molecular layers from the same single cell enables more comprehensive characterization of cellular heterogeneity compared with conventional single-modality approaches. A key example is co-detection of chromatin accessibility and gene expression that offers the opportunity to investigate cell type-resolved gene regulatory mechanisms. Here we describe a sensitive and robust protocol for in situ sequencing hetero RNA-DNA-hybrid after assay for transposase-accessible chromatin using sequencing (ISSAAC-seq) for the concurrent measurement of chromatin accessibility and gene expression from the same single nucleus. The method begins with dual Tn5 tagging of open chromatin regions and the RNA-cDNA hybrid produced by reverse transcription that take place in bulk nuclei. Then, various single-nucleus isolation strategies, including plate and droplet barcoding-based approaches, can be used based on the experimental purpose of the user. The protocol is highly modular with a flexible throughput ranging from several hundreds to tens of thousands of nuclei. The generated data are of high quality in both modalities. The entire workflow can be finished within 1 or 2 days, and the procedures work on multiple different single-nucleus isolation and barcoding platforms.}, }
@article {pmid41524665, year = {2026}, author = {Pibaque, P and Porporato, G and Cescutti, S and Cruz-Flores, A and Busche, T and Winker, A and Rapp, TM and Bergkamp, P and Doneva, A and Chakarov, N}, title = {Domination Versus Sisterhoods in the Blood Microbiota of Migrating Birds: Patterns of Within- and Between-Individual Blood Parasite Diversity Revealed Through Metabarcoding.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70056}, pmid = {41524665}, issn = {1749-4877}, abstract = {Avian blood parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon are typically identified through Sanger sequencing of a partial cytochrome b fragment, the MalAvi barcoding region. This approach limits the detection of mixed infections and the relative frequencies of co-infecting parasites. In contrast, next-generation sequencing (NGS) can resolve these problems but has been underused for haemosporidian lineage identification in samples from the wild. We used an improved PCR protocol and sequencing with Illumina MiSeq to determine haemosporidian assemblages in wild birds captured at a migration stopover site in Bulgaria, Europe. From 406 samples obtained from 52 bird species, we detected 81 haemosporidian lineages in 131 infected samples from 32 species (32% prevalence). On average, individuals were infected with 2.4 lineages, with 59 birds infected by a single lineage, and 21 birds infected with 5-9 lineages. A subset of samples was Illumina- and Sanger-sequenced in parallel, finding mixed infections in 72 samples and 8× higher detection rate of mixed and co-infections through high-throughput sequencing. Both methods identified the same dominant (co-infecting) lineage (91%). Metabarcoding identified common mixed infections of sister lineage groups ("sisterhoods") known for prevalent lineages and morphospecies, including Plasmodium relictum p_SGS1, Haemoproteus motacillae h_YWT2, and Haemoproteus parabelopolskyi h_SYAT01. Some other lineages appeared consistently more dominant. Our study shows that in some host communities, metabarcoding can reveal a great diversity of mixed infections. This opens new horizons to the study of assemblages of haemosporidian parasites, their interactions within individual hosts, and co-evolution with other members of the blood microbiome and the hosts.}, }
@article {pmid41522876, year = {2025}, author = {Crous, PW and Groenewald, JZ and Bensch, K and Gené, J and Guarro, J}, title = {Genera of phytopathogenic fungi known from culture: 1-379.}, journal = {Studies in mycology}, volume = {112}, number = {}, pages = {261-633}, pmid = {41522876}, issn = {0166-0616}, abstract = {Approximately 200000 species of fungi have been described to date, representing nearly 8000 currently recognised genera. Many of these genera are regarded as plant pathogenic, as they include at least one species proven to cause pre- or postharvest plant disease. Following the abandonment of dual nomenclature and the advent of DNA sequencing and phylogenetic approaches, numerous para- and polyphyletic clades were resolved into distinct genera. These genera are now defined based on morphology, ecology, and DNA phylogeny. The present paper represents the first in a series that aims to provide descriptions, classification, illustrations, significant species, disease symptoms, and DNA data for the common genera of phytopathogenic fungi known from culture, including the first treatment of 379 genera. In addition, several new combinations, lecto-, epi-, or neotypes are also proposed. Taxonomic novelties: New combinations: Anisogramma coryli (Batsch) Crous, Helostroma bacarum (Buhagiar) Aime &amp; Bensch, Hymenella cerealis (Ellis &amp; Everh.) Crous &amp; J.Z. Groenew., Hypomyces multiseptatus (de Hoog) Crous &amp; Bensch, Hypomyces verticillatus (Link) Crous &amp; Bensch, Mastigocladium capsici (S.Q. Tong &amp; Y.J. Wu) Lin Zhao &amp; Crous, Mastigocladium lepidopterorum (L.W. Hou et al.) Lin Zhao &amp; Crous, Microstroma glucosiphilum (T. Kij. &amp; Aime) Aime &amp; Bensch, Paraconiothyrium coniothyrium (Fuckel) Crous &amp; Bensch, Sclerophomella aquilegiicola (M. Petrov) Crous &amp; Bensch, Sclerophomella clematidina (Thüm.) Crous &amp; Bensch, Sclerophomella clematidis-rectae (Petr.) Crous &amp; Bensch, Sclerophomella glaucii (Brunaud) Crous &amp; Bensch, Sclerophomella humulicola (Chaiwan et al.) Crous &amp; Bensch, Sclerophomella hydei (Maharachch. et al.) Crous &amp; Bensch, Sclerophomella parvula (L.W. Hou et al.) Crous &amp; Bensch, Sclerophomella petasitis (Tibpromma et al.) Crous &amp; Bensch, Sclerophomella rosae (Qian Chen et al.) Crous &amp; Bensch, Sclerophomella sandfjordenica (Crous &amp; Rämä) Crous &amp; Bensch, Sclerophomella vincetoxici (De Not.) Crous &amp; Bensch, Sclerophomella vodakii (E. Müll.) Crous &amp; Bensch; New name: Sclerophomella humuligena Crous &amp; Bensch for Calophoma humuli V. Thiyag. et al. New typifications (basionyms): Ascochyta pisi Lib., Cryptosphaeria glaucopunctata Grev., Diaporthe cubensis Bruner, Geotrichum candidum Link, Hymenula cerealis Ellis &amp; Everh., Lanosa nivalis Fr., Mauginiella scaettae Cavara, Phaeophleospora eugeniae Rangel, Pilidium acerinum Kunze, Seiridium marginatum Nees, Sphaeria melanostyla DC., Sporendonema sebi Fr., Tubercularia chaetospora Pat., Wallemia ichthyophaga Johan-Olsen. Citation: Crous PW, Groenewald JZ, Bensch K, Gené J, Guarro J (2025). Genera of phytopathogenic fungi known from culture: 1-379. Studies in Mycology 112: 261-633. doi: 10.3114/sim.2025.112.05.}, }
@article {pmid41522517, year = {2026}, author = {Rehsen, PM and Honka, MS and Impiö, M and Madge Pimentel, I and Leese, F and Beermann, AJ}, title = {Improving taxonomic resolution, biomass and abundance assessments of aquatic invertebrates by combining imaging and DNA megabarcoding.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20501}, pmid = {41522517}, issn = {2167-8359}, mesh = {Animals ; *Biomass ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; *Aquatic Organisms/classification/genetics ; *Invertebrates/genetics/classification ; Neural Networks, Computer ; *Insecta/genetics/classification ; Ecosystem ; }, abstract = {Understanding biodiversity change requires a comprehensive assessment of not only the identity of species inhabiting an ecosystem but also their biomass and abundance. However, assessing biodiversity on the species level with precise biomass information is a time-consuming process and thus rarely applied. While DNA-based approaches like DNA barcoding offer precise species identification, they lack information on specimen size and biomass. In contrast, high-throughput imaging techniques enable rapid measurements of a specimen's size and morphological features but may have low taxonomic resolution. In this study, we combined DNA megabarcoding, i.e., high-throughput barcoding of single specimens, with semi-automated imaging and deep neural networks to produce accurate taxonomic identifications, abundance, and biomass estimations for insects. In a multiple stressor field experiment, we collected a dataset of 743 specimens from 14 species of the orders Ephemeroptera, Plecoptera, and Trichoptera (EPT), which are routinely used as aquatic biological quality indicator taxa. Each specimen was imaged, weighed, and megabarcoded using the COI barcode gene. From the images captured using the semi-automated imaging device BIODISCOVER, we curated a final dataset of 146,439 images taken from two perpendicular cameras. We trained convolutional neural networks (CNNs) with these pictures for species identification and biomass estimation and evaluated their performance. In addition, we investigated whether models pre-trained for species identification perform better on the biomass estimation task, compared to models trained solely for biomass estimation, thus potentially reducing the need for extensive labelled data in future studies. Our findings demonstrate that combining DNA megabarcoding with automated imaging and deep neural networks enables fast, reliable, but also comprehensive assessment of species composition and biomass on the specimen level, contributing to the urgently needed methods in conservation biology, ecology, and evolution.}, }
@article {pmid41522508, year = {2026}, author = {Campos-Yánez, F and García-Ruilova, AB and Inclán, DJ}, title = {A new species of aposematic grasshopper of the genus Pseudoutanacris (Acrididae: Gomphocerinae) from the Andean cloud forest of the Ecuadorian Amazon basin.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20376}, pmid = {41522508}, issn = {2167-8359}, mesh = {Animals ; Ecuador ; Male ; Female ; *Grasshoppers/classification/anatomy &amp; histology/physiology ; Forests ; Amazona ; }, abstract = {We have identified a new grasshopper species belonging to the genus Pseudoutanacris Jago, 1971, in the montane forests of the eastern Andes in Ecuador. This discovery expands the known distribution of the genus, previously limited to a single species in the Bolivian tropics, by over 2,000 kilometers. For the first time, a female of the genus is described, and notes on the ecology and natural history of the species are presented. We also provide the first barcodes of the genus Pseudoutanacris Jago, 1971. The males of a newly described species, Pseudoutanacris grilla sp. nov. shares a striking coloration pattern with their Bolivian congener, Pseudoutanacris chromobapta Jago, 1971, setting them apart from other members of the tribe Amblytropidiini. However, the females maintain a cryptic coloration pattern, similar to that of the tribe members, and display different behavior from the males. During our study, we also observed Ps. grilla sp. nov. on the same plant as Megacheilacris graminicola (Descamps &amp; Amédégnato, 1971) (Bactrophorinae: Romaleidae), a species with similar chromatic characteristics. This finding also marks the first formal documentation of the new geographical records of M. graminicola (Descamps &amp; Amédégnato, 1971) in Ecuador.}, }
@article {pmid41522495, year = {2026}, author = {Bao, S and Deng, L and Shi, Y and Duan, N}, title = {Comparative genomics and phylogenetic analysis of seven Ficus species based on chloroplast genomes.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20531}, pmid = {41522495}, issn = {2167-8359}, mesh = {*Ficus/genetics/classification ; *Genome, Chloroplast/genetics ; *Phylogeny ; *Genomics/methods ; }, abstract = {BACKGROUND: The genus Ficus (Moraceae) is a large and ecologically important group, known for its intricate fig-wasp pollination mutualism and role as a keystone resource in tropical ecosystems. Despite its significance, the phylogenetic relationships within Ficus remain partially unresolved, necessitating more comprehensive genomic data. Chloroplast (cp) genomes are valuable resources for plant phylogenetic and comparative genomic studies. Here, we sequenced, assembled, and comparatively analyzed the complete chloroplast genomes of seven Ficus species, including Ficus esquiroliana, Ficus pandurata, Ficus formosana, Ficus erecta, Ficus carica, Ficus hirta, and Ficus stenophylla.<br><br>RESULTS: The complete cp genomes were successfully assembled, ranging in size from 160,340 bp to 160,669 bp, and exhibited a typical quadripartite structure with highly conserved gene content and arrangement. Critically, while some of these species have previously published plastomes, our assemblies consistently encoded 130 genes, contrasting with reported gene counts (e.g., 129 for F. formosana (NC_059898), 119 for F. carica (KY635880), 131 for F. erecta (MT093220)) in earlier studies. Numerous repeat sequences and simple sequence repeats (SSRs) were identified, predominantly in non-coding regions, which serve as valuable resources for developing novel genetic markers. Analysis of codon usage revealed a strong bias towards A/T endings, a common feature in plant cp genomes. While inverted repeat (IR) boundary regions were largely conserved, minor variations, including partial gene duplications (rps19, rpl2), were observed. Comparative genome alignment and nucleotide diversity analysis showed high sequence conservation, with most variations concentrated in single-copy and non-coding regions. We identified three hypervariable regions (ccsA, ccsA - ndhD, and rpoB - trnC-GCA) with elevated nucleotide diversity (Pi >&#xa0;0.012, ccsA up to 0.0141), suggesting their utility as candidate DNA barcodes for Ficus. Phylogenetic analysis using 79 protein-coding genes from 26 species robustly supported the monophyly of Ficus and resolved the seven newly sequenced species into two well-supported clades, consistent with previous classifications.<br><br>CONCLUSIONS: Our study provides new, consistently assembled and rigorously annotated chloroplast genome data for Ficus, including clarified data for previously studied species with notable gene content discrepancies. These data identify candidate molecular markers with potential applications for systematics and population genetics, and offer robust insights into relationships among sampled taxa. These data will facilitate future studies of Ficus evolution and conservation when complemented by broader taxon sampling and nuclear/mitochondrial data.}, }
@article {pmid41522476, year = {2025}, author = {Seokho, S and Sohn, J and Kim, H}, title = {First records of Opius and Apodesmia (Hymenoptera, Braconidae, Opiinae) from South Korea, with descriptions of newly-recorded species.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e176155}, pmid = {41522476}, issn = {1314-2828}, abstract = {BACKGROUND: The subfamily Opiinae comprises more than 2,000 valid species worldwide. Members of this subfamily are koinobiont endoparasitoids, with parasitism generally culminating in the eventual death of the host. Several species of Opiinae have been utilised for biological control of agricultural pests. The genus Opius is the largest genus within Opiinae, with more than 1,000 valid species worldwide. It is divided into several subgenera, classification of which remains under active discussion. The genus Apodesmia was formerly regarded as a subgenus of Opius, but was elevated to genus level, based on differences in the form of the occipital carina.<br><br>NEW INFORMATION: Opius youi Li &amp; van Achterberg, 2013 is recorded for the first time from South Korea, representing the first record of the species outside China. Apodesmia incisula Fischer, 1963 is also newly recorded from South Korea, constituting the first record of the species outside Europe, where it was previously known from Germany and the Netherlands. For each species, detailed morphological descriptions are provided, accompanied by diagnostic characters illustrated with photographs of the relevant body structures. The barcode region of mitochondrial cytochrome c oxidase I (COI) was also analysed for the species.}, }
@article {pmid41522231, year = {2026}, author = {Gu, F and Yang, L}, title = {Structural Characteristics, Comparative Analyses, and Conservation Significance of the Complete Chloroplast Genome of the Critically Endangered Lithocarpus yongfuensis (Fagaceae).}, journal = {Ecology and evolution}, volume = {16}, number = {1}, pages = {e72833}, pmid = {41522231}, issn = {2045-7758}, abstract = {This study aims to delineate the chloroplast (cp) genome of the critically endangered Lithocarpus yongfuensis (Fagaceae), with fewer than 10 wild individuals known. Genomic information for this species is scarce, hindering conservation strategies. We sequenced, assembled, and annotated its complete cp genome, analyzed its structure, and conducted comparative and phylogenetic analyses within the genus Lithocarpus. The cp genome is 161,258 bp in length, exhibiting a typical quadripartite structure and containing 131 annotated genes (86 protein-coding, 8 rRNA, and 37 tRNA genes). Comparative analysis revealed a conserved genomic architecture across the genus, with two protein-coding genes (rpoC2 and matK) showing evidence of positive selection. The rps16-trnK-UUU intergenic spacer was identified as a potential DNA barcode for distinguishing L. yongfuensis. Phylogenetic analysis based on complete cp genomes placed L. yongfuensis within the Southeast China clade, closely allied to L. crassifolius, L. litseifolius, and L. brevicaudatus. These findings provide essential genomic resources for conservation genetics and offer insights into the adaptive evolution of this rare species.}, }
@article {pmid41520911, year = {2026}, author = {McKenzie, M and Irac, SE and Chen, Z and Moradi, A and Jenner, A and Nguyen, Q and Rashidieh, B}, title = {Integrative Spatial Omics and Artificial Intelligence: Transforming Cancer Research with Omics Data and AI.}, journal = {Seminars in cancer biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcancer.2026.01.002}, pmid = {41520911}, issn = {1096-3650}, abstract = {The integration of multi-omics data, including genomics, transcriptomics, proteomics, epigenomics, and metabolomics, coupled with the histological spatial data have transformed biomedical research, offering unprecedented insights into cellular functions and disease mechanisms. However, the sheer volume and complexity of these datasets present a significant challenge in terms of interpretation and clinical translation. Artificial intelligence (AI) and machine learning (ML) are revolutionizing data analysis, enabling the extraction of meaningful patterns from high-dimensional datasets and facilitating the development of predictive models. This shift is particularly transformative in cancer research, where understanding the tumor microenvironment (TME) and its spatial dynamics is crucial for improving therapeutic outcomes. This review explores recent advancements in spatial Omics (SO) including spatial transcriptomics (ST) and spatial proteomics (SP), and AI-driven computational models, focusing on their applications in oncology. We discuss key methodologies, including spatial barcoding, in situ sequencing, and digital spatial profiling, and highlight major platforms. AI-powered tools, including deep learning models and spatial graph-based analyses, enhance data interpretation, allowing for robust predictive modeling, biomarker discovery, and personalized therapeutic strategies. Despite their transformative potential, ST and AI-driven approaches face challenges, including high-dimensional data complexity, computational constraints, and standardization of analytical pipelines. Addressing these challenges requires advanced mathematical frameworks such as spatial graph theory, topological data analysis, and agent-based modeling, which refine data integration and improve biological insights. Future research should focus on enhancing spatial resolution, cross-platform data harmonization, and AI-driven predictive models to advance precision oncology. By integrating ST, SP, and AI, researchers can develop dynamic, patient-specific treatment strategies, ultimately improving clinical outcomes and deepening our understanding of cancer progression and immune system interactions.}, }
@article {pmid41518826, year = {2026}, author = {Palm, ER and Santini, G and Niccolai, A and Vergine, M and Negro, C and Nissim, WG and Sabbatini, L and Balestrini, R and de Pinto, MC and Gohari, G and Fotopoulos, V and Mancuso, S and Luvisi, A and De Bellis, L and Rodolfi, L and Vita, F}, title = {Improving yield of a bean ecotype using biostimulants: focus on bean amino acid profiles and plant responses.}, journal = {Plant physiology and biochemistry : PPB}, volume = {231}, number = {}, pages = {110988}, doi = {10.1016/j.plaphy.2025.110988}, pmid = {41518826}, issn = {1873-2690}, abstract = {Biostimulants have emerged as having the potential to sustainably enhance crop performance as well as yield quantity and nutritional quality. Although naturally rich in lysine, beans are generally deficient in sulfur-containing amino acids like methionine and cysteine. Improving the nutritional imbalance in beans is highly desirable, especially in those with cultural and economic value, like Fagiolo di Sorana, a high-quality Protected Designation of Origin (PDO) bean variety from Pistoia, Italy. A spirulina-based (1 g/L and 3 g/L) and a commercially available (MC EXTRA; 1 g/L) biostimulant were applied as foliar sprays for two consecutive years to Fagiolo di Sorana plants grown under both open field and semi-controlled greenhouse conditions. Productivity was higher in treated plants: a 7 % increase (p-value, 0.036) was found in whole pod weight in the first year of the trial with 3 g/L and in the second year trial (p-value, 0.020) for MC EXTRA compared to the control. Improved amino acid composition of the beans were found, specifically an increase of 200 % (p-value, 0.040) and 400 % (p-value, 0.053) in methionine content with 3 g/L spirulina and MC EXTRA, respectively, compared to the control, thus addressing the bean's typical deficiency in sulfur amino acids. Bean digestibility increased 3 % (p-value, 0.013) with the higher concentration (3 g/L) of the spirulina-based biostimulant relative to the control-grown plants. Molecular barcoding identified genetic differences within a collection of ten Tuscan bean landraces, including the Fagiolo di Sorana variety, thus offering a first attempt at the genetic characterization essential for preserving landrace germplasm. These genetic data were then coupled with the assessment of protein digestibility to identify differences within the landrace collection. Thus, the use of biostimulants presents an opportunity to further enhance the yield and nutritional profile of this PDO without compromising its environmental integrity.}, }
@article {pmid41515439, year = {2026}, author = {Ísleifsdóttir, D and Xu, M and Biwersi, M and Leblanc, MJ and Heiðmarsson, S and Pálsson, S and Sorensen, JL and Viktorsson, E&#xd6; and Ólafsdóttir, ES}, title = {Is the Reindeer Lichen Cladonia arbuscula Really Producing Isousnic Acid? A Chemotaxonomy Query.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {1}, pages = {}, pmid = {41515439}, issn = {1420-3049}, support = {2310001-051//Icelandic Research Fund/ ; V&#xcd;S2023-93104//University of Iceland Science Park Fund/ ; 92257//University of Iceland research fund/ ; N&#xdd;R-14-2023//Landsvirkjun Fund/ ; ALLP 585977-23//Natural Sciences and Engineering Research Council of Canada Alliance International Collaboration/ ; }, mesh = {*Lichens/chemistry/metabolism/genetics/classification ; Chromatography, High Pressure Liquid ; *Ascomycota/genetics/metabolism/chemistry/classification ; DNA Barcoding, Taxonomic ; *Benzofurans/metabolism/chemistry ; *Reindeer/microbiology ; Animals ; Phylogeny ; }, abstract = {Isousnic acid (isoUA) has been detected in a few usnic acid (UA)-producing lichens with chemotaxonomic values. IsoUA was first isolated from a specimen belonging to Cladonia arbuscula s.l. (referred to as C. mitis in the publication). However, the isolation and detection of isoUA in this Cladonia species have not been reproduced and confirmed with clear evidence. This study focused on C. arbuscula s.l. collected in Iceland and aimed to (1) identify the lichen specimen using DNA barcoding and (2) investigate whether isoUA is produced using a series of chromatographic methods. The fungal nuclear ribosomal internal transcribed spacer (nrITS) barcode was sequenced, and the specimen was identified as C. arbuscula, following recent circumscription recommendations. Routine metabolite profiling did not detect isoUA, and it could only be identified after vigorous chromatographic purification and concentration steps using flash chromatography and preparative high-performance liquid chromatography. IsoUA was found in trace quantities (~24 µg/g dry weight), which likely explains its absence in routine metabolite profiling. A rapid ultra-high-performance liquid chromatography (UHPLC) method using a pentafluorophenyl column was developed to separate UA and isoUA. Our study highlights the importance of an integrative approach combining DNA barcoding and detailed chromatographic analyses for lichen chemistry research.}, }
@article {pmid41514962, year = {2025}, author = {Todorov, K and Antova, G and Petkova, Z and Teneva, O and Angelova-Romova, M and Mladenov, R and Naimov, S and Apostolova, E and Gyuzeleva, D and Mladenova, T and Panayotova, H and Stoyanov, P}, title = {Anatomical, Molecular-Genetic, and Phytochemical Study of Species from the Genus Equisetum in Bulgaria.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, pmid = {41514962}, issn = {2223-7747}, support = {project &#x2116; BG-RRP-2.004-0001-C01//European Union-NextGenerationEU, through the National Recovery and Resilience Plan of the Republic of Bulgaria/ ; }, abstract = {Five species of the genus Equisetum distributed in Bulgaria were studied: four species from the subgenus Equisetum (Equisetum arvense, E. telmateia, E. sylvaticum, and E. palustre) and one from the subgenus Hippochaete (E. ramosissimum). The anatomical, taxonomic, and phylogenetic characteristics of the selected species were established. In species belonging to the subgenus Equisetum, the endodermis was arranged in the form of a continuous ring, while in the representatives of the subgenus Hippochaete, a two-layered endodermis surrounding each vascular bundle was observed. The results from the DNA barcoding supported the taxonomic treatment of the studied species. The chemical and lipid compositions of the plants were also investigated. The Equisetum species had a similar chemical composition and a high content of sterols and phospholipids. In the glyceride oils, palmitic acid predominated, ranging from 69.5% to 78.7%. β-sitosterol was the main component in the sterol fraction, while the tocopherol content was found to be remarkably low in two of the samples (37.6-82.8 mg/kg), with α-tocopherol being predominant. In the phospholipid fraction, the major classes were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and phosphatidic acids. The chemical composition of the studied species and their high biologically active lipid constituents suggested that they were suitable for application in various directions.}, }
@article {pmid41514857, year = {2025}, author = {Zhan, Q and Tang, Y and Zhao, Y and Hou, S and Huang, Y and Zhao, X and Chen, Y and Xue, X}, title = {Complete Mitochondrial Genome Sequencing of Brachypelma albiceps and Comparative Codon Usage Bias Analysis Across Seven Mygalomorphae Species.}, journal = {Biology}, volume = {15}, number = {1}, pages = {}, pmid = {41514857}, issn = {2079-7737}, support = {LGZD202507//Fundamental Research Funds for the Central Universities/ ; 2025//Qinglan Project" of Jiangsu Province in 2025/ ; 32100366//National Natural Science Foundation of China/ ; 2022YFC2601200//National Key R&amp;D Program of China/ ; "Public Security Technology" project (2022)//the Jiangsu Province "14th Five-Year Plan" Key Construction Discipline/ ; }, abstract = {Tarantulas (family Theraphosidae) are ecologically significant invertebrate predators in terrestrial ecosystems, but many species face threats from habitat fragmentation and unsustainable collection for the international pet trade. Brachypelma albiceps, a CITES Appendix II-listed species, lacks comprehensive mitochondrial genome characterization, limiting phylogenetic and evolutionary studies. Here, we report a complete mitochondrial genome sequence for B. albiceps (13,856 bp; GC content 32.84%) and provide detailed annotation. The genome exhibits typical metazoan mitochondrial organization, containing 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs, with an AT-rich nucleotide composition (67.16%) characteristic of arthropod mitochondria. Comparative analyses of B. albiceps and six other Mygalomorphae species revealed strong biases toward A/T-ending codons and avoidance of G/C-ending codons. ENC-GC3s, neutrality, and PR2 analyses consistently indicate that natural selection plays a dominant role in shaping synonymous codon usage, with mutation pressure also contributing. Phylogenetic reconstruction based on 10 high-quality mitochondrial protein-coding genes from 23 spider species confirmed the placement of B. albiceps within the family Theraphosidae and its close phylogenetic relationship to Cyriopagopus species. These results provide valuable genomic resources for the Theraphosidae systematics, enhance our understanding of codon bias evolution, and provide critical DNA barcode data for forensic identification of CITES-regulated specimens in the illegal wildlife trade.}, }
@article {pmid41513884, year = {2026}, author = {Balsamo, JA and Mendoza, M and Kelly-Baker, L and G Thacker, S and Verthelyi, D}, title = {Multiplexed Immunophenotyping for Innate Activation Assessment Detects Single-Cell Responses to Immunomodulatory Nucleic Acid Impurities in Therapeutics.}, journal = {The AAPS journal}, volume = {28}, number = {1}, pages = {49}, pmid = {41513884}, issn = {1550-7416}, mesh = {Humans ; *Immunity, Innate/drug effects/immunology ; *Immunophenotyping/methods ; *Single-Cell Analysis/methods ; Flow Cytometry/methods ; *Nucleic Acids/immunology ; Oligodeoxyribonucleotides/immunology/pharmacology ; Monocytes/immunology/drug effects ; }, abstract = {Innate immune response modulating impurities (IIRMI) with adjuvant potential have emerged as important factors in the immunogenicity risk assessment of protein, peptide, and oligonucleotide therapeutics, particularly for follow-on products where minimal or no clinical studies are available. To assess the impact of differences in impurities on specific cell types, we developed a new IIRMI assay termed multiplexed immunophenotyping for innate activation assessment (MIIAA) that employs spectral flow cytometry to capture single-cell responses to drug products and potential impurities. This technique introduces a new live fluorescent cell barcoding platform that enables sample multiplexing for homogeneous staining with a single fluorescent antibody cocktail composed of identity and activation markers that are acquired simultaneously with a five laser Cytek Aurora. Samples are digitally reassigned to their original testing conditions by positive and negative gating of barcode dyes. Cellular subsets are identified by dimensionality reduction of surface markers with UMAP then gated using cell-specific markers. Here we use trace levels of TLR3, 7/8 and 9 agonists (Poly(I:C), R848, and CpG ODN) to characterize specific responses in B cells, monocytes, cDC and pDC. Importantly, MIIAA captures single-cell responses to nucleic acid impurities in the presence of therapeutic oligonucleotides or monoclonal antibodies with high sensitivity. Taken together, MIIAA offers a powerful immunophenotyping tool to characterize single-cell responses to drug products and potential immunomodulatory impurities that may find utility in drug pipelines to characterize the impact of therapeutics on specific immune cells and to interrogate immunogenic or immunomodulatory risk in comparisons between reference and follow-on products.}, }
@article {pmid41513017, year = {2026}, author = {Cao, J and Poyarkov, NA and Wei, P and Tie, M and Matsukoji, T and Suwannapoom, C and Ai, R and Lu, W and Sucharitakul, P and Wang, H and Chomdej, S and Yuan, Z and Yan, F}, title = {Diversity, Phylogeny, and biogeography of the subgenus Japonigekko (Gekkonidae: Gekko).}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {108530}, doi = {10.1016/j.ympev.2025.108530}, pmid = {41513017}, issn = {1095-9513}, abstract = {The subgenus Japonigekko, a monophyletic lineage, represents the most ecologically and morphologically diverse group within the genus Gekko, with a wide distribution across East Asia. Given the ecological significance and high diversity of Japonigekko, understanding its true species diversity and biogeographic history is crucial for biodiversity conservation in East Asia. However, research on this subgenus remains limited compared to other well-studied vertebrate groups such as mammals and amphibians. In this study, we conducted extensive sampling and integrated molecular data from 34 of the 38 known Japonigekko species using barcoding techniques for 331 samples from 129 sites, systematically elucidating their phylogenetic relationships. Further genomic analysis addressed longstanding taxonomic controversies, revealed previously underestimated species diversity, and clarified the historical biogeography of this group. Ultimately, we identified nine candidate new species. Phylogenetic analyses and ancestral area reconstructions suggest that Japonigekko originated in the Indochina Peninsula and southern China, subsequently dispersing northward and eastward during the Miocene in response to geological events and climatic fluctuations. The recurrent formation and disappearance of land bridges between the mainland and East Asian islands provided critical opportunities for both dispersal and isolation, revealing a unidirectional mainland-to-island dispersal pattern. These findings support to the "Ancient Species Divergence Hypothesis" in East Asia.}, }
@article {pmid41510249, year = {2025}, author = {Skene, P and Hart, M and Thomson, Z and Kaul, S and Ilkisin, S and Landreau, M and Stuckey, T and Wittig, P and Keller, M and McCann, C and Torgerson, T}, title = {Massively Scalable Single-cell Multiomic Profiling of T Cell Repertoire with REFLEX.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7915855/v1}, pmid = {41510249}, issn = {2693-5015}, abstract = {Single-cell profiling of T cell state with immune repertoire is critical for understanding heterogenous T cell phenotypes and responses to antigen, however, existing technologies struggle to generate this information at sufficient throughput to match biological complexity. We present "REFLEX", a novel single-cell method enabling highly scalable, cost-efficient, multiomic profiling with paired-chain TCR sequencing. REFLEX utilizes in-situ reverse transcription with integrated sample multiplexing barcodes in a way that merges seamlessly with the commonly used 10x FLEX platform to allow capture of TCR sequences at unprecedented scale and depth. We profile >2 million cells from CMV-peptide-pulsed T cell expansions, capturing TCR sequences and rich multiomic information from 1.4M T cells, identifying many putative novel CMV reactive clonotypes and illustrating the scale and transformative impact on our understanding of T cell mediated adaptive immunity achievable with REFLEX.}, }
@article {pmid41509721, year = {2025}, author = {Xiong, Y and Li, D and Xu, X}, title = {Five new species of the trapdoor spider genus Latouchia Pocock, 1901 (Araneae, Halonoproctidae) from China.}, journal = {ZooKeys}, volume = {1265}, number = {}, pages = {103-127}, pmid = {41509721}, issn = {1313-2989}, abstract = {Five new species of the trapdoor spider genus Latouchia Pocock, 1901 are described from southern China based on both morphological and molecular evidence: L. jihe sp. nov. (♂♀), L. wufeng sp. nov. (♂♀), L. wuhan sp. nov. (♂♀), L. yinggen sp. nov. (♂♀), and L. zhangping sp. nov. (♂♀). The male and female of L. jinyun Hao, Yu &amp; Zhang, 2025 are also redescribed from specimens collected in Nanchong City, Sichuan Province, China, located over 100 km from the type locality in Chongqing Municipality. Species delimitation is supported by genetic distance analyses of the mitochondrial DNA barcode gene (cytochrome c oxidase subunit I, COI), comparing the five new species with five previously described taxa. GenBank accession codes for the five new species and L. jinyun are provided to facilitate future identification and taxonomic research.}, }
@article {pmid41509719, year = {2025}, author = {Wang, JX and Zhu, XJ and Xiao, YL}, title = {Phylogenetic analysis of the genus Semioscopis (Lepidoptera, Depressariidae), with description of a new species from China.}, journal = {ZooKeys}, volume = {1265}, number = {}, pages = {175-187}, pmid = {41509719}, issn = {1313-2989}, abstract = {This study describes Semioscopis sinicella Wang, Zhu &amp; Xiao, sp. nov. of the genus Semioscopis Hübner, 1825 (Lepidoptera, Depressariidae) from China. The new species is similar in external morphology and male genitalia to the European S. avellanella (Hübner, 1793) and the Japanese S. similis Saito, 1989, but it can be distinguished in female genitalia mainly by the distinctly shorter sclerotised section of the ductus bursae and the length ratios of the ductus bursae and corpus bursae to the papillae anales. Morphological descriptions and illustrations of the new species are provided. Furthermore, a phylogenetic analysis based on COI gene sequences using IQ-tree supports S. sinicella sp. nov. as a monophyletic lineage and further divides the genus Semioscopis into seven species groups.}, }
@article {pmid41509718, year = {2025}, author = {Salah, M and Baleela, R and Ahmed, EY and Isam, B and Abdalla, A and Masri, M and Elfaki, E}, title = {Paragomphus alami sp. nov. (Odonata, Gomphidae): a new dragonfly species described from the White Nile River, Sudan.}, journal = {ZooKeys}, volume = {1265}, number = {}, pages = {159-174}, pmid = {41509718}, issn = {1313-2989}, abstract = {Sudan's unique biogeographic position at the Afrotropical-Palearctic interface, coupled with the ecological gradient of the Nile River, fosters a diverse odonate fauna. Despite this, the genus Paragomphus Cowley, 1934 remains understudied in the region. This study describes Paragomphus alami sp. nov., a new species of Paragomphus from the White Nile floodplain in Sudan, based on integrated morphological and molecular evidence. Field surveys conducted between 2017 and 2022 documented adult populations across the Sudanese floodplains. Specimens were morphologically analysed using microscopy compared to congeners P. lacustris Karsch, 1890 and P. elpidius Ris, 1921. DNA barcoding (COI gene) was performed on two specimens, with maximum-likelihood phylogenetic reconstruction using 28 sequences of Paragomphus and related species in addition to an outgroup. Mean interspecific genetic distance was computed manually. Morphological comparisons with congeners revealed unique diagnostic traits in P. alami sp. nov., including short, thick cerci ending with a black tooth, and an epiproct that is noticeably shorter than those of P. lacustris and P. elpidius. The phylogenetic analysis revealed that P. alami forms a well-supported monophyletic clade (bootstrap value = 100%), which is corroborated by morphological evidence, and no observed intraspecific variation, which supports the recognition of this species as distinct; this was further supported by the mean interspecific distance of 12.34%. This discovery highlights Sudan's role as a biogeographic crossroads and the need for further research of Odonata in the region. Habitat sensitivity highlights conservation urgency. The species seasonal emergence, habitat specificity, and sensitivity to deforestation underscore its conservation importance.}, }
@article {pmid41509389, year = {2026}, author = {Wang, CC and Dorsey, E and Wu, C}, title = {Expanding High-Fidelity Multiplexing in Ultrasensitive Single-Molecule Protein Detection via Proximity Barcoding.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.01.03.697469}, pmid = {41509389}, issn = {2692-8205}, abstract = {The human proteome presents a vast information reservoir for basic and diagnostics research, yet the low abundances of many proteins in biofluids pose an analytical challenge. While ultrasensitive methods such as digital enzyme-linked immunosorbent assay have expanded the window of detectable proteins, multiplexing with high accuracy, sensitivity, and throughput remains limited by cross-reactivity and signal readout channels To address this challenge, we introduce PRO-MOSAIX (PROximity-barcoded Molecular On-bead Signal Amplification for Individual MultipleXing), a high-accuracy, ultrasensitive multiplex digital immunoassay platform that integrates high-throughput single-molecule protein detection with DNA barcode-based proximity ligation. PRO-MOSAIX generates "ON" signals only from matched affinity reagents in proximity, minimizing false positives from cross-reactive binding. This approach overcomes the multiplexing ceiling imposed by fluorescence spectral overlap by employing a single signal readout channel and DNA barcoding. In conjunction, we further improve multiplexing accuracy by mitigating a secondary source of false positives from DNA-based signal amplification. As a proof of principle, we establish and validate a 15-plex PRO-MOSAIX assay in human plasma, with low femtomolar sensitivities and high measurement accuracies. PRO-MOSAIX is modular and utilizes common laboratory instrumentation with a high-throughput flow cytometric readout, providing a broadly accessible tool that bridges the gap between analytical sensitivity and high-order multiplexing.}, }
@article {pmid41504599, year = {2026}, author = {Fang, C and Lindsey, JW and Abbott, LF and Aronov, D and Chettih, SN}, title = {Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {41504599}, issn = {2050-084X}, support = {DBI-1707398//National Science Foundation/ ; DP2-AG071918//NIH Office of the Director/ ; 1K99NS136846/NS/NINDS NIH HHS/United States ; DE-SC0020347//U.S. Department of Energy/ ; }, mesh = {*Hippocampus/physiology ; Animals ; *Models, Neurological ; *Neurons/physiology ; Passeriformes/physiology ; *Memory, Episodic ; *Memory/physiology ; *Nerve Net/physiology ; }, abstract = {Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an 'index' - a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ('barcodes') that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems.}, }
@article {pmid41503923, year = {2026}, author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H}, title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70231}, pmid = {41503923}, issn = {1744-7917}, support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; }, abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.}, }
@article {pmid41503381, year = {2026}, author = {Zanovello, L and Eisendle, D and Casari, S and Ennemoser, M and Grund, H and Favrin, G and Rossi, S and Modesti, A and Luchelli, M and Rüber, L and Meraner, A and Gandolfi, A}, title = {Origin and Genetic Diversity of Barbatula (Cypriniformes: Nemacheilidae) in Italy.}, journal = {Ecology and evolution}, volume = {16}, number = {1}, pages = {e72832}, pmid = {41503381}, issn = {2045-7758}, abstract = {Recent morphological and molecular studies suggested the existence of several undescribed species within the genus Barbatula. The stone loach (Barbatula barbatula) is considered, according to the Italian Red List, as native in Northern Italy and classified as vulnerable (VU), having a limited and fragmented distribution from Lombardy to Friuli-Venezia Giulia regions. In the present study, 248 specimens of Barbatula sp., collected from 17 sampling sites in Italy-spanning its entire known distribution area-and from one site in Austria, were analysed by sequencing the Cytochrome C Oxidase I (COI) and the Cytochrome B (CytB) mitochondrial regions. Sequencing results were then compared with reference samples from the literature. Three highly divergent mitochondrial lineages were observed in Italian populations, which can be associated with three different species: Barbatula pironae in Friuli-Venezia Giulia, Barbatula fluvicola in Trentino-Alto Adige and Lombardy, and Barbatula aff. barbatula coexisting with the latter in Lombardy. The three species, with the first having a distribution limited to the upper Adriatic area, and the other two having a wider distribution north of the Alps, should therefore be considered as different Management Units. Therefore, the integration of the Italian freshwater fish species checklist and the update of their taxonomy are strongly advised. Our data together with other available evidence suggest that the three species are likely native to Italy, and hence a revision or definition of their conservation status might be needed.}, }
@article {pmid41502534, year = {2026}, author = {Weatherford, E and Grauer, A and Sirochinsky, C and Lehman, IF and Thummala, N and Callahan, M and Sittig, DF and Singh, H and Salmasian, H and Jurgens, M and Adelman, JS}, title = {Developing updated and new guidance to promote reliable patient identification.}, journal = {JAMIA open}, volume = {9}, number = {1}, pages = {ooaf160}, pmid = {41502534}, issn = {2574-2531}, abstract = {OBJECTIVES: To describe the process of updating the Patient Identification Safety Assurance Factors for EHR Resilience (SAFER) Guide and to review new practices and refinements to the Guide.<br><br>MATERIALS AND METHODS: We conducted a review of literature on the topic of patient identification in healthcare settings, focusing on papers published after 2016. Titles and abstracts were screened by a team of reviewers, and the full text of retained articles was used to inform the revision.<br><br>RESULTS: The updated SAFER Guide strengthens recommendations for displaying patient photographs and using electronic patient identification, including barcoding and radiofrequency identification on patient wristbands. The Guide also recommends the use of biometric identification at registration and point of care. Finally, the updated Guide removes a recommendation to restrict the number of concurrently open patient records permitted in the electronic health record.<br><br>DISCUSSION: The revised SAFER Guide includes new recommendations aimed at supporting accurate patient identification at registration, order placement, and the point of care.<br><br>CONCLUSION: The updated Patient Identification SAFER Guide provides evidence-based national recommendations to help reduce patient misidentification.}, }
@article {pmid41501532, year = {2026}, author = {Demesa-Arevalo, E and Dӧrpholz, H and Vardanega, I and Maika, JE and Pineda-Valentino, I and Eggels, S and Lautwein, T and Kӧhrer, K and Schnurbusch, T and von Korff, M and Usadel, B and Simon, R}, title = {Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, pmid = {41501532}, issn = {2055-0278}, support = {EXC2048 CEPLAS//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048 CEPLAS//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CSCS FOR5235//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC2048//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Grass inflorescences are composite structures, featuring complex sets of meristems as stem cell niches that are initiated in a repetitive manner. Meristems differ in identity and longevity, generate branches or split to form flower meristems that finally produce seeds. Within meristems, distinct cell types are determined by positional information and the regional activity of gene regulatory networks. Understanding these local microenvironments requires precise spatio-temporal information on gene expression profiles, which current technology cannot achieve.Here we investigate transcriptional changes during barley development, from the specification of meristem and organ founder cells to the initiation of distinct floral organs, on the basis of an imputation approach integrating deep single-cell RNA sequencing with spatial gene expression data. The expression profiles of more than 40,000 genes can now be analysed at cellular resolution in multiple barley tissues using the new web-based graphical interface BARVISTA, which enables precise virtual microdissection to analyse any sub-ensemble of cells. Our study pinpoints previously inaccessible key transcriptional events in founder cells during primordia initiation and specification, characterizes complex branching mutant phenotypes by barcoding gene expression profiles, and defines spatio-temporal trajectories during flower development. We thus uncover the genetic basis of complex developmental processes, providing novel opportunities for precisely targeted manipulation of barley traits.}, }
@article {pmid41501049, year = {2026}, author = {Moore, ST and Lian, X and Vaidya, A and Chatterjee, S and Santelli, J and Sun, Y and Farbiak, L and Zhu, H and Siegwart, DJ}, title = {Multiplexed lipid nanoparticle barcoding reveals tissue-dynamic kinetic insights and enriched cellular tropism in hepatic zones.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-68103-7}, pmid = {41501049}, issn = {2041-1723}, support = {P30CA142543//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 5R01EB025192-06//U.S. Department of Health &amp; Human Services | NIH | National Institute of Biomedical Imaging and Bioengineering (NIBIB)/ ; }, abstract = {Lipid nanoparticles (LNPs) efficiently deliver nucleic acids to cells in vivo and facilitate clinical applications including RNA-based vaccines and therapies. Discovery and optimization of LNPs remain challenging due to the complexity of input variables and low throughput workflows. To accelerate these processes, we report a broadly compatible barcoded Cre recombinase mRNA barcode platform that enables multiplexed LNP tracking in vivo in tdTomato reporter mice. We evaluate accumulation and degradation kinetics of mRNA encapsulated in Selective Organ Targeting (SORT) LNPs in the liver, lung, and spleen, and show that functional protein activity is associated with rapid organ enrichment. We further demonstrate how barcode multiplexing can streamline systematic kinetic studies, distinguish nanoparticles with distinct biological outcomes, and differentiate subtle, yet important, variations within a series of similar formulations. Finally, we use barcoding to identify and characterize nanoparticles with hepatic zonal bias and previously overlooked extrahepatic tropism. This approach could accelerate high resolution characterization of nanoparticles with desirable properties, enable large-scale systematic studies of diverse LNPs, and provide insights into optimizable parameters of LNP-mRNA delivery.}, }
@article {pmid41500013, year = {2025}, author = {Rani, V and Chauhan, C and Sengar, RS}, title = {DNA barcoding markers: A comprehensive review and taxonomic classification across species.}, journal = {Computational biology and chemistry}, volume = {122}, number = {}, pages = {108872}, doi = {10.1016/j.compbiolchem.2025.108872}, pmid = {41500013}, issn = {1476-928X}, abstract = {DNA barcoding has revolutionized species identification and biodiversity assessment by employing short, standardized genetic sequences as molecular markers. Since its inception by Hebert in 2003, it has become a cornerstone of taxonomy, ecology, conservation, agriculture, and medicine. This review traces the historical development of DNA barcoding, highlighting the strengths and limitations of widely used markers such as COI in animals, ITS in fungi, rbcL and matK in plants, and alternative loci in algae. The discussion emphasizes how barcoding enables accurate identification of cryptic taxa, supports food and forensic authentication, and strengthens biodiversity monitoring across ecosystems. Advancements in multi-locus strategies, genome-based markers, and DNA metabarcoding have enhanced resolution and scalability, while next-generation sequencing, environmental DNA, and nanotechnology promise to overcome persistent challenges of low variability, amplification barriers, and incomplete reference databases. Despite ongoing limitations, DNA barcoding continues to be an indispensable, cost-effective tool that bridges classical taxonomy with modern genomics. By integrating emerging technologies and fostering global collaboration, it holds immense potential for transforming biodiversity science and ensuring sustainable ecosystem management in the genomic era.}, }
@article {pmid41499369, year = {2026}, author = {Chen, K and Luo, S and Jiang, C and Gu, S and Yang, F and Liu, X and Wang, S and Qu, X and Zhang, Q and Zhang, P and Gong, Y and Zeng, H and Qiu, D and Miao, W and Xiong, J}, title = {HiMBar: A High-Fidelity Metagenomic Barcoding Approach for Transkingdom Species Detection and Interaction Analysis in Aquatic Ecosystems.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70092}, pmid = {41499369}, issn = {1755-0998}, support = {2023S016//Ningbo Public Welfare Science and the Technology Program Project/ ; 2022xjkk0204//Third Xinjiang Scientific Expedition Program/ ; SNJNP2022008//Background Resources Survey in Shennongjia National Park/ ; 2019 QZKK0304//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; SNJGKL2022008//Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; 32122015//National Natural Science Foundation of China/ ; 32300355//National Natural Science Foundation of China/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Ecosystem ; *Metagenomics/methods ; *Aquatic Organisms/classification/genetics ; Fungi/genetics/classification ; Computational Biology/methods ; Bacteria/classification/genetics ; }, abstract = {Aquatic ecosystems host diverse organisms across all six life kingdoms, yet their complex interactions remain poorly understood, primarily due to limitations in transkingdom species detection methods. To address this limitation, we developed HiMBar (https://github.com/Xchenkai2019/HIFI_barcoding), a high-fidelity (HiFi) metagenomic barcoding approach that utilises long, highly accurate reads to extract multiple full-length marker genes (such as rRNA genes, COI, rbcL) directly from environmental DNA sequencing reads. These genes are subsequently clustered into operational taxonomic units (OTUs) for species identification, eliminating the need for PCR amplification or sequence assembly. HiMBar outperforms existing DNA-based methods in accuracy, recall and consistency. Applying HiMBar, we identified a stable interaction network among Cyanobacteria, Planctomycetota, Verrucomicrobiota and Fungi. Further analysis revealed that glucose metabolism plays a key role in maintaining these interactions. Our study offers a powerful tool for transkingdom species monitoring and provides a case study for exploring transkingdom interactions and their molecular mechanisms.}, }
@article {pmid41493178, year = {2026}, author = {Piątek, M and Lutz, M and Yorou, NS and Guelly, KA and Piątek, J}, title = {Smut fungi on Trachypogon spicatus in Africa: Sporisorium trachypogonis-spicati and Tilletia afrotrachypogonis, sp. nov.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/00275514.2025.2588503}, pmid = {41493178}, issn = {1557-2536}, abstract = {Two smut fungi infecting the crinkle-awn grass Trachypogon spicatus (Poaceae) in Africa are characterized morphologically, illustrated, and linked to DNA barcodes (rDNA ITS, 28S). Sporisorium trachypogonis-spicati is reported for the first time from Benin, South Africa, and Togo, far from the previously known localities in the Democratic Republic of the Congo and Zimbabwe. This species is morphologically similar and closely related but genetically divergent to Sporisorium trachypogonicola, which infects Trachypogon spicatus in the Americas. Tilletia afrotrachypogonis is described as a new species from Togo and is also known from southeastern Africa (Malawi, Zambia). This species is morphologically almost identical to but genetically distinct from Tilletia trachypogonis, which infects Trachypogon spicatus in Mexico. The phylogenetic sister relationship, phenotype, and ecological similarity for the two species pairs Sporisorium trachypogonis-spicati/S. trachypogonicola and Tilletia afrotrachypogonis/T. trachypogonis, but occurrence in different geographic areas (Africa and the Americas/North America, respectively), suggest a common ancestral species, allopatric speciation, and duplication, i.e. speciation on the same host species.}, }
@article {pmid41490555, year = {2026}, author = {Wei, R and Gao, Z and Cui, D and Zou, Y and Dong, Y and Tian, Q and Wen, R and Li, X and Yang, W}, title = {Aucklandia lappa, Vladimiria souliei, and Inula helenium: A comprehensive review on the ethnomedicines, phytochemicals, quality control and pharmacology of three confusable Muxiang varieties (2015-2025).}, journal = {Journal of ethnopharmacology}, volume = {360}, number = {}, pages = {121163}, doi = {10.1016/j.jep.2026.121163}, pmid = {41490555}, issn = {1872-7573}, abstract = {The dried roots of Aucklandia lappa (Mu-Xiang), Vladimiria souliei (Chuan-Mu-Xiang), and Inula helenium (Tu-Mu-Xiang), perennial species of the Asteraceae family, are commonly used in traditional Chinese medicine for their therapeutic properties.<br><br>AIM OF THE REVIEW: Morphological and phytochemical similarities among three Muxiang varieties, particularly between A. lappa and V. souliei, lead to confusion. This review aimed to provide a comprehensive analysis of their ethnomedicinal uses, phytochemistry, quality control, pharmacological properties, and modern applications.<br><br>MATERIALS AND METHODS: Relevant literatures between January 2015 and September 2025 were retrieved from the Web of Science, PubMed, ScienceDirect, and CNKI.<br><br>RESULTS: A total of 429 compounds were identified from three Muxiang varieties, mainly including the sesquiterpene lactones (SLs), monoterpenoids, triterpenoids, phenylpropanoids, and flavonoids. Among these, the contained SLs (149 compounds) were the principal bioactive constituents responsible for the effects of anticancer, anti-inflammation, gastrointestinal protection, anti-microorganism, hepatoprotection and neuroprotection. Advanced analytical methods, such as HPLC, GC-MS, DNA barcoding, and hyperspectral imaging coupled with machine learning, were established to enable accurate species differentiation and quality control. The review further provided a comparative analysis of the similarities and differences among three Muxiang varieties.<br><br>CONCLUSION: This review synthesizes the current knowledge on three Muxiang varieties, establishing a foundational resource for their botany, traditional uses, phytochemistry, pharmacology, and quality control. Despite historical confusion due to morphological and ethnopharmacological similarities, modern research has revealed differences in their chemical composition and pharmacological activities. Future validation of distinctions is essential to ensure the rational and targeted utilization of these Muxiang resources.}, }
@article {pmid41489363, year = {2026}, author = {Pipas, JM and Sullivan, CS}, title = {mGem: Deciphering how polyomaviruses coexist with their hosts for a lifetime.}, journal = {mBio}, volume = {}, number = {}, pages = {e0231125}, doi = {10.1128/mbio.02311-25}, pmid = {41489363}, issn = {2150-7511}, abstract = {Small DNA tumor viruses such as polyomaviruses have evolved persistent, in some cases lifelong infections despite their compact genomes and host immune pressure. This review synthesizes historical and recent insights into the mechanisms underlying polyomavirus persistence and shedding, including dynamic host cell cycle regulation, viral non-coding control region modulation, and viral microRNA-mediated repression. We highlight modes of shedding consistent with concurrent latent/lytic and smoldering infections, discuss emerging evidence of reversible latency, and identify unresolved questions in viral-host interplay. Understanding these strategies is critical for managing viral reactivation and disease in immunocompromised patients and exemplifies the remarkable evolutionary success of polyomaviruses.}, }
@article {pmid41488798, year = {2026}, author = {Yan, R and Abdullah,  and Jia, J and Islam, M and Li, H and Liu, M and Yir-Erong, B and Tian, X}, title = {Characterization of Verbesina encelioides (Asteroideae, Asteraceae) Chloroplast Genome and Phylogenetic Insights.}, journal = {Ecology and evolution}, volume = {16}, number = {1}, pages = {e72897}, pmid = {41488798}, issn = {2045-7758}, abstract = {Verbesina encelioides (Cav.) Benth. &amp; Hook.f. ex A.Gray (Asteroideae, Asteraceae) is a widespread annual herb native to southwestern North America that has naturalized globally. Here, we report the first de novo assembly and comprehensive annotation of the complete chloroplast (cp) genome of V. encelioides, generated using Illumina NovaSeq sequencing. The circular genome is 152,213 bp and exhibits the characteristic quadripartite structure, comprising a large single-copy (83,911 bp) region, a small single-copy (18,248 bp) region, and two inverted repeat regions (25,027 bp each). The genome encodes 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 16 genes duplicated in the IRs. Comparative analysis with Verbesina alternifolia revealed high structural conservation regarding gene content and arrangement, codon usage, amino acid frequency, and simple sequence repeats. Codon usage showed bias toward A/T-ending codons (RSCU > 1), whereas leucine was the most abundant amino acid, and cysteine was the least frequent. Simple sequence repeat analysis predominantly identified A/T-rich mononucleotide repeats. Nucleotide diversity analysis highlighted several variable regions-including trnD-trnY, atpA-trnR, rpl32-trnL, ccsA-ndhD, and trnL-ccsA-which may serve as molecular markers. Analysis of adaptive evolution in Verbesina species and related genera identified codons under positive selection in 19 chloroplast genes: atpB, ccsA, clpP, ndhD, ndhI, psaB, psbB, rpl14, rpoB, rpoC1, rps8, ycf3, accD, matK, rbcL, ndhF, rpoC2, ycf2, and ycf1. Maximum likelihood phylogenetic analysis placed Verbesina within the tribe Heliantheae. This complete cp genome provides a valuable genetic resource for phylogenetic studies, DNA barcoding, and population genetics of Verbesina and related Asteraceae taxa.}, }
@article {pmid41484813, year = {2026}, author = {Silva-Ramos, CR and Sierra-González, MC and Chacón Gómez, ME and Melby, PC and Aguilar, PV and Cabada, MM and Hidalgo, M}, title = {Francisella spp. as an overlooked cause of acute undifferentiated febrile illness in Colombia? Unexpected evidence from febrile patients negative for other common and neglected etiologies in Villeta municipality.}, journal = {Tropical medicine and health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s41182-025-00883-6}, pmid = {41484813}, issn = {1348-8945}, support = {D43TW010331/TW/FIC NIH HHS/United States ; }, abstract = {BACKGROUND: Acute undifferentiated febrile illness (AUFI) represents a major health challenge in tropical regions due to its wide range of etiologies. In Villeta, Colombia, previous studies investigated common causes such as malaria, arboviral diseases, leptospirosis and rickettsiosis, as well as several neglected bacterial agents. However, some patients remained without an identified etiology, underscoring the need for broader approaches to uncover other potential causes. Therefore, the aim of the present study was to investigate into other potential bacterial causes of AUFI through advanced molecular strategies utilizing 16S rRNA sequencing.<br><br>METHODS: The study analyzed AUFI patient samples previously screened for fourteen pathogens. The V3-V9 hypervariable region of the 16S rRNA gene was amplified from whole-blood DNA of unresolved cases and sequenced using the Oxford Nanopore GridION platform. Reads were filtered, quality-checked, and taxonomically classified using the SILVA database.<br><br>RESULTS: Eight samples from individuals without evidence of infection or recent exposure to previously screened pathogens were selected for 16S rRNA sequencing. DNA quality and integrity were confirmed, and enrichment produced high-quality amplicons for all samples. Sequencing generated high-quality reads overwhelmingly dominated by Francisella, representing over 93% of classified reads, followed by Coxiella and Arcobacter.<br><br>CONCLUSIONS: This study provides the first molecular evidence of Francisella in whole-blood from febrile patients in Colombia. Findings highlight its potential role in AUFI, demonstrate the value of 16S rRNA barcoding, and underscore the need for expanded surveillance of highly neglected bacterial taxa.}, }
@article {pmid41481685, year = {2026}, author = {Harper, RL and Lelliott, PM and Bender, SB and Pinto, AR}, title = {Unraveling Cardiovascular Development and Function: Insights From Single-Cell Omics.}, journal = {Circulation research}, volume = {138}, number = {1}, pages = {e325793}, doi = {10.1161/CIRCRESAHA.125.325793}, pmid = {41481685}, issn = {1524-4571}, mesh = {Humans ; *Single-Cell Analysis/methods ; Animals ; *Cardiovascular System/metabolism/embryology/growth &amp; development/cytology ; Transcriptome ; Cell Lineage ; *Heart/embryology ; Gene Expression Profiling ; *Genomics/methods ; }, abstract = {The cardiovascular system, composed of the heart and vasculature, is essential for blood circulation, nutrient exchange, and waste removal. In the past, our understanding of cardiovascular development and function has largely been shaped by bulk tissue analyses, which obscures cellular heterogeneity. The emergence of single-cell omics has transformed the field by enabling unbiased transcriptional profiling of individual cells, revealing the diversity of stem cells and progenitor cells driving embryogenesis, resulting in the various mature cardiovascular cell types in the adult heart and vasculature. This technology has provided unprecedented insights into the molecular mechanisms governing cardiovascular development and function by identifying novel cell subpopulations, characterizing their unique properties, and tracing their temporal evolution through advanced analytical approaches. In this review, we discuss how single-cell omics has reshaped our understanding of cardiovascular developmental biology, highlight key analytical tools and emerging approaches, examine preclinical models that have facilitated these discoveries, and explore how these technologies have defined the cellular landscape of the heart and vasculature. We conclude by looking ahead to emerging technologies such as spatial transcriptomics and clonal barcoding for lineage tracing, as well as new strategies in addressing the gender gap in cardiovascular research.}, }
@article {pmid41481464, year = {2026}, author = {Ashok, Y and Bubb, KL and Oy, C and Gorjifard, S and Cuperus, JT and Queitsch, C and Fields, S}, title = {Dosa: A method to covalently barcode proteins for high-throughput biochemistry.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {1}, pages = {e2529762123}, doi = {10.1073/pnas.2529762123}, pmid = {41481464}, issn = {1091-6490}, support = {RM1HG010461//HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; R21HG013504//HHS | NIH | National Human Genome Research Institute (NHGRI)/ ; }, mesh = {Escherichia coli/genetics/metabolism ; Humans ; *Escherichia coli Proteins/genetics/metabolism/chemistry ; *tRNA Methyltransferases/genetics/metabolism/chemistry ; RNA, Transfer/genetics/metabolism ; }, abstract = {Deep mutational scanning couples a protein's activity to DNA sequencing for high-throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like cell proliferation, as proxy for protein activity. Here, we covalently link variant proteins in vivo to an RNA barcode by fusing them to Escherichia coli tRNA (m5U54) methyltransferase TrmA (E358Q). This methyltransferase mutant forms a covalent bond with a tRNA T-arm stem-loop sequence, which we embed in an RNA along with a unique barcode. Following cell lysis, variant proteins are separated in vitro according to their biochemical properties and identified by sequencing their covalently linked barcodes. The in vitro assays can be carried out in highly denaturing conditions, such as 8 M urea, due to the covalent RNA-protein linkage. We use this method, Dosa, to analyze a large pool of FLAG epitope variants for binding to an anti-FLAG-antibody, to profile substrate variants for their cleavage by enteropeptidase and human rhinovirus 3C protease, and to measure the solubility of several hundred Aβ(1-42) variants. This method should be amenable to numerous biochemical assays with proteins produced in E. coli or mammalian cells.}, }
@article {pmid41478996, year = {2026}, author = {Fanli, M}, title = {Single-Cell 3' mRNA Sequencing with 10× Chromium Gel Beads-in-Emulsion (GEM) Kits.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2983}, number = {}, pages = {473-492}, pmid = {41478996}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; Humans ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; *RNA, Messenger/genetics ; *Sequence Analysis, RNA/methods ; Emulsions ; Chromium/chemistry ; Gene Expression Profiling/methods ; }, abstract = {Single-cell RNA sequencing is widely used in developmental biology, immunology, cancer research, and clinical applications, providing a scalable and reliable approach for single-cell transcriptomics. The Chromium Next GEM Single Cell 3' Reagent kits by 10× Genomics provide an advanced method for generating single-cell gene expression libraries using microfluidic partitioning and barcoding technology. These kits enable the profiling of thousands of individual cells in a single experiment by encapsulating single cells with uniquely barcoded Gel Beads-in-Emulsion (GEMs). Reverse transcription (RT) occurs within each GEM, producing barcoded cDNA, which is subsequently purified, amplified, and converted into a dual-indexed sequencing library. The workflow consists of four major steps: GEM generation and barcoding, post-GEM-RT cleanup and cDNA amplification, 3' gene expression library construction, and sequencing. Quality control measures, including SPRIselect bead cleanup, Bioanalyzer/TapeStation validation, and PCR optimization, ensure high-quality sequencing results. The final library is compatible with Illumina sequencing platforms, allowing researchers to analyze cellular heterogeneity, gene expression dynamics, and rare cell populations. This protocol is based on the 10× Chromium Single Cell 3' Reagent Kits user guide (v3.1-Dual Index), which can be downloaded from the 10× Genomics website (https://www.10xgenomics.com). It is recommended to refer to the original official guide for more details when carrying out the experiments with these kits, ensuring you stay updated with any revisions or updates.}, }
@article {pmid41478954, year = {2026}, author = {Dong, X and Edwards, S and Deng, YM and Dapat, C and Hirankitti, A and Barr, IG}, title = {Sequencing RSV Whole Genome Using a Long Amplicon-Based Method with Oxford Nanopore Technologies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3003}, number = {}, pages = {149-163}, pmid = {41478954}, issn = {1940-6029}, mesh = {Humans ; *Genome, Viral ; *Whole Genome Sequencing/methods ; *Respiratory Syncytial Virus, Human/genetics ; *Respiratory Syncytial Virus Infections/virology ; *Nanopore Sequencing/methods ; *High-Throughput Nucleotide Sequencing/methods ; Multiplex Polymerase Chain Reaction/methods ; Nanopores ; }, abstract = {Respiratory syncytial virus (RSV) infection continues to be a significant burden on public health care systems and is a global health concern. Whole genome sequencing (WGS) provides a useful tool to better understand the viral transmission and emerging mutations that may impact antibody treatments, antiviral drug sensitivity, and vaccine effectiveness. Here, we describe a rapid and sensitive protocol for sequencing clinical samples of both human RSV-A and RSV-B viruses based on the Oxford Nanopore Technology (ONT) sequencing platform. It involves long amplicon generation by setting up two one-step multiplex reverse-transcription polymerase chain reactions (mRT-PCR) for each sample, library preparation with the ONT rapid barcoding kit and NGS data analysis with the ARTIC pipeline.}, }
@article {pmid41477882, year = {2026}, author = {Campbell, IW and Hullahalli, K and Waldor, MK}, title = {Quantifying host-microbe interactions with bacterial lineage tracing.}, journal = {Science (New York, N.Y.)}, volume = {391}, number = {6780}, pages = {34-40}, doi = {10.1126/science.adx5362}, pmid = {41477882}, issn = {1095-9203}, mesh = {*Host Microbial Interactions/genetics ; *Bacteria/genetics/classification ; *DNA Barcoding, Taxonomic ; Animals ; Humans ; *Host-Pathogen Interactions ; *Bacterial Infections/microbiology ; }, abstract = {Using genomic barcodes to trace bacterial lineages within a host reveals previously unobservable dynamics of infection, including the impact of infection bottlenecks, routes of bacterial dissemination, and patterns of within-host evolution. Barcoding introduces trackable diversity to otherwise isogenic bacterial populations. Comparing the barcodes within an inoculum to those within the host quantifies the "founding population," which reveals the magnitude of population collapse caused by host bottlenecks. Furthermore, comparisons of the founders between tissues can reveal the patterns of pathogen dissemination. On longer timescales, the emergence of dominant barcoded lineages can also be used to detect within-host evolution. Collectively, barcoding studies quantify the hidden parameters that underlie bacterial colonization and create a quantitative framework for modeling and preventing infectious disease.}, }
@article {pmid41476166, year = {2025}, author = {Chen, Q and Sriram, A and Das, A and Matic, K and Hendija, M and Tonry, K and Ross, JL and Das, M and McGorty, RJ and Robertson-Anderson, RM and Valentine, MT}, title = {BARCODE: high throughput screening and analysis of soft active materials.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67963-3}, pmid = {41476166}, issn = {2041-1723}, support = {NSF DMR-2119663//National Science Foundation (NSF)/ ; NSF DMR-2118403//National Science Foundation (NSF)/ ; NSF DMR-2118449//National Science Foundation (NSF)/ ; NSF DMR-1933487//National Science Foundation (NSF)/ ; CS-PBP-2023-019//Research Corporation for Scientific Advancement (RCSA)/ ; }, abstract = {Active, responsive, non-equilibrium materials-at the forefront of materials engineering-offer dynamical restructuring, mobility and other complex life-like properties. Yet, this enhanced functionality comes with significant amplification of the size and complexity of the datasets needed to characterize their properties, thereby challenging conventional approaches to analysis. To meet this need, we present BARCODE: Biomaterial Activity Readouts to Categorize, Optimize, Design and Engineer, an open-access software that automates high throughput screening of microscopy video data to enable non-equilibrium material optimization and discovery. BARCODE produces a unique fingerprint or 'barcode' of performance metrics that visually and quantitatively encodes dynamic material properties with minimal file size. Using three complementary material-agnostic analysis branches, BARCODE significantly reduces data dimensionality and size, while providing rich, multiparametric outputs and rapid tractable characterization of activity and structure. We analyze a series of datasets of cytoskeleton networks and cell monolayers to demonstrate BARCODE's abilities to accelerate and streamline screening and analysis, reveal unexpected correlations and emergence, and enable broad non-expert data access, comparison, and sharing.}, }
@article {pmid41474525, year = {2025}, author = {Unitt, A and Krisna, MA and Parfitt, KM and Jolley, KA and Maiden, MCJ and Harrison, OB}, title = {Neisseria gonorrhoeae LIN codes provide a robust, multi-resolution lineage nomenclature.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {41474525}, issn = {2050-084X}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 10.35802/218205/WT_/Wellcome Trust/United Kingdom ; 10.35802/214374/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Neisseria gonorrhoeae/genetics/classification ; Multilocus Sequence Typing/methods ; *Terminology as Topic ; Phylogeny ; Gonorrhea/microbiology ; Humans ; *DNA Barcoding, Taxonomic/methods ; }, abstract = {Investigation of the bacterial pathogen Neisseria gonorrhoeae is complicated by extensive horizontal gene transfer: a process which disrupts phylogenetic signals and impedes our understanding of population structure. The ability to consistently identify N. gonorrhoeae lineages is important for surveillance of this increasingly antimicrobial resistant organism, facilitating efficient communication regarding its epidemiology; however, conventional typing systems fail to reflect N. gonorrhoeae strain taxonomy in a reliable and stable manner. Here, a N. gonorrhoeae genomic lineage nomenclature, based on the barcoding system of Life Identification Number (LIN) codes, was developed using a refined 1430 core gene MLST (cgMLST). This hierarchical LIN code nomenclature conveys lineage information at multiple levels of resolution within one code, enabling it to provide immediate context to an isolate's ancestry, and to relate to familiar, previously used typing schemes such as Ng cgMLST v1, 7-locus MLST, or NG-STAR clonal complex (CC). Clustering with LIN codes accurately reflects gonococcal diversity and population structure, providing insight into associations between genotype and phenotype for traits such as antibiotic resistance. These codes are automatically assigned and publicly accessible via the https://pubmlst.org/organisms/neisseria-spp database.}, }
@article {pmid41472846, year = {2025}, author = {Wang, G and Zhao, L and Shi, Y and Qu, F and Ding, Y and Liu, W and Liu, C and Luo, G and Li, M and Bai, X and Li, L and Wang, L and Wong, CC and Ho, YP and Yu, J}, title = {High-throughput generic single-entity sequencing using droplet microfluidics.}, journal = {iMeta}, volume = {4}, number = {6}, pages = {e70087}, pmid = {41472846}, issn = {2770-596X}, abstract = {Single-cell sequencing has revolutionized our understanding of cellular heterogeneity by providing a micro-level perspective in the past decade. While heterogeneity is fundamental to diverse biological communities, existing platforms are primarily designed for eukaryotic cells, leaving significant gaps in the study of other single biological entities, such as viruses and bacteria. Current methodologies for single-entity sequencing remain limited by low throughput, inefficient lysis, and highly fragmented genomes. Here, we present the Generic Single-Entity Sequencing (GSE-Seq), a versatile and high-throughput framework that overcomes key limitations in single-entity sequencing through an integrated workflow. GSE-Seq combines (1) one-step generation of massive barcodes, (2) degradable hydrogel-based in situ sample processing and whole genome amplification, (3) integrated in-droplet library preparation, and (4) long-read sequencing. We applied GSE-Seq to profile viral communities from human fecal and marine sediment samples, generating thousands of high-quality single-entity genomes and revealing that most are novel. GSE-Seq identified not only dsDNA and ssDNA viruses, but also hard-to-detect giant viruses and crAssphages. GSE-Seq of bacterial genomes also revealed putative novel bacterial species, validating the versatility of this platform across different microbial kingdoms. Collectively, GSE-Seq represents a robust framework that addresses persistent challenges in high-throughput profiling for generic applications and holds immense promise for single-cell deconvolution of diverse biological entities.}, }
@article {pmid41472828, year = {2025}, author = {Bonet, DF and Blumenthal, JI and Lang, S and Dahlberg, SK and Hoffecker, IT}, title = {Spatial coherence in DNA barcode networks.}, journal = {Patterns (New York, N.Y.)}, volume = {6}, number = {12}, pages = {101428}, pmid = {41472828}, issn = {2666-3899}, abstract = {DNA barcode networks are the basis of sequencing-based microscopy, an emerging family of chemical imaging methods aiming to reconstruct spatial information, without optics, using sequencing technology. These methods capture microscopic spatial information by forming networks composed of many local chemical interactions, each marked by a unique, DNA-based barcode. However, the fundamental laws governing such networks are not yet understood, and spatial barcode networks are influenced by structural distortions such as false or shortcut edges. Current methods lack ground-truth-free tools to validate spatial quality, and we address this with a framework for topology-based quality control. We define a fundamental feature of spatial networks, spatial coherence, which quantifies geometric self-consistency in a network. By formalizing this relationship into quantitative metrics adapted from classical geometric rules, we could quantify spatial distortions by using only network data and show how these can be used as an optimization criterion to iteratively improve spatial reconstruction.}, }
@article {pmid41472539, year = {2025}, author = {Gustafsson, DR and Lee, L and Grossi, AA and Zou, F and Tan, DJX and Song, HW and Meier, R}, title = {From host to host, and continent to continent: Two phoresy-enabled Guimaraesiella hitchhiker louse species revealed by integrative taxonomy (Phthiraptera: Ischnocera).}, journal = {Medical and veterinary entomology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mve.70045}, pmid = {41472539}, issn = {1365-2915}, support = {GIABR-GJRC201701//Introduction of Full-Time High-Level Talent Fund of the Institute of Zoology, Guangdong Academy of Sciences/ ; 31961123003//National Natural Science Foundation of China/ ; 32001098//National Natural Science Foundation of China/ ; //Foreign Young Talent Plan/ ; //Guangdong Academy of Sciences Special Project of Science and Technology Development/ ; //Pearl River Talent Recruitment Program of Guangdong Province/ ; }, abstract = {The 'core Guimaraesiella' comprise a morphologically rather homogeneous group of avian chewing lice (Phthiraptera), most of which remain undescribed. Based on an integrative approach combining morphological characters and analyses of COI barcoding sequences, we here describe two new species within this group: Guimaraesiella impiger new species and Guimaraesiella stellana new species. Both species were collected from hippoboscid flies in Singapore, suggesting that they are capable of moving phoretically between hosts. In at least G. impiger, this was confirmed as louse specimens from another 30 host species that were found to be conspecific with the holotype of G. impiger in our mOTU analysis. This, together with limited morphological variability between species, highlights the need to combine genetic and morphological data when identifying 'core Guimaraesiella' species from southeast Asia. Moreover, both louse species appear to be able to cross vast geographical distances. Guimaraesiella impiger is known from across southeast Asia as well as in Malawi, despite none of the known hosts occurring in both Asia and Africa. Guimaraesiella stellana is known from two host species, one in Singapore and one in Australia, separated by several known biogeographical barriers, which seem to have limited the range of all known closely related species to the Australo-Papuan region; how G. stellana arrived in Singapore on a nonmigratory host is presently unknown. These cases highlight that comparisons with only locally occurring louse species may not be a valid identification method for this group. As both species described here are morphologically similar, identification of cryptic species of lice in this group within Guimaraesiella may need to rely on COI barcodes or other molecular markers.}, }
@article {pmid41471855, year = {2025}, author = {Cova, BO and Saranholi, BH and Gestich, CC and Machado, PR and Monte-Alegre, AF and Schriefer, A}, title = {Invertebrate-Derived DNA (iDNA) to Identify Sand Flies' Bloodmeal: A Molecular Approach to Identifying Hosts in Blood-Feeding Vectors of Leishmaniasis.}, journal = {Microorganisms}, volume = {13}, number = {12}, pages = {}, pmid = {41471855}, issn = {2076-2607}, support = {1U01AI136862-18/NH/NIH HHS/United States ; }, abstract = {DNA metabarcoding data obtained by next generation sequencing (NGS) has been used to identify species in mixed biological samples, such as DNA from the gut content of invertebrates that feed on vertebrates (invertebrate-derived DNA, iDNA). This investigation employed DNA metabarcoding approach to determine vertebrate hosts of female phlebotomine sand flies, blood-feeding leishmaniasis vectors. We evaluated performance across three mitochondrial markers: a mammal-specific mini-barcode (16S rRNA), a pan-vertebrate mini-barcode (12S rRNA), and a standard CytB barcode region. Phlebotomine sand flies collections occurred in the Cacao Region of Southeastern Bahia, Brazil, an American Tegumentary Leishmaniasis (ATL) endemic zone. Our analysis examined iDNA from forty female specimens pooled in thirteen samples of seven sand fly species, including confirmed ATL vectors. Metabarcoding-derived operational taxonomic units (OTUs) underwent taxonomic assignment through comparison with GenBank NCBI[®] reference databases. Results identified twenty vertebrate OTUs: primates (four OTUs), rodents (four), ungulates (five), marsupials (one), plus a domestic dog and a chicken. Notably, non-mammalian taxa, including reptiles (one OTU) and amphibians (three), were detected. The iDNA metabarcoding approach allowed us to accurately sample the diversity of phlebotomine sandflies' bloodmeals in a single specimen of a non-engorged female sand fly with mixed feeding.}, }
@article {pmid41471226, year = {2025}, author = {Apaa, TT and Oke, PO and Shima, FK and Fidelis, GA and Dunham, S and Tarlinton, R}, title = {Canine Ticks, Tick-Borne Pathogens and Associated Risk Factors in Nigeria.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, doi = {10.3390/pathogens14121271}, pmid = {41471226}, issn = {2076-0817}, support = {00000//University of Nottingham/ ; }, mesh = {Animals ; Dogs ; Nigeria/epidemiology ; *Dog Diseases/epidemiology/parasitology/microbiology ; Risk Factors ; *Tick-Borne Diseases/epidemiology/veterinary/parasitology ; *Tick Infestations/veterinary/epidemiology/parasitology ; Male ; *Ticks/microbiology/parasitology ; Female ; Prevalence ; Ehrlichia/isolation &amp; purification/genetics ; Anaplasma/isolation &amp; purification ; Rhipicephalus sanguineus ; Babesia/isolation &amp; purification/genetics ; }, abstract = {Tick-borne pathogens (TBPs) pose a significant threat to canine health in Nigeria. Despite this, there is little data on the molecular identification of ticks and TBPs of dogs in Nigeria. This study assessed the prevalence of ticks and TBPs in Nigerian dogs, along with associated risk factors. A total of 259 dogs were enrolled in the study, from which 112 adult ticks were collected. Of these, 40 were characterized by molecular barcoding confirming Rhipicephalus sanguineus (R. sanguineus, 35/40) and Haemphysalis leachi (H. leachi, 5/40) infestations. Nucleotide sequences showed high percentage similarity to R. sanguineus tropical lineage and H. leachi sequences from Chad. Point-of-care (POC) testing of 259 dogs detected antibodies to TBPs in 40.9% of blood samples, with Ehrlichia (29.7%), Anaplasma (10.8%), and Dirofilaria (0.4%) species identified. PCR assays revealed a prevalence of 58.7% for TBPs, including Ehrlichia (40.5%) and Babesia (17.4%), with 7.3% co-infected. Risk factor analysis showed that adult dogs and those infested with ticks had a higher likelihood of TBP seropositivity. Exotic breeds and dogs examined during the rainy season were more likely to test positive for TBPs via PCR. Overall, this study demonstrates the high prevalence of diverse TBPs in Nigerian dogs and suggests that dog breed may play a role in susceptibility to diseases.}, }
@article {pmid41470621, year = {2025}, author = {Krivina, E and Sinetova, M and Starikov, A and Portnov, A and Temraleeva, A}, title = {Evaluating Species Delimitation Methods in Chloroidium (Trebouxiophyceae, Chlorophyta): Efficacy of DNA Barcodes and Description of Chloroidium pseudoellipsoideum sp. nov. from Arctic Soils.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {24}, pages = {}, pmid = {41470621}, issn = {2223-7747}, support = {# 075-15-2025-485//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Despite extensive research into green microalgae belonging to the genus Chloroidium, their species diversity and biotechnological potential remain poorly characterized. The strain VKM Al-418, the subject of this study, was isolated from the soil of Duvannyi Yar (Russian Federation). The independent species status of this strain is supported by distinct morphological characteristics, robust phylogenetic placement based on the 18S-ITS1-5.8S-ITS2 fragment, and unique features in the secondary structures of both ITS1 and ITS2, including one compensatory base change (CBC) in the highly conserved helix III of ITS2. Additionally, the species delimitation was also confirmed using five independent algorithmic approaches analyzing four different DNA barcodes. The concatenated ITS1-5.8S-ITS2 fragment is more reliable for species discrimination than the individual ITS1 or ITS2 barcodes. Of the species delimitation methods evaluated, ASAP (Assemble Species by Automatic Partitioning) and GMYC (Generalized Mixed Yule Coalescent) performed best in distinguishing Chloroidium species across multiple barcode regions in our analysis. The fatty acid profile of strain VKM Al-418 was analyzed at 9 °C, 22 °C, and 27 °C and exhibited high plasticity in response to temperature, indicative of an adaptive strategy to its harsh environment. Using this integrative taxonomic approach, we describe Chloroidium pseudoellipsoideum sp. nov., a new species with a distinct phylogenetic positioning and promising biotechnological properties.}, }
@article {pmid41470043, year = {2025}, author = {Martin, PA and Pacheco-Sierra, G and Mestre, AP and Siroski, P and Amavet, PS}, title = {DNA Barcoding for Species Identification and Conservation of Caimans (Crocodilia: Alligatoridae).}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.70060}, pmid = {41470043}, issn = {2471-5646}, support = {//Student Research Assistance Scheme (SRAS)/ ; PICT-2013-1402//Agencia (FONCyT)/ ; }, abstract = {Systematics has become an essential aspect of managing and conserving species from the order Crocodilia. All members of the group are listed in CITES appendices, and to control illegal traffic of animals and subproducts, we must be able to correctly assess the specific identity of the samples. Genetic DNA barcoding is a very efficient tool for species identification in the animal kingdom, based on the sequencing of a region of a mitochondrial gene, the Cytochrome oxidase subunit I (COI). Our principal aims were to design specific primers that allow obtaining this sequence from the genetic material of the caiman species and test the potential utility of barcoding in forensic studies, as well as verify the correct identification of different collections. We successfully obtained barcodes using our designed primers to amplify caiman samples, studying a fragment of 610 bp. We also compared sequences (N = 290) from public databases of all the species included in the Order Crocodilia, obtaining a tree that resulted in a similar current crocodilian phylogeny. The primers designed can be applied to obtain barcodes from samples of other crocodilian species, and this information can contribute significantly to forensic and systematic studies.}, }
@article {pmid41469971, year = {2025}, author = {Bradley, DD and Schimke, EJ and Alvey, AP and Hofmann, HA and Solomon-Lane, TK}, title = {Tagging Very Small Fish: Two Effective and Low Impact Methods.}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.70058}, pmid = {41469971}, issn = {2471-5646}, support = {IOS-1354942//NSF/ ; #947 (2016)//BEACON Center for the Study of Evolution in Action/ ; #1081 (2017, 2018)//BEACON Center for the Study of Evolution in Action/ ; IOS-2341006//NSF/ ; //Department of Natural Sciences/ ; }, abstract = {Identifying individuals over time and across contexts is essential in many scientific fields. There are a variety of well-established methods for uniquely marking individuals (e.g., visible implant elastomer, barcodes, paint). However, for some species, life history stages, and/or experiments, existing methods are not sufficient. Here, we describe procedures for how two tagging methods-a tattoo ink injection method and a fishing line piercing method - can be used with the youngest, smallest juveniles of the African cichlid fish, Astatotilapia burtoni, which are too small for the methods used with adults. With the tattoo method, we injected tattoo ink into the dorsal muscle. Different colors and injection locations can be used to distinguish among individuals over a period of weeks (up to 4 weeks, average 2.5-3 weeks under our conditions). Because fish this young and small are sensitive to handling and injection, we also include physiological data showing fish recover well from anesthetization and tagging. With the piercing method, very thin fishing line is threaded through the dorsal muscle and tied into a barbell or loop. Unique colors and patterns can be used to distinguish among individuals over a period of months. Because a physical tag might impede normal movement in a very small fish, we also include data from an open field exploration test showing similar behavior between tagged and control (non-tagged) juveniles. We expect these effective and inexpensive methods to be useful for a variety of small species and will facilitate early-life, developmental, and longitudinal research.}, }
@article {pmid41465714, year = {2025}, author = {Rincón, JA and Del Río, MG and Marvaldi, AE}, title = {Taxonomic Revision of the South American Genus Eudius and First Insights into the Phylogeny of the Tribe Eudiagogini (Curculionidae: Entiminae).}, journal = {Insects}, volume = {16}, number = {12}, pages = {}, pmid = {41465714}, issn = {2075-4450}, support = {PIP 3108//CONICET/ ; }, abstract = {The genus Eudius Schoenherr is classified in the broad-nosed weevil tribe Eudiagogini (Entiminae) and harbors two species, Eudius quadrisignatus Gyllenhal and Eudius jocosus Fahraeus, which are only known from their original descriptions. It is endemic to the Brazilian Atlantic Forest, which is one of the most threatened biomes in the world despite being a biodiversity hotspot. In this contribution, and as part of a wider systematic and phylogenetic study on tribe Eudiagogini, we performed a taxonomic revision of the genus Eudius and made preliminary phylogenetic analyses of Eudiagogini based on morphology and molecular evidence. Specimens from seven collections in Argentina, Brazil, and Europe were examined. Diagnosis and redescription of the genus and its species are provided, along with photographs of habits, and illustrations of diagnostic characters and new geographic distribution data. Additionally, a lectotype is designated for each species. The morphology-based phylogenetic analysis was performed under maximum parsimony, using 60 characters from adults coded for representative species from eight genera of Eudiagogini and other related tribes of Entiminae. As a result, monophyly of the genus Eudius and its placement within the tribe Eudiagogini are confirmed, while placement of the genus Chileudius Kuschel in Eudiagogini is refuted. A first molecular phylogenetic analysis of the tribe was also designed, using DNA sequences (of the COI barcode and two ribosomal markers) available for some representatives of Eudiagogini and outgroup taxa, analyzed under parsimony and maximum likelihood. The molecular results are consistent with morphology in recovering a monophyletic tribe Eudiagogini, excluding the genus Chileudius, which is now placed as incertae sedis in Entiminae, pending further analyses. Informative characters within the tribe are discussed, with Eudius supported as a clade by the basally connate tarsal claws and by the sclerites present in the bursa of female genitalia. Synapomorphies justifying the revised concept of Eudiagogini as a natural tribe are highlighted, like the presence of a cavernous prementum and the metaventrite with a spine-like swelling anterior to each metacoxa.}, }
@article {pmid41465705, year = {2025}, author = {Shapoval, NA and Nokkala, S and Nokkala, C and Shapoval, GN and Labina, ES and Romanovich, AE and Kuznetsova, VG}, title = {Genetic Differentiation of Bisexual and Parthenogenetic Populations of Plant Louse Cacopsylla ledi (Hemiptera, Psylloidea).}, journal = {Insects}, volume = {16}, number = {12}, pages = {}, pmid = {41465705}, issn = {2075-4450}, support = {FZMW-2023- 0006//Ministry of Science and Higher Education of the Russian Federation/ ; 125012901042-9//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The psyllid genus Cacopsylla comprises mainly bisexually reproducing species; however, some members of this genus exhibit a unisexual mode of reproduction. Using an integrative approach that combines molecular and cytogenetic methods, as well as Wolbachia screening, we conducted a comprehensive study of the Palaearctic species C. ledi. We show that this species uses various reproductive strategies (bisexual and parthenogenetic) across its distribution range. Our findings indicate that the bisexual mode of reproduction has emerged at least twice in the evolutionary history of C. ledi. Bisexual populations in southern Fennoscandia are of ancestral origin, whereas the bisexual mode of reproduction observed in northern Fennoscandia represents a recent secondary transition from parthenogenesis. We report that in the first case, parthenogenetic and bisexual lineages can be easily distinguished not only cytogenetically but also by DNA barcoding, while in the second case, "bisexual" individuals share DNA barcodes with parthenogenetic ones. A comprehensive Wolbachia screening (1140 specimens across the entire distribution range) revealed Wolbachia infection in every specimen of C. ledi, indicating a significant role of the endosymbiont in the biology and evolution of this species.}, }
@article {pmid41465176, year = {2025}, author = {Budowle, B and Sajantila, A and Vanek, D}, title = {Animal Species and Identity Testing: Developments, Challenges, and Applications to Non-Human Forensics.}, journal = {Genes}, volume = {16}, number = {12}, pages = {}, pmid = {41465176}, issn = {2073-4425}, support = {VJ01010026//Ministry of Interior, Czech Republic/ ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Forensic Genetics/methods ; Humans ; *DNA Barcoding, Taxonomic/methods ; Species Specificity ; Genetic Markers ; }, abstract = {Biological samples of non-human origin, commonly encountered in wildlife crime investigations, present distinct challenges regarding forensic DNA analysis efforts. Although the types of samples encountered in human identity testing can vary to some degree, analyzing DNA from one species is facilitated by unified processes, common genetic marker systems, and national DNA databases. In contrast, non-human animal species identification is confounded by a diverse range of target species and a variety of sampling materials, such as feathers, processed animal parts in traditional medicine, and taxidermy specimens, which often contain degraded DNA in low quantities, are contaminated with chemical inhibitors, and may be comingled with other species. These complexities require specialized analytical approaches. Compounding these issues is a lack of validated non-human species forensic sampling and typing kits, and the risk of human DNA contamination during evidence collection. Markers residing on the mitochondrial genome (mtDNA) are routinely sought because of the large datasets available for comparison and their greater sensitivity of detection. However, the barcoding results can be complicated at times for achieving species-level resolution, the presence of nuclear inserts of mitochondrial DNA (NUMTs), and the limitation of mtDNA analysis alone to detect hybrids. Species-specific genetic markers for identification have been developed for a few high-profile species; however, many CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora)-listed organisms lack specific, validated forensic analytical tools, creating a significant gap in investigative enforcement capabilities. This deficiency stems in part from the low commercial nature of wildlife forensics efforts, a government research-driven field, the difficulty of obtaining sufficient reference samples from wild populations, limited training and education infrastructure, and inadequate funding support.}, }
@article {pmid41465154, year = {2025}, author = {Xu, D and Zhang, L and Zhang, C and Song, L and Qian, W and Luo, H and Zhao, Q}, title = {Comparative Analysis and Characterization of Plastid Genomes of Mycetia (Rubiaceae).}, journal = {Genes}, volume = {16}, number = {12}, pages = {}, pmid = {41465154}, issn = {2073-4425}, support = {32200169//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Plastid ; Phylogeny ; Microsatellite Repeats/genetics ; *Rubiaceae/genetics/classification ; Base Composition ; Genome, Chloroplast ; Codon Usage ; Evolution, Molecular ; Plastids/genetics ; }, abstract = {BACKGROUND: Mycetia, a subshrub genus within the subfamily Rubioideae (Rubiaceae), is predominantly distributed in tropical Asia, lacking comprehensive plastid genomic resources. This study aimed to characterize the complete plastid genomes of two Mycetia species and explore their structural features and evolutionary relationships.<br><br>METHODS: The plastid genomes of Mycetia hirta and Mycetia sinensis were sequenced and assembled. We analyzed genome structure, simple sequence repeats (SSRs), long repeats, codon usage, nucleotide diversity (&#x3c0;), and Ka/Ks and conducted phylogenetic analysis.<br><br>RESULTS: Both genomes exhibited a typical quadripartite structure (153,989-154,588 bp; GC content 37.7-37.8%), encoding 126 genes (86 protein-coding, 8 rRNA, and 32 tRNA). Both chloroplast genomes contained 52-60 SSRs and three repeat types with minor interspecific differences. Junction regions and codon usage were highly conserved, with slight variations in RSCU values. The average &#x3c0; was 0.0096, and the non-coding trnE-trnT (&#x3c0; = 0.0817) emerged as a potential DNA barcode. The average Ka/Ks was 0.2900, indicating purifying selection. Phylogenetic analysis confirmed the monophyly of Mycetia within Argostemmateae.<br><br>CONCLUSIONS: This study provides the first comparative plastid genomic analysis for Mycetia, enhancing our understanding of its genetic diversity and supporting future phylogenetic and taxonomic research on the genus.}, }
@article {pmid41465096, year = {2025}, author = {Karbarz, M and Lebioda, E and Leśko, A}, title = {DNA Barcoding Protocol for Masdevallia Orchids: A Tool for CITES-Based Identification and Trade Control.}, journal = {Genes}, volume = {16}, number = {12}, pages = {}, pmid = {41465096}, issn = {2073-4425}, support = {Agreement No. RID/SP/0010/2024/1//Minister of Science of the Republic of Poland under the Program "Regional Initiative of Excellence"/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; Endangered Species ; DNA, Plant/genetics ; Conservation of Natural Resources ; }, abstract = {Background: Orchids of the Masdevallia genus are characterized by their beautiful esthetic qualities. However, they are vulnerable to habitat destruction, illegal harvesting, tourism and climate change. These extinction threats have led to the listing of all Masdevallia species in Appendix II of CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) and their selection by the IUCN (International Union for Conservation of Nature). Orchids are sold in various forms, e.g., stems or tubers, rendering them impossible to identify based on morphology alone. DNA barcoding is a method that enables reliable identification of organisms using DNA barcodes, and it offers an excellent solution to the need for efficient identification of Masdevallia orchids. The aim of this study was to determine the most effective locus for DNA barcode identification of Masdevallia orchids in order to develop a quick and practical identification method for this genus. Such a method can be used by CITES verification authorities to detect illegal trade. This is the first focused study to validate a DNA barcoding protocol for Masdevallia for CITES enforcement purposes. Methods: Three genetic regions were analyzed: matK, rbcL, and ITS. The effectiveness of identification was verified based on results obtained from the new version of the BOLD Systems v.5 reference database. Results: Although Masdevallia is not well represented in this database, successful identification to the genus level was achieved. Conclusions: The highest identification efficiency at the genus level was achieved for the ITS region (91%).}, }
@article {pmid41463928, year = {2025}, author = {Barua, S and Tarannum, A and Rupprecht, CE and Simonis, MC and Barrantes Murillo, DF and Willoughby, JR and Wang, C}, title = {A Simple Yet Reliable 12S rRNA-Based Molecular Approach for Identifying Bat Species.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {24}, pages = {}, doi = {10.3390/ani15243643}, pmid = {41463928}, issn = {2076-2615}, support = {G0018155//Alabama Department of Conservation &amp; natural Resources/ ; }, abstract = {Bats (Chiroptera) represent nearly one-fifth of all mammalian species and play vital ecological roles as pollinators, pest controllers, and reservoirs of zoonotic pathogens. Accurate identification of bat species is essential for biodiversity monitoring, conservation, and disease surveillance. Traditional methods based on morphology or acoustic calls are often limited by overlapping features, while DNA barcoding using the cytochrome oxidase I (COI) gene can be hindered by sequence variability. In this study, we developed a simple, single-step PCR assay targeting a short, variable region of the mitochondrial 12S rRNA gene. Alignment of sequences from 232 bat species allowed the design of a single primer pair producing a 203-224 bp amplicon that successfully distinguished all species analyzed. The assay achieved 100% amplification success across 241 bat samples, with 97.2% concordance between molecular and morphological identification. Two samples showed sequence divergence suggestive of an undescribed species. Overall, ten bat species from six genera were identified, with Eptesicus fuscus being the most frequent. This assay offers a practical and robust approach for bat identification, supporting biodiversity assessment and pathogen surveillance in ecological and public health research.}, }
@article {pmid41460495, year = {2025}, author = {Podlipec, R and Krišelj, A and Zorc, M and Matjan Štefin, P and Usaar, S and Humar, M}, title = {Nanometer-Precision Tracking of Adipocyte Dynamics via Single Lipid Droplet Whispering-Gallery Optical Resonances.}, journal = {ACS sensors}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssensors.5c03272}, pmid = {41460495}, issn = {2379-3694}, abstract = {Biophotonics─and more recently, biointegrated photonics─offer transformative tools for probing cellular processes with unprecedented precision. Among these, whispering-gallery-mode (WGM) resonators (optical microcavities formed in spherical structures) have emerged as powerful biosensors and intracellular barcodes. Lipid droplets (LDs), with their high refractive index and intrinsic spherical geometry, are ideal candidates for supporting intracellular lasing. Although lasing in LDs has been previously demonstrated, it has not yet been harnessed to study live-cell biology. Here, we report the first use of WGM resonances in LDs of live primary adipocytes, employing a continuous-wave (CW) laser at powers below the biological damage threshold. By measuring these resonances, we achieved nanometer-scale precision in size estimation, enabling real-time observation of rapid LD dynamics and deformations on the minute scale─far beyond the spatiotemporal resolution of conventional microscopy. We systematically characterized this photonic sensing approach, demonstrating its ability to resolve adipocyte heterogeneity, monitor lipolytic responses to forskolin and isoproterenol, and detect early signs of cell viability loss─well before conventional assays. This proof-of-concept establishes intracellular LD WGM resonances as a robust platform for investigating live single-cell metabolism. The technique enables rapid, cost-effective assessment of adipocyte function, reveals cell-to-cell variability obscured by bulk assays, and lays the foundation for high-throughput analysis of metabolism- and obesity-related diseases at both the cellular and tissue levels.}, }
@article {pmid41459143, year = {2025}, author = {Fleming, AJ and Smith, MA and Hallwachs, W and Janzen, D}, title = {A new genus and a new species in the tribe Eryciini (Diptera, Tachinidae) from Area de Conservación Guanacaste in north-western Costa Rica.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e161853}, pmid = {41459143}, issn = {1314-2828}, abstract = {BACKGROUND: A new genus and species of within the tribe Eryciini are described from the Area de Conservación Guanacaste (ACG) in north-western Costa Rica. Specimens were reared from wild-caught caterpillars collected during an ongoing biodiversity inventory within the ACG. An integrative taxonomic approach was used to characterise the new taxa, incorporating morphological analysis, life history data and DNA barcodes, supported by high-resolution photographs. Furthermore, two new combinations are proposed and the associated species are re-described. A lectotype is designated for Exorista loxostegae (Reinhard, 1922) and an identification key to the species of the new genus is provided.<br><br>NEW INFORMATION: The description of the new genus Santarosamyia Fleming and Wood, 2024 gen. nov. along with the new species: Santarosamyia woodorum Fleming &amp; Wood sp. nov. are provided.The following new combinations are proposed: Nilea erecta (Coquillett, 1902) as Santarosamyia erecta (Coquillett, 1902) comb. nov.; Nilea uniplilum (Aldrich &amp; Webber, 1924) as Santarosamyia unipilum (Aldrich &amp; Webber, 1924) comb. nov.A lectotype is designated for Exorista loxostegae (Reinhard, 1922).Tachinidae, Diptera, Costa Rica, CO1, Parasitoid, Guanacaste.}, }
@article {pmid41458355, year = {2025}, author = {Qian, Y and Wang, F and Gao, J and Jiang, Z and Gao, X and Chen, Z}, title = {Integrating Extracellular Vesicles Proteomics and Clinical Parameters to Develop a High-Precision Predictive Model for Severe Asthma.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {17945-17960}, pmid = {41458355}, issn = {1178-7031}, abstract = {INTRODUCTION: This study aimed to identify biomarkers and develop a predictive model for distinguishing severe asthma (SA) from non-severe asthma (NSA) by integrating clinical data and extracellular vesicles (EVs) proteomics.<br><br>METHODS: Plasma-derived EVs were isolated from 44 individuals, including 15&#xa0;healthy controls, 15 SA patients, and 14 NSA patients. Proteomic profiling of EVs was performed using proximity barcoding assay (PBA). Clinical indicators such as FEV1/FVC ratio, DLCO% predicted, and blood neutrophil count were recorded. A multivariate model incorporating both clinical and EV-derived protein data was constructed and evaluated using ROC curve analysis. Candidate biomarkers were further validated in cell-based and murine SA models.<br><br>RESULTS: Although total EV counts and protein load did not differ significantly across groups, specific EV proteins (eg, SELL, PECAM1, ITGB3, CD9) were consistently elevated. Notably, protein combinations such as ITGB3&amp;CLDN1 and ESAM&amp;ITGA6 showed strong discriminatory power between SA and NSA (AUC > 0.8). The integrative model combining clinical metrics and EV proteins (IL6, NGFR, NFASC, PCDHA1) achieved a high predictive accuracy (AUC = 0.97 &#xb1; 0.075). Expression of IL6, NGFR, and NFASC was significantly upregulated in SA cellular and animal models, aligning with patient data.<br><br>CONCLUSION: This study presents a reliable multi-parameter model for distinguishing severe from non-severe asthma, leveraging both clinical indicators and EV proteomics. These findings support the potential of EV-based biomarkers in early diagnosis and personalized management of SA.}, }
@article {pmid41455508, year = {2025}, author = {Bassini-Silva, R and da Cruz, LF and Carvalho, JT and de Souza Mello-Oliveira, V and Pesenato, IP and Calchi, AC and Castro-Santiago, AC and de Oliveira Andrade, L and da Silva Zampim, G and de Oliveira Bonaldo, R and Miranda, LFD and Subutzki, MEBS and Perrone, RF and de Quadros, RM and Ueno, TEH and Hoppe, EGL and André, MR and Duarte, JMB and Dos Santos Cruz Piveta, C and Labruna, MB and Barros-Battesti, DM and Dowling, APG and de Castro Jacinavicius, F}, title = {Sleeping with the enemy II: Expanding the ecological, molecular, and epidemiological knowledge of the tropical fowl mite, Ornithonyssus bursa (Berlese, 1888).}, journal = {Parasitology international}, volume = {}, number = {}, pages = {103226}, doi = {10.1016/j.parint.2025.103226}, pmid = {41455508}, issn = {1873-0329}, abstract = {Ornithonyssus bursa (Berlese), the tropical fowl mite from the family Macronyssidae, is a hematophagous ectoparasite of birds with increasing importance in human and animal health. This study reports new cases of human parasitism associated with O. bursa in Brazil, involving direct contact with avian hosts or their nests. These cases include new geographic records in the states of São Paulo and Santa Catarina, and new associations with bird species, including the first known record in Amazona aestiva (Psittaciformes). Molecular analysis was performed on individual mites to characterize the species and investigate associated microorganisms. This study provides the first partial sequence of the cox1 gene for O. bursa and the first phylogenetic analysis for the family using this marker. Additionally, we report the first detection of Ehrlichia and Wolbachia in Brazilian specimens. Phylogenetic analyses based on the 16S rRNA sequences placed the Ehrlichia haplotype close to strains previously detected in Haemaphysalis spp. ticks and the Wolbachia haplotype within supergroup E. These findings expand our understanding of the ecological and microbial diversity of O. bursa, highlighting its public health relevance, and emphasize the need for further studies on its vector potential and evolutionary relationships.}, }
@article {pmid41453807, year = {2025}, author = {Hanna, AR and Shepherd, SJ and Datto, GA and El-Mayta, R and Anderson, T and Navarro, IB and Ricciardi, AS and Padilla, MS and Srikumar, N and Zhang, S and Yamagata, HM and Meng, NY and Buser, JR and Alameh, MG and Mitchell, MJ and Issadore, DA}, title = {Automated and Parallelized Microfluidic Generation of Large and Precisely Defined Lipid Nanoparticle Libraries.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.5c15613}, pmid = {41453807}, issn = {1936-086X}, abstract = {Lipid nanoparticles (LNPs) are being developed for a broad set of therapeutic applications by changing both the structures of the lipids used to formulate each LNP and their relative proportions. Because lipid synthesis and in vivo screening have been parallelized using combinatorial chemistry and LNP barcoding, respectively, the manual and sequential microfluidic formulation of LNPs remains the primary rate-limiting step during early-stage discovery. In this work, we present a parallelized, automated microfluidic platform capable of generating large, precisely defined LNP libraries in parallel, with throughput on the order of 1000 distinct formulations per hour. Each formulation is defined by varying the reagent flow ratios into one of eight microscale mixers using lithographically encoded fluidic resistors and dynamically controlled external pressure supplies. The microfluidic chip is integrated with custom robotic plate handling for the rapid collection of each distinct formulation. To evaluate this platform, we characterized 96 formulations generated on-chip in terms of both physicochemical properties and transfection efficiency in vitro. We further validated our lead candidate against the state of the art in vivo. We demonstrate the ability to rapidly discover a formulation and scale its production to liters per hour under identical mixing conditions, bridging from early discovery to manufacturing through microfluidic parallelization.}, }
@article {pmid41452897, year = {2025}, author = {Fontaine, A and Djigo, OKM and Gomez, N and Boukhary, AOMS and Basco, L and Briolant, S}, title = {Amplicon-based DNA sequencing to characterize Duffy antigen polymorphisms and analysis of Duffy blood system and glucose-6-phosphate dehydrogenase deficiency in Mauritania.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {12}, pages = {e0013882}, doi = {10.1371/journal.pntd.0013882}, pmid = {41452897}, issn = {1935-2735}, abstract = {BACKGROUND: Both Duffy blood antigen expression and G6PD deficiency are known to be associated with ethnic origin. Updates in epidemiological data on the prevalence of polymorphisms in these two human genes are key information for guiding national programs to eliminate Plasmodium vivax malaria.<br><br>METHODS: Duffy genotypes and their predicted phenotypes were determined in 943 blood samples from Mauritanian patients belonging to different ethnic groups (n&#x2009;=&#x2009;432 White Moors and n&#x2009;=&#x2009;511 individuals of black African ancestry) with a known G6PD genotype determined by PCR-restriction fragment length polymorphism in our previous study, using a cost-saving multiplexed barcoding technique that allows simultaneous analysis of a large number of samples and next-generation DNA sequencing (NGS).<br><br>RESULTS: Duffy-negative phenotype predicted from Duffy genotype was predominant in individuals with black African ancestry (65-88%), while 16% of white Moors were Duffy-negative. Among 432 samples with interpretable Duffy sequence data from white Moors, 7/356 (2.0%) were Duffy-positive and G6PD A- deficient; 8/76 (10.5%) were Duffy-negative and G6PD A- deficient, mostly (n&#x2009;=&#x2009;6) in heterozygous females. By contrast, among 511 patients of black African ancestry, 13 (13/140, 9.3% including heterozygous females) were Duffy-positive and G6PD A- deficient; 65 (65/371, 17.5%) were Duffy-negative and G6PD A- deficient, mostly (n&#x2009;=&#x2009;44) in heterozygous females.<br><br>CONCLUSION: A large majority of white Moors are Duffy-positive and susceptible to P. vivax infection, but most are eligible for anti-hypnozoite therapy with primaquine at the standard dose. About 15.4% of individuals with black African ancestry were affected by G6PD A- deficiency, independently of their Duffy receptor status. This population requires G6PD screening before primaquine therapy in rare cases of P. vivax infection. These results provide important clues about the feasibility to implement an efficient anti-hypnozoite treatment in Mauritania and identify priority areas for targeted interventions against P. vivax malaria.}, }
@article {pmid41446374, year = {2025}, author = {Fan, Y and Chen, L and Wu, Y and Wang, X and Tian, W and Ge, M and Li, C and Xie, Y}, title = {The Complete Chloroplast Genome of Synotis solidaginea and Phylogenetic Analysis.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72806}, pmid = {41446374}, issn = {2045-7758}, abstract = {Synotis is an important genus within the Asteraceae family. The genus comprises numerous species, many of which exhibit highly similar morphology, making identification using traditional taxonomic methods challenging. Therefore, developing a scientifically sound and effective identification method for Synotis plants is of significant importance. In this study, the complete chloroplast (cp) genome of Synotis solidaginea was sequenced using the Illumina HiSeq 4000 platform, analyzed, and compared with its closely related species. The results revealed that the complete chloroplast genome of S. solidaginea is 150,899 bp in length with a GC content of 37.47%. It exhibits the typical quadripartite structure, consisting of a large single-copy (LSC) region (83,338 bp), a small single-copy (SSC) region (17,885 bp), and two inverted repeat (IR) regions (each 24,838 bp). The genome encodes a total of 127 genes, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Thirty-two simple sequence repeats (SSRs) were identified. Four highly variable regions (trnG-UCC, ndhC-trnV-UAC_2, trnY-GUA-trnE-UUC, and trnH-GUG-psbA) were identified as potential DNA barcodes for species identification. Phylogenetic analysis revealed that S. solidaginea is closely related to its congeneric species Synotis cavaleriei, Synotis erythropappa, Synotis duclouxii, and Synotis nagensium. This study provides a reference for the phylogenetic analysis of Synotis using chloroplast genomics, and offers data support for the hybrid breeding of S. solidaginea to cultivate desirable ornamental traits or stress resistance traits. Furthermore, chloroplast genome research can also assist researchers in gaining a deeper understanding of the species origin of S. solidaginea and contribute to the study of species conservation and utilization.}, }
@article {pmid41446238, year = {2025}, author = {Sohn, S and Morgan, D and Callahan, C and Dockery, K and Brock, A and Zoldan, J}, title = {Cell Barcoding Reveals Lineage-dependent Outcomes in hiPSC Cardiac Differentiation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2025.12.12.694049}, pmid = {41446238}, issn = {2692-8205}, abstract = {UNLABELLED: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have potential applications in treating cardiovascular disease but are currently limited in their clinical translation. A primary limitation is the poor clinical scalability of hiPSC-CMs, with the heterogeneity of hiPSC cardiac differentiation significantly contributing to this limitation. We hypothesize that clinical scalability can be improved by tracking and controlling hiPSC clonal heterogeneity, a variable often overlooked in current differentiation approaches. "Fate priming", wherein clonal lineage identity determines differentiation fate, has been demonstrated in other stem cell differentiation pathways. We investigated fate priming in hiPSC cardiac differentiation using the ClonMapper cell barcoding platform to label, track, and isolate distinct hiPSC lineages from the same cell line. We show that certain hiPSC lineages preferentially differentiate into hiPSC-CMs or non-CMs. After isolating lineages with apparent fate priming, we found significant differences in cardiac differentiation outcomes between these single-clone populations and heterogeneous, multi-clone hiPSC populations. These findings indicate that lineage identity influences hiPSC cardiac differentiation outcomes.<br><br>SIGNIFICANCE STATEMENT: Cardiovascular disease is a significant global health concern that can be addressed by engineering artificial tissues to develop new treatments for heart disease or to directly replace damaged heart tissue. Stem cells are a useful tool for engineering these tissues because of their ability to become cardiomyocytes. However, their clinical translation is limited by variability in the process of differentiating stem cells into cardiomyocytes. This article reports findings that show different lineages of genetically identical human induced pluripotent stem cells have different capacities for differentiating into cardiomyocytes, which may contribute to the variability observed.}, }
@article {pmid41444830, year = {2025}, author = {Yang, Z and Zhang, Y and Fang, Y and Zhang, Y and Du, J and Shen, X and Zhang, K and Zou, P and Chen, Z}, title = {Spatial barcoding reveals reaction radii and contact-dependent mechanism of proximity labeling.}, journal = {Nature chemical biology}, volume = {}, number = {}, pages = {}, pmid = {41444830}, issn = {1552-4469}, support = {2022YFA1304700//Chinese Ministry of Science and Technology | Department of S and T for Social Development (Department of S&amp;T for Social Development)/ ; 32088101//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Proximity labeling techniques such as TurboID and APEX2 have become pivotal tools for studying protein interactions. However, the spatial patterns of labeling methods within the submicrometer range remain poorly understood. Here we used DNA nanostructure platforms to precisely measure the labeling radii of TurboID and APEX2 through in vitro assays. Our DNA nanoruler design enables the deployment of oligonucleotide-barcoded labeling targets with nanometer precision near the enzymes. By quantifying labeling yields using qPCR and mapping them against target distances, we uncovered surprising insights into the labeling mechanisms. Contrary to the prevailing diffusive labeling model, our results demonstrate that TurboID primarily operates through contact-dependent labeling. Similarly, APEX2 shows high labeling efficiency within its direct contact range. In parallel, it exhibits low-level diffusive labeling toward more distant phenols. These findings reframe our understanding in the mechanism of proximity labeling enzymes while highlighting the potential of DNA nanotechnology in spatially profiling reactive species.}, }
@article {pmid41440705, year = {2025}, author = {Tangthirasunun, N and Gautier, V and Lalanne, C and Bonometti, L and Cros-Arteil, S and Hayes, RD and Calhoun, S and Riley, R and Pangilinan, J and Lipzen, A and Ng, V and Grigoriev, IV and Gladieux, P and Giraud, T and Silar, P}, title = {Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {41440705}, issn = {2309-608X}, support = {DOE DE-AC02-05CH11231//the U.S. Department of Energy Joint Genome Institute/ ; KREF206612//King Mongkut's Institute of Technology Ladkrabang/ ; }, abstract = {Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type locus. In vitro fruiting was obtained for 16 strains, enabling the definition of seven new species, namely Pseudorhypophila gallica, Pseudorhypophila guyanensis Rhypophila alpibus, Rhypophila brasiliensis, Rhypophila camarguensis, Rhypophila reunionensis and Rhypophila thailandica, as well as two new combinations, namely Pseudorhypophila latipes and Pseudorhypophila oryzae. Eight strains for which in vitro fruiting was not obtained may belong to additional new species. These results expand the known diversity of the Naviculisporaceae and greatly enlarge the genomic data available for the family.}, }
@article {pmid41438958, year = {2025}, author = {Zhou, C and Ma, K and Wang, T and Tang, Y and Zhang, M and Yu, J and Liu, R and Ding, Q and Qiu, S and Li, Y and Ma, Z and Nie, G}, title = {Assessing Current Fish Diversity in the Yellow River Basin by Integrating Large-Scale Barcoding and Morphological Data.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72617}, pmid = {41438958}, issn = {2045-7758}, abstract = {In recent years, fish populations in the Yellow River (YR) basin have declined sharply due to human activities. Some studies even suggest that nearly half of the native fish species in the YR have disappeared. There are also significant differences among the literature on the systematic discussion of fish species in the Yellow River Basin. The construction of a standardized and complete DNA barcode database for YR fish is urgently needed. In this study, 127 sampling points were sampled in the YR basin from 2013 to 2023, and a DNA barcode database of 3011 sequences and 110 species was constructed. A total of 124 operable taxonomic units (OTUs) were identified via four sequence-based species classification methods. The barcode and morphological results of 84 (77.1%) species remained consistent. Some species cannot be described in the literature and are assigned to unique OTUs, and some widely distributed species are also assigned multiple OTUs. These findings indicate that the fish diversity in the YR basin has been severely underestimated, and more detailed investigations and further research are needed. This study constructed the first fish DNA barcode database in the YR basin and provided new insights for the study of fish diversity in the region.}, }
@article {pmid41438953, year = {2025}, author = {Schoenemann, K and Lim, HC and Keady, MM and Carr, DE}, title = {Pollen Foraging by Bumble Bee Queens During a Critical Nesting Period Revealed by DNA Metabarcoding.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72733}, pmid = {41438953}, issn = {2045-7758}, abstract = {The nest-founding stage represents an especially vulnerable period of the bumble bee (Bombus) life cycle, during which solitary queens must locate and collect sufficient foraging resources to sustain themselves and their brood. Yet, we lack contemporary information about floral foraging resources used by queens in early spring. Here, we use next-generation sequencing to characterize the floral species used by queens for pollen provisions during early nest establishment. We collected pollen loads from over 100 wild bumble bee queens at working farms, rural and city parks, and nature preserves across the Piedmont region of Virginia, USA. Using metabarcoding of two universal DNA barcodes for plants, ITS2 and rbcL, we determined the taxonomic composition of pollen used by queens. Pollen loads contained native and non-native woody (e.g., Cercis: Fabaceae, Prunus: Rosaceae, Salix: Salicaceae), herbaceous (e.g., Lamium: Lamiaceae, Viola: Violaceae), and vine (e.g., Lonicera: Caprifoliaceae) taxa. The non-native Lamium and Elaeagnus (Elaeagnaceae) most frequently hosted foraging queens, owing in part to their abundance across sites and the season. Pollen composition varied more over time than among bumble bee species or across sites, but land cover predicted a small amount of variation in pollen composition. Specifically, the percentage of crop land within 1 km increased the representation of Lamium in queen pollen loads, likely reflecting the abundance of the disturbance-adapted flower in fallow cornfields. Finally, the pollen communities detected by rbcL were twice as diverse as those by ITS2, perhaps owing to the better taxonomic resolution afforded by the fast-evolving rbcL marker. This study demonstrates that queens are flexible foragers and that among the most common Bombus species, plant phenology drives pollen use more than species identity. Further, this study highlights the importance of monitoring pollen diets to inform regional management strategies and considerations about metabarcoding techniques.}, }
@article {pmid41435415, year = {2025}, author = {Argue, BM and Gate, D}, title = {Basic Science and Pathogenesis.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {21 Suppl 1}, number = {Suppl 1}, pages = {e100419}, doi = {10.1002/alz70855_100419}, pmid = {41435415}, issn = {1552-5279}, mesh = {Humans ; *Alzheimer Disease/cerebrospinal fluid/genetics/blood ; *Cognitive Dysfunction/cerebrospinal fluid/genetics/blood ; Aged ; Male ; Protein Isoforms/genetics/cerebrospinal fluid ; Female ; Single-Cell Analysis ; }, abstract = {BACKGROUND: Single-cell long-read sequencing was performed on immune cells from cerebrospinal fluid (CSF) and blood to assess isoform diversity in healthy aging individuals and those diagnosed with mild cognitive impairment (MCI) or Alzheimer's disease (AD).<br><br>METHOD: cDNA from single-cell experiments was subjected to long-read sequencing using Oxford Nanopore Technologies. The dataset included immune cells from CSF (45 controls, 13 MCI/AD) and blood (22 controls, 28 AD). Computational analysis incorporated scNanoGPS for extracting cell barcodes and mapping reads to the genome, IsoQuant for isoform modeling, and SQANTI3 for filtering artifacts.<br><br>RESULTS: Single-cell long-read sequencing identified 97,920 unique transcripts, with half of all genes exhibiting multiple isoforms. Notably, 20% of the detected isoforms were previously unannotated in the human genome. Novel isoforms were observed in AD-associated genes, including BIN1 and PTK2B, with BIN1 displaying lymphoid cell-specific isoforms.<br><br>CONCLUSION: Human immune cells demonstrate extensive isoform diversity, including previously unannotated isoforms, particularly in genes implicated in AD.}, }
@article {pmid41432445, year = {2025}, author = {Giorgio, RT and Le, MT and Zhang, T and Holmes, CL and Hullahalli, K}, title = {Accurate interpretation of within-host dissemination using barcoded bacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0146025}, doi = {10.1128/msystems.01460-25}, pmid = {41432445}, issn = {2379-5077}, abstract = {Bacterial dissemination across tissues is a critically important process influencing infection outcomes. Monitoring within-host dissemination is challenging because conventional measures of bulk bacterial burden cannot distinguish between lineages that are shared between tissues and those that replicate locally. This limitation can be overcome using barcoded bacteria, where deep sequencing of the barcode locus and comparisons of barcodes between tissues define which lineages spread within the host. Numerous studies have used barcoded bacteria to generate high-resolution maps of dissemination. However, since multiple cells in the infectious inoculum can contain identical barcodes, inferences about dissemination can be confounded when distinct lineages from the inoculum with identical barcodes are observed in different tissues. Thus, even though the same barcodes can be observed in different tissues, dissemination between these tissues may not have occurred. Here, we aimed to develop an approach that would provide a solution to this confounding effect. We developed a simulation-based distance metric that quantifies the significance of observing shared barcodes between tissues. We validated this approach using simulated data sets spanning three orders of magnitude in barcode diversities and on three published experimental infection data sets. Our reanalysis reveals previously unappreciated patterns of Escherichia coli spread during liver abscess formation, clarifies the role of the Muc2 mucin in Listeria monocytogenes systemic spread, and quantifies how Klebsiella pneumoniae replication in the lungs drives systemic dissemination. As barcoding studies expand across diverse infection models, this approach provides an essential tool for accurate interpretation of within-host bacterial dissemination.IMPORTANCEHow microbes move between tissues in the host is an important factor that controls the outcome and severity of infections. A powerful method to monitor within-host microbial dissemination is the use of barcoded bacteria and lineage tracing. Comparisons of barcodes between tissues enable inferences of microbial dissemination, and this method has been applied to diverse contexts of bacterial infections. Here, we demonstrate that inferences of microbial dissemination are confounded, where observing identical barcodes in different tissues does not always signify that dissemination has occurred. To overcome this limitation, we define a metric to quantify the extent to which sharing of barcodes is meaningful and provide new insights into previous barcoding studies in Escherichia coli, Listeria monocytogenes, and Klebsiella pneumoniae. As bacterial lineage tracing continues to be applied across diverse models, our method will help ensure accurate interpretations of microbial dissemination.}, }
@article {pmid41431142, year = {2025}, author = {Shaw, AJ and Duffy, AM and Aguero, B and Nieto-Lugilde, M and Imwattana, K and Robinson, SC and Schuette, S and Wilkens, RT and Yavitt, J and Weston, DJ and Piatkowski, B and Granath, G}, title = {Climate niches structure a regional hybrid zone in Sphagnum (peatmoss, Bryophyta).}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e70143}, doi = {10.1002/ajb2.70143}, pmid = {41431142}, issn = {1537-2197}, abstract = {PREMISE: Hybridization is an important evolutionary process across all groups of embryophyte land plants, but relatively little is known about hybridization and introgression in plants with a dominant gametophyte life cycle stage. This paper focuses on hybridization between four closely related species of the moss genus Sphagnum.<br><br>METHODS: Analyses utilized three types of molecular data: restriction-site-associated DNA sequencing (RADseq), RADseq-like data derived from in silico digestion of genome sequences, and species-specific barcode markers developed previously for this group. Sampling included 582 gametophytes from 79 collecting sites from 27&#xb0; to 56&#xb0;N. A range of analytical methods were employed: phylogeny reconstruction, genetic analyses using the program structure, demographic modeling, and comparative genomics.<br><br>RESULTS: Gene flow was detected among all pairwise combinations of extant species and between ancestral lineages and those species. Hybridization between S. diabolicum and S. magniae was especially pronounced and plants in a regional zone from North Carolina to New Jersey were genetically admixed. Demographic analyses indicated that this admixture reflects hybridization. Introgressed SNPs were detected across all chromosomes, but introgressed SNPs fixed in genetically pure samples of the two species were concentrated on four autosomes: 2, 7, 14, and 19. Patterns of genomic admixture/introgression were significantly correlated with climate variation across collection sites within the hybrid zone.<br><br>CONCLUSIONS: The genomic structure of plants in a regional hybrid zone between S. magniae and S. diabolicum was structured by climate adaptation and strengthens the value of this group for learning more about speciation and climate adaptation.}, }
@article {pmid41428017, year = {2025}, author = {Brehm, G and Böttger, D and Diniz, UM and Donoso, DA and Kortmann, M and Müller, J and Rabl, D and Keller, A and Laguerre, M}, title = {Illustrated Catalogue and Phylogenetic Relationships of 330 Species of Arctiinae Moth Species from the Chocó Rainforest in NW Ecuador: Most Species are Undescribed.}, journal = {Neotropical entomology}, volume = {54}, number = {1}, pages = {127}, pmid = {41428017}, issn = {1678-8052}, support = {FOR 5207//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Moths/classification/anatomy &amp; histology/genetics ; Rainforest ; *Phylogeny ; Ecuador ; DNA Barcoding, Taxonomic ; Male ; Female ; }, abstract = {Tropical rain forests are the most species rich terrestrial habitats on Earth, but their insect diversity is understudied, and it is unclear how many species are already scientifically described. A model group to study description patterns are tiger moths (Erebidae: Arctiinae), a species-rich moth clade that comprises subtaxa that differ considerably in appearance. We inventoried Arctiinae moths in a lowland rainforest in the Canandé and Tesoro Escondido Reserves, NW Ecuador, and sorted 12,335 individuals into 330 species, of which 303 had DNA barcode (COI) data extracted. We found 52 species of Lithosiini, 4 species of Arctiina, 17 species of Pericopina, 132 species of Phaegopterina, 52 species of Euchromiina and 71 species of Ctenuchina. A total of 45% of the species can be assigned by us to known named species, but the numbers vary considerably within the subtaxa: while in the conspicuous butterfly-like Pericopina 82% are described, this figure is only 26% for the smaller and cryptic Lithosiini, indicating a strong description bias even within a relatively well-known group of macromoths. This may indicate that particularly small and inconspicuous moth species have so far been neglected and that museum collections might often not be representative archives of insect diversity. Therefore, more systematic and non-biased collection campaigns should be carried out for better estimates of insect diversity. All 330 Arctiinae species are listed in three electronic catalogues, which contain all barcoded individuals as well as corresponding type material from museums, allowing a transparent and straightforward verification of all identifications. We constructed a preliminary phylogeny using literature data as backbone in combination with our DNA COI sequence data which provides a unique and useful data base for future studies in the Chocó rainforest.}, }
@article {pmid41427923, year = {2025}, author = {Mamani, MM and Catacora, L and Nina, N and Alarcon, WDT and Cai, FM and Rydén, J and Druzhinina, IS and Jensen, DF and Crespo, CF and Karlsson, M and Dubey, M}, title = {Diversity of Trichoderma in the unexplored Bolivian Amazon region and their potential for coffee diseases control.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf142}, pmid = {41427923}, issn = {1574-6968}, abstract = {Trichoderma fungi are colonizers of plant substrates and rhizosphere and are valued for their antagonism against phytopathogens and ability to promote plant health. We investigated Trichoderma diversity in coffee-growing soils in Caranavi region of Yungas-La Paz, Bolivia, where high humidity and fungal diseases threaten yield, and evaluated their potential as biocontrol agents against coffee pathogens. A total of 440 Trichoderma were isolated from coffee rhizosphere, fallow lands, and forest ecosystems across an altitudinal gradient in Caranavi. DNA barcode analyses using ITS, rpb2, and tef1 loci identified only four species. However, 47 taxa comprising 344 isolates were ambiguous, and 41 isolates were previously unrecognised species. The diversity of Trichoderma spp. was significantly affected by ecosystem type and altitude, with more species isolated from coffee rhizosphere than fallow lands and forest ecosystems, and from lower altitudes than higher ones. Evaluation of 100 isolates against a native coffee wilt pathogen Fusarium sp. C22 identified 70 potent antagonists, with 30 achieving 90-100% disease control. This is the first comprehensive study of Trichoderma diversity in Yungas, identifying indigenous Trichoderma for biocontrol applications against coffee diseases. It also emphasizes the need to refine the Trichoderma species concept and improve the taxonomic resolution within the genus.}, }
@article {pmid41427718, year = {2026}, author = {Kanjo, K and Bhasin, M and Dey, C and Bakshi, N and Ashok, A and Singh, R and Kumar, S and Ringe, RP and Varadarajan, R}, title = {Charged scanning mutagenesis as a high-throughput approach for epitope mapping.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {1}, pages = {e70433}, pmid = {41427718}, issn = {1469-896X}, support = {JBR/2021/000033//JC Bose Fellow of the Department of Science and Technology, Ministry of Science and Technology, India/ ; BT/IN/EU-INF/15/RV/19-20//ENDFLU: the Department of Biotechnology, Ministry of Science and Technology, Government of India/ ; CRG/2022/004425//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Epitope Mapping/methods ; *SARS-CoV-2/immunology/genetics/chemistry ; Mice ; *Mutagenesis ; *Spike Glycoprotein, Coronavirus/genetics/immunology/chemistry ; *Epitopes/immunology/genetics/chemistry ; COVID-19/immunology/virology ; Humans ; }, abstract = {Identifying neutralizing epitopes is important for developing vaccines and inhibitors against viral pathogens. We describe a rapid method for epitope mapping, employing barcoded charged scanning mutagenesis libraries displayed on the yeast surface, and screening using flow cytometry coupled with deep sequencing. Prior scanning mutagenesis data suggest that mutations to a charged residue, such as Aspartic acid or Arginine, will be well tolerated at exposed positions of an antigen and minimally affect protein stability and expression. Yet such substitutions at epitope residues strongly perturb binding to a cognate partner. We constructed an Aspartate scanning library of SARS-CoV-2 receptor binding domain and linked every mutation in the library to a defined unique barcode. The approach was used to map epitopes targeted in polyclonal sera of mice immunized with different SARS-CoV-2 immunogens. In contrast to complete mutational scans, charged scanning mutagenesis with the introduced barcoding strategy employs libraries with >50-fold lower diversity, facilitating library construction, screening, and downstream analysis, and also allowing for further multiplexing of samples, thus accelerating interaction site identification, as well as vaccine and inhibitor development.}, }
@article {pmid41426548, year = {2025}, author = {Gerwin, S and Deng, X and He, F and Pauls, SU}, title = {Diversity of Rhyacophila (Trichoptera, Rhyacophilidae) in the Hengduan Mountains.}, journal = {ZooKeys}, volume = {1263}, number = {}, pages = {69-88}, pmid = {41426548}, issn = {1313-2989}, abstract = {Aquatic insects are particularly dependent on environmental conditions because their life cycles are directly linked to physico-chemical conditions in freshwater habitats. Here, we combine DNA barcoding and ecological analysis to determine general distributional patterns for an unknown fauna of Rhyacophila (Trichoptera, Rhyacophilidae) in the Hengduan Mountains in China. In total 415 larval and 109 adult specimens from four major Hengduan Mountain river basins (1022 m - 4381 m a.s.l.) were sequenced and analyzed. Molecular operational taxonomic units (MOTUs) were delimited as putative species analogs. MOTUs were derived from mitochondrial COI (mtCOI) and nuclear wingless (nuWG) data using the tree-based GMYC method. As expected, based on a higher mutation rate, mtCOI delimitation resulted in a much higher number of MOTUs (66) than in WG (27), but not all mtCOIMOTUs were nested within nuWGMOTUs. Many mtCOIMOTUs were geographically restricted and rare, often occurring in only one or two sampling sites. Multivariate GLM analyses confirmed the importance of basins as the primary factor for explaining the diversity of RhyacophilaMOTUs. The high level of geographical restriction of MOTUs among basins and along elevational gradients indicates that Rhyacophila in the Hengduan Mountains are largely range-restricted, dispersal limited and consequently vulnerable to local changes in environmental conditions.}, }
@article {pmid41426536, year = {2025}, author = {Kučinić, M and Previšić, A and Ćukušić, A and Vučković, I and Žalac, S and Cerjanec, D and Ćuk, R and Stojanović, KZ and Akimbekova, N and Vuković, M and Skejo, J and Hlebec, D and Božić, A and Kutnjak, H}, title = {Fauna, distribution, and DNA barcoding data of caddisflies (Insecta, Trichoptera) in Croatia.}, journal = {ZooKeys}, volume = {1263}, number = {}, pages = {179-288}, pmid = {41426536}, issn = {1313-2989}, abstract = {This study presents a thorough overview of the diversity of the Trichoptera fauna in Croatia, encompassing several key aspects. First, it offers a historical overview of Trichoptera research conducted within the country, tracing the development and major milestones of this field. Second, it provides a detailed analysis of the distribution and species diversity of caddisflies across Croatia's three geographical regions, the Continental, Alpine, and Mediterranean, as well as within two ecoregions (ER5 - Dinaric Western Balkan and ER11 - Pannonian Lowlands) and two major river basins (AS - Adriatic Sea basin and BS - Black Sea basin). This biogeographic assessment is based on comprehensive records of adult specimens and, in certain cases, on DNA barcoding data obtained from larval stages. Third, the study includes a thorough examination of species synonyms and a critical review of the existing literature. Finally, it delivers a faunistic and taxonomic review of selected species and subspecies. A total of 225 species belonging to 18 families and 74 genera have been identified. Two of these species are represented by two and three subspecies, respectively, bringing the total number of recorded Trichoptera taxa in Croatia to 228. The presence of 223 species was confirmed in the adult stage. Only two species were identified by DNA barcoding as larvae. In the Continental region 170 species were recorded, in the Alpine region 155, and in the Mediterranean part 131 species. The Black Sea basin contains 203, and the Adriatic basin 141 species. In the Pannonian Lowland region (Ecoregion 11) we determined 152 and in the Dinaric Western Balkan (Ecoregion 5) 197 species. The BOLD Systems database currently contains about 593 DNA barcoded Trichoptera specimens from Croatia comprising 176 species, identifying 211 BINs, covering 78% of Croatian Trichoptera fauna.}, }
@article {pmid41424079, year = {2025}, author = {Waki, T and Sekine, H and Aou, A and Nitta, M and Yamamoto, G and Toshino, S and Nakano, H and Okawa, T and Takano, K and Yamazaki, D and Hagihara, R}, title = {Metacercariae infecting seven cnidarian species with their life cycle information including their adult stages in Japan.}, journal = {Journal of helminthology}, volume = {100}, number = {}, pages = {e4}, doi = {10.1017/S0022149X25100989}, pmid = {41424079}, issn = {1475-2697}, mesh = {Animals ; Japan ; *Metacercariae/classification/genetics/isolation &amp; purification/growth &amp; development ; *Life Cycle Stages ; *Trematoda/classification/genetics/isolation &amp; purification/growth &amp; development/anatomy &amp; histology ; Phylogeny ; *Cnidaria/parasitology/classification ; Fishes/parasitology ; DNA Barcoding, Taxonomic ; Fish Diseases/parasitology ; }, abstract = {This study examined the metacercariae of trematodes in cnidarian jellyfish around Japan to demonstrate the importance of the jellyfish as the second intermediate or paratenic hosts. Trematodes were sampled from cnidarian jellyfish in seven coastal regions of Japan between 2024 and 2025. Trematodes (adults and metacercariae) were also obtained from marine fish and arrow worms and included for data comparisons. DNA barcoding was used for the species identification of metacercariae in the jellyfish and for elucidating their partial life cycles. Eight cnidarian species (245 individuals) were sampled, with metacercarial infection detected in seven host species. Based on morphological and molecular analyses, the metacercariae were classified into nine species belonging to three families, Accacoeliidae, Hemiuridae, and Lepocreadiidae. Six of these species were identified as the same species of adults isolated from fish hosts around Japan, although species names of two of the six remained unclear. The remaining three trematode species were assumed to belong to Lepocreadiidae, a major group of fish trematodes. These findings indicate that cnidarian jellyfish are important intermediate or paratenic hosts of fish trematodes in Japanese waters, as has been reported in other areas in previous studies. Moreover, a metacercaria occasionally detected in an arrow worm was identified as the same species as those in jellyfish, suggesting predator-prey relationships between these hosts. The study also synonymised Tetrochetus hamadai Fukui and Ogata, 1935, T. aluterae (Hanson, 1955), and T. mitenevi Zubchenko, 1978, with T. coryphaenae Yamaguti, 1934, based on molecular and morphological data.}, }
@article {pmid41423517, year = {2025}, author = {Chambwe, N and Kennedy, SR and Kohrn, BF and Lazarchuk, P and Leutert, M and Qin, G and Tercan, B and Sanchez-Contreras, M and Tang, W and Graber, JJ and Paddison, PJ and Villén, J and Shmulevich, I and Monnat, RJ}, title = {Cellular heterogeneity and therapeutic response profiling of human IDH + glioma stem cell cultures.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-33082-8}, pmid = {41423517}, issn = {2045-2322}, abstract = {Glioblastoma stem cell (GSC) cultures are initiated from glioblastoma (GBM) surgical resection tissue. When grown appropriately they can capture and propagate key GBM molecular and cellular features. We have characterized cellular, genomic and proteomic features of four isocitrate dehydrogenase (IDH)-expressing (IDH +) GSC cultures as cellular models for ~ 90% of adult GBMs. We demonstrate that GSC cultures can be continuously propagated in defined, serum-free media and 5% oxygen without specialized growth substrates; have culture-specific genomic and mtDNA variants together with gene/protein expression profiles; and display reproducible dose-survival curves for the GBM standard-of-care therapies ionizing radiation (IR) and temozolomide (TMZ). In order to better define GSC culture cellular heterogeneity and dynamics, we used lentiviral DNA barcoding, mtDNA variants and single cell gene expression profiling over 40 days after IR treatment. GSC cultures are versatile in their ability to support many in vitro protocols including high throughput screens as well as xenograft, organoid and other disease modeling protocols. They provide a simple cellular disease model for better understanding GBM biology, and for identifying new, potentially more effective GBM therapies and treatment regimens.}, }
@article {pmid41420443, year = {2025}, author = {Torres, A and Lee, L and Srivathsan, A and Meier, R}, title = {UITOTO: a software for generating molecular diagnoses for species descriptions.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/cla.70023}, pmid = {41420443}, issn = {1096-0031}, abstract = {Millions of species remain undescribed, and each eventually will require a species description with a diagnosis. Yet, we lack software that can derive state-specific and contrastive molecular diagnoses and allows the user to validate them based on all available sequences for the taxon under study. Here we introduce UITOTO, which addresses this shortcoming by facilitating the identification, testing, and visualization of diagnostic molecular combinations (DMCs). The software uses a weighted random sampling algorithm based on the Jaccard Index for building candidate DMCs. It then selects DMCs with the highest specificity stability, meeting user-defined thresholds for exclusive character states. If multiple optimal DMCs are identified, UITOTO derives a majority-consensus DMC. To verify whether the generated DMCs are contrastive, UITOTO includes a validation module that tests DMCs against databases, efficiently handling thousands of aligned or unaligned sequences. We here, not only propose UITOTO, but also assess its performance relative to other software that can derive DMCs (e.g. MOLD). For this purpose, we analyse three large empirical datasets: (i) Megaselia (Diptera: Phoridae: 69 species, 2229 training and 30 289 testing barcodes); (ii) Mycetophilidae (Diptera: 118 species, 1456 training, 60 349 testing barcodes); and (iii) European Lepidoptera (49 species, 591 training, 21 483 testing barcodes). Based on classification metrics (e.g. F1 Score), UITOTO's DMCs outcompete DMCs from other software. We furthermore provide guidelines for generating molecular diagnoses and a user-friendly Shiny App-GUI that includes a module for obtaining publication-quality DMC visualizations. Overall, our study confirms that the biggest challenge for generating molecular and morphological diagnoses is similar: balancing specificity and length; short diagnoses often lack specificity, while excessively long DMCs are often so specific that they do not accommodate intraspecific variation.}, }
@article {pmid41419930, year = {2025}, author = {Rodrigues, BL and Vasconcelos Dos Santos, T and Brilhante, AF and de Souza Pinto, I and Rocha, EG and Pereira Júnior, AM and da Silva Costa, G and de França, KP and de Souza Cavalcante, K and Shimabukuro, PHF and Medeiros, JF and Galati, EAB}, title = {On the integrative taxonomy of Trichophoromyia Barretto, 1962 and its relationship with Nyssomyia Barretto, 1962 (Diptera, Psychodidae, Phlebotominae): species delimitation, phylogeny, genus and subgenus description.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-025-07155-6}, pmid = {41419930}, issn = {1756-3305}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2023/03715-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, abstract = {BACKGROUND: The sand fly genus Trichophoromyia Barretto, 1962 is one of the most diverse inthe subfamily Phlebotominae. The taxonomy and systematics of this group is complex due toboth a high similarity among species and unclear relationships among other sand fly groupswithin the subtribe Psychodopygina Galati, 1995. Despite their great relevance as vectors of Leishmania spp., few studies have explored the usefulness of molecular markers in studyingthe diversity of this group.<br><br>METHODS: Here, we evaluated the use of barcode sequences of the cytochrome coxidasesubunit I gene (COI) for identifying several Trichophoromyia spp., by inferring intra- andinterspecific genetic distances, in addition to performing a set of several single-locus speciesdelimitation approaches using discovery methods. Moreover, we employed a multilocusdataset of four independent molecular markers (COI , ITS2 , 28S and PARA) to infer thephylogenetic species tree, estimate divergence times and delimit species under a validationmodel.<br><br>RESULTS: The phylogenetic inferences confirmed the paraphyly of Trichophoromyia and Nyssomy ia Barretto, 1962. Thus, two new genera, named Reburrus gen. nov. and Shawmyia gen. nov., were proposed to accommodate sand flyspecies that did not fit in the aforementioned groups. Additionally, a new subgenus wasproposed: Trichophoromyia (Dilermandomyia) subg. nov., containing most speciesof Trichophoromyia . A recent speciation history was also estimated, with most of the speciesstudied diversifying during the Pleistocene. However, our dataset was insufficient to fullyresolve relationships within Trichophoromyia (Dilermandomyia) subg. nov. Many speciesshowed paraphyletic patterns in the gene trees, and some could not be reliably identified anddelimited using both COI barcodes and multilocus tools.<br><br>CONCLUSIONS: The sand fly genus Trichophoromyia exhibits a complex diversification history.Our phylogenetic inference and morphological observations of Nyssomyia and Trichophoromy ia, allowed us to propose new groups for the Psychodopygina subtribe. However, theprevalence of species-level paraphyletic patterns for Trichophoromyia (Dilermandomyia) subg.nov., showed that further assessment of this group requires a broader locus sampling combined with detailed morphological analysis.}, }
@article {pmid41419813, year = {2025}, author = {El-Demerdash, MM and El-Sayed, ASA and Yassin, MA and Elsehely, HH}, title = {Pyrene morphology and molecular identification of some garden ornamental palms of the family Arecaceae based on the plastid rbcL gene in Egypt morphological and molecular identification of ornamental palms (Arecaceae) in Egypt based on pyrene traits and rbcL gene sequence.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1715}, pmid = {41419813}, issn = {1471-2229}, mesh = {Egypt ; *Arecaceae/genetics/anatomy &amp; histology/classification ; Phylogeny ; *Ribulose-Bisphosphate Carboxylase/genetics ; DNA Barcoding, Taxonomic ; *Pyrenes/analysis ; Fruit/anatomy &amp; histology/genetics ; Plastids/genetics ; }, abstract = {The ornamental palms represent a diverse species in the national botanical gardens, and roadsides; however, the accurate identification of the palm trees (Arecaceae) is a problematic due to the numerous overlapped morphological traits, especially with the environmental conditions. So, the objective of this study was to implement the different morphological traits, especially based on the pyrene morphology, with the molecular barcoding markers of the plastid rbcL on delineation and revising the taxonomical identification of the most common Palm trees in Egypt in addition to their pharmacological and Ethnobotanical applications. An obvious variation on the surface of pyrenes among the studied Palm taxa ranged from ovoid to globose or discoid, with brown to pale brown, was recorded. The pyrene's fruit dimensions were ranged with S. yaba Becc. (5.65 × 6.85 mm), Washingtonia robusta (7.19 × 4.4 mm) and Sabal palmetto (Walter) Lodd. ex Schult. &amp; Schult.f. (7.24 × 9.58 mm), while Syagrus romanzoffiana (Cham.) Glassman is (19.8 × 12.15 mm). The color of the pyrene of W. robusta, S. romanzoffiana, and Livistona decora (W.Bull) Dowe was brown, while was dark brown in Butia capitata (Mart.) Becc. Sabal yapa and S. palmetto. The SEM analysis of the pyrene surface microsculpture, the studied taxa of S. palmetto, S. yaba, Livistona, Brahea, and Sabal could be easily delimited at the generic level. The taxonomical identification of plant taxa based on their morphological characteristics, such as color, surface smoothness, and geometric shapes, was confirmed based on their molecular barcoding. The Principal Component Analysis (PCA) scatter plot based on the morphological traits distinguishes the taxa of tribe Cocoeae, subfamily Arecoideae and taxa of tribe Corypheae, subfamily Coryphoideae. From the UPGMA dendrogram based on the micromorphological characteristics, the studied taxa were grouped into two major clusters (I, II), the cluster I includes S. palmatto, S, yaba and W. robusta which belongs to subtribe Sabalinae, tribe corypheae, while cluster II includes L. decora, L. chinensis, (Jacq.) R.Br. ex Mart.and B. armata which belongs to subtribe Livistoninae and tribe Corypheae. Thus, the classification of the experimental plants based on the morphological traits of pyrene fruit microsculpturing was closely matched with the molecular barcoding based on the rbcL sequences.}, }
@article {pmid41418522, year = {2025}, author = {Martel, C and Kreidt, J and Scott, J and Griffiths-Lee, J and Rázuri-Gonzales, E and Wright, GA and Stevenson, PC}, title = {Pollen and sterol content differentially affect solitary bee development.}, journal = {The Science of the total environment}, volume = {1012}, number = {}, pages = {181213}, doi = {10.1016/j.scitotenv.2025.181213}, pmid = {41418522}, issn = {1879-1026}, abstract = {Pollen sterols are essential micronutrients for bees, with roles as membrane components, hormone precursors and for regulating gene expression. It is historically accepted that bees are unable to produce sterols de novo or modify them and use them as they occur in pollen. This may require adaptation by bees to specific plants because pollen sterols vary dramatically across taxa. Here we investigated the effects of pollen with different sterol composition or supplementation on development of solitary red mason bees, Osmia bicornis, comparing bee provisioned pollen, with Castanea sativa pollen containing campesterol a key Osmia sterol, a sterol supplemented C. sativa pollen, a polyfloral pollen from which the key campesterol and cholesterol sterols were almost absent, and a combination of polyfloral and C. sativa pollen. DNA barcoding was used to characterise the Osmia pollen, which comprised at least 38 taxa but was mostly Quercus spp. Pollen diet significantly affected the larval final weight, larval development time and development over time. Larvae fed chestnut pollen supplemented with sterols developed significantly faster over time compared to those from the other treatments, including the chestnut pollen with no sterol supplementation. Despite sterol composition being distinctive among pollen diets, sterol profiles were more similar among bees from different pollen foods (i.e., different treatments) than between bees and their pollen foods. Moreover, bees fed on polyfloral pollen had much higher relative concentrations of campesterol (~8.5 %) and cholesterol (~26 %) than the pollen itself (~3 % and ~ 0.7 %, respectively), addressing the possibility that Osmia bees are highly efficient in sterol selective accumulation or possible transformation of sterols in Osmia bees. Our results suggest greater flexibility in sterol handling in bees than previously assumed.}, }
@article {pmid41413444, year = {2025}, author = {Hookabe, N and Hiruta, SF and Yabuki, A and Yoshino, H and Hisasue, Y and Sawada, N and Ueshima, R and Kajihara, H}, title = {Unrecognized species-level diversity of terrestrial nemerteans in the UNESCO world heritage Ogasawara Islands revealed by mitogenomics.}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {135}, pmid = {41413444}, issn = {2730-7182}, support = {23KJ2222//Japan Society for the Promotion of Science/ ; 25K09751//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Genome, Mitochondrial ; Japan ; Islands ; *Invertebrates/genetics/classification/anatomy &amp; histology ; *Biodiversity ; Phylogeny ; *Genetic Variation ; }, abstract = {BACKGROUND: The terrestrial ribbon worm Geonemertes pelaensis Semper, 1863 (phylum Nemertea) is widely reported from tropical regions worldwide. In Japan, this species has been recorded from subtropical islands including the Ogasawara Islands, a UNESCO World Heritage Site south of Tokyo recognized for its unique biodiversity, where it has been implicated in the decline of native soil invertebrates. Here, we demonstrate that the nemerteans in the Ogasawara Islands are genetically and morphologically distinct from those found on Yonaguni Island (Okinawa, Japan), indicating the presence of at least two separate species in Japan.<br><br>RESULTS: We sequenced the complete mitochondrial genomes of both populations (18,755&#xa0;bp for Ogasawara; 31,745&#xa0;bp for Yonaguni), revealing substantial differences in genome size and gene arrangement. The mitochondrial genome of the Yonaguni population is unusually large, exceeding typical sizes reported for metazoans. Uncorrected p-distances in cytochrome c oxidase subunit I (COX1) sequences between the two populations ranged from 6.75 to 8.59%, which is above the widely used threshold for intraspecific variation in nemerteans. Morphological comparisons also support species-level distinction: live specimens from Yonaguni have a pale body with a prominent mid-dorsal stripe (body width-to-stripe ratio: 1:0.078-0.110), whereas individuals from Ogasawara are pale to light brown with a narrower and fading stripe (ratio: 1:0.042-0.050). Moreover, accessory-stylet pouches differ between populations: Yonaguni specimens possess four to five pouches, each containing 3-5 stylets, while Ogasawara specimens have two pouches, each with two stylets. Examination of museum specimens collected in the 1980s from Chichijima showed the extremely similar external morphology as our recent Ogasawara specimens, indicating that this form has been the only Geonemertes species in the Ogasawara Islands for nearly half a century.<br><br>CONCLUSIONS: Our results indicate the presence of species-level diversity in Japanese terrestrial nemerteans and demonstrate that accurate species identification using molecular barcodes is essential in insular ecosystems. Recognizing cryptic or pseudocryptic lineages is critical for effective biodiversity monitoring and for preventing mismanagement in ecologically sensitive regions such as the Ogasawara Islands.}, }
@article {pmid41411409, year = {2025}, author = {Mazelis, I and Sun, H and Kulkarni, A and Torre, TL and Klein, AM}, title = {Multistep genomics on single cells and live cultures in subnanoliter capsules.}, journal = {Science (New York, N.Y.)}, volume = {}, number = {}, pages = {eady7209}, doi = {10.1126/science.ady7209}, pmid = {41411409}, issn = {1095-9203}, abstract = {Single-cell sequencing methods uncover natural and induced variation between cells. Many functional genomic methods, however, require multiple steps that cannot yet be scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells and large analytes while being freely accessible to media, enzymes and reagents. Capsules enable high-throughput multistep assays combining live-cell culture with genome-wide readouts. We establish methods for barcoding CAGE DNA libraries, and apply them to measure persistence of gene expression programs in cells by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and their extension to live-cell assays.}, }
@article {pmid41410945, year = {2025}, author = {Ramkrishna,  and Negi, N and Pandey, S}, title = {Discovery of Trichoderma frianum sp. nov. from India: a new member of the Trichoderma harzianum species complex (Harzianum clade).}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41410945}, issn = {1618-1905}, support = {FRI-703/FPT-11//Indian Council of Forestry Research and Education/ ; }, abstract = {Trichoderma frianum sp. nov., a wood-inhabiting species from India, is described based on morphological characteristics and molecular phylogenetic analyses. This taxon is congruent with the morphological species concept of T. harzianum sensu lato, characterized by pyramidal conidiophores and cruciate phialidic whorls with fewer than five phialides. However, it differs by producing verticils that bear up to seven divergent phialides. Phylogenetic analyses based on a combined dataset of the translation elongation factor 1-alpha (tef1) and RNA polymerase II second-largest subunit (rpb2) gene regions confirmed the placement of T. frianum within the T. harzianum species complex (THSC) of the Harzianum clade. This species forms a sister lineage to T. anaharzianum, T. neotropicale, T. lixii, T. xixiacum, and T. lentinulae, with the pairwise homoplasy index (PHI) test supporting their classification as distinct species. Comparative sequence analyses revealed that T. frianum possesses unique tef1 and rpb2 sequences that do not meet the ∃!(rpb299 ≅ tef197) standard for known species, fulfilling the criteria of the International Commission on Trichoderma Taxonomy (ICTT) for new species delineation. However, deviations from the tef1 and rpb2 thresholds were observed in some comparisons within THSC and are discussed. Functionally, T. frianum exhibited strong antagonistic activity against major Eucalyptus pathogens and showed robust growth under high-salinity conditions in vitro, suggesting its potential for biocontrol and stress-resilient forestry systems.}, }
@article {pmid41409049, year = {2026}, author = {Lv, M and Zhu, T}, title = {First report of mitochondrial genome of Cloeon viridulum (Ephemeroptera: Baetidae) from Hebei, China.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {11}, number = {1}, pages = {74-78}, pmid = {41409049}, issn = {2380-2359}, abstract = {Baetidae is a globally diverse mayfly family. While COI DNA barcode studies are abundant, its mitogenomic data remain scarce. In this study, we present the first mitochondrial genome of Cloeon viridulum Navás, 1931. The mitogenome of C. viridulum spans 14,431 bp and includes 13 protein-coding genes, 22 transfer RNA genes, and one 16S ribosomal RNA (rRNA) gene. However, it features an incomplete 12S rRNA gene and lacks a control region. This mitogenome has a GC content of 32.4%. Phylogenetic analysis strongly supports a sister relationship between C. viridulum and C. dipterum. Our findings offer genomic insights into Baetidae evolution.}, }
@article {pmid41408638, year = {2025}, author = {Vestal, G and Zhou, Z and Sergent, S and Sheth, M and Lee, J and Otieno, K and Kariuki, S and Hill, A and Ter Kuile, FO and Lindblade, KA and Slutsker, L and Hamel, MJ and Desai, M and Gimnig, JE and Samuels, AM and Vigfusson, Y and Shi, YP}, title = {Assessing the impact of temporal changes in transmission on Plasmodium falciparum strains in Asembo, western Kenya (1996-2017) using within-host metrics via 24-SNP barcodes.}, journal = {Malaria journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12936-025-05700-3}, pmid = {41408638}, issn = {1475-2875}, support = {132//AMD fund from the CDC/ ; }, abstract = {BACKGROUND: Genomic surveillance of malaria parasites offers important insights into the impact of interventions on transmission reduction and changes in pathogen populations over time, especially in low-transmission areas. However, such surveillance faces challenges in high-transmission regions. Detecting temporal changes in transmission in high-transmission settings requires analytical methods tailored to high-diversity parasite populations that can differentiate between superinfection (infection through multiple mosquito bites, each bearing an unrelated strain) and co-transmission (infection through a single mosquito bite bearing more than one strain).<br><br>METHODS: This study applied a previously developed novel Next Generation Sequencing (NGS) 24-SNP barcode assay for genotyping smear-positive samples obtained from a 2017 cross-sectional survey in the Asembo area, western Kenya, building on previous work on samples collected in the surveys conducted in 1996, 2001, 2007, and 2012. Algorithms StrainRecon and STIM were used to identify parasite strains within a sample and measure multiplicity of infection (MOI). Population genetic metrics of FST (Fixation Index), strain-relatedness by IBD (Identity by Descent), Hs (Modified Heterozygosity) and Ne (Effective Population Size) were evaluated using the same 24-SNP data. This study further explored a novel slope metric of the relationship between within-host strain relatedness and MOI to infer superinfection and co-transmission. Temporal changes in the above metrics were assessed.<br><br>RESULTS: There was no significant differentiation in FST, Hs, Ne, and strain-relatedness at the population level over time. In contrast, the average MOI significantly decreased from 4.32 in 1996 to 3.34 in 2012, although it increased to 3.49 in 2017. Insecticide-treated bednet distribution campaigns from 1997 to 2017 did track these temporal changes in MOI. Additionally, the value of strain relatedness within-host (IBD) was inversely correlated with MOI (number of strains), and the change in the inverse relationship (within-host slopes) over time was verified by two different correlation analysis and modelling. The temporal trends in this within-host slope metric suggested that transmission dynamics shifted towards co-transmission from 2001 to 2012, and then returned to similar levels of superinfection in 2017 as in 1996.<br><br>CONCLUSION: The within-host MOI, IBD-based strain-relatedness, and their mathematical relationship (slope) provide useful metrics for understanding the transmission dynamics in our study. Notably, this study presents the first simple slope-based method using 24-SNP barcodes to distinguish superinfection from co-transmission in a high transmission area, warranting further evaluation of the novel tool in other high transmission settings.}, }
@article {pmid41406413, year = {2025}, author = {Kumano, S and Tanaka, K and Kawakami, S and Yamamoto, M and Akahori, R and Nojima, A}, title = {Scaling Peptide-Barcode Approach for Parallel Evaluation of Protein Expression from Multiple mRNA Variants.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c02991}, pmid = {41406413}, issn = {1520-6882}, abstract = {Messenger RNA (mRNA) technology has revolutionized therapeutic design, yet optimizing untranslated regions (UTRs) and synonymous codons still depends on low-throughput, trial-and-error workflows. We previously reported a peptide-barcode method that quantifies protein expression from pooled mRNAs, but only two variants were tested. For this study, we extend the approach to nine mRNA variants produced by combining three different 5' UTRs with three codon-modified enhanced green fluorescent protein (eGFP) coding sequences. All nine template plasmids were assembled in a single Gibson reaction, transcribed together, and cotransfected into HEK293T cells. At least five distinct ten-residue peptide barcodes were assigned to each mRNA variant in the pooled library. After translation, the barcodes were enzymatically released and analyzed in a single liquid chromatography-mass spectrometry (LC-MS) run. To correct for differences in transcript abundance within the pool, the LC-MS signals were normalized to the corresponding barcode read counts obtained by nanopore sequencing of the same pooled mRNA library. Averaging the barcode signals assigned to each variant partially reduced barcode-specific bias and yielded a moderate correlation coefficient of 0.53 relative to the eGFP fluorescence measured from nine separate single-transfection controls. While not intended for precise quantification, the results indicate that peptide barcoding can discriminate variants with higher protein output within a single pooled experiment and is useful for first-pass, rank-order screening. Thus, this peptide-barcode method provides a scalable route toward higher-throughput optimization of larger mRNA libraries.}, }
@article {pmid41405917, year = {2025}, author = {Gowert, YG and Lemos, VM and Corrêa, F and Vollrath, S and Vieira, JP and Condini, MV and Bastos, RF and Freire, MCC and Farro, APC and Junior, ASV and Albuquerque, C and Hostim-Silva, M and Garcia, AM}, title = {Multiple tools to investigate the origin of the exotic species Chinook salmon Oncorhynchus tshawytscha (Walbaum, 1792) (Salmonidae) in the world's largest chocked coastal lagoon.}, journal = {Journal of fish biology}, volume = {107}, number = {5}, pages = {1800-1806}, pmid = {41405917}, issn = {1095-8649}, support = {313008/2021-3//CNPq/ ; 307678/2022-9//CNPq/ ; }, mesh = {Animals ; *Salmon/genetics/anatomy &amp; histology/physiology/classification ; Female ; DNA Barcoding, Taxonomic ; }, abstract = {Salmonid species have increasingly been established in South America for aquaculture and recreational fishing purposes. This study provides the first scientific record of the Chinook salmon (Oncorhynchus tshawytscha) in the Patos Lagoon (32°S), the world's largest choked coastal lagoon. The specimen was a female with 770 mm (total length), 3992.1 g, estimated age of 6 years and an advanced sexual maturation stage. Based on multiple tools (DNA barcoding, stable isotopes in eye lens, otolith growth layers and egg's histological analysis), we discussed potential entry routes for this species into the lagoon.}, }
@article {pmid41404612, year = {2025}, author = {Tischbirek, CH and Fang, L and Chadly, DM and Lobbia, S and Aguirre, JD and Takei, Y and Chen, CH and Sternberg, PW and Lois, C and Elowitz, MB and Cai, L}, title = {Synaptic MEMOIR: mapping individual synapses of neurons with protein barcodes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.25.690442}, pmid = {41404612}, issn = {2692-8205}, abstract = {Obtaining wiring diagrams of brains has been a major achievement for neuroscience. However, an underlying challenge in connectomics is the fundamental tradeoff between the imaging resolution needed to resolve synapses and the volume of the brain that can be imaged. For example, electron microscopy (EM) visualizes synaptic sites with ~5 nm resolution, but is difficult to scale beyond volumes of 1 mm [3] . Here, we present Synaptic MEMOIR (Memory with Engineered Mutagenesis with Optical in situ Readout) that enables imaging of neuronal projections in animal brains with single-synapse resolution. Synaptic MEMOIR is built around three key design features. First, protein barcodes are transported to synapses to allow matching of synaptic barcodes to cell body barcodes without high resolution imaging and the error-prone process of tracing neuronal processes across long distances. Second, Synaptic MEMOIR uses continuous mutagenesis to generate a large diversity of barcodes to uniquely label cell bodies and synapses. Last, the timing of recombination and transport can be tuned to record synaptic age or projection information. Combining these features, we demonstrated projection mapping of 113 neurons in the Drosophila melanogaster optic lobe in a volume of 9.5 million μm [3] . Because synapses are identified by transported barcodes with optical microscopy at 300 nm resolution, this approach can potentially scale to much larger volumes, similar at least to those imaged in recent mouse brain transcriptomics atlases. In addition, synaptic MEMOIR can match barcodes across brain sections, and does not require tissue clearing to track long-range projections. Together, these results provide the foundation for a scalable optical image-based system for reconstructing the neural wiring diagrams of brains across different developmental stages, genetic backgrounds and perturbations.}, }
@article {pmid41403643, year = {2025}, author = {Wang, B and Zhang, Y and Li, J and Wu, M and Shi, Y and Sun, X and Xiao, X and Zhang, P and Shi, Y and Li, Y and Tian, H}, title = {Revealing dietary habits and intestinal microbiome composition of the Beijing swift (Apus apus pekinensis) through regurgitated pellets and fecal samples.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1693396}, pmid = {41403643}, issn = {1664-302X}, abstract = {INTRODUCTION: The Beijing swift, an important insectivorous bird, is a key protected wild animal in Beijing. Current research on this species primarily focuses on distribution surveys and population dynamics, while systematic studies on its diet and intestinal microbiome composition remain lacking, a knowledge gap that constrains in-depth understanding of its ecological adaptability.<br><br>METHODS: This study integrated DNA barcoding and high-throughput 16S rRNA gene sequencing to systematically analyze regurgitated pellets and fecal samples from ringed and rescued individuals, revealing the following findings.<br><br>RESULTS: The dietary composition primarily encompasses insects from five orders, Diptera, Coleoptera, Hemiptera, Hymenoptera and Lepidoptera, with significant differences observed between adults and nestlings. Dominant intestinal bacterial phyla included Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota. Correlation network analysis indicated that Stenotrophomonas, Aminobacter, etc., exhibit extensive mutually promotive interactions with other bacteria, suggesting their potential roles as core functional bacterial communities in the intestine.<br><br>DISCUSSION: This research provides the first evidence of dietary differentiation patterns and intestinal microbial composition characteristics of Beijing swifts, providing key foundational data for assessing its survival and adaptation mechanisms. It is highly significant for developing scientific rescue strategies and conservation initiatives.}, }
@article {pmid41401069, year = {2025}, author = {Handler, JS and Li, Z and Dveirin, RK and Lin, JD and Fang, W and Wu, S and Forsmo, JE and Goodarzi, H and Fertig, EJ and Kalhor, R}, title = {A cell-state axis underlying colonization in carcinomas with implications for metastasis risk prediction and interception.}, journal = {Cell reports}, volume = {44}, number = {12}, pages = {116701}, doi = {10.1016/j.celrep.2025.116701}, pmid = {41401069}, issn = {2211-1247}, abstract = {Metastasis to the liver drives mortality in pancreatic ductal adenocarcinoma (PDAC), yet mechanisms of colonization remain unclear. Using genomic barcoding, we developed a clonal competition model under immune surveillance, isolating murine PDAC subclones with high or low liver-colonization potential. Combined transcriptome and chromatin-accessibility analyses revealed a distinct "metastatic-potential axis," separate from the normal-to-PDAC and classical-basal axes. We established "MetScore" as a biomarker of this axis. MetScore distinguishes metastases from primary PDAC tumors in patients, predicts outcomes beyond classical-basal classifications, and generalizes across carcinoma subtypes, suggesting conserved colonization mechanisms. High-MetScore PDAC cells preferentially occupy immune cell-enriched niches, suggesting they remodel the metastatic microenvironment. Functional screening identified c-Fos as a positive mediator of colonization and a candidate anti-metastatic target. Collectively, we identify a cell-state axis underpinning PDAC liver colonization, introduce MetScore as a broadly applicable biomarker, and nominate actionable targets for peri-operative therapeutic intervention.}, }
@article {pmid41400440, year = {2025}, author = {Bolshakov, DT and Weix, EWZ and Galateo, TM and Rajasekaran, R and Coyle, SM}, title = {Noise-Guided Design of Synthetic Protein Waves in Living Cells.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00599}, pmid = {41400440}, issn = {2161-5063}, abstract = {Protein circuits organize cell biology, but synthetic dynamics are challenging to engineer due to stochastic genetic and biochemical variation. Genetically encoded oscillators (GEOs) built from bacterial MinDE-family ATPases and activators generate synthetic protein waves that act as novel frequency-domain imaging barcodes in eukaryotic cells, providing a platform for understanding, engineering, and applying synthetic protein dynamics. Using budding yeast, we disentangle how expression levels and expression noise govern the GEO waveform and encodability. While the GEO amplitude is sensitive to extrinsic noise, the GEO frequency is stably encoded by the activator:ATPase ratio. By integrating GEO components into the yeast modular cloning toolkit, we developed different noise-guided expression strategies that act like filters on the GEO waveform. We paired these filters with hundreds of biochemically distinct GEO variants to engineer clonal populations that oscillate at distinct frequencies and to design waveform libraries with customizable spectral features and tunable waveform variation. Our work establishes a robust platform for precision genetic encoding of synthetic GEO oscillations and highlights the utility of noise-guided strategies for dynamic protein circuit design.}, }
@article {pmid41399041, year = {2025}, author = {Noffsinger, CR and Caboň, M and Matheny, PB and Adamčíková, K and Looney, BP and Kõljalg, U and Abarenkov, K and Adamčík, S}, title = {Biogeography and host associations of Russula subsection Xerampelinae based on large-scale analysis of UNITE sequence data.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70833}, pmid = {41399041}, issn = {1469-8137}, support = {PRG1170//Eesti Teadusagentuur/ ; VEGA 1/0346/22//Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and the Slovak Academy of Sciences/ ; VEGA 2/0050/22//Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and the Slovak Academy of Sciences/ ; DEB 2030779//Directorate for Biological Sciences/ ; APVV-20-0257//Slovak Research and Development Agency project/ ; }, abstract = {Estimating fungal geographic ranges and niche potential is limited by the ephemeral nature of fruiting bodies. While environmental DNA offers broader insights, species-level identification remains difficult due to uncertain sequence clustering thresholds, low interspecific variation in barcoding regions, and limited taxonomic resolution. To address this, we analyzed large-scale environmental sequence data to investigate biogeographic patterns and ectomycorrhizal host associations in Russula subsection Xerampelinae, a group widely distributed across boreal and arctic ecosystems. We used maximum likelihood phylogenetic methods to identify internal transcribed spacer sequences from the UNITE database for 13 previously defined Russula species. Additionally, we retrieved sequence-associated metadata on locality and host association from PlutoF. In total, 1363 sequences were resolved in clades with our target species, expanding known distributions and plant host associations. Integrating environmental metadata with phylogenetic analyses revealed widespread distributions and host generalism across the Northern Hemisphere. However, UNITE's species hypotheses clustering thresholds often failed to reflect phylogenetically defined species boundaries, even at conservative levels. Our phylogeny-based assignment approach applied on metabarcoding data improves species resolution and biogeographic inference, providing a step-by-step workflow for sequence-based identification and for addressing ecologically and evolutionarily driven research questions.}, }
@article {pmid41397565, year = {2025}, author = {Ganuza, M and Yoshimoto, M}, title = {HSC-independent and -dependent hematopoiesis: new insights and lineage tracing methods.}, journal = {Experimental hematology}, volume = {}, number = {}, pages = {105352}, doi = {10.1016/j.exphem.2025.105352}, pmid = {41397565}, issn = {1873-2399}, abstract = {Recent advancement in developmental hematology has revealed unappreciated hematopoietic waves and origins during development, in addition to unexpected hematopoietic stem cell (HSC)-independent progenitors that provide lifelong hematopoiesis, using in vivo barcoding technologies and various lineage-tracing mouse models. Also, these tools estimate HSC numbers and display HSC behaviors that have not been anticipated. This review introduces such new discoveries in blood development and discusses the data and controversies. Tease Abstract: Recent advances in developmental hematology have uncovered previously unappreciated waves and origins of hematopoiesis in the embryo, including unexpected HSC-independent progenitors that contribute to lifelong hematopoiesis, using cutting-edge approaches such as in vivo barcoding and various lineage-tracing mouse models. These tools have also identified haematomesoblast, early erythroid and megakaryocytic differentiation pathways, estimated HSC numbers, and revealed unanticipated HSC behavior during the perinatal period. Together, these insights are reshaping our fundamental concepts of hematopoiesis and changing the paradigm.}, }
@article {pmid41396975, year = {2025}, author = {Hsueh, YW and Chiang, PM}, title = {USPPAR is a cost-effective, scalable, and highly sensitive single-cell RNA sequencing workflow compatible with diverse specimens.}, journal = {PLoS biology}, volume = {23}, number = {12}, pages = {e3003537}, pmid = {41396975}, issn = {1545-7885}, mesh = {*Single-Cell Analysis/methods/economics ; Humans ; Animals ; HEK293 Cells ; Mice ; *Sequence Analysis, RNA/methods/economics ; Cost-Benefit Analysis ; Workflow ; RNA/genetics ; }, abstract = {Single-cell RNA sequencing (scRNA-seq) requires high sensitivity, throughput, and broad compatibility across specimens. Current high-capacity methods lack sensitivity compared to low-capacity counterparts. Moreover, tissue-specific methods for collecting cells/nuclei limit unbiased comparisons across samples. Here, we propose a Unified framework by Split-Pool barcoding with optimal-efficiency PolydeoxyAdenylation for scRNA detection (USPPAR). Using short and long dsDNA substrates, low Co[2+] concentration, while eliminating all other metal-ion components, enabled terminal deoxynucleotide transferase to efficiently polydeoxyadenylate intractable blunt and 3' recessed dsDNA ends, which was unattainable with other systems. By benchmarking against six state-of-the-art technologies using HEK293, the efficient addition of PCR handles for cDNA amplification made USPPAR's gene detection sensitivity comparable to high-sensitivity methods and significantly higher than existing high-cell-capacity platforms. In primary PBMCs, USPPAR enabled high-sensitivity, high-resolution scRNA-seq, and lysine conjugation improved sensitivity as an RNase inactivator. Based on nuclease reporter and mRNA protection assays, partially chelated Cu[2+] served as a potent, non-precipitating, broad-spectrum nuclease inhibitor across various pH levels. Beyond demonstrating high sensitivity in liver tissue, an organ with low nuclease activity, single-nucleus RNA sequencing (snRNA-seq) with this inhibitor enabled one-pot extraction of RNA-stable nuclei from nuclease-rich tissues, such as the pancreas. Finally, comparisons with reference datasets from the 10× platform using mouse spleen and maize tissues showed that USPPAR matched cell-type coverage while achieving higher gene-detection efficiency. With five key enzymes available and quality-controlled, USPPAR provides a unified, cost-effective, sensitive method for high-cell-capacity scRNA profiling of diverse specimens without special equipment.}, }
@article {pmid41396839, year = {2025}, author = {Zhang, Y and Li, X and Yi, J and Lyu, W and Wang, H and Guo, Q and Tang, T and Ou, F and Gu, H and Shen, F and Wang, Y and Xu, H}, title = {Barcode-Based SlipChip for High-Multiplexed and Trace Sample Digital Quantification with Femtomolar Sensitivity.}, journal = {ACS sensors}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssensors.5c02362}, pmid = {41396839}, issn = {2379-3694}, abstract = {The development of the digital enzyme-linked immunosorbent assay (ELISA) has improved the detection of low-abundance protein biomarkers in biological samples, achieving a 1000-fold increase in sensitivity compared to conventional protein detection methods. However, existing digital ELISA technologies encounter difficulties in simultaneously identifying numerous protein biomarkers at ultralow concentrations, particularly in trace samples. This limitation calls for improvements in both detection multiplicity and sensitivity. Herein, a simple digital ELISA platform, the Barcodes Integrated SlipChip (BIS-chip), was developed for the ultrasensitive identification of multiple proteins from trace samples. The BIS-chip employs a two-step loading method that eliminates substrate precatalysis, thereby ensuring the specificity of 10-plex target detection. Additionally, its high bead-loading efficiency improves the assay sensitivity for each target. By counting digital "On" and "Off" signals, the BIS-chip quantifies a panel of 10 cytokines with low limits of detection (LoD) in the femtogram per milliliter (fg/mL) range, achieving a sensitivity improvement of several orders of magnitude compared with standard highly multiplexed suspension array technology. To validate its clinical applicability, the BIS-chip was used to simultaneously measure 10 cytokines from only 20 μL of intralesional plasma of patients diagnosed with oral lichenoid reactions (OLRs), a condition where cytokines are typically undetectable via commercial multiplexed immunoassays. Supported by machine-learning algorithms, the OLR diagnostic models were successfully developed with 95.7% sensitivity and 100% specificity. With its exceptional detection multiplicity, ultrasensitivity, and straightforward workflow, the BIS-chip provides an innovative solution for the quantitative analysis of clinical low-abundance biomarkers in trace samples.}, }
@article {pmid41394887, year = {2025}, author = {Mwamula, AO and Bae, CH and Kim, YS and Lee, DW}, title = {Description of A New Cryptic Species of the Papillosa Group, Pellioditis koreana n. sp. (Nematoda: Rhabditidae) from Korea.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250056}, pmid = {41394887}, issn = {0022-300X}, abstract = {Pellioditis koreana n. sp. was recovered from cadavers of Protaetia brevitarsis seulensis larvae and is herein characterized using morphometric and DNA barcode data. P. koreana n. sp. is characterized by its lateral fields with four lines, anterior part of the pharynx longer than posterior part, hemizonid prominent, located adjacent to the middle or posterior part of isthmus, excretory pore located anterior to basal bulb or within the anterior part of basal bulb, tail cupola-shaped, with angular sides, with a slender spike, phasmids prominent, papilla-like, flanking the cupola part, male tail region with nine pairs of genital papillae with a 1 + (1 + 1) + 2 + 1 + 3 pattern, spicules 48.0-70.5 μm long, gubernaculum less than half of spicule length long, dauer juvenile with a long tail, and tapering to a filiform posterior end. The phylogenetic relationships were reconstructed using 18S-, 28S-, and ITS-rRNA gene sequences. The phylogenies showed that P. koreana n. sp. is a sister species to P. zhejiangensis. This species represents the first record of an entomo-parasitic relationship within this predominantly gastropod-parasitic genus.}, }
@article {pmid41394730, year = {2025}, author = {Sun, R and Yang, P and Wang, L and Hu, Y and Yang, Y and Deng, F and Li, S and Fan, M and Xia, X and Li, Y}, title = {PKU tags, novel genetically encoded shape tags for cell labeling in light and electron microscopy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.25.690457}, pmid = {41394730}, issn = {2692-8205}, abstract = {Distinguishing among neuronal cell types is crucial for deciphering complex neural networks and brain functions. However, the current repertoire of cell-labeling tools compatible with light microscopy (LM) and/or electron microscopy (EM) is limited compared to the vast number of cell types in the brain. Here, we introduce PKU (polymer king-size unit) tags, genetically encoded "shape tags" that leverage the polymerization of self-assembling proteins, spectrally distinct fluorescent proteins and, optionally, a nuclear targeting sequence to generate a series of multi-shaped (spherical or filamentous), multi-colored (blue, green, red, near-infrared) and multi-localized (cytosolic or nuclear) tags. By co-expressing multiple PKU tags within the same cell, a combinatorial strategy further expands the repertoire, which can theoretically yield hundreds of unique labeling patterns. Expressing PKU tags in vivo provides multi-cell-type labeling and neuronal circuit tracing, without altering the animal's behavior or transcriptomic profiles. Moreover, when fused to the peroxidase APEX2, PKU tags maintain their shape-specific features, providing shape "barcoding" using EM. Thus, PKU tags represent a versatile and efficient toolkit for studying connectomics using both LM and EM.}, }
@article {pmid41394686, year = {2025}, author = {Hart, MR and Thomson, ZJ and Kaul, SN and Ilcisin, S and Landreau, M and Stuckey, TJ and Wittig, PJ and Keller, M and McCann, CD and Torgerson, TR and Skene, PJ}, title = {REFLEX, a Novel Immune Profiling Assay, Combining TCR Repertoire and Multiome at Massively Scalable Single-cell Resolution to Catapult Exploration of T-cell Derived Immunity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.24.684243}, pmid = {41394686}, issn = {2692-8205}, abstract = {Single-cell profiling of T cell state with immune repertoire is critical for understanding heterogenous T cell phenotypes and responses to antigen, however, existing technologies struggle to generate this information at sufficient throughput to match biological complexity. We present "REFLEX", a novel single-cell method enabling highly scalable, cost-efficient, multiomic profiling with paired-chain TCR sequencing. REFLEX utilizes in-situ reverse transcription with integrated sample multiplexing barcodes in a way that merges seamlessly with the commonly used 10x FLEX platform to allow capture of TCR sequences at unprecedented scale and depth. We profile >2 million cells from CMV-peptide-pulsed T cell expansions, capturing TCR sequences and rich multiomic information from 1.4M T cells, identifying many putative novel CMV reactive clonotypes and illustrating the scale and transformative impact on our understanding of T cell mediated adaptive immunity achievable with REFLEX.}, }
@article {pmid41394655, year = {2025}, author = {Zhang, P and Law, BK and Goodwin, K and Chan, MM and Nelson, CM}, title = {Mapping embryonic mouse lung development using enhanced spatial transcriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.22.688293}, pmid = {41394655}, issn = {2692-8205}, abstract = {The mature mammalian lung contains ~50 different cell types that are located in precise positions along and around the airway epithelial tree. Here, we investigated how these spatial patterns are progressively established during development. Specifically, we optimized a microfluidics-enabled, deterministic barcoding-based sequencing (DBiT-seq) workflow to achieve highly sensitive spatial mapping of tissue sections from early embryonic mouse lungs. Spatial mapping of epithelial populations revealed that Sox9+ epithelial progenitors are located throughout the epithelial tree at early stages before becoming confined to the distal ends. Spatial mapping of mesenchymal populations revealed a previously unrecognized mesenchymal cluster that expresses high levels of extracellular matrix proteins and appears to promote embryonic lung innervation. These findings provide new insights into the spatial organization and cellular dynamics underlying early lung development, and demonstrate the power of spatial transcriptomics to uncover hidden patterns and populations of cells.}, }
@article {pmid41394078, year = {2025}, author = {Nanni, L and Brahnam, S and Fusaro, D}, title = {Matrix-based vector representations in neural networks for classifying molecular biology data.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf251}, pmid = {41394078}, issn = {2635-0041}, abstract = {SUMMARY: Selecting an appropriate classifier is essential for achieving accurate classification. In this study, we propose novel neural network (NNs)-based alternatives to standard classifiers as support vector machines. NNs, particularly convolutional neural networks and transformer networks, have shown exceptional performance in processing image data. To leverage this capability, we explore methods for transforming 1D vector data into 2D matrix representations, enabling the application of NNs pre-trained on large-scale image datasets. Specifically, we introduce a new data restructuring technique based on Wigner transforms, and we compare many methods proposed in the literature. The effectiveness and robustness of our approach are assessed using various benchmark datasets, from peptide classification to DNA barcoding classification, demonstrating consistently strong performance.<br><br>All source code and related resources used in this work are made publicly available at https://github.com/LorisNanni/Matrix-Representation-of-Vectors-in-Neural-Networks-for-Data-Classification.}, }
@article {pmid41391287, year = {2025}, author = {Guzik, MT and Thornhill, J and van der Heyde, M and Stringer, DN and White, NE and Saccò, M and Beasley-Hall, PG and Nevill, P and King, RA and Cooper, SJB and Austin, AD}, title = {Towards a global barcode reference library for subterranean fauna.}, journal = {The Science of the total environment}, volume = {1011}, number = {}, pages = {181078}, doi = {10.1016/j.scitotenv.2025.181078}, pmid = {41391287}, issn = {1879-1026}, abstract = {Implementation of environmental DNA (eDNA) metabarcoding for biodiversity discovery and assessment offers a unique opportunity to gain new insights into subterranean communities around the world. However, for effective and meaningful identification of species from anonymous eDNA barcodes, a library of known reference sequences with associated correct taxonomic metadata - also called a barcode reference library (BRL) - is required. Here we propose an open, publicly accessible information resource for eDNA biomonitoring of subterranean fauna following findable, accessible, interoperable and reusable (FAIR) principles that can be expanded globally. While similar proposals have been made by other authors for individual taxon groups, here we have analysed a curated BRL of subterranean fauna compiled from existing GenBank and BOLD DNA sequence databases for a minimum of five genes (COI, 18S, 12S, 28S and 16S rRNA). We demonstrate the value of such an initiative to eDNA metabarcoding where custom libraries are used to characterise entire ecosystems under examination. To examine the effectiveness of a custom BRL, we generated metabarcoding data for an exemplar system at Bungaroo Creek in the Pilbara (Australia), a globally significant location of stygofaunal diversity. We compared results of BLAST queries of eDNA Operational Taxonomic Units (OTUs) to our BRL and the GenBank nucleotide database, and observed that for all barcoding regions, the custom BRL identified subterranean zero-radius OTUs (ZOTUs) (i.e., error-corrected biological sequences) that could not be identified using GenBank and worked better in tandem. We use the BRL presented here to propose a six-stage plan for developing data infrastructure for subterranean fauna, especially with respect to eDNA metabarcoding data. To our knowledge, this represents the first published instance of a subterranean BRL being tested against real eDNA metabarcoding data. These findings provide a step forward towards robust DNA-based bioassessments for subterranean biodiversity and further emphasise the need for the eDNA community to work together in facilitating a global BRL.}, }
@article {pmid41390472, year = {2025}, author = {Tian, D and Yang, J and Zhang, L and Yang, H and Wang, S and Su, X}, title = {Spatial fluorescence barcode by transiently luminescent DNA beads.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-67410-3}, pmid = {41390472}, issn = {2041-1723}, abstract = {Multiplexed nucleic-acid detection is essential for molecular diagnostics and spatial genomics, but conventional fluorescence methods are often limited by spectral overlap, nonspecific signals, and restricted encoding capacity. We present a spatial fluorescence barcode (SFB) platform based on transiently luminescent DNA beads (TLDBs) that enables single-color, high-plex readout. In this method, targets are encoded through the spatial arrangement of DNA-functionalized beads, eliminating the need for multicolor labeling or spectral unmixing. Target recognition is achieved through toehold-mediated strand displacement, and built-in nucleases enable autonomous enzymatic resetting for repeated use of probes. The system employs monochromatic spatial encoding, decoupling encoding capacity from spectral channels, and features a simplified probe design and decoding workflow. Self-resetting probes not only streamline the encoding process but also enhance practicality by allowing repeated assays without the need to re-prepare costly probe combinations. We demonstrate robust detection of pathogen-derived nucleic acids in infected blood and cancer-associated microRNAs in tissue samples, validating the platform's clinical applicability. Compared to existing barcoding strategies, SFB integrates monochromatic spatial encoding, simplified design, and autonomous reusability, offering a practical, scalable, and cost-effective solution for high-throughput nucleic acid analysis.}, }
@article {pmid41387894, year = {2025}, author = {Osman, T and Chiuya, T and Fèvre, EM and Junglen, S and Borgemeister, C}, title = {Impact of invasive weed Parthenium hysterophorus (Asteraceae) on mosquito abundance and plant-feeding behavior in an arboviral endemic region in Kenya.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-025-07174-3}, pmid = {41387894}, issn = {1756-3305}, support = {TRR 228//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Invasive alien species (IAS) are rapidly altering ecosystems, undermining biodiversity, ecosystem processes, and interspecies interactions. Although IAS ecological and economic effects are well recognised, their impact on mosquito populations and the dynamics of infectious diseases is poorly understood. Plant-derived sugars are crucial for mosquito biology, supporting nectarivorous male survival and enhancing female blood feeding.<br><br>METHODS: In this study, we investigated how Parthenium hysterophorus, a rapidly proliferating invasive weed, shapes the population structure and nectar-feeding behaviour of the mosquito vector in the Rift Valley area of Kenya. Across six villages, three heavily infested with P. hysterophorus and three uninfested controls, we collected 48,489 mosquitoes representing 35 species from two subfamilies (Anophelinae and Culicinae) and nine genera, including Anopheles, Aedes, Culex, Mansonia, and Coquillettidia. Mosquito plant feeding was confirmed using the anthrone test, and the ingested flora were identified via DNA barcoding of chloroplast markers, specifically matK, rbcL, and ITS2.<br><br>RESULT: Mosquito abundance was significantly higher in Parthenium-infested villages, particularly during the dry season (p < 0.001), despite similar species diversity across sites. Medically important vectors, including Mansonia africana, Coquillettidia metallicus, Culex pipiens, and Anopheles funestus, were notably more common in invaded habitats. Overall fructose positivity was significantly high in mosquitoes from Parthenium sites (p = 0.046), with females showing especially higher rates (28.1% vs 18.0%; p = 0.0038). DNA barcoding indicated a clear feeding preference for P. hysterophorus among Coq. metallicus, Mn. africana, and An. funestus, alongside other plants such as Lantana camara.<br><br>CONCLUSION: Our findings indicate that P. hysterophorus has a notable impact on mosquito population composition and stimulates sugar-feeding behavior among important vector species. This IAS acts as a sustainable nutritional source, potentially enhancing mosquito survival, extending vector activity in dry seasons, and heightening the risk of arboviral disease transmission. The findings highlight the critical need to integrate invasive plant management within comprehensive mosquito control strategies.}, }
@article {pmid41386828, year = {2025}, author = {Nasernakhaei, F and Zahraei, M}, title = {Genetic differentiation and conservation insights into Salicornia iranica subsp. sinus-persica from Musa Bay using SCoT markers and DNA barcodes.}, journal = {Journal, genetic engineering &amp; biotechnology}, volume = {23}, number = {4}, pages = {100563}, pmid = {41386828}, issn = {2090-5920}, abstract = {Understanding genetic diversity is essential for the conservation and management of halophyte species, especially in ecologically sensitive and industrially impacted regions. In this study, 52 accessions of Salicornia iranica subsp. sinus-persica were collected from diverse microhabitats across Musa Bay, including coastal zones, islands, and petrochemical sites. Following comprehensive morphological assessments showing high phenotypic similarity, and to ensure broad ecological coverage, 16 accessions representing all major microhabitats were selected for molecular analysis. SCoT markers and DNA barcoding (ITS and trnH-psbA regions) were employed to investigate their genetic structure. The SCoT markers revealed considerable polymorphism and partial genetic differentiation, especially between accessions from petrochemical and natural saline habitats. ITS sequencing identified five haplotypes without forming a monophyletic clade, indicating shallow divergence and possible ancestral polymorphism. In contrast, no variation was detected in the plastid region trnH-psbA. These results represent the first global report of ITS and trnH-psbA haplotypes for this subspecies. While the findings are preliminary due to limited sample size and marker coverage, they provide a critical baseline for future studies employing high-resolution genomic tools. Our findings underscore the influence of habitat fragmentation and anthropogenic pressures on genetic patterns and emphasize the importance of conserving genetically distinct accessions in ecologically vulnerable habitats to support the long-term survival and sustainable utilization of this coastal halophyte.}, }
@article {pmid41383658, year = {2025}, author = {Oset, M and Flakus, A and Guzow-Krzemińska, B}, title = {Two new species of Cora (lichenized Basidiomycota, Lichenomphaliaceae) and additional records from Bolivia.}, journal = {MycoKeys}, volume = {126}, number = {}, pages = {1-18}, pmid = {41383658}, issn = {1314-4049}, abstract = {Two new species of lichens, Cora neoparabovei Oset, Flakus &amp; Guzow-Krzem. and C. neopseudobovei Oset, Flakus &amp; Guzow-Krzem., are described based on material collected in Bolivia. The study is based on morphological and anatomical examinations, molecular phylogenetic analysis and haplotype network analysis of the nuITS rDNA sequences. Phenotypically, Cora neoparabovei is characterised by the long, concentrically arranged setae on the surface of the thallus and densely pilose margins, whereas in C. neopseudobovei the diagnostic features are the brown upper surface thallus when fresh, pale yellow to orange-yellow when dry, with slightly visible concentric colour zonation when dry and also with involute, creamy white margins. In addition, three species, i.e., Cora arcabucana B. Moncada, C. Rodr. &amp; Lücking, C. cuzcoensis Holgado, Rivas Plata &amp; Perlmutter, and C. undulata L.Y. Vargas, B. Moncada &amp; Lücking, are reported as new to Bolivia. New records of C. aspera Wilk, Lücking &amp; E. Morales from Bolivia are reported.}, }
@article {pmid41383654, year = {2025}, author = {Sihvonen, P and Lee, KM and Söderholm, M and Rajaei, H and Hausmann, A and Staude, HS}, title = {Drepanogynis insciata (Felder &amp; Rogenhofer, 1875), a South African geometrid moth lost to science rediscovered after more than 140 years (Lepidoptera, Geometridae, Ennominae).}, journal = {ZooKeys}, volume = {1261}, number = {}, pages = {261-276}, pmid = {41383654}, issn = {1313-2989}, abstract = {The geometrid moth Drepanogynis insciata (Felder &amp; Rogenhofer, 1875) has been known only from two specimens in the Natural History Museum, London, UK: the holotype male collected before 1875 from South Africa, and a second male specimen without date and collecting locality data but probably collected before 1879. Unexpectedly, 13 specimens of this species-long considered lost to science-were observed in four locations between 2020 and 2023 in the Western Cape, near the type locality of the species. These observations were based on photographs available on iNaturalist, apart from a single male attracted to light, which was collected and vouchered for study from the Western Cape on 28 January 2022. We illustrate D. insciata and the newly collected specimen using both classical dissection and non-destructive micro-CT imaging. Phylogenetic analysis based on the multi-gene maximum-likelihood method places the species within Ennominae, tribe Drepanogynini. DNA barcodes reveal its nearest genetic neighbor to be Drepanogynis smaragdaria Krüger, 2002, with 5.9% sequence divergence. We discuss the conservation implications of this rediscovery.}, }
@article {pmid41382136, year = {2025}, author = {Pfuderer, L and Friedl, A and Wiggli, B and Grass, R}, title = {Doffing procedures of personal protective equipment evaluated with lipid nanoparticles as viral surrogates: uncovering potential blind spots.}, journal = {Antimicrobial resistance and infection control}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13756-025-01680-w}, pmid = {41382136}, issn = {2047-2994}, abstract = {BACKGROUND: Personal protective equipment (PPE) should effectively protect health care workers (HCWs) when treating infectious patients. However, during doffing contamination from outside of the PPE could be transferred and might cause serious infection. Therefore, complex doffing procedures have been developed, which include disinfection steps and would thereby protect the HCWs even if a contamination event occurred during doffing. However, assessing these complex multi-step procedures regarding risk of contamination and infection is challenging. The use of harmless surrogates with pathogen mimicking properties such as lipid nanoparticles encapsulating DNA (LNPs) could provide valuable insights into the effectiveness of doffing and disinfection procedures. Compared to the state-of-the-art method of contamination monitoring using fluorescent lotions LNPs promise to be more sensitive and give additional insights into the value of the disinfection steps.<br><br>METHODS: After pre-testing the suitability of LNPs as viral surrogates in terms of detection limit and susceptibility to ethanolic disinfection, LNPs with different barcodes were used to evaluate the PPE doffing procedure in place at the Cantonal Hospital Baden (Switzerland). During the biannual HCWs' PPE training, several sites of the PPE were deliberately contaminated with LNPs after donning. After completion of the doffing procedure, the hands and faces of the HCWs and several environmental sites were analysed for LNP contamination via qPCR.<br><br>RESULTS: The analysis showed that no contamination of HCWs' hands and faces was detectable, indicating the effective protection of HCWs. But some environmental sites were contaminated during the doffing procedure. Owing to the disinfection sensitivity of the LNPs it could be shown that the LNPs detected were disintegrated during one of the disinfection steps of the procedure.<br><br>CONCLUSIONS: This study demonstrates that LNPs can be used as viral surrogates during the evaluation of PPE doffing procedures. LNPs can lead to insightful results due to their low detection limit and the susceptibility towards disinfection, making this method superior to fluorescent lotions. Consequently, indications for the procedures' effectivity in inhibiting pathogen transfer to HCWs were found using LNPs. At the same time, blind spots in environmental contamination were uncovered, and the necessity of the disinfection steps in the protocol was displayed.}, }
@article {pmid41379560, year = {2025}, author = {Doorenweerd, C and Barr, NB}, title = {A Cytochrome C Oxidase I Barcode distance threshold for genus-level identification of pest fruit flies (Tephritidae).}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf330}, pmid = {41379560}, issn = {1938-291X}, support = {//United States Department of Agriculture (USDA)/ ; //USDA Animal and Plant Health Inspection Service/ ; AP22PPQS&amp;T00C065//University of Hawaii's College of Tropical Agriculture and Human Resources/ ; AP23PPQS&amp;T00C073//University of Hawaii's College of Tropical Agriculture and Human Resources/ ; }, abstract = {Accessible and accurate methods of pest identification are a cornerstone of pest management. When identifications are not feasible using morphology, molecular methods such as DNA Barcoding provide an option to complete a diagnosis. However, previous studies have shown that some pests cannot be identified to species using DNA Barcodes. In such cases, a genus-level identification could guide subsequent response to pests, but few studies have examined the performance of DNA Barcoding methods to diagnose pest genera as opposed to pest species. We datamined 6,582 previously published Cytochrome C Oxidase I (COI) Barcode region sequences for 12 genera of tephritid fruit flies that include the six main pest genera. After filtering short sequences and duplicate haplotypes, a dataset with 3,077 sequences remained for a pairwise-distance and tree-based genus-level identification test. Our results show that a 5% pairwise distance threshold provides reliable genus-level identifications using sequences of 400 to 658 base pairs. This threshold can easily be implemented with widely available tools such as the Basic Local Alignment Search Tool (BLAST) algorithm. The 5% distance cutoff value is set conservatively and could be refined further by including more species and genera in the reference set. We additionally find that the 3՛ end of the COI Barcode region has greater pairwise distances between genera than the 5՛ end. Our findings provide an additional use of the COI Barcode region for identification that can readily be implemented in pest fruit fly management protocols.}, }
@article {pmid41377849, year = {2025}, author = {Yu, M and Kim, S and Sohn, J and Kim, H}, title = {New records of the genus Aleiodes (Hymenoptera, Rogadinae) from South Korea.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e170343}, pmid = {41377849}, issn = {1314-2828}, abstract = {BACKGROUND: The subfamily Rogadinae comprises several genera, amongst which Aleiodes Wesmael, 1838 is the most species-rich, with more than 632 species described worldwide and many others likely remaining undiscovered.<br><br>NEW INFORMATION: In this study, we report three species of Aleiodes newly recorded from South Korea: Aleiodes angustipterus van Achterberg &amp; Shaw, 2016, Aleiodes euproctis He &amp; Chen, 1990 and Aleiodes malichi Butcher et al., 2012.}, }
@article {pmid41377505, year = {2025}, author = {Huberman, LB and Villalobos-Escobedo, JM and Skerker, JM and Shi, R and Rico-Ramírez, AM and Adams, C and Arkin, AP and Deutschbauer, AM and Glass, NL}, title = {Construction of a randomly barcoded insertional mutant library in the filamentous fungus Trichoderma atroviride.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.30.691285}, pmid = {41377505}, issn = {2692-8205}, abstract = {Filamentous fungi play key roles in ecosystems, agriculture, biotechnology, symbiosis, and disease, yet the large-scale characterization of gene function in these organisms remains limited by low transformation efficiencies and their multinucleate, syncytial cells, which complicate high-throughput screening strategies. To address the challenge of high-throughput screening in filamentous fungi, we developed methods to construct a genome-wide barcoded insertional mutant library in Trichoderma atroviride , a filamentous fungus widely used as a biocontrol agent against bacterial and fungal plant pathogens. Our strategy leveraged randomly barcoded transfer DNA insertions from plasmid libraries containing hundreds of millions of unique DNA barcodes and a broad host-range drug resistance marker delivered via Agrobacterium tumefaciens into T. atroviride . By optimizing transformation conditions, we achieved up to 600 independent transformants per infection event, resulting in a library of over 31,000 mapped insertions disrupting 7,104 of the 11,863 predicted genes in the T. atroviride genome. This resource establishes a scalable platform for high-throughput functional genomics in filamentous fungi, enabling both fundamental investigations of fungal biology and engineering approaches toward improved medical applications, biotechnology, and sustainable agriculture.}, }
@article {pmid41377107, year = {2025}, author = {Janka, E and Alagappan, RP and Das, D and Kjeldsberg, LA and Wang, S and Haugen, T and Wentzel, A}, title = {Diverse microbial communities colonize biofilm carriers in moving bed and intermittent cleaning reactors for municipal and industrial wastewater treatment.}, journal = {Biofilm}, volume = {10}, number = {}, pages = {100337}, pmid = {41377107}, issn = {2590-2075}, abstract = {Conventional biofilm reactors are widely used for the removal of organic constituents and nutrients (i.e., nitrogen and phosphorus) in municipal and industrial wastewater treatment. Moving bed biofilm reactor (MBBR) and continuously flow intermittent cleaning reactor (CFIC) have been developed as more compact, small footprint, and highly efficient biofilm-based systems for wastewater treatment. However, despite the advancements in reactor technology, there is limited scientific information on the microbial composition of the biofilms in these systems. This study aimed to characterize and provide early insights into the microbial diversity of biofilms grown on biofilm carriers and liquid suspensions of the biofilm-based wastewater treatment systems. Microbial samples were collected from biofilm carriers and liquid suspension in four full-scale MBBR plants and two CFIC plants in Norway, all treating municipal and industrial wastewater. DNA was extracted from the samples and subjected to meta-barcode sequencing for taxonomic classification of microbial communities in each treatment plant. The results revealed significant variation in microbial compositions across treatment plants, influenced by wastewater characteristics, biofilm carrier types, and reactor operational characteristics. On the biofilm carriers, the dominant bacterial taxa included TM7-1 (Saccharibacteria), Burkholderiales, Clostridiales, Actinomycetales, Pseudomonadales, Rickettsiales, and Rhodobacteriales. In liquid suspensions, the dominant groups were Clostridiales, Methanosarcinales, Pseudomonadales, Flavobacteriales, and Rhodobacteriales. In conclusion, this study highlights the diverse microbial populations on biofilm carriers and liquid suspensions, which collectively contribute to the enhanced treatment efficiency of both MBBR and CFIC systems.}, }
@article {pmid41375363, year = {2025}, author = {Lobo-Torres, M and Mantilla-Escalante, DC and Anaya, BJ and Tirado, DF and Arenas-Gómez, CM}, title = {Uncovering the Floral Origins of Honey Bee Pollen in Colombian Tropical Dry Forest: A Low-Cost DNA Barcoding Approach Reveals Cactaceae Dominance.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {23}, pages = {}, doi = {10.3390/plants14233652}, pmid = {41375363}, issn = {2223-7747}, support = {934 CT391-2023//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (MinCiencias)-Programa de Becas postdoctorales orientadas por misiones 934 CT391-2023 y el Fondo Nacional para el Financiamiento de la Ciencia, la Tecnolog&#xed;a y la Innovaci&#xf3;n Francisco Jos&#xe9; de Caldas/ ; }, abstract = {Characterizing the botanical composition of pollen is essential to understanding the floral resources used by bees. While microscopy is the traditional method, it is time-consuming and limited in taxonomic resolution. Molecular tools such as DNA barcoding offer a more precise and cost-effective alternative for identifying plant taxa in mixed pollen samples. This study implemented a preliminary and cost-effective molecular approach to identify the botanical origin of pollen stored in bee bread from Apis mellifera hives in a tropical dry forest fragment in La Paz, Cesar, using rbcL and matK genes as markers. The chloroplast markers rbcL and matK were amplified and Sanger-sequenced from three independent bee hives, each processed in duplicate as technical replicates. The BLAST+ 2.17.0 results from Sanger sequences showed a sequence identity ranging from 89%-99%, with rbcL showing higher and more consistent matches than matK, suggesting stronger discriminatory power, while the lower identity in one hive indicated a more complex pollen mixture. However, matK detected a greater number of taxa overall (i.e., 70% of the total, 64 genera) compared with rbcL (i.e., 50%, 46 genera). Both markers overlapped in approximately 20% of the taxa, most of which (i.e., 94%) belonged to the family Cactaceae. This indicated that, although rbcL provided more reliable matches, matK contributed to broader taxonomic coverage, highlighting the complementarity of both markers for mixed pollen analyses. This approach highlights its value as an exploratory tool prior to applying high-throughput sequencing strategies. Furthermore, such studies may support the development of local honey brands by validating that their products originate mainly from the biodiversity of tropical dry forests, an ecosystem currently at risk, thereby conferring both ecological and market value.}, }
@article {pmid41374505, year = {2025}, author = {Cheng, Y and Liu, Y and Li, Q and Jiang, T and Ji, C and Liu, L and Zhong, Y and Wu, J and Chen, G}, title = {An Intelligent System for Pigeon Egg Management: Integrating a Novel Lightweight YOLO Model and Multi-Frame Fusion for Robust Detection and Positioning.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {23}, pages = {}, doi = {10.3390/s25237132}, pmid = {41374505}, issn = {1424-8220}, mesh = {*Columbidae/physiology ; Animals ; Algorithms ; Eggs ; *Ovum ; Image Processing, Computer-Assisted/methods ; Intelligent Systems ; }, abstract = {To address the issues of high breakage rates and substantial labor costs in pigeon egg farming, this study proposes an intelligent pigeon egg recognition and positioning system based on an improved YOLOv12n object detection algorithm and OpenCV barcode recognition technology. Visual sensors installed on feeding machines were used to collect real-time video data of pigeon cages, with images obtained through frame extraction. The images were annotated using LabelImg to construct a pigeon egg detection dataset containing 1500 training images, 215 validation images, and 215 test images. After data augmentation, the dataset was used to train the pigeon egg recognition model. Additionally, customized barcodes were designed according to actual farm conditions and recognized using OpenCV through preprocessing steps including grayscale conversion, filtering, and binarization to extract positional information. Experimental results demonstrate that the proposed YOLOv12n-pg recognition model requires only 4.9 GFLOPS computational load, contains 1.56 M parameters, and has a model size of 3.5 MB, significantly lower than other models in the YOLO-n series. In inference tests, it achieved 99.4% mAP50 and 83.6% mAP50-95. The implementation of a majority voting method in practical testing further reduced the missed detection rate. The system successfully records "cage location-egg count" information as key-value pairs in a database. This system effectively enables automated management of pigeon eggs, improves recognition performance, and demonstrates higher efficiency and accuracy compared to manual operations, thereby establishing a foundation for subsequent research in pigeon egg recognition.}, }
@article {pmid41372213, year = {2025}, author = {Song, F and Lian, J and Liu, ZL and Li, XJ and Huang, WD and Zhao, X and Yan, X and Jin, L and Jin, GZ and Zhao, XY and Ge, XJ}, title = {A DNA Barcode Reference Library of Native Seed Plants in Chinese Dryland Regions.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-025-06259-z}, pmid = {41372213}, issn = {2052-4463}, abstract = {Approximately 6.6 million km[2] of China's territory consists of drylands at high desertification risk. Despite ecological vulnerability, these regions remain understudied in biodiversity research. DNA barcoding provides an efficient tool for rapid species identification, offering significant potential for biodiversity conservation and ecological surveys in drylands. However, comprehensive reference data for China's drylands are currently lacking, underscoring the urgent need for a reliable, extensive, and traceable DNA barcode reference library. To address this gap, we systematically surveyed plant diversity across nearly all Chinese drylands from 2013 to 2021. Our study documented 1,140 species, representing 434 genera, 76 families, and 29 orders. Based on this effort, we constructed the most comprehensive DNA barcode reference library for native dryland seed plants in China, comprising 13,246 sequences across five markers: rbcL (3,056), matK (3,332), ITS (3,358), psbA-trnH (1,770), and trnL-F (1,730). This resource establishes a critical foundation for integrated taxonomic research, biodiversity monitoring, and environmental impact assessments. Moreover, it supports initiatives in desertification control, plant conservation, and sustainable development in China's dryland regions.}, }
@article {pmid41368503, year = {2025}, author = {Hakimzadeh, A and Mikryukov, V and Metsoja, M and Tedersoo, L and Anslan, S}, title = {Are we throwing away good data? Evaluation of chimera detection algorithms on long-read amplicons reveals high false-positive rates across algorithms.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20456}, pmid = {41368503}, issn = {2167-8359}, mesh = {*Algorithms ; False Positive Reactions ; *DNA Barcoding, Taxonomic/methods ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; Detection Algorithms ; }, abstract = {Long-read amplicon sequencing has enabled us to return to full-length DNA barcodes, which benefit from the higher taxonomic resolution in metabarcoding-based biodiversity studies. However, chimeric sequences (artificial constructs formed when incomplete amplicons fuse during polymerase chain reaction (PCR)) remain challenging, potentially skewing diversity estimates and ecological inferences. Here, we benchmark three de novo chimera detection algorithms, uchime_denovo, removeBimeraDenovo, and chimeras_denovo, on simulated and empirical eukaryotic full-ITS (rRNA ITS1-5.8S-ITS2) datasets to evaluate their precision, sensitivity, and effects on the final OTUs composition/community structure. Upon simulated data, uchime_denovo achieved the highest precision even with default settings, whereas other algorithms displayed high false-positive chimera rates without setting adjustments. Similarly, the tests upon empirical data showed that uchime_denovo had lower false positive rates, whereas about half of the sequences in the putative chimeric batch were false positives when using chimeras_denovo and removeBimeraDenovo. We found that most of the false-negative chimeras contained multiple 5.8S regions, indicating PacBio library preparation artifacts rather than PCR artifacts. However, OTU-level comparisons indicated that overall richness and community-ordination patterns remain largely consistent across different chimera-filtering approaches with or without accounting for false positives and negatives.}, }
@article {pmid41359104, year = {2025}, author = {Kikkawa, HS and Tsuge, K}, title = {Identification of toxic plants from poisonous samples using massively parallel sequencing.}, journal = {Forensic toxicology}, volume = {}, number = {}, pages = {}, pmid = {41359104}, issn = {1860-8965}, support = {17K15886//Japan Society for the Promotion of Science/ ; 20392269//Japan Society for the Promotion of Science/ ; }, abstract = {PURPOSE: Some toxic plants have strong morphological similarities with edible wild plants. Therefore, poisoning often occurs due to accidental ingestion. It is important to identify poisonous plants in edible plant mixtures, even if the samples have been digested. In the present study, we developed a method for genus and species identification in mixed samples using massive parallel sequencing (MPS).<br><br>METHODS: Veratrum oxysepalum and Colchicum autumnale are the most common causative plants of such accidents and their morphological features are similar to those of the edible Hosta sieboldiana. In this study, we used V. oxysepalum and C. autumnale as the target poisonous plant species. We developed and optimized an MPS analysis method for trnL and rbcL regions that are commonly used in plant species identification. Initially, DNA from poisonous plants (V. oxysepalum and C. autumnale) and edible plants (H. sieboldiana) were mixed in various ratios and analyzed using MPS. Next, we prepared cooked materials and simulated gastric contents from V. oxysepalum, C. autumnale, and H. sieboldiana and analyzed them using MPS.<br><br>RESULTS: We detected both poisonous and edible plant DNA when mixed in equal amounts. Poisonous plants were also detected in cooked or simulated gastric acid content. These results suggest that our method can be used to identify the genera or species of plants present in cooked materials and simulated gastric contents.<br><br>CONCLUSIONS: These results indicate that MPS techniques are useful for the forensic analysis of plant materials.}, }
@article {pmid41320931, year = {2025}, author = {López-Jiménez, A and García-Varela, M and Aguilar-Aguilar, R}, title = {Species delimitation of Apharyngostrigea Ciurea, 1927 (Digenea: Diplostomoidea) based on morphology and molecular data from the Neotropical region of Mexico.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1017/S0031182025101315}, pmid = {41320931}, issn = {1469-8161}, abstract = {The genus Apharyngostrigea comprises a group of diplostomoidean digeneans that parasitize birds of the family Ardeidae (herons), with approximately 20 species described worldwide. Despite numerous efforts, a robust phylogenetic framework to delimit species within the genus is still lacking, mainly due to the limited morphological variation among its members. This study employed an integrative taxonomic approach, combining nuclear and mitochondrial DNA sequences with morphological data to assess species boundaries within Apharyngostrigea based on specimens collected from southeastern Mexico. Using a combination of species discovery (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partition, General Mixed Yule Coalescent and Poisson Tree Processes) and validation methods based on Bayesian gene tree topologies (BPP and PHRAPL). We found high diversity within this genus in southeastern Mexico. Our analyses supported the delimitation of four nominal species that were previously described and validated in this study, along with the redescription of three of them. In addition, through species delimitation methods and morphological examination, we identified two candidate species and/or lineages that require further evidence to be formally described. This study demonstrates that an integrative taxonomic approach provides a robust framework for species delimitation in taxonomically complex groups such as Apharyngostrigea.}, }
@article {pmid41357975, year = {2025}, author = {Yuan, X and Chen, K and Ahmed, AY and Shao, M}, title = {MELO-ED: learning locality-sensitive multi-embeddings for edit distance.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.23.689944}, pmid = {41357975}, issn = {2692-8205}, abstract = {Edit distance is a fundamental metric for quantifying similarity between biological sequences, but its high computational cost limits large-scale applications. Previously, we proposed learned locality-sensitive bucketing (LSB) functions that achieved superior performance and efficiency compared to classical seeding methods for identifying similar and dissimilar sequences. How-ever, each component of an LSB function is represented as a one-dimensional hash value that can only be compared for identity, which constrains the method's accuracy. Here, we intro-duce MELO-ED, a multi-embedding locality-sensitive framework that upgrades each hash value to a higher-dimensional embedding capable of efficiently approximating edit distance. MELO-ED employs a Siamese convolutional neural architecture that learns complementary embeddings capturing both global sequence context and fine-grained edit operations. By integrating locality-sensitive bucketing with multi-embedding representations, MELO-ED achieves near-perfect ac-curacy without increasing the number of buckets required. Leveraging mature indexing methods in the embedding space, MELO-ED transforms time-consuming edit distance computations into scalable similarity searches across massive genomic databases. Comprehensive evaluations on simulated DNA sequences and real barcode datasets demonstrate that MELO-ED outperforms both traditional alignment-free methods and contemporary machine learning approaches, in-cluding our previously developed learned LSB functions. These results establish MELO-ED as a state-of-the-art framework for fast and accurate classification of similar and dissimilar sequences. MELO-ED is available at https://github.com/Shao-Group/MELO-ED .}, }
@article {pmid41354705, year = {2025}, author = {Pavia, PX and Patiño, LH and Méndez, C and Romero, Y and Duque, MC and Cruz, C and Ramírez, JD}, title = {Response and therapeutic failure to meglumine antimoniate, the first-line drug for cutaneous leishmaniasis infections in Colombian soldiers.}, journal = {Parasitology research}, volume = {124}, number = {12}, pages = {152}, pmid = {41354705}, issn = {1432-1955}, mesh = {Humans ; *Leishmaniasis, Cutaneous/drug therapy/epidemiology/parasitology ; *Meglumine Antimoniate/therapeutic use ; Colombia/epidemiology ; *Military Personnel ; *Antiprotozoal Agents/therapeutic use ; Adult ; Male ; Female ; Treatment Failure ; Young Adult ; *Leishmania/drug effects/classification/genetics/isolation &amp; purification ; Risk Factors ; Adolescent ; Animals ; Middle Aged ; }, abstract = {Leishmaniasis is a vector-borne disease caused by Leishmania protozoa, transmitted through infected female phlebotomine sandflies. Cutaneous leishmaniasis (CL), its most common form, causes considerable morbidity, particularly among Colombian military personnel in endemic areas. Although meglumine antimoniate (MA) remains the first-line treatment, increasing reports of therapeutic failure (TF) raise concerns about its efficacy and highlight the need to identify associated risk factors. The objective of this study was to identify risk factors linked to MA treatment outcomes in Colombian soldiers with CL and to characterise the Leishmania species involved and their geographic distribution. A total of 128 soldiers diagnosed with CL (2018-2019) were followed for treatment response. Sociodemographic, clinical and lesion data were collected. Leishmania species were identified through HSP70 and MPI gene barcoding, and geographic origins were mapped. Selected isolates from TF patients underwent in vitro susceptibility testing to MA. The cure proportion was 67.9%, with TF in 32%. Factors significantly associated with TF included previous infections (p = 0.001), prior MA use (p = 0.000), lymphadenopathy (p = 0.008) and lesion type (p = 0.002). Multivariate analysis identified previous treatment (p = 0.000), lesion size and infections acquired in the Orinoquía (p = 0.013) and Pacific (p = 0.014) regions as risk factors. L. (V.) braziliensis predominated, especially in Orinoquía and Amazon regions; L. (V.) panamensis was widespread, and L. (L.) mexicana appeared only in the Andean region. In vitro resistance to MA was not observed in analysed isolates; thus, this factor does not appear related to TF. TF is linked to specific clinical and epidemiological variables, supporting their integration into patient monitoring during MA therapy. Clinical trial number: not applicable.}, }
@article {pmid41354528, year = {2025}, author = {Ebmer, D and Czerny, J and Unterköfler, MS and Karbe, M and Gruber, R and Stimac, I and Fuehrer, HP and Joachim, A and Pikalo, J}, title = {Reports of Microthoracius mazzai (Phthiraptera: Anoplura) infestations in alpaca (Vicugna pacos) herds from Austria and Germany.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {66}, number = {}, pages = {101371}, doi = {10.1016/j.vprsr.2025.101371}, pmid = {41354528}, issn = {2405-9390}, mesh = {Animals ; Austria/epidemiology ; Germany/epidemiology ; *Lice Infestations/veterinary/parasitology/epidemiology ; *Anoplura/genetics/classification/anatomy &amp; histology ; Male ; Female ; *Camelids, New World/parasitology ; *Camelidae/parasitology ; Electron Transport Complex IV/genetics ; Phylogeny ; }, abstract = {Sucking lice (Phthiraptera: Anoplura) constitute obligate and permanent insect ectoparasites of mammals and exhibit a hematophagous lifestyle. In South American camelids, three species of the genus Microthoracius have been described, however, reports outside South America are scarce. Here we describe infestations with Microthoracius mazzai in three alpaca (Vicugna pacos) herds from Austria (Styria and Salzburg), and Germany (Bavaria). Overall, lice infestations were detected in eight animals. Four of them exhibited a massive generalized infestation. Lice specimens were identified as M. mazzai using morphological keys. First molecular characterization of M. mazzai, including DNA barcodes based on mitochondrial cytochrome oxidase subunit 1 gene, is provided. Although rarely reported outside South America, lice of the genus Microthoracius should be considered as the cause for pruritus and dermatitis in South American camelids worldwide.}, }
@article {pmid41354072, year = {2025}, author = {Shneyer, VS and Rodionov, AV}, title = {20 Years of DNA Barcoding - Achievements and Problems.}, journal = {Biochemistry. Biokhimiia}, volume = {90}, number = {11}, pages = {1602-1619}, doi = {10.1134/S0006297925602977}, pmid = {41354072}, issn = {1608-3040}, mesh = {*DNA Barcoding, Taxonomic/methods/history ; Animals ; High-Throughput Nucleotide Sequencing ; *DNA/genetics ; }, abstract = {Over 20 years of extensive studies on DNA barcoding of various types of multicellular organisms have resulted in the selection of specific markers for multiple taxonomic groups, development of primers for many selected markers, establishment of DNA barcodes for more than 400 thousand species, and creation of the BOLD database. Next-generation sequencing methods allow DNA barcodes to be obtained immediately for many samples, including those stored in museum collections. DNA barcode analysis has revealed many previously unknown and undescribed species in various animal groups. DNA barcoding has been successfully used in many practical applications. However, certain problems and controversial issues remain, primarily, regarding description of new species based on DNA barcodes and the accuracy of sample identification using reference libraries.}, }
@article {pmid41351823, year = {2025}, author = {Howard-Stone, R and Măndoiu, II}, title = {MHASS: Microbiome HiFi Amplicon Sequencing Simulator.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf656}, pmid = {41351823}, issn = {1367-4811}, abstract = {SUMMARY: Microbiome HiFi Amplicon Sequence Simulator (MHASS) creates realistic synthetic PacBio HiFi amplicon sequencing datasets for microbiome studies, by integrating genome-aware abundance modeling, realistic dual-barcoding strategies, and empirically derived pass-number distributions from actual sequencing runs. MHASS generates datasets tailored for rigorous benchmarking and validation of long-read microbiome analysis workflows, including ASV clustering and taxonomic assignment.<br><br>Implemented in Python with automated dependency management, the source code for MHASS is freely available at https://github.com/rhowardstone/MHASS along with installation instructions. Our code is also published on Zenodo at https://doi.org/10.5281/zenodo.17486364.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41351680, year = {2025}, author = {Fang, XY and Lin, S and Zhong, XP and Zhang, XL and Zhang, YT and Chen, JM and Zhou, KL}, title = {Morphological and Molecular Analyses of Cladonema cf. Californicum (Hydrozoa: Anthoathecata) from China.}, journal = {Zoological science}, volume = {42}, number = {6}, pages = {596-604}, doi = {10.2108/zs240009}, pmid = {41351680}, issn = {0289-0003}, mesh = {Animals ; China ; Phylogeny ; *Hydrozoa/genetics/anatomy &amp; histology/classification ; Electron Transport Complex IV/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, hydrozoan medusae collected from a home aquarium in Sanming, China, were tentatively identified as Cladonema cf. californicum Hyman, 1947, based on DNA barcoding. Morphologically, these specimens differed from known Cladonema medusae, including C. californicum, by possessing a manubrium with protuberances and tentacles with one to three (typically two) adhesive branches, along with three to six (usually four) stinging branches emerging laterally from the main tentacle shaft. These morphological distinctions were supported by molecular phylogenetic analyses using the mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) gene sequences. Nonetheless, COI sequences revealed that C. cf. californicum clustered with juvenile Cladonema californicum medusae from California, USA, with a minimal genetic distance of 0.008, indicating potential conspecificity. Given the morphological similarities among juvenile Cladonema medusae, the Californian specimens may have been misidentified. Further investigations focusing on the polyp stage and geographic distribution are necessary to fully resolve the taxonomic status of these medusae and clarify their relationship with C. californicum.}, }
@article {pmid41351674, year = {2025}, author = {Hikosaka, A and Nishimoto, A and Takeda, N and Hikosaka-Katayama, T}, title = {Occurrence of 12 Acoela Species in the Seto Inland Sea.}, journal = {Zoological science}, volume = {42}, number = {6}, pages = {540-555}, doi = {10.2108/zs240106}, pmid = {41351674}, issn = {0289-0003}, mesh = {Animals ; Phylogeny ; Japan ; RNA, Ribosomal, 18S/genetics ; Oceans and Seas ; Electron Transport Complex IV/genetics ; *Animal Distribution ; Species Specificity ; }, abstract = {The Acoela is a notable taxon in terms of the early evolution of bilaterians and the photosynthetic symbiosis between animals and microalgae. There are approximately 416 described species of Acoela worldwide, which are classified into 16 families. In total, 21 species have been reported in Japan, of which five have been reported in the Seto Inland Sea. We surveyed acoels in the intertidal zone of beaches along the Seto Inland Sea coast of Hiroshima Prefecture and collected specimens. A comparison of mitochondrial cytochrome oxidase subunit I (COI) sequences and molecular phylogenetic analysis suggested that they could be divided into 12 species. Molecular phylogenetic analysis using 18S rRNA sequences suggested that these species belonged to five families: Convolutidae, Otocelididae, Dakuidae, Actinoposthiidae, and Isodiametridae. There have been no previous reports of Dakuidae or Actinoposthiidae in Japan and no reports of Isodiametridae in the Seto Inland Sea. These results suggested that the diversity of Acoela in Japan and the Seto Inland Sea is far richer than is currently known.}, }
@article {pmid41351070, year = {2025}, author = {Allsopp, RC and Page, K and Wren, E and Nteliopoulos, G and Gleason, KLT and Lall, GM and Bhagani, S and Acheampong, E and Wadsley, MK and Coombes, RC and Shaw, JA}, title = {Concurrent genomic assessment of circulating tumour cells and ctDNA to guide therapy in metastatic breast cancer.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {1858}, pmid = {41351070}, issn = {1471-2407}, mesh = {Humans ; *Neoplastic Cells, Circulating/pathology/metabolism ; *Breast Neoplasms/genetics/pathology/blood/therapy/drug therapy ; Female ; *Circulating Tumor DNA/genetics/blood ; Middle Aged ; *Biomarkers, Tumor/genetics/blood ; Genomics/methods ; Mutation ; DNA Copy Number Variations ; Neoplasm Metastasis ; High-Throughput Nucleotide Sequencing ; Adult ; Aged ; Precision Medicine ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Molecular analysis of actionable driver mutations and somatic copy number alterations (sCNAs) in circulating tumour DNA (ctDNA) and circulating tumour cells (CTCs) is increasingly being used to guide personalised medicine in patients with cancer. In previous CTC studies, high numbers of CTCs were needed for successful recovery of individual CTCs for molecular analysis at a time when patients typically have very short survival, limiting clinical applicability. Here, by performing longitudinal analyses of ctDNA and CTCs across a broad range of CTC counts, we hypothesized that CTCs could reveal synergistic and additional genomic information to ctDNA at points when therapeutic interventions could be considered in the follow up of patients with metastatic breast cancer (MBC).<br><br>METHODS: Eight patients underwent serial blood sampling. CTCs were captured via CellSearch-DEPArray from 7.5&#xa0;mL (CellSave tubes), while 15&#xa0;mL (EDTA tubes) was used for cfDNA extraction. A total of 58 cfDNA samples and 192 CTCs from the 8 patients were compared by shallow whole genome sequencing sWGS and targeted next generation sequencing using custom designed mutation panels (cfDNA; dual barcoding Ion AmpliSeq HD technology (556 hotspots across 24 genes) and CTCs; SingleSeq-compatible AmpliSeq technology across 539 of the 556 (97%) hotspots).<br><br>RESULTS: The majority of patient samples showed complementary genomic information in CTCs and ctDNA from the same blood sample. However, genome changes were detected in CTCs from some blood samples that were ctDNA negative despite progression providing actionable information at times when ctDNA analysis was not informative. Across the CTCs and ctDNA, common regions of loss included chromosome 13q14 containing the RB1 gene, detected in 3 of 4 patients receiving CDK4/6 inhibitors and amplification of 17q12 containing the ERBB2 gene in 2 of the 7 patients with HER2 negative metastatic disease, suggesting evolution to HER2 positive disease.<br><br>CONCLUSIONS: Our study shows that CTCs provide key information that would have been missed by ctDNA monitoring alone and extends CTC and cfDNA genomic profiling to patients with a broad range of CTC counts for blood-based monitoring of HER2 status and other clinically actionable targets for informing treatment decisions in metastatic disease.}, }
@article {pmid41347007, year = {2025}, author = {Réblová, M and Nekvindová, J and Bauchová, L and Hernández-Restrepo, M}, title = {Pleurophragmium parvisporum (Ascomycota): One name, seven stories - a case highlighting the need for verification of strains from public culture collections.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e173033}, pmid = {41347007}, issn = {2210-6340}, abstract = {Public repositories of living fungal strains provide essential reference points and support diverse scientific outcomes. Current best practices for preserving fungal strains emphasise the generation of DNA barcodes and the management of comprehensive metadata. However, challenges arise when type material or authentic reference strains are lacking, as this prevents direct comparison of DNA barcodes and forces identifications to rely solely on morphology. This problem is particularly pronounced for strains deposited during the pre-molecular era, especially those belonging to species with simple or convergent morphologies. In this study, we re-examined seven strains deposited in a public culture collection under the name Pleurophragmium parvisporum, including synonymous designations. Our approach combined cultivation experiments, comparative morphological analyses, multi-locus phylogenetic reconstruction of six nuclear markers, and biogeographic assessments. Our analyses revealed that these strains are scattered across four distinct families or orders in three classes. Two strains belong to Thysanorea (Chaetothyriales, Eurotiomycetes): T. acropleurogena sp. nov. and a sterile strain identified as the already known T. melanica. Two other strains were resolved within Wongia (Papulosaceae incertae sedis, Sordariomycetes) and introduced as W. pallidopolaris sp. nov. and W. rhachidophora sp. nov. Finally, two strains represent novel taxa within the Tubeufiales (Dothideomycetes), described here as Zaanenomyces hilifer sp. nov. and Skoliomycella flava gen. et sp. nov. Of the seven examined strains, only one conformed to the species concept of P. parvisporum and is here regarded as its reference strain. The phylogenetic analyses resolved P. parvisporum within Neomyrmecridium (Myrmecridiales, Sordariomycetes). Consequently, Neomyrmecridium was reduced to synonymy of Pleurophragmium, leading to the proposal of 11 new combinations (P. asiaticum comb. nov., P. asymmetricum comb. nov., P. fusiforme comb. nov., P. gaoligongense comb. nov., P. guizhouense comb. nov., P. luguense comb. nov., P. naviculare comb. nov., P. pteridophytophilum comb. nov., P. septatum comb. nov., P. sichuanense comb. nov., and P. sorbicola comb. nov.), and two new names (P. fluviale nom. nov. and P. jiulongheense nom. nov.). In addition, three species formerly placed in Uncispora are transferred to Thysanorea, with new combinations proposed based on congruent morphology and multi-locus phylogenetic evidence: T. hainanensis comb. nov., T. sinensis comb. nov., and T. wuzhishanensis comb. nov. This study refines the generic limits of Pleurophragmium and morphologically similar genera and reveals several previously unrecognised lineages. It highlights how misinterpretation of subtle morphological features may lead to strains being misidentified and deposited under incorrect names in public collections, where they risk perpetuating taxonomic errors.}, }
@article {pmid41345699, year = {2025}, author = {Yilmaz, A and Kasap, OE}, title = {Prevalence of Wolbachia in natural sand fly (diptera: psychodidae) populations from Türkiye and its potential role in mitochondrial divergence.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-025-07157-4}, pmid = {41345699}, issn = {1756-3305}, support = {2211-A National PhD Scholarship Program//T&#xdc;B&#x130;TAK/ ; 101057690//European Commission/ ; 10038150 and 10038150//UK Research and Innovation/ ; TBAG 105T205 and SBAG 114S999//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; 09D01601002 and 01001601001//Hacettepe University Scientific Research Unit/ ; W911QY-16-C-0160//AFHSB-GEIS/ ; }, abstract = {BACKGROUND: Phlebotomine sand flies are vectors of various pathogens, most notably Leishmania spp. Symbiotic bacteria have recently gained considerable attention owing to their effects on hosts and on other organisms co-infecting the same host. In this study, we investigated the natural Wolbachia infection status of sand fly taxa distributed in Türkiye and examined its potential role in driving the deep mitochondrial divergence observed within certain taxa.<br><br>METHODS: We analysed 858 sand fly specimens, mostly collected between 2005 and 2016, with additional samples obtained in 2023. Specimens were morphologically identified, and the mitochondrial cox1 gene was sequenced for DNA barcoding. For selected taxa showing marked mitochondrial divergence, species delimitation methods were applied, and genetic diversity indices and neutrality tests were calculated. Wolbachia infection was detected via PCR amplification of the wsp gene, and strain diversity was characterised using multilocus sequence typing (MLST) of five housekeeping genes. Logistic regression was used to evaluate associations between infection status and mitochondrial lineage, sex or collection period.<br><br>RESULTS: Wolbachia infection was detected in 16.67% of specimens, occurring exclusively in Phlebotomus papatasi, Ph. major s.l., Ph. tobbi, Ph. economidesi and Sergentomyia minuta. Analyses of wsp and MLST data identified all sequences as belonging to Supergroup A, with multiple strains present within and across host taxa. Infection among the five Ph. major s.l. lineages delineated by species delimitation was significantly associated with lineage, with lineages 3-5 showing a higher probability of infection. The reduced haplotype and nucleotide diversity, along with a significant negative deviation from neutrality observed in lineage 5, suggest a selective sweep likely driven by Wolbachia infection.<br><br>CONCLUSIONS: This study represents the first comprehensive screening of Wolbachia infection in sand fly taxa distributed across T&#xfc;rkiye, during which several novel Wolbachia strains were identified. Our findings suggest a potential role of Wolbachia infection in driving lineage differentiation within certain sand fly taxa. However, further detailed investigations are required to elucidate the mechanisms by which Wolbachia influences sand fly diversification and to assess the broader epidemiological implications related to sand fly-borne diseases (SFBDs).}, }
@article {pmid41341958, year = {2025}, author = {Chaves, M and Hashish, A and Goraichuk, IV and Casserta, LC and Mears, MC and Gadu, E and Bakre, A and Alexander Morris, ER and Shelkamy, MMS and Nadendla, S and Perez, DR and El-Gazzar, M}, title = {Nanopore sequencing in veterinary medicine: from concepts to clinical applications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1701570}, pmid = {41341958}, issn = {2235-2988}, mesh = {*Nanopore Sequencing/methods/veterinary ; Animals ; *Veterinary Medicine/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Nanopores ; Genomics/methods ; }, abstract = {Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.}, }
@article {pmid41340599, year = {2025}, author = {Hébert, C and Favret, C}, title = {Large-Scale Integrative Taxonomy of the Smallest Insects Reveals Astonishing Temperate Diversity (Hymenoptera: Chalcidoidea: Mymaridae).}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70197}, doi = {10.1111/mec.70197}, pmid = {41340599}, issn = {1365-294X}, support = {RGPIN-2024-05502//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche du Qu&#xe9;bec-Nature et technologies/ ; }, abstract = {Fairyflies (Hymenoptera: Chalcidoidea: Mymaridae) are a diverse but taxonomically understudied group of parasitoid wasps that attack the eggs of other insects. Being among the very smallest of all insects, they are often ignored in biodiversity surveys despite being one of the most abundant microhymenoptera in many habitats. The traditional approach of morphological species delimitation can be challenging due to their minute size and meticulous slide-mounting technique. Ways to accelerate their discovery are needed. We conducted the first large-scale study of Mymaridae in temperate forests, combining DNA megabarcoding and the large-scale integrative taxonomy (LIT) workflow to describe their diversity. We obtained COI barcodes from 2098 specimens and used ASAP and RESL for species delimitation. Between 42 and 114 molecular clusters were delimited. Reducing morphological validation to only 9% of the sample enabled accurate delimitation while limiting time and effort. We confirmed the presence of 55 species, including many potentially new to science. The LIT workflow was effective for Mymaridae, although cryptic diversity remains unresolved in some large clusters, especially in the genera Alaptus and Anagrus, where high haplotype diversity and morphological ambiguity suggest additional hidden species. DNA reference databases proved unreliable, with less than 1% correct species matches, highlighting the taxonomic gap for this group. Nonetheless, we contributed 16 new identified reference barcodes to public databases and added new provincial and national species records for Canada. Our results demonstrate the value of combining molecular and morphological data in a standardised workflow and underscore the importance of improving reference databases for effective biodiversity assessments of dark taxa like microhymenoptera.}, }
@article {pmid41339720, year = {2025}, author = {Alsulami, F and Jhanjhi, NZ}, title = {Deep learning framework for barcode localization and decoding using simulated UAV imagery.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-29720-w}, pmid = {41339720}, issn = {2045-2322}, abstract = {Automated warehouse stock tracking is becoming increasingly important for improving logistics and reducing manual errors. Unmanned Aerial Vehicles (UAVs) offer a promising solution by enabling automated barcode scanning from above. However, challenges such as poor lighting, shadows, and partial occlusions still limit the reliability of real-time barcode detection and decoding. This research presents a deep learning framework evaluated on simulated UAV imagery for barcode inventory management. The proposed system uses the YOLOv8 object detection model to accurately localize both 1D and 2D barcodes in images captured from a UAV perspective. With a mean Average Precision (mAP) of 92.4%, the model demonstrates strong performance even in complex warehouse conditions. Once localized, the barcode regions are decoded using OpenCV's barcode module. The extracted data, including product ID and quantity, is then automatically updated into a MySQL database to simulate real-time stock updates. Although tested using simulated aerial imagery, the system is designed to be drone-ready with minimal adjustments. This modular approach shows potential for real-world UAV deployment and contributes to reducing human effort and errors in inventory tracking.}, }
@article {pmid41339471, year = {2025}, author = {Priyadarshini, A and Mahalakshmi, K and Venkatesan, NK and Dhanalakshmi, M}, title = {Whole genome sequencing of a hypermucoviscous, multidrug-resistant Klebsiella pneumoniae subsp. pneumoniae K219 isolated from human sputum.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-30811-x}, pmid = {41339471}, issn = {2045-2322}, abstract = {Multidrug-resistant (MDR) strains of Klebsiella pneumoniae pose a significant public health threat due to their ability to evade commonly used antibiotics, restricting therapeutic options and increasing mortality rates especially among immunocompromised individuals. This study aimed to sequence the genome of MDR K. pneumoniae subsp. pneumoniae K219 isolate procured from a tertiary care hospital, Chennai which was isolated from a human sputum sample. Sequencing was performed using third-generation Oxford Nanopore Technologies (MinION platform, FLO-MIN106 flow cell, R9.4.1 pore type) with the EXP-NBD114 barcoding kit and SQK-LSK109 sequencing kit. The genome was analysed using a suite of bioinformatics tools to identify virulence factors, resistance genes, mobile elements, and clustered regularly interspaced short palindromic repeats (CRISPR). The assembled genome of K. pneumoniae K219 comprises a single circular chromosome and four plasmids, with a total genome size of 5,038,803 base pairs. The plasmids measured 229,745; 134,193; 33,455; and 183,631 base pairs, respectively. One CRISPR array was identified. Genomic characterization of K. pneumoniae K219, including its four plasmids and a CRISPR array, offers valuable insights into the genetic architecture of this MDR strain. The data enhance our understanding of its resistance mechanisms, virulence determinants, and interaction with mobile genetic elements. These findings can guide targeted treatment strategies and infection control measures in clinical settings.}, }
@article {pmid41338874, year = {2025}, author = {Villegas, NK and Tran, MH and Keller, A and Plesa, C}, title = {BAR-CAT: Targeted Recovery of Synthetic Genes via Barcode-Directed CRISPR-dCas9 Enrichment.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1177/25731599251401526}, pmid = {41338874}, issn = {2573-1602}, abstract = {Modern gene synthesis platforms enable investigations of protein function and genome biology at an unprecedented scale. Yet, the proportion of error-free constructs in diverse gene libraries decreases with length due to the propagation of oligo synthesis errors. To rescue these error-free constructs, we developed Barcode-Assisted Retrieval CRISPR-Activated Targeting (BAR-CAT), an in vitro method that uses multiplexed dCas9-single-guide RNA (sgRNA) complexes to extract barcodes corresponding to error-free constructs. After a 15-min incubation and wash regimen, three low-bundance targets in a 300,000-member test library were enriched 600-fold, greatly reducing downstream requirements. When applied to a 384-gene DropSynth gene library, BAR-CAT enriched 12 targets up to 122-fold and revealed practical limits imposed by sgRNA competition and library complexity, which now guide ongoing protocol scaling. By eliminating laborious clone-by-clone validation and working directly on plasmid libraries, BAR-CAT provides a platform for recovering perfect synthetic genes, subsetting large libraries, and ultimately lowering the cost of functional genomics at scale.}, }
@article {pmid41337486, year = {2025}, author = {Jang, J and Ko, KP and Zhang, J and Jun, S and Park, JI}, title = {Deciphering precursor cell dynamics in esophageal preneoplasia via genetic barcoding and single-cell transcriptomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {49}, pages = {e2509534122}, doi = {10.1073/pnas.2509534122}, pmid = {41337486}, issn = {1091-6490}, support = {CA286761//HHS | NIH | National Cancer Institute (NCI)/ ; CA193297//HHS | NIH | National Cancer Institute (NCI)/ ; CA278971//HHS | NIH | National Cancer Institute (NCI)/ ; CA279867//HHS | NIH | National Cancer Institute (NCI)/ ; CA256207//HHS | NIH | National Cancer Institute (NCI)/ ; CA278967//HHS | NIH | National Cancer Institute (NCI)/ ; P30 CA016672/CA/NCI NIH HHS/United States ; RP180672//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200504//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; CA125123//HHS | National Institutes of Health (NIH)/ ; RR024574//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Animals ; *Esophageal Neoplasms/genetics/pathology/metabolism ; Mice ; Single-Cell Analysis/methods ; *Precancerous Conditions/genetics/pathology/metabolism ; *Transcriptome ; Humans ; Esophagus/pathology/metabolism ; Tumor Suppressor Protein p53/genetics/metabolism ; Cell Lineage ; Receptor, Notch1/genetics ; }, abstract = {Although histologically normal, esophageal preneoplastic cells harbor early genetic alterations and likely exhibit lineage plasticity. However, their origins and trajectories remain unclear. To address this, we combined genetic barcoding with single-cell RNA sequencing to trace the lineage of esophageal preneoplastic cells. We identified a distinct progenitor-like cell population with high plasticity. Through a scoring system, these high-plasticity cells are mapped, revealing their contributions to proliferative and basal cell populations. This approach uncovers molecular markers, including Nfib and Qk, that define these precursor cells, validated by spatial transcriptomics and a Trp53 Cdkn2a Notch1 mouse model. These findings provide critical insights into early tumorigenesis, highlighting the potential of precursor cells as biomarkers for early detection and therapeutic targets of esophageal squamous cell cancer. By elucidating the cellular dynamics underlying esophageal preneoplasia, this research lays the foundation for strategies to prevent malignant progression, offering broader implications for improving cancer diagnostics and treatment approaches.}, }
@article {pmid41335224, year = {2026}, author = {Bronnec, P and Dalmon, S and Briand, C and Allatif, O and Broly, M and Marcotte, M and Lombardi, G and Barthes, K and Martel, N and Hughes, S and Gillet, B and Milhavet, F and Atilgan, A and Bachelez, H and Palmeri, S and Prigione, I and Madrange, M and Savey, L and Moutschen, M and Jeru, I and El Moussaoui, M and Belot, A and Sbidian, E and Carbone, A and Jamilloux, Y and Gattorno, M and Smahi, A and Georgin-Lavialle, S and Boursier, G and Magnotti, F and Henry, T}, title = {SpeckSeq enables high-throughput functional stratification of MEFV variants in autoinflammatory diseases.}, journal = {The Journal of experimental medicine}, volume = {223}, number = {2}, pages = {}, doi = {10.1084/jem.20251065}, pmid = {41335224}, issn = {1540-9538}, support = {779295//Agence Nationale pour la Recherche/ ; ANR-21-CE17-0046//Agence Nationale pour la Recherche/ ; EQU202103012640//Fondation pour la Recherche M&#xe9;dicale/ ; }, mesh = {*Pyrin/genetics/chemistry ; Humans ; *Familial Mediterranean Fever/genetics ; High-Throughput Nucleotide Sequencing/methods ; Mutation/genetics ; *Hereditary Autoinflammatory Diseases/genetics ; Inflammasomes/metabolism ; }, abstract = {Variants of uncertain significance (VUS) are a major obstacle in genetic diagnosis, particularly when involving gain-of-function (GoF) mutations that are poorly predicted in silico. MEFV, which encodes the inflammasome sensor pyrin, is mutated in two autoinflammatory diseases, familial Mediterranean fever (FMF) and pyrin-associated autoinflammation with neutrophilic dermatosis (PAAND). Here, we developed SpeckSeq, a method that combines DNA bar-coding, ASC speck-based single-cell sorting and next-generation sequencing to systematically identify hypermorphic MEFV variants in response to different stimuli. SpeckSeq identified 49 GoF mutations separated into two distinct groups containing either PAAND variants or FMF variants. SpeckSeq was validated using patients' cells and supported a reclassification of MEFV variant pathogenicity, leading to novel diagnoses. As a large-scale mutagenesis approach, using human genetics as a guide, SpeckSeq revealed structural and functional pyrin features, including a putative ligand-accommodating cavity in the B30.2 domain. Altogether, SpeckSeq classifies VUS to refine molecular diagnostics and improve our knowledge on the pyrin inflammasome.}, }
@article {pmid41334765, year = {2025}, author = {Kmentová, N and Topić, M and Vanhove, MPM and Atkinson, SD}, title = {Monomyxum ligophori n. sp. in a ParasiteBlitz: monopisthocotylans as myxozoan hosts in South Carolina and monophyly of a cosmopolitan hyperparasitic clade.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e127}, doi = {10.1017/S0022149X25100904}, pmid = {41334765}, issn = {1475-2697}, support = {DIOS/OEYLRODE/2022/001//Universiteit Hasselt/ ; BOF20TT06//Universiteit Hasselt/ ; BOF21PD01//Universiteit Hasselt/ ; Prf-2022-049//Belgian Federal Science Policy Office/ ; NA22OAR4170114//U.S. Department of Commerce/ ; 2021H1D3A2A02081767//National Research Foundation of Korea/ ; Tartar Research Fund//Oregon State University/ ; F22AP01952//U.S. Fish and Wildlife Service/ ; 23KP05VHOM//Universiteit Hasselt/ ; }, mesh = {Animals ; *Myxozoa/genetics/classification/isolation &amp; purification/physiology/growth &amp; development ; *Fish Diseases/parasitology ; South Carolina ; Phylogeny ; Life Cycle Stages ; *Platyhelminths/parasitology ; *Smegmamorpha/parasitology ; Parasitic Diseases, Animal/parasitology ; DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; }, abstract = {A ParasiteBlitz event offers a brief, intense opportunity to discover diverse parasite species and to reveal life cycles of heteroxenous parasite taxa. In this study, we describe Monomyxum ligophori n. sp., a hyperparasitic myxozoan (Monomyxidae) proliferating in two dactylogyrid monopisthocotylan flatworms (Ligophorus saladensis, Ligophorus mugilinus) infecting mugilid fishes (Mugil cephalus, Mugil curema) on the Atlantic coast of North America. Furthermore, we used DNA barcoding to infer the parasite's complex life cycle, matching its hyperparasitic myxospore stages with actinospore stages infecting the polychaete Streblospio benedicti found in the same locality during the ParasiteBlitz and also reported previously from the same region. Thus we report the first life cycle of a myxozoan that most likely does not require a vertebrate host. Hyperparasitic myxozoans are rare with only five species reported worldwide to infect flatworms. This study provides more information on the previously discussed host specificity towards monopisthocotylan hosts of these monomyxid myxozoan hyperparasites. Notably, Monomyxum ligophori n. sp. was detected in two out of four gill-infecting parasitic flatworms (being absent in Ligophorus uruguayensis and Metamicrocotyla macracantha) found infecting the same fish individuals during the ParasiteBlitz. Our molecular data and phylogenetic analysis support the previously suggested common origin of Monomyxum species infecting monopisthocotylan flatworms, and contribute to understanding the life cycle and host interactions of this unique hyperparasitic myxozoan lineage.}, }
@article {pmid41333291, year = {2025}, author = {Chávez-López, Y}, title = {A new species of Ampharete Malmgren, 1866 (Annelida: Ampharetidae) from Washington and redescription of A. cirrata Webster &amp; Benedict, 1887 and A. labrops Hartman, 1961.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e20457}, pmid = {41333291}, issn = {2167-8359}, mesh = {Washington ; Animals ; Electron Transport Complex IV/genetics ; Phylogeny ; *Polychaeta/anatomy &amp; histology/classification/genetics ; }, abstract = {Ampharete acutifrons (Grube, 1860), originally described from Greenland, has long been considered a widely distributed arctic-boreal species. However, recent morphological re-assessment of the holotype indicates that most previous records of A. acutifrons were misidentifications, and molecular sequence data also suggest that A. acutifrons is a multispecies complex. This study focuses on specimens of the A. acutifrons species complex from Washington, USA, with publicly available cytochrome c oxidase subunit I (COI) sequence data. Specimens from Washington belonging to the Invertebrate Zoology Collection of the Florida Museum of Natural History were examined. Additional specimens were examined for morphological comparison, including type material of A. cirrata Webster &amp; Benedict, 1887, and A. labrops Hartman, 1961. Detailed morphological descriptions of specimens and photographs of the diagnostic characters were made. The molecular analysis includes 37 published COI sequences of Ampharete and Anobothrus species sourced from public databases. Redescriptions of type material of A. cirrata and A. labrops are provided. Ampharete paulayi n. sp. is described as a new species from Washington, USA, based on morphological and COI sequences data. Photographs of living specimens are presented, a hypothesis on the development of buccal tentacles in Ampharete species is proposed, and the use of Methyl green stain is recommended as a standard practice in future descriptions of ampharetids.}, }
@article {pmid41332668, year = {2025}, author = {Hartman, A and Takacsi-Nagy, O and Kernick, C and Theberath, NE and Lu, J and Wu, L and Mantilla, M and Mittra, S and McClellan, A and Johnson, N and Mohamad, L and Castillo-Colin, L and Hoque, F and Eapen, A and Chen, A and Moser, LM and Rogando, T and Hernandez, A and Santostefano, K and Satpathy, AT and Roth, TL}, title = {A unified genetic perturbation language for human cellular programming.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.20.689421}, pmid = {41332668}, issn = {2692-8205}, abstract = {Evolution simultaneously and combinatorially explores complex genetic changes across perturbation classes, including gene knockouts, knockdowns, overexpression, and the creation of new genes from existing domains. Separate technologies are capable of genetic perturbations at scale in human cells, but these methods are largely mutually incompatible. Here we present CRISPR-All, a unified genetic perturbation language for programming of any major type of genetic perturbation simultaneously, in any combination, at genome scale, in primary human cells. This is enabled by a standardized molecular architecture for each major perturbation class, development of a functional syntax for combining arbitrary numbers of elements across classes, and linkage to unique single cell compatible barcodes. To facilitate use, CRISPR-All converts high level descriptions of desired complex genetic changes into a single DNA sequence that can rewire genomic programs within a cell. Using the CRISPR-All language allowed for head-to-head functional comparisons across perturbation types in a comprehensive analysis of all previously identified genetic enhancements of human CAR-T cells. Combining CRISPR-All programs with single cell RNA sequencing revealed a greater diversity of phenotypic states, including improved functional performance, only accessible through distinct perturbation classes. Finally, CRISPR-All combinatorial genome scale screening of up to four distinct perturbations simultaneously revealed additive functional improvements in human T cells accessible only through iterative multiplexing of modifications across perturbation classes. CRISPR-All enables exploration of a combinatorial genetic perturbation space, which may be impactful for biological and clinical applications.}, }
@article {pmid41331945, year = {2025}, author = {David, O and Munabi, IG and Joseph, O and Mwaka, E and William, B}, title = {A dataset of HLA-A allele sequences and periodontal disease status in people living with HIV.}, journal = {BMC research notes}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13104-025-07590-9}, pmid = {41331945}, issn = {1756-0500}, support = {R56DE032217/DE/NIDCR NIH HHS/United States ; }, abstract = {OBJECTIVES: This dataset was generated to investigate the distribution of HLA-A alleles in people living with HIV (PLWH) with and without periodontitis in Uganda. The data were collected as part of the parent study Oral papillomavirus, microbiota and cancer in people living with HIV (OHPVMC). The dataset provides valuable information about host genetic factors that may influence periodontal disease susceptibility in HIV-positive populations.<br><br>DATA DESCRIPTION: The dataset includes nanopore sequencing data (FASTQ format) for HLA-A alleles obtained from 64 PLWH participants (32 with periodontitis and 32 without). It also contains accompanying clinical metadata including periodontitis severity scores, age, sex, antiretroviral therapy duration, number of drinks per day and number of cigarettes per day. Processed files include HLA-A allele calls in CSV format, and file linking the barcodes to the unique identification numbers. All data files have been deposited in public repositories to facilitate reuse in immunogenetics and oral health research. The raw sequencing data are available through NCBI's Sequence Read Archive, while processed data and metadata are hosted on Figshare. This dataset will be particularly valuable for researchers studying genetic susceptibility to oral diseases, HLA diversity in African populations, and the application of nanopore sequencing for HLA typing.}, }
@article {pmid41331487, year = {2025}, author = {Tan, H and Dong, X and Kang, J and Bu, N and Zhang, Y and Qi, Z and Li, Z and Zhang, Z and Zhang, X and Wang, H and Ding, Y and Liu, Y and Zhao, L}, title = {Molecular characterization of livestock-associated ticks and tick-borne bacteria in Xinjiang, northwestern China.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-025-07178-z}, pmid = {41331487}, issn = {1756-3305}, support = {32260887//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; BR251303//Scientific Innovation Team Project/ ; }, abstract = {BACKGROUND: Xinjiang Uygur Autonomous Region represents a critical pastoral zone at the livestock-tick-human interface in northwestern China, yet molecular data on tick-borne pathogens in this region remain scarce.<br><br>METHODS: Between 2017 and 2018, 6172 ticks were collected from cattle, sheep, goats, horses, and dogs across 18 counties in Xinjiang. Tick species identification was performed through morphological examination and cytochrome oxidase I (COI) gene barcoding. Pooled samples (n&#x2009;=&#x2009;55) were screened using polymerase chain reaction (PCR) and sequencing targeting Rickettsia (glutamate transporter A [gltA], outer membrane protein A [ompA] genes), Anaplasma (16S ribosomal RNA [16S rRNA]), Borrelia (heat shock protein GroEL [groEL]), and broad-range bacterial diversity (16S rRNA).<br><br>RESULTS: Seven tick species were identified: Alveonasus lahorensis (33.7%), Dermacentor marginatus (32.3%), Rhipicephalus turanicus (21.9%), Dermacentor silvarum (5.7%), Hyalomma asiaticum (4.0%), and Haemaphysalis sulcata (2.5%). Rickettsia DNA was detected in 28 of 55 pools (50.9%), with sequences showing relatedness to Rickettsia raoultii, Rickettsia massiliae, and Rickettsia barbariae. Anaplasma capra was identified in D. marginatus collected from goats (1.8% of pools), while Borrelia miyamotoi was detected in R. turanicus from sheep (1.8% of pools). Additional bacterial genera detected included Arsenophonus in D. marginatus, Coxiella in R. turanicus, and Francisella in H. asiaticum. Notably, R. massiliae was detected in both eggs and unfed larvae of R. turanicus, consistent with transovarial transmission.<br><br>CONCLUSIONS: This study represents the first comprehensive molecular survey of livestock-associated ticks in Xinjiang, revealing high prevalence of spotted fever group rickettsiae and the presence of emerging tick-borne pathogens. Our findings underscore potential zoonotic risks within pastoral systems and emphasize the critical need for enhanced One Health surveillance strategies at the livestock-human interface in this region.}, }
@article {pmid41329648, year = {2025}, author = {Vihavainen, J and Kiljunen, N and Pohjola, P and McKeown, J and Oinonen, E and Mutanen, M and Pohjoismäki, J}, title = {Megabarcoding dark taxa - Assessing the utility of mass DNA barcoding for phorid fly species discovery.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0334948}, pmid = {41329648}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Diptera/genetics/classification/anatomy &amp; histology ; Female ; Male ; Electron Transport Complex IV/genetics ; Phylogeny ; Finland ; Species Specificity ; }, abstract = {Many hyperdiverse, small-bodied insect families contain numerous undescribed species, generally termed "dark taxa". Scuttle flies (Diptera: Phoridae), being among the most diverse insect groups globally, are a prime example. DNA barcoding can help delineate dark taxa, particularly when integrated with morphology, and/or additional molecular evidence. We sequenced COI-barcodes from 9,120 Finnish phorid specimens and initially identified them using the BOLD database. Furthermore, species identifications of all 843 specimens, belonging to other genera than Megaselia, were confirmed morphologically. Initially, the BOLD-based identifications matched the morphological identifications only in 68% of the cases, primarily due to numerous misidentifications in BOLD. After adjusting the BOLD reference identifications based on morphological analyses of male features, we established a reliable framework for female identification. This is advantageous for future identification of females, as they are often excluded from traditional identification keys. Only two species were discovered as new to Finland, demonstrating that Finnish fauna is well-known, except Megaselia. Although DNA barcodes show great promise for identifying phorids, incorrectly identified reference sequences remain challenging, not the functionality of barcode gene Cytochrome c oxidase subunit I (COI) itself. The number of Megaselia BINs greatly exceeded the known Finnish species count, with many sequences lacking matches in BOLD. This further highlights Megaselia as a particularly dark group, for which genetic tools are essential for uncovering species identities and assessing diversity.}, }
@article {pmid41328580, year = {2025}, author = {Goodsell, C and Jung, P and Maslakova, S and Allen, J}, title = {Baseodiscus the Eldest: First Report of a Decades-Long Lifespan in a Nemertean Species.}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.70052}, pmid = {41328580}, issn = {2471-5646}, support = {//The authors received no specific funding for this work./ ; }, abstract = {Nemertea is a speciose phylum of marine invertebrate predators ubiquitous in the world's oceans, which includes Lineus longissimus (Gunnerus, 1770)-the world's longest documented extant animal, yet much about the life histories of these remarkable animals remains poorly understood. For example, it is not known how long nemerteans live. We report a maximum known age of a nemertean individual, identified by morphology and DNA-barcoding as belonging to Baseodiscus punnetti (Coe, 1904), which has been kept in aquaria for at least 26 years. This finding confirms previous speculations that at least some species of nemerteans may live for many years and highlights a dearth of knowledge of the longevity of nemerteans and of marine invertebrates more broadly.}, }
@article {pmid41328418, year = {2025}, author = {Hajri, S and Bahri, L and Harris, DJ}, title = {New Insights on Genetic and Morphological Divergence Among a Buthus Species Complex From Tunisia With the Identification of a New Species.}, journal = {Ecology and evolution}, volume = {15}, number = {12}, pages = {e72556}, pmid = {41328418}, issn = {2045-7758}, abstract = {The taxonomy of the scorpion genus Buthus is complex due to the considerable increase in newly reported species, their high degree of similarity, and consequently, the great difficulty in their morphological differentiation. Tunisian species are not exempt from this issue, with several references highlighting the need for taxonomic revisions. This study integrates DNA sequence data and morphological assessments to investigate the diversity present in Tunisia and to provide morphological details that facilitate species identification. The results show that most Tunisian specimens are distributed within two clades. One clade comprises four subclades corresponding to B. tunetanus Herbst, 1800, B. paris C. L. Koch, 1839, B. chambiensis Kovařík 2006 and a southern group corresponding probably to B. lourencoi Rossi, Tropea &amp; Yağmur, 2013. The second clade represents a new species described in this study as B. saidnouirai Hajri, Bahri &amp; Harris, sp. nov. No evidence of B. dunlopi Kovařík 2006 have been recorded in the studied samples. Distances between all five species exceed the minimum divergence thresholds for Buthus species. The greatest distance was observed between B. saidnouirai. sp. nov. and the southern group, while the smallest distance was between B. tunetanus and B. paris. Although the genetic differences revealed considerable divergence of the new group from the four remaining species, the morphological assessment did not identify the same pattern. These five species demonstrate a morphological shape gradient in which B. paris and the southern group represent the two extremes, with B. paris being the most ornamented and the latter the least. The new species presents an intermediate morphology. The geographic distributions of the five reported species are discussed in this work according to the topography and orography of the region. Additional lineages known from Algeria may also enter the western fringes of Tunisia.}, }
@article {pmid41327488, year = {2025}, author = {Song, Z and Klyuchnikov, E and Badbaran, A and Tan, L and Dress, RJ and Czajkowski, E and Weßler, S and Massoud, R and Wolschke, C and Schimrock, A and Zhang, Y and Ly, C and Gagelmann, N and Rathje, K and Fehse, B and Bonn, S and Ravens, S and Gagliani, N and Krebs, CF and Panzer, U and Ayuk, F and Kröger, N and Prinz, I}, title = {Mega-scale single-cell profiling reveals novel biomarkers associated with acute GvHD after allogeneic hematopoietic stem cell transplantation.}, journal = {Biomarker research}, volume = {13}, number = {1}, pages = {155}, pmid = {41327488}, issn = {2050-7771}, abstract = {BACKGROUND: Alloreactive T cells mediate graft-versus-leukemia (GvL) reactions and acute graft-versus-host disease (aGvHD) in AML patients following allogeneic hematopoietic stem cell transplantation.<br><br>METHODS: To investigate biomarkers that identify alloreactive T cells associated with either beneficial GvL or detrimental aGvHD, we collected graft samples and two post-transplant follow-up blood samples (day 30 and day 100) of ten AML patients undergoing hematopoietic stem cell transplantation and profiled over 777,000 CD45[+] leukocytes in total by combinatorial barcoding-based mega-scale single-cell RNA sequencing.<br><br>RESULTS: Using immune receptor sequences as intrinsic clonal barcodes, we observed that especially CD8[+] graft-derived T cells persisted and displayed enhanced proliferation, clonal expansion, and likely alloreactivity. Notably, patient-derived peripheral leukocytes that survived the conditioning, as identified by sex-chromosome-related genes, were primarily CD4[+] T helper cells. MDGA1 expression on T cells and NK cells emerged as a novel biomarker potentially associated with aGvHD. Additionally, we observed a significant deficiency of ADGRG1 expression, a marker of alloreactive cytotoxic T cells, by &#x3b1;&#x3b2; and &#x3b3;&#x3b4; T cells from relapsed patients.<br><br>CONCLUSIONS: In conclusion, mega-scale single-cell monitoring of graft and hematopoietic immune cell reconstitution allowed us to demonstrate that MDGA1 and ADGRG1 may function as complementary biomarkers expressed by distinct circulating T cells that are associated with divergent outcomes in AML patients, enabling precise risk stratification of alloHSCT outcomes and presenting potential therapeutic targets.}, }
@article {pmid41325363, year = {2025}, author = {Dvirnas, A and Leal-Garza, LM and Abbaspour, Z and Fröbrant, E and Frykholm, K and Wrande, M and Sandegren, L and Westerlund, F and Ambjörnsson, T}, title = {DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.}, journal = {PloS one}, volume = {20}, number = {12}, pages = {e0335633}, pmid = {41325363}, issn = {1932-6203}, mesh = {*Algorithms ; *Chromosome Mapping/methods ; Escherichia coli/genetics ; *DNA/genetics ; Software ; }, abstract = {In optical genome mapping (OGM), large numbers of individual DNA maps-sequence-specific data series along single DNA molecules-are produced. Such individual maps have to be stitched together in a process called de novo OGM assembly in order to create consensus OGM maps for corresponding regions along the chromosomes. While there are several types of experimental OGM assays, not all of them have de novo OGM assembly tools available. In particular, in densely-labelled OGM there are no such tools. Here, we present and evaluate DOGMA, a de novo OGM assembly algorithm for densely labelled OGM data which uses matrix profiles. Matrix profile has transformed how data mining problems are approached in time series analysis. Yet, this algorithm has not been widely explored outside of the time series community- we here use it for OGM de novo assembly for the first time. Further novelties in our algorithm are the introduction of two scores for each individual alignment, use of p-values, a visual representation as barcode islands and the introduction of a method for generating consensus barcodes using amplitude adjustment. Utilizing p-values helps mitigate the risk of errors in the assemblies as caused by false positives. We demonstrate our algorithm by applying it for de novo OGM assembly of synthetic datasets and of an experimental dataset from an Escherichia coli genome. We validate the assemblies using corresponding reference genomes and investigate the strengths and limitations of the algorithm. De novo OGM assembly of dense optical DNA maps shows promise as a complement or an alternative to current OGM techniques for other types of genome mapping assays. The code is available at: https://github.com/dnadevcode/dogma.}, }
@article {pmid41318587, year = {2025}, author = {Platzgummer, K and Oerther, SI and Bečvář, T and Dvořák, V and Sádlová, J and Bečvářová, B and Volf, P and Obwaller, AG and Bakran-Lebl, K and Trájer, AJ and Walochnik, J and Kniha, E}, title = {The knowns and unknowns of phlebotomine sand flies (Diptera: Psychodidae) in selected countries of Central Europe.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-025-07160-9}, pmid = {41318587}, issn = {1756-3305}, support = {bo/00896/24/5//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; 101057690//European Commission/ ; }, abstract = {BACKGROUND: Sand flies are vectors of the protozoan Leishmania spp. and phleboviruses. In Europe, several species are widely distributed in the Mediterranean region and a northward spread can be observed. They can be found regularly also in some regions of Central Europe, with Phlebotomus mascittii being the most cold-tolerant and northerly distributed species, but the knowledge on their distribution in countries such as Germany, Austria, Czechia, Slovakia, and Hungary remains fragmentary because of a lack of comprehensive field studies and a poor understanding of the ecological requirements and phylogeographic history.<br><br>METHODS: A comprehensive literature review of sand fly occurrence in five Central European countries was complemented by entomological surveys, including sand fly and rodent screening for sand fly-borne pathogens. Nucleic acid extraction, COI barcoding, blood meal analysis, and phylogenetic and environmental analyses incorporating unsupervised machine learning techniques were conducted.<br><br>RESULTS: This study significantly advances the understanding of the current distribution of six sand fly species in Central Europe. Among them, only Ph. mascittii was present in all analyzed countries, except Czechia, with its seasonal activity peaking in July. Phlebotomus papatasi, Ph. perfiliewi and Ph. neglectus were recorded in Hungary, while Ph. perniciosus and Phlebotomus simici were found in Germany and Austria, respectively. Although Leishmania DNA was absent in sand flies and rodents, DNA from two distinct Trypanosoma lineages was detected in several specimens, suggesting Ph. mascittii feeds on both birds and ruminants. Trypanosomatid lineages identified in local rodents differed, indicating distinct lineages between sand flies and rodents. Environmental analysis identified 15 Corine land cover classes associated with sand fly presence, with urban locations being the most frequently occupied. Linear regression models comparing presence versus absence revealed significantly higher sand fly presence in forested and urban landscapes. Furthermore, Ph. mascittii populations formed four distinct ecological clusters, which broadly grouped into two main geographic groups: one in the Upper Rhine Valley of southwestern Germany and the other spanning the Carpathian Basin.<br><br>CONCLUSIONS: This study provides new insights into the current distribution, ecological preferences, seasonal activity, and potential vector capacity of sand fly species in Central Europe.}, }
@article {pmid41317321, year = {2025}, author = {Shin, HJ and Sharma, S and Kronheim, S and Cheung, M and Nguyen, LV}, title = {Protocol to track single-cell-derived clones using DNA barcoding combined with single-cell RNA sequencing.}, journal = {STAR protocols}, volume = {6}, number = {4}, pages = {104229}, doi = {10.1016/j.xpro.2025.104229}, pmid = {41317321}, issn = {2666-1667}, abstract = {Clonal fitness and plasticity drive tumor heterogeneity contributing to disease progression and treatment resistance. Here, we provide a protocol to track the clonal outputs from uniquely marked cells. We describe steps for constructing and validating lentiviral DNA barcode libraries. We then detail procedures for single-cell RNA sequencing. This approach links clonal growth activity with transcriptomic profiles and enables permanent cellular labeling to track clonal dynamics in various model systems, which can provide insight into molecular processes underlying clone function. For complete details on the use and execution of this protocol, please refer to Nguyen et al.[1].}, }
@article {pmid41316409, year = {2025}, author = {Leta, S and Mulatu, T and Yalew, B and Chibssa, TR and Paeshuyse, J}, title = {DNA barcoding and blood meal profiling of Ethiopian mosquitoes (Diptera: Culicidae): insights into species identification and host preferences.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {493}, pmid = {41316409}, issn = {1756-3305}, support = {4520196970//Global Minds PhD scholarship program, KU Leuven/ ; }, mesh = {Animals ; Ethiopia ; *DNA Barcoding, Taxonomic ; *Culicidae/classification/physiology/genetics ; *Mosquito Vectors/classification/physiology/genetics ; Phylogeny ; Feeding Behavior ; Host Specificity ; Genetic Variation ; Humans ; Female ; Aedes/classification/genetics/physiology ; Anopheles/classification/genetics/physiology ; }, abstract = {BACKGROUND: Arboviruses continue to threaten global health because of their rapid geographical expansion and significant disease burden. Of the over 500 recognized arboviruses, approximately 150 affect humans, and around 50 affect domestic animals and wildlife. The spread and impact of these viruses have increased significantly over the past three decades, driven by the proliferation of their vectors and the rise of global trade and travel.<br><br>METHODS: In this study, we used molecular methods to characterize mosquito species diversity and host feeding preferences across Ethiopia's Great Rift Valley. Mosquitoes were collected from diverse habitats in the Great Rift Valley of Ethiopia using Centers for Disease Control and Prevention (CDC) light traps, BG-Sentinel traps, and hand aspirators. The area was chosen for its high vector diversity, suitable breeding habitats, and the epidemiological importance of arboviruses. Morphological identification was conducted, and 204 blood-fed mosquitoes were selected. Genomic DNA was extracted, followed by polymerase chain reaction (PCR) amplification targeting the COI gene. Blood meal analysis was performed using vertebrate-specific primers targeting the 12S rRNA gene. Mosquito species identification, genetic diversity analysis, and phylogenetic analyses were conducted.<br><br>RESULTS: Of 6601 collected mosquitoes, 4977 were identified morphologically, comprising 399 Aedes, 2861 Culex, 1841 Anopheles, and 275 Mansonia species. COI DNA barcode analysis identified 142 mosquito specimens belonging to 16 species, with Anopheles coustani, Cx. tritaeniorhynchus, Cx. pipiens complex, Mansonia africana, and Ma. uniformis being the predominant species. Blood meal analysis (n&#x2009;=&#x2009;71 successful amplifications) revealed a primary reliance on humans and cattle. Cx. pipiens complex showed a strong anthropophilic tendency, while Cx. tritaeniorhynchus and Ma. uniformis exhibited broader host ranges. Genetic diversity indices showed significant Fu's Fs statistics for Cx. pipiens complex, Cx. tritaeniorhynchus, Ma. africana, and Ma. uniformis.<br><br>CONCLUSIONS: This study offers valuable preliminary insights into the diversity of mosquito species, genetic variation, and host-feeding preferences within the Ethiopian Rift Valley. The findings emphasize the potential of molecular techniques to enhance traditional entomological methods and improve the accuracy of mosquito identification. While the study is limited in both geographic and temporal scope, it highlights mosquito species of medical and veterinary significance and suggests implications for arboviral disease surveillance.}, }
@article {pmid41315888, year = {2025}, author = {van der Windt, N and Paix, B and Biesmeijer, JC and Ambo-Rappe, R and Huang, YM and Nirbadha, KGS and Sipkema, D and de Voogd, NJ}, title = {Host Evolutionary History Drives Prokaryotic Diversity in the Globally Distributed Sponge Family Petrosiidae.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70186}, doi = {10.1111/mec.70186}, pmid = {41315888}, issn = {1365-294X}, support = {101000392//Horizon 2020 Framework Programme/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //European Regional Development Fund/ ; //Collectivit&#xe9; Territoriale de Martinique/ ; CRG-1-814 2012-BER-002//King Abdullah University of Science and Technology/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology/ ; MNPH104403//Marine National Parks Headquarters/ ; }, abstract = {Sponge microbial communities play a crucial role in marine ecosystem functioning and serve as a rich source of bioactive compounds. While host identity is recognised as a major determinant of microbiome diversity, the underlying evolutionary mechanisms remain poorly understood. This study aimed to comprehensively assess phylosymbiosis patterns within the sponge family Petrosiidae. In total 21 sponge species, collected across a broad geographic scale, were examined to investigate how host phylogeny influences microbiome composition. Using 28S rRNA, 18S rRNA and COI gene barcoding to identify host sponges, combined with 16S rRNA gene amplicon sequencing to characterise prokaryotic communities, we provide evidence of phylosymbiosis through multiple analytical approaches, including distance-based metrics and topological congruence. Our results show that host phylogeny and identity play a significant role in structuring sponge microbiomes, even at finer taxonomic resolutions. However, we observed notable incongruencies, where closely related sponge species exhibit divergent microbial communities that appear to be associated with depth or geographical location. This study represents the first large-scale investigation of phylosymbiosis in sponges at the family level, providing valuable insights into the evolutionary and ecological drivers shaping sponge microbiomes, particularly in the sponge family Petrosiidae.}, }
@article {pmid41315366, year = {2025}, author = {Sahu, A and Singh, M and Sarkar, UK}, title = {Building a DNA barcode library of commercially exploited fish genetic resources (FGR) of the Gomti River, Ganga basin, implications for conservation and management.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42721}, pmid = {41315366}, issn = {2045-2322}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; Rivers ; Phylogeny ; *Conservation of Natural Resources ; India ; Biodiversity ; Electron Transport Complex IV/genetics ; *Gene Library ; }, abstract = {The Gomti River is a vital tributary of the largest Gangetic Riverine system, flowing in the northern part of Uttar Pradesh, India. This habitat serves as one of India's most precious repository for fish genetic resources (FGR), contributing significantly to regional biodiversity, and is a source of livelihood. It has diverse climatic conditions, which have led to a distinctive fish community structure and the presence of native species. The application of DNA barcoding for assessing FGR in the north Himalayan region, particularly in UP, presents a notable research gap. This study established the first DNA barcodes of voucher specimens identified through classical taxonomy, creating a molecular catalogue of commercially important fish species. DNA barcoding was accomplished using the cytochrome oxidase subunit I gene (COI) for species identification and phylogenetic analysis. We identified 37 commercially important fish species (34 native &amp; 3 exotics) using classical taxonomy and molecular biology, which belonged to 8 orders, 18 families, and 29 genera. The IUCN conservation status revealed that 30 species (81.08%) were categorized as Least Concern (LC), followed by 4 species (10.81%) as Near Threatened (NT), 2 species (5.41%) as Vulnerable (VU), and 1 species (2.70%) as Endangered (EN). Cypriniformes order and Cyprinidae family emerged as the most dominant groups, contributing 40.54% and 29.73%, respectively. Average read lengths of all sequences were 630.82 bp (range 578-655 bp). Overall nucleotide composition of Adenine (A) = 25.81%, Thymine (T) = 28.88%, Cytosine (C) = 27.53%, and Guanine (G) = 17.78%. Average GC content (54.69%) was higher than AT content (45.31%). As expected, the uncorrected p-genetic distances showed a progressive increase in genetic divergence from lower to higher taxonomic levels. p-distance values ranged from 0-0.48% (mean 0.06%) within species, 0-11.37% (1.56%) within genera, 0-12.27% (5.00%) within families, and 0-15.31% (8.88%) within orders. Among families, Cyprinidae (12.27%) and Danionidae (11.57%) exhibited the highest genetic divergence. Whereas at the order level, the greatest divergence was observed in Perciformes (15.31%), followed by Siluriformes (15.22%). The constructed phylogenetic tree shows that all species are clearly separated based on similar groups and clustered into independent clades. Assemble Species by Automatic Partitioning (ASAP) analysis identified ten partitions with the best ASAP score (4.00). It reveals a barcode gap of 1-9% (0.01-0.09) and delimits approximately 31-37 putative fish species. The GTR + G + I model revealed a strong transition bias in the COI gene of the barcoded fishes, with higher pyrimidine substitutions and transition/transversion ratios (k1 = 10.80; k2 = 26.98; R = 3.09). Our dataset comprised 110 COI nucleotide sequences with 592 positions in the final alignment, including 236 polymorphic sites and 39 distinct haplotypes. We also estimated haplotype diversity (Hd = 0.975) and nucleotide diversity (π = 0.194). Our findings highlighted that efficacy of traditional taxonomy and DNA barcoding method (also known as integrative taxonomy) is complementary to each other for identifying and authenticating fish taxa. Additionally, the developed COI library will be valuable for future environmental DNA (eDNA) studies for detecting indigenous and exotic fish species and useful for nature conservation. We conclude that it serves as an effective tool for sustainable conservation, fishery management, and future monitoring of freshwater fish genetic resources.}, }
@article {pmid41310420, year = {2025}, author = {Al-Andal, A}, title = {Plastome diversity and phylogenetic insights among modern Egyptian wheat cultivars: Genome-Wide and Gene-Level perspectives.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-025-07739-5}, pmid = {41310420}, issn = {1471-2229}, support = {RGP2/310/46//Deanship of Research and Graduate Studies at King Khalid University/ ; }, abstract = {This study presents a genome-wide and gene-level characterization of plastome diversity and phylogenetic relationships among ten modern Egyptian wheat cultivars, representing both hexaploid and tetraploid lineages. Raw sequencing data for all cultivars were retrieved from NCBI BioProject PRJNA1290394, and plastome assemblies were generated using the published wheat chloroplast genome (GenBank accession MW889057.1) as the seed reference under default settings. Comprehensive plastome sequencing revealed an exceptionally conserved genome structure and gene content across cultivars, yet identified distinct mutation hotspots, with the rps2 gene exhibiting the highest single-gene SNP burden (up to 21 SNPs in cultivar Sahel 1). SNP profiling demonstrated clear differentiation between genetically divergent cultivars such as Sahel 1 and GMZ9, and documented variation in overall mutational load-ranging from 7 to 74 SNPs per cultivar-mirroring phylogenetic clade structure. Chloroplast heteroplasmy analysis uncovered cultivar-specific genome stability patterns, informing breeding decisions and highlighting cytoplasmic diversity. SSR motif analysis confirmed predominant AT-rich homopolymers and subtle motif-length differences distinguishing tetraploid and hexaploid genotypes. Codon usage analysis showed a highly conserved AT-bias and effective translational optimization across ploidy levels. Phylogenetic reconstruction using complete plastome sequences resolved finer relationships than gene-based approaches, while matK emerged as a superior biomarker for distinguishing Poaceae lineages. mVISTA comparison revealed conserved plastome structure with divergence hotspots at atpH-atpI and atpA regions, underscoring their value as potential molecular markers for phylogenetic and barcoding applications. Taken together, these findings provide deep insights into plastome-driven genetic diversity, robust cultivar identification, and the evolutionary context for Egyptian wheat breeding and conservation programs. (253 words).}, }
@article {pmid41309703, year = {2025}, author = {Salamon, S and Mikołajczak, K and Basińska-Barczak, A and Banachewicz, P and Błaszczyk, L}, title = {Intergenerational and horizontal transmission of wheat endophytic fungi.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {42275}, pmid = {41309703}, issn = {2045-2322}, support = {2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; 2017/27/B/NZ9/01591//National Science Center in Poland/ ; }, mesh = {*Triticum/microbiology ; *Endophytes/genetics/physiology/classification ; *Fungi/genetics/classification ; Mycobiome ; Seedlings/microbiology ; }, abstract = {Understanding the mechanisms of endophytic fungal transmission is crucial for deciphering plant-microbe interactions and leveraging microbiomes in crop improvement. In this study, we examined the potential for intergenerational inheritance and external recruitment of endophytic fungi in common wheat. Fungal community structure was compared in generation G1 and parental G0 plants using ITS2 metabarcoding data and culture-based identification in four tissues (roots, stems, leaves, and seeds) in ten cultivars. A set of 27 operational taxonomic units (OTUs) was consistently detected in both generations, suggesting the presence of a core mycobiome dominated by genera such as Fusarium, Trichoderma, Penicillium, Cladosporium, Sarocladium and Lecanicillium. Experimental inoculation of axenic wheat seedlings with fungi Fusarium proliferatum, Penicillium expansum, Trichoderma hamatum originating from the wheat endosphere confirmed the ability of these species to recolonize host tissues and thus their role in stable association with plants. However, several other taxa (Engyodontium album, Sarocladium spinificis, Clonostachys candelabrum, and Nigrospora gorlenkoana) originating from internal wheat tissues failed to recolonize axenic plants, suggesting transient colonization via horizontal pathways. These findings highlight the dual contribution of vertical inheritance and environmental recruitment in shaping the wheat endomycobiome, offering a foundation for targeted manipulation of beneficial fungi in cereal crops.}, }
@article {pmid41309632, year = {2025}, author = {Hosogane, T and Santana, LS and Eling, N and Moch, H and Bodenmiller, B}, title = {Compressed sensing expands the multiplexity of imaging mass cytometry.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-025-66629-4}, pmid = {41309632}, issn = {2041-1723}, support = {310030_205007//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 316030_213512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; UC4 DK108132/DK/NIDDK NIH HHS/United States ; IMAXT Grand Challenge//Cancer Research UK (CRUK)/ ; 866074//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {The multiplexity of current antibody-based imaging is limited by the number of reporters that can be detected simultaneously. Compressed sensing can be used to reconstruct high-dimensional information from low-dimensional measurements. Previously, compressed sensing using composite in situ imaging (CISI) of transcriptomic data leveraged gene co-regulation structure to recover spatial expression of 37 RNA species from images of 11 composite channels. Here, we extend the CISI framework to protein expression data measured by imaging mass cytometry (IMC). CISI-IMC accurately recovers spatial expression of 16 immune and stromal marker proteins from images of 8 composite channels with an average Pearson's correlation of 0.8 across protein. Training the CISI-IMC framework using data collected on multiple human tissues enables universal decompression of composite data from a wide range of tumor and healthy tissue types. The expression dictionary and barcoding matrix described here are immediately implementable for general immune and stromal cell type classification, but CISI-IMC can in principle be applied to other markers or other antibody-based imaging methods. Our work lays the foundation for much higher plex protein imaging.}, }
@article {pmid41307211, year = {2025}, author = {Ramsey-Coleman, C and Youngner, C and Singletary, T and Wright, D and Payton, C and Sargent, M and Kettel Khan, L and Lavinghouze, SR}, title = {Scanning for Wellness: QR Code Strategies to Promote Public Health Programs.}, journal = {Health promotion practice}, volume = {}, number = {}, pages = {15248399251391141}, doi = {10.1177/15248399251391141}, pmid = {41307211}, issn = {1524-8399}, abstract = {This article discusses the importance of effective communication tools in public health, highlighting innovations like Quick Response (QR) codes and QR wallet reference cards (QR cards) for enhancing outreach and education. QR codes are scannable barcodes that link to digital content. QR cards are compact cards, similar to business cards, with codes that lead to relevant health information. To our knowledge, there is little published literature on using QR codes and cards for public health programs and health communication outside of health care clinics and education settings. The North Carolina Department of Health and Human Services, Division of Public Health, Community and Clinical Connections for Prevention and Health Branch has successfully implemented QR codes in various public health programs, particularly in diabetes management and nutrition, physical activity, and obesity initiatives. Key lessons learned include using reputable QR code generators, ensuring visibility and scanability of the codes, testing links before use, providing clear calls to action, and considering dynamic versus static codes based on needs. QR codes can be leveraged in public health practice for program promotion, evaluation sharing, and community resource accessibility. However, limitations such as smartphone dependency among some populations should be acknowledged. In conclusion, while QR codes are a simple tool, they hold significant potential for improving public health communication. Research on QR code use in public health settings could help inform best practices for public health programs and health promotion across different contexts.}, }
@article {pmid41304618, year = {2025}, author = {Djebaili, R and Farda, B and Gialdini, O and Vaccarelli, I and Rezaee Danesh, Y and Pellegrini, M}, title = {Microbial Consortium of Streptomyces spp. from Mining Environments Enhances Phytoremediation Potential of Lemna minor L.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {22}, pages = {}, doi = {10.3390/plants14223467}, pmid = {41304618}, issn = {2223-7747}, abstract = {The presence of substantial amounts of heavy metals in the environment can result in various significant ecological issues and human health risks. Currently, bioremediation employing microorganisms is garnering significant interest due to its effectiveness. The present investigation aimed to isolate actinobacterial strains from an Italian mine and to characterise them for heavy metals resistance and plant growth-promoting characteristics. The different samples were processed for DNA extraction and 16S rRNA gene metabarcoding to investigate the bacteria and archaea communities. Cultivable microbiota were isolated and evaluated for heavy metals tolerance and different PGP traits. The most pertinent strains were tested for compatibility, merged into a consortium, and tested on Lemna minor L. Metabarcoding analysis revealed that amplicon sequence variants (ASVs) at the phylum level were mostly assigned to proteobacteria and bacteroidota. Uncultured and unknown taxa were the most prevalent in the samples at the genus level. A total of ten strains were obtained from the culture-dependent approach exhibiting interesting heavy metals tolerance and plant growth-promoting traits. The best strains (MTW 1 and MTW 5) were selected and further characterised by 16S barcoding. These strains were identified as Streptomyces atratus (99.57% identity). An in planta experiment showed that the metal-tolerant consortium MTW 1-5 improved plant physiology by significantly optimising plant growth and tolerance to heavy metals. The experiment conducted provided evidence for the possibility of using actinobacteria as bioaugmentation agents to improve the phytoextraction abilities of L. minor.}, }
@article {pmid41303671, year = {2025}, author = {Jang, W and Lee, SH and Kim, WJ and Yang, S and Moon, BC}, title = {PCR-Based Molecular Authentication Method for Sources of Agrimoniae Herba via Comparative Analyses of Complete Chloroplast Genomes.}, journal = {International journal of molecular sciences}, volume = {26}, number = {22}, pages = {}, doi = {10.3390/ijms262211189}, pmid = {41303671}, issn = {1422-0067}, support = {KSN2511030//Korea Institute of Oriental Medicine/ ; }, mesh = {*Genome, Chloroplast ; Phylogeny ; Polymorphism, Single Nucleotide ; *Polymerase Chain Reaction/methods ; DNA Barcoding, Taxonomic/methods ; *Agrimonia/genetics/classification ; INDEL Mutation ; Plants, Medicinal/genetics ; Species Specificity ; Drugs, Chinese Herbal ; }, abstract = {Accurate species identification is essential for the quality control and standardization of herbal medicines. Agrimonia species, the authentic sources of Agrimoniae Herba, have long been used in traditional medicine, yet limited genomic resources have hindered the establishment of reliable molecular approaches for accurate species discrimination within this genus. Here, we report the newly assembled complete chloroplast genomes (155,156-155,302 bp) of four Agrimonia species, which exhibit the typical quadripartite structure and contain 112 unique genes. Comparative analysis revealed 684 variable sites, including 497 single nucleotide polymorphisms (SNPs) and 187 insertions/deletions (InDels), predominantly located in the single-copy regions. Based on these species-specific variations, we developed nine PCR-based molecular markers that distinguished the four species. The markers were validated using herbarium specimens and commercial herbal products, demonstrating reproducibility and practical applicability. Phylogenetic analysis supported the monophyly of the genus Agrimonia and resolved each species into distinct clusters within the subtribe Agrimoniinae. These results showed that chloroplast genome sequences of the genus Agrimonia can serve as effective super DNA barcodes for species identification. Our study provides fundamental genomic resources for Agrimonia and reliable molecular tools for species authentication, providing a basis for ensuring the authenticity and safety of Agrimoniae Herba.}, }
@article {pmid41302919, year = {2025}, author = {Yakimenko, EV and Romanovich, AE and Lukhtanov, VA}, title = {Questionable Species Names for Distinct Species Clusters: An Empirical Test of the BOLD Molecular Identification Engine.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111172}, pmid = {41302919}, issn = {2075-4450}, support = {24-14-00047//Russian Science Foundation/ ; }, abstract = {DNA barcoding is an effective method for species identification, but its practical application, as implemented in the Barcode of Life Data System (BOLD), faces numerous challenges. In our work, we conducted an empirical test of this approach using butterflies of the Volga River region in eastern Europe as a model system. We demonstrate that DNA barcoding is a powerful tool for identifying species clusters of the local fauna studied. However, assigning the identified clusters to scientific species names using BOLD was problematic for more than half of the species analyzed. The reasons for these problems are numerous errors in (1) species and even (2) generic identifications of DNA barcodes in the BOLD database (30% and 26% of all problematic cases, respectively), (3) similarity of DNA barcodes in different species (22%), (4) unresolved taxonomic problems associated with the species names that BOLD suggests as identifications (18%), (5) anomalous barcodes (2%), and (6) incompleteness of the BOLD database (2%). Solving problems 1, 2 and 5 requires improving the DNA barcode curation system and minimization of the identification errors in the BOLD database. Problems 3 and 6 can be partly solved by accumulating DNA barcodes, especially barcodes of local faunas, since populations of different species with identical DNA barcodes often have non-overlapping areas. Problem 4 is the most difficult and requires further intensive taxonomic research to solve it.}, }
@article {pmid41302916, year = {2025}, author = {Stonis, JR and Remeikis, A and Orlovskytė, S}, title = {New Discoveries Supporting the Exceptional Species Diversity of Opostegidae in Central America and the Caribbean, Alerting on Misidentified Barcodes.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111170}, pmid = {41302916}, issn = {2075-4450}, abstract = {The aim of this study was to supplement current knowledge on the species diversity of Opostegidae in Central America and the Caribbean and to compare this diversity with that of other regions. We examined historical material and conducted fieldwork in Honduras during 2023-2025, a true tabula rasa in terms of Opostegidae diversity. Collected specimens were dissected, with genitalia photographed and analyzed. Molecular divergence was assessed using Neighbor-Joining and Maximum Likelihood methods, as well as Bayesian inference; creation of a mitotype network (TCS algorithm) and species delimitation (bPTP method) were also performed. The study of historical material revealed that Pseudopostega saltatrix (Walsingham) is not conspecific with taxa previously published under the same name, resulting in the description of one new Pseudopostega species. Fieldwork in Honduras yielded 11 additional Pseudopostega species-all new national records, six of which are new to science. The paper introduces 33 new molecular sequences, bringing the total to 114 mtDNA COI-5' sequences currently deposited in the National Genomics Data Center (China). With these discoveries, the number of Opostegidae in Central America and the Caribbean rises to 63 species, representing 30.9% of the global fauna. The Neotropical realm (103 spp.) exhibits markedly higher Opostegidae diversity than other biogeographical regions, underscoring its importance as a center of diversification. Our analysis also revealed an alarmingly high proportion of doubtful molecular barcodes-nearly one-third (27%) appear erroneous due to species misidentification in Neotropical Opostegidae.}, }
@article {pmid41302912, year = {2025}, author = {Liu, Y and Triapitsyn, SV and Zhang, D and Wang, J and Aishan, Z}, title = {Integrative Taxonomy of Polynema (Doriclytus) (Hymenoptera: Mymaridae) from Oriental China: Three New Species and Five New Records Revealed by Morphological and Molecular Analyses.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111166}, pmid = {41302912}, issn = {2075-4450}, support = {32260123//Zhulidezi Aishan/ ; }, abstract = {Polynema Haliday, 1833 (Hymenoptera: Chalcidoidea: Mymaridae), one of the most species-rich genera in the family, comprises egg parasitoids with diverse hosts across multiple insect orders, some serving as biological control agents for agricultural and forestry pests. The subgenus Polynema (Doriclytus Foerster, 1847), characterized by pronounced morphological conservatism, has historical taxonomic challenges due to reliance on external morphological characteristics. This study employed an integrative taxonomic approach, combining morphological and molecular analyses, to investigate P. (Doriclytus) diversity in the Oriental region of China. Eight species were identified, including three new species-P. (Doriclytus) acutum Wang &amp; Aishan, sp. nov., P. (Doriclytus) daliense Wang &amp; Aishan, sp. nov., and P. (Doriclytus) longicornia Wang &amp; Aishan, sp. nov.-and five species newly recorded from China: P. (Doriclytus) alalatum Rehmat &amp; Anis, 2016, P. (Doriclytus) bicolorigastra Rehmat &amp; Anis, 2016, P. (Doriclytus) dhenkunde Mani &amp; Saraswat, 1973, P. (Doriclytus) dunense Hayat &amp; Anis, 1999, and P. (Doriclytus) tyakshiense Irfan &amp; Anis, 2023. Comprehensive morphological descriptions and diagnostic illustrations are provided for all new taxa, with key diagnostic features detailed for the newly recorded species. Molecular analysis of COI sequences using both the Assemble Species by Automatic Partitioning (ASAP) and Generalized Mixed Yule Coalescent (GMYC) models yielded congruent species delimitation results, with genetic distances between delimited species showing maximum intraspecific divergence of 1.51% and interspecific divergences of 3-12% within the 470 bp COI barcode region. The deposition of 32 novel COI sequences in GenBank significantly enhances molecular resources for Mymaridae systematics.}, }
@article {pmid41302893, year = {2025}, author = {Liang, F and Zeng, W and Li, S and Liu, X}, title = {Species Delimitation in the Bark Louse Genus Neostenopsocus Liang &amp; Liu, 2024 (Psocodea: Stenopsocidae) Based on DNA Barcoding.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111147}, pmid = {41302893}, issn = {2075-4450}, support = {32100362, 32200366//National Natural Science Foundation of China/ ; 23B0490//Scientific Research Fund of Hunan Provincial Education Department/ ; }, abstract = {The family Stenopsocidae exhibits a rich biodiversity in China, yet species identification based on morphological characters remains problematic due to insufficient study and absent molecular data. DNA barcoding has been widely employed for rapid species identification in insects, particularly through standardized COI gene sequencing. In this study, we conducted species delimitation for Neostenopsocus in China based on the morphological characters and DNA barcodes, comprising 20 morphological species with 110 barcodes. We redescribed 13 species from China and proposed 39 new synonyms. This study supports the applicability of DNA barcoding for species identification in Neostenopsocus. The K2P distance between the morphological species of Neostenopsocus ranges from 0.0051 to 0.2040, with most exceeding 0.10. The maximum intraspecific divergence reaches 0.0778 in N. nepalensis. The external morphology of Neostenopsocus shows considerable structural uniformity, and the genitalia provide limited diagnostic value for species identification. Instead, the marking patterns of the head and forewing are considered to be useful for species identification. Therefore, delimiting closely related species demands an integrated taxonomy approach that combines extensive geographical sampling, detailed morphological analysis, and nuclear DNA data.}, }
@article {pmid41302869, year = {2025}, author = {Toševski, I and Caldara, R and Jović, J and Baviera, C and Ugarte San Vicente, I and Krstić, O}, title = {An Integrative Revision of the Genus Rhamphus (Curculionidae) from the Western Palearctic: Morphological and Molecular Data Reveal the Radiation of Multiple Species.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111123}, pmid = {41302869}, issn = {2075-4450}, support = {451-03-136/2025-03/200010//Ministry of Science, Technological Development, and Innovation of the Republic of Serbia/ ; }, abstract = {Here, we report on the complexity of the taxonomy and species evolution within the monophyletic genus Rhamphus, which includes some of the smallest members of the Curculionidae family and whose species are morphologically almost indistinguishable from each other. Despite their similar appearance, we found high divergence and varying evolutionary rates among observed species groups living both in sympatry and allopatry in the western Palearctic. On the basis of subtle morphological differences and molecular evidence, we defined eight morphotypic groups and 14 species, of which 6 are newly described in this paper: R. diottiisp. nov. and R. ibericussp. nov. (monzinii-group), R. cypricussp. nov. and R. macedonicussp. nov. (cypricus-group), R. betulaesp. nov. and R. crypticussp. nov. (pulicarius group). Rhamphus morphotypic groups showed intense species radiation and cryptic speciation, with an estimated genetic divergence of 4.2-18.8% (uncorrected) in the barcoding region of the mitochondrial COI gene. The estimated divergence of the two nuclear markers, nEF-1α and nCAD, ranged from 1 to 11.9% and 0.5 to 15%, respectively. Phylogenetic analyses using both single and partitioned multigene adequately resolved the relationships between Rhamphus species and identified all groups and the species with high nodal support. According to our study, Rhamphus species cluster into monophyletic groups that are partly defined by their host plant associations and by subtle differences in penis shape. No substantial differences in female genitalia were found. Most of the species exhibit relatively rapid species radiation, which is cryptic by nature.}, }
@article {pmid41302845, year = {2025}, author = {Xun, H and Jiang, K and Zhu, W}, title = {Review of the Genus Mictis (Hemiptera: Heteroptera: Coreidae: Coreinae) from China, with Description of a New Species.}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111099}, pmid = {41302845}, issn = {2075-4450}, support = {32400356//Biological Resources Programme, Chinese Academy of Sciences, and National Natural Science Foundation of China/ ; }, abstract = {Species of the genus Mictis Leach, 1814, notable for their large body size and wide distribution, have attracted significant attention in physiological and phylogenetic studies. However, taxonomic issues surrounding these insects have long been overlooked, with the validity and taxonomic status of several species remaining unresolved. This study systematically reviews the nomenclatural and taxonomic issues of the genus Mictis within China, resulting in the proposal of two new synonyms and one new combination: Mictis serina (Dallas, 1852) = Mictis fuscipes (Hsiao, 1963) syn. n., Mictis longicornis (Westwood, 1842) = Mictis tuberosa (Hsiao, 1965) syn. n., and Ochrochira falloui (Reuter, 1888) comb. n. All known Mictis species from the region are diagnosed, and a new species, Mictis arcuatasp. n., is described. An identification key and DNA barcoding data for the Mictis species are provided. The intra-specific chromatic variation and distribution of the genus are also discussed.}, }
@article {pmid41302835, year = {2025}, author = {Lukhtanov, VA}, title = {Integrative Taxonomic Analysis Doubles Number of Species in the Central Asian Butterfly Genus Lyela (Lepidoptera, Nymphalidae, Satyrinae).}, journal = {Insects}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/insects16111089}, pmid = {41302835}, issn = {2075-4450}, support = {24-14-00047//Russian Science Foundation/ ; }, abstract = {Lyela Swinhoe, 1908 is a small Central Asian butterfly genus, in which three species were previously recognized based on comparison of wing patterns. The present study, based on an extensive population sample across the entire range of Lyela and using integrative taxonomy methods, confirmed the monophyly of the genus and revealed the paraphyly of the most widespread species, Lyela myops sensu auct. The genus is shown to include six species, L. myops (Staudinger, 1881) (Kazakhstan, northern Kyrgyzstan, northwestern China, and southwestern Mongolia), L. tashkumirica Lukhtanov, 2024, stat. nov. (Fergana Valley in Kyrgyzstan), L. babatagi Tshikolovets, 1998, stat. nov. (southern Uzbekistan and eastern Turkmenistan), L. tekkensis (Staudinger, 1886), stat. nov. (southwestern Turkmenistan and northeastern Iran), L. macmahoni Swinhoe, 1908 (Pakistan and Afghanistan), and L. amirica Wyatt, 1961 (Afghanistan). Each of these species represents a monophyletic unity with respect to the COI gene and is separated from the other species by a distinct barcoding gap and structural differences in the male genitalia.}, }
@article {pmid41300814, year = {2025}, author = {Karbarz, M and Grzyb, F and Szlachcikowska, D and Leśko, A}, title = {Untangling Coelogyne: Efficacy of DNA Barcodes for Species and Genus Identification.}, journal = {Genes}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/genes16111361}, pmid = {41300814}, issn = {2073-4425}, support = {Agreement No. RID/SP/0010/2024/1.//Minister of Science of the Republic of Poland under the Program "Regional initiative of excellence"./ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; Phylogeny ; DNA, Plant/genetics ; Species Specificity ; }, abstract = {Background/Objectives: While morphological similarity and incomplete specimens pose a challenge to the precise identification of Coelogyne orchids, accurate species and genus assignment is essential for conservation and CITES enforcement. This study evaluated the efficacy of five DNA barcode regions-rbcL, matK, trnH-psbA, atpF-atpH, and ITS2-and their combinations for species- and genus-level discrimination within the genus Coelogyne, aiming to develop a rapid and simple diagnostic tool for use by customs officers and trade inspectors. This is the first comprehensive comparative analysis of these five barcode regions specifically within Coelogyne, a genus underrepresented in molecular identification studies, and the first to propose multi-locus combinations for potential practical use. This study identified DNA barcode regions with high resolution and reliability, providing a solid basis for practical identification kits. Such tools will enhance CITES enforcement by enabling rapid detection of Coelogyne species in trade, directly supporting their conservation and contributing to the reduction in illegal orchid trade. Methods: Using a CTAB protocol, genomic DNA was extracted from leaf samples belonging to 19 Coelogyne species. Sanger sequencing was performed after PCR amplification using published primer sets for every barcode region. Sequences were modified in BioEdit, and BLASTn (accessed 15 June 2025) was used to compare them to GenBank (NCBI Nucleotide). Amplification efficiency was calculated per locus. Species and genus identification success rates were determined by the congruence of top BLAST hits with morphologically pre-identified taxa. Multi-barcode combinations (matK + rbcL, ITS2 + matK, matK + trnH-psbA, rbcL + trnH-psbA, and matK + rbcL + trnH-psbA) were also assessed. Results: With rbcL, atpF-atpH, and ITS2 yielding ≤11%, the highest single-locus species identification rates were for trnH-psbA (21%) and matK (16%). Among single-locus barcodes, matK showed the highest performance, with 84% genus assignment. ITS2 reached 27%, but genus-level resolution remained limited for the rbcL, trnH-psbA and atpF-atpH barcodes. Multi-barcode approaches maintained species resolution: matK + rbcL + trnH-psbA, matK + rbcL, and matK + trnH-psbA correctly identified 16% of species and achieved 74-79% genus assignment. Conclusions: No single locus achieves robust species discrimination in Coelogyne, but trnH-psbA, matK and atpF-atpH provide the best single-marker performance. Using the matK locus alone, in combination with either trnH-psbA or rbcL, or all three together ensures consistent genus-level identification and significantly improves taxonomic resolution. This study introduces a novel multi-locus barcode strategy tailored to Coelogyne, offering a practical solution for identification and enforcement. While promising, this approach represents a potential application that requires further validation before routine implementation.}, }
@article {pmid41300785, year = {2025}, author = {Chen, Z and Zeng, Q and Gong, M and Wu, H and Chen, W and Xu, X}, title = {DNA Barcoding Identification of Angelicae Sinensis Radix and Its Adulterants Based on Internal Transcribed Spacer 2 Region and Secondary Structure Prediction.}, journal = {Genes}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/genes16111333}, pmid = {41300785}, issn = {2073-4425}, support = {No. 2023YFD1601400//the National Key Research and Development Program for Young Scientists of China/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; *Angelica sinensis/genetics/classification ; *DNA, Ribosomal Spacer/genetics/chemistry ; DNA, Plant/genetics ; Nucleic Acid Conformation ; Drug Contamination ; }, abstract = {Background: Morphological similarities among Angelicae Sinensis Radix and related species often lead to market substitution. This study develops a DNA barcoding method to authenticate these herbs and identify adulterants derived from Angelica, Heracleum, and Peucedanum genera. Methods: Phylogenetic analysis was conducted using MEGA 11.0 software with ITS2 sequences from Angelicae Sinensis Radix, Ligusticopsis Pubescens Radix, Angelicae Pubescens Radix, and their related species within the genera Angelica, Peucedanum, and Heracleum. Additionally, ITS2 secondary structures were predicted for the three herbs to provide supplementary evidence for identification. Results: The amplification success rate was 86.67%, and the interspecific genetic distance, ranging from 0.009~0.220, was significantly greater than the intraspecific genetic distance range from 0.000~0.062, indicating that the ITS2 sequence is suitable for differentiating three herbs and their related species. Additionally, their ITS2 secondary structures exhibited significant differences, which can also serve as a reliable criterion for their identification. Conclusions: This study not only validated the identification efficacy of ITS2 sequences and their secondary structures for the three herbs, but more importantly, enabled precise traceability of adulterants through the construction of a comprehensive phylogenetic framework.}, }
@article {pmid41300772, year = {2025}, author = {Xiang, P and Phua, YW and Rosli, AR and Loh, KJ and Syn, CK}, title = {Forensic Identification of Cannabis with Plant DNA Barcodes and Cannabinoid Synthesis Genes.}, journal = {Genes}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/genes16111320}, pmid = {41300772}, issn = {2073-4425}, mesh = {*Cannabis/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Cannabinoids/biosynthesis/genetics ; *DNA, Plant/genetics ; Humans ; Plant Proteins/genetics ; }, abstract = {Background/Objectives: According to the World Drug Report 2025, cannabis is the most abused drug in the world, being sold in illicit markets in various physical forms ranging from herbal cannabis to cannabis resin and liquid cannabis. Currently, the methods used for cannabis identification are largely based on the morphological features and chemical content of the product. In this respect, identification could be severely impacted if the product is highly fragmented or pulverised. As such, DNA-based molecular techniques offer a viable alternative detection approach. In this study, we have developed a robust DNA testing method for cannabis identification, with high sensitivity and specificity. Methods/Results: Two plant DNA barcode regions, rbcL and matK, were successfully amplified in a cohort of 54 cannabis plant samples. DNA sequences obtained from these samples were blast-searched against GenBank and resulted in returned matched identity of at least 99% compared to their corresponding Cannabis sativa reference sequences. In addition, the amplification of two cannabis-unique markers, the tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes, produced amplicons with expected sizes only in cannabis samples; these amplicons were not detected in those plants closely related to cannabis. Sequence comparison of the majority of samples yielded at least 97% matched identity against C. sativa reference sequences in GenBank. The THCAS and CBDAS markers detected only the cannabis DNA in varying levels of cannabis-hops and cannabis-tobacco DNA mixtures. Lastly, the use of the four markers could effectively differentiate between cannabis and non-cannabis in 27 blinded samples, including 18 actual casework samples. Conclusions: In conclusion, these four genetic markers can be used to discriminate cannabis from other plant species at the genus level, especially in challenging forensic samples lacking morphological features which therefore cannot be determined by traditional detection methods. As such, this method can complement existing techniques to identify a myriad of cannabis samples.}, }
@article {pmid41300762, year = {2025}, author = {Wang, Y and Xiang, Z and Liu, K and Lin, Y and Dong, S}, title = {Complete Chloroplast Genome and Phylogenomic Analysis of Davallia trichomanoides (Polypodiaceae).}, journal = {Genes}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/genes16111310}, pmid = {41300762}, issn = {2073-4425}, support = {QDZK112022022//National Natural Science Foundation of China Cultivation Project/ ; }, mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; *Polypodiaceae/genetics/classification ; Evolution, Molecular ; }, abstract = {Background/Objectives: Chloroplast genomes (plastomes) are valuable for fern systematics, yet the epiphytic lineages have remained underexplored. Methods: The Davallia trichomanoides plastome was de novo assembled from Illumina data and annotated. Results: The plastome measures 154,217 bp with a GC content of 40.82% and contains 115 genes. Comparative analysis reveals two inverted repeat (IR) size classes (~24.0-24.6 kb vs. ~27.4-27.5 kb) and lineage-specific shifts at the IR junctions. For instance, the ndhF gene remains in the small single copy (SSC) region in D. trichomanoides and Drynaria acuminata, but it crosses into the IRb region in other species. We observed nucleotide diversity hotspots in the large single copy (LSC) and SSC regions. The IR regions are highly conserved. The ratios of nonsynonymous to synonymous substitutions (Ka/Ks) are mostly less than 1, indicating purifying selection. Phylogenetic analysis places D. trichomanoides as the sister to D. acuminata. Conclusions: This study highlights the stable plastome structure of D. trichomanoides and identifies candidate loci for barcoding. It also supports the stable placement of Davallia within the epiphytic Polypodiineae.}, }
@article {pmid41300739, year = {2025}, author = {Yin, D and Li, X and Xiao, Z and Zhou, L}, title = {Chloroplast Genome Features and Phylogeny of Two Nationally Protected Medicinal Plants, Euchresta tubulosa and Euchresta japonica: Molecular Resources for Identification and Conservation.}, journal = {Genes}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/genes16111286}, pmid = {41300739}, issn = {2073-4425}, mesh = {*Genome, Chloroplast/genetics ; Phylogeny ; *Plants, Medicinal/genetics/classification ; Endangered Species ; DNA Barcoding, Taxonomic/methods ; }, abstract = {[Objectives]: By performing genome assembly, annotation, comparative characterization, and phylogenetic analysis on the complete chloroplast genomes of E. tubulosa and E. japonica-two medicinal plants belonging to the genus Euchresta-this study aims to identify their differential genes, thereby providing fundamental research for screening candidate genes as DNA barcodes for species identification and facilitating the conservation of these endangered species. [Methods]: Illumina PE150 sequencing was performed. Chloroplast genomes (plastomes) were assembled and annotated with GetOrganelle/SPAdes. Comparative analyses assessed gene content, IR/LSC/SSC structure, repeat profiles, and codon-usage bias. Using related Fabaceae as references, we conducted mVISTA alignments and sliding-window nucleotide diversity (Pi) analyses to identify candidate DNA barcodes. Phylogenies from whole-plastome sequences were inferred with Maximum Likelihood, Bayesian Inference, and Maximum Parsimony. [Results]: The plastomes measured 153,960 bp (E. japonica) and 150,146 bp (E. tubulosa), with GC contents of 36.30% and 36.20%, respectively, each exhibiting a typical quadripartite structure. IR/SC boundaries were highly conserved without evident expansion or contraction. Repeat statistics were 20/30 palindromic repeats, 57/64 tandem repeats, and 156/159 simple sequence repeats (SSRs) in E. japonica/E. tubulosa, respectively. Leucine was the most frequently encoded amino acid, cysteine the least, and codon usage favored A/U at third positions. Five hypervariable loci-rps19, psbA, trnK, matK, and rps16 (Pi > 0.03)-were identified as candidate DNA barcodes. All trees consistently placed both species within Papilionoideae (Fabaceae) and recovered the closest relationship to Sophora macrocarpa. [Conclusions]: This study provides, for the first time, complete plastomes and candidate barcoding regions for two protected Euchresta species, supplying foundational resources for species identification, resource assessment, and conservation planning.}, }
@article {pmid41299646, year = {2025}, author = {Bunchom, N and Saijuntha, W and Andrews, RH and Agatsuma, T and Valencia, J and Revolteado, MJ and Prasayasith, P and Soundala, P and Sannikone, S and Hansana, P and Sato, MO and Banouvong, V and Buchy, P and Iwagami, M}, title = {Molecular insights into seasonal trematode infections in Bithynia Snails: host lineages, parasite diversity, and Opisthorchis viverrini susceptibility in southern Lao PDR.}, journal = {Tropical medicine and health}, volume = {53}, number = {1}, pages = {173}, pmid = {41299646}, issn = {1348-8945}, support = {Grant No. 6518003/2565//Mahasarakham University/ ; Grant No. JP25jm0110028; 2022-2028//Japan International Cooperation Agency (JICA) and the Japan Agency for Medical Research and Development (AMED) through the SATREPS project, titled "Project for Malaria and Neglected Parasitic Diseases Control and Elimination using Advanced Research Technique, Communication Tools, and Eco-Health Education"/ ; }, abstract = {BACKGROUND: Opisthorchiasis, caused by Opisthorchis viverrini, is a major public health concern in Southeast Asia. Despite control programs, O. viverrini infection persists and contributes to severe liver diseases, including cholangiocarcinoma. This study aimed to assess seasonal variation in trematode prevalence and diversity, evaluate the susceptibility of Bithynia siamensis sensu lato lineages II and III to O. viverrini infection, and examine the phylogenetic and haplotype network of identified trematode and their snail hosts in Champasak Province, southern Lao PDR.<br><br>METHODS: Snail samples were collected quarterly in 2024 (February, May, August, and November) from Khong and Mounlapamok Districts using handpicking and scooping. Trematode infections were detected by the crushing method, identified morphologically, and confirmed by molecular analysis. DNA barcoding of nuclear and mitochondrial genes was used to verify trematode species and snail lineages.<br><br>RESULTS: Of 1,764 Bithynia snails examined, 169 (9.58%) were infected. Five cercarial types were identified: amphistome (3.40%), xiphidiocercariae (2.78%), monostome (2.61%), mixed monostome and amphistome (0.34%), cystophorous (0.28%), and O. viverrini (0.17%). Infection rates of O. viverrini did not differ between lineages II and III, but other trematodes were significantly more frequent in lineage III (76.67%).<br><br>CONCLUSIONS: Trematode infection rates and species diversity in B. s. goniomphalos show marked seasonal variation in Champasak Province, southern Lao PDR. These findings highlight the complexity of host-parasite interactions and the role of environmental factors shaping transmission, providing insights for targeted prevention and control.}, }
@article {pmid41297683, year = {2025}, author = {Zheng, M and Zhao, Y and Gao, M and Huang, M and Song, X}, title = {Chloroplast structure, codon usage bias, and machine learning-based molecular identification using DNA barcoding of Sophorae Tonkinensis Radix et Rhizoma(Shan Dou gen) and its analogues.}, journal = {Fitoterapia}, volume = {}, number = {}, pages = {107005}, doi = {10.1016/j.fitote.2025.107005}, pmid = {41297683}, issn = {1873-6971}, abstract = {To investigate the complete chloroplast genome sequences and codon usage bias of "Shan Dou Gen" (Sophorae Tonkinensis Radix et Rhizoma) and its six easily confused species, analyze their evolutionary patterns, and evaluate the identification efficiency of four DNA barcodes combined with two machine learning methods for these seven plant species. Chloroplast gene structures of the seven species were aligned to construct phylogenetic trees. Codon usage bias was analyzed using CodonW and CUSP. Genetic distances were calculated based on the Kimura-2-Parameter model to assess the barcoding gap and reconstruct phylogenetic trees.Species discrimination capabilities of four DNA barcodes (ITS2, matK, psbA-trnH, and rbcL) were compared. Species identification was performed using BLOG and WEKA machine learning algorithms. Single-nucleotide SSRs predominated in chloroplast genomes, primarily composed of A/T bases. Complete species differentiation was achieved using cpDNA. Natural selection was the primary factor influencing codon usage bias, followed by mutation pressure. Among synonymous codons, A > T and G > C in base composition, with optimal codons ending in A/U at the third position across all seven species. All four DNA barcodes successfully discriminated Shandougen from its confusable species. The BLOG algorithm achieved >85 % identification accuracy, outperforming WEKA. This research provides a theoretical foundation for ensuring clinical medication safety, elucidating plant phylogeny, facilitating species identification, and guiding resource conservation and utilization of Shandougen and its analogues.}, }
@article {pmid41296748, year = {2025}, author = {Prudente, ALC and Silva, FM and Santos, MMD and Vasconcelos, S and Rojas-Runjaic, FJM and Becerra-Rondón, AC and Maciel, AO and Sarmento, JF and Graboski, R and Teixeira, C and Guimarães, AC and Nascimento, A and Oliveira, AMS and Molina, M and Silva, P and Carvalho Neto, CS and Nunes, GL}, title = {Unraveling the herpetofauna diversity in canga and forest ecosystems of the Eastern Amazon.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0332753}, pmid = {41296748}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Brazil ; *Forests ; *Reptiles/genetics/classification ; *Amphibians/genetics/classification ; Phylogeny ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Conservation of Natural Resources ; Lizards/genetics/classification ; }, abstract = {Species inventories are essential for discovering new taxa, improving knowledge of species' geographic distributions, characterizing local richness, evaluating biodiversity loss, and contributing to the conservation of endangered areas, including those with endemic and rare species. The southeastern region of Pará, Brazil, encompasses a transitional zone between the Amazon and Cerrado biomes, marked by a mosaic of natural environments with high variability in relief, substrates, and geological attributes. We conducted a comprehensive survey of the region's herpetofauna, combining taxonomic surveys with molecular characterization, with a particular focus on species associated with savanna-like environments known as canga. We selected four sampling sites: one within the Serra dos Carajás mosaic of protected areas and three in the surrounding region, including São Geraldo do Araguaia, Conceição do Araguaia, and Ourilândia do Norte/São Félix do Xingu. Our inventory recorded a total of 242 species (99 amphibians and 143 squamate reptiles), including ten new records for the state of Pará and two notable range extensions. We also generated a DNA barcode reference library of 860 sequences (436 COI and 424 16S rRNA) from 500 specimens. Approximately 58.4% of amphibian species and 32.2% of squamate reptile species were supported by at least one reference barcode. Our dataset includes five novel COI and two novel 16S rRNA records for amphibians, and 25 novel COI and 13 novel 16S rRNA records for squamate reptiles.}, }
@article {pmid41295111, year = {2025}, author = {Sun, Y and Wang, J and Yin, R}, title = {RepSAU-Net: Semantic Segmentation of Barcodes in Complex Backgrounds via Fused Self-Attention and Reparameterization Methods.}, journal = {Journal of imaging}, volume = {11}, number = {11}, pages = {}, pmid = {41295111}, issn = {2313-433X}, abstract = {In the digital era, commodity barcodes serve as a bridge between the physical and digital worlds and are widely used in retail checkout systems. To meet the broader application demands for product identification, this paper proposes a method for locating, semantically segmenting barcodes in complex backgrounds, decoding hidden information, and recovering these barcodes in wide field-of-view images. This method integrates self-attention mechanisms and reparameterization techniques to construct a RepSAU-Net model. Specifically, this paper first introduces a barcode image dataset synthesis strategy adapted for deep learning models, constructing the SBS (Screen Stego Barcodes) dataset, which comprises 2000 wide field-of-view background images (Type A) and 400 information-hidden barcode images (Type B), totaling 30,000 images. Based on this, a network architecture (RepSAU-Net) combining a self-attention mechanism and RepVGG reparameterization technology was designed, with a parameter count of 32.88 M. Experimental results demonstrate that this network performs well in barcode segmentation tasks, achieving an inference speed of 4.88 frames/s, a Mean Intersection over Union (MIoU) of 98.36%, and an Accuracy (Acc) of 94.96%. This research effectively enhances global information capture and feature extraction capabilities without significantly increasing computational load, providing technical support for the application of data-embedded barcodes.}, }
@article {pmid41294086, year = {2026}, author = {Vu, D and de Vries, M and van den Ende, BG and Houbraken, J and Nilsson, RH and Brankovics, B and Hernández-Restrepo, M and Groenewald, JZ and Crous, PW and Hagen, F and Meyer, W and Verkley, GJM and Groenewald, M}, title = {Advancing Yeast Identification Using High-Throughput DNA Barcode Data From a Curated Culture Collection.}, journal = {Molecular ecology resources}, volume = {26}, number = {1}, pages = {e70082}, doi = {10.1111/1755-0998.70082}, pmid = {41294086}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Yeasts/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics/chemistry ; High-Throughput Nucleotide Sequencing/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Sequence Analysis, DNA ; }, abstract = {Yeast identification is essential in fields ranging from microbiology and biotechnology to food science and medicine. While DNA barcoding has become the standard for identifying cultured strains, environmental DNA (eDNA) metabarcoding has revolutionised microbial community profiling, providing deeper insights into yeast communities across diverse ecosystems. A major challenge in DNA (meta)barcoding remains the limited availability of high-quality reference sequences, which are critical for accurate species identification and comprehensive taxonomic profiling of both environmental and clinical samples. To address this gap, the Westerdijk Fungal Biodiversity Institute (WI) launched a DNA barcoding initiative in 2006 to generate high-quality, often type-derived ITS and LSU barcodes for all ~100,000 fungal strains preserved in the CBS culture collection, including approximately 15,000 yeasts. Building on the yeast barcode dataset released in 2016, we now present an expanded set of 2856 ITS and 3815 LSU sequences, representing 911 and 1137 yeast species, respectively. Notably, 27%-29% of these sequences are derived from ex-type cultures. Using both newly generated and previously published barcodes, we assess the taxonomic resolution of commonly used yeast metabarcoding markers (ITS, ITS1, ITS2 and LSU) and propose marker-specific similarity cutoffs for different yeast taxonomic groups. These results provide actionable guidance for marker selection and improve the interpretation of metabarcoding data. We further demonstrate the impact of well-curated reference databases with up-to-date taxonomy by reanalyzing Human Microbiome Project data, revealing how diet and environment shape the gut mycobiota.}, }
@article {pmid41292861, year = {2025}, author = {Unverdorben, LV and Mason, S and Wu, W and Noda, M and Castaneda, S and Vornhagen, J and Snitkin, ES and Rao, K and Bachman, MA}, title = {A Novel Technique to Characterize Klebsiella pneumoniae Populations Indicates that Mono-Colonization is Associated with Risk of Infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.05.686704}, pmid = {41292861}, issn = {2692-8205}, abstract = {UNLABELLED: Klebsiella pneumoniae and related species are a common cause of healthcare-associated infections. The gut is a major Klebsiella reservoir and gut colonization is a risk factor for developing an extraintestinal Klebsiella infection. Patients can be colonized by multiple Klebsiella strains or even species in the gut simultaneously, and there is high concordance between the gut colonizing- and infection causing-strains. The detection and characterization of colonizing strains is critical for a better understanding of the progression to infection and for developing interventions for colonized patients. However, the association between mixed or mono-colonization and subsequent infection is unknown. In this study, we developed an amplicon-based sequencing method called wzi -Seq that enables the detection and quantification of Klebsiella strains from complex samples and mixtures using the conserved capsule gene wzi as a molecular barcode. This method is highly accurate and precise with a sensitivity of 93% and specificity of 99.8% in mixtures containing as many as 58 unique wzi types. The assay was validated analytically and applied to an established case and control cohort. We determined that 63.2% (108/171) patients were mono-colonized with a single Klebsiella strain while 36.8% (63/171) had mixed colonization with multiple Klebsiella strains. Controlling for patient variables in multivariate analysis, we determined that mono-colonization was significantly (p = 0.034) associated with infection. Characterization of Klebsiella colonizing populations could improve the accuracy of assessing infection risk and enable targeted interventions to prevent these healthcare-associated infections.<br><br>IMPORTANCE: Klebsiella gut colonization is a major risk factor the development of extraintestinal Klebsiella infections in hospitalized settings. However, it is unknown if patients are colonized by one or multiple strains of Klebsiella and how the population structure of Klebsiella in the gut impacts infection risk. Here we describe the development of a novel technique, wzi -Seq, to detect and quantify multiple Klebsiella strains from complex samples using standard techniques and rapid DNA sequencing. We applied wzi -Seq to rectal swabs from a well-characterized patient cohort and found that Klebsiella colonization with a single strain was more prevalent than colonization with multiple strains. Furthermore, mono-colonized patients had a significantly higher risk of developing a Klebsiella infection than mixed colonized patients. This work validates a new tool to study Klebsiella populations and reveals that population structure in the gut influences the risk of healthcare associated infections.}, }
@article {pmid41292775, year = {2025}, author = {Stuart, H and McKenna, A}, title = {SCOUT: Ornstein-Uhlenbeck modelling of gene expression evolution on single-cell lineage trees.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.12.688020}, pmid = {41292775}, issn = {2692-8205}, abstract = {Understanding the evolutionary dynamics of clonal populations is essential for uncovering the principles of development, disease progression, and therapeutic resistance. Recent advances in single-cell lineage tracing and transcriptomics enable such analyses by combining heritable barcodes with cell-state information. Here, we present SCOUT (s ingle- c ell O rnstein- U hlenbeck t rees), a framework that models gene expression dynamics along single-cell lineage trees using Ornstein-Uhlenbeck processes to distinguish neutral drift from selective pressure. Using simulations, we demonstrate that SCOUT accurately classifies genes based on their underlying evolutionary models. We further validate SCOUT in Caenorhabditis elegans development, identifying biological processes under selection across distinct developmental contexts. Finally, we apply SCOUT to a lung adenocarcinoma xenograft model, revealing key regulators of metastatic progression and tumor microenvironmental adaptation. By integrating lineage and transcriptomic data, SCOUT provides a powerful evolutionary lens for dissecting the forces that shape cell fate.}, }
@article {pmid41292737, year = {2025}, author = {Choudhary, K and McManus, MT}, title = {Scalable imaging-based profiling of CRISPR perturbations with protein barcodes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.11.687767}, pmid = {41292737}, issn = {2692-8205}, abstract = {Imaging-based CRISPR screens enable high-content functional genomics by capturing phenotypic changes in cells after genetic perturbation. Protein barcodes provide cost-effective, easy-to-implement, and imaging-compatible barcoding for pooled perturbations, yet their scalability has been constrained by the need for arrayed cloning, lentiviral recombination between barcodes and guides, and difficulties in decoding barcodes with high confidence. Here, we introduce poolVis and cellPool, an integrated experimental and computational platform designed to address these limitations. poolVis uses Cre-lox-mediated reconfiguration to position barcode-sgRNA pairs in proximity during viral integration, which greatly reduces barcode shuffling during pooled cloning and delivery. cellPool leverages a scalable computational workflow and the unique aspects of protein barcodes to produce unpooled image galleries from multi-terabyte scale datasets. Applying this platform to single- and double-CRISPRi profiling of cell-cycle genes and chromokinesins in the MCF10A cells uncovered established and previously unrecognized phenotypes, including nuclear morphology changes and reciprocal sign epistasis in DNA damage.}, }
@article {pmid41292433, year = {2025}, author = {Lan, F and Chen, A and Ding, Y and Yang, C and Zhang, P and Fang, X}, title = {Sensitive and Specific Analysis of miRNAs in Single Tumor-Derived Extracellular Vesicles Using CRISPR-Based Nanoflow Cytometry.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c04700}, pmid = {41292433}, issn = {1520-6882}, abstract = {Tumor-derived extracellular vesicle (TEV) microRNAs (miRNAs) are promising cancer biomarkers but pose detection challenges due to their low abundance and sequence homology. Here, we present a CRISPR/Cas13a-based nanoflow cytometry (nFCM) platform integrated with a DNA-guided orthogonal membrane fusion strategy for ultrasensitive miRNA detection of TEVs at the single particle level. TEVs were identified with aptamers against CD63 and EpCAM markers to create an orthogonal barcode-anchored TEV (Orth-TEV). Meanwhile, liposomes preloaded with CRISPR/Cas13a molecular sensing components were modified with cholesterol-tagged DNA probes to produce Tags-CRISPR/Cas13a@Lipo. The complementary DNA sequences on the Orth-TEV and Tags-CRISPR/Cas13a@Lipo vesicles facilitated zipper-like hybridization, thereby achieving specific membrane fusion to effectively eliminate the interference of nontarget vesicles or free molecules. The resulting TEV-CRISPR/Cas13a@Lipo vesicles allow in situ detection of three prostate cancer (PCa)-associated miRNAs in a single TEV via nFCM with a low detection limit (LOD) of 14.7 (miR-153), 16.0 (miR-183), and 23.7 (miR-940) particles/mL, respectively. The approach was further applied to plasma samples from PCa patients and healthy donors, showing significantly elevated miRNA signals in PCa-derived TEV. ROC analysis yielded AUC values of 0.931, 0.923, and 0.869 for the three target miRNAs, confirming excellent diagnostic performance. To enhance classification accuracy, we conducted a statistical multivariate analysis based on the PCA-LDA model, which achieved perfect group separation and a diagnostic accuracy of 91.3%. Overall, this CRISPR/Cas13a-based nFCM platform offers a robust, accurate, and clinically applicable platform for single-vesicle miRNA profiling with broad potential in liquid biopsy-based cancer diagnosis.}, }
@article {pmid41290749, year = {2025}, author = {Silva, MI and Viegas, MB and Sousa, F and Gordo, LS and Paulo, OS and Vieira, AR}, title = {Identification of tuna species used by the Portuguese canning industry through a DNA-based approach.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41802}, pmid = {41290749}, issn = {2045-2322}, support = {CEECIND/01528/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {Animals ; *Tuna/genetics/classification ; Portugal ; *DNA Barcoding, Taxonomic/methods ; Seasons ; *Food Preservation/methods ; Seafood ; Fisheries ; *DNA/genetics ; Species Specificity ; }, abstract = {Despite the popularity of canned tuna in Portugal, limited research has explored how tuna species vary across brands and seasons. Accurate species identification is crucial to preserve both the economy and ecology of global tuna fisheries, as mislabelling and the use of certain species can have far-reaching implications. Our study analysed the diversity of tuna species used by the Portuguese tuna canning industry, focusing on brand-specific and seasonal variations, using molecular barcoding methods. In this industry, the occurrence of different species was observed only in products using water as a preservation medium. Skipjack tuna was predominant across all preservation media and brands analysed. Nonetheless, other species like Thunnus obesus and T. albacares, or Auxis spp. (not considered true tuna) were also detected. The use of different species was limited to cans produced during the second quarter of the year, which could reflect differences in seasonal availability of different tuna species or in sourcing strategies/market preferences of each company. Finally, more than one species was detected inside the same container in four brands, violating current European legislation. These results provide the first broad assessment of species used in the Portuguese tuna canning industry and showed the inclusion of vulnerable species is limited.}, }
@article {pmid41290175, year = {2025}, author = {Pakrashi, A and Thompson, KA and Hebert, PDN}, title = {Haplodiploidy accelerates mitogenome evolution in insects.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2059}, pages = {20251813}, doi = {10.1098/rspb.2025.1813}, pmid = {41290175}, issn = {1471-2954}, support = {//Canada Foundation for Innovation (MSI)/ ; //Ontario Ministry of Colleges and Universities/ ; //Government of Canada through Genome Canada and Ontario Genomics/ ; //The New Frontiers in Research Fund/ ; }, mesh = {Animals ; *Genome, Mitochondrial ; *Insecta/genetics ; *Evolution, Molecular ; Phylogeny ; *Diploidy ; *Haploidy ; Electron Transport Complex IV/genetics ; }, abstract = {Rates of mitogenome evolution differ among animal lineages, and this variation has been linked to life history, to ecological traits and-potentially-to the sex-determination system. Insects are a compelling model for examining the latter factor because haplodiploid (HD) has evolved on multiple occasions from a diplodiploid (DD) ancestral state. We tested for rate differences between DD and HD taxa by examining sequence change in a sentinel segment of the mitogenome, the 658 bp barcode region of the cytochrome c oxidase subunit I (COI) gene. Specifically, we investigated if amino acid substitutions and indels are more frequent in HD than DD lineages by inspecting COI sequences from over 86 000 BINs (a species proxy) representing 783 insect families and 26 orders. Among them, 10 lineages, varying in rank from tribe to order, are HD. Our analysis, which accounts for phylogeny, indicates that HD lineages have higher rates (1.7×) of amino acid substitution, higher Ka/Ks (3.5×) and far more indels than DD taxa. While our results demonstrate that HD accelerates mitogenome evolution, future work is needed to clarify its mechanistic basis. We hypothesize that HD facilitates positive selection for mitochondrial mutations which encode proteins that interact with nuclear gene products. Such coevolutionary interactions should be facilitated because recessive mutations in the nuclear genome are fully exposed to selection in males of the HD but not the DD lineages.}, }
@article {pmid41288610, year = {2025}, author = {Shu, L and Zhuang, D and Tang, J and Zhao, J and Shao, W and Guan, X and Zhang, D}, title = {DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {11}, pages = {}, pmid = {41288610}, issn = {1367-4811}, support = {62136004//National Natural Science Foundation of China/ ; 62276130//National Natural Science Foundation of China/ ; 2023YFF1204803//National Key R&amp;D Program of China/ ; BE2022842//Key Research and Development Plan of Jiangsu Province/ ; }, mesh = {*Nanopore Sequencing/methods ; *Deep Learning ; *Sequence Analysis, RNA/methods ; *Software ; Nanopores ; }, abstract = {MOTIVATION: Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-seq) offers high-resolution, single-molecule analysis but is hindered by the lack of robust multiplex barcoding methods. Existing approaches struggle to accurately demultiplex raw nanopore signals, failing to capture both local patterns and long-range dependencies. This limitation underscores the requirement for advanced solutions to improve accuracy, efficiency, and adaptability in sequencing workflows. We present DemuxTrans, a hybrid deep learning framework that integrates Multi-Layer Feature Fusion, Transformers, and Temporal Convolutional Networks (TCN) for precise barcode demultiplexing.<br><br>RESULTS: DemuxTrans achieves state-of-the-art performance across multiple datasets by effectively balancing local feature extraction, global context modeling, and long-term dependency capture, excelling in metrics such as accuracy, recall and F1-score. These results demonstrate DemuxTrans as a scalable, efficient solution for barcode demultiplexing in nanopore sequencing, enabling precise identification of multiplexed RNA samples and improving throughput in transcriptomic and epigenomic analyses.<br><br>The code and datasets are publicly available on https://github.com/LiyuanShu116/Demuxtrans.}, }
@article {pmid41288389, year = {2025}, author = {Taheri, S and Schwarzkopf, E and Berman, HL and Brandt, N and McNeill, J and Sevier, N and Ruffieux, M and Dunn, RR and Smukowski Heil, C}, title = {The role of flour type and feeding schedule on the sourdough microbiome.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0238025}, doi = {10.1128/spectrum.02380-25}, pmid = {41288389}, issn = {2165-0497}, abstract = {Sourdough starters are fermentations of various grains by bacteria and yeast and are of worldwide economic and cultural importance. Sourdoughs are sometimes spontaneously inoculated, and their resident microbial communities are in part shaped by environmental factors, potentially including flour, water, air, human microbiota, equipment, geography, and temperature. The number of different genera of bacteria and yeast found in sourdoughs is large; however, only a handful of species typically dominate an individual sourdough starter. Understanding how and why certain species form a mature climax community in a particular environment is a key question in microbial ecology. To investigate this question, we used a meta-barcoding approach and tested whether different baking flours (all-purpose, bread, and whole wheat) and frequency of feeding, also known as backslopping, shape the sourdough starter microbial community over the course of one month. We found that the yeast genus Kazachstania rapidly rose in frequency and became the most abundant yeast in all starters, regardless of flour type or feeding schedule. In contrast, flour type did affect the bacterial community. Mature sourdoughs all contained the bacterial genera Companilactobacillus, Levilactobacillus, Lactiplantibacillus, Furfurilactobacillus, and Acetobacter, with Companilactobacillus detected at higher relative abundance in whole wheat flour and Levilactobacillus detected at higher relative abundance in bread flour. We conclude that flour can shape the microbial community of sourdough and has potential implications for functional traits.IMPORTANCEHow organisms disperse and colonize new environments is central to our understanding of biodiversity. Sourdough, the often spontaneously inoculated fermentation of grains by bacteria and yeast, represents a great system to test and observe how microorganisms come to inhabit a particular niche. In our study, we investigate how environmental parameters such as flour type and feeding frequency influence the microbial community. We find that the common sourdough yeast genus Kazachstania is most abundant in all starters regardless of treatment, but we also find a significant effect of flour type on the lactic acid bacteria composition of the sourdough starters. This work shows how the environment can impact the presence and abundance of particular microorganisms and prompts future studies to test how particular lactic acid bacteria species can specialize on certain resources.}, }
@article {pmid41288263, year = {2025}, author = {Creedy, TJ and Ding, Y and Gregory, KM and Swaby, L and Zhang, F and Vogler, AP}, title = {Bioinformatics of Combined Nuclear and Mitochondrial Phylogenomics to Define Key Nodes for the Classification of Coleoptera.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syaf031}, pmid = {41288263}, issn = {1076-836X}, support = {//NHM Biodiversity Initiative (2013-2017)/ ; //iBioGen consortium/ ; 810729//EU Horizon 2020/ ; //Chinese Scholarship Council/ ; IAF-2018-038//Leverhulme International Fellowship/ ; }, abstract = {Nuclear genome sequencing for phylogenetics is resource-intensive while mitochondrial genomes can be sequenced and analyzed with relative ease for building densely sampled phylogenetic trees of the most species-rich lineages of animals. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from > 2,000 BUSCO loci mined from GenBank's Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 491 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at the family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with 3 recent nuclear phylogenomic studies resulted in the recognition of > 80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.}, }
@article {pmid41284889, year = {2025}, author = {Shang, F and Nizharadze, T and Thiele, R and Cirovic, B and Frank, L and Busch, K and Pei, W and Feyerabend, TB and Höfer, T and Wang, X and Rodewald, HR}, title = {Multipotent progenitors with distinct origins, clonal lineage fates, transcriptomes, and surface markers yield two hematopoietic trees.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {48}, pages = {e2505510122}, doi = {10.1073/pnas.2505510122}, pmid = {41284889}, issn = {1091-6490}, support = {32170742 and 92374117//MOST | National Natural Science Foundation of China (NSFC)/ ; SFB 873-B11//Deutsche Forschungsgemeinschaft (DFG)/ ; SFB 873-B11//Deutsche Forschungsgemeinschaft (DFG)/ ; Helmholtz I &amp; I Initiative program//Helmholtz Association ()/ ; Leibniz Award//Deutsche Forschungsgemeinschaft (DFG)/ ; Advanced Grant 742883//EC | European Research Council (ERC)/ ; }, mesh = {Animals ; *Hematopoietic Stem Cells/cytology/metabolism ; *Cell Lineage ; Mice ; *Transcriptome ; *Multipotent Stem Cells/cytology/metabolism ; *Hematopoiesis/physiology ; Cell Differentiation ; Biomarkers/metabolism ; Mice, Inbred C57BL ; }, abstract = {Multipotent progenitors (MPP) are the quantitative source of native hematopoiesis that have been thought to be replenished slowly by hematopoietic stem cells (HSC). However, recent fate mapping studies have revealed two developmentally distinct populations of MPP, HSC-derived MPP (hMPP), and HSC-independent, embryonic MPP (eMPP). These data raise fundamental questions on the distinctions and functions of these progenitors. Here, we mapped the clonal dynamics of the two independent MPP systems, using in situ barcoding, and barcode linkage (hMPP), or disconnect (eMPP), with HSC. The cumulative output of eMPP to hematopoiesis was 35%, and their output was enriched for lymphoid fates. Conversely, hMPP output was enriched for myeloid-restricted fates. Distinguishing HSC from eMPP outputs revealed that only ~15% of adult HSC clones underwent multilineage differentiation (lymphoid, myeloid, and erythroid). To prospectively identify eMPP, we developed PolySMART for joint profiling of PolyloxExpress RNA barcodes, surface markers, and transcriptomes, and we found that the plasma cell marker CD138 enriches for eMPP. CD138[+] MPP are primed for self-renewal and toward lymphoid fate, and become largely but not completely replaced by CD138[-] MPP over time, which may contribute to the loss of lymphoid output with age. Taken together, adult hematopoiesis consists of two distinct lineage trees. The source of the "eMPP tree" substantially contributes to hematopoiesis before it declines, while the HSC-hMPP tree supplies hematopoiesis life-long. Our molecular determinants distinguishing the two MPP systems may open avenues to further explore these unexpected layers of hematopoiesis.}, }
@article {pmid41282751, year = {2025}, author = {Fu, Y and English, AC and Paulin, LF and Jhangiani, SN and Weissenberger, G and Vee, V and Han, Y and Mehta, HH and Muzny, DM and Gibbs, RA and Posey, JE and Calame, DG and Sedlazeck, FJ}, title = {Enriching for Answers in Rare Diseases.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.21.25338483}, pmid = {41282751}, abstract = {We present Trio-barcoded ONT Adaptive Sampling (TBAS), a cost-efficient long-read sequencing strategy combining sample barcoding and adaptive enrichment to sequence rare-disease trios on a single PromethION flow cell. TBAS achieved near-complete variant phasing and detection of small variants, structural variants, and tandem repeats with high accuracy and 77% potential solve rate. This scalable approach retains methylation data and enables clinically relevant, phenotype-guided long-read diagnostics at a fraction of current costs.}, }
@article {pmid41282438, year = {2025}, author = {Jin, YL and Bu, Y}, title = {Four new species of Symphylella (Symphyla, Scolopendrellidae) from Chongqing, southwest China with DNA barcoding analysis.}, journal = {ZooKeys}, volume = {1259}, number = {}, pages = {349-379}, pmid = {41282438}, issn = {1313-2989}, abstract = {The symphylans from Chongqing, Southwest China were investigated and studied for the first time. Four new species of the genus Symphylella, S. obtusa sp. nov., S. yintiaolingensis sp. nov., S. flabella sp. nov., and S. micropora sp. nov., are identified and described. They were compared with similar species in detail. The DNA barcodes for all new species were sequenced and analyzed together with other congeners and the genetic distance analysis further support our morphological determination. In addition, two groups, the isabellae group and oligosetosa group, of the genus Symphylella are proposed based on the pattern of inserted setae on the tergal processes, and their respective species are listed.}, }
@article {pmid41282325, year = {2025}, author = {}, title = {Correction to Application of Invertebrate-Derived DNA Barcoding (iDNA) in Blood-Sucking Leeches From West Sumatra: A Discovery of Blue-Eyed Litter Frog Leptobrachium waysapuntiense.}, journal = {Ecology and evolution}, volume = {15}, number = {11}, pages = {e72553}, doi = {10.1002/ece3.72553}, pmid = {41282325}, issn = {2045-7758}, abstract = {[This corrects the article DOI: 10.1002/ece3.72235.].}, }
@article {pmid41280501, year = {2025}, author = {Kamra, J and Saini, P and Prakash, O and Kumar, V and Tiwari, R}, title = {A comprehensive review on biotechnological approaches for improvement of medicinal plants: techniques for qualitative and quantitative production.}, journal = {3 Biotech}, volume = {15}, number = {12}, pages = {435}, pmid = {41280501}, issn = {2190-572X}, abstract = {Recent advancements in biotechnology have opened new avenues for enhancing both the qualitative and quantitative production of medicinal plants. This review highlights various genetic modification approaches, including transgenesis, recombinant DNA technology (RDT), and gene amplification through polymerase chain reaction (PCR), which enable the targeted improvement of plant traits. Complementary techniques such as omics technologies and RNA interference (RNAi) further allow precise regulation of gene expression, elucidation of metabolic pathway and enhancement of metabolite biosynthesis (e.g., alkaloids, terpenoids). In addition, this review discusses innovative strategies to improve plant yield and quality, including genetic marker-based identification, cryopreservation for long-term conservation, plant tissue culture for large-scale propagation, nanotechnology-based delivery systems, bio-fortification, DNA barcoding, and metabolomics for sustainable utilization. The integration of these biotechnological tools signficantly contributes to the production of high-value bioactive compounds, secondary metabolites, and recombinant proteins, while also facilitating drug discovery pipelines. Moreover, these interventions enhance tolerance to environmental stresses, promoting adaptation under adverse conditions.}, }
@article {pmid41280488, year = {2025}, author = {Barman, R and Banik, D}, title = {DNA barcoding clubbed with morphomatrix of commonly distributed species of Myristicaceae from North East India.}, journal = {3 Biotech}, volume = {15}, number = {12}, pages = {424}, pmid = {41280488}, issn = {2190-572X}, abstract = {UNLABELLED: The depauperate and paleopolyploid family Myristicaceae face challenges for correct species identification. Majority rule consensus trees of morphomatrix of NER species reflected diagnostic group traits (ca. 41.70%) and variable traits (ca. 58.30%) respectively. Amplification and sequencing success rates with DNA barcode loci rbcL, matK and, trnL-F were > 90% while 45% and 76% with psbA-trnH, respectively in Horsfieldia and Knema. 178 sequences of 8 species of the region were submitted to GenBank including trnL-F spacer mostly for the first time. The highest parsimony informative sites were exhibited by trnL-F and highest variable sites by matK. Mean inter-specific distances with trnL-F, matK + trnL-F in Horsfieldia and with psbA-trnH, rbcL + trnL-F in Knema were ≥ 2 times mean intraspecific distances. trnL-F in Horsfieldia and rbcL + trnL-F in Knema, and trnL-F + psbA-trnH in Horsfieldia and Knema showed barcode gaps. Identification success by 'best match' was 98% with matK + trnL-F and 96-97% with trnL-F + psbA-trnH in Horsfieldia and Knema. The Maximum Parsimony and Bayesian Inference (BI) trees with trnL-F and BI tree with trnL-F + psbA-trnH was monophyletic and resolved 100% and 60% species. Dynamic DNA QR codes generated with Knema erratica-matK, Horsfieldia kingii-psbA-trnH, Endocomia macrocoma subsp. prainii-trnL-F. The loci trnL-F, trnL-F + psbA-trnH were exhibited as candidate barcodes, additionally matK + trnL-F for Horsfieldia and rbcL + trnL-F for Knema. The DNA barcode library of NER Myristicaceae would aid in species identification, ecological variation and conservation biology.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04625-7.}, }
@article {pmid41280400, year = {2025}, author = {Ensing, DJ and Nelson, TD and Moffat, CE and Joslin, L and Eckert, L and Kraml, MM and Eckert, CG}, title = {Together again: the invasive mustard Hesperis matronalis suffers devastating seed predation by a recently adventive specialist weevil.}, journal = {BioControl (Dordrecht, Netherlands)}, volume = {70}, number = {6}, pages = {835-847}, pmid = {41280400}, issn = {1386-6141}, abstract = {UNLABELLED: The enemy release hypothesis underpins classical (or importation) biocontrol as a management technique for invasive species. Classical biocontrol has had resounding success when prospective control agents have been subject to appropriate screening before release. Occasionally, however, natural enemies have been reunited with their hosts accidentally. Such adventive agents may provide effective control but have also avoided the careful screening characteristic of modern importation biocontrol programmes. We were studying the invasive mustard, Hesperis matronalis L. (Dame's rocket; Brassicaceae: Hesperidae), when we discovered rampant seed predation by an unknown seed predator. Using DNA barcoding, we identified this seed predator as Ceutorhynchus inaffectatus Gyllenhal (Coleoptera: Curculionidae), a recently (2018) detected species in North America. Comparing potential and realised seed production, we found that seed predation by C. inaffectatus strongly reduces H. matronalis fecundity, and that this effect was not moderated by infection with turnip mosaic virus (TuMV), a commercially important pathogen hosted by H. matronalis and transmitted by polyphagous aphid species. C. inaffectatus is expected to be highly host-specific, and the absence of native Hesperidae species in North America suggests the potential for C. inaffectatus as a classical, but adventive, biocontrol agent of H. matronalis. We suggest population genetic research to identify the origin of C. inaffectatus, and host specificity testing before any intentional redistribution of this species for H. matronalis biocontrol. More generally, this system acts as a model for biocontrol prospects with adventive insect herbivore species.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10526-025-10338-w.}, }
@article {pmid41280082, year = {2025}, author = {Mosadeghi, R and Foyt, D and Sharp, L and Taylor, C and Tay, N and Oberlin, S and Fan, J and Bourke, S and Kattah, M and Huang, B and McManus, MT}, title = {RainBar: Optical Barcoding for Pooled Live-Cell Imaging with Single-Cell Resolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.04.686676}, pmid = {41280082}, issn = {2692-8205}, abstract = {High-throughput pooled screening has advanced functional genomics, but most existing methods rely on endpoint sequencing and are blind to dynamic, time-resolved phenotypes. We developed RainBar (Rainbow Barcodes), an optical barcoding system that supports pooled live-cell imaging with single-cell resolution. RainBar uses lentiviral co-delivery of spectrally distinct nuclear and cytoplasmic fluorescent proteins to encode up to 64 unique perturbations per well. To mitigate barcode recombination and improve decoding accuracy, we employed single-template viral production, codon diversification, and a ratio-based spectral unmixing pipeline tailored to overlapping fluorophores. An inverted cytoplasmic segmentation approach and multilayer perceptron classifier enabled accurate barcode identification in both arrayed and pooled formats. As a proof of concept, we applied RainBar to dissect NF-κB signaling dynamics in epithelial cells. Live imaging of RelA translocation uncovered stimulus-specific kinetics: IL-1β triggered rapid recovery, while TNF induced prolonged nuclear localization. In pooled CRISPRi screens, RainBar recovered known NF-κB regulators (e.g., IL1R1, MYD88, TNFRSF1A) and highlighted additional modulators, including the Ino80 chromatin remodeling complex subunits and KAT2A acetyltransferase. Together, these results position RainBar as a flexible platform for multiplexed, image-based functional genomics, with potential to reveal dynamic signaling architectures across diverse cellular contexts in live cells.}, }
@article {pmid41279805, year = {2025}, 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.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.11.03.686270}, pmid = {41279805}, issn = {2692-8205}, abstract = {UNLABELLED: 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) virus. The inclusion of a diverse genetic barcode enabled high-resolution tracing of viral dispersal for the H1N1 virus. While infectious virus was consistently detected in the URT, the H1N1 virus could be detected in LRT while the H3N2 virus could not. To determine whether replication of the H1N1 virus in the LRT extends to other modes 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 contracted upon dispersal to the lungs. This loss of diversity was associated with increased distance to and branching from the major airways, implicating long distance dispersal through the airways in imposing within-host population bottlenecks. These data underline the implications for within-host viral dynamics of the distinct environments of the upper and lower respiratory tracts.<br><br>IMPORTANCE: The 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 {pmid41279755, year = {2025}, author = {Hickey, JW and Li, H and Caraccio, C and Yan, Y and Marx, K and Martin, P and Leng, HT and Fayiah, J and Towalid, E and Dighero-Kemp, B and Nolan, GP and Prakash, M and McIlwain, DR}, title = {Fluid-Squid: DIY Multiplexed Imaging of Cells and Tissues.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.09.680291}, pmid = {41279755}, issn = {2692-8205}, abstract = {Recent advances in multiplexed single-cell characterization have revolutionized our insight into cell biology, but many available technologies remain limited by high costs or a lack of customizability. To address these challenges, we developed Fluid-Squid, a cost-effective, quantitative imaging platform that integrates automated fluidics to support customizable, do-it-yourself multiplexed imaging workflows. Using Fluid-Squid, we successfully imaged fresh frozen human intestinal tissues with a 36-plex oligonucleotide-barcoded antibody panel and further demonstrated the feasibility of lyophilizing such multiplexed panels. We also adapted existing multiplexed imaging workflows to characterize individual cells to identify immune cell populations, phenotype, and antigen-specific cells from mouse splenocytes and human peripheral blood mononuclear cells (PBMCs) with a 39-antibody panel. To further expand its utility, we developed a barcoding strategy that allows for the pooling and simultaneous staining of multiple samples, reducing time, costs, and batch effects in single-cell experiments. This approach facilitated rapid titration to optimize antibody concentrations and assess the impact of various blood preparation methods on cell type retention. Overall, our work provides a new open-source framework for automated fluidics and microscopy in a flexible, cost-effective platform, empowering adaptable multiplexed characterization of both single cells and tissues.}, }
@article {pmid41279741, year = {2025}, author = {Bradley, NJ and Pendyala, S and Partington, K and Fowler, DM}, title = {STARCall integrates image stitching, alignment, and read calling to enable scalable analysis of in situ sequencing data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.31.685785}, pmid = {41279741}, issn = {2692-8205}, abstract = {UNLABELLED: Fluorescent in situ sequencing involves imaging-based sequencing by synthesis in intact cells or tissues to reveal target nucleotide sequences inside each cell. Often, the target sequences are barcodes that indicate a perturbation (e.g. CRISPR guide or genetic variant) delivered to the cell. However, processing in situ sequencing data presents a considerable challenge, requiring stitching and aligning tens of thousands of images with millions of cells, detecting small amplicon colonies across sequencing cycles, and calling reads. To address these challenges, we introduce STARCall: STitching, Alignment and Read Calling for in situ sequencing, a software package that analyzes raw in situ sequencing images to produce a genotype-to-phenotype mapping for each cell. STAR-Call improves upon previous solutions by combining stitching and alignment of images into a single step that minimizes both inter-cycle and intra-cycle alignment error. STARCall also improves detection and extraction of sequencing reads, incorporating filters and normalization to combat background fluorophore signal. We compare STARCall to other methods using a diverse set of images that include commonly encountered imaging problems such as variable intensity across channels and cycles and high levels of background. Specifically, this comprises ∼250,000 images from a pooled screen of ∼3,500 barcoded LMNA variants expressed in U2OS cells and ∼1,200 bar-coded PTEN variants in induced pluripotent stem cells (iPSC) and iPSC-derived neurons. Overall, STARCall aligned more than 50% of tiles with <1 pixel error on all nine image sets while alternative packages had higher error on four. STARCall also yielded an 8-40% increase in genotyped cells due to improved filtering and normalization methods that address background fluorescence. STARCall can call tools like CellPose to segment cells and CellProfiler to compute cell features from the phenotyping images. STARcall is open-source and freely available, providing a robust solution for the analysis of in situ sequencing data.<br><br>AUTHOR SUMMARY: Short regions of RNA or DNA can be sequenced inside intact cells or tissues (i.e. in situ) by combining a microscope and sequencing by DNA synthesis. Multiple cycles of sequencing are performed, in which incorporation of a single fluorescently labeled nucleotide is imaged, and the corresponding base detected. Recently, in situ sequencing has proved useful in optical pooled screens, where a library of perturbations such as CRISPR-mediated gene knockouts or genetic variants is introduced into cells, and in situ sequencing is used to reveal the specific perturbation in each cell. However, processing in situ sequencing data presents a considerable challenge, requiring stitching and aligning tens of thousands of images, detecting small amplicon colonies across sequencing cycles, and calling reads. To address these challenges, we introduce STARCall: STitching, Alignment and Read Calling for in situ sequencing. STARCall uses a novel stitching algorithm that minimizes both inter-cycle and intra-cycle alignment error, and improved filters and normalization for base calling. When applied to a set of 9 in situ sequencing image sets, STARCall yielded an 8-40% increase in genotyped cells. STARCall is open-source and applicable to a variety of experiments, providing a robust pipeline for in situ sequencing data.}, }
@article {pmid41279580, year = {2025}, author = {Yoon, CJ and Nam, CH and Lee, SM and Choi, ES and Bae, JH and Kim, H and Jung, YM and Lim, J and Kim, R and Derom, C and Meireson, E and Weyers, S and Park, JW and Lee, J and Sung, J and Griffith, OL and Griffith, M and Jun, JK and Ju, YS}, title = {Clonal dynamics of monozygotic twinning in early human embryogenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.05.680569}, pmid = {41279580}, issn = {2692-8205}, abstract = {Monozygotic twins are derived from the split of a single zygote early in embryogenesis. Although it was hypothesized that the timing of twining is overall associated with fetal membrane configuration of twins, i.e., chorionicity and amnionicity, our understanding of early embryonic clonal dynamics underlying human twinning is limited. Here we explored the segregations of early embryonic lineages in 7 dichorionic diamniotic (DCDA), 7 monochorionic diamniotic (MCDA), 8 monochorionic monoamniotic (MCMA) monozygotic twins, and 1 dichorionic triamniotic (DCTA) monozygotic triplets, using post-zygotic early embryonic mutations (EEMs) as endogenous lineage barcodes. Patterns of the early lineage distributions among monozygotic twins revealed three apparent clonal categories, referred to as para-identical, sub-identical, and full-identical twins, which largely correlated with the amnionicity of the twins. Rather, despite conventional wisdom, chorionicity was not substantially associated with early clonal compositions, but with blood exchanges in utero . In sub-identical twins, where one co-twin was clonally a part of the other, our data suggested that the foundation of the latter co-twin was established after acquisition of a median of 6 additional post-zygotic mutations (range: 2-13), corresponding to ∼5 early cell divisions. Additional in-depth analysis on the matched placenta from an MCDA twin suggested that separation of two co-twins can precede the separation of the placenta and embryonic proper, and a single chorion can be formed even with multiclonal origin. Our findings provide insights into the clonal dynamics, twinning processes, and cell fate decisions in early human embryogenesis.}, }
@article {pmid41279260, year = {2025}, author = {Wu, YC and Schwartz, D and Khalil, EA and Upadhye, A and Rehman, J and Lee, SS}, title = {NicheProt : Cell-type-resolved proteomics of tissue compartments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.23.684231}, pmid = {41279260}, issn = {2692-8205}, abstract = {Spatial proteomics uncovers the molecular underpinnings of cellular function in intact tissues. Laser capture microdissection coupled with mass spectrometry enables comprehensive proteomic profiling of selected tissue regions, but typically does not support cell-type-specific proteomic analysis. We present NicheProt , a 3D optical microscopy-guided, photobleaching-mediated cell barcoding approach for isolating intact specific cell types from defined microanatomical tissue compartments or niches. Using sequential bottom-up proteomic analysis, we defined two distinct phenotypes of CD11c[+] dendritic cells based on their spatial locations in the inflamed mouse spleen. These two compartment-specific dendritic cell populations were characterized by proteomic signatures differing in the levels of 54 proteins. This 3D tissue microscopy-guided method offers cell-type and microregion-resolved proteomic analysis, facilitating the proteomic discovery of previously unrecognized cell subtypes and their functional roles in distinct tissue compartments.}, }
@article {pmid41279235, year = {2025}, author = {Baranowska, P and Lam, T and Herr, AE}, title = {Deterministic DNA barcoding using vacuum-driven loading of free oligonucleotides to microwell arrays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.29.684720}, pmid = {41279235}, issn = {2692-8205}, abstract = {Achieving high-throughput and cost-effective next-generation sequencing requires sample (samples, cells/beads) pooling. A key approach to pooling samples while maintaining unambiguous sample identification is to employ DNA barcoding, which assigns each specimen a unique nucleotide (index) sequence. For barcoding in droplets and microwells, one widely used approach is to randomly seed a unique oligo-coated bead into each compartment. Synthesis of oligonucleotide-coated beads (e.g., split-pooling) is exceptionally intensive and random seeding can result in errors. As an alternative, we present deterministic, aqueous barcoding of 512 arrayed microwells using a multi-layer, vacuum-driven microfluidic network. To uniquely barcode each of the 512 microwells, the oligonucleotide solutions are designed using a Combinatorial Dual Indexing (i5, i7) scheme with the deterministic loading. Deterministic loading of the solutions is achieved by sequentially mating two bifurcated and complementary microchannel-network layers to the microwell array. Vacuum-assisted flow and dead-end channel design yields uniform barcode patterning in the microwell array (∼20% CV), reasonable barcode loading times (30 - 40 min per one step), and reduced reagent use (∼ 8-16 µL at 25 µM oligos vs. 10-50 µL at 100 µM for bead systems). Cross-contamination occurred in ∼4% of the microwells, well within the acceptable range. Following DNA barcode delivery, on-chip PCR of nuclear DNA from a breast cancer cell line having the characteristics of the differentiated mammary epithelium (MCF7) was successfully performed, with off-chip quality control of the amplified breast cancer DNA. Overall, we describe a deterministic and bead-free DNA barcoding strategy for efficient barcoding of widely used microwell arrays.}, }
@article {pmid41278540, year = {2025}, author = {Twa, GM and Phillips, RA and Robinson, NJ and Day, JJ}, title = {Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {4}, pages = {lqaf156}, pmid = {41278540}, issn = {2631-9268}, mesh = {Animals ; Male ; Female ; Rats ; *RNA, Small Nuclear/genetics ; Machine Learning ; *RNA-Seq/methods ; *Sequence Analysis, RNA/methods ; *Gene Expression Profiling/methods ; Sex Characteristics ; }, abstract = {Single-nucleus RNA sequencing (snRNA-seq) technology offers unprecedented resolution for studying cell type-specific gene expression patterns. However, snRNA-seq poses high costs and technical limitations, often requiring the pooling of independent biological samples and the loss of individual sample-level data. Deconvolution of sample identity using inherent features would enable the incorporation of pooled barcoding and sequencing protocols, thereby increasing data throughput and analytical sample size without requiring increases in experimental sample size and sequencing costs. In this study, we demonstrate a proof of concept that sex-dependent gene expression patterns can be leveraged for the deconvolution of pooled snRNA-seq data. Using previously published snRNA-seq data from the rat ventral tegmental area, we trained a range of machine learning models to classify cell sex using genes differentially expressed in cells from male and female rats. Models that used sex-dependent gene expression predicted cell sex with high accuracy (93%-95%) and generalizability and outperformed simple classification models using only sex chromosome gene expression (88%-90%). This work provides a model for future snRNA-seq studies to perform sample deconvolution using a two-sex pooled sample sequencing design and benchmarks the performance of various machine learning approaches to deconvolve sample identification from inherent sample features.}, }
@article {pmid41277841, year = {2025}, author = {Gopal, K and Burnett, C and Kharytonchyk, S and Emery, A and Atindaana, E and Swanstrom, R and Kidd, JM and Telesnitsky, A}, title = {RNA splicing patterns contribute to burst size variation among HIV-1-infected Jurkat cell clones.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0133425}, doi = {10.1128/jvi.01334-25}, pmid = {41277841}, issn = {1098-5514}, abstract = {UNLABELLED: Accurately quantifying virus release from HIV-1-infected cells is central to predicting infection outcomes and evaluating treatment strategies. Recent studies suggest that viral shedding can vary strikingly among infected cells. To identify predictors of virus release levels, a previously developed high-throughput molecular barcoding system was used to track the expression properties of individual infected clones within a polyclonal population. Consistent with previous reports, virus release spanned four orders of magnitude among clonal integrants. While reporter gene expression correlated poorly with virus release, intracellular viral RNA levels correlated well, and levels of unspliced HIV-1 RNA correlated most closely. Comparing clones with different virus release levels showed that they varied not only in total intracellular HIV-1 RNA levels but also in levels of viral RNA splicing. Remobilizing proviruses revealed that splicing differences were largely due to cell-intrinsic properties, although splicing differences were due to heritable features of the parent provirus for at least one clone. This clone displayed high levels of reporter gene expression from an HIV-1spliced RNA, but low levels of unspliced viral RNA and virus release. This over-splicing clone, which contained a non-synonymous substitution in rev, did not respond to treatment with the latency-reversing agent JQ1 but displayed increased virus release in response to treatment with pladienolide B, a splicing inhibitor. These findings demonstrate that splicing differences can contribute to virus production levels and suggest that future studies on proviral populations that include expanded clones may benefit from assessing clone-specific splicing properties.<br><br>IMPORTANCE: Many models of HIV-1 infection rely on the assumption that actively infected cells release similar amounts of virus, despite recent reports that suggest shedding differs drastically among infected cells. In this study, the expression phenotypes of hundreds of integrant clones were analyzed to identify factors contributing to burst size variation. In agreement with previous reports, virus release spanned over four orders of magnitude within the infected pool. Both proviral expression levels and variation in splicing contributed to these burst size differences. While cell-intrinsic factors appeared to be the primary contributors to heterogeneous shedding patterns, viral point mutations were also observed and, in at least one case, contributed to particle release levels. Together, these findings demonstrate that expression variation among proviruses is both large and multifaceted and suggest that clone-specific differences in HIV-1 expression properties may contribute to unpredicted responses to treatment interventions.}, }
@article {pmid41277803, year = {2025}, author = {Guðmundsson, T and Randhawa, HS}, title = {Parasite diversity in haddock (Melanogrammus aeglefinus) from Icelandic waters.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e125}, doi = {10.1017/S0022149X2510076X}, pmid = {41277803}, issn = {1475-2697}, support = {//H&#xe1;sk&#xf3;li &#xcd;slands/ ; }, mesh = {Animals ; Iceland/epidemiology ; *Fish Diseases/parasitology/epidemiology ; *Biodiversity ; *Gadiformes/parasitology ; *Parasites/classification/isolation &amp; purification/genetics ; DNA Barcoding, Taxonomic ; *Helminths/isolation &amp; purification/classification/genetics ; }, abstract = {It is assumed that the biology and ecology of commercial fish species are relatively well-known, given that many of these parameters are key for stock assessment in fisheries management. Surprisingly (or not), several new parasite species are described annually from fish that are of commercial and cultural importance. Haddock (Melanogrammus aeglefinus) is an important commercial fish species in the North Atlantic with more than 50 parasite species having been reported from it. Despite its commercial importance in Icelandic waters, only 11 parasite species have been reported from Icelandic haddock. In February and March 2023, 26 haddock were sampled, including 16 and 10 from the north and south of Iceland, respectively. Fish were examined for parasites, with a focus on macroparasites (large, usually visible to the eye). Parasites were identified morphologically with identifications of helminths confirmed using DNA barcoding (Sanger sequencing). Overall, 19 different parasite species were recovered with 17 being shared between haddock sampled from the north and south of Iceland. Of these, eight represent new geographical records for parasites of haddock in Icelandic waters. Our study indicates that monitoring for parasites remains important, regardless of how well a species has been studied. Furthermore, reporting parasites per organ and per region, especially when areas are known to be influenced by different abiotic and physical features, is important in the context of parasites as biological tags for stock identification. Despite a small sample size, our study suggests that some parasites might act as potential biological tags for stock identification of haddock in Icelandic waters.}, }
@article {pmid41273043, year = {2025}, author = {González, ML and Camps, GA and Sérsic, AN and Cosacov, A and Acosta, MC and Aguilar, DL and Almirón, NEA and Chiapero, AL and Lauenstein, DL and Scaldaferro, M and Sosa-Pivatto, M and do Pico, GV and Moreno, EMS and Vega, C and Neffa, VS and Baranzelli, MC}, title = {Mind the Gaps: Shortfalls in Studies of the Intraspecific Genetic Diversity of Plants Across the Gran Chaco.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70187}, doi = {10.1111/mec.70187}, pmid = {41273043}, issn = {1365-294X}, support = {PIBAA-28720210100101CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PIP-11220210100320CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PIP-11220210100536CO//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PICT 2020-00602//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT-3050//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT-2021-273//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PIP-33620230100570CB//Secretaria de Ciencia y Tecnolog&#xed;a - Universidad Nacional de C&#xf3;rdoba/ ; }, abstract = {Intraspecific genetic diversity (IGD) is a fundamental component of biodiversity, essential for understanding the evolutionary histories and demographic processes of species, and is key to effective conservation planning. However, ecologically important regions such as the Gran Chaco, South America's second-largest forested biome, remain largely underexplored. Encompassing diverse vegetation across climatic and altitudinal gradients, it harbours more than 3400 vascular plant species, 11% of which are endemic. Despite its ecological importance, genetic research in the region is limited and often biased. We reviewed IGD studies on vascular plants in the Gran Chaco from 1985 to 2024, identifying 85 studies covering 74 species. Coverage remains alarmingly low, with only 2.14% of species and 9.95% of the phylogenetic diversity represented. Research is skewed towards perennial (91%) and tree (46%) species, with limited representation of annuals and herbaceous taxa. Most studies relied on nuclear DNA (66%), fewer used chloroplast DNA (27%) and only 7% combined both genomes. Geographically, 33% of the Gran Chaco has no IGD data, and a further 22% includes data from a single species. Genetic sampling is concentrated in more accessible areas with higher road density and proximity to research institutions, particularly at higher altitudes. We found that in the Argentine Chaco ecoregions, 4.4 species have been genetically studied for every 100 species recorded, while in the Bolivia and Paraguay Chaco ecoregions, this proportion drops to 1.1 species for every 100 in each country. Future research on IGD in the Gran Chaco should broaden its taxonomic scope, diversify genomic tools and expand geographic coverage. Addressing these gaps will provide critical insights into the biogeographic history of the Gran Chaco and strengthen conservation strategies in this threatened and understudied biome.}, }
@article {pmid41272223, year = {2025}, author = {Atsma, H and Burkett-Cadena, ND and Wisely, SM and Urlaub, A and Botero-Cañola, S and Reeves, LE}, title = {Monitoring biodiversity and detection of diverse vertebrate species with mosquito blood meal analysis at the DeLuca Preserve, Florida, USA.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-28062-x}, pmid = {41272223}, issn = {2045-2322}, abstract = {Biodiversity monitoring is essential to conservation, yet field surveys are expensive, labor-intensive, and require substantial taxonomic expertise. DNA-based approaches are increasingly implemented to indirectly detect the presence of species at diverse types of field sites. In terrestrial ecosystems, invertebrate-derived DNA (iDNA) has potential to contribute to monitoring efforts that aim to characterize the diversity of vertebrate communities or to detect the presence of vertebrate species. We investigated the feasibility of using mosquito blood meals to detect vertebrate animals, focusing on the diversity of species detected by mosquitoes collectively and by individual species. Mosquitoes were collected at the DeLuca Preserve, Osceola County, Florida, USA over an eight-month period using sampling methods known to be effective for blood-fed mosquitoes. Blood-fed mosquitoes were identified and screened for host DNA using DNA barcoding-based blood meal analysis. From a sample of 2,051 identified blood meals, representing 21 mosquito species, mosquitoes collectively detected 86 vertebrate species. This assemblage of vertebrates was taxonomically diverse with species from all four terrestrial vertebrate classes, 22 orders, including large- and small-bodied species, and species that are nocturnal, diurnal, migratory, resident, fossorial, arboreal, and semiaquatic, and those that are imperiled, invasive, and cryptic. The host detection efficiency, a measure of the number of detected vertebrate species relative to the number of identified blood meals, varied among mosquito species, indicating that species do not contribute equally to detecting vertebrate species within a community. Our results demonstrate the feasibility of mosquito-based iDNA as a detection method for vertebrates, capable of detecting diverse vertebrate species with a single sampling technique. Because of variation in mosquito diversity patterns between geographic sites and habitats, and in the host associations and host detection efficiency among mosquito species, preliminary surveys to identify and target mosquito species appropriate to the goals of the monitoring effort would be expected to optimize return on investment in mosquito-based vertebrate surveys.}, }
@article {pmid41271826, year = {2025}, author = {Sugi, T and Reteng, P and Gaithuma, AK and Kawai, N and Namangala, B and Mutengo, MM and Ishiguro, N and Hayashida, K and Yamagishi, J}, title = {Enhanced blood parasite species identification using V4-V9 18S rDNA barcoding by universal primers on a nanopore platform.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {41249}, pmid = {41271826}, issn = {2045-2322}, support = {JP24ym0126801//Japan Agency for Medical Research and Development/ ; JP20wm0125008//Japan Agency for Medical Research and Development/ ; JPJSCCB20230007//Japan Society for the Promotion of Science Core-to-Core program/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *RNA, Ribosomal, 18S/genetics ; Cattle ; Humans ; *DNA Primers/genetics ; *Nanopores ; Plasmodium falciparum/genetics/isolation &amp; purification ; *DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Parasites/genetics/classification ; DNA, Protozoan/genetics ; }, abstract = {Microscopic examination is commonly used for blood parasite detection in resource-limited settings due to its low cost and simplicity. However, it requires microscopy experts and has poor species-level identification. This study proposes a targeted next-generation sequencing (NGS) approach using a portable nanopore platform to enable accurate and sensitive parasite detection in such settings. To improve species identification on the error-prone nanopore sequencer, we designed a DNA barcoding strategy targeting the 18S rDNA V4-V9 region, which outperformed the commonly used V9 region. To enrich parasite DNA and reduce host contamination, two blocking primers were developed: a C3 spacer-modified oligo competing with the universal reverse primer and a peptide nucleic acid (PNA) oligo that inhibits polymerase elongation. These were combined to selectively reduce the amplification of host's DNA from blood samples. The developed targeted NGS test successfully detected Trypanosoma brucei rhodesiense, Plasmodium falciparum, and Babesia bovis in human blood samples spiked with as few as 1, 4, and 4 parasites per microliter, respectively. Validation study using field cattle blood samples revealed that this test could detect multiple Theileria species co-infections in the same cattle. The established parasite targeted NGS test using a portable nanopore platform enables comprehensive parasite detection with high sensitivity and accurate species identification.}, }
@article {pmid41267691, year = {2025}, author = {Kaltenbach, T}, title = {Mayflies of the Fiji Islands (Ephemeroptera).}, journal = {ZooKeys}, volume = {1259}, number = {}, pages = {205-276}, pmid = {41267691}, issn = {1313-2989}, abstract = {Material collected in 2024 in nine different rivers on the two main islands of Fiji, Viti Levu and Vanua Levu, is the basis for this taxonomic study of mayflies of the Fiji Islands. Apart from one larva of Caenidae, not treated in this study, all other larvae and three female imagos belong to two genera of the family Baetidae (Baetis Leach and Papuanatula Lugo-Ortiz &amp; McCafferty). A new subgenus of Papuanatula, Fijifiliola subgen. nov., based on the larvae of ten new species, and the larva and female imago of one new species of Baetis are described and illustrated. DNA barcodes (COI) were obtained for most species, and their genetic distances were analysed (Kimura-2 parameter). A key to all species of Papuanatula (Fijifiliola)subgen. nov. is provided. Amongst the new species of Papuanatula (Fijifiliola)subgen. nov., a case of parthenogenesis and likely ovoviviparity is discussed.}, }
@article {pmid41263605, year = {2025}, author = {Terra, M and Brescovit, A and Dias, A and Rincão, M and da Rosa, R}, title = {Cryptic diversity identified by DNA barcoding reveals the impact of pleistocene climate oscillations on a forest interior spider.}, journal = {Genome}, volume = {68}, number = {}, pages = {1-12}, doi = {10.1139/gen-2025-0028}, pmid = {41263605}, issn = {1480-3321}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Genetic Variation ; Forests ; Brazil ; Haplotypes ; *Spiders/genetics/classification ; DNA, Mitochondrial/genetics ; Phylogeography ; Climate Change ; }, abstract = {Quaternary climate oscillations significantly influenced the configuration of the Brazilian Atlantic Forest. In this study, mitochondrial DNA analysis of Enoploctenus cyclothorax (Bertkau, 1880) was conducted to investigate potential cryptic diversity within populations across the state of Paraná, Brazil. Two divergent genetic lineages were identified based on genetic distances, haplotype network, and phylogenetic inference. A phylogeographical break separates the lineages into two geographic regions; one lineage is found exclusively in the eastern region and the other is found mainly in the northern and western regions of the state. The coalescence tree estimates the divergence time between 1.8 million years and 500 000 years ago, period marked by glaciation, suggesting historical forest fragmentation as a potential isolating mechanism. These findings support the hypothesis of independently evolving units within E. cyclothorax, possibly representing cryptic species, though broader sampling and integrative approaches are necessary for taxonomic validation.}, }
@article {pmid41262462, year = {2025}, author = {Lewis, JH and Kojima, H and Campbell, EO}, title = {A Japan-focused review of East Asian Acicnemis Fairmaire, 1849 (Coleoptera, Curculionidae) reveals cryptic diversity in a well-studied region.}, journal = {ZooKeys}, volume = {1259}, number = {}, pages = {103-167}, pmid = {41262462}, issn = {1313-2989}, abstract = {The East Asian species of Acicnemis Fairmaire, 1849 (Coleoptera: Curculionidae: Molytinae) are reviewed using a combination of traditional morphological approaches (microscopy, dissections) and DNA barcoding. Three new species, A. cryptica Lewis &amp; Kojima, sp. nov., A. koguma Lewis &amp; Kojima, sp. nov. and A. squamata Lewis &amp; Kojima, sp. nov. are described from mainland Japan. The former two species are cryptic and sister to more widespread, previously described taxa. Based on examination of name-bearing type material and morphological considerations Acicnemis cruciata Kleine, 1924 syn. nov. is a junior subjective synonym of Acicnemis postica Hubenthal, 1919, Acicnemis yakushimana Morimoto &amp; Miyakawa, 1995 syn. nov. is a junior subjective synonym of A. dividicincta Morimoto &amp; Miyakawa, 1995, and Acicnemis dorsonigrita Voss, 1941 syn. nov. is a junior subjective synonym of Acicnemis palliata Pascoe, 1872. Lectotypes are designated for Acicnemis albofasciata (Ter-Minasian, 1953), A. laeta Hubenthal, 1919, A. postica Hubenthal, 1919 and A. sauteri Hubenthal, 1919. Important morphological characters used in Acicnemis species identification are reviewed and a key to the East Asian species is provided. DNA (CO1) barcoding is used to supplement our morphology-based species hypothesis, and the first published barcodes for most species covered here are presented.}, }
@article {pmid41259660, year = {2025}, author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A}, title = {Raxtax: A k-mer-based non-Bayesian Taxonomic Classifier.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf620}, pmid = {41259660}, issn = {1367-4811}, abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.<br><br>RESULTS: We validate raxtax on three widely used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100,000 and 1,000,000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.<br><br>raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.}, }
@article {pmid41256401, year = {2025}, author = {Rosen, JD and Vasanthakumari, AD and Salomon, K and de Lange, N and Dash, PM and Keukeleire, P and Hassan, A and Barrera, A and Kircher, M and Love, MI and Schubach, M}, title = {Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.25.678548}, pmid = {41256401}, issn = {2692-8205}, abstract = {As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains challenging. In particular, the study of non-coding genomic variation remains a major challenge due to the lack of accurate functional annotation for activity in a given context and across alleles. Experimental evidence is critical for prioritizing and interpreting functional effects of genetic alterations. Massively Parallel Reporter Assays (MPRAs) have emerged as a powerful high-throughput approach, enabling quantification of regulatory element activity and allelic effects, and systematic dissection of gene regulatory logic and variant effects across different contexts. However, the diversity of MPRA designs, lack of standardized formats, and many potential processing parameters hamper data integration, reproducibility, and meta-analyses across studies. To address these challenges, the Impact of Genomic Variation on Function (IGVF) Consortium established an MPRA focus group to develop community standards, including harmonized file formats, and robust analysis pipelines for a wide range of library types and experimental designs. Here, we present these formats and comprehensive computational tools, MPRAlib and MPRAsnakeflow, for uniform processing from raw sequencing reads to counts, processing and visualization. Using diverse MPRA datasets, we characterize technical variability sources including barcode sequence bias, outlier barcodes, and delivery method (episomal vs. lentiviral). Our results establish best practices for MPRA data generation and analysis, facilitating robust, reproducible research and large-scale integration. The presented tools and standards are publicly available, providing a foundation for future collaborative efforts in regulatory genomics.}, }
@article {pmid41255016, year = {2025}, author = {Li, X and Zhang, X and Zhai, J and Lei, R and Li, H}, title = {DNA barcode-targeted triplex droplet digital PCR for three high-risk soybean fungal pathogens in soybean seeds.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70388}, pmid = {41255016}, issn = {1526-4998}, support = {2021YFD1400100//National Key Research and Development Program of China/ ; 2021YFD1400103//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Soybean crops face significant threats from the fungal pathogens Diaporthe aspalathi, Diaporthe caulivora, and Cadophora gregata, which cause stem canker and brown stem rot leading to substantial yield losses. Current detection methods rely on time-consuming isolation and culturing, underscoring the need for rapid, sensitive, and direct diagnostic tools. This study aimed to develop a triplex droplet digital polymerase chain reaction (ddPCR) assay for simultaneous detection of these three pathogens without requiring fungal cultivation.<br><br>RESULTS: A triplex ddPCR assay was designed using specific regions of the translation elongation factor 1-&#x3b1; (EF-1&#x3b1;) and &#x3b2;-tubulin (TUB2) genes, which were identified via comparative DNA barcode analysis of fungi infecting soybean plants. The assay achieved high sensitivity with absolute quantification limits of 0.20 copies/&#x3bc;L for D. aspalathi, 0.34 copies/&#x3bc;L for D. caulivora, and 2.58 copies/&#x3bc;L for C. gregata. Recovery rates from fungal-mycelium-spiked soybean seed samples ranged from 58.8% to 91.7%. When applied to field samples, the assay detected the target pathogens in 60% of imported soybean seeds.<br><br>CONCLUSION: The triplex ddPCR method enables accurate, sensitive, and rapid simultaneous detection of three high-risk fungal pathogens in soybean seeds. This assay supports large-scale screening of imported commodities, facilitates early disease management, and has the potential to reduce significant economic losses in soybean production. &#xa9; 2025 Society of Chemical Industry.}, }
@article {pmid41254144, year = {2025}, author = {Abu El-Hassan, GMM and Abo El-Ela, RH and Sawaby, R and El-Hamouly, H and El Sawaf, BM and Ghallab, EH}, title = {Morphology, molecular phylogeny and record verification of Sarcophaga ruficornis Fabricius (Diptera: Sarcophagidae) from Egypt.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40357}, pmid = {41254144}, issn = {2045-2322}, mesh = {Animals ; *Sarcophagidae/genetics/anatomy &amp; histology/classification ; Egypt ; *Phylogeny ; DNA Barcoding, Taxonomic/methods ; Male ; Female ; Electron Transport Complex IV/genetics ; Forensic Entomology/methods ; }, abstract = {In forensic entomology, accurate species identification is essential for calculating the exact minimum postmortem interval (minPMI), as insect developmental rates are highly species-specific. Sarcophaga (Liopygia) ruficornis (Fabricius, 1794) is a species of medical and forensic significance. Recently, it was recorded from Egypt for the first time. The current study aimed to conclusively identify S. ruficornis in Egypt through DNA barcoding and morphological examination of both adult males and females, for the first time, to our knowledge. A segment of the mitochondrial cytochrome oxidase subunit one gene (COI) of S. ruficornis was amplified, and a sequence length of 817 bp was obtained and submitted to GenBank. The genitalia of both sexes and the diagnostic morphological characters of the species were examined and illustrated. In addition, the phylogenetic relationship of the Egyptian population of S. ruficornis was investigated. This study demonstrates the utility of DNA barcoding for investigating the genetic composition and variation of S. ruficornis populations and provides essential data for the identification of S. ruficornis in Egypt, which makes it possible to identify a specimen correctly even when only limited morphological evidence is available.}, }
@article {pmid41249436, year = {2025}, author = {Zhuo, W and Liu, Y and Wang, H and Lu, S and Xiao, B and Yang, M and Xiong, C and Zhou, N and Zhang, G and Qi, J and Zhu, J and Wang, L and Ren, F}, title = {Chloroplast genome analysis reveals intraspecific variation and phylogenetic conflicts in Bletilla.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {40297}, pmid = {41249436}, issn = {2045-2322}, support = {2024jbky-032//Basic Research Expenses of Chongqing Science and Technology Bureau/ ; cstc2022ycjh-bgzxm0029//Chongqing Talent Program/ ; CQYC20210309793//Chongqing Talent Program/ ; 2Y201402128//Chongqing Traditional Chinese Medicine Technology Projec/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; *Orchidaceae/genetics/classification ; *Genetic Variation ; DNA Barcoding, Taxonomic ; Chloroplasts/genetics ; }, abstract = {The genus Bletilla Rchb.f., an endangered taxon of Orchidaceae Juss. with significant medicinal value, faces persistent controversies in taxonomic identification and phylogenetic relationships. In this study, we analyzed a dataset of 57 complete chloroplast genomes (CPGs) from five subfamilies of Orchidaceae, including five newly sequenced Bletilla CPGs and publicly available data. These CPGs were combined with corresponding nuclear ribosomal internal transcribed spacer (nrITS) sequences obtained from public databases to resolve taxonomic uncertainties and phylogenetic relationships within Bletilla. Our results revealed significant intraspecific variation in Bletilla CPGs with overlapping intraspecific and interspecific genetic distances (GDs), alongside non-monophyletic clades of B. striata, B. ochracea, and B. formosana in species-level phylogenies. Consequently, the CPG 'super barcodes'-proposed as high-resolution markers for plant identification-demonstrated limited discriminatory power in Bletilla, challenging their universal reliability. Phylogenetic analysis revealed conflicting placements between Bletilla and B. sinensis in CPG and nrITS trees: while nrITS data supported a monophyletic Bletilla within the subtribe Coelogyninae Benth., CPG data placed B. sinensis outside Bletilla, forming a sister clade with Calanthe triplicata and Tainia dunnii. Collectively, this study provides new evidence for the taxonomic identification and phylogenetic relationships of Bletilla through chloroplast-nuclear genome integration, offering a preliminary framework for taxonomic re-evaluation of complex plant groups.}, }
@article {pmid41248424, year = {2025}, author = {Af Geijerstam, P and Johansson, E and Fägerstam, S and Wu, JH and Ghafouri, B and Karlsson, K and Hebib, L and Kastbom, L and Wennberg, P and Gustafson Hedov, E and Storgärds, M and Sundström, J and Rådholm, K}, title = {Effect of the FoodSwitch application on type 2 diabetes in Sweden: a study protocol for the randomised controlled DIgitAl diabeTES Treatment - the Healthy Eating, heaLthy Patients trial (DIATEST-HELP).}, journal = {BMJ open}, volume = {15}, number = {11}, pages = {e110141}, doi = {10.1136/bmjopen-2025-110141}, pmid = {41248424}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 2/diet therapy ; Sweden ; *Mobile Applications ; *Diet, Healthy ; Randomized Controlled Trials as Topic ; Glycated Hemoglobin/analysis ; Quality of Life ; Adult ; Female ; *Food Labeling/methods ; Male ; Middle Aged ; Smartphone ; }, abstract = {INTRODUCTION: A healthy diet improves glycaemic control and reduces cardiovascular risk in type 2 diabetes (T2D). However, access to dietitians is limited. Several countries have implemented mandatory interpretive front-of-pack labelling to guide consumers towards healthier food choices, but Sweden has not. Smartphone applications may offer an alternative platform to provide such information. This study evaluates the dietary and clinical impact of a novel application providing interpretive labelling to Swedish adults with T2D.<br><br>METHODS AND ANALYSIS: This is a fully decentralised randomised controlled trial. 900 individuals with T2D for &#x2265;2 years who regularly shop for groceries will be recruited via general practices and community advertisements. Participants will be randomised to receive either: (1) access to the FoodSwitch mobile application plus standard written dietary advice, or (2) standard written dietary advice only. The FoodSwitch application allows users to scan barcodes on packaged foods to receive recommendations of healthier alternatives within the same category. The primary outcome is the difference in change in mean self-measured glycated haemoglobin between groups after 6 months. Secondary outcomes include differences in changes in waist circumference, body weight, quality of life, medication use, hospitalisations and all-cause mortality at 26 weeks. Exploratory outcomes include omics analyses. Recruitment is ongoing. Expected study completion on 31 December 2026.<br><br>ETHICS AND DISSEMINATION: The trial has received ethical approval from the Swedish Ethical Review Authority (2023-06622-01, 2024-06668-02, 2024-07357-02 and 2025-01095-02) and is performed in line with World Medical Association Declaration of Helsinki and the General Data Protection Regulation. Results will be published in a peer-reviewed international journal.<br><br>TRIAL REGISTRATION NUMBER: NCT05977218.}, }
@article {pmid41248068, year = {2025}, author = {Casasent, AK and Stolley, DL and Gamal, BT and Dahay, A and Mok, S and Rocha, L and Li, V and Nguyen, AT and Zhang, B and Brasuell, CT and Thompson, EJ and Huynh, T and Burks, JK and Ferri-Borgogno, S}, title = {Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {224}, pages = {}, doi = {10.3791/68619}, pmid = {41248068}, issn = {1940-087X}, mesh = {*Transcriptome ; Animals ; *Gene Expression Profiling/methods ; Paraffin Embedding/methods ; Mice ; Humans ; *Sequence Analysis, RNA/methods ; }, abstract = {The spatial composition of cells within the host, as well as the bacteria or viral loads within the tissue, can impact the interaction of cell types and analytes that drive the cell through cell-type-specific processes. Stereo-seq for FFPE tissues uses random priming to spatial barcodes, which is different from standard spatial transcriptomics methods, which use A'tailing to capture messenger RNA (mRNA) or probe-based to capture species-specific transcripts. These methods do not embrace the more current knowledge about the impact and importance of other types of RNA from long non-coding RNA, mitochondrial RNA, microRNA, or other species, RNA, such as microbial, viral, and fungal. Outlined here is a step-by-step procedure from tissue sectioning through library preparation for spatial species-agnostic stereo-seq application with RNA detection using a randomer probe methodology, which is compatible with formalin fixed paraffin embedded (FFPE) tissues. This Stereo-seq method has a random capture bead of 0.22 µm in size that reoccurs in an array every 0.5 µm, allowing for subcellular resolution from a sequencing-based technology. As this method detects both host and non-host RNA, the protocol requires specific considerations to allow for the determination of what is inside the tissue versus what was deposited on the tissue during the collection, preservation, cutting, and detection process (i.e., environmental and handling contaminants). Lastly, this protocol allows one to have high (single-cell) level resolution of multi-RNA species within a spatial context, providing insight into the intra- and inter-actome of cell types and pathological species.}, }
@article {pmid41247050, year = {2025}, author = {Inman, B and Butler, J and George-Nichol, S and Kovalenko, G and Savidge, T and Vergnetti, Y and Pongratz, C and Bee, E and DiNardo, AR and Kay, A and Mandalakas, A and Bortz, E and Ness, TE}, title = {Application of FreezeTB, a targeted nanopore sequencing assay, for identification of drug resistance and lineages among pulmonary tuberculosis cases in Alaska.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0233525}, doi = {10.1128/spectrum.02335-25}, pmid = {41247050}, issn = {2165-0497}, abstract = {Alaska has the highest incidence of tuberculosis (TB) in the United States, with 8% mortality while undergoing TB treatment. With a quarter of TB cases lacking sputum culture to enable drug resistance testing, FreezeTB aimed to develop tools tailored to meet the challenges in Alaska while being translatable to other settings. We designed a rapid and cost-effective laboratory workflow and software to identify drug-resistant mutations in Mycobacterium tuberculosis using targeted next-generation sequencing (tNGS). FreezeTB, a Fast, Reliable, Economical Evaluation tool to Zap Endemic Tuberculosis, amplifies 22 gene loci associated with resistance to 16 anti-tuberculosis drugs. M. tuberculosis isolates from Alaska (2011-2024) were blinded and underwent analysis with FreezeTB, then compared with phenotypic drug susceptibility testing (pDST) and whole genome sequencing (WGS). Compared with WGS (n = 79), FreezeTB provided the same mutations in 96% (n = 76/79) of samples with 100% lineage agreement (n = 79/79). Compared with pDST using Cohen's kappa, FreezeTB had almost perfect agreement for rifampin (RIF, 0.90; n = 97/98) and ethambutol (EMB, 1.00; n = 98/98), strong agreement for isoniazid (INH, 0.80; n = 88/98), moderate agreement for ethionamide (ETO, 0.78; n = 95/98), weak agreement for streptomycin (STR, 0.56; n = 95/98), and no agreement for pyrazinamide (PZA, 0.20; n = 91/98). Using a portable nanopore sequencer, each sample cost under $30 for sequencing, which included a flow cell, a barcoding kit, a flow cell wash kit, a polymerase, and primers. FreezeTB provides a portable, 1-day laboratory and bioinformatic workflow for sequencing M. tuberculosis. Freeze TB can accurately determine mycobacterial lineage and resistance for RIF, INH, ETH, and ETO at a low cost.IMPORTANCEGlobally, tuberculosis is the leading infectious cause of mortality with 10.8 million new cases and 1.25 million deaths occurring in 2024. Targeted next-generation sequencing (tNGS) is a rapid, cost-effective method for identifying mutations in the Mycobacterium tuberculosis genome associated with drug resistance. FreezeTB was created to provide low-cost, portable sequencing and tNGS analysis for drug resistance. FreezeTB selectively amplifies and sequences 24 targets of the M. tuberculosis genome that cover regions the WHO has designated as containing mutations conferring drug resistance, as well as provides species confirmation and rapid lineage determination. Freeze TB is a laboratory workflow and free, open-source (OS) low dependency bioinformatic software that can be downloaded onto a computer with no further need for internet access. Using M. tuberculosis isolates from Alaska, FreezeTB provided the same mutations in 96% (n = 76/79) of samples with 100% lineage agreement (n = 79/79) compared with whole genome sequencing.}, }
@article {pmid41246444, year = {2025}, author = {Park, J and Ra, DK and Kim, S}, title = {A newly-recorded species, Roeslerstammia erxlebella (Fabricius, 1787) (Lepidoptera, Roeslerstammiidae) from Korea, with a key to species of the genus and DNA barcoding analysis.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e171683}, doi = {10.3897/BDJ.13.e171683}, pmid = {41246444}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Roeslerstammia Zeller, 1839, the type genus of the family Roeslerstammiidae, comprises a total of four species on a global scale. The type species, Roeslerstammia erxlebella (Fabricius, 1787) is distributed across the Palaearctic Region, from Europe to Japan. However, the presence of this species has only been confirmed in European countries, Russia and Japan.<br><br>NEW INFORMATION: The present study reports the first record of Roeslerstammia erxlebella in Korea, specifically from Odae-san National Park. This paper constitutes a review of the taxonomic history of the family Roeslerstammiidae and the genus Roeslerstammia. A thorough taxonomic account of the recently documented species, R. erxlebella, is presented, accompanied by a taxonomic key and an illustrated map delineating the geographical distribution of the genus Roeslerstammia. Furthemore, the DNA Barcode data of a Korean individual was made available, alongside public data from BOLD systems. The DNA Barcoding analysis further indicates that the Korean individual is R. erxlebella.}, }
@article {pmid41245217, year = {2025}, author = {Ojeda-Perez, I and Bustos, A and Selvaraj, S and Fañanas-Baquero, S and Alberquilla-Fernandez, O and Serrano, LJ and Bonafont, J and Garcia-Torralba, A and Torres-Ruiz, R and Rodriguez-Perales, S and Lang, V and Trigueros, C and Mayo-Garcia, R and Quintana-Bustamante, O and Porteus, M and Sánchez-Dominguez, R and Segovia, JC}, title = {Harnessing DNA barcoding to enhance and sustain polyclonality in gene-edited hematopoietic stem cells.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {33}, number = {4}, pages = {101615}, doi = {10.1016/j.omtm.2025.101615}, pmid = {41245217}, issn = {2329-0501}, abstract = {A challenge in gene editing for hematopoietic stem and progenitor cells (HSPCs) is achieving efficient editing while preserving long-term engraftment and clonal diversity. Tracking edited clones with high resolution is essential to understand the impact of editing on hematopoiesis. We developed a barcoded AAV6 donor template (BC-AAV) to precisely monitor the fate of edited HSPCs following transplantation. Our findings reveal that, despite initial barcode diversity in vitro, human hematopoiesis generated by edited HSPCs transplanted in immunodeficient mice is driven by a limited number of dominant clones. The engraftment of gene-edited cells follows an oligo/polyclonal pattern, indicating that editing does not alter clonal dynamics in this model. Using BC-AAV, we optimized a gene editing protocol for correcting the PKLR gene, responsible for pyruvate kinase deficiency, a rare disorder that causes severe anemia due to red blood energy imbalance. We implemented key improvements. GMP-grade StemSpan AOF medium and StemRegenin-1 increased clonal diversity while maintaining hematopoietic potential. NHEJ inhibitor AZD-7648, significantly boosted editing efficiency in vitro, and a shorter transduction period enhanced engraftment and clonal balance without compromising editing outcomes. This refined strategy for gene editing in human HSPCs optimizes both efficiency and long-term polyclonal dynamics and has important implications for clinical applications.}, }
@article {pmid41239062, year = {2025}, author = {Ayadi, ZEM and Rebah, MA and Gey, D and Tazerouti, F}, title = {Morphological and Molecular Characterization of Hexostoma auxisi Palombi, 1943 (Polyopisthocotylea: Hexostomatidae) from Auxis rochei (Risso, 1810) (Teleostei: Scombridae) off Algerian Waters, Western Mediterranean.}, journal = {Acta parasitologica}, volume = {70}, number = {6}, pages = {222}, pmid = {41239062}, issn = {1896-1851}, mesh = {Animals ; Mediterranean Sea ; *Trematoda/genetics/anatomy &amp; histology/classification/isolation &amp; purification ; Algeria ; *Fish Diseases/parasitology/epidemiology ; *Trematode Infections/veterinary/parasitology ; Electron Transport Complex IV/genetics ; Gills/parasitology ; Phylogeny ; *Perciformes/parasitology ; }, abstract = {INTRODUCTION: Hexostoma auxisi Palombi, 1943 was originally described by Palombi (1943) from Auxis thazard off Italy, Mediterranean Sea. The original description of this species lacks morphological and morpho-metrical data. In addition, no published sequence of this species is available in molecular engines.<br><br>MATERIALS AND METHODS: Specimens of Hexostoma auxisi were collected from the gills of Auxis rochei (Risso, 1810) off the Algerian coast, Western Mediterranean. Monogenean were stained with acetic carmine, measured and drawn. Furthermore, molecular study was conducted using partial fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) of parasites and a tissue sample of the fish's gills on which the monogeneans were found.<br><br>RESULTS: In this study, we provide morpho-anatomical and morpho-metrical data of Hexostoma auxisi. Our specimens are morphologically close to those described by Palombi (1943) off Italy, Mediterranean Sea. The morphological study was supported by a molecular analysis of cox1 gene that reveals that our sequence of H. auxisi is distinct from its congener H. thynni by 20.51%.<br><br>CONLUSION: The present study allowed us to confirm the taxonomic status of Hexostoma auxisi which belongs to the genus Hexostoma and the family Hexostomatidae.}, }
@article {pmid41238550, year = {2025}, author = {Yadav, RP and Xing, P and Zhao, M and Hollander, P and Strell, C and Xie, M and Salehi, M and Torell, E and Sjöblom, T and Enblad, G and Amini, RM and Swartling, FJ and Glimelius, I and Micke, P and Hellström, M and Chen, X}, title = {scFFPE-ATAC enables high-throughput single cell chromatin accessibility profiling in formalin-fixed paraffin-embedded samples.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {10022}, pmid = {41238550}, issn = {2041-1723}, support = {2024-03756//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 24 3484 Pj//Swedish Cancer Foundation/ ; 22 0491 JIA//Swedish Cancer Foundation/ ; KAW 2023.0046//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; KAW 2024.0166//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, mesh = {Humans ; *Chromatin/metabolism/genetics ; Animals ; *Paraffin Embedding/methods ; Formaldehyde/chemistry ; Mice ; *Single-Cell Analysis/methods ; Tissue Fixation/methods ; Transposases/metabolism/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Epigenesis, Genetic ; Lung Neoplasms/genetics/pathology ; Lymph Nodes/pathology/metabolism ; Spleen ; Lymphoma, Large B-Cell, Diffuse/genetics/pathology ; }, abstract = {Formalin-fixed paraffin-embedded (FFPE) samples are the gold standard for tissue preservation in clinical and research settings. Current single-cell chromatin accessibility technologies cannot resolve cell-type-specific epigenetic profiles in FFPE tissues due to extensive DNA damage. We present scFFPE-ATAC, a high-throughput single-cell chromatin accessibility assay for FFPE samples that integrates an FFPE-adapted Tn5 transposase, ultra-high-throughput DNA barcoding (>56 million barcodes per run), T7 promoter-mediated DNA damage repair, and in vitro transcription. We benchmark scFFPE-ATAC on FFPE mouse spleen and validate its performance against fresh tissue. We apply it to human lymph node samples archived for 8-12 years and to lung cancer FFPE tissues, revealing distinct regulatory trajectories between tumor center and invasive edge. Analysis of archived follicular lymphoma and transformed diffuse large B-cell lymphoma samples identifies relapse- and transformation-associated epigenetic dynamics. scFFPE-ATAC enables retrospective, spatial, and mechanistic epigenetic studies in long-term archived specimens.}, }
@article {pmid41236296, year = {2025}, author = {Albogami, A}, title = {Genetic diversity and phylogenetic structure of Marawh and Bidah pomegranate landraces from Al-Baha, Saudi Arabia, using ITS DNA barcoding.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {10}, pages = {89-93}, doi = {10.14715/cmb/2025.71.10.12}, pmid = {41236296}, issn = {1165-158X}, mesh = {Saudi Arabia ; *Phylogeny ; *Pomegranate/genetics/classification ; *Genetic Variation ; *DNA Barcoding, Taxonomic/methods ; DNA, Plant/genetics ; }, abstract = {Pomegranate (Punica granatum L.) plays a vital cultural and economic role in the Al-Baha region of Saudi Arabia. Despite its significance, limited molecular data exist on the genetic structure of local landraces, particularly the distinct red and green fruit colour variants of the Marawh and Bidah cultivars. This study investigates the genetic diversity and phylogenetic relationships among these landraces using the nuclear internal transcribed spacer (ITS) DNA region. Maximum likelihood phylogenetic tree construction and network analysis (SplitsTree) were employed. Results reveal that red- and green-fruited landraces cluster into distinct clades, with red variants exhibiting reticulate patterns suggestive of introgression or incomplete lineage sorting. Genetic distance analysis confirmed a high similarity (~99.15%) between the green variants, despite their placement in separate clades. The findings provide crucial insights into the evolutionary history, cultivar authentication, and conservation strategies for pomegranate germplasm in Al-Baha. Future directions include genome-wide SNP analyses and expanded sampling to refine our understanding of these valuable genetic resources.}, }
@article {pmid41234542, year = {2025}, author = {Lapeva-Gjonova, A and Pramatarova, M and Borowiec, L and Gjonov, I and Kostova, R and Bekchiev, R and Borissov, S}, title = {DNA barcoding of Messor ants of Bulgaria with insights into their taxonomic diversity.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e168586}, pmid = {41234542}, issn = {1314-2828}, abstract = {BACKGROUND: Despite ongoing efforts to catalogue European ant species, studies focusing on the genetic diversity of Balkan ants remain limited. An integrative approach combining morphology, genetics, ecology and biogeography is preferable for accurately identifying species and resolving taxonomic uncertainties, particularly amongst challenging insect taxa, such as the ants in the genus Messor (Hymenoptera, Formicidae).<br><br>NEW INFORMATION: In this study, we analyse ants of the genus Messor using DNA barcode sequences, with a particular focus on the Bulgarian fauna. A total of 85 COI sequences were examined, including 84 from Messor specimens and one from Aphaenogaster, which was used as an outgroup. Of these, 81 sequences were newly generated, while four were retrieved from GenBank. The majority of specimens were collected in Bulgaria (61), with additional samples from Greece (13), T&#xfc;rkiye (4), Albania (1) and North Macedonia (2), providing broader genetic and geographic representation.Althogether, 11 Messor morphospecies were identified, based on specimens used for molecular analysis. To assess the degree of congruence between morphological and molecular data, six species delimitation analyses were conducted: RESL, GMYC, ASAP, ABGD, bPTP and mPTP. In addition, haplotype network analysis of all sequences identified 35 distinct and coherently clustered haplotypes, providing insights into genetic diversity.The COI barcode region successfully distinguished Messor wasmanni Krausse, 1910, M. oertzeni Forel, 1910 and M. ibericus Santschi, 1931. In contrast, species pairs, such as M. atanassovii Atanassov, 1982 and M. creticus Salata &amp; Borowiec, 2019, as well as M. ponticus Steiner et al., 2018 and M. hellenius Agosti &amp; Collingwood, 1987, could not be reliably differentiated using COI data. Furthermore, Messor structor (Latreille, 1798) showed high intraspecific genetic diversity. Finally, the structor and instabilis species groups were recovered with moderate to high support in both Maximum Likelihood and Bayesian Inference analyses, confirming that M. oertzeni and M. hellenius belong to the structor group.Our results provide a reference for future research and underscore the value of integrative taxonomic approaches in ant biodiversity studies.}, }
@article {pmid41233723, year = {2025}, author = {Ollivier, M and Marquisseau, A and Dufrêne, E and Rudelle, R and Rougerie, R and Perrard, A and Pichon, M and , }, title = {CODABEILLES: a reliable reference library of COI DNA barcodes for French wild bees monitoring (Apoidea: Anthophila).}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {121}, pmid = {41233723}, issn = {2730-7182}, support = {ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; ANR-22-CE02-0028//ANR JCJC/ ; }, abstract = {UNLABELLED: In the Anthropocene, the decline of insect pollinators poses a significant threat to ecosystem services, particularly to wild bee populations essential for plant biodiversity and agricultural productivity. France, with 983 species, hosts one of the most diverse bee faunas in Europe, yet these species face growing pressures from habitat loss, climate change, and intensive agriculture. Addressing this crisis requires robust taxonomic frameworks and efficient species identification methods to support long-term monitoring initiatives such as the European Pollinator Monitoring Scheme, EU-PoMS. DNA barcoding, utilizing the COI-5P gene, has proven effective for species delineation and biodiversity monitoring, particularly in detecting cryptic diversity among genera with large numbers of species such as Andrena, Nomada or Lasioglossum. However, significant gaps remain in reference libraries, particularly for the species from the Mediterranean Basin. To bridge this gap, the CODABEILLES initiative was launched in 2021 to enhance barcode data for the French bee fauna. Initially, only 25% of species had barcodes from French voucher specimens, increasing to 62% when considering voucher specimens from other countries. By 2025, thanks to collaboration with sixteen specialists and institutions, CODABEILLES contributed 1477 reference barcodes, covering approximately 560 species and raising barcode coverage to 82%. When integrating data published under other initiatives over the same period the coverage reaches 94% of the French bee fauna. This dataset significantly enhances species identification accuracy and supports large-scale pollinator monitoring through metabarcoding and environmental DNA approaches. Despite the success of COI-5P barcoding, taxonomic inconsistencies persist, necessitating further integrative research. This study underscores the need for continued collaboration among taxonomists, molecular biologists, and conservationists to refine species classifications and ensure comprehensive reference databases. The improved barcode coverage provided by CODABEILLES paves the way for more accurate DNA-based monitoring of wild bee populations and their ecological interactions, crucial for guiding conservation strategies in the face of ongoing environmental change.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12862-025-02429-0.}, }
@article {pmid41233332, year = {2025}, author = {Comstock, WJ and Navarro, MVAS and Maybee, DV and Rho, Y and Wagner, M and Jaber, K and Wang, Y and Smolka, MB}, title = {Proteomic sensors for quantitative multiplexed and spatial monitoring of kinase signaling.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9902}, pmid = {41233332}, issn = {2041-1723}, support = {R35GM141159//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01HD095296//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F31CA281247//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, mesh = {*Proteomics/methods ; *Signal Transduction ; Humans ; Checkpoint Kinase 1/metabolism ; Ataxia Telangiectasia Mutated Proteins/metabolism/genetics ; Peptides/metabolism/chemistry ; *Biosensing Techniques/methods ; Protein Kinases/metabolism ; Mass Spectrometry ; DNA Damage ; }, abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we develop a proteomic kinase activity sensor technique (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a versatile system for systematically and spatially probing kinase action in cells.}, }
@article {pmid41232800, year = {2025}, author = {Ma, P and Ma, H and Li, J and Bi, W and Zhang, S and Hou, W and Xu, H}, title = {Combinatorial chemistry and click chemistry for the optimization of lipid nanoparticles to enhance RNA delivery.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {104532}, doi = {10.1016/j.drudis.2025.104532}, pmid = {41232800}, issn = {1878-5832}, abstract = {Lipid nanoparticle (LNP)-based gene therapy holds great promise to revolutionize modern medicine. To address the challenges associated with LNP-based mRNA delivery, we systematically examine combinatorial chemistry approaches that facilitate the rapid synthesis of ionizable lipid libraries for high-throughput LNP screening, the application of click and bioorthogonal chemistry for the surface modification of LNPs with targeting ligands, and recent advances in barcoding technologies enabling comprehensive in vitro and in vivo evaluation of LNP performance. Furthermore, we outline the key design considerations and crucial challenges associated with developing LNPs for effective mRNA delivery, and propose strategic approaches to expand lipid libraries and enhance high-throughput screening (HTS) capabilities.}, }
@article {pmid41229993, year = {2025}, author = {Tongkerd, P and Janjai, T and Pholyotha, A and Gojšina, V and Panha, S and Sutcharit, C}, title = {The microsnail genera Clostophis and Acinolaemus (Eupulmonata, Pupilloidea, Hypselostomatidae) from central Thailand, with description of three new species.}, journal = {ZooKeys}, volume = {1258}, number = {}, pages = {35-71}, pmid = {41229993}, issn = {1313-2989}, abstract = {Hypselostomatid microsnails of the genera Clostophis and Acinolaemus from limestone hills in central Thailand were studied and three new species are described. Clostophis rhynchotes Tongkerd &amp; Panha, sp. nov. is diagnosed by a conical spire, long and descending tuba, 14 spiral striations on the last whorl, and only a single parietal lamella. In addition, a previously known species, C. proboscideus, is redescribed, and variations in its apertural dentition are also documented. In the genus Acinolaemus, two new sympatric species that clearly differ in shell shape are described. Acinolaemus rhamphodontis Tongkerd &amp; Panha, sp. nov. is characterised by a depressed conical spire with a long and descending tuba, and eight apertural dentitions, while A. corusticorus Tongkerd &amp; Panha, sp. nov. possesses a conical shell without a tuba and nine apertural dentitions. Specimens from the type locality of A. ptychochilus (the type species), A. cryptidentatus and A. mueangonensis are re-described and compared with the new species. The living snails of A. mueangonensis and A. rhamphodontis Tongkerd &amp; Panha, sp. nov. possess blackish to translucent bodies. In addition, COI barcoding data for Clostophis and Acinolaemus are provided for the first time.}, }
@article {pmid41227545, year = {2025}, author = {Xue, F and Zhu, X and Qin, L and Guo, Y and Sun, J and Dang, Z and Hua, L and Chu, B and Hua, R}, title = {Sex-Based Dietary Divergence in Plateau Pikas (Ochotona curzoniae) but Not Plateau Zokors (Eospalax baileyi).}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {21}, pages = {}, pmid = {41227545}, issn = {2076-2615}, support = {GAU-QDFC-2024-02//Bin Chu/ ; 32201478//Bin Chu/ ; }, abstract = {Quantifying sex-specific dietary differences in small mammals reveals the internal resource allocation mechanisms within a species and provides new insights for ecosystem management and conservation practices. The plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi) are dominant small mammals that exhibit distinct lifestyles and social structures on the Qinghai-Tibetan Plateau. Despite the fact that the diets of both species have been extensively studied, sex-specific dietary differences have rarely been investigated. This study employed DNA metabarcoding combined with a self-constructed plant DNA barcode database to analyze the diet composition and trophic niche of male and female plateau pika and plateau zokor during the growing season. The results showed that male and female plateau pika consumed 39 and 37 plant species, respectively, and male and female plateau zokor consumed 38 and 39 plant species, respectively. With respect to the plateau pika, males showed a significantly higher intake of Phlomoides umbrosa than females (p < 0.05), whereas females consumed a significantly greater proportion of tuberous plants (p < 0.05). Females also exhibited a significantly greater dietary diversity and trophic niche breadth than males. But there was no significant difference in dietary diversity and trophic niche breadth between the sexes in the plateau zokor. In conclusion, our results show that dietary differences between males and females depend on each species' lifestyle. Social, surface-living pikas show apparent sex-based differences, while solitary, underground-living zokors do not.}, }
@article {pmid41223485, year = {2025}, author = {Zhao, M and Song, H and Zheng, Y and Qin, L and Liu, X and Deng, S and Liu, J and Chen, L and Du, W and Wang, Z}, title = {A proof-of-principle study: Species identification based on mitochondrial 12S rRNA gene using QNome nanopore sequencing.}, journal = {Forensic science international. Genetics}, volume = {81}, number = {}, pages = {103388}, doi = {10.1016/j.fsigen.2025.103388}, pmid = {41223485}, issn = {1878-0326}, abstract = {Accurate species identification can provide crucial evidence to aid criminal investigations and preserve species diversity. DNA barcoding is an effective tool to ascertain the origin of degraded, trace, or processed samples, and the mitochondrial 12S rRNA gene serving as a potential marker due to its low intraspecific variation and high interspecific variation. QNome nanopore sequencing, with its flexible read lengths, real-time analysis, and portable device size, offers new means for species identification. In this proof-of-principle study, we collected 12S rRNA gene reference sequences of 120 common species from Genbank genetic sequence database and conducted sequence similarity analysis to evaluate the applicability of this genetic marker. The automated species identification pipeline, ClassIdent, based on QNome nanopore sequencing of the 12S rRNA gene, was subsequently developed as an open-source tool. We sequenced 60 tested samples from different animals using the QNome sequencer, and ClassIdent was employed to detect matching proportions and generate consensus sequences. Out of the 60 tested samples, 53 matched the sequences of their corresponding species, while the remaining seven matched sequences from closely related species within the same genus or family. The average proportion of sequencing reads assigned to the reference sequence was 95.66 %, with an average sequence similarity of 99.11 %. The consensus sequences generated by ClassIdent demonstrated high accuracy, showing an average sequence similarity of 99.34 % compared to Sanger sequences. Overall, this pipeline demonstrated the potential of using 12S rRNA gene for species identification via Qnome nanopore sequencing. However, further research is needed to incorporate more DNA barcoding markers or to detect the whole mitochondrial genome based on long read sequencing technology.}, }
@article {pmid41223244, year = {2025}, author = {Pontes, A and Silva, MR and Rutkowski, D and Carvalho, C and Coito, J and Capela, N and Groenewald, M and Brito, PH and Gonçalves, C and Vannette, RL and Sampaio, JP}, title = {Zygosaccharomyces progenitor sp. nov., a new yeast species associated with bees of the genera Apis and Bombus.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006957}, pmid = {41223244}, issn = {1466-5034}, mesh = {Animals ; *Phylogeny ; Bees/microbiology ; DNA, Fungal/genetics ; Sequence Analysis, DNA ; Mycological Typing Techniques ; *Zygosaccharomyces/classification/genetics/isolation &amp; purification ; Japan ; DNA Barcoding, Taxonomic ; Portugal ; United States ; Honey/microbiology ; Genome, Fungal ; }, abstract = {A novel ascomycetous yeast species of the genus Zygosaccharomyces is proposed, based on isolates obtained in Japan, Portugal and the USA, and on a combination of conventional DNA barcode sequence analyses and whole-genome phylogenies. The new species is described as Zygosaccharomyces progenitor sp. nov. (PYCC 7198[T]) and was found in association with bees (Apis mellifera and Bombus spp.) and their honey, besides being found in plants and soil. The novel species belongs to a Zygosaccharomyces subclade that also harbours Zygosaccharomyces rouxii. Although the two species can be differentiated at the sequence level, they cannot be distinguished at the phenotypic level. As is typical of the genus, Z. progenitor sp. nov. produces spherical ascospores after cell conjugation.}, }
@article {pmid41222779, year = {2025}, author = {Wei, R and Li, Q}, title = {Comparative plastomes and phylogenetic relationships of Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon from plastomes and ITS.}, journal = {Genetica}, volume = {153}, number = {1}, pages = {33}, pmid = {41222779}, issn = {1573-6857}, mesh = {*Phylogeny ; *Genome, Plastid ; Evolution, Molecular ; *Phyllanthus/genetics/classification ; RNA, Transfer/genetics ; *Plastids/genetics ; RNA, Ribosomal/genetics ; }, abstract = {Phylogenomic approaches effectively minimize topological incongruences caused by heterogeneous gene evolutionary rates among lineages. The taxonomic status of Breynia, Glochidion, Synostemon, and Sauropus-whether they should be merged into Phyllanthus or retain their separate generic status-remains controversial. Moreover, these taxonomic revisions lack evidences from phylogenomic evidence. In this study, we assembled the first complete plastid genomes of Breynia disticha, Glochidion eriocarpum, G. hirsutum, G. lanceolarium, Phyllanthus fluitans, Sauropus androgynus, and Synostemon bacciformis to elucidate plastome evolutionary dynamics and resolve phylogenetic relationships among these five genera. The plastomes ranged in size from 152,927 to 157,460 bp, encoding a conserved set of 78 protein-coding genes, 35-36 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes, totaling 117-118 unique genes. Notably, 12 novel tRNA secondary structures were identified, potentially linked to lineage-specific adaptations. Structural variation at the LSC/IRb boundary, driven by IRb expansion-contraction dynamics, resulted in significant gene length and content heterogeneity. Divergence hotspot analyses identified petA-psbJ, rpl22, ndhF-rpl32, and ycf1 as hypervariable loci suitable for DNA barcoding applications. Positive selection signals were detected in five genes (ndhB, rpl33, rps15, ycf2, ycf4), suggesting their critical roles in environmental adaptation. Phylogenomic discordance between plastid and nuclear ribosomal DNA (nrDNA) datasets was pervasive across Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon, likely attributable to historical hybridization or chloroplast capture events. Given that the intergeneric boundaries among Breynia, Glochidion, Phyllanthus s.s., Sauropus, and Synostemon are obscure and that extensive cytonuclear discordance exists, we recommend accepting a broad circumscription of Phyllanthus.}, }
@article {pmid41219063, year = {2025}, author = {Hulevata, I and M Porteiro, F and Giacomello, E and Catarino, D}, title = {On the occurrence of the snakefish Trachinocephalus myops (Aulopiformes: Synodontidae) in the Azores archipelago.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70266}, pmid = {41219063}, issn = {1095-8649}, support = {UIDB/05634/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/05634/2025//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/05634/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; M1.1.A/FUNC.UI&amp;D/003/2021-2024//Azores Government/ ; M1.1.A/REEQ.CIENT&#xcd;FICO UI&amp;D/2021/010//Azores Government/ ; }, abstract = {The snakefish Trachinocephalus myops is an Atlantic species distributed in tropical and temperate coastal waters on sandy substrates. This study reports the validated record of an adult T. myops in the Azores archipelago caught by a fisherman at Faial Island. Meristic, morphometric characters and molecular analyses supported species identity. The possibilities of recurrent misidentification or recent colonization of the species in the region and its biogeographic affinities are discussed. T. myops is hereby included as a native species in the Azores.}, }
@article {pmid41218139, year = {2025}, author = {He, L and Dang, K and Sun, Q and Wang, W and Li, W and Zhang, W and Ye, K and Wang, H and Li, Z and Guo, Y and Li, Z and Yao, C and Li, P and Huang, Y and Zhao, X}, title = {High-Resolution Multiplexed Sequencing of Single-Cell Full-length Transcriptome Via Combinational Barcoded Tn5 Transposon Insertion.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e16013}, doi = {10.1002/advs.202516013}, pmid = {41218139}, issn = {2198-3844}, support = {82361138570//National Natural Science Foundation of China/ ; 81827901//National Natural Science Foundation of China/ ; 32371393//National Natural Science Foundation of China/ ; 2022YFC2702701//National Key R&amp;D Program of China/ ; }, abstract = {The technological advancements in single-cell transcriptome analysis make significant progress in both depth and breadth. However, balancing the cell analysis throughput with full-length transcript coverage remains a persistent challenge. Here, CBTi-seq (Combinational Barcoded Tn5 Transposon Insertion sequencing) is reported, leveraging Tn5 transposase-mediated molecular assembly of combinatorial barcodes and unique molecular identifiers (UMIs) to enable high-resolution multiplexed sequencing of the full-length transcriptome in single cells. This approach achieves molecular resolution by end-to-end sequencing, enabling unambiguous reconstruction of splice variants and structural variations with base-pair precision. The design of orthogonal combination barcode Tn5 reduces DNA barcode diversity while enhancing multiplexing flexibility, and Tn5-delivered UMIs insertion eliminates read bias, providing accurately quantifies transcript abundance through the tagging of each fragment. The method is compatible with both single-cell and spatially resolved tissue microenvironment. Compared with commercial terminal library and other full-length sequencing methods, CBTi-seq achieves superior sensitivity and resolution while significantly reducing costs and work time (≈5 h). Moreover, cell-type-specific alternative splicing patterns are robustly identified in both gene-edited cells and human testicular cells, leveraging this high-resolution capability to further reveal modality dynamic events and isoform switching independent of gene expression changes during spermatogenesis with the potential to reproductive development and diagnostic treatment.}, }
@article {pmid41218017, year = {2025}, author = {Patterson, EC and Morrison-Lanjouw, S and Jobling, MA and Wetton, JH}, title = {Rapid on-site universal vertebrate species identification via multi-barcode nanopore sequencing.}, journal = {PloS one}, volume = {20}, number = {11}, pages = {e0336383}, pmid = {41218017}, issn = {1932-6203}, abstract = {The growing illegal wildlife trade (IWT) threatens biodiversity and is a conduit for zoonotic disease, yet its risk of detection is low. Once processed, trafficked species are difficult to identify morphologically, and currently require DNA-based approaches that are time-consuming, costly, and lab-based. There is thus a need for a rapid, cheap, on-site method for species identification. We describe VeRIF-ID (Vertebrate Rapid In-Field Identification via DNA), a method that employs simultaneous on-site nanopore sequencing of four different mitochondrial DNA barcodes. Primers were designed to produce short amplicons to aid analysis of damaged DNA, and to be effective over a broad taxonomic range of vertebrates from lamprey to chimpanzee. Validation demonstrated species-level identification in 91% of 83 tested species, and genus/tribe-level identification of the remaining species (which are also problematic with existing approaches). DNA extraction, PCR and library preparation steps were simplified and optimised so that sampling to species identification takes <3 h for a single sample. Species components are identifiable non-quantitatively in prepared mixtures of muscle tissue from up to five species, and laboratory tests of Traditional East Asian Medicine samples reveal DNA from species including critically endangered saiga antelope and black rhinoceros. In conjunction with a portable Bento Lab device the necessary equipment and reagents are easily portable, and we apply the method to analyse seized bushmeat and fish samples within an airport customs zone, identifying mammal and fish species in 15 samples within 6 h. The initial equipment costs for VeRIF-ID are ~ $8K, and the cost per sample of ~$10-48 (depending on set-up), considerably cheaper than current conventional lab-based approaches. The method requires only basic hands-on skills. Ongoing trials with potential end-users will focus on establishing forensic reporting criteria prior to casework implementation. Future development of user-friendly bioinformatic interfaces will aim to fully democratise species identification.}, }
@article {pmid41216496, year = {2025}, author = {Zhou, LN and Wu, SZ and Ma, Q and Jia, XW and Li, P and Jin, XJ and Zhang, YH}, title = {Phylogenomic Analyses and DNA Barcoding Development Within Moraceae: Insights Into Genomic Features, Mutational Hotspots, and Adaptive Evolution.}, journal = {Ecology and evolution}, volume = {15}, number = {11}, pages = {e72399}, pmid = {41216496}, issn = {2045-7758}, abstract = {Moraceae, with its seven tribes, 45 genera, and approximately 1200 species, is of significant value in food, medicine, ecological restoration, and as a source of industrial raw materials. However, determination of the taxonomy and phylogeny of Moraceae species remains challenging due to their diverse morphological features. To address this issue, we sequenced seven complete plastomes and analyzed online datasets for 46 other species at the tribal level within Moraceae. Our analysis revealed that all the plastomes within this family had a typical quadripartite structure and ranged from 158,459 to 162,594 bp in length. Comparative plastome analyses revealed 10 highly variable regions (ndhF-rpl32, rps4-trnT, rps15-ycf1, trnC-petN, ycf1). A total of 5350 dispersed and tandem repeats along with 4751 simple sequence repeats (SSRs) were identified, highlighting their potential for the development of molecular markers in Moraceae. While the evolutionary rates across the various tribes of Moraceae were found to be similar, the genes ndhK, ndhD, rps2, and rps12 displayed evidence of positive selection. Codon usage bias was shaped by mutation and selection, with significant natural selection observed on genes such as clpP, ndhC, ndhI, etc. Additionally, 13 optimal codons were identified for 10 genes. This study confirms that the seven tribes within the Moraceae family are monophyletic, with divergence estimated to have occurred approximately 79.43 million years ago. This timing coincides with the formation of modern rainforests and a burst in angiosperm diversity toward the end of the Cretaceous period. Overall, the resolution of Moraceae tribal-level phylogeny provides a foundational framework for revising taxonomic classifications. Furthermore, our genomic resources will be available for genetic engineering and germplasm exploration within this versatile plant family.}, }
@article {pmid41210971, year = {2025}, author = {Wu, JW and Yang, M and Chen, CC and Au, G and Wang, S and Xu, Y and Chern, GW and Huang, CH}, title = {Robust calibration and quantification of FRET signals using multiplexed biosensor barcoding.}, journal = {iScience}, volume = {28}, number = {11}, pages = {113743}, pmid = {41210971}, issn = {2589-0042}, abstract = {Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) underpins many genetically encoded fluorescent biosensors for monitoring biochemical activities in live cells. However, the FRET ratio (acceptor-to-donor signal ratio), commonly used as a proxy for FRET efficiency, is highly sensitive to imaging parameters, complicating data interpretation. Using FP-based barcodes, we introduced calibration standards into subsets of cells for normalization of fluorescence signals. Theoretical analysis indicated the need for both high- and low-FRET standards for calibration under different excitation intensities. We validated this prediction using engineered "FRET-ON" and "FRET-OFF" standards, demonstrating that calibrated FRET ratios are independent of imaging conditions. Including donor-only and acceptor-only cells enabled simultaneous determination of FRET efficiency for multiple biosensors. Calibration also restored expected reciprocal changes in donor and acceptor signals, often obscured by imaging fluctuations and photobleaching. Together, our studies introduce a simple strategy for robust, multiplexed FRET biosensor imaging, facilitating cross-experimental and long-term studies.}, }
@article {pmid41210617, year = {2025}, author = {Neo, I and Loh, RK and Cho, TJY and Puniamoorthy, N and Yeo, DCJ and Tan, MK}, title = {First DNA barcodes and morphometric analysis of Singaporean Tetrigidae (Orthoptera, Caelifera) support color variations as intraspecific polymorphism through integrative taxonomy.}, journal = {ZooKeys}, volume = {1257}, number = {}, pages = {305-326}, pmid = {41210617}, issn = {1313-2989}, abstract = {Integrative taxonomy refers to the practice of incorporating multiple lines of evidence, including morphology and genetics, to delineate species. While both morphology and genetic markers, such as the Cytochrome c oxidase subunit I (COI), have been widely applied in insect taxonomy, their use remains limited in the taxonomic studies of pygmy grasshoppers (Orthoptera: Tetrigidae). Currently, DNA barcodes for tetrigids, especially from Southeast Asia, remain scarce. This limitation is especially pressing given the extensive color variation documented in pygmy grasshoppers, which has rarely been systematically tested to determine whether such variation represents intraspecific polymorphisms or species differences. Historically, color polymorphism has even led to erroneous species delimitation. In this study, we examined taxa from Singapore previously reported to exhibit color variation and applied an integrative taxonomic framework to investigate whether these morphs represent intraspecific polymorphism or species-level differences. Our analyses combined morphometrics of 22 characters with principal component analyses, and DNA barcoding using short gene fragments of COI and small ribosomal RNA subunit III (12S). We focused on four taxa: two morphospecies of Coptotettix, Loxilobus insidiosus (Bolívar, 1887), and Thoradonta nodulosa (Stål, 1861). DNA barcoding revealed that color morphs are genetically similar, and morphometric analysis likewise showed no distinct clustering. Together, these results indicate that different color morphs indeed represent intraspecific polymorphisms. More importantly, we demonstrate that combining molecular data with morphological evidence offers an effective, integrative framework for resolving taxonomic challenges within tetrigids and highlights the value of integrative approaches for clarifying species boundaries in morphologically variable taxa.}, }
@article {pmid41210614, year = {2025}, author = {Theron, GL and Ellis, AG and Midgley, JM}, title = {A revision of a spring-active clade of Prosoeca Schiner, 1867 (Diptera, Nemestrinidae), keystone pollinators from the Greater Cape Floristic Region in South Africa, with descriptions of three new species.}, journal = {ZooKeys}, volume = {1257}, number = {}, pages = {249-284}, pmid = {41210614}, issn = {1313-2989}, abstract = {Prosoeca Schiner, 1867 is the most diverse genus of Nemestrinidae in Africa and is endemic to southern Africa. The 37 described species in this genus are all thought to be important pollinators for the plants that they visit. A recent phylogenetic study has shown that the diversity of this group is far larger than is formally recognised. Using of the phylogeny published by Theron et al. (2020), the monophyletic clade of six species from the Succulent Karoo that are on the wing during the spring flowering season are revised. The known species are redescribed and three new species are described: Prosoeca ora sp. nov., P. aquilo sp. nov., and P. parva sp. nov. A lectotype is designated for Prosoeca peringueyi Lichtwardt, 1920. DNA barcodes have been generated for five species to aid molecular identification of species.}, }
@article {pmid41210188, year = {2025}, author = {Lv, X and Zhang, X and Azad, R and Zaman, M}, title = {Biosystematics of Angulitermes dehraensis in the Northwestern Indomalayan region by integrating morphometrics and distributional data with DNA barcoding.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1695789}, pmid = {41210188}, issn = {2673-8600}, abstract = {Termites are eusocial and economically important insects which are found in the world's tropical regions as a harmful or beneficial organism. They play a dual role, both as pests damaging crops and urban structure and as an ecological engineer sustaining the ecosystem. Pakistan is part of the Indomalayan realm hosting diverse flora and fauna including termites; however, the status (diversity, distribution, feeding hosts, pest and non-pest) of the genus Angulitermes in the northwestern region (Khyber Pakhtunkhwa, Pakistan) has been largely neglected. Termite cultures were collected from diverse ecosystems, cleaned, and preserved in alcohol-filled vials for subsequent morphometric identification and DNA barcoding. Coordinates with relevant ecological data were also recorded. Soldiers were used for capturing refined images and morphometric identification through available literature, which resulted as an Angulitermes dehraensis and a new locality record. A revised and updated world's species list for the genus was made along with the distribution map of this study via ArcGIS. The identified representative soldier's leg was processed for mtDNA extraction followed by amplification and sequencing. The received sequence was subjected to BLASTn search, and only top 15 sequences via BLASTn search and then via manual search for taxon Angulitermes were retrieved from GenBank. Aligned and trimmed sequences were processed for phylogenetic tree (neighbor-joining and maximum-likelihood) construction and validation of understudy species sequence analogy. A novel sequence was submitted to GenBank for accession number (PX423737). Based on the available and recorded feeding host substrate data, it is a pest species which needs management.}, }
@article {pmid41209357, year = {2025}, author = {Fraga Dornellas, L and Mata, VA and Mendes, S and Leitão, R and Bartz, M and Nascimento, E and Costa, J and Sousa, JP and Cunha, L}, title = {Establishing DNA-Based Strategies for Soil Biodiversity Assessment: Insights From Carabid Beetles.}, journal = {Ecology and evolution}, volume = {15}, number = {11}, pages = {e72461}, pmid = {41209357}, issn = {2045-7758}, abstract = {Molecular-based methods offer valuable opportunities for assessing soil biodiversity in different ecosystems. However, their reliability and large-scale applicability depend on developing, optimizing protocols and establishing high quality, curated local reference databases. This study aimed to evaluate key steps in soil macroinvertebrate metabarcoding workflow, including the sample decontamination process and the efficiency of taxa recovery. Specifically, we sought to: (1) determine the impact of sample decontamination, (2) validate species-level recovery efficiency of the metabarcoding pipeline spiked with a curated mock community of morphologically identified and barcoded carabid beetles, and (3) compare traditional morphological identification and metabarcoding for specimens' taxonomic assignment and recovery. Our results showed that the commonly used decontamination process did not significantly impact OTU richness, suggesting it is not essential for this fauna. Compared to morphology, to metabarcoding provided a more comprehensive taxonomic overview at higher level taxa. However, validation with the mock community revealed discrepancies in species-level recovery, underscoring that its accuracy is highly contingent on the quality of the reference database. DNA metabarcoding is a currently used and promising technique for macroinvertebrate assessment regarding time, efficiency, and costs, yet reaching greater depth in taxonomic resolution. Yet, its species-level accuracy remains dependent on comprehensive and well-curated barcode reference databases. We recommend an integrative approach, combining molecular data with targeted validation, for the most robust outcomes. For this reason, we recommend the use of integrative methodologies for robust and rapid biodiversity assessments. We found that the common decontamination step is not crucial for soil macrofauna metabarcoding accuracy. Consequently, its removal streamlines sample processing.}, }
@article {pmid41208904, year = {2025}, author = {Pykälä, J and Myllys, L}, title = {Unexpected species richness of the lichen genus Protoblastenia (Lecanorales, Psoraceae) in Finland.}, journal = {MycoKeys}, volume = {124}, number = {}, pages = {193-226}, pmid = {41208904}, issn = {1314-4049}, abstract = {The taxonomy of Protoblastenia in Finland was studied, based on morphology and molecular data (nuITS rDNA sequences). Twenty species were recognised, with sixteen species being newly described here: P. arupii sp. nov., P. borealis sp. nov., P. compressa sp. nov., P. dolomitica sp. nov., P. ekmanii sp. nov., P. fennoarctica sp. nov., P. minuta sp. nov., P. oulankaensis sp. nov., P. pseudocompressa sp. nov., P. pseudoterricola sp. nov., P. remota sp. nov., P. rikkinenii sp. nov., P. saanaensis sp. nov., P. timdalii sp. nov., P. violacea sp. nov. and P. westbergii sp. nov. All species are confined to calcareous rocks, except P. terricola which also grows on calcareous soil. The calcareous fells in Enontekiö in NW Finland were identified as hot spots of Protoblastenia diversity. Nine newly-described species (P. arupii, P. fennoarctica, P. minuta, P. pseudoterricola, P. rikkinenii, P. saanaensis, P. timdalii, P. violacea and P. westbergii) are restricted to this area in Finland. Several of the species are semi-cryptic. On average, they may have minor morphological differences, but many specimens cannot be identified, based on morphology only. Protoblastenia rikkinenii is reported from Norway and P. oulankaensis from Italy, based on GenBank sequences. Full descriptions and a preliminary key of Protoblastenia in Finland are provided.}, }
@article {pmid41204963, year = {2025}, author = {Diani Gohar, S and Soorni, A}, title = {Plastome diversity and phylogenomic analysis of Satureja (Lamiaceae): uncovering evolutionary patterns and diagnostic markers.}, journal = {Planta}, volume = {262}, number = {6}, pages = {149}, pmid = {41204963}, issn = {1432-2048}, mesh = {Phylogeny ; *Genome, Chloroplast/genetics ; *Satureja/genetics/classification ; Evolution, Molecular ; Genetic Markers ; Genetic Variation ; }, abstract = {The chloroplast genomes of Satureja are highly conserved but contain hypervariable loci like ndhF and ycf1. These loci provide powerful molecular tools for precise species identification, phylogenetic resolution, and future conservation efforts in this important genus. The genus Satureja (Lamiaceae) comprises a valuable number of aromatic herbs and shrubs with significant ecological, medicinal, and economic value, particularly in the Mediterranean and Southwest Asia. Satureja species are renowned for their therapeutic essential oils, yet their chloroplast (cp) genomic resources remain vastly understudied, with only S. montana complete cp genome available. To address this gap, we sequenced and analyzed the complete cp genomes of three taxonomically and ecologically distinct Satureja species (S. hortensis, S. khuzestanica, and S. montana subsp. variegata) and a new individual of S. montana, using Illumina sequencing and comparative genomic approaches. The assembled cp genomes exhibited a conserved quadripartite structure, with sizes ranging narrowly from 151,777 to 151,924 bp, featuring typical large (LSC) and small (SSC) single-copy regions flanked by inverted repeats (IRs). Genome annotation revealed 128-130 genes, including core photosynthetic and ribosomal genes, with notable interspecific variation in tRNA copy numbers. Comparative analyses identified hypervariable loci (ndhF, ycf1, petN) as promising DNA barcodes for species discrimination, while codon use bias strongly favored A/T-ending codons. Simple sequence repeats (SSRs) were predominantly mononucleotide (A/T), and long repetitive sequences showed species-specific length polymorphisms. Phylogenetic reconstruction using the whole cp genomes strongly supported the monophyly of Satureja and resolved infrageneric relationships with high bootstrap confidence (> 90%), placing these species in a distinct clade sister to Thymus and Mentha. Our study provides the first comprehensive cp genomic resource for Satureja, elucidating evolutionary patterns, identifying molecular markers for taxonomy, and establishing a foundation for future conservation and biotechnological applications in this economically important genus.}, }
@article {pmid41204855, year = {2025}, author = {Viruel, J and Sweeney, CJ and Day, R and White, K and Dawson, W and Myer, B and Floyd, K and Corcoran, M and Kelting, C and Poncet, S and Forest, F and Clubbe, C and Newton, RJ}, title = {Phylogenomic Barcoding of Soil Seed Bank-Persistent and Wind-Dispersed Non-Native Plant Species in South Georgia.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70068}, doi = {10.1111/1755-0998.70068}, pmid = {41204855}, issn = {1755-0998}, support = {DPLUS080//Darwin Initiative/ ; RYC2023-042611-I//MCIU/AEI/10.13039/501100011033 and FSE+/ ; }, abstract = {Climate change and invasive species are leading drivers of biodiversity loss, with island ecosystems being especially vulnerable. South Georgia, a remote sub-Antarctic island, is 170 km long with approximately 30,000 ha of vegetated coastal areas, as snow and ice dominate the inland regions. Human activities on the island have historically introduced non-native species, resulting in 41 introduced vascular plant species compared with only 24 native ones. To address this imbalance, the South Georgia Non-Native Plant Management Strategy was implemented (2016-2020) to control non-native plant populations. We assessed emergent seedlings from South Georgia soil samples and wind-dispersed seeds to determine which species persist in the soil seed bank and contribute to dispersal. Using a molecular barcoding approach, we evaluated traditional markers (rbcL and matK) and optimized a high-throughput Angiosperms353 sequencing pipeline for accurate seedling identification. We generated a reference library covering all native and non-native species and applied this to 1,498 emergent seedlings and 737 trapped seeds. Molecular barcoding identified 21 species, including 10 non-natives and 11 natives. Strikingly, 84% of emergent seedlings were non-native, with Class III invasive species (Cerastium fontanum, Poa annua, Taraxacum officinale) dominating across most sites and in all wind traps. By contrast, Class I and II species occurred rarely and only at a few sites, indicating that management efforts have substantially reduced their spread, though viable seeds persist in the soil. These findings highlight both the continued threat from persistent seed banks of dominant invaders and the value of molecular barcoding for long-term monitoring. Our approach provides a framework for biosecurity and restoration management in South Georgia and other vulnerable ecosystems under climate change pressures.}, }
@article {pmid41204321, year = {2025}, author = {Wang, Y and Xie, Y and Jin, J and Li, J and Lai, X and Qiu, X and Tong, Y and Zhang, Z}, title = {New insights into the phylogenetic and biogeographic analysis of Elaeocarpus (Elaeocarpaceae) in China, and further consolidated 'Acronodia' as a distinct group.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1524}, pmid = {41204321}, issn = {1471-2229}, support = {190781//Key Science and Technology Research Project in Jiangxi Province Department of Education/ ; 31110103911//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; China ; *Genome, Chloroplast/genetics ; Phylogeography ; DNA, Chloroplast/genetics ; }, abstract = {BACKGROUND: Elaeocarpus is the most species-rich genus in Elaeocarpaceae (Oxalidales), comprising 39 species of trees that grow in tropical and subtropical forests in China, 14 of which are endemic. Few studies to focus on the phylogeny of Elaeocarpus in China. Limited available evidence indicates a close phylogenetic relationship between Sect. Ganitrus and Sect. Dicera, while the question of whether the 'Acronodia' group warrants taxonomic separation from Sect. Monocera remains unresolved. The status of group 'Acronodia' in Elaeocarpus is uncertain because the combination of molecular fragments available to construct the phylogenetic tree has not been evaluated.<br><br>RESULTS: In this study, we compared chloroplast genome sequences on the basis of the alignment of 4 chloroplast genome sequences with the mVISTA and KaKs_Calculator tools. The results revealed that the phylogeny has good bootstrap value for ycf1, ITS and trnS-atpA and that 27 Elaeocarpus species (40 samples), including 3 species that are distributed naturally outside China, are grouped into 2 major clades: one comprising Sect. Ganitrus and Sect. Dicera, and the other consisting of Sect. Monocera and the 'Acronodia' group. Furthermore, the results of the phylogenetic analysis with the BEAST tool suggest that Elaeocarpus originated from Southwest China during the early Eocene (40&#xa0;Ma) and started to diversify south of the Yangtze River during the early Miocene (15&#xa0;Ma).<br><br>CONCLUSION: Overall, this study highlights the taxonomic utility of chloroplast genomes in Elaeocarpus, and the time and regions of origin will facilitate future studies on conservation.}, }
@article {pmid41203862, year = {2025}, author = {Dagher, M and Ongo, G and Robichaud, N and Kong, J and Rho, W and Teahulos, I and Tavakoli, A and Bovaird, S and Merjaneh, S and Tan, A and Edwardson, K and Scheepers, C and Ng, A and Hajjar, A and Sow, B and Vrouvides, M and Lee, A and DeCorwin-Martin, P and Rasool, S and Huang, J and Erps, T and Coffin, S and Rashidi, NM and Han, Y and Chandrasekaran, SN and Miller, L and Kost-Alimova, M and Skepner, A and Singh, S and Carpenter, AE and Munzar, JD and Juncker, D}, title = {nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {41203862}, issn = {1548-7105}, abstract = {Existing high-plex protein measurement tools compromise on quantification, precision and cost efficiency. Here, to address this, we present nELISA, a platform that combines a DNA-mediated, bead-based sandwich immunoassay with advanced multicolor bead barcoding. Antibody pairs are preassembled on target-specific, barcoded beads, which ensures spatial separation between noncognate assays. Detection antibodies are tethered via flexible single-stranded DNA to enable efficient ternary sandwich formation. Detection is achieved through toehold-mediated strand displacement, where fluorescently labeled DNA oligos simultaneously untether and label detection antibodies. nELISA delivers sub-picogram-per-milliliter sensitivity across seven orders of magnitude. Using a 191-plex inflammation panel, we profiled cytokine responses in 7,392 peripheral blood mononuclear cell samples, generating ~1.4 million protein measurements and revealing over 440 robust cytokine responses, including previously unreported effects. nELISA thus provides a simple, scalable and cost-efficient solution for large-scale, high-fidelity phenotypic screening.}, }
@article {pmid41203832, year = {2025}, author = {Lewis, SM and Berthelet, J and Whitehead, LW and Rajasekhar, P and El-Saafin, F and Bell, C and Naik, S and Merino, D and Wimmer, VC and Rogers, KL}, title = {LeGO-3D: 3D imaging of lung metastases and vascularisation using light sheet fluorescence microscopy.}, journal = {Npj imaging}, volume = {3}, number = {1}, pages = {58}, pmid = {41203832}, issn = {2948-197X}, support = {GNT2036844//National Health and Medical Research Council/ ; GNT2027459//National Health and Medical Research Council/ ; MCRF21011//Victorian Cancer agency/ ; IIRS0049//National Breast Cancer Foundation/ ; }, abstract = {Cancer metastasis involves a complex cascade of events, where cancer cells migrate from their site of origin to secondary sites via the lymphatic and circulatory system. During this process, some cancer subclones will successfully 'seed' at distant organs to generate lethal metastases. Here, we optimised a method for tracking cancer cells in metastatic breast cancer tumours and investigated their complex interplay with the lung vasculature using lentiviral-based optical barcoding (LeGO). Given the regional heterogeneity in lung tissue microenvironments as well as lobar asymmetry, we used light sheet microscopy to perform three-dimensional (3D) imaging of wholemount lung lobes. The results revealed that polychromatic metastases occurred less frequently than monochromatic metastases and were more likely to be located nearer to blood vessels in both spontaneous (i.e. mammary fat pad injections) and experimental (i.e. tail vein injections) mouse assays of metastasis. This 3D imaging and analytic pipeline can provide unique insights about metastatic heterogeneity and dynamics, and represents a new avenue for studying therapeutic response across large volumes of lung tissue.}, }
@article {pmid41202131, year = {2025}, author = {Liu, Y and Ban, Y and Gao, D}, title = {Oligo-CALL: A next-generation barcoding platform for studying resistance to targeted therapy.}, journal = {Science advances}, volume = {11}, number = {45}, pages = {eadw9990}, doi = {10.1126/sciadv.adw9990}, pmid = {41202131}, issn = {2375-2548}, mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; Cell Line, Tumor ; CRISPR-Cas Systems ; *Lung Neoplasms/genetics/drug therapy/pathology ; Single-Cell Analysis ; Molecular Targeted Therapy ; Proto-Oncogene Proteins p21(ras)/genetics/antagonists &amp; inhibitors ; }, abstract = {Understanding therapy resistance requires deconvolving heterogeneous cell populations and tracking clonal trajectories. While CRISPR-based cellular barcoding is powerful for lineage tracing, many platforms suffer from low efficiency and limited compatibility with single-cell transcriptomics. We developed Oligo-CALL (Oligonucleotide-inducible CRISPR transcriptional activator-Assisted Lineage Labeling), an advanced barcoding system enabling precise lineage tracing, live clone isolation, and seamless integration with single-cell RNA sequencing. Applied to lung cancer cells treated with a KRAS[G12C] inhibitor, Oligo-CALL identified clones consistently enriched posttreatment, supporting a model of predestined resistance. Oligo-CALL achieved >95% efficiency in linking lineage identity to transcriptomes, uncovering diverse clone-specific pathways with underlying resistance. Paired analysis of barcode-matched clones from naïve and resistant populations revealed transient and fixed resistance phenotypes. Notably, DNA repair pathways are recurrently altered in resistant clones, and inhibition of poly(adenosine 5'-diphosphate-ribose) polymerase synergizes with KRAS G12C inhibition to overcome resistance. Together, Oligo-CALL provides a versatile platform for dissecting lineage evolution and molecular dynamics of targeted therapy resistance.}, }
@article {pmid41198699, year = {2025}, author = {Lin, R and Xu, Y and Yang, S and Chen, S and Wang, Z and Wang, K and Gao, Z and Zhao, YS}, title = {Regioselective on-surface crystallization of one-dimensional organic barcode-like heterostructures of MOFs with fluorescent stripe patterns.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9810}, pmid = {41198699}, issn = {2041-1723}, support = {2022YFA1204403//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; }, abstract = {Heterostructures, integrating different semiconducting materials in a single structure, are key components for various modern electrical and optoelectronic devices. However, it is difficult to maintain the sequential epitaxial nucleation due to the passivation of crystal seeds, thus resulting in limited spatial segments in heterostructures. Here, we report an interface-recognition assembly strategy assisted by Plateau-Rayleigh instability (PRI) to spontaneously form one-dimensional (1D) heterostructures featuring abundant fluorescent stripe patterns. Guided by 1D metal-organic frameworks (MOFs) templates with exposed electron-donating sites, the de-wetting process promotes the effective regioselective crystallization of solute molecules with electron-withdrawing feature on template surface, thus forming 1D barcode-like heterostructures. The spatial locations and number of the stripes are effectively controlled by PRI and template parameters, while their emission colors are primarily governed by the charge-transfer (CT) interactions between solutes. On this basis, we have achieved full-color and heterogeneous stripe patterns by tuning the CT strengths and controlling the stripe nucleation sequences, thus creating abundant 1D barcode-like heterostructures. Through integrating the photoisomers into stripes, these heterostructures exhibit time-dependent graphical patterns and enable construction of 2D photonic barcodes. Our work offers a supramolecular approach for patterning of well-aligned organic heterostructures and rational design of optoelectronic devices that have potential in anti-counterfeiting applications.}, }
@article {pmid41193635, year = {2025}, author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R}, title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41193635}, issn = {2058-5276}, support = {991222//Simons Foundation/ ; }, abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.}, }
@article {pmid41193241, year = {2025}, author = {Kawabata, H and Miura, O}, title = {Excess of non-synonymous mutations and structural variations in mitogenomes of freshwater snails in the genus Semisulcospira.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/24701394.2025.2583076}, pmid = {41193241}, issn = {2470-1408}, abstract = {Mitochondrial DNA has unique biological characteristics, such as a high mutation rate and clonal inheritance, which make it an appropriate marker in molecular biology. However, exceptionally high mitochondrial divergences have been reported in terrestrial and marine invertebrates, plants, and certain vertebrate lineages, which complicates the interpretation of the results in DNA barcoding and evolutionary studies. The freshwater snails in the genus Semisulcospira have two mitochondrial DNA lineages: a normal mitochondrial lineage (mt-A type) and a highly divergent 'enigmatic' lineage (mt-B type). We assembled thirty-two mitogenomes of Semisulcospira to understand the molecular evolution of the mt-B type. We found that the mt-B type evolves faster than the mt-A type, has more non-synonymous mutations, and exhibits structural variations with truncated cob and cox3 genes. Our results showed that the observed molecular evolution of the mt-B type could result from a decreased efficiency of natural selection due to small population size and/or the accumulation of slightly deleterious mutations caused by mitochondrial sex ratio distortion.}, }
@article {pmid41193180, year = {2025}, author = {Hormiga, G and Lavery, AH and Arnedo, MA}, title = {The spider genus Stictonanus Millidge, 1991 in the Juan Fernandez Archipelago (Araneae, Linyphiidae): systematics and biogeography.}, journal = {Invertebrate systematics}, volume = {39}, number = {11}, pages = {}, doi = {10.1071/IS25046}, pmid = {41193180}, issn = {1447-2600}, mesh = {Animals ; *Spiders/classification/anatomy &amp; histology/genetics ; *Phylogeny ; Phylogeography ; Male ; }, abstract = {We studied the systematics of the Juan Fernandez linyphiid species originally classified in the genus Juanfernandezia Koçak &amp; Kemal, 2008. In an earlier study, we had hypothesized that the two Juanfernandezia species, each endemic to a single island, form a clade that was sister to the southern South American genus Notholepthyphantes Millidge, 1985. We have carried out a multi-locus phylogenetic analysis to infer the relationships of Juanfernandezia based on an extended taxon sampling. Our study shows that Juanfernandezia is sister to the South American genus Stictonanus Millidge, 1991, which until recently remained poorly known. The striking similarity of the somatic and genitalic morphology of these two genera suggest that the clade is better classified as a single genus, with Stictonanus being the oldest available generic name for this lineage. Stictonanus, circumscribed now to include five species, is sister to a lineage composed of two small genera, Notholepthyphantes and Falklandoglenes Usher, 1986. Stictonanus fernandezi (Berland, 1924) comb. nov. and Stictonanus paolae Hormiga &amp; Arnedo, sp. nov., both from the Juan Fernandez Islands, are described and illustrated. The type species of the genus, Stictonanus paucus Millidge, 1991, and the second continental species, S. exiguus Millidge, 1991, are here redescribed and illustrated (the male of S. exiguus is described here for the first time). We further infer a time calibrated tree to discuss the biogeographic history of Stictonanus. ZooBank: urn:lsid:zoobank.org:pub:C6D833D0-0422-401C-B010-B12618B1633C.}, }
@article {pmid41192368, year = {2025}, author = {Lin, YT and Lin, YH and Shiu, YW and Han, YS}, title = {Morphological and molecular evidence reveal the Sarotherodon melanotheron invasion off Taiwan, East Asia.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118898}, doi = {10.1016/j.marpolbul.2025.118898}, pmid = {41192368}, issn = {1879-3363}, abstract = {The blackchin tilapia, Sarotherodon melanotheron Rüppell, 1852, is a highly euryhaline cichlid native to West and Central Africa. Due to its broad salinity tolerance and rapid reproduction, it has become a high-risk invasive species in brackish and coastal ecosystems worldwide. This study reports the first and northernmost confirmed record of wild blackchin tilapia population in East Asia, based on 13 specimens collected from coastal waters of Kaohsiung City, Southern Taiwan. Morphological and meristic data, together with cytochrome c oxidase subunit I (COI) gene sequencing, confirmed species identity and consistency with native and invasive populations elsewhere. The occurrence of mature individuals and a substantial wild population confirms the establishment of invasion population in Taiwanese coastal environment. Given its wide salinity tolerance and omnivorous diet, this species poses potential ecological and economic threats to native ecosystems and aquaculture. This finding also represents the northernmost record of blackchin tilapia in the western Pacific.}, }
@article {pmid41187829, year = {2025}, author = {Simonson, AW and Chao, MC and Hood, LE and Donlan, RA and Hopkins, F and Chase, MR and Vickers, AJ and Callendrello, A and Klein, E and Borish, H and Malin, M and Maiello, P and Scanga, CA and Lin, PL and Fortune, SM and Flynn, JL}, title = {Protection against reinfection with Mycobacterium tuberculosis extends across heterologous Mtb lineages.}, journal = {Mucosal immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mucimm.2025.10.010}, pmid = {41187829}, issn = {1935-3456}, abstract = {Immunological memory elicited either through previous or ongoing M. tuberculosis (Mtb) infection provides a critical mechanism by which hosts protect against re-infection and disease progression upon Mtb re-exposure. Conversely, the uneven competition between distinct Mtb strains suggest certain bacterial clades have enhanced ability to spread across communities and circulate globally, potentially by evading memory responses gained by prior infection with genomically different strains. To address whether memory responses induced by one strain can protect against a genetically distinct strain, we conducted a heterologous reinfection study in cynomolgus macaques involving primary infection by a Lineage 4 Erdman Mtb strain and subsequent re-challenge by a Lineage 2 strain, HT-L2. Recent epidemiologic studies have shown that the clade to which HT-L2 belongs has been spreading successfully over the last decade in Lima, Peru. Here, through microbiologic, PET-CT imaging and sequencing of Mtb genomic barcodes, we show that reinfected animals developed fewer lung lesions and controlled both pulmonary and disseminated forms of infection better than naïve animals without prior exposure to Mtb. Our data support that protection against reinfection is not limited by Mtb lineage, providing optimism that vaccines can be effective across populations and geographic locations.}, }
@article {pmid41187186, year = {2025}, author = {Altaha, S and Al-Qaoud, K and Al-Omari, M and Al-Shawaheen, A}, title = {Development of multiplex immuno-PCR diagnostic platform using chicken IgY antibodies for COVID-19 diagnosis.}, journal = {Journal of infection in developing countries}, volume = {19}, number = {10}, pages = {1455-1463}, doi = {10.3855/jidc.21414}, pmid = {41187186}, issn = {1972-2680}, mesh = {Animals ; Chickens/immunology ; *Immunoglobulins/immunology ; *COVID-19/diagnosis ; *SARS-CoV-2/immunology/genetics ; *Multiplex Polymerase Chain Reaction/methods ; *Antibodies, Viral/immunology ; Sensitivity and Specificity ; Humans ; Enzyme-Linked Immunosorbent Assay ; *COVID-19 Serological Testing/methods ; Spike Glycoprotein, Coronavirus/immunology ; }, abstract = {INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic has significantly accelerated the development of diagnostic techniques. Real‑time quantitative polymerase chain reaction (RT‑qPCR) was the method of choice for diagnosis and was considered as the gold standard. However, limited specificity of RT-PCR was noticed during the pandemic. This research aimed to develop a combined highly specific immune-based and highly sensitive molecular-based diagnostic technique.<br><br>METHODOLOGY: Groups of chicken were immunized with commercial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N, S, and E antigens. The IgY antibodies were purified from eggs using a High-Trap IgY affinity column. Three unique DNA barcodes were designed, synthesized, and amplified using 5'-amine-labeled forward primers. DNA barcodes purified form PCR products were coupled to IgY antibodies using the (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide) - N-hydroxysuccinimide (EDC-NHS) coupling chemistry. ELISA; SDS-PAGEs; immunoblot (IB); and uniplex-, duplex- and multiplex immuno-PCR (IPCR) were used to confirm system validity.<br><br>RESULTS: Amplification of single barcodes using RT-PCR showed a Ct value of 15, with no significant variation when amplified in duplex or multiplex formats. Chicken IgY-DNA barcode conjugation and reactivity were verified using IB and ELISA. IPCR resulted in efficient amplification of all three DNA barcodes in uniplex, duplex, and multiplex formats after binding to commercial N, S, and E antigens.<br><br>CONCLUSIONS: The successful combination of the specific antibody-based techniques, low-cost chicken IgY antibodies, and RT-PCR sensitivity achieved in this study present a promising approach to meet the demand for sensitive and accurate diagnostics. This generic platform can be adopted in any analyte detection system.}, }
@article {pmid41184589, year = {2025}, author = {Bernadskaya, YY and Kuan, A and Tjärnberg, A and Brandenburg, J and Zhang, P and Wiechecki, K and Kaplan, N and Failla, M and Bikou, M and Madilian, O and Bruderer, N and Wang, W and Christiaen, L}, title = {Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.}, journal = {The EMBO journal}, volume = {}, number = {}, pages = {}, pmid = {41184589}, issn = {1460-2075}, support = {HL108643//HHS | NIH | NHLBI | Division of Intramural Research (DIR)/ ; HD096770//HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; 32270870//National Natural Science Foundation of China/ ; }, abstract = {During development, stem and progenitor cells divide and transition through multipotent states to generate the diverse cell types by undergoing defined changes in biomolecular composition, which underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, the cardiac and pharyngeal muscle programs are jointly primed in multipotent cardiopharyngeal progenitors, and segregate in distinct daughter cells only after cell division. Here, using the tunicate Ciona, we showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10 (+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single-cell RNA-sequencing (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S, and G2 phases. We refer to this process as "transcriptome maturation", and identified candidate mature genes, including the Rho GAP-coding gene Depdc1b, which peaks in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and by enabling asymmetric cell division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". We show that both classic regulatory circuits and coupling with the G1-S transition drive transcriptome maturation, ensuring the timely deployment of lineage-specific programs.}, }
@article {pmid41183194, year = {2025}, author = {Gentry, K and Lian, L and Kim, H and Celik, O and Jones, C and Podilapu, AR and Shakked, A and Loughrey, D and Zenhausern, R and Jang, B and Doan, J and Rudden, S and Dahlman, JE}, title = {Glycolipid nanoparticles target the spleen and detarget the liver without charge.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {45}, pages = {e2409569122}, doi = {10.1073/pnas.2409569122}, pmid = {41183194}, issn = {1091-6490}, support = {Dahlman Lab//Amgen Inc. | Amgen Foundation (The Amgen Foundation)/ ; }, mesh = {*Liver/metabolism/drug effects ; *Spleen/metabolism/drug effects ; Animals ; *Glycolipids/chemistry ; *Nanoparticles/chemistry/administration &amp; dosage ; Mice ; Humans ; Mice, Inbred C57BL ; }, abstract = {Lipid nanoparticles (LNPs) formulated with a neutral helper lipid can deliver RNA to the liver in humans. However, clinically relevant delivery to other tissues has remained challenging. To avoid the liver, scientists often add antibodies or helper lipids with a permanent charge. Here, we report an alternative approach: antibody- and charge-independent liver detargeting. Using DNA barcoding to test 109 chemically distinct LNPs in vivo, we found that replacing a neutral helper lipid with a neutral glycolipid reduced liver delivery and increased splenic delivery. Consistent with this differential tropism, these glycolipid nanoparticles caused differences in downstream cellular signaling in vivo compared to traditional LNPs. These data suggest that extrahepatic LNPs can be designed without the imposition of a net negative or positive charge.}, }
@article {pmid41181664, year = {2025}, author = {Monckton, SK and Levesque-Beaudin, V and Thompson, KA and Barnes, A and French, K and Hampton, H and Hebert, PDN}, title = {The brown copper moth, Tridentaforma browncopper: DNA barcoding reveals a second species in the family Tridentaformidae (Lepidoptera, Adeloidea).}, journal = {ZooKeys}, volume = {1257}, number = {}, pages = {25-38}, pmid = {41181664}, issn = {1313-2989}, abstract = {A biodiversity monitoring program in south-central British Columbia, Canada, at sites on traditional nłeʔképmx territory near the Highland Valley Copper mine, collected many specimens of an unknown moth. DNA barcode analysis revealed its affinity but deep divergence (14.3%) from Tridentaforma fuscoleuca (Braun, 1923), the only species in the family Tridentaformidae. The new species was assigned to the BIN (Barcode Index Number) BOLD:AFK8960. Morphological study confirmed its placement in this family but revealed marked genitalic differences from T. fuscoleuca. Given its genetic and morphological divergence, we describe Tridentaforma browncopper Monckton &amp; Levesque-Beaudin, sp. nov. The scientific name is a translation of the name, skʷúnkʷl̓itkax̣n̓I, chosen by nłeʔképmx Elders and Knowledge Keepers, which means "brown copper moth". Its discovery and naming reflect an effective collaboration among biodiversity scientists, industry representatives, and Indigenous communities. It also demonstrates how DNA barcoding can facilitate species descriptions without requiring taxonomists with specialist expertise in the group under investigation.}, }
@article {pmid41179342, year = {2025}, author = {Bang, WJ and You, JY and Bae, Y and Chuang, MF and Shin, S}, title = {Preliminary Study on Host Use and Phylogenetic Analysis of Corethrella nippon in Taiwan.}, journal = {Ecology and evolution}, volume = {15}, number = {11}, pages = {e72405}, pmid = {41179342}, issn = {2045-7758}, abstract = {This study investigated frog-biting dipteran species using newly designed frog-calling traps in Taiwan. The trap effectively collected specimens from both families, Culicidae and Corethrellidae, demonstrating its utility. Host preference analysis revealed that Odorrana swinhoana (Boulenger, 1903) and Kurixalus eiffingeri (Boettger, 1895) were most frequently associated with collected specimens of Corethrellidae. Additionally, the corethrellids were predominantly attracted to a sound frequency around 2200 to 2700 Hz. Then, DNA barcoding was also conducted on the four collected species of Culicidae: Armigeres subalbatus (Coquillett, 1898), Uranotaenia nivipleura Leicester, 1908, Ur. macferlanei Edwards, 1914, and Mimomyia luzonensis (Ludlow, 1905), and the mitochondrial genome of Corethrella nippon Miyagi 1980 was first sequenced and annotated. Mitogenome-based phylogenetic analysis confirmed that C. nippon formed a clade with Corethrella condita Borkent, 2008. In our analysis, family Corethrellidae clustered with Culicidae; however, the inter-family phylogenetic relationships within Culicoidea appeared paraphyletic, particularly concerning family Chaoboridae. Future studies should explore a greater variety of frog species across more diverse regions and use other genomic datasets beyond the mitogenome to infer a more robust deep topology at the superfamily level and further broaden our understanding of host preference.}, }
@article {pmid41179240, year = {2025}, author = {Harefa, T and Haryono, H and Gustiano, R and Sukmono, T and Wahyudewantoro, G}, title = {Desmopuntius mahakamensis, a new cyprinid species (Teleostei, Cyprinidae) from East Kalimantan, Indonesia.}, journal = {ZooKeys}, volume = {1256}, number = {}, pages = {371-391}, pmid = {41179240}, issn = {1313-2989}, abstract = {Desmopuntius mahakamensis sp. nov., is described based on specimens from East Kalimantan, Indonesia. The new species, D. mahakamensis is distinguished from all congeners by the following combination of characters: anal-fin rays iii,5½; lateral line scales 26-27 (mode 26); predorsal scales 9-11 (mode 10); gill rakers 9-11 (mode 10); total vertebrae 29; axial streak present; presence of 5-6 black lateral stripes in adults (>30 mm SL), with stripe +1 extending from behind the gill opening along scale row 1 and reaching only to midbody, between the origin and end of the dorsal-fin base. Molecular evidence further supports the assignment of the new species in the genus Desmopuntius and its clear separation from congeners.}, }
@article {pmid41176652, year = {2025}, author = {Yang, X and Gao, Z}, title = {Regulation of Supramolecular Interactions: RNA:DNA Folding and Nanopore Sensing Applications.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {e202500709}, doi = {10.1002/cbic.202500709}, pmid = {41176652}, issn = {1439-7633}, support = {22176080//National Natural Science Foundation of China/ ; ZR2023YQ015//Natural Science Foundation of Shandong Province/ ; }, abstract = {The intersection of DNA/RNA nanotechnology and single-molecule solid-state nanopore sensing enables precise detection of low-abundance biomolecules. However, a significant challenge persists that nucleic acid molecules readily fold during nanopore translocation, which gives rise to ambiguous current signatures, reduces the number of usable data points, and compromises detection accuracy. Herein, a recent advancement by the Platnich group is highlighted, wherein urea is employed as a noncovalent modulator to participate in the isothermal assembly of MS2 bacteriophage RNA with DNA barcodes. This modulator stably binds to the RNA:DNA hybrids through supramolecular interactions after removal of free urea by buffer exchange. Nanopore assays showed a ≈50% reduction in fold-shift events in the urea-treated group. Atomic force microscopy characterization shows that the persistence length of the hybrids is enhanced by ≈40%. This strategy provides a new noncovalent regulatory tool for nucleic acid nanotechnology and pushes the nanopore sensing technology toward the precision detection of low-abundance RNA.}, }
@article {pmid41174477, year = {2025}, author = {Ren, T and Xun, L and Jia, Y and Zhou, H and Li, B}, title = {Insights into the plastome evolution and phylogenetic relationships of Lepidium (Brassicaceae).}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1489}, pmid = {41174477}, issn = {1471-2229}, support = {2023K-25//Science and Technology Program of Shaanxi Academy of Science/ ; 2023K-14//Science and Technology Program of Shaanxi Academy of Science/ ; 2022K-04//Key Scientific Research Project of Shaanxi Academy of Sciences/ ; 32300314//National Natural Science Foundation of China/ ; [KRDL] K6-2207039//First Investigation of Wild Plants Resources in Xi'an/ ; }, mesh = {*Phylogeny ; *Lepidium/genetics/classification ; *Evolution, Molecular ; *Genome, Plastid/genetics ; *Plastids/genetics ; }, abstract = {BACKGROUND: Lepidium represents one of the most species-rich genera in the Brassicaceae, encompassing numerous taxa with excellent medicinal value. Although the plastome architecture of Brassicaceae has been extensively characterized, its evolutionary dynamics within Lepidium remain poorly understood. Besides, the intrageneric taxonomy has long been problematic, primarily due to subtle morphological differences or overlapping morphological characteristics. Here, 15 Lepidium plastomes (11 newly sequenced and 4 published) were subject to comparative genomic and phylogenetic analyses to investigate plastome evolution and phylogenetic relationships.<br><br>RESULTS: The total length of the 11 newly sequenced Lepidium plastomes varied from 153,803&#xa0;bp to 154,997&#xa0;bp, with 111-112 unique genes. The Lepidium plastomes exhibited strong conservatism in genome size, gene order, plastome structure, IR/SC borders, codon usage, mVISTA analysis, Pi value, and genetic distance. However, minor variations were observed in IR border shifts. Analysis of repeat sequences revealed interspecific differences in both long repeat sequences (24-40) and simple sequence repeats (78-98) among 15 Lepidium plastomes. Six divergence hotspots (ycf1, ccsA, matK, rps15-ycf1, trnH-GUG-psbA, and rpl32-trnL-UAG) were identified as potential DNA barcodes for both species identification and phylogenetic analyses of Lepidium. The ycf1 gene was under relaxed selection. Furthermore, our phylogenetic studies clarified that all 15 Lepidium species formed a strongly supported monophyletic group within the tribe Lepidieae, while the cytonuclear discordance between ITS and plastome trees was found within Lepidium.<br><br>CONCLUSION: Our findings suggested that cytonuclear discordance within Lepidium likely results from hybridization/introgression and incomplete lineage sorting. Meanwhile, we proposed the reclassification of L. perfoliatum within Section Lepia. This study clearly documented global patterns of plastome structural evolution, and constructed a well-supported phylogeny of Lepidium. The reliable phylogenetic tree not only provides a new viewpoint into the intrageneric relationships and sectional classification of Lepidium, but also advances our understanding of the evolutionary history of this genus.}, }
@article {pmid41173855, year = {2025}, author = {Dahlberg, SK and Bonet, DF and Franzén, L and Ståhl, PL and Hoffecker, IT}, title = {Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9652}, pmid = {41173855}, issn = {2041-1723}, support = {949624//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2020-05368//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, mesh = {*Gene Expression Profiling/methods ; *Oligonucleotide Array Sequence Analysis/methods ; Humans ; Animals ; Mice ; Transcriptome ; }, abstract = {Spatial transcriptomics technologies aim to spatially map gene expression in tissues and typically use oligonucleotide array surfaces that have undergone spatial indexing. These arrays are used to capture nucleic acids diffusing from adjacently placed tissues, allowing subsequent sequencing to reveal both gene and position. Slide-tags is a recently developed method by Russell et al. that inverts this principle. Instead of capturing molecules released from the tissue, probes are detached from a pre-decoded bead array and diffused into tissues, tagging nuclei with spatial barcodes. In this work we reanalyze this data and discover a latent, spatially informative cell-bead network formed incidentally from barcode diffusion and the biophysical properties of the tissue. This allows us to treat Slide-tags as a network-based imaging-by-sequencing approach. By optimizing spatial constraints encoded in the cell-bead network structure, we can achieve unassisted tissue reconstruction, a fundamental shift from classical spatial technologies based on pre-indexed arrays.}, }
@article {pmid41172905, year = {2025}, author = {Huang, X and Lu, L and Yan, Y and Wu, L and Qi, H and Li, M and Lin, Y and Zhou, Q and Lu, Y}, title = {DNA self-assembly-based direct fluorescence encoding of targets enables simultaneous 10-plex microRNA detection.}, journal = {Biosensors &amp; bioelectronics}, volume = {293}, number = {}, pages = {118130}, doi = {10.1016/j.bios.2025.118130}, pmid = {41172905}, issn = {1873-4235}, abstract = {As crucial post-transcriptional regulators, microRNAs (miRNAs) serve as valuable biomarkers for disease diagnosis and precision medicine. Current detection technologies (e.g., Luminex xMAP), however, suffer from technical limitations including elevated coefficient of variation and suboptimal sensitivity. To address these challenges, we developed an innovative imaging-based detection system leveraging DNA self-assembly and fluorescence barcoding technologies. Our system demonstrates two breakthrough features: (1) Programmable DNA assemblies facilitate highly specific target recognition with built-in signal amplification, achieving enhanced sensitivity through magnetic bead-mediated target enrichment; and (2) A rationally designed four-color fluorescent encoding system can generate 33 unique barcode combinations, from which we select 10 barcode combinations that allow multiplexed detection of 10 miRNAs in a single-tube reaction vessel. Validation studies using breast cancer cell lines (MCF-7) confirmed the system's robust performance in complex biological matrices. Our platform offers distinct advantages of streamlined workflow, cost-effectiveness and superior reproducibility, and is expected to provide a new technical means for early tumor screening and precision medicine.}, }
@article {pmid41171823, year = {2025}, author = {Khudamrongsawat, J and Krajangdara, T and Panithanarak, T and Karuwancharoen, R and Klangnurak, W and Promnun, P and Senanan, W}, title = {DNA barcoding for elasmobranch diversity assessment in Thailand: Its advantages and limitations.}, journal = {PloS one}, volume = {20}, number = {10}, pages = {e0334640}, pmid = {41171823}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Thailand ; *Biodiversity ; *Elasmobranchii/genetics/classification ; Phylogeny ; Genetic Variation ; DNA, Mitochondrial/genetics ; Species Specificity ; }, abstract = {The assessment of elasmobranch biodiversity in Thailand benefits greatly from the application of DNA barcoding, which helps mitigate the challenge posed by a shortage of expert taxonomists. Fragments of COI and ND2 mitochondrial DNA were examined, and the strengths and weaknesses of these two markers were compared. In this study, DNA products from 153 elasmobranch samples were amplifiable and revealed a total of 28 shark species and 32 batoid species. Many species could be confidently identified as their morphological characteristics aligned with DNA barcodes. However, several exceptions were recognized. The absence of reference sequences for rare species presented a challenge for species verification, and the misidentification of reference sequences, as well as changes in species names due to taxonomic revisions, added complexity when comparing DNA barcoding sequences. Conflicts between morphology and genetics were also observed. While intraspecific genetic variation based on both DNA barcodes generally indicated 0-2% variation, this metric could not always be used for species delimitation. This was particularly true for species displaying low genetic variation among closely related species and species where cryptic diversity remained hidden and yet to be uncovered. In such cases, the morphological characteristics of the samples served as the primary means of species identification. Despite these challenges, DNA barcoding remains an invaluable tool for biodiversity assessment, especially in light of the shortage of skilled experts, and for identification of products made from vulnerable species. However, it is essential to exercise caution and be aware of these complexities in its application.}, }
@article {pmid41169085, year = {2025}, author = {Ferreira da Silva, MJ and Colmonero-Costeira, I and Djaló, SL and Camará, T and Sá, RM and Minhós, T and Kiebler, A and Grethlein, M and Pikkarainen, N and Prost, S}, title = {Using miniaturized laboratory equipment and DNA barcoding to improve conservation genetics training and identify illegally traded species.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {e70165}, doi = {10.1111/cobi.70165}, pmid = {41169085}, issn = {1523-1739}, support = {232533027//Mohamed bin Zayed Species Conservation Fund/ ; NORTE-01-0145-FEDER-000046//European Regional Development Fund/ ; //Genetic Society/ ; PCI#1694//Primate Conservation Incorporated/ ; Biodiverse Anthropocenes research//Academy of Finland PROFI6 336449/ ; PRIMACTION//Born Free Foundation/ ; UID/00713/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {Illegal wildlife trade (IWT) is one of the largest global illegal activities, and it negatively affects biodiversity and sustainable development worldwide. DNA barcoding coupled with high-throughput sequencing (i.e., metabarcoding) is useful in identifying taxa affected by IWT and has been used routinely for decades. However, for countries lacking laboratory infrastructure, sequencing units, and trained staff, the application of DNA barcoding tools in conservation is limited and depends on slow sample transport processes and molecular analyses carried out abroad. Guinea-Bissau, on the West African coast, has one of the lowest human development indices in the world and is a biodiversity hotspot threatened by IWT. We explored the potential use of inexpensive and portable miniaturized laboratory equipment (MLE) and DNA barcoding tools to improve training in conservation genetics and identification of traded species. We tested these technologies in tissue samples collected at different times and contexts in Guinea-Bissau and used 3 primer pairs amplifying mitochondrial DNA fragments. We successfully identified 33 tissue samples to the species level; thus, MLE may accelerate the use of DNA and metabarcoding methods in countries that have low research funding and limited infrastructure. The use of these technologies has the potential to advance the discipline of conservation genetics in Guinea-Bissau and other countries and to train students and employees of government agencies dedicated to investigating environmental crimes.}, }
@article {pmid41168956, year = {2025}, author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD}, title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70069}, doi = {10.1111/1755-0998.70069}, pmid = {41168956}, issn = {1755-0998}, abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.}, }
@article {pmid41168495, year = {2025}, author = {Chang, T and Zhao, S and Deng, K and Liao, Z and Tang, M and Zhu, Y and Han, W and Yu, C and Fan, W and Jiang, M and Wang, G and Liu, D and Peng, J and Pang, Y and Fei, P and Wang, J and Zheng, C and Huang, Y}, title = {High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41168495}, issn = {1546-1696}, support = {T2188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; T2225005//National Natural Science Foundation of China (National Science Foundation of China)/ ; Z221100007022003//Beijing Municipal Science and Technology Commission/ ; }, abstract = {Spatial RNA imaging has not been widely adopted because conventional fluorescence microscopy is limited to only a few channels and the cyclic reactions needed to increase multiplexing in techniques such as sequential fluorescence in situ hybridization require sophisticated instrumentation. Here, we introduce 'profiling of RNA in situ through single-round imaging' (PRISM), a method that expands coding capacity through color intensity grading. Using a radius vector filtering strategy to ensure the distinguishability of codewords in color space, PRISM achieves up to 64-plex color-barcoded RNA imaging in a single imaging round with conventional microscopes. We validate PRISM's versatility across various tissues by generating a three-dimensional (3D) atlas of mouse embryonic development from E12.5 to E14.5, a quasi-3D tumor-normal transition landscape of human hepatocellular carcinoma and a 3D cell atlas and subcellular RNA localization landscapes of mouse brain. Additionally, we show the critical role of cancer-associated fibroblasts in mediating immune infiltration and immune response heterogeneity within and between tumor microenvironments.}, }
@article {pmid41168426, year = {2025}, author = {Tian, X and Peng, Y and Liu, S and Shafiei, G and Wang, M and Sun, Y and Lou, J and Xian, J and Hu, K and He, Y and Wang, Q and Ding, C and Gao, T and Huang, S and Li, K and Wang, Q and Zuo, XN and Zhang, Z and Li, A and Liu, B}, title = {Spontaneous brain regional dynamics contribute to generalizable brain-behaviour associations.}, journal = {Nature human behaviour}, volume = {}, number = {}, pages = {}, pmid = {41168426}, issn = {2397-3374}, support = {82171543//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82425024 &amp; 82372049//National Natural Science Foundation of China (National Science Foundation of China)/ ; 20250484761//Beijing Nova Program/ ; 20230484425//Beijing Nova Program/ ; }, abstract = {Spontaneous brain activity is fundamental to understanding the neural basis of inter-individual differences, making its characterization central to brain-wide association studies. While inter-regional coupling patterns have been extensively studied, intra-regional dynamics remain largely unexplored. Here, analysing data from four neuroimaging cohorts (ages 8-82 years; N = 30,148), we extracted ~5,000 time-series features from resting-state haemodynamic signals across 271 brain regions, offering a comprehensive characterization of intra-regional dynamics. We identified a reliable subset that serves as an individual-specific 'barcode', capturing multifaceted dynamic dimensions that stably reflect inter-individual variation across datasets. These barcodes linked nonlinear autocorrelations in unimodal regions to substance use traits and random walk dynamics in higher-order networks to general cognitive abilities. Importantly, these brain-behaviour associations generalized across life stages and populations, with substance use showing age-specific variation and cognition exhibiting consistent patterns across age groups. This work advances large-scale, generalizable brain-wide association studies by highlighting the potential of intra-regional dynamics.}, }
@article {pmid41167558, year = {2025}, author = {Zhang, Q and Li, M and Shen, L and Chen, L and Yuan, Z and Zhang, X and Wang, H and Yu, Y and Luo, F and Peng, G and Hu, J and Bao, Z and Song, N and Chen, K}, title = {A universal cost-efficient sample labeling approach for multiplexed single cell RNA-seq based on recombinant HUH-endonuclease-agglutinin tagging.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2025.10.004}, pmid = {41167558}, issn = {1673-8527}, abstract = {Recent advances in single-cell transcriptomics have revolutionized our understanding of cellular diversity and tissue heterogeneity, providing unprecedented insights into biological and medical research. However, the high per-assay cost limits broader applications of this technology. Although sample-labeling strategies enabling multiplexing have emerged, current methods suffer from either impractical complexity for barcoding or high cost for preparing the index labeling reagents. To address these challenges, here we present HEATag, a universal cell membrane labeling approach that combines Duck circovirus HUH endonuclease (DCV) with wheat germ agglutinin (WGA) to efficiently tag cell membranes with indexed single-stranded DNA (indexed ssDNA). The DCV domain enables rapid, sequence-specific conjugation of indexed ssDNA, while the WGA domain ensures robust labeling of fresh or fixed cells across diverse species. This method is compatible with both commercial platforms and custom systems, readily adaptable to various single cell omics workflows. Therefore, HUH-endonuclease-agglutinin tagging (HEATag) provides a universal, cost-effective and scalable solution for high-throughput single-cell studies, enhancing library preparation efficiency and minimizing batch effects for single-cell researchers.}, }
@article {pmid41164792, year = {2025}, author = {Suciu, SRA and Jung, JL and Azevedo, JMN}, title = {MONICEPH project: Monitoring cephalopods during whale-watching activity in the Azores (2020-2024).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e158822}, pmid = {41164792}, issn = {1314-2828}, abstract = {BACKGROUND: The study of oceanic cephalopods off the Azores Archipelago began decades ago with the analysis of stomach contents from sperm whales that were hunted for the whaling industry. The identification of numerous cephalopod species contributed significantly to cephalopod taxonomy, as well as enhancing understanding of the sperm whale diet. In the 1990s, the shift from whaling to whale-watching created new opportunities to continue studying deep-ocean ecology: participatory research involving the actors of the new industry.<br><br>NEW INFORMATION: MONICEPH (MONItoring CEPHalopods during whale-watching activity in the Azores) is a collaborative platform designed to collect, organise and disseminate cephalopod occurrence data gathered by whale-watching companies in the Azores. From 2020 to 2024, cephalopod remains found at the water's surface during sightings of cetaceans were collected in partnership with companies from four islands: S&#xe3;o Miguel, Terceira, Pico and Faial. The deep-ocean cephalopod remains at the water's surface were likely brought up by their predators during feeding activity. We assume that sperm whales, in particular, occasionally release cephalopods at the surface due to incomplete consumption during a hunt or for feeding of their calves. Trained staff collected the samples, which were subsequently identified using DNA barcoding and/or morphological characteristics. The dataset includes 182 cephalopod records across 16 species. One species, Onykia carriboea Lesueur, 182, has been newly identified in the region, expanding the list of species previously documented in the published data for the Northeast Atlantic.}, }
@article {pmid41164282, year = {2025}, author = {Almerekova, SS and Yermagambetova, MM and Yerbolatov, DY and Ishmuratova, MY and Turuspekov, YK}, title = {Complete plastome sequences of Lonicera L. species: implications for phylogeny and comparative analysis.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {29}, number = {6}, pages = {883-895}, doi = {10.18699/vjgb-25-95}, pmid = {41164282}, issn = {2500-0462}, abstract = {Lonicera L. is one of the largest and economically significant genera in the family Caprifoliaceae Juss., with a controversial taxonomy. To contribute to its molecular taxonomy, we sequenced the plastomes of Lonicera species: Lonicera caerulea (two subspecies), L. tatarica, and L. micrantha - using next-generation sequencing technology and conducted a comparative analysis. Plastome sizes ranged from 153,985 bp in L. micrantha to 164,000 bp in L. caerulea subsp. pallasii, each containing 130 genes, including 85 protein-coding, 37 tRNA, and 8 rRNA genes. Five protein-coding (rps7, rps12, ndhB, ycf2, and ycf15), 7 tRNA (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC), and 4 rRNA (rrn4.5, rrn5, rrn16, and rrn23) genes were duplicated. Comparative analysis of Lonicera plastome boundaries revealed structural variations in L. caerulea subsp. altaica and L. caerulea subsp. pallasii, particularly in ndhA gene distribution. Three highly variable, two intergenic (ycf1-trnN-GUU and trnN-GUU-ndhF) and one genic (accD) region were identified. A total of 641 simple sequence repeats were detected in four plastomes. Phylogenetic analyses grouped Lonicera samples into two clades corresponding to subgenera Periclymenum and Chamaecerasus. In this study, the plastid genomes of two subspecies of L. caerulea and species L. micrantha were sequenced for the first time. The maximum likelihood tree derived from complete plastid genome sequences proved to be the most informative, showing a topology consistent with previous studies. The nucleotide sequences of variable regions (accD-ycf1-ndhF-trnN-GUU) demonstrate high potential for use in DNA barcoding and may serve as valuable molecular markers for species phylogenetic studies within the genus Lonicera.}, }
@article {pmid41162144, year = {2025}, author = {Hutchings, P and McLaren, E and Kupriyanova, E and Gunton, LM and Lavesque, N and Przeslawski, R}, title = {The taxonomy of Australian polychaetes: current understanding, knowledge gaps and steps forward for management.}, journal = {Advances in marine biology}, volume = {101}, number = {}, pages = {27-56}, doi = {10.1016/bs.amb.2025.07.001}, pmid = {41162144}, issn = {2162-5875}, mesh = {Animals ; Australia ; *Polychaeta/classification ; *Conservation of Natural Resources ; *Biodiversity ; }, abstract = {Amid the current global biodiversity crisis, understanding and conserving marine invertebrates is more urgent than ever. Marine invertebrates are key components of biodiversity in benthic ecosystems, however, in Australia they remain underrepresented in biodiversity data and conservation planning. Australia's coastline extends from the tropics to subpolar environments and the surrounding waters comprise the Australian Territorial Seas and the Exclusive Economic Zone (EEZ). Currently there are 60 Australian Federal and 98 State Marine Parks which by law must ensure the sustainable management of their biodiversity. Polychaetes are dominant in benthic communities both in terms of species richness and diversity and play a critical role in the functioning of marine ecosystems. Polychaetes are also sensitive to environmental disturbance and change and must be considered in developing marine park zoning and monitoring plans. Here we review the history of species discovery (1791-2025) in shallow (0-300 m) and deep waters (300-5,000 m) within Australia. We highlight that many species remain undescribed, especially in the deep sea, and vast areas in Australian waters have little or no data on the polychaetes that occur there. Finally, we propose what can be done to ensure that polychaetes are included in management plans, including (1) increased availability of information for benthic ecologists from museums, (2) the development of reference DNA barcode libraries by museums, (3) increased tertiary education opportunities and (4) increased philanthropic funding sources.}, }
@article {pmid41162141, year = {2025}, author = {Knorrn, AH and Sonnewald, M and Moctar, SMM and El-Hacen, EHM and Dia, M and Cherif, A and Sidi, MTO and Freiwald, A}, title = {The need for taxonomic expertise in protecting Mauritania's marine ecosystems and biological resources.}, journal = {Advances in marine biology}, volume = {101}, number = {}, pages = {105-151}, doi = {10.1016/bs.amb.2025.08.001}, pmid = {41162141}, issn = {2162-5875}, mesh = {Mauritania ; *Conservation of Natural Resources/methods ; Animals ; *Ecosystem ; *Biodiversity ; *Aquatic Organisms/classification ; }, abstract = {Seasonal upwelling events have a significant impact on the Mauritanian waters, which are a component of the Canary Current Large Marine Ecosystem (CCLME). These events frequently provide nutrient-rich waters to Mauritania's coastal waters. This influx of nutrients supports some of the most productive fish stocks in the Atlantic and sustains the development of a rich and diverse marine biodiversity. Despite its ecological and economic importance, a significant part of Mauritania's marine fauna remains insufficiently investigated, with significant taxonomic gaps spanning over a variety of taxa. A comprehensive understanding of regional biodiversity is essential for the implementation of sustainable fisheries management and the effective protection of marine ecosystems. Such understanding depends on accurate taxonomic knowledge, which forms the basis for assessing species distributions, ecological interactions and trophic networks. This review provides a synthesis of past research initiatives and campaigns conducted along the Mauritanian coast and identifies key coastal ecosystems of particular ecological relevance. It further highlights current gaps in taxonomic knowledge and points out the importance of an integrative approach to biodiversity research that combines classical morphological taxonomy with modern genetic species identification techniques. Additionally, the review advocates for the establishment and maintenance of a scientific reference collection of the Mauritanian marine fauna as a foundational resource for ongoing and future biodiversity assessments. Ultimately, this article proposes an integrative and interdisciplinary biodiversity research strategy for Mauritania's unique marine environment, thereby contributing to long-term conservation efforts and the sustainable use of marine resources at times of climate change and overexploitation of biological resources.}, }
@article {pmid41159105, year = {2025}, author = {Hoxha, I and Dervović, J and Unterköfler, MS and Schlamadinger, L and Situmorang, T and Fuehrer, HP and Obwaller, AG and Sekulin, K and Camp, JV and Harl, J and Walochnik, J and Alić, A and Kniha, E}, title = {A cross section through mosquitoes of Bosnia and Herzegovina: Barcodes, blood meals and pathogens.}, journal = {One health (Amsterdam, Netherlands)}, volume = {21}, number = {}, pages = {101246}, pmid = {41159105}, issn = {2352-7714}, abstract = {Mosquitoes are important vectors of human and animal pathogens, yet data on their diversity and vector potential remain scarce for the central Balkan country Bosnia and Herzegovina. This study aimed to assess mosquito species composition, associated pathogens, and the potential public health risks in BIH. Adult mosquitoes were collected with light traps, identified morphologically and by barcoding, and screened molecularly for various pathogens, including West Nile virus (WNV), Dirofilaria spp., Trypanosoma spp., and Plasmodium spp. A total of 2691 mosquitoes of 17 species were identified, with Culex pipiens/torrentium being most abundant and new records of Aedes albopictus and Ae. japonicus japonicus. The first detection of WNV (lineage 2) RNA in mosquitoes in BIH highlights the potential risk of circulation in the region, aligning with findings from neighboring countries. In addition, DNA of filarioid nematodes (Dirofilaria immitis, D. repens, and Setaria tundra) were detected, underscoring their role as potential vectors of zoonotic dirofilariasis. Also, Trypanosoma and Plasmodium DNA was detected, warranting further investigation into the possible involvement of mosquitoes in their transmission. The detection of invasive Aedes species and mosquito-borne pathogens emphasize the need for strengthened vector surveillance in southeastern Europe, particularly in BIH. This study provides the first barcode inventory of 17 mosquito species and novel molecular evidence of mosquito-borne pathogens in BIH, offering valuable baseline data for future epidemiological assessments and sustained entomological surveillance.}, }
@article {pmid41152343, year = {2025}, author = {Khode, PP and Sylvester, MN and Naumov, NG and Pethe, AM and Dhoble, SJ}, title = {Tuning photoluminescence in Gd2O3 via lattice engineering for advanced barcode and LEDs applications.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37706}, pmid = {41152343}, issn = {2045-2322}, abstract = {UNLABELLED: The utilization of luminescent phosphors in barcode technology can enhance the security feature. Using NaOH as a reducing agent, we have prepared Gd2O3:Eu[3+]/Er[3+] for luminescent phosphor. The cubic structure of Gd2O3 phosphor is confirmed by the structural analysis conducted using XRD. Dopant Eu and Er induce lattice contraction and expansion in the host lattice, respectively. Based on SEM analysis, porous and irregular particles with an average size of 401 nm were observed. In Tem analysis of prepared phosphor have some particle are in spherical in shape. The formation of Gd2O3 was confirmed by Gd-O band stretching as shown in the FTIR analysis. The emission in the red and green regions is emitted by Gd2O3:Eu[3+] and Gd2O3:Er[3+], respectively. The emission peaks of Gd2O3:Eu[3+]/Er[3+] are observed at 524 nm, 539 nm, 549 nm, 563 nm, 593 nm, 612 nm, and 629 nm when it is triggered by 363 nm, with a maximum energy transfer efficiency of 95.93%. Enhancing the security of barcodes can be achieved through the use of color-tunable Gd2O3:Eu[3+]/Er[3+] phosphor. Gd2O3:Er[3+] (1.5 mol%) is a prominent candidate for LED bulbs due to its CCT (5765 K).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-21434-3.}, }
@article {pmid41156631, year = {2025}, author = {Munir, M and Naeem, M and Wu, X and Zeng, W and Sun, Z and Li, Y and Yong, T and Yang, F and Chang, X}, title = {Morpho-Molecular Identification and Pathogenic Characterization of Fusarium and Colletotrichum Species Associated with Intercropped Soybean Pod Decay.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, doi = {10.3390/pathogens14101020}, pmid = {41156631}, issn = {2076-0817}, support = {2023YFD1401000//National Key R&amp;D Program/ ; 23ZDYF3037//Key Research and Development Plan of Sichuan Province/ ; AB23026107//Guangxi Key Research and Development Program/ ; }, mesh = {*Glycine max/microbiology ; *Fusarium/genetics/classification/isolation &amp; purification/pathogenicity ; *Colletotrichum/genetics/classification/pathogenicity/isolation &amp; purification ; *Plant Diseases/microbiology ; Phylogeny ; China ; Seeds/microbiology ; DNA, Fungal/genetics ; }, abstract = {The fruiting stage of soybean (Glycine max L.) is critical for determining both its yield and quality, thereby influencing global production. While some studies have provided partial explanations for the occurrence of Fusarium species on soybean seeds and pods, the fungal diversity affecting soybean pods in Sichuan Province, a major soybean cultivation region in Southwestern China, remains inadequately understood. In this study, 182 infected pods were collected from a maize-soybean relay strip intercropping system. A total of 10 distinct pod-infecting fungal genera (132 isolates) were identified, and their pathogenic potential on soybean seeds and pods was evaluated. Using morphological characteristics and DNA barcode markers, we identified 43 Fusarium isolates belonging to 8 species, including F. verticillioides, F. incarnatum, F. equiseti, F. proliferatum, F. fujikuroi, F. oxysporum, F. chlamydosporum, and F. acutatum through the analysis of the translation elongation factor gene (EF1-α) and RNA polymerases II second largest subunit (RPB2) gene. Multi-locus phylogenetic analysis, incorporating the Internal Transcribed Spacer (rDNA ITS), β-tubulin (β-tubulin), Glyceraldehyde 3-phosphate dehydrogenase (GADPH), Chitin Synthase 1 (CHS-1), Actin (ACT), Beta-tubulin II (TUB2), and Calmodulin (CAL) genes distinguished 37 isolates as 6 Colletotrichum species, including C. truncatum, C. karstii, C. cliviicola, C. plurivorum, C. boninense, and C. fructicola. Among these, F. proliferatum and C. fructicola were the most dominant species, representing 20.93% and 21.62% of the isolation frequency, respectively. Pathogenicity assays revealed significant damage from both Fusarium and Colletotrichum isolates on soybean pods and seeds, with varying isolation frequencies. Of these, F. proliferatum, F. acutatum, and F. verticillioides caused the most severe symptoms. Similarly, within Colletotrichum genus, C. fructicola was the most pathogenic, followed by C. truncatum, C. karstii, C. cliviicola, C. plurivorum, and C. boninense. Notably, F. acutatum, C. cliviicola, C. boninense, and C. fructicola were identified for the first time as pathogens of soybean pods under the maize-soybean strip intercropping system in Southwestern China. These findings highlight emerging virulent pathogens responsible for soybean pod decay and provide a valuable foundation for understanding the pathogen population during the later growth stages of soybean.}, }
@article {pmid41154061, year = {2025}, author = {Hu, J and Wei, H and Jiang, Y and Xue, Q and Wang, F}, title = {DNA Barcoding in Meat Authentication: Principles, Applications, and Future Perspectives.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {20}, pages = {}, doi = {10.3390/foods14203522}, pmid = {41154061}, issn = {2304-8158}, support = {ZCLZ24C1301//Basic Public Welfare Research Plan of Zhejiang Province, China, grant number/ ; 2023YW15//Fundamental Research Funds of China Jiliang University, grant number/ ; CY2023327//Zhejiang Provincial Administration for Market Regulation Eagle Plan Cultivation, grant number/ ; }, abstract = {DNA barcoding technology, as a species identification method based on specific DNA sequence variations, has been widely applied in meat product authentication in recent years. This paper reviews the technical principles, current applications, and comparative advantages of DNA barcoding in meat identification, particularly in contrast to traditional authentication methods. It further highlights the critical role of DNA barcoding in ensuring meat authenticity, enhancing food safety, and contributing to biodiversity conservation efforts. Furthermore, the paper explores the strategic implications and future trends of DNA barcoding in food regulation and ecological protection, demonstrating its practical feasibility and broad prospects in meat products. By highlighting its applications in detecting food adulteration and verifying species origin, this review aims to promote the safety and sustainable development of the meat industry while providing valuable insights for related fields. Ultimately, the implementation of DNA barcoding technology serves as a crucial safeguard for public food safety and health, aligning with the growing demand for improved food control systems.}, }
@article {pmid41153436, year = {2025}, author = {de Virgilio, M and De Paola, D and Selvaggi, M and Carbonara, C and Ragni, M and Caputi Jambrenghi, A and Giannico, F and Colonna, MA and Tarricone, S}, title = {DNA Barcoding and Analysis of Nutritional Properties as a Tool for Enhancing Traceability of Anchovies (Engraulis encrasicolus L.) Fished in the Italian Southern Adriatic Sea.}, journal = {Genes}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/genes16101219}, pmid = {41153436}, issn = {2073-4425}, support = {B91B17001140009//Regione Puglia/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Seafood/analysis ; Italy ; *Nutritive Value ; Mediterranean Sea ; Fatty Acids/analysis ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Seasons ; Pilot Projects ; }, abstract = {Background: Anchovies (Engraulis encrasicolus L.) are a component of the Mediterranean diet and among the most fished species. Despite Italian consumers showing a strong preference and willingness to pay more for locally caught anchovies, cases of mislabeling with non-local or different species have been documented. Molecular techniques like DNA barcoding offer reliable species identification, even in processed products, where morphological traits are no longer detectable. This pilot study applied a DNA barcoding technique targeting the mitochondrial cytochrome b gene to authenticate anchovies caught in the Italian Southern Adriatic Sea. Objectives: The study evaluated seasonal variations in the chemical and nutritional composition of anchovies, particularly the fatty acid profiles, highlighting their health benefits. Methods: During 2021, two fish samplings of anchovies were conducted per season from two fishing areas in Southern Adriatic Sea, one sample was used for mitochondrial DNA analyses, the other was used for morphometric measurements, physical, bromatological and chemical analyses. Results: Fish collected in summer showed higher total weight and edible yield relative to those fished in winter (p < 0.05). Anchovies fished in summer contained the highest concentration of proteins (p < 0.05) as compared to those caught during winter and autumn, while, in turn, they showed the highest amount of fat (p < 0.01). Fillets from anchovies fished during spring and summer contained a greater (p < 0.05) concentration of polyunsaturated fatty acids, and n-3 fatty acids than samples collected in autumn and winter. Conclusions: This study paves the way for further investigation to refine and validate the genetic identification and nutritional features of anchovies caught in the Italian Southern Adriatic Sea and marketed to consumers.}, }
@article {pmid41153363, year = {2025}, author = {Guo, X and Bai, Y and Ruan, J and Jin, X and Wang, S and Xue, D and Wu, Y}, title = {Comparative Analysis of Artemisia Plastomes, with Implications for Revealing Phylogenetic Incongruence and Evidence of Hybridization.}, journal = {Genes}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/genes16101145}, pmid = {41153363}, issn = {2073-4425}, support = {32270215//National Natural Science Foundation of China/ ; LQ24C020002//Zhejiang Provincial Natural Science Foundation of China/ ; YB202406//University Laboratory Research Project of Zhejiang Province/ ; }, mesh = {*Artemisia/genetics/classification ; *Phylogeny ; *Hybridization, Genetic ; *Plastids/genetics ; Evolution, Molecular ; DNA Barcoding, Taxonomic ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; }, abstract = {Background: With the advancement of the next-generation sequencing technology, it is becoming more cost-effective to obtain plastomes from genome skimming data at shallow sequencing depth. Artemisia is a species-rich genus, comprising species of great medicinal or economic value. However, plastomes of Artemisia have not been thoroughly and comparatively analyzed, and the phylogenetic relationships within the genus are still not well resolved. Methods: In this study, 19 Artemisia plastomes were obtained from genome skimming data. Together with the plastomes retrieved from the public database, comparative analyses of their structure were also conducted. We further used sequences of plastomes and nuclear internal transcribed spacer sequences to conduct phylogenetic reconstruction. Results: The Artemisia plastomes are conserved in terms of structure, GC content, gene number, and order. Some regions, i.e., accD, ccsA, ndhE, ycf1, ccsA-ndhD, trnG[GCC]-trnfM[CAU], were found to be variable and could be chosen as candidates for the DNA barcode. Phylogenetic analyses also confirmed that the four subgenera of Artemisia are not monophyletic. The incongruence between plastid and nuclear phylogenies indicated that hybridization events have occurred during the evolution of the genus. Conclusions: Reconstructed phylogenies using plastome sequences and nuclear internal transcribed spacers improved our understanding of the phylogenetic backbone of Artemisia. In the future, more taxa of Artemisia should be sequenced and analyzed to clarify the evolutionary history.}, }
@article {pmid41151664, year = {2025}, author = {Laojun, S and Changbunjong, T and Kamoltham, T and Chaiphongpachara, T}, title = {An integrative approach to DNA barcoding, geometric morphometrics, and machine learning for field identification of Culex mosquitoes (Diptera: Culicidae), with implications for vector-borne disease surveillance.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107885}, doi = {10.1016/j.actatropica.2025.107885}, pmid = {41151664}, issn = {1873-6254}, abstract = {Culex mosquitoes are of considerable medical and veterinary importance, acting as vectors of arboviruses such as Japanese encephalitis, Rift Valley fever, and West Nile virus, as well as the filarial parasite Wuchereria bancrofti. Accurate identification of Culex species, however, remains challenging due to their close morphological similarity, frequent damage to field-collected specimens, and the limited availability of trained taxonomists. To address these challenges, this study employed an integrative framework combining DNA barcoding, wing geometric morphometrics (GM), and Random Forest (RF) to improve the identification of 12 Culex species (Cx. bicornutus, Cx. bitaeniorhynchus, Cx. brevipalpis, Cx. fuscocephala, Cx. gelidus, Cx. hutchinsoni, Cx. nigropunctatus, Cx. pseudovishnui, Cx. quinquefasciatus, Cx. sinensis, Cx. sitiens, and Cx. tritaeniorhynchus) in Thailand. DNA barcoding successfully validated the morphological identifications, with nucleotide sequences from representative specimens showing strong concordance with the GenBank and Barcode of Life Data Systems (BOLD) databases (≥97-100%), confirming the reliability of morphological diagnoses. Complementarily, wing GM demonstrated stronger discriminatory power: Mahalanobis distance analysis revealed all species to be significantly different (p < 0.05), and a cross-validated reclassification test achieved 82.18% performance with an adjusted total accuracy of 80%. For field identification of unknown specimens, both Mahalanobis distance and RF produced comparable results, yielding very high accuracy (80%-100%) for eight species. Overall, the integration of DNA barcoding, wing GM, and machine learning offers a robust and practical framework for strengthening mosquito-borne disease surveillance. Nonetheless, as each method has distinct strengths and limitations, their application should be carefully adapted to specific epidemiological and operational contexts.}, }
@article {pmid41151578, year = {2025}, author = {Zhang, X and Wu, Z and He, H and Guan, Q and Ouyang, Q and Wang, R and Xie, L and Zhou, Y and Feng, B and Luo, Z and Xu, P and Yan, W and Hu, G and Li, J and Zhang, M and Zou, Y and Xu, X and Zhou, C and Cheng, Q and Liu, J and Gao, Q and Yang, S and Xiong, M and Chen, Y}, title = {3D-generation of high-purity midbrain dopaminergic progenitors and lineage-guided refinement of grafts supports Parkinson's disease cell therapy.}, journal = {Cell stem cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.stem.2025.10.001}, pmid = {41151578}, issn = {1875-9777}, abstract = {The low in vivo yield of midbrain dopaminergic (mDA) neurons and uncertain lineage fates of donor cells following transplantation impede clinical application of human pluripotent stem cell (hPSC)-based cell therapy for Parkinson's disease (PD). We developed a three-dimensional (3D) differentiation method, SphereDiff, to generate high-purity mDA progenitors (mDAPs), leading to a significant enrichment of mDA neurons post transplantation. Grafted mDA neurons fully restored dopamine levels and corrected motor deficits in PD model mice. Single-cell spatial transcriptomics revealed a patterned distribution of mDA neuron subtypes and glial cells. Using cross-transplantation single-cell split barcoding (TX-SISBAR), we elucidated the clonal lineage fates of donor cells post transplantation, revealing the mDA neuron and astrocyte fates of mDAPs and glutamatergic neuron fates of diencephalic progenitors. Leveraging these lineage insights, we further refined SphereDiff and eliminated off-target lineage cells. Producing high in vivo efficacy, lineage-defined donor cells supports safer and more effective PD cell therapy in regenerative medicine.}, }
@article {pmid41148924, year = {2025}, author = {Zangl, L and Fischer, I and Sittenthaler, M and Chovanec, A and Gros, P and Holzinger, W and Kunz, G and Lienhard, A and Macek, O and Mayerhofer, C and Mladinić, M and Topić, M and Schäffer, S and Sefc, KM and Sturmbauer, C and Haring, E and Koblmüller, S}, title = {A DNA Barcode Inventory of Austrian Dragonfly and Damselfly (Insecta: Odonata) Species.}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, pmid = {41148924}, issn = {2075-4450}, support = {na//Austrian Federal Ministry of Science, Research and Economy/ ; W-UNS-01/17//Municipal Department 22 - Environmental Protection (MA22)/ ; W-UNS-01/17//European Agricultural Fund for Rural Development 2014-2020/ ; }, abstract = {Dragonflies and damselflies are important indicator species for quality and health of (semi-)aquatic habitats. Hitherto, 78 species of Odonata have been reported for Austria. Ecological data, Red List assessments, and a dragonfly association index exist, but population- and species-level genetic data are largely lacking. In this study, we establish a comprehensive reference DNA barcode library for Austrian dragonflies and damselflies based on the standard barcoding marker COI. Because of the increasing significance of environmental DNA (eDNA) analyses, we also sequenced a segment of the mitochondrial 16S rRNA gene, a marker often used in eDNA metabarcoding approaches. In total, we provide 786 new COI barcode sequences and 867 new 16S sequences for future applications. Sequencing success was >90 percent for both markers. Identification success was similar for both markers and exceeded 90 percent. Difficulties were only encountered in the genera Anax Leach, 1815, Chalcolestes Kennedy, 1920, Coenagrion Kirby, 1890 and Somatochlora Selys, 1871, with low interspecific genetic distances and, consequently, BIN (barcode index number) sharing. In Anax, however, individual sequences clustered together in species-specific groups in the COI tree. Irrespective of these challenges, the results suggest that both markers perform well within most odonate families in terms of sequencing success and species identification and can be used for reliably delimiting Austrian species, monitoring, and eDNA approaches.}, }
@article {pmid41148905, year = {2025}, author = {Melone, G and Andretta, L and Guastaferro, VM and Romito, E and Formisano, G and Giorgini, M and Laudonia, S}, title = {The Parasitoid Complex of Aleurothrixus floccosus (Hemiptera: Aleyrodidae) in the Citrus Groves of Central-Southern Italy.}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/insects16101037}, pmid = {41148905}, 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 = {The woolly whitefly, Aleurothrixus floccosus, is likely a Neotropical origin species that has spread globally. Introduced to France in 1969, it became a pest in southern European citrus groves, first reported in Italy in 1974. Integrated management using biological control agents is crucial due to the low efficacy of chemical controls. Nymphs produce waxy filaments and honeydew, limiting insecticide contact. Natural enemies, especially from Neotropics, have been documented. The parasitoids Amitus spiniferus and Cales noacki were released in France in 1970 and later observed in Liguria, Italy. In the Campania region, C. noacki was first found on Aleurotuba jelineki in 1984 and this finding preceded the first report of A. floccosus in the same area. Subsequently, C. noacki was also introduced in other regions where it showed better adaptation throughout the Italian territory, reaching high parasitization levels on the woolly whitefly nymphs. After many years since the last field investigations, surveys in 2024-2025 in organic citrus groves in central and southern Italy identified additional parasitoids. Besides C. noacki and A. spiniferus, Eretmocerus paulistus and Signiphora xanthographa were found for the first time in Italy. Both species were originally described from the Neotropical ecozone. The aphelinid finding represents its first documented establishment in Italy, while the signiphorid one represents a new record for the European fauna. E. paulistus is a primary parasitoid, while S. xanthographa is a hyperparasitoid that can limit the effectiveness of other parasitoids. The interaction of these parasitoids resulted in high parasitism rates for A. floccosus nymphs. Preserving the current complexity of parasitoids in integrated pest management (IPM) programs could effectively control the woolly whitefly in central and southern Italy.}, }
@article {pmid41148902, year = {2025}, author = {Thongsahuan, S and Aupalee, K and Yakoh, A and Kaewnoi, D and Maleewong, W and Srisuka, W and Wannasan, A and Saeung, A and Takaoka, H}, title = {Integrative Description and Redescription of Black Fly (Diptera: Simuliidae) Species in the Simulium (Gomphostilbia) ceylonicum Species-Group from Thailand.}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/insects16101034}, pmid = {41148902}, issn = {2075-4450}, support = {N42A670561//National Research Council of Thailand/ ; }, abstract = {Utilizing the COI barcoding approach, cryptic diversity has previously been detected within the morphologically recognized Simulium (Gomphostilbia) trangense Jitklang, Kuvangkadilok, Baimai, Takaoka &amp; Adler, 2008 and S. (G.) sheilae Takaoka &amp; Davies, 1995, of the S. (G.) ceylonicum species-group. Here, an unknown black fly species belonging to the S. ceylonicum species-group from southern Thailand was discovered and described as a new species, S. (G.) sipoense sp. nov. In addition, S. (G.) trangense is herein fully redescribed based on specimens collected from its type locality. Based on an integrative taxonomic approach combining morphological and molecular data, the validity of the newly described S. sipoense sp. nov. and the redescribed S. trangense is confirmed. Comparative morphological characteristics and phylogenetic analysis, inferred from COI sequences, suggest that the new species is conspecific with the species redescribed as S. trangense, using specimens collected from Malaysia, and is morphologically and phylogenetically closely related to S. sheilae, particularly to the specimens from Indonesia. The redescribed S. trangense is genetically highly similar or even identical to the species that was apparently misidentified as S. sheilae from southern and western Thailand, and is morphologically very similar to the new species, from which it is clearly distinguished by the relative length of the female claw tooth, shape of the male ventral plate, and color of the larval body. A detailed information on the morphological characteristics separates the new species, and the redescribed S. trangense from all other known species of the same species-group in Thailand and neighboring countries is provided. Further studies are warranted to clarify the taxonomic status of several cryptic species recognized within the morphologically defined S. trangense and S. sheilae.}, }
@article {pmid41148898, year = {2025}, author = {Kasparek, M and Schmid-Egger, C and Roberts, H}, title = {Cryptic and Non-Cryptic Diversity in Cleptoparasitic Bees of the Genus Stelis Panzer, 1806, Subgenus Stelidomorpha Morawitz, 1875, with a Description of New Species from the Arabian Peninsula (Hymenoptera, Megachilidae).}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/insects16101030}, pmid = {41148898}, issn = {2075-4450}, abstract = {Cleptoparasitic bees of the subgenus Stelis (Stelidomorpha) occur mainly in the Mediterranean and Middle East. In this study, we elevate Stelis aegyptiaca ssp. canaria Warncke, 1992 to species rank (S. canaria Warncke, 1992) and describe two new species, Stelis alainensis Kasparek sp. nov. and Stelis surica Kasparek sp. nov., both discovered in Oman and the United Arab Emirates. Morphological differences between these species and their closest relatives (S. aegyptiaca Radoszkowski, 1876, S. pentelica Mavromoustakis, 1963, and S. nasuta (Latreille, 1809)) are corroborated by genetic divergence in the mitochondrial COI barcode region, with Kimura 2-parameter (K2P) distances of 7.6-15.2%. A notable case is Stelis nasuta, which shows deep genetic subdivision into three clusters: (1) Iberian Peninsula and North Africa, (2) southeastern France, Italy, and the Balkans, (3) eastern Balkans, Turkey, and the Levant. Moderate genetic K2P distances of 2.9-3.3% complicated species delimitation. Analyses with ABGD, ASAP, bPTP, and RESL algorithms consistently supported recognition of these lineages as putative species. As multivariate analyses of 11 morphometric traits revealed no consistent diagnostic differences, we treat these lineages as phylospecies rather than formal taxa. Our findings demonstrate that bee diversity in the Palaearctic remains underestimated, and that expanded sampling and integrative approaches continue to reveal hidden lineages.}, }
@article {pmid41148888, year = {2025}, author = {Yetchom Fondjo, JA and Wandji, AC and Zahiri, R and Hawlitschek, O and Hemp, C}, title = {Integrative Taxonomy Revealed Cryptic Diversity in the West African Grasshopper Genus Serpusia Karsch, 1891 (Orthoptera: Catantopinae).}, journal = {Insects}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/insects16101020}, pmid = {41148888}, issn = {2075-4450}, abstract = {BACKGROUND/OBJECTIVES: Despite their ecological significance, DNA barcoding data for African rainforest Orthoptera remain underrepresented globally, limiting progress in species discovery, biodiversity assessment, and conservation. This study aimed to generate molecular data for morphologically identified Serpusia Karsch, 1891 species to evaluate their taxonomic status.<br><br>METHODS: Specimens were collected from multiple sites in Cameroon and analyzed using DNA barcoding with COI-5P and 16S rDNA markers. Species delimitation was performed with Automatic Barcode Gap Discovery, and phylogenetic relationships were inferred using Maximum Likelihood and Bayesian Inference. Additionally, external morphology and the male phallic complex were examined.<br><br>RESULTS: Molecular analyses delineated 19 MOTUs, five corresponding to Serpusia opacula, seven to Serpusia succursor and the remainder to outgroups. Similarity-based assignments matched these MOTUs to 19 BINs. Phylogenetic reconstruction revealed S. opacula and S. succursor as two genetically distinct clades, with the S. opacula group more closely related to Aresceutica Karsch, 1896 than to the S. succursor group. Accordingly, we established a new genus, Paraserpusia gen. nov., to accommodate S. succursor. Within the S. opacula group, five species are recognized: one previously described (S. opacula) and four new species (S. kennei sp. nov., S. missoupi sp. nov., S. seinoi sp. nov., and S. verhaaghi sp. nov.). The former S. succursor, now Paraserpusia succursor, is divided into six well-supported lineages, five of which are formally described here (P. hoeferi sp. nov., P. husemanni sp. nov., P. kekeunoui sp. nov., P. tamessei sp. nov., and P. tindoi sp. nov.). A haplotype network based on COI-5P sequences corroborates three major clades corresponding to the S. opacula group, the S. succursor group, and Aresceutica. Diagnostic morphological differences between Serpusia and Paraserpusia are consistently supported across characters.<br><br>CONCLUSIONS: This integrative approach reveals substantial hidden diversity within Serpusia and highlights the importance of combining molecular and morphological data to uncover and formally describe previously overlooked taxa.}, }
@article {pmid41147142, year = {2025}, author = {Yadav, V and Tiwari, AK and Siddhanta, S}, title = {Generative Adversarial Network-driven high-resolution Raman spectral generation for accurate molecular feature recognition.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5an00354g}, pmid = {41147142}, issn = {1364-5528}, abstract = {Through the probing of light-matter interactions, Raman spectroscopy provides invaluable insights into the composition, structure, and dynamics of materials. Obtaining such data from portable and cheap instruments is of immense practical relevance in several domains. Here, we propose the integration of a Generative Adversarial Network (GAN) to generate high-resolution Raman spectra with a portable hand-held spectrometer to facilitate concurrent spectral analysis and compound classification. Portable spectrometers generally have a lower resolution, and the Raman signal is usually buried under the background noise. The GAN-based model could not only generate high-resolution data but also reduce the spectral noise significantly. The generated data was further tested on a trained Artificial Neural Network (ANN) model for the classification of organic and pharmaceutical drug molecules, which was further used for spectral barcoding for the identification of unknown pharmaceutical drugs. This integrated system holds the potential for achieving accurate and real-time monitoring of noisy inputs to obtain high throughput output, thereby opening new avenues for applications in different domains. This synergy between spectroscopy and machine learning (ML) facilitates improved data processing, noise reduction, and feature extraction and paves the way for predictive modeling and automated decision-making using cost-effective portable devices.}, }
@article {pmid41145626, year = {2025}, author = {Wang, Y and Salama, YE and Amer, KE and Elsayed, WF and Orabi, SA and El-Sappah, AH and Mahdy, EMB and Zayed, EM and Elashtokhy, MMA}, title = {Molecular and agronomic assessment of faba bean genotypes identifies resistance to Orobanche crenata infestation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {37535}, pmid = {41145626}, issn = {2045-2322}, mesh = {*Vicia faba/genetics/parasitology/growth &amp; development ; *Orobanche/physiology ; Genotype ; *Plant Diseases/genetics/parasitology ; *Disease Resistance/genetics ; }, abstract = {Faba bean (Vicia faba L.)(V. faba), an essential legume in Egypt, is severely impacted by broomrape (Orobanche crenata) (O. crenata), a parasitic weed that feeds on roots, making chemical control difficult without harming the crop. Three faba bean genotypes (Giza-843, Misr-3, and Sakha-3) along with nine pure lines were evaluated for resistance to broomrape in field trials (2021-2023) using gene barcoding (rbcL, rpoC1), ten Start Codon Targeted (SCoT) markers, and phonological and agronomic traits to identify resistance sources. Five faba bean genotypes-Giza 843, Lines 2, 7, 8, and 9-significantly reduced all broomrape growth and productivity traits. Line 5 had the lowest spike length, fresh and dry spike weight, number of spikes/m[2], and number of capsules/spike across both seasons. Genotypes Line 5, Line 6, and Misr 3 exhibited the highest seed yield per plot and hectare under normal and broomrape-infested conditions. Line 4 showed the lowest yield reductions, followed by Lines 9 and 8. The study generated 103 amplicons with a polymorphism rate of 51.46%, with SCoT-10 being the most informative marker, revealing 69% polymorphism and affecting 13 amplicons. Three faba bean genotypes showed significant genetic diversity, high seed output, and effectively reduced broomrape growth, highlighting their potential for genetic improvement and sustainable use in future research. Four faba bean genotypes, namely Sakha 3, Line 2, Line 4, and Line 9, are promising genotypes for combating broomrape infestation.}, }
@article {pmid41145427, year = {2025}, author = {van der Nol, E and Haupt, NA and Gao, QQ and Smit, BAM and Hoffmann, MA and Engler-Lukajewski, M and Ludwig, M and McKenna, S and Mata, JM and Béquignon, OJM and van Westen, G and Wendel, TJ and Noordermeer, SM and Böcker, S and Pomplun, S}, title = {Barcode-free hit discovery from massive libraries enabled by automated small molecule structure annotation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {9479}, pmid = {41145427}, issn = {2041-1723}, support = {VFE 0003//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; VFE 0029//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; 101039354//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Small Molecule Libraries/chemistry/pharmacology ; *Drug Discovery/methods ; Humans ; Carbonic Anhydrase IX/antagonists &amp; inhibitors/metabolism ; Tandem Mass Spectrometry ; Software ; }, abstract = {Affinity-selection platforms are powerful tools in early drug discovery, but current technologies - most notably DNA-encoded libraries (DELs) - are limited by synthesis complexity and incompatibility with nucleic acid-binding targets. We present a barcode-free self-encoded library (SEL) platform that enables direct screening of over half a million small molecules in a single experiment. SELs combine tandem mass spectrometry with custom software for automated structure annotation, eliminating the need for external tags for the identification of screening hits. We develop efficient, high-diversity synthesis protocols for a broad range of chemical scaffolds and benchmark the platform in affinity selections against carbonic anhydrase IX, identifying multiple nanomolar binders. We further apply SELs to flap endonuclease 1 (FEN1) - a disease related DNA-processing enzyme inaccessible to DELs - and discover potent inhibitors. Taken together, screening barcode-free libraries of this scale all at once represents an important development, enables access to novel target classes, and promises substantial impact on both academic and industrial early drug discovery.}, }
@article {pmid41143289, year = {2025}, author = {Sosa, SOSA and Andrade, LF and Boyko, CB and Brandt, A and Buge, B and Dávila Jiménez, Y and Henseler, M and Hernández Alcántara, P and Jóźwiak, P and Knauber, H and Marcondes Machado, F and Martínez-Muñoz, CA and Momtazi, F and Nakadera, Y and Qiu, JW and Riehl, T and Rouse, GW and Sigwart, JD and Sirenko, B and Souza-Filho, JF and Steger, J and Stępień, A and Tilic, E and Trautwein, B and Vončina, K and Williams, JD and Zhang, J}, title = {Ocean Species Discoveries 13-27 - Taxonomic contributions to the diversity of Polychaeta, Mollusca and Crustacea.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e160349}, pmid = {41143289}, issn = {1314-2828}, abstract = {BACKGROUND: Despite centuries of exploration, marine invertebrate biodiversity remains notably under-described. The majority of species in major marine groups are still unnamed, limiting our ability to understand and conserve ecosystems facing rapid environmental change. The rate of species discovery continues to outpace the formal process of species description. This gap creates an urgent need for streamlined, scalable approaches to taxonomy. The SENCKENBERG OCEAN SPECIES ALLIANCE was founded to help meet this challenge by facilitating global collaboration, offering technical support for species documentation and promoting efficient taxonomic publishing. Within this framework, Ocean Species Discoveries provides a forum for concise, but data-rich descriptions of marine invertebrate taxa. This second collection presents a diverse set of taxonomic contributions, based on recent and historical collections, including newly-described species and a re-description of a previously poorly-known taxon. The integrative documentation of the taxa treated herein was facilitated by the newly-established Discovery Laboratory at the Senckenberg Research Institute, the first service unit dedicated to supporting alpha taxonomists.<br><br>NEW INFORMATION: This article presents 14 new species and one re-description, two new genera, with taxa spanning three phyla. Newly-described taxa comprise two polychaete annelids: Nicon salinus Hern&#xe1;ndez-Alc&#xe1;ntara &amp; D&#xe1;vila-Jim&#xe9;nez, sp. nov. and Spinther bohnorum Tilic &amp; Rouse, sp. nov. Molluscs span four classes, with three polyplacophorans: Craspedochiton zefranki Von&#x10d;ina, sp. nov., Ferreiraella charazata Sigwart, sp. nov. and a new genus with type species Pycnodontochiton sinensis Sirenko, Zhang &amp; Sigwart, gen. et sp. nov. and Pycnodontochiton tenuidontus (Saito and Okutani, 1990), comb. nov. The new monoplacophoran Veleropilina gretchenae Sigwart &amp; Steger, sp. nov. is one of the first species of this class with a high-quality genome, published from the specimen that is now the holotype. The scaphopod Laevidentalium wiesei Sahlmann, 2012 represents a re-description and range extension and the bivalve Myonera aleutiana Machado &amp; Sigwart, sp. nov. is the second bivalve including an anatomical description with non-invasive methods using micro-CT. Amongst crustaceans, there are two new amphipod species: Apotectonia senckenbergae Momtazi &amp; Riehl, sp. nov. and Metharpinia hirsuta Souza-Filho &amp; Andrade, sp. nov. Three isopod species were described, including the parasitic species Zeaione everta Boyko &amp; Williams, sp. nov. that is the only species in the new genus Zeaione Boyko &amp; Williams, gen. nov. and two free-living isopods: Haploniscus bulbosus Henseler, Knauber &amp; Riehl, sp. nov. and Macrostylis peteri Riehl, sp. nov. Finally, there are two new tanaidaceans: Hoplopolemius olo J&#xf3;&#x17a;wiak &amp; St&#x119;pie&#x144;, sp. nov. and Nesotanais thalassinus St&#x119;pie&#x144;, sp. nov.The data used for the description of ten of the species and one of the new genera treated herein were wholly or partially obtained at the SOSA Discovery Laboratory using integrative methods including light and electron microscopy, confocal imaging, molecular barcoding and micro-CT scanning. Additional novel findings include the first record of the family Macrostylidae and the genus Macrostylis G. O. Sars, 1864 from Australian waters (Macrostylis peteri, sp. nov.) and novel host associations: Ferreiraella charazata, sp. nov. is documented with epibiotic tubeworms on its tail valves that are typical of this genus and the decapod Eucalliaxiopsis aequimana (Baker, 1907) is newly recorded as a host for bopyrid isopods, representing the first such record for the family Eucalliacidae.}, }
@article {pmid41143268, year = {2025}, author = {Cu, HL and Nguyen, HD and Pham, LT and Chu, MH}, title = {Dataset on some chloroplast DNA regions of Strobilanthes bantonensis Lindau in Vietnam.}, journal = {Data in brief}, volume = {62}, number = {}, pages = {111932}, pmid = {41143268}, issn = {2352-3409}, abstract = {Strobilanthes bantonensis is used in traditional medicine to treat gastritis, lung inflammation, high fever, heat reduction, and tumors. S. bantonensis is a plant species of scientific interest for the discovery of novel physiologically active compounds. The Strobilanthes species exhibit considerable morphological similarity and significant homoplasy, which together with deformed or powdered specimens, complicate further classification and distinction. This dataset contains the nucleotide sequences of PCR-specific primer pairs, the sequences of the trnE-trnT, psbK-psbI, ycf1, and matK regions isolated from the S. bantonensis, and the phylogenetic trees constructed from the sequences of these chloroplast DNA regions. In the phylogenetic trees constructed based on the two intergenic regions, trnE-trnT and psbK-psbI, and the matK gene region, S. bantonensis (CB_VN) is in the same subgroup as S. bantonensis (GenBank: MT576695.1), with bootstrap coefficients of 100 %, 100 %, and 98 %, respectively. Notably, in all three phylogenetic trees, S. bantonensis (CB_VN) is distributed in the monophyletic group (Strobilanthes). The trnE-trnT, psbK-psbI, and matK markers are viable candidates for DNA barcoding to assist in the identification of Strobilanthes species. The primer pairs trnE-trnT_F/trnE-trnT_R, psbK-psbI_F/psbK-psbI_R, ycf1_F/ycf1_R, and matK_F/matK_R can be used to amplify the trnE-trnT, psbK-psbI, ycf1, and matK regions from species of the Strobilanthes genus, Acanthaceae family and other higher plants. This dataset is the first report on the trnE-trnT, psbK-psbI, ycf1, and matK markers and the phylogeny based on these sequences of S. bantonensis.}, }
@article {pmid41142504, year = {2025}, author = {Chen, W and Song, S and Samanta, A and Sethi, S and Drees, C and Kappl, M and Butt, HJ and Walther, A}, title = {Growing functional artificial cytoskeletons in the viscoelastic confinement of DNA synthetic cells.}, journal = {Nature chemical engineering}, volume = {2}, number = {10}, pages = {627-639}, pmid = {41142504}, issn = {2948-1198}, abstract = {Intracellular structures, such as cytoskeletons, form within a crowded cytoplasm with viscoelastic properties. While self-assembly in crowding is well studied, the effects of coupled viscoelastic environments remain elusive. Here we engineer all-DNA synthetic cells (SCs) with tunable viscoelastic interiors to investigate this phenomenon. We introduce facile DNA barcode engineering to selectively enrich DNA tiles with adjustable concentrations into SCs to form artificial cytoskeletons coupled to their interior. Distinct mechanistic differences in assembly occur compared with solution or simple crowding. Furthermore, we develop light, molecular and metabolic switches to direct structure formation and create self-sorted SC populations with distinct artificial cytoskeletons. These cytoskeletons strengthen SCs and support stable contacts with mammalian cells. By bridging molecular-scale DNA nanotube assembly with mesoscale condensate structures, our SCs provide a versatile platform to investigate self-assembly under viscoelastic confinement and to harness subcellular architectures for emerging applications.}, }
@article {pmid41140631, year = {2025}, author = {Wen, B and Cheng, R}, title = {A taxonomic study of Gandaritis flavomacularia and related species (Lepidoptera, Geometridae), with description of a new species from western China.}, journal = {ZooKeys}, volume = {1255}, number = {}, pages = {333-341}, pmid = {41140631}, issn = {1313-2989}, abstract = {The taxonomic status of Gandaritis flavomacularia has recently undergone revision. This study evaluates the validity of G. flavomacularia based on both morphological and molecular evidence. Furthermore, a new, closely related species, Gandaritis stueningi Wen &amp; Cheng, sp. nov. from Sichuan, China, is described, supported by both molecular and morphological data. Key morphological characters, including the male and female genitalia, are illustrated and compared with those of three related species.}, }
@article {pmid41139833, year = {2025}, author = {Neo, DM and Ben-Zion, I and Bagnall, J and Solomon, MY and Bond, AN and Gath, E and Zhang, S and Shoresh, N and Gomez, J and Hung, DT}, title = {A Multiplexed, Target-Based Phenotypic Screening Platform Using CRISPR Interference in Mycobacterium abscessus.}, journal = {ACS infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsinfecdis.5c00623}, pmid = {41139833}, issn = {2373-8227}, abstract = {The rise of difficult-to-treat Mycobacterium abscessus infections presents a growing clinical challenge due to the immense arsenal of intrinsic, inducible and acquired antibiotic resistance mechanisms that render many existing antibiotics ineffective against this pathogen. Moreover, the limited success in discovery of novel compounds that inhibit novel pathways underscores the need for innovative drug discovery strategies. Here, we report a strategic advancement in PROSPECT (PRimary screening Of Strains to Prioritize Expanded Chemistry and Targets), which is an antimicrobial discovery strategy that measures chemical-genetic interactions between small molecules and a pool of bacterial mutants, each depleted of a different essential protein target, to identify whole-cell active compounds with high sensitivity. Applying this modified strategy to M. abscessus, in contrast to previously described versions of PROSPECT which utilized protein degradation or promoter replacement strategies for generating engineered hypomorphic strains, here we leveraged CRISPR interference (CRISPRi) to more efficiently generate mutants each depleted of a different essential gene involved in cell wall synthesis or located at the bacterial surface. We applied this platform to perform a pooled PROSPECT pilot screen of a library of 782 compounds using CRISPRi guides as mutant barcodes. We identified a range of active hits, including compounds targeting InhA, a well-known mycobacterial target but under-explored in the M. abscessus space. The unexpected susceptibility to isoniazid, traditionally considered to be ineffective in M. abscessus, suggested a complex interplay of several intrinsic resistance mechanisms. While further complementary efforts will be needed to change the landscape of therapeutic options for M. abscessus, we propose that PROSPECT with CRISPRi engineering provides an increasingly accessible, high-throughput target-based phenotypic screening platform and thus represents an important step toward accelerating early stage drug discovery.}, }
@article {pmid41138890, year = {2025}, author = {Rodrigues Alves, MT and Aluotto Scalzo Júnior, SR and Nunes da Silva, W and de Almeida Costa, RA and Dias Moura Prazeres, PH and de Oliveira Costa, RB and Cordeiro Guimarães, L and de Oliveira Guarnieri, L and Marta Figueiredo, M and de Araujo Moreira, F and de Toledo Ribas, V and Ricardo Massensini, A and Goulart Guimarães, PP}, title = {High-Throughput in vivo and in vitro screening of lipid nanoparticles for nucleic acid delivery to the brain.}, journal = {International journal of pharmaceutics}, volume = {}, number = {}, pages = {126278}, doi = {10.1016/j.ijpharm.2025.126278}, pmid = {41138890}, issn = {1873-3476}, abstract = {Gene therapy is a promising approach for correcting acquired or inherited brain diseases, nevertheless, faces a challenge in effectively delivering nucleic acids to the brain. Ionizable lipid nanoparticles (LNPs) are commonly used as delivery systems, however they are often screened in in vitro settings which poorly replicates in vivo biological barriers. Here, we used a high-throughput in vivo and in vitro screening methods to assess a library of LNPs for nucleic acid delivery to neurons and brain tissue. LNPs were formulated via microfluidic mixing with different helper lipid and molar ratios, each containing a unique barcode DNA (b-DNA). LNPs were characterized and pooled for intravenous injection in C57BL/6 mice, and their biodistribution was assessed via next-generation sequencing. The top-performing LNPs, which exhibited higher b-DNA delivery to the brain, were further assessed for transfection efficiency in primary neurons using pDNA and mRNA. We established concentration-response curves, monitored protein expression overtime, and performed cell viability assays. Our results showed that DOPE-based LNPs outperformed other formulations in brain delivery and neuronal transfection. Additionally, altering the ionizable lipid in our top formulation to FDA-approved options did not improve neuronal transfection efficiency. Finally, our identified top performing LNP4 was able to induce luciferase expression in brain after intravenous administration. No signs of neurological damage, inflammation or behavioral impairments were observed. Our results demonstrate that our LNPs efficiently deliver nucleic acids to neurons and the brain, while our screening strategy accelerates the design of LNPs for brain gene therapy.}, }
@article {pmid41134309, year = {2025}, author = {Cardeñosa, D and Grogan, PA and Chapman, DD}, title = {Bite, swab, identify: Validating molecular tools for detecting depredating shark species.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70264}, pmid = {41134309}, issn = {1095-8649}, support = {//The Roe Foundation/ ; }, abstract = {Depredation, the partial or complete removal of hooked fish by predators, poses significant challenges for fisheries worldwide. Shark depredation in recreational fisheries has become a growing concern, influencing both fisheries management and public perceptions of shark conservation. Although DNA swabbing of depredated fish has been used to identify responsible shark species, the reliability of this technique remains uncertain due to potential environmental DNA (eDNA) contamination. In this study, we evaluated the accuracy of swab-based molecular identification by comparing genetic results to video-confirmed depredation events. Four depredation events were recorded in Jupiter, Florida, involving a bull shark (Carcharhinus leucas), lemon shark (Negaprion brevirostris), great hammerhead shark (Sphyrna mokarran) and great barracuda (Sphyraena barracuda). DNA analysis of swab samples from depredated fish correctly identified the responsible shark species in all three shark cases. Barracuda depredation yielded no amplification. Our findings validate the use of swab-based molecular techniques for accurately identifying depredating shark species and confirm the absence of misleading eDNA signals. This approach provides a valuable, non-invasive tool for studying predator-prey interactions and informing fisheries management strategies.}, }
@article {pmid41133790, year = {2025}, author = {Bonneau, P and Renkema, JM and Gariepy, T and Firlej, A and Fournier, V}, title = {Effects of multiple biological control agents on Drosophila suzukii (Diptera: Drosophilidae) in the laboratory, greenhouse, and field.}, journal = {Journal of economic entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jee/toaf245}, pmid = {41133790}, issn = {1938-291X}, support = {IA116618//Programme Innov'Action Agroalimentaire/ ; //Centre S&#xc8;VE/ ; }, abstract = {Drosophila suzukii Matsumura is a nearly worldwide invasive pest that causes damage to ripening fruit, particularly raspberries. Biological control in an integrated pest management strategy may be an alternative to repeated insecticide applications. We evaluated the effects of using multiple commercially available agents against D. suzukii in raspberries. In the laboratory, the combination of the pupal parasitoid Muscidifurax raptorellus Kogan and Legner (Hymenoptera: Pteromalidae) and predators Orius insidiosus Say (Heteroptera: Anthocoridae) and Chrysoperla carnea Stephens (Neuroptera: Chrysopidae) reduced D. suzukii to the lowest level compared to any 1 species or 2 species combinations in a substitutive design. However, in caged plants with ripening fruit in a greenhouse, M. raptorellus and O. insidiosus together were more effective against D. suzukii than the 3 species combination. In high tunnels, M. raptorellus and O. insidiosus were ineffective against D. suzukii, and spinosad applications with or without M. raptorellus and O. insidiosus resulted in equally low numbers of D. suzukii. In the field, M. raptorellus and O. insidiosus and Pachycrepoideus vindemmiae Rondani (Hymenoptera: Pteromalidae) releases in raspberry plots with sweet alyssum were less effective against D. suzukii than spinosad applications to plots with or without sweet alyssum as a banker plant. Hymenoptera, particularly Figitidae: Eucoilinae as determined by barcoding, were more abundant in raspberries adjacent to sweet alyssum than in raspberry plots without sweet alyssum. With the discovery and redistribution of figitid parasitoids of larval D. suzukii, future research on their effects in combination with banker plants like sweet alyssum and releases of predators is needed.}, }
@article {pmid41131974, year = {2025}, author = {Ben Ahmed, R and Gajda, &#x141; and Raś, D and Świątek, P}, title = {Taxonomic update and DNA barcoding of Tunisian nasal leeches (Annelida: Hirudiniformes; Praobdellidae): confirming Limnatis nilotica and revealing a second Limnatis species in North Africa.}, journal = {Invertebrate systematics}, volume = {39}, number = {4}, pages = {}, doi = {10.1071/IS24074}, pmid = {41131974}, issn = {1447-2600}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Leeches/classification/genetics/anatomy &amp; histology/ultrastructure ; Tunisia ; Species Specificity ; Phylogeny ; Africa, Northern ; Electron Transport Complex IV/genetics ; RNA, Ribosomal, 28S/genetics ; }, abstract = {Leeches of the genus Limnatis are known ectoparasites of vertebrates, including humans and domestic animals, with some species causing significant health complications. In this study, we describe Limnatis anouarensis sp. nov., a new nasal leech species from Tunisia and compare it with Limnatis nilotica sensu stricto from Tunisia and Morocco. Morphological analyses were conducted using light and scanning electron microscopy, focusing on external and internal structures. Additionally, mitochondrial (cytochrome c oxidase subunit I, COI; 12S rRNA, 12S) and nuclear (28S rRNA, 28S) gene fragments were sequenced for molecular characterisation. The new species is distinguished by its larger size, distinct reproductive system morphology and unique dorsal colouration, characterised by a median orange band and marginal orange stripes, in contrast to the black-striped pattern of L. nilotica (Moore, 1938). Molecular analyses confirmed that mitochondrial markers provide reliable species identification, whereas the analysed fragment of 28S gene was fully conserved and unsuitable for differentiation. These findings confirm the presence of at least two distinct Limnatis species in North Africa, emphasising the need for further taxonomic and ecological studies to clarify their distribution, host specificity and potential medical significance. ZooBank: urn:lsid:zoobank.org:pub:7CA59D0E-1D42-4A02-B886-D198DD88E698.}, }
@article {pmid41130498, year = {2025}, author = {Said, MB}, title = {Advances in molecular taxonomy of Hyalomma ticks: from classical markers to next-generation omics.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107881}, doi = {10.1016/j.actatropica.2025.107881}, pmid = {41130498}, issn = {1873-6254}, abstract = {Ticks of the genus Hyalomma are important vectors of pathogens affecting humans and animals, including viruses, bacteria, and protozoans, and their expanding geographic range, driven by climate change and migratory birds, raises concerns about emerging disease outbreaks, specifically tick-borne diseases (TBDs) in previously unaffected regions. Despite this epidemiological significance, Hyalomma taxonomy remains challenging due to morphological variability and cryptic species complexes, particularly in immature stages. This review traces how molecular taxonomy has evolved from classical to next-generation approaches, emphasizing how successive methodological innovations have transformed species identification, phylogenetic reconstruction, and vector surveillance. Molecular systematics has greatly advanced species identification and phylogeographic understanding. For instance, mitochondrial markers enable reliable barcoding and reveal broad geographic patterns, while nuclear markers complement these insights and support functional genomics studies. Yet, earlier molecular tools have often fallen short in resolving closely related species or detecting fine-scale genetic differentiation essential for understanding vector competence and adaptation. More recently, high-throughput approaches such as population genomics, sialotranscriptomics, and MALDI-TOF MS have enhanced species discrimination and allowed rapid field-based identification. These next-generation omics platforms represent the new frontier of Hyalomma systematics, enabling comprehensive genetic, proteomic, and transcriptomic characterization that bridges taxonomy with function. However, despite these advances, significant challenges persist, including the scarcity of reference genomes for several Hyalomma species, limited integration of multi-omics datasets, and the lack of standardized bioinformatics pipelines that hinder data comparability across studies. Moreover, uneven geographic sampling and inconsistent marker selection continue to restrict our capacity to delineate cryptic lineages and link genetic diversity to epidemiological outcomes. By bridging taxonomy with function, these omics innovations establish an integrated framework linking genetic diversity to epidemiological risk and provide a roadmap for predictive, standardized, and applied Hyalomma taxonomy to improve vector surveillance and disease preparedness. This review provides the first comprehensive synthesis integrating classical, mitochondrial, nuclear, and multi-omics approaches for Hyalomma systematics.}, }
@article {pmid41127325, year = {2025}, author = {Tong, Y and Liu, Z and Liu, H and Hou, Z}, title = {A new terrestrial talitrid genus, Kachinorchestia, with a new species from Myanmar (Crustacea, Amphipoda, Arcitalitridae).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e162403}, pmid = {41127325}, issn = {1314-2828}, abstract = {BACKGROUND: The Arcitalitridae (Amphipoda, Senticaudata, Talitrida, Talitroidea) is a diverse family containing 15 genera, of which Myanmarorchestia Hou, 2017 and Solitroides Suzuki, Nakano, Nguyen, Nguyen, Morino &amp; Tomikawa, 2017 were reported in Southeast Asia. During research of terrestrial amphipods in Myanmar, we found character traits of some specimens did not match any existing genus of the family Arcitalitridae. These specimens should belong to a new genus.<br><br>NEW INFORMATION: This new genus Kachinorchestia Hou, gen. nov. with one new species Kachinorchestia putao Hou, sp. nov. is described from terrestrial habitats in Myanmar. This new genus is characterised by mandible left lacinia mobilis with four teeth, gnathopod II propodus of male enlarged, oval and subchelate, with hook posteriorly, simplidactylate pereopods, complex and lobed gills and telson uncleft. Photos, molecular and morphological descriptions of new genus are provided.}, }
@article {pmid41125033, year = {2025}, author = {Rabbani, G and Chan, KH and Wainwright, BJ}, title = {Shark and ray meat sold for human consumption contains toxic metal concentrations above safe limits with concentrations varying by species and habitat.}, journal = {Marine pollution bulletin}, volume = {222}, number = {Pt 3}, pages = {118822}, doi = {10.1016/j.marpolbul.2025.118822}, pmid = {41125033}, issn = {1879-3363}, abstract = {Due to the high trophic positions sharks and rays occupy as apex predators, they are known to biomagnify toxic metals. This is problematic because shark meat consumption is increasing throughout the world where it is frequently seen as a cheap and accessible source of dietary protein. This increased consumption has the potential to expose humans to concentrations of toxic metals above those deemed safe by regulatory authorities. Shark and ray meat is frequently dried or sold as fillets making it difficult to identify the species. To overcome these identification challenges we used DNA barcoding to determine the species of shark used for meat. Two hundred and ninety-five samples were collected from retail establishments in Singapore and barcoded, this resulted in the identification of 17 species, 12 are predominantly inhabitants of coastal waters, while five are identified as oceanic species. Using inductively coupled plasma mass spectrometry the concentrations of mercury, arsenic, cadmium, and lead in each was determined. In all samples, across all species we found multiple instances where mandated safe concentrations for each metal were exceeded, with these concentrations differing significantly by species analysed. Further analysis, grouping samples by habitat type revealed significant differences in the concentrations of toxic metals between species from coastal and oceanic habitats. The results show that consumption of shark and ray meat can expose consumers to high concentrations of toxic metals, with these concentrations varying significantly by species and habitat. Given these differences, accurate and detailed product labelling that indicates the species of origin and habitat would allow consumers to avoid species that pose the highest risk to health.}, }
@article {pmid41124029, year = {2025}, author = {Cunniffe, NJ and Gold, KM and Hamelin, FM and Navas-Cortés, JA and Potnis, N and Weisberg, AJ and Garrett, KA}, title = {From Chaos to Clarity: Deriving Meaningful Biology from Big Data in Plant Pathology.}, journal = {Phytopathology}, volume = {115}, number = {10}, pages = {1240-1244}, doi = {10.1094/PHYTO-10-25-0328-FI}, pmid = {41124029}, issn = {0031-949X}, mesh = {*Big Data ; *Plant Diseases ; *Plant Pathology ; *Plants ; }, abstract = {This Focus Issue was inspired by the vast volumes of data now being generated from both laboratory experiments and field studies. These complex, high dimensional data sets demand new analytic approaches. We invited contributions that apply novel statistical, machine learning, or artificial intelligence methods, or that integrate multiple 'omics approaches to reveal new aspects of pathogen biology, host interactions, or emergent system-level properties. The Focus Issue contains 13 articles falling into five broad themes and drawing upon a diverse range of data types, from disease imaging to meta-barcoding data to optical sensing to genetic data to expert knowledge. Together, these papers show how integrating technology, data, and biology is already transforming plant pathology. We hope this Focus Issue inspires new collaborations, new methods, and a continued commitment to turning data into understanding and chaos into clarity. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.}, }
@article {pmid41122926, year = {2025}, author = {Zhang, B and Jiang, W and Fang, Z and Chen, H and Jiang, N and Zhou, J and Wan, R and Li, S and Li, T and Cai, L and Song, H and Li, L and Gao, L and Chen, L and Peng, H}, title = {Development of a High-Resolution MNP Marker System for Aquatic Biodiversity Monitoring: A Case Study With Schizothorax prenanti in the Yangtze River.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70063}, doi = {10.1111/1755-0998.70063}, pmid = {41122926}, issn = {1755-0998}, support = {2021041-ZHX//Open Research Fund of Key Laboratory of Three Gorges Project for Conservation of Fishes/ ; 2023XKZ024//Excellent Discipline Cultivation Project by Jianghan University/ ; NBZZ20220230//The Research Projects of China Three Gorges Corporation/ ; 2024JCYJ06//The Research Fund of Jianghan University/ ; 2023010201020447//Wuhan Municipal Knowledge Innovation Special Project/ ; 2025AFB113//Natural Science Foundation of Hubei Province/ ; }, abstract = {Effective monitoring of aquatic biodiversity is critical for conservation, yet current approaches such as mitochondrial COI barcoding and microsatellite markers exhibit limitations in resolution, sensitivity, and scalability, particularly for detecting low-abundance or degraded DNA in mixed aquatic samples. To address these challenges, we developed a novel Multiple Nucleotide Polymorphism (MNP) marker system tailored to S. prenanti, an endangered endemic fish species emblematic of biodiversity crises in the Yangtze River. Through restriction-site associated DNA sequencing, we identified 115 genome-wide MNP markers. These markers demonstrated ultrasensitive detection (~1 DNA copy/reaction) and high specificity (mean discriminative power = 0.77, calculated as the probability that two random samples differ at a locus). When applied to environmental DNA from the Yangtze River, the MNP system revealed substantial genetic diversity among 86 samples (84% average differentiation rate) and quantified the contribution of artificially stocked fish to natural populations, identified 567 shared alleles between stocked and wild populations. By outperforming traditional methods in analysing fragmented DNA and enabling high-throughput applications, this MNP framework provides a transformative approach for conservation genetics. Our scalable solution bridges the gap between genetic research and conservation action, offering global applicability for aquatic biodiversity monitoring.}, }
@article {pmid41120480, year = {2025}, author = {Johansen, NS and Eiken, HG and Rossmann, SL and Brurberg, MB and Skogen, M and Fajardo, MB and Glorvigen, B and Eklo, TS and Haugen, FA and Hagen, S and Lysøe, E}, title = {Aphid populations and virus vector potential in potato fields across seasons and regions in Norway.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36675}, pmid = {41120480}, issn = {2045-2322}, mesh = {*Aphids/virology/classification/genetics ; *Solanum tuberosum/virology/parasitology ; Animals ; Norway ; Seasons ; *Insect Vectors/virology ; *Plant Diseases/virology ; Potyvirus ; }, abstract = {Several aphid species pose serious treats to potato crops by causing direct damage to the plants and/or indirectly by transmitting viruses. Different morphological forms and phenotypic plasticity among aphids complicates taxonomy and identification and thus makes targeted pest management in potatoes challenging. To obtain an overview of aphids frequenting potato fields in Norway, we investigated seasonal and annual changes in aphid populations in five potato fields (58-64 °N) over a three-year period (2016-2018), using yellow pan traps. In total 2218 of the 6136 collected aphids were identified by traditional barcoding, meaning sequencing a ~ 650 fragment of the mitochondrial COI gene. This revealed 137 different species, of which 111 were identified at the species level. The remaining were identified only to the genus level, indicating potential novel species. The southernmost sampling location yielded the highest number of species and individual counts, although no clear correlations to climate factors (temperature/precipitation) was observed. Of the 111 species identified, at least 39 are potential vectors of potato virus Y (PVY) and nine species may also transmit potato virus A (PVA). Knowledge on virus vector and non-vector aphid abundance and phenology have the potential to improve pest management of potato cultivation.}, }
@article {pmid41119951, year = {2025}, author = {Geci, D and Ibrahimi, H and Strohmeier, T and Koblmller, S and Bilalli, A and Zamani, A}, title = {First DNA barcoding of Dysderidae (Araneae) from Kosovo, with new records and the description of a new species of Harpactea Bristowe, 1939.}, journal = {Zootaxa}, volume = {5653}, number = {4}, pages = {486-500}, doi = {10.11646/zootaxa.5653.4.2}, pmid = {41119951}, issn = {1175-5334}, mesh = {Animals ; *Spiders/classification/genetics/anatomy &amp; histology/growth &amp; development ; Male ; DNA Barcoding, Taxonomic ; Female ; Kosovo ; Animal Distribution ; Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {New taxonomic and faunistic data on the dysderid spiders of Kosovo are presented, along with a survey of previous records. Harpactea dardanica Geci &amp; Zamani sp. nov., belonging to the lepida species-group, is described as new to science based on male specimens collected in the Bjeshkt-e-Nemuna National Park, western Kosovo. Dysdera adriatica Kulczyski, 1897, Dy. lata Reuss, 1834, Dasumia kusceri (Kratochvl, 1935), H. rubicunda (C.L. Koch, 1838), H. srednagora Dimitrov &amp; Lazarov, 1999, and H. tenuiemboli Deltshev, 2011, as well as the genus Dasumia Thorell, 1875, are reported from Kosovo for the first time. Additional records are provided for Dy. longirostris Doblika, 1853 and H. lepida (C.L. Koch, 1838). DNA barcodes (partial sequences of the mitochondrial cytochrome c oxidase subunit 1 gene) were generated for all species. Photographic illustrations are provided for the newly described species, as well as for H. srednagora and H. tenuiemboli.}, }
@article {pmid41121673, year = {2024}, author = {Dai, YT and Chen, ZG and Hu, CL and Ning, PF and Ouyang, S and Huang, XC and Wu, XP}, title = {Taxonomic reassessment of Scabies (Bivalvia: Unionidae) species in China based on multilocus and mitogenomic phylogenetic analyses.}, journal = {Invertebrate systematics}, volume = {38}, number = {6}, pages = {}, doi = {10.1071/IS24020}, pmid = {41121673}, issn = {1447-2600}, mesh = {Animals ; *Phylogeny ; China ; Species Specificity ; *Genome, Mitochondrial ; *Bivalvia/classification/genetics/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; }, abstract = {Effective species conservation necessitates the ability to accurately differentiate among species, a challenge compounded by taxonomic uncertainties in freshwater mussels due to substantial intraspecific variation and pronounced phenotypic plasticity in shell morphology. The taxonomic status and species validity of Scabies longata and S. chinensis, two species endemic in China, have been under continuous debate since establishment. The lack of essential molecular data required for a comprehensive systematic study has resulted in the unresolved taxonomic status of these two species. This study presents molecular data, including COI barcoding, COI + 28S rRNA, and mitogenomic data combined with morphological characteristics to assess the validity of S. longata and S. chinensis. Both morphological and COI barcoding data support the conclusion that S. longata and S. chinensis are junior synonyms of Nodularia douglasiae and N. nuxpersicae respectively. Our findings suggest the absence of Scabies species in China. Mitochondrial phylogenetic analyses were used to further elucidate intrageneric relationships within the genus Nodularia, revealing the following relationships: (N. breviconcha (Nodularia sp. 1 (N. douglasiae (N. nuxpersicae, N. nipponensis)))). We underscore the significance of employing an integrated taxonomic approach for species identification, especially given the considerable morphological disparities between larvae and adult freshwater mussels. Proper morphological identification of adult specimens is essential for extracting meaningful taxonomic characters. Furthermore, our findings suggest a notable resemblance between the freshwater bivalve fauna in southern China and those east of the Mekong River. ZooBank: urn:lsid:zoobank.org:pub:DA87D330-5E23-4F4B-8CC2-CBA3CD191BE8.}, }
@article {pmid41119938, year = {2025}, author = {Zheng, Y and Badano, D and Aspck, U and Aspck, H and Hayashi, F and Liu, X}, title = {Revision of the antlion genus Epacanthaclisis Okamoto, 1910 (Neuroptera: Myrmeleontidae: Dendroleontinae).}, journal = {Zootaxa}, volume = {5657}, number = {1}, pages = {1-100}, doi = {10.11646/zootaxa.5657.1.1}, pmid = {41119938}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Animal Distribution ; *Neoptera/classification/anatomy &amp; histology/growth &amp; development ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Asia ; }, abstract = {The antlion genus Epacanthaclisis of the subfamily Dendroleontinae is herein revised. A total of 22 species (including 11 new species) are recorded from East to Central Asia and classified into four species groups: 1) the E. continentalis group: E. alaica Krivokhatsky, 1998, E. continentalis Esben-Petersen, 1935, E. darman Zheng, Badano, U. Aspck, H. Aspck &amp; Liu sp. nov., E. hamata Krivokhatsky, 1998, E. kuldurguch Krivokhatsky, 1998, E. liuyingqiae Zheng, Badano, U. Aspck, H. Aspck &amp; Liu sp. nov., E. victor Badano, Zheng &amp; Liu sp. nov., E. zhiweii Zheng, Badano, U. Aspck, H. Aspck &amp; Liu sp. nov., and E. zuqii Zheng, Badano, U. Aspck, H. Aspck &amp; Liu sp. nov.; 2) the E. tuyuezhengi group: E. tuyuezhengi Zheng &amp; Liu sp. nov., E. zhihaoi Zheng &amp; Liu sp. nov.; 3) the E. maculosa group: E. jiazhii Zheng, U. Aspck, H. Aspck, Hayashi &amp; Liu sp. nov., E. maculata (Yang, 1986), E. maculosa (Yang, 1986), E. minana (Yang, 1999), E. wuchaoi Zheng, Badano &amp; Liu sp. nov., and E. xiaohongae Zheng &amp; Liu sp. nov.; 4) the E. moiwana group: E. banksi Krivokhatsky, 1998, E. longwai Zheng, Hayashi &amp; Liu sp. nov., E. moiwana (Okamoto, 1905), and E. ningshana Wan &amp; Wang, 2010. Besides, E. batangana Yang, 1992, is not assigned to any species group. E. amydrovittata Wan &amp; Wang, 2010 syn. nov. and E. samarkandica Krivokhatsky, 1998 syn. nov. are respectively synonymized as E. banksi and E. continentalis. Immature stages of five species (E. zuqii sp. nov., E. jiazhii sp. nov., E. minana, E. banksi, and E. ningshana) from China are reported after identification through rearing and COI barcoding. A key to the species of Epacanthaclisis is provided. The specialized morphological characters, systematic position, distribution pattern, and biology of Epacanthaclisis are discussed.}, }
@article {pmid41119906, year = {2025}, author = {Pyrcz, TW and Boyer, P and Garlacz, R and Fhraeus, C and Andrade-C, MG and Blint, Z and Mahecha-J, O}, title = {Out of the blue: a new blue Lymanopoda butterfly from the pramo of northern Colombia raises questions about disjunct distributions (Lepidoptera: Nymphalidae, Satyrinae).}, journal = {Zootaxa}, volume = {5659}, number = {4}, pages = {547-564}, doi = {10.11646/zootaxa.5659.4.5}, pmid = {41119906}, issn = {1175-5334}, mesh = {Animals ; *Butterflies/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; Colombia ; Female ; Animal Distribution ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Body Size ; Ecosystem ; Organ Size ; Phylogeny ; }, abstract = {A new, striking species of satyrine butterfly, Lymanopoda chysquyco sp. nov. (Nymphalidae, Satyrinae, Satyrini, Pronophilina) is described from the Pramo de Guerrero, the northern extremity of high-altitude grasslands in the Colombian Eastern Cordillera. Among approximately 70 known Lymanopoda species, only five exhibit blue colour on the upperside of their wings, with no evidence of close relationships among them. The new species superficially resembles L. samius Westwood which occurs parapatrically at slightly lower elevations and belongs to a distantly related lineage within the genus. Remarkably, external morphology and male genitalia suggest a strong similarity of the new species to L. hazelana found in southern Ecuador and northernmost Peruover 1300 km away. Molecular analysis using COI barcoding confirms that L. hazelana and a few other closely related species also found in southern Ecuador are the closest known relatives of L. chysquyco sp. nov. This substantial geographic disjunction is unlikely to be a sampling artefact, as intermediate pramo regions of the Eastern and Central Colombian Cordillera and central Ecuador have been extensively surveyed. The origin of L. chysquyco sp. nov. in northern Colombia remains unclear, and two possible scenarioslong-distance dispersal or vicariance accompanied by large-scale extinction in intervening areasare considered.}, }
@article {pmid41119904, year = {2025}, author = {Li, SL and Zhou, YC and Liu, P and Liu, F and Peng, XJ}, title = {Three new species of the genus Draconarius Ovtchinnikov, 1999 (Araneae: Agelenidae) from Hunan Province, China.}, journal = {Zootaxa}, volume = {5659}, number = {4}, pages = {581-588}, doi = {10.11646/zootaxa.5659.4.7}, pmid = {41119904}, issn = {1175-5334}, mesh = {Male ; Animals ; China ; Female ; *Spiders/classification/anatomy &amp; histology/genetics/growth &amp; development ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Phylogeny ; }, abstract = {Three new species of the genus Draconarius Ovtchinnikov, 1999 are described as such: D. circinatus sp. nov. (male, female), D. jiemuxiensis sp. nov. (female) and D. latus sp. nov. (male, female), from Hunan province, China. Detailed descriptions, photos of somatic features and copulatory organs, as well as the distribution map are provided. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI) of D. circinatus sp. nov. (male, female) are provided.}, }
@article {pmid41119897, year = {2025}, author = {Seong, JW and Park, JG and Nam, DH}, title = {Revisiting subspecies identification of Common Kestrels (Falco tinnunculus): A critical look at Zhang et al. (2008).}, journal = {Zootaxa}, volume = {5659}, number = {4}, pages = {536-546}, doi = {10.11646/zootaxa.5659.4.4}, pmid = {41119897}, issn = {1175-5334}, mesh = {Animals ; *Falconiformes/genetics/classification ; DNA, Mitochondrial/genetics ; Phylogeny ; China ; Male ; }, abstract = {Zhang et al. (2008) investigated subspecific variation of Common Kestrels (Falco tinnunculus) wintering in Beijing, China, using a partial mtDNA control region (394395bp), and concluded that two subspecies were present. However, analysis of their raw data revealed mostly double peaks at each nucleotide position, indicating ambiguity in the DNA sequence. These likely arose from a combination of factors, including irregular PCR efficiencies and slight primer mismatches. Zhang et al. (2008) likely misinterpreted these double peaks as evidence of distinct subspecies. This resulted in an inflated number (56) of variation sites. Their interpretation was further confounded by potential issues with their primers, designed from a sequence of F. peregrinus with a one-nucleotide difference. To address these limitations, we sequenced the full mtDNA control region (1,266bp) of 38 Common Kestrel samples using newly designed primers. This analysis yielded clean, single-peak profiles for each sequence, confirming that all samples belonged to F. t. interstinctus. We therefore propose reclassifying these populations as a single subspecies, F. t. interstinctus. Erroneous barcode sequences can distort subspecific identification and population structure, leading to inaccurate data and misleading phylogenetic inferences. Our study underscores the critical need for robust methods to minimize barcode sequencing errors. This would not only ensure accurate phylogenetic inferences for Common Kestrels but also support reliable population genetic studies across diverse taxa.}, }
@article {pmid41119886, year = {2025}, author = {Wang, RH and Zhang, ZC and Feng, HY and Lin, XL}, title = {Larval morphology and DNA barcode of Synorthocladius bifidus Liu &amp; Wang, 2005 (Diptera: Chironomidae).}, journal = {Zootaxa}, volume = {5660}, number = {1}, pages = {139-146}, doi = {10.11646/zootaxa.5660.1.11}, pmid = {41119886}, issn = {1175-5334}, }
@article {pmid41119879, year = {2025}, author = {Kamyab, F and Makhov, IA and Mokhtari, A}, title = {A new species of the genus Dzhugesia Wehrli (Lepidoptera: Geometridae, Ennominae) from Iran.}, journal = {Zootaxa}, volume = {5660}, number = {2}, pages = {255-266}, doi = {10.11646/zootaxa.5660.2.6}, pmid = {41119879}, issn = {1175-5334}, mesh = {Animals ; Iran ; *Moths/classification/anatomy &amp; histology/growth &amp; development/genetics ; Male ; Female ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; }, abstract = {A series of geometrid moths belonging to the little-known genus Dzhugesia Wehrli, 1936, were collected in southern Iran (Kerman Province). Both morphological characters and DNA barcoding confirm that the specimens represent a new species, herein described as D. alierfani Makhov &amp; Kamyab sp. nov. Additional remarks on the diagnostic characters of the genus Dzhugesia are provided. The relationships between Dzhugesia and the closely related genera Crocallis and Scodiomima are also discussed. Furthermore, the misidentification of a specimen previously submitted to the BOLD database is corrected. This study constitutes the first record of the genus Dzhugesia from Iran. D. miatleuskii is recorded as new species for the fauna of Iran.}, }
@article {pmid41119869, year = {2025}, author = {Ruengsawang, N and Sangpradub, N and Cubeddu, T and Erpenbeck, D and Wrheide, G and Pronzato, R and Manconi, R}, title = {Bangkok urban census of aquatic invertebrate fauna by an integrative taxonomic approach: the case of Suan Luang Rama IX Park and its freshwater sponges (Spongillida: Spongillidae).}, journal = {Zootaxa}, volume = {5660}, number = {3}, pages = {371-388}, doi = {10.11646/zootaxa.5660.3.4}, pmid = {41119869}, issn = {1175-5334}, mesh = {Animals ; *Porifera/classification/anatomy &amp; histology/genetics/growth &amp; development ; Thailand ; Fresh Water ; Ecosystem ; Animal Distribution ; Phylogeny ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Body Size ; }, abstract = {Faunistic investigations on freshwater bodies of the Bangkok Metropolitan Area resulted in the discovery of a freshwater sponge population fragmented in small lentic microhabitats at the Suan Luang Rama IX Park. Sponges living in the lotus and waterlily garden and tropical greenhouse were photographed in situ, and some representative, small samples were collected and stored at the Division of Biology (Porifera Collection), Rajamangala University of Technology Krungthep, Bangkok. The taxonomic integrative analyses focused on diagnostic morphotraits, barcoding, and biogeography. The sponge population was ascribed to Radiospongilla cf. cerebellata (Porifera: Demospongiae: Spongillida: Spongillidae) and is a new record for the Bangkok area and the entire Thai inland water. Comparative integrative analyses vs spongillid taxa worldwide resulted in the discovery of new gemmular morphotraits for the genus. Although the Thai Radiospongilla cf. cerebellata diverges from the Indian type of Radiospongilla cerebellata at the level of gemmular theca architecture, molecular analyses highlighted the matching of the former with the Radiospongilla cluster. A possible allochthonous origin of the Bangkok Radiospongillas population is hypothesised. This investigation on botanical gardens aquatic fauna and a review of appropriate literature highlights that sponges are able to inhabit very confined and fragmented, shallow water bodies, i.e., scattered terracotta pots, plastic containers, and small ponds with aquatic plants also in megalopolis gardens.}, }
@article {pmid41119858, year = {2025}, author = {Kawashima, I and Matsui, Y and Yagi, S}, title = {Taxonomic study of Japanese species of the genus Gibberifera Obraztsov (Lepidoptera: Tortricidae: Olethreutinae), with a description of a new species.}, journal = {Zootaxa}, volume = {5660}, number = {4}, pages = {547-559}, doi = {10.11646/zootaxa.5660.4.5}, pmid = {41119858}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; Japan ; Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Gibberifera xylosmae sp. nov., whose larvae feed on Xylosma congesta (Salicaceae), is described in Japan. Photographs of adults, male and female genitalia of the three Japanese Gibberifera species are provided. The diagnosis, a key, and DNA barcodes of Japanese Gibberifera species are also presented. Intraspecific and interspecific genetic distances between Japanese Gibberifera species and other congeners are also provided.}, }
@article {pmid41119853, year = {2025}, author = {Mengual, X and Hauser, M}, title = {Atriadops Wandolleck, 1897 (Diptera: Nemestrinidae) recorded for the first time from Ecuador.}, journal = {Zootaxa}, volume = {5660}, number = {4}, pages = {596-600}, doi = {10.11646/zootaxa.5660.4.10}, pmid = {41119853}, issn = {1175-5334}, mesh = {Animals ; Ecuador ; Female ; *Diptera/classification/anatomy &amp; histology/growth &amp; development/genetics ; Animal Distribution ; Male ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; DNA Barcoding, Taxonomic ; }, abstract = {The genus Atriadops Wandolleck, 1897 (Diptera: Nemestrinidae) occurs in the Neotropical, Afrotropical, Indomalayan and Australasian Regions. It is easily recognized by not having ocelli and the vestigial mouthparts. Out of the seven recognized species worldwide, only one is present in the Neotropics, A. macula (Wiedemann, 1824). We report the first record of Atriadops from Ecuador, a female of A. macula, from the Napo Province, provide the first DNA barcode for the species, and discuss the possible reasons for the low number of records of this genus.}, }
@article {pmid41119850, year = {2025}, author = {Zheng, T and Wu, K and Zhang, F}, title = {First record of the subfamily Megaschizominae Rowland, 1973 from China, with description of a new species of Megaschizomus Lawrence, 1969 (Schizomida: Hubbardiidae).}, journal = {Zootaxa}, volume = {5661}, number = {1}, pages = {80-94}, doi = {10.11646/zootaxa.5661.1.3}, pmid = {41119850}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {The subfamily Megaschizominae Rowland, 1973 is recorded from China for the first time through the description of a new species in the genus Megaschizomus Lawrence, 1969: M. zhongshanensis sp. nov. (male, female). This study presents the first illustrated description of male genital structures for a species within this subfamily. In addition to the detailed description, illustrations, diagnosis, and a distribution map are provided. Additionally, the DNA barcode of the new species is also provided.}, }
@article {pmid41119838, year = {2025}, author = {Huemer, P and Mayr, T and Nel, J and Stark, W}, title = {Epermenia reinhardgaedikei sp. nov., an overlooked species from central-southern Europe (Lepidoptera, Epermeniidae).}, journal = {Zootaxa}, volume = {5661}, number = {2}, pages = {237-248}, doi = {10.11646/zootaxa.5661.2.5}, pmid = {41119838}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Animal Distribution ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Body Size ; Organ Size ; Europe ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Epermenia reinhardgaedikei sp. nov. is described from material collected in central Italy, south-eastern France, and eastern Austria. The species was hitherto mixed with the congeners E. theimeri Gaedike, 2001 and E. profugella (Stainton, 1856) due to superficial similarity in male genitalia. However, the new species is closest to E. iniquellus (Wocke, 1867), differing from that species and congeners in structures of male genitalia and by DNA barcodes. Adults, male and female genitalia are figured.}, }
@article {pmid41119791, year = {2025}, author = {Lim, W and Bang, WJ and Shin, S}, title = {New records of Macrocera Meigen 1803 (Diptera, Keroplatidae) from the Korean Peninsula with description of a new species.}, journal = {Zootaxa}, volume = {5665}, number = {2}, pages = {239-255}, doi = {10.11646/zootaxa.5665.2.5}, pmid = {41119791}, issn = {1175-5334}, mesh = {Animals ; Republic of Korea ; Male ; Female ; *Diptera/classification/anatomy &amp; histology/genetics/growth &amp; development ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; Organ Size ; Phylogeny ; }, abstract = {A new speciesMacrocera interrupta sp. nov.is described from Wando, South Korea. We also report the first records of M. abdominalis Okada 1937 and M. maculosa Matsumura 1915 from South Korea. DNA barcoding data for all three species are presented. Their relationships with other Macrocera species from the Palearctic Region are briefly discussed.}, }
@article {pmid41119769, year = {2025}, author = {Sohn, JC}, title = {A new species of Oruza Walker, 1861 (Lepidoptera, Erebidae, Boletobiinae) from Korea with barcode-based pairing.}, journal = {Zootaxa}, volume = {5665}, number = {4}, pages = {592-596}, doi = {10.11646/zootaxa.5665.4.8}, pmid = {41119769}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Republic of Korea ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {A new species of the genus Oruza, O. koreana sp. nov. is described, based on 14 specimens collected in Korea. The species is closely related to Oruza obliquaria Marumo, 1932 but can be distinguished from the latter by the shapes of the costal process in the male genitalia and the lamella postvaginalis in the female genitalia. The occurrence of Oruza obliquaria in Korea is discussed. Two COI barcodes of O. koreana sp. nov. are provided to facilitate pairing and reliable identification.}, }
@article {pmid41119705, year = {2025}, author = {Golovatch, SI and Enghoff, H and Efeykin, BD}, title = {Chondrodesmus riparius Carl, 1914, a millipede species new to the fauna of Costa Rica, originally described from Colombia, and introduced to and presently widespread across Europe (Diplopoda, Polydesmida, Chelodesmidae).}, journal = {Zootaxa}, volume = {5692}, number = {1}, pages = {161-174}, doi = {10.11646/zootaxa.5692.1.8}, pmid = {41119705}, issn = {1175-5334}, mesh = {Animals ; Costa Rica ; Male ; Female ; Colombia ; *Arthropods/classification/anatomy &amp; histology/growth &amp; development/genetics ; Europe ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Introduced Species ; Ecosystem ; }, abstract = {The fairly large-bodied Neotropical millipede genus Chondrodesmus Silvestri, 1897, includes 23 species described from Central America, to Costa Rica in the north, and 25 more from South America, to Colombia, Venezuela, Peru and central-western Amazonia of Brazil in the south. Among them, seven species have hitherto been described or recorded from Costa Rica, including Chondrodesmus hoffmanni (Peters, 1865), from an unknown place, and here revised based on the holotype. Unexpectedly, it appears to differ markedly from all Costa Rican congeners, and instead it shows profound similarities to Chondrodesmus riparius Carl, 1914, from Colombia. The status of the European introduction heretofore provisionally referred to either as C. cf. riparius or C. riparius is confirmed here, since morphologically the European and Tropical American C. riparius populations represent the same species. To support this, comparative molecular studies using COI barcoding data, freshly obtained from a population from Costa Rica, with a European population of C. riparius show a congruence of 99.2%. This not only indicates the conspecificity of C. riparius from South America and Europe, but it also suggests the source area whence its introduction to Europe could have occurred.}, }
@article {pmid41119695, year = {2025}, author = {Semenchenko, AA and Palatov, DM and Makarchenko, EA}, title = {A review of the taxonomy, distribution and population genetic analysis of the Diamesa cinerella group (Diptera: Chironomidae: Diamesinae), with a description of D. soktoshensis sp. nov. and DNA barcoding of known species.}, journal = {Zootaxa}, volume = {5692}, number = {1}, pages = {121-147}, doi = {10.11646/zootaxa.5692.1.6}, pmid = {41119695}, issn = {1175-5334}, mesh = {Animals ; Male ; DNA Barcoding, Taxonomic ; Animal Distribution ; *Chironomidae/classification/genetics/anatomy &amp; histology/growth &amp; development ; Phylogeny ; Female ; Body Size ; Organ Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; }, abstract = {We provide original identification keys for adult males, brief redescriptions of the seven known species, a description of a new species, D. soktoshensis sp. nov., and a molecular genetic analysis of species of the Diamesa cinerella group. Population genetic analysis of Diamesa cinerella group revealed 109 haplotypes for 183 samples and a high level of haplotype diversity0.984 0.004. We identified four haplogroups, including Diamesa tsutsuii (1), Diamesa lavillei (2), Diamesa. soktoshensis sp. nov. (3) and the remaining species (4). The four haplogroups were significantly different from each other by FST values (P < 0.01). We explored the use of the internal transcribed spacers (ITS) region as an alternative nuclear DNA barcode forspecies delimitation of the Diamesa cinerella group. Three haplogroups were identified with no obvious connection to the species or sampling location.}, }
@article {pmid41119691, year = {2025}, author = {Zhang, H and Li, Q and Yang, Z and Zhang, F}, title = {Description of five new species of Zodariidae Thorell, 1881 (Araneae) from Yunnan, China.}, journal = {Zootaxa}, volume = {5692}, number = {2}, pages = {256-276}, doi = {10.11646/zootaxa.5692.2.3}, pmid = {41119691}, issn = {1175-5334}, mesh = {Animals ; *Spiders/classification/anatomy &amp; histology/genetics/growth &amp; development ; China ; Male ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {Five new ant-eating spiders from Yunnan, China, are described: Asceua banlaoensis sp. nov. (), A. nangunhe sp. nov. (), Euryeidon cervicornis sp. nov. (), Mallinella acutidentata sp. nov. () and M. tongbiguan sp. nov. (); the habitus and copulatory organs are documented, and a distribution map is provided for all new species. The association between males and females of Euryeidon cervicornis sp. nov. was confirmed by genetic similarity (COI barcoding).}, }
@article {pmid41119662, year = {2025}, author = {Schmidt, BC and Gartshore, M}, title = {Ecology, morphology and distribution of Anisota finlaysoni Riotte (Lepidoptera, Saturniidae).}, journal = {Zootaxa}, volume = {5646}, number = {1}, pages = {63-77}, doi = {10.11646/zootaxa.5646.1.3}, pmid = {41119662}, issn = {1175-5334}, mesh = {Animals ; Animal Distribution ; Male ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Female ; Ecosystem ; Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Ontario ; Body Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; DNA Barcoding, Taxonomic ; }, abstract = {Identifying the conservation needs of the short-horned oakworm, Anisota finlaysoni Riotte, has been hampered by incomplete resolution of species boundaries and geographic ranges of the Anisota senatoria species-group. Here, the life history, morphology, occurrence, and DNA barcode variation of A. finlaysoni and A. senatoria are compared across a transect of three key geographic regions in Ontario, Canada. Contrary to recent range depictions, our results show that A. finlaysoni is currently confirmed to occur only in the region of eastern Lake Ontarios north shore. Previous information on morphological characters used to distinguish A. finlaysoni is incomplete or erroneous. Lake Erie populations most recently assigned to A. finlaysoni exhibit some finlaysoni-like larval traits, but adult phenotype of all examined material is indistinguishable from A. senatoria of the Lake Huron region, and unlike topotypical A. finlaysoni. Although the cryptic occurrence of A. finlaysoni in the Lake Erie region cannot be ruled out, current data indicate that this species has a much smaller global range than previously believed, and is separated by a geographic gap of about 200 km from the nearest A. senatoria populations. Re-assignment of the Lake Erie populations from A. finlaysoni to A. senatoria, and the recognition of some peripheral occurrence records as historical errors, results in a significantly smaller global range for A. finlaysoni. DNA barcode data for the genus Anisota are at odds with current taxonomy, limiting the utility of barcodes in discriminating species of the senatoria-group. Because A. finlaysoni is distinct morphologically as adults and larvae from geographically nearby populations of A. senatoria, it should continue to be treated as a distinct species pending convincing evidence to the contrary.}, }
@article {pmid41119576, year = {2025}, author = {Debnath, R and Reddy, BT and Rajmohana, K and Dinesh, KP}, title = {Morphological and molecular characterization of a new species of Hadronotus Frster (Hymenoptera: Scelionidae) reared from reduviid eggs in India.}, journal = {Zootaxa}, volume = {5711}, number = {3}, pages = {424-434}, doi = {10.11646/zootaxa.5711.3.7}, pmid = {41119576}, issn = {1175-5334}, mesh = {Animals ; India ; Female ; Phylogeny ; Male ; Animal Distribution ; *Reduviidae/parasitology ; *Wasps/anatomy &amp; histology/classification/genetics/growth &amp; development ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Ovum/parasitology ; }, abstract = {Hadronotus omnistriatus Debnath, Rajmohana and Thirupam Reddy sp. nov. (Hymenoptera: Scelionidae) is described herein as new to science from India under the muscaeformis species group. The specimens were reared from eggs of a reduviid host (Hemiptera: Reduviidae). A detailed morphological description is provided, along with its DNA barcode data. A single gene-based molecular phylogenetic analysis on the mitochondrial cytochrome c oxidase I is presented to support the delineation of the new species. Additionally, a checklist of Hadronotus species reported from India is provided.}, }
@article {pmid41119552, year = {2025}, author = {Timossi, G}, title = {Micropterix vulcanica sp. nov. (Lepidoptera, Micropterigidae) discovered on the island of Pantelleria (Italy, Sicily).}, journal = {Zootaxa}, volume = {5683}, number = {2}, pages = {282-288}, doi = {10.11646/zootaxa.5683.2.7}, pmid = {41119552}, issn = {1175-5334}, mesh = {Animals ; Sicily ; Male ; Female ; Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; Islands ; Ecosystem ; *Butterflies/anatomy &amp; histology/classification/genetics/growth &amp; development ; Italy ; }, abstract = {Micropterix vulcanica sp. nov. is described, found during research on the biodiversity of Lepidoptera on Pantelleria Island National Park (Italy, Sicily). The new species has a unique combination of color pattern of the wings, genital morphology and DNA barcode.}, }
@article {pmid41119529, year = {2025}, author = {Lvarez, Y and Nez, R and Magaldi, LM and Matthews, D and Freitas, AVL and Espeland, M}, title = {Phenotypes, natural history and barcodes unveil cryptic species within the Caribbean Metalmark Dianesia carteri (Holland) (Lepidoptera: Riodinidae).}, journal = {Zootaxa}, volume = {5686}, number = {1}, pages = {5-48}, doi = {10.11646/zootaxa.5686.1.2}, pmid = {41119529}, issn = {1175-5334}, mesh = {Animals ; *Butterflies/classification/anatomy &amp; histology/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Female ; Male ; Phylogeny ; Animal Distribution ; Body Size ; Organ Size ; Caribbean Region ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Phenotype ; Ecosystem ; }, abstract = {The butterfly genus Dianesia Harvey &amp; Clench, 1980 is the only known representative of the family Riodinidae in the West Indies with a single described species containing two subspecies, represented by rare, little-known populations occurring only in the Bahamas and Cuba. Until now, the genus has been regarded as monotypic, but differences in morphology, DNA barcodes and life history suggest that it contains multiple cryptic species. Our assessment led to recognize the existence of at least nine species within Dianesia: Dianesia carteri (Holland, 1902), Dianesia ramsdeni (Skinner, 1912) (previously regarded as a subspecies of the first), Dianesia galindoensis Barro, Hernndez &amp; Torres, 2025, and the newly herein described Dianesia aberrans sp. nov., Dianesia sheylae sp. nov., Dianesia alayoi sp. nov., Dianesia flammata sp. nov., Dianesia abscondita sp. nov. and Dianesia serpentinicola sp. nov. These species remained unnoticed due to their superficial resemblance and lack of information about their biology, but can be differentiated by a combination of their DNA barcodes, wing length and shape, and elements of the color pattern, particularly the forewing postdiscal white band. Genitalia, habitat, host plant, and larval morphology also serve to differentiate the species. Bayesian and maximum likelihood COI gene trees recovered a similar topology in which all species are reciprocally monophyletic except for D. alayoi nested inside D. flammata. Species delimitation analyses supported the described species, including those that are not monophyletic, and suggested the presence of three additional species, but we regard them as artifacts produced by specimens with slightly different barcodes. Future research employing more genetic and ecological data is necessary to clarify the relationships among these species, as well as to understand their biogeographical history, ecology, and behavior, and to provide baseline knowledge for their conservation.}, }
@article {pmid41119491, year = {2025}, author = {Zhou, YC and Qin, XY and Zhou, GC and Peng, XJ and Liu, P}, title = {Two new species of the genus Tmarus Simon, 1875 (Araneae: Thomisidae) from China.}, journal = {Zootaxa}, volume = {5666}, number = {1}, pages = {105-114}, doi = {10.11646/zootaxa.5666.1.5}, pmid = {41119491}, issn = {1175-5334}, mesh = {Animals ; China ; Male ; Female ; *Spiders/classification/anatomy &amp; histology/genetics/growth &amp; development ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Phylogeny ; }, abstract = {Two new species of the genus Tmarus Simon, 1875 are described and named as T. yueluensis sp. nov. () and T. rostratus sp. nov. () from Hunan Province. Detailed description, photographs of somatic features and copulatory organs, as well as a distribution map are provided. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI) of T. yueluensis. sp. nov. () are provided.}, }
@article {pmid41119488, year = {2025}, author = {Garzn-Ordua, IJ and Brower, AVZ}, title = {A new cryptic Phyllodonta Warren (Lepidoptera: Geometridae) from Mexico City with documentation of its life history.}, journal = {Zootaxa}, volume = {5666}, number = {1}, pages = {136-144}, doi = {10.11646/zootaxa.5666.1.8}, pmid = {41119488}, issn = {1175-5334}, mesh = {Animals ; Mexico ; Female ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Male ; Animal Distribution ; Larva/anatomy &amp; histology/classification/growth &amp; development ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {A new species of Phyllodonta is described and illustrated from Mexico: P. coztomatlivora sp. nov. The new species is superficially indistinguishable from others in the so-called latrata species group, from which three other cryptic species from Costa Rica were recently described. However, it differs from them in features of the female genitalia, caterpillar morphology, larval food plant choice and DNA barcode. The new entity may be restricted to high elevations of the Trans Mexican Volcanic Belt; in Mexico City, the species is found inside a protected natural area which should warrant some level of conservation.}, }
@article {pmid41119451, year = {2025}, author = {Jaume-Schinkel, S}, title = {Morpho-Molecular species delimitation within Tonnoira Enderlein (Diptera, Psychodidae): Updates on COI barcode data and the description of five new species.}, journal = {Zootaxa}, volume = {5673}, number = {1}, pages = {1-26}, doi = {10.11646/zootaxa.5673.1.1}, pmid = {41119451}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Male ; Female ; Animal Distribution ; Panama ; *Psychodidae/classification/anatomy &amp; histology/genetics/growth &amp; development ; Electron Transport Complex IV/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {This work describes five new species of Tonnoira Enderlein, namely, T. acantha sp. nov., T. asymmetrica sp. nov., T. sinuosa sp. nov., T. stria sp. nov., and T. wachi sp. nov., increasing the total number of species in this genus to 33. Additionally, T. conistylus Jaume-Schinkel, 2022 is documented for the first time in Panama. COI barcodes are provided for four of these newly described species and for T. fusiformis Quate &amp; Brown, 2004. Molecular species delimitation analyses demonstrate the effectiveness of COI barcodes in identifying and discovering Psychodidae species in the Neotropics. This work highlights the current state of COI barcoding for Tonnoira species, emphasizing the importance of integrating molecular tools with traditional taxonomy to enhance species identification and conservation strategies. These findings contribute to a more comprehensive understanding of species diversity within this genus and support ongoing biodiversity conservation efforts.}, }
@article {pmid41119442, year = {2025}, author = {Hoang, QD and Truong, BP and Tran, TTT}, title = {ReclassificationofCoelotes songae(Araneae:Agelenidae:Coelotinae)withdescriptionofitsunknownfemaleconfirmedbymorphologyandDNAbarcoding.}, journal = {Zootaxa}, volume = {5673}, number = {1}, pages = {143-150}, doi = {10.11646/zootaxa.5673.1.10}, pmid = {41119442}, issn = {1175-5334}, mesh = {Animals ; Female ; *Spiders/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; Animal Distribution ; Vietnam ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; DNA Barcoding, Taxonomic ; }, abstract = {The genus Sinocoelotes Zhao &amp; Li, 2016 is recorded from Vietnam for the first time based on the reclassificationof Coelotes songae Liu, Li &amp; Pham, 2010 as Sinocoelotes songae (Liu, Li &amp; Pham, 2010) comb. nov. The previously unknown female is described for the first time from type locality, as confirmed through DNA barcoding and morphological analysis.}, }
@article {pmid41119438, year = {2025}, author = {Beljaev, VA and Gorbunov, PY and Makhov, IA}, title = {An enigmatic new species of the genus Catarhoe (Lepidoptera: Geometridae: Larentiinae) from Kyrgyzstan and taxonomic notes to the genus.}, journal = {Zootaxa}, volume = {5618}, number = {3}, pages = {372-392}, doi = {10.11646/zootaxa.5618.3.4}, pmid = {41119438}, issn = {1175-5334}, mesh = {Animals ; Male ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; Kyrgyzstan ; Female ; Animal Distribution ; Body Size ; Organ Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {The paper presents a new species of geometrid moth of the genus Catarhoe Herbulot, 1951 from Kyrgyzstan, and offers a concise taxonomic review of the genus based on existing literature and on an analysis of COI barcode mitochondrial DNA fragment in Epirrhoini. A new species and new monotypic subgenus are described: Catarhoe (Hyporhoe subgen. nov.) narynensis sp. nov. The species is distinguished by a unique set of characters in the male genitalia, which markedly differs from those of other congeneric species, and has significant genetic distances from the rest of the Catarhoe spp. but not exceeding genetic distances into the genus at whole. The current species composition of the genus Catarhoe has been clarified and includes 13 species. Taxonomic status of Catarhoe nyctichroa (Hampson, 1912), Catarhoe arachne hissarica Viidalepp, 1988, and Catarhoe semnana sensu Kemal et al. (2020) requires clarification. A high level of morphological and genetic diversity of the genus Catarhoe was revealed. The genetic distances between the morphological groups of Catarhoe spp. are comparable to those between the genera of Epirrhoini. The generic name Microcalcarifera Inoue, 1982, is revived from its synonymy with Catarhoe. The genus includes type species Microcalcarifera obscura (Butler, 1878: 450) (Cidaria), comb. rev., and two subspecies: Microcalcarifera obscura fecunda (Swinhoe, 1891), comb. rev. and Microcalcarifera obscura multilinea (Hampson, 1891), comb. rev.}, }
@article {pmid41119392, year = {2025}, author = {Kosterin, OE and Vierstraete, A and Schneider, T and Kompier, T and Hu, FS and Jr, LE and Makbun, N and Onishko, VV and Papazian, M and Dumont, HJ}, title = {Molecular phylogenetic analysis of the family Macromiidae (Odonata) worldwide based on a mitochondrial and two nuclear markers, with a short overview of its taxonomic history.}, journal = {Zootaxa}, volume = {5620}, number = {4}, pages = {501-545}, doi = {10.11646/zootaxa.5620.4.1}, pmid = {41119392}, issn = {1175-5334}, mesh = {Animals ; *Phylogeny ; Female ; Male ; Animal Distribution ; }, abstract = {Three molecular markers (two traditional and a new one), the barcoding fragment of the mitochondrial COI gene, the nuclear ITS region of the nucleolus organiser, and the nuclear histone H3H4 region including partial sequences of the highly conserved genes of core histones H3 and H4 and the non-coding spacer between them, were sequenced in 38 (31% of all) species of Macromiidae, representing all its four genera. Besides, 15 species of the related incertae sedis genera Macromidia Martin, 1907, Idionyx Hagen, 1867 and Oxygastra Selys, 1870 were sequenced. Available sequences of the concerned groups were also adopted from GenBank. All markers resolved Macromiidae as a monophyletic clade with the highest support. In contrast, our markers did not resolve the expected monophyletic branch containing the incertae sedis genera. Didymops transversa (Say, 1840) clustered with Macromia Rambur, 1842 in most trees as an inner lineage in the Macromia cluster. For this reason, we restored the synonymy of Didymops Rambur, 1842 with Macromia. Epophthalmia Burmeister, 1839 and Phyllomacromia Selys, 1878 were resolved as sister branches, as proposed before on morphological basis. On the species level, Macromia fraenata Martin, 1907, Macromia clio Ris, 1916 and Macromia kubokaiya Asahina, 1964 were restored as valid species names. Macromia flavocolorata Fraser, 1922 was downgraded to the subspecies Macromia calliope flavocolorata, stat rev., but the name Macromia miniata Fraser, 1924 was restored as valid species name to denote the species of the Western Ghats of India once considered as M. flavocolorata as well. The synonymy of M. cupricincta Fraser, 1924 and M. berlandi Lieftinck, 1941 at the species level were confirmed but the latter was treated as M. cupricincta berlandi stat. rev. Macromia hamata Zhou, 2003 was synonymised to Macromia manchurica Asahina, 1964. The presence of Epophthalmia vittata Burmeister, 1839 in Indochina as a common species was confirmed. The situation with Macromia callisto Laidlaw, 1922 remains obscure.}, }
@article {pmid41119380, year = {2025}, author = {Can, L and Aydemr, HB}, title = {New records with DNA barcodes of the family Proctotrupidae (Hymenoptera: Proctotrupoidea) from Trkiye.}, journal = {Zootaxa}, volume = {5621}, number = {1}, pages = {131-143}, doi = {10.11646/zootaxa.5621.1.6}, pmid = {41119380}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Female ; Male ; Animal Distribution ; Phylogeny ; Body Size ; Turkey ; Organ Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Electron Transport Complex IV/genetics ; *Wasps/classification/genetics/anatomy &amp; histology/growth &amp; development ; }, abstract = {The current study presents faunistic data concerning the Proctotrupidae family from the Central Black Sea region, specifically the Yeilrmak Delta in Samsun Province, Trkiye. Specimens were collected using Malaise traps over a period from March to September 2023. A total of five species across five genera of Proctotrupidae were identified. Notably, the genera Codrus Panzer, 1805, Cryptoserphus Kieer, 1907, and Mischoserphus Townes, 1981, along with the species Codrus picicornis Foerster, 1856, Cryptoserphus aculeator (Haliday, 1839) and Mischoserphus obesus Townes, 1981 are reported for the first time in Trkiye. An identification key for the existing genera of Turkish Proctotrupidae is included. The study also investigated the use of mitochondrial cytochrome oxidase subunit 1 (COI) gene-based DNA barcoding for species identification. Partial sequence data for Proctotrupidae species Cryptoserphus aculeator, Exallonyx crenicornis, Mischoserphus obesus, Phaneroserphus calcar, and Phaenoserphus viator were obtained and submitted to the NCBI database under accession numbers PQ423217PQ423221.The COI barcode sequences for M. obesus, which were previously undocumented in databases, are also presented. A phylogenetic tree constructed from COI sequences facilitates the identification and comparison of taxa. Despite observable morphological differences, certain species were found to be closely related, indicating the necessity for further research encompassing a wider array of species and specimens. The findings suggest that COI barcoding serves as an effective tool for the accurate and expedient identification of Proctotrupidae species.}, }
@article {pmid41119377, year = {2025}, author = {Oliveira-Filho, RR and Antunes, M and Tamburus, AF and Oliveira-Rogeri, L and Bochini, GL and Hostim-Silva, M and Mantelatto, FL}, title = {New records of decapod crustaceans (Crustacea, Decapoda) in the central coast of Brazil supported by integrative analysis.}, journal = {Zootaxa}, volume = {5621}, number = {2}, pages = {196-210}, doi = {10.11646/zootaxa.5621.2.2}, pmid = {41119377}, issn = {1175-5334}, mesh = {Animals ; Brazil ; *Decapoda/classification/anatomy &amp; histology/growth &amp; development/genetics ; Male ; Animal Distribution ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; Organ Size ; }, abstract = {The decapod fauna of the coast of Esprito Santo, southeastern Brazil, is poorly studied. Herein we report for the first time, for the region, the occurrence of eight species of crustaceans, representing an important contribution to the knowledge about the Brazilian biodiversity. The specimens were collected near the mouths of four estuaries (So Mateus, Ipiranga, Doce and Piraqu-A). For identification of the newly recorded species, Apiomithrax violaceus (A. Milne-Edwards, 1867), Notolopas brasiliensis Miers, 1886, Speloephorus elevatus Rathbun, 1898, Acantholobulus caribbaeus (Stimpson, 1871), Hexapanopeus angustifrons (Benedict &amp; Rathbun, 1891), Hexapanopeus paulensis Rathbun, 1930, Mesorhoea sexspinosa Stimpson, 1871 and Leander paulensis Ortmann, 1897, morphology was assessed using specific literature. DNA barcoding was used as a complementary tool for the species identification. The present study fills many gaps in the geographic distribution of crustaceans in the Western Atlantic and will serve as an updated record and baseline for future studies along the Brazilian coast.}, }
@article {pmid41119374, year = {2025}, author = {Timossi, G and Huemer, P}, title = {Adela paludicolella Zeller, 1850, and Adela orientella Staudinger, 1870 sp. rev. (Lepidoptera, Adelidae): two distinct species revealed by morphological analysis and DNA barcoding.}, journal = {Zootaxa}, volume = {5621}, number = {2}, pages = {249-261}, doi = {10.11646/zootaxa.5621.2.5}, pmid = {41119374}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Male ; Female ; Animal Distribution ; Organ Size ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Phylogeny ; Greece ; Italy ; }, abstract = {The morphological study of A. paludicolella specimens collected in Italyspecifically from the island of Elba (Tuscany) and Sardiniaas well as from Greece, has revealed differences in habitus and reproductive organs between the Italian and Greek specimens. Subsequent genetic analysis confirmed the genetic distinction between A. paludicolella Zeller, 1850, and A. orientella Staudinger, 1870 (sp. rev.), which are distributed in the western and eastern Mediterranean, respectively.}, }
@article {pmid41119367, year = {2025}, author = {Garzn-Ordua, IJ and Matson, TA and Vzquez, AM}, title = {Four new species of Acronyctodes Edwards (Geometridae: Ennominae) from Mesoamerica.}, journal = {Zootaxa}, volume = {5621}, number = {3}, pages = {335-352}, doi = {10.11646/zootaxa.5621.3.3}, pmid = {41119367}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Animal Distribution ; Body Size ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Larva/anatomy &amp; histology/classification/growth &amp; development ; }, abstract = {Four new species of Acronyctodes are described and illustrated: A. gabrieli Matson sp. nov., A. asignum Matson sp. nov., A. bisbili Murillo-Vzquez sp. nov., and A. corrugata Matson &amp; Garzn-Ordua sp. nov. Each species is distinguished by unique genitalic features, different DNA barcode data, and in some cases, interspecific larval color patterns. With the addition of these new species and the exclusion of Acronyctodes thinballa from the genus, the total number of species in Acronyctodes has doubled to eight.}, }
@article {pmid41119359, year = {2025}, author = {Lu, M and Yao, Z and Liu, T}, title = {Leaf-mining moths of the genus Phyllonorycter Hbner (Lepidoptera: Gracillariidae: Lithocolletinae) associated with Juglandaceae in China, with descriptions of two new species and one newly recorded species.}, journal = {Zootaxa}, volume = {5621}, number = {4}, pages = {453-464}, doi = {10.11646/zootaxa.5621.4.4}, pmid = {41119359}, issn = {1175-5334}, mesh = {Animals ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; China ; Female ; Male ; Body Size ; Organ Size ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Plant Leaves/parasitology ; Pupa/anatomy &amp; histology/classification/growth &amp; development ; }, abstract = {Until recently, no species of Phyllonorycter Hbner, 1822 had been recorded to feed on Juglandaceae in China. In this study, we describe two new species, P. stenopterae Lu &amp; Liu, sp. nov. and P. tumoris Lu &amp; Liu, sp. nov., both discovered in Shandong Province, China, feeding on Pterocarya stenoptera C. DC. (Juglandaceae). Additionally, this paper provides the first record of P. pterocaryae (Kumata, 1963) in China, along with its newly identified host plant, Pterocarya stenoptera. Detailed images of the adults, genitalia, pupae, host plants, leaf mines, and DNA barcode data of the new species are presented.}, }
@article {pmid41119347, year = {2025}, author = {Zhang, ZC and Chen, JW and Zhang, Y and Lin, XL}, title = {First record of the genus Krenopelopia (Diptera: Chironomidae) from China, with a description of Krenopelopia wangi sp. nov.}, journal = {Zootaxa}, volume = {5673}, number = {2}, pages = {280-290}, doi = {10.11646/zootaxa.5673.2.7}, pmid = {41119347}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; *Chironomidae/anatomy &amp; histology/classification/genetics/growth &amp; development ; Animal Distribution ; Female ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {The genus Krenopelopia Fittkau, 1962 is recorded from China for the first time. Krenopelopia wangi Zhang &amp; Lin, sp. nov. is described and illustrated as adults. Species status is supported by COI DNA barcodes. A key to adult males of Krenopelopia worldwide is presented.}, }
@article {pmid41119323, year = {2025}, author = {Pei, V and Bankowska, A and Goldschmidt, T and Hrsaker, K and Jovanovi, M and Kaitetzidou, E and Krakowiak, M and Kozowska, A and Michaloudi, E and Michoski, G and Milia, M and Pozojevi, I and Rewicz, T and Rusiniak, O and Sobolak, K and Szuko, I and Stryjecki, R and Stur, E and Szlauer-Ukaszewska, A and Szenejko, M and Zawal, A}, title = {Checklist of water mites from the Balkan Peninsula: second supplement, new DNA barcodes and description of a new species.}, journal = {Zootaxa}, volume = {5676}, number = {1}, pages = {1-74}, doi = {10.11646/zootaxa.5676.1.1}, pmid = {41119323}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; *Mites/classification/anatomy &amp; histology/genetics/growth &amp; development ; Balkan Peninsula ; Male ; Female ; Animal Distribution ; Checklist ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Knowledge of the water mite fauna in the Balkans is still very heterogeneous and far from complete. A compilation of published data is considered the first step in creating an up-to-date comprehensive checklist of water mites of the Balkans. In this supplement, we list all species reported from the Balkans from November 2017 to date and provide an updated checklist of water mites that inhabit the Balkan countries. With the additions in this study, the number of water mite species inhabiting the Balkan Peninsula has increased to 426 species and subspecies. One species, Sperchon balcanicus Pei, sp. nov. (Sperchontidae), is described as new to science. This study adds 299 new barcodes to the existing DNA barcode reference library that now includes 1032 COI DNA barcodes from the Balkans publicly available through the Barcode of Life Data Systems (BOLD). Still, only one-third of the currently known species of water mites in the Balkans now have reference barcodes in BOLD, indicating the need for future integrative research on the morphological and genetic diversity of Balkan water mites.}, }
@article {pmid41119322, year = {2025}, author = {Stadie, D and Lszl, GM and Fiebig, R}, title = {Integrative taxonomic revision of the Xenimpia-Psilocladia-Coenina generic complex with a review of the genus Procypha Warren, 1897 stat. rev. (Lepidoptera, Geometridae, Ennominae, Gonodontini).}, journal = {Zootaxa}, volume = {5677}, number = {1}, pages = {1-69}, doi = {10.11646/zootaxa.5677.1.1}, pmid = {41119322}, issn = {1175-5334}, mesh = {Animals ; Male ; *Moths/classification/anatomy &amp; histology/growth &amp; development/genetics ; Female ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Phylogeny ; DNA Barcoding, Taxonomic ; Ecosystem ; }, abstract = {Using an integrative approach, the classification of the Afrotropical ennomine genera Xenimpia Warren, 1895, Coenina Walker, 1860, and Psilocladia Warren, 1898, is revised. As a result of the DNA barcoding combined with morphological data, eight distinct genera are delimited and characterised to include the current species content of Xenimpia, Coenina and Psilocladia: Bambenga Lszl, Stadie &amp; Fiebig gen. nov. (type species Xenimpia repudiosa Prout, 1915), Arebatia Lszl, Stadie &amp; Fiebig gen. nov. (type species Xenimpia tetracantha Herbulot, 1973), Claudimpia Lszl, Stadie &amp; Fiebig gen. nov. (type species Xenimpia soricina Herbulot, 1973) and Paracoenina Lszl, Stadie &amp; Fiebig gen. nov. (type species Coenina dentataria Swinhoe, 1904) are established. Furthermore, Xenimpia Warren, 1895 (type species: X. erosa Warren, 1895), Coenina Walker, 1860 (type species: Geometra poecilaria Herrich-Schffer, 1854) and Psilocladia Warren, 1898 (type species: P. obliquata Warren, 1898) are retained as valid genera and the latter is excluded from the tribe Gonodontini; in addition, Procypha Warren, 1897 stat. rev. (type species P. maculosata Warren, 1897) is reinstated from synonymy with Xenimpia. As a consequence of the revised generic classification, the following new combinations are established: Bambenga repudiosa (Prout, 1915) comb. nov., Arebatia albicaput (Fletcher, 1956) comb. nov., A. angusta (Prout, 1915) comb. nov., A. burgessi (Carcasson, 1964) comb. nov., A. ceres (Karisch, 2020) comb. nov., A. chalepa (Prout, 1915) comb. nov., A. clenchi (Viette, 1980) comb. nov., A. conformis (Warren, 1898) comb. nov., A. crassimedia (Herbulot, 1996) comb. nov., A. crassipecten (Herbulot, 1961) comb. nov., A. fletcheri (Herbulot, 1954) comb. nov., A. flexuosa (Herbulot, 1996) comb. nov., A. informis (Swinhoe, 1904) comb. nov., A. kala (Herbulot, 1973) comb. nov., A. karischi (Herbulot, 1996) comb. nov., A. loile (Carcasson, 1964) comb. nov., A. loxostigma (Prout, 1915) comb. nov., A. luxuriosa (Herbulot, 1961) comb. nov., A. spinosivalvis (Herbulot, 1996) comb. nov., A. tetracantha (Herbulot, 1973) comb. nov., A. vastata (Herbulot, 1996) comb. nov., Claudimpia diaereta (Prout, 1923) comb. nov., C. misogyna (Carcasson, 1962) comb. nov., C. soricina (Herbulot, 1973) comb. nov., Paracoenina dentataria (Swinhoe, 1904) comb. nov., P. aegyptiaca (Rebel, 1906) comb. nov., P. islamitica (Amsel, 1935) comb. nov., Procypha transmarina (Herbulot, 1961) comb. nov. and P. dohertyi (Herbulot, 1961) comb. nov. Moreover, the genus Procypha is taxonomically revised, including descriptions of five new taxa (P. paradohertyi sp. nov., P. strutzbergi sp. nov., P. strutzbergi caputgalli ssp. nov., P. insolita sp. nov. and P. meyi sp. nov.) and synonymisation of Xenimpia lactesignata Warren, 1914 syn. nov. regarded as a junior synonym of X. maculosata Warren, 1897. Based on diagnostic morphology, the genus Procypha is subdivided into four species groups. The early stages of Procypha maculosata, P. dohertyi and P. strutzbergi Stadie, Lszl &amp; Fiebig sp. nov. are described and depicted, as well as wing patterns and genitalia of all species in this genus are figured. The paper is illustrated with two dendrograms inferred from ML genetic analyses, four distribution maps and 83 colour figures demonstrating the type species of each genus discussed and the adults, genitalia, early stages and habitats of Procypha taxa.}, }
@article {pmid41119317, year = {2025}, author = {Bartolo, AG and Cassar, LF and Massa, B and Schembri, S and Ghana, S}, title = {Genetic analysis of a Mediterranean Red-Listed species Brachytrupes megacephalus (Lefbvre, 1827) (Orthoptera, Gryllidae).}, journal = {Zootaxa}, volume = {5679}, number = {1}, pages = {83-100}, doi = {10.11646/zootaxa.5679.1.4}, pmid = {41119317}, issn = {1175-5334}, mesh = {Animals ; *Gryllidae/genetics/classification/growth &amp; development/anatomy &amp; histology ; Phylogeny ; Male ; Animal Distribution ; Female ; Mediterranean Region ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Body Size ; Organ Size ; Ecosystem ; }, abstract = {Brachytrupes megacephalus, the Giant Sand-dune Cricket, which has a restricted distribution across some locations in the Mediterranean and the more arid Sahara, typically colonises psammophilous biocoenoses within coastal and desert regions, including cultivated land where the substrate is characteristically sandy. Recent assessments reported that the species European population trend is in decline. Despite being a Red-listed species of conservation interest, it has not yet been studied genetically. The present study examines B. megacephalus specimens from Mediterranean locations in Sicily, Linosa, Sardinia, Malta, Gozo, and Libya, in addition to specimens of allied taxa from West Africa and the Far East. Barcode sequencing was carried out for fragments of the small (12SrRNA, ~400 bp) and large (16srRNA, ~500 bp) mitochondrial ribosomal subunits, the small nuclear ribosomal subunit (18SrRNA, ~650 bp), the large nuclear ribosomal unit (28SA, ~400 bp rRNA), the gene coding for H3 protein (H3, ~330 bp) and cytochrome c oxidase subunit 1 (CO1 ~600 bp). Subsequent phylogenetic analyses supported this clade as separate (at species level) from Brachytrupes membranaceus, which is the only other congener for which sequence data exists in online DNA libraries.}, }
@article {pmid41119313, year = {2025}, author = {Huemer, P and Umpich, J}, title = {New species and interesting records of Spiniphallellus Bidzilya &amp; Karsholt, 2008, from Kyrgyzstan (Lepidoptera, Gelechiidae).}, journal = {Zootaxa}, volume = {5679}, number = {1}, pages = {133-142}, doi = {10.11646/zootaxa.5679.1.8}, pmid = {41119313}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Kyrgyzstan ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {Spiniphallellus minimus sp. nov., a new species of the recently described gelechiid genus Spiniphallellus Bidzilya &amp; Karsholt, 2008, is described from Kyrgyzstan. Key diagnostic characters are found in the external morphology, particularly the short forewing length, and in the male genitalia, supported by divergence in DNA barcodes. In addition, S. stonisi Bidzilya &amp; Karsholt, 2008, previously known only from the holotype, is reported from Kyrgyzstan for the first time and redescribed, including its previously unknown female. Adults and male genitalia of both species, as well as the female genitalia of S. stonisi, are illustrated.}, }
@article {pmid41119291, year = {2025}, author = {Matsushima, Y and Blcu, MJ and Kakui, K}, title = {Atlantapseudes tridens sp. nov. (Tanaidacea: Apseudidae) from the Okinawa Trough, Japan, with a note on the taxonomic status of Atlantapseudes curvatus.}, journal = {Zootaxa}, volume = {5679}, number = {4}, pages = {484-500}, doi = {10.11646/zootaxa.5679.4.2}, pmid = {41119291}, issn = {1175-5334}, mesh = {Animals ; Japan ; Female ; Male ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; *Crustacea/classification/anatomy &amp; histology/growth &amp; development/genetics ; Ecosystem ; Phylogeny ; }, abstract = {The deep-sea apseudid genus Atlantapseudes Bcescu, 1978 currently contains six described species. The distinction between the type species (A. nigrichela Bcescu, 1978) and A. curvatus Esquete &amp; Cunha, 2017 is problematic, because it is unclear whether the holotype for A. nigrichela has a tridentate or monodentate rostrum. We observed and redescribed the type material of A. nigrichela and concluded that A. nigrichela and A. curvatus are conspecific, i.e., the latter is a junior synonym of the former. Additionally, we amended the diagnosis of A. nigrichela and treated the form of A. nigrichela with a monodentate rostrum in Bcescu (1978) as an unidentified species. We also found that Atlantapseudes sp. sensu Kakui et al. (2011), the first record of this genus from the North Pacific, was undescribed; here we describe it as Atlantapseudes tridens sp. nov. The new species resembles A. nigrichela in having a tridentate rostrum but differs in having (1) pereonites 13 without posterolateral spines; (2) a tiny anterolateral spine on pereonite-6; (3) two distal bifurcate spiniform setae on the labial palp; and (4) one outer distal seta on maxillipedal palp article-2. We present a partial nucleotide sequence for the cytochrome c oxidase subunit I (COI) gene from A. tridens sp. nov. for future DNA barcoding.}, }
@article {pmid41119272, year = {2025}, author = {Pei, V and Zawal, A and Bankowska, A and Arajo, R and Sugocki, U and Rewicz, T and Krakowiak, M and Michoski, G and Giro, D and Silva, LPD and Rfo, I and Raposeiro, PM and Ballini, L and Stryjecki, R and Ekrem, T and Ferreira, S}, title = {Exploring the water mite fauna (Acari, Hydrachnidia) of the Madeira archipelago: DNA Barcoding reveals a remarkable species endemicity.}, journal = {Zootaxa}, volume = {5621}, number = {5}, pages = {501-513}, doi = {10.11646/zootaxa.5621.5.1}, pmid = {41119272}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; *Mites/classification/genetics/anatomy &amp; histology/growth &amp; development ; Animal Distribution ; Female ; Male ; Phylogeny ; Ecosystem ; }, abstract = {Water mites represent the group with the highest degree of endemism among all macroinvertebrates living in freshwater habitats of Madeira. The water mite fauna of this archipelago has been well known for a long time, but until now they have not been molecularly investigated. So far, 25 species of water mites have been recorded, most of them endemic to Madeira. The library presented here covers 584 COI DNA barcodes grouped into 23 Barcode Index Numbers (BINs), which represent the genetic barcodes of 23 species (more than 80% of the known Madeira water mite fauna). Our study shows that COI barcode clusters generated by the Barcode of Life Data Systems (BOLD) matches to morphological identifications of specimens, with one exception in the family Lebertiidae. A large-scale comparison of the new sequences with those available in public databases such as BOLD confirmed the uniqueness of the genetic diversity of water mites inhabiting Madeira. Neumania atlantida Lundblad, 1941, a species previously synonymized with N. uncinata Walter, 1927, is resurrected as a valid species. Additionally, genetic data revealed that Sperchon brevirostris Koenike, 1895, a species common in freshwaters of Europe and Macaronesia, consists of multiple genetic lineages, one of which is restricted to Madeira. Finally, our research revealed three species new to the water mite fauna of Madeira, i.e., Hydrachna skorikowi Piersig, 1900, Arrenurus bicuspidator Berlese, 1885 and Lebertia algeriensis Lundblad, 1942. The latter species, found to be common in the running waters of the island, may be the first species of water mite documented as potentially, if not invasive, then non-indigenous in freshwater ecosystems of Madeira.}, }
@article {pmid41119270, year = {2025}, author = {Ancillotto, L and Serafini, E and Viviano, A and Labadessa, R and Martino, J and Annessi, M and Bruni, G and Repetto, E and Nabholz, B and Mori, E and Baratti, M}, title = {DNA-barcoding and ecological niche analysis of Wart Biters (Decticus spp.) from an endemism hotspot (Tettigoniidae: Tettigoniinae).}, journal = {Zootaxa}, volume = {5621}, number = {5}, pages = {547-559}, doi = {10.11646/zootaxa.5621.5.3}, pmid = {41119270}, issn = {1175-5334}, mesh = {Animals ; Ecosystem ; Phylogeny ; Male ; Animal Distribution ; Female ; DNA Barcoding, Taxonomic ; *Orthoptera/genetics/classification/growth &amp; development/physiology ; Italy ; DNA, Mitochondrial/genetics ; }, abstract = {Understanding biogeographical patterns is a challenging task, particularly in the case of poorly studied organisms, whose phylogenetic affinities and ecological needs are not yet understood. Such a case is common among invertebrates and particularly among insects, whose extensive diversity may hamper full and deep comprehension of their ecological and evolutionary patterns. Within insects, orthopterans also represent a relatively poorly studied group. Building knowledge upon biogeography and evolution of orthopterans may provide key insights to their conservation, especially in the case of range-restricted taxa that are inherently more vulnerable, and prone to extinction. In this study we thus applied an integrated approach, combining DNA-barcoding and ecological niche modelling, for investigating the diversity of wart biters (Orthoptera Tettigoniidae, genus Decticus). We particularly aimed at providing a first screening of the molecular identity of species within the genus, and an assessment of their macro-ecological needs. We analysed mitochondrial DNA (cytochrome oxidase I COI) and bioclimatic niche data for the four Decticus species that occur in the Italian Peninsula (D. verrucivorus, D. albifrons, D. loudoni, and D. aprutianus), reconstructing their phylogenetic relationships based on molecular approaches, and comparing their ecological preferences. We provide COI sequences for all the species found in Italy, including the first one available for two endemic ones. We found a clear molecular differentiation among the four species, with D. albifrons being the most distinct and basal taxon, as based on the COI sequence adopted. Our results also bring evidence of significant ecological niche differentiation, with each species occupying a distinct portion of the climatic space available within Italy. Notably, the two range-restricted and short-winged species, D. loudoni and D. aprutianus, result as sister taxa according to COI, and exhibit greater ecological specialisation compared to the more widespread species. Besides, we also highlight significant intra-taxon diversity for both D. verrucivorus sensu stricto and D. albifrons, suggesting that further research on potential intraspecific variability may be needed to clarify the taxonomic position of Italian populations. The observed genetic divergence and ecological niche differentiation found among wart biters suggest that adaptation to different ecological conditions may have played a role in the diversification of these range-restricted species. Our results confirmed the importance of the Italian Peninsula as a biodiversity hotspot for Orthoptera and provide a solid baseline for more in-depth molecular studies, besides providing novel sequences that may be used for e.g., DNA metabarcoding or eDNA campaigns. Further research is in fact needed to explore the specific ecological factors driving niche differentiation in this and other taxa, and to investigate the evolutionary pathways that led to the genus current diversity and distribution.}, }
@article {pmid41119269, year = {2025}, author = {Xu, ZB and Grehan, JR and Yang, ZY and Gan, HL and Hu, SJ}, title = {Two new species of Palpifer Hampson (Lepidoptera: Hepialidae) from Yunnan, China.}, journal = {Zootaxa}, volume = {5621}, number = {5}, pages = {560-570}, doi = {10.11646/zootaxa.5621.5.4}, pmid = {41119269}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; Female ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {Two new species of the genus Palpifer Hampson, 1893 are described. The first species, named P. qinglai sp. nov. from Yunnan University in Kunming, Yunnan, China, is similar to P. sexnotatus (Moore, 1879) but distinguished by differences in forewing pattern, male genitalia structure and DNA barcode sequence. The second species, named P. bazi sp. nov. from Mengzi, Honghe, Yunnan, China, resembles P. boonei Grehan &amp; Mielke, 2019 but also differs in the same characteristics.}, }
@article {pmid41119263, year = {2025}, author = {Shafaie, S and Pekr, S and Ortiz, D}, title = {Integrative taxonomy of the Iberian Zodarion species of the rubidum and styliferum groups (Araneae: Zodariidae).}, journal = {Zootaxa}, volume = {5624}, number = {1}, pages = {1-69}, doi = {10.11646/zootaxa.5624.1.1}, pmid = {41119263}, issn = {1175-5334}, mesh = {Animals ; *Spiders/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; Female ; Phylogeny ; Animal Distribution ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Body Size ; Organ Size ; Spain ; }, abstract = {Zodarion, one of the most diverse zodariid spider genera, has recently garnered significant interest due to its peculiar adaptations for stringent ant-eating specialization. However, species identification within this genus remains challenging, as many Zodarion species are still insufficiently documented. This study revisits the taxonomy of Iberian species within the rubidum and styliferum groups, which together comprise 25 of the 171 species in the genus. Detailed morphological documentation is provided, including photographs and SEM images of key taxonomic characters, presented here for the first time. Molecular characterizations were also conducted to facilitate future species identification and to investigate patterns of mitochondrial variation within and between species. Notably, Z. extraneum has been reinstated as a distinct species. The male of Z. extraneum and the female of Z. alentejanum are described for the first time, while the female of Z. viduum is redescribed. Additionally, the species Z. alentejanum, Z. bosmansi, Z. guadianense and Z. lusitanicum have been assigned to the styliferum group. Three new synonyms are proposed: Z. brevicephalus with Z. styliferum, Z. duriense with Z. bacelarae, and Z. parastyliferum with Z. extraneum. Pairwise interspecific divergences between individual sequences generally exceeded intraspecific variation, and the mitochondrial gene tree recovered all but one species as monophyletic groups, underscoring the utility of molecular barcoding for identifying Zodarion species. However, interspecific distances between consensus sequences often blurred species boundaries. Our integrative taxonomic study provides tools for improved identification of Zodarion species, facilitating further research into their biology.}, }
@article {pmid41119237, year = {2025}, author = {Haas, MC and Bahder, BW and Bartlett, CR}, title = {A new species of Anotia Westwood from Bonaire and Curaao (Fulgoromorpha: Fulgoroidea: Derbidae: Otiocerini).}, journal = {Zootaxa}, volume = {5627}, number = {3}, pages = {539-550}, doi = {10.11646/zootaxa.5627.3.7}, pmid = {41119237}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; Body Size ; Organ Size ; DNA Barcoding, Taxonomic ; }, abstract = {A new species in the genus Anotia Kirby, 1821 was collected in a malaise trap during a recent collecting event on Bonaire, Dutch Antilles. A single female of the same species, collected at light on Curaao in 1957, was found in the collection of the Naturalis Biodiversity Center. Here Anotia posa sp. nov. is described and molecular data for the barcoding region (5 half) of the cytochrome c oxidase subunit I (COI), 18S rRNA gene and D9D10 expansion region of the 28S rRNA gene is provided. Some records of a second undescribed Anotia from Curaao are included.}, }
@article {pmid41119222, year = {2025}, author = {Wang, B and Li, X and Kong, F}, title = {Female association of seven species of the genus Amphinemura Ris, 1902 (Nemouridae: Amphinemurinae) in China based on morphological and molecular data.}, journal = {Zootaxa}, volume = {5631}, number = {1}, pages = {137-152}, doi = {10.11646/zootaxa.5631.1.6}, pmid = {41119222}, issn = {1175-5334}, mesh = {Animals ; Female ; China ; Male ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {Females of seven known species of nemourid stoneflies, Amphinemura claviloba (Wu, 1973), A. dabanshana Li, Du &amp; Yang, 2017, A. hastata (Wu, 1973), A. multispina (Wu, 1973), A. ningxiana Li &amp; Yang, 2011, A. pediformis Li &amp; Yang, 2008 and A. qiliana Li, Teslenko &amp; Yang, 2020, are described in this paper. DNA barcoding analysis confirmed the association between males and females, thus validating the morphological taxonomic conclusions.}, }
@article {pmid41119183, year = {2025}, author = {Naderi, A and Hagen, WT and Nazari, V}, title = {Molecular phylogeny of Hipparchia Fabricius, 1807 (Lepidoptera: Nymphalidae: Satyrinae) with description of an overlooked species from the Zagros mountains, Iran.}, journal = {Zootaxa}, volume = {5636}, number = {2}, pages = {361-375}, doi = {10.11646/zootaxa.5636.2.9}, pmid = {41119183}, issn = {1175-5334}, mesh = {Animals ; Iran ; Phylogeny ; Male ; Female ; Animal Distribution ; *Butterflies/classification/genetics/anatomy &amp; histology/growth &amp; development ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {Using sequence data from four nuclear genes alongside DNA barcodes, we reconstructed the evolutionary history of genus Hipparchia Fabricius, 1807. Our phylogeny supported the previously proposed subgeneric classification for the genus and revealed an overlooked taxon close to H. fatua (Freyer, 1845) from the Zagros mountain range in Western Iran, here described as a new species, Hipparchia lunulata sp. nov. We also confirm that the range of H. fatua sichaea (Lederer, 1857), originally described from Beirut, extends to the westernmost part of the Zagros mountains in Iran.}, }
@article {pmid41119175, year = {2025}, author = {Semenchenko, AA and Makarchenko, EA}, title = {On the taxonomy and distribution of Diamesa gregsoni Edwards, (Diptera: Chironomidae: Diamesinae), with morphological redescription and DNA barcoding of species from the Far East.}, journal = {Zootaxa}, volume = {5636}, number = {3}, pages = {499-510}, doi = {10.11646/zootaxa.5636.3.5}, pmid = {41119175}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Male ; *Chironomidae/classification/genetics/anatomy &amp; histology/growth &amp; development ; Animal Distribution ; Female ; Phylogeny ; Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Pupa/anatomy &amp; histology/classification/growth &amp; development/genetics ; Organ Size ; }, abstract = {By analyzing the DNA barcoding data of the Diamesa gregsoni Edwards syntype, we carried out a genetic study of this species from the Far East and made a comparison with DNA barcodes of North American populations. A morphological redescription of the adult male and a description of the pupa and larva are given, and the taxonomy and distribution of the species are clarified in this study. The Bayesian tree revealed two well-supported clades of D. gregsoni from Nearctic and Palaearctic. The average K2P genetic divergence between these clades was 1.67%, which corresponds to intraspecific differences. Overall intraspecific p-distances within 23 DNA barcodes of D. gregsoni were 1.19%. The Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Multi-rate Poisson tree processes (mPTP) approaches for the species delimitation confirmed that Nearctic and Palaearctic DNA barcodes belong to a single molecular taxonomic unit, while general mixed Yule-coalescent (GMYC) delimit the dataset into three different molecular operational taxonomic units (mOTU).}, }
@article {pmid41119164, year = {2025}, author = {David, KJ and Mahammed, NRN and Hancock, DL and Gracy, RG and Ningthoujam, K and Sushil, SN}, title = {Taxonomic notes on Oriental bamboo-shoot fruit fly genus Acroceratitis Hendel (Diptera: Tephritidae: Dacinae: Gastrozonini), with description of a new species from India.}, journal = {Zootaxa}, volume = {5637}, number = {1}, pages = {83-98}, doi = {10.11646/zootaxa.5637.1.3}, pmid = {41119164}, issn = {1175-5334}, mesh = {Animals ; India ; Male ; Female ; *Tephritidae/classification/anatomy &amp; histology/genetics/growth &amp; development ; Phylogeny ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {A new species of Acroceratitis Hendel, namely Acroceratitis sachini David, Hancock &amp; Noor is described from Western Ghats, Karnataka, India. Diagnoses of all 11 species of Acroceratitis recorded from India along with an updated key to all described species is provided. DNA barcode sequences of A. sachini, A. parastriata David &amp; Hancock, A. ceratitina (Bezzi), A. incompleta Hardy, A. histrionica (Meijere) and A. tomentosa Hardy were obtained and are reported. Phylogenetic analysis using mt COI revealed Acroceratitis to be monophyletic.}, }
@article {pmid41119143, year = {2025}, author = {Rajgopal, NN and Ramaiah, M and Rai, S and Dey, D and Singaravel, M and Meshram, NM}, title = {Shanaya: A new leafhopper genus of the tribe Mukariini (Cicadellidae: Deltocephalinae) with two new species discovered and described from India.}, journal = {Zootaxa}, volume = {5637}, number = {2}, pages = {383-393}, doi = {10.11646/zootaxa.5637.2.11}, pmid = {41119143}, issn = {1175-5334}, mesh = {Animals ; India ; Female ; Male ; Animal Distribution ; *Hemiptera/classification/anatomy &amp; histology/genetics/growth &amp; development ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Phylogeny ; Ecosystem ; }, abstract = {A new genus, Shanaya gen. nov., is proposed within the tribe Mukariini, based on the discovery of two new species from India that could not be assigned to any previously described genera. Detailed morphological descriptions and photographic illustrations are provided for both species: Shanaya spatulata gen. et sp. nov. (Type species, India: Himachal Pradesh) and Shanaya abeeri gen. et sp. nov. (India: Karnataka). Morphological evidence supports their classification under this new genus. A distribution map, along with identification keys to the genera of Mukariini of India and species of the new genus, are included. Its tribal placement, as well as similarities and differences with related genera, are also discussed. DNA barcodes (partial mitochondrial COI sequences) were generated for Shanaya spatulata gen. et sp. nov. and submitted to NCBI GenBank. All type specimens are housed in the National Pusa Collection (NPC), ICARIndian Agricultural Research Institute, New Delhi, University of Agricultural Sciences, Bengaluru (UASB) and National Insect Museum, ICARNational Bureau of Agricultural Insect Resources, Bengaluru (NIM).}, }
@article {pmid41119117, year = {2025}, author = {Divelec, RL and Michez, D}, title = {Taxonomic revision of the garrulus species group in the bee genus Hylaeus Fabricius, 1793 (Hymenoptera: Apoidea, Colletidae).}, journal = {Zootaxa}, volume = {5642}, number = {2}, pages = {127-146}, doi = {10.11646/zootaxa.5642.2.2}, pmid = {41119117}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; Bees/classification/anatomy &amp; histology/growth &amp; development/genetics ; Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The species group of Hylaeus garrulus (Warncke, 1981) encompasses three rare Iberian endemics. Because of the dubious association of sexes and species concepts, their consistent identification have remained difficult. By the mean of barcoding and morphology, we aim to accurately associate males and females of the group. As a result, H. convergens Dathe 2000 is found to be a junior synonym of H. teruelus (Warncke, 1981) syn. nov., and the female previously assigned to H. teruelus belongs to a new species, H. woodi Le Divelec, sp. nov. This study also revealed that the previous lack of a clear diagnosis for the garrulus group resulted in the erroneous report of H. gazagnairei (Vachal, 1891) in Europe; this species is actually absent from this region. A comparative diagnosis of the garrulus group is therefore provided to facilitate the identification of its members.}, }
@article {pmid41119019, year = {2025}, author = {Han, S and Shin, S}, title = {First records of the genus Acerocnema Becker (Diptera: Scathophagidae) from South Korea, with a new species and a newly recorded species using DNA barcodes.}, journal = {Zootaxa}, volume = {5653}, number = {3}, pages = {440-450}, doi = {10.11646/zootaxa.5653.3.9}, pmid = {41119019}, issn = {1175-5334}, mesh = {Animals ; Male ; Republic of Korea ; DNA Barcoding, Taxonomic ; *Diptera/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; Body Size ; Organ Size ; }, abstract = {This study reports the first Korean records of the genus Acerocnema Becker, 1894, with one new species, Acerocnema saurischia sp. nov., and one newly recorded species, A. flavifrons Iwasa. A key to the Korean Acerocnema is provided with morphological diagnosis and images of habitus and male genitalia structures. To assist in species identification, mitochondrial cytochrome c oxidase subunit I (COI) gene sequences were obtained from all specimens to assess DNA barcoding.}, }
@article {pmid41118963, year = {2025}, author = {Costa, DA and Rocha, S and Martins, D and Venncio, M and Urea, M and Almeida, J and Ferreira, GG and Christoffersen, ML and Antunes, C}, title = {Filling in another piece of the puzzle: Using Integrative Taxonomy to establish yet another new species of Hediste (Annelida, Polychaeta, Nereididae).}, journal = {Zootaxa}, volume = {5696}, number = {1}, pages = {28-40}, doi = {10.11646/zootaxa.5696.1.2}, pmid = {41118963}, issn = {1175-5334}, mesh = {Animals ; *Polychaeta/classification/anatomy &amp; histology/genetics/growth &amp; development ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Mediterranean Sea ; Ecosystem ; Female ; DNA Barcoding, Taxonomic ; Male ; Phylogeny ; }, abstract = {One of the most prevalent autochthonous polychaete taxa in the European Atlantic and Mediterranean seas is the genus Hediste (Nereididae, Polychaeta, Annelida). Its species provide food for aquatic life, such as fish and crustaceans, playing significant ecological roles in trophic webs. Until 2022, only the species Hediste diversicolor was referenced for Atlantic and Mediterranean waters; nonetheless, it is a cryptic species, in which Hediste pontii in the Adriatic Sea, and Hediste astae in the Aegean, Black, Caspian, and Baltic seas have recently been established. In this paper, we propose a new species of polychaete, Hediste sinesimplex sp. nov. for the Western Mediterranean, Baltic and Eastern North seas, based on an integrative approach, focusing on traditional taxonomy and DNA barcoding analysis. In addition to the morphological description, we have also included 3D models of this new species to exemplify the use of this technique for in-depth morphological description.}, }
@article {pmid41118942, year = {2025}, author = {Fiemapong, ARN and Blandenier, Q and Tamesse, JL and Mitchell, EAD}, title = {Taxonomic review of the Afrotropical millipede genus Scaptodesmus Cook, 1896 (Diplopoda, Polydesmida, Chelodesmidae), with integrative descriptions of three new species from Cameroon.}, journal = {Zootaxa}, volume = {5696}, number = {3}, pages = {361-384}, doi = {10.11646/zootaxa.5696.3.3}, pmid = {41118942}, issn = {1175-5334}, mesh = {Animals ; Cameroon ; *Arthropods/classification/anatomy &amp; histology/genetics/growth &amp; development ; Phylogeny ; Female ; Male ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; DNA Barcoding, Taxonomic ; Ecosystem ; }, abstract = {The genus Scaptodesmus Cook, 1896, is revised based on recent material collected from Cameroon. Three new species are described and illustrated: S. kala sp. nov., S. manengouba sp. nov., and S. vandenspiegeli sp. nov. Additionally, the diagnoses of two old and well-defined species of the genus, S. porati Cook, 1896, and S. granulosus (Attems, 1931), are revised. The species Scaptodesmus dentatus Silvestri, 1909, previously regarded as incertae sedis, is here confirmed as such, since its taxonomic affiliation remains uncertain. An identification key to and a distribution map for all Scaptodesmus species known so far are provided. Barcoding base on COI sequencing was successfully performed for all three new species and compared with previously published sequences from the family Chelodesmidae. The results reveal that the three new species are all genetically distinct from one another. A maximum likelihood phylogenetic tree constructed using the dataset of available species resulted in a well-resolved and well-supported phylogeny. In all cases, barcoding data were consistent with traditional morphological taxonomic classifications. This work highlights the importance of integrated taxonomy in resolving relationships within millipede species groups below the family level.}, }
@article {pmid41118913, year = {2025}, author = {Gao, Y and Bu, Y}, title = {Three new species of Philotella (Collembola, Neanuridae, Pseudachorutinae) from China with the DNA barcoding analysis.}, journal = {Zootaxa}, volume = {5701}, number = {2}, pages = {179-190}, doi = {10.11646/zootaxa.5701.2.6}, pmid = {41118913}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; China ; Male ; Female ; Animal Distribution ; Phylogeny ; *Arthropods/classification/anatomy &amp; histology/genetics/growth &amp; development ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {Three new species of the genus Philotella are reported from China, Philotella huadongensis sp. nov. from Jiangsu, Shanghai and Zhejiang, Philotella varisensillata sp. nov. from Hubei, Philotella fuxii sp. nov. from Henan. An updated key to the world species of the genus is also provided. In addition, the DNA barcodes of P. huadongensis sp. nov. were sequenced and genetic distances of the species in the subfamily Pseudachorutinae was analyzed.}, }
@article {pmid41118871, year = {2025}, author = {Fang, Z and Hu, W and McCormack, K and Pos, DD and Tang, CT and Zhu, Y and Mao, K and Stone, GN and Zhang, YM}, title = {New species of rose gall wasp Diplolepis Geoffroy, 1762 (Hymenoptera: Diplolepididae) and its parasitoid Orthopelma Taschenberg, 1865 (Hymenoptera: Ichneumonidae) on a rare endemic rose species in Sichuan, China.}, journal = {Zootaxa}, volume = {5706}, number = {2}, pages = {231-246}, doi = {10.11646/zootaxa.5706.2.5}, pmid = {41118871}, issn = {1175-5334}, mesh = {Animals ; *Wasps/classification/anatomy &amp; histology/genetics/growth &amp; development/physiology ; China ; Male ; Female ; Animal Distribution ; *Rosa/parasitology ; *Plant Tumors/parasitology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {We describe a new species of rose gall wasp from Sichuan, China, Diplolepis nezha Hu, Zhang, McCormack &amp; Fang, sp. nov. (Diplolepididae: Diplolepidinae), which induces galls on the rare, endemic rose Rosa chinensis var. spontanea (Rehder &amp; E.H. Wilson) T.T. Yu &amp; T.C. Ku. In association with these galls, we also describe a new parasitoid species, Orthopelma aobing Hu, Zhang, Dal Pos, McCormack &amp; Fang, sp. nov. (Ichneumonidae: Orthopelmatinae). DNA barcodes were used to confirm the identities of both new species. We provide updated dichotomous keys incorporating these taxa and briefly discuss their biology in the context of other East Asian species, informed by phylogenetic analyses.}, }
@article {pmid41118797, year = {2025}, author = {Saldaitis, A and Lien, VV and Junnila, A and Ihle, S and Sulak, H and Yakovlev, RV and Volkova, JS and Mller, GC and Revay, EE and Prozorova, TA and Prozorov, AM}, title = {Two new mainland sister species for the Taiwanese Bharetta owadai (Lepidoptera, Lasiocampidae, Lasiocampinae, Argudini).}, journal = {Zootaxa}, volume = {5633}, number = {3}, pages = {470-484}, doi = {10.11646/zootaxa.5633.3.3}, pmid = {41118797}, issn = {1175-5334}, mesh = {Animals ; Male ; Taiwan ; Female ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; Phylogeny ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Vietnam ; Ecosystem ; }, abstract = {Bharetta owadai Kishida, 1986, was considered a widespread Indomalayan species occurring in Taiwan (type-locality), mainland China and Vietnam. Study of the genitalia of adults and barcoding showed that the taxon is a group of sister species. Allopatric Taiwanese and mainland populations have a slight difference in male genitalia and a distinct genetic distance of 3.264.56 %, which allowed description of the mainland population as a new species, Bharetta sarah sp. nov. known from Guanxi (type-locality) and Jianxi Provinces in China, and northern Vietnam. The second new species, Bharetta hanne sp. nov., has distinct male genitalia and is found on Fansipan Mountain (type-locality) and a nearby mountain ridge. Adults, their genitalia, distribution map, and phylogenetic tree are illustrated.}, }
@article {pmid41118786, year = {2025}, author = {Joshi, R and Zahiri, R and Banerjee, D and Singh, N}, title = {A catalogue of the Erebidae of India (Lepidoptera, Noctuoidea).}, journal = {Zootaxa}, volume = {5635}, number = {1}, pages = {1-247}, doi = {10.11646/zootaxa.5635.1.1}, pmid = {41118786}, issn = {1175-5334}, mesh = {Animals ; India ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; Female ; Animal Distribution ; Phylogeny ; Organ Size ; DNA Barcoding, Taxonomic ; Body Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; }, abstract = {The present catalogue comprises 2,203 valid species in 562 genera of Erebidae from India. Of the 19 known subfamilies of Erebidae (including Strepsimaninae as incertae sedis), all are represented in the subcontinent except for the New World subfamily Scolecocampinae. Arctiinae are the most diverse, with 737 species, and Eulepidotinae and Strepsimaninae are the least diverse, each represented by a single species. We follow the classification proposed by Zahiri et al. (2012) and utilized DNA barcoding combined with multigene data analysis to determine the phylogenetic position of uncertain moth species. The taxonomic status of Strepsimaninae is still unclear and thus is included here as incertae sedis. The type locality, first reference, synonymy, and distribution within and outside India are provided for each of the included species. A replacement name Ophiusa neotirhaca Singh &amp; Joshi, nom. nov. is provided for Ophiusa pseudotirhaca Singh &amp; Ranjan, 2016, a junior homonym of Ophiusa pseudotirhaca (Berio, 1956: 24). Artaxa guttata, syn. nov. is synonymised with Artaxa digramma. Lygephila sanjauliensis Rose &amp; Srivastava, 1989, comb. nov. is established.}, }
@article {pmid41116189, year = {2025}, author = {Hohl, T and Bönisch, U and Manke, T and Arrigoni, L}, title = {Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {437}, pmid = {41116189}, issn = {1756-0500}, mesh = {Humans ; *Cryopreservation/methods ; *Formaldehyde/chemistry ; *Single-Cell Analysis/methods ; Hep G2 Cells ; *Chromatin Immunoprecipitation Sequencing/methods ; *Tissue Fixation/methods ; Reproducibility of Results ; }, abstract = {OBJECTIVE: The need for freshly isolated cells in bulk or single cell ATAC-seq experiments creates considerable logistical barriers and increases susceptibility to batch effects. This makes it difficult to coordinate complex or longitudinal studies. Our goal was to develop a sample preservation strategy that overcomes these limitations, enabling consistent and high-quality chromatin accessibility profiling from archived samples.<br><br>RESULTS: We established a workflow that incorporates mild formaldehyde fixation prior to cryopreservation, preserving both bulk and single-cell ATAC-seq data quality at levels comparable to fresh samples in HepG2 cells. This protocol reliably maintains key data quality metrics, including signal-to-noise ratio and fragment distributions. Furthermore, the method is fully compatible with transposase-based sample multiplexing using custom Tn5 barcodes. To address barcode hopping inherent to multiplexing, we introduced a computational demultiplexing strategy based on fragment ratios, which accurately assigns single cells to their sample of origin. Our approach streamlines experimental logistics and ensures reproducibility across diverse and temporally dispersed samples, broadening the scope for ATAC-seq-based studies, including those in clinical research settings where coordinated sample collection is challenging.}, }
@article {pmid41113180, year = {2025}, author = {Jin, H and Wang, Y and Song, C and Qi, X}, title = {First morphological description of the larval stages of three Microtendipes species (Diptera, Chironomidae) from South China with molecular confirmation.}, journal = {ZooKeys}, volume = {1255}, number = {}, pages = {27-40}, pmid = {41113180}, issn = {1313-2989}, abstract = {This study presents the first integrated morphological and molecular characterization of larvae from three Microtendipes species, Microtendipes baishanzuensis Song &amp; Qi, 2023, Microtendipes robustus Song &amp; Qi, 2023 and Microtendipes tuberosus Qi &amp; Wang, 2006, collected from subtropical streams in China, providing important insights for advancing Chironomidae taxonomy. Using detailed morphometric analysis (head capsule ratios, mandibular pecten length, and striae counts) in conjunction with mitochondrial COI barcoding, we established larval-adult associations and differentiated these species from their congeners. Microtendipes baishanzuensis is characterized by a brownish head capsule with distinctly paler median teeth compared to the lateral teeth, the longest mandibular pecten within the genus, the highest number of body striae, and an exceptionally anteriorly positioned ring organ. Microtendipes robustus is distinguished by a uniformly dark brown mentum, remarkably wide ventromental plates, the most variable striae count, and a medium-sized mandibular pecten. Microtendipes tuberosus exhibits a uniformly dark brown mentum with median teeth conspicuously shorter than the second lateral teeth, the smallest body size in the genus, the shortest mandibular pecten, the fewest striae, and the most posteriorly located ring organ. A revised larval key for Chinese Microtendipes is presented, improving freshwater biomonitoring and addressing challenges associated with cryptic diversity.}, }
@article {pmid41113177, year = {2025}, author = {Zhang, J and Zhang, C and Xing, Y and Yu, H and Mi, X}, title = {A survey of the spider genus Lipocrea Thorell, 1878 (Araneae, Araneidae) from Guiyang City, Southwest China: An integrated morphological and molecular approach.}, journal = {ZooKeys}, volume = {1255}, number = {}, pages = {207-237}, pmid = {41113177}, issn = {1313-2989}, abstract = {A survey was undertaken to study the spider genus Lipocrea Thorell, 1878, from Guiyang City, Guizhou Province, southwest China. A total of two species is here addressed based on morphology and five methods of molecular species delimitation, comprising L. guiyang J. Zhang, Yu &amp; Mi, sp. nov. and L. fusiformis (Thorell, 1877), the type species of the genus as well as a new record for mainland China. These two species are distributed in Huaxi District and Kaiyang County of Guiyang, respectively, providing the first formal record of this genus from mainland China.}, }
@article {pmid41112752, year = {2025}, author = {Sousa, J and Lutz, &#xcd; and Santana, P and Martins, T and Ferreira, C and Santa Brígida, N and Miranda, J and da Silva, R and Barbosa, AJ and Matos, S and Mendes, C and Cardoso, B and Silva, A and da Silva, I and da Costa, J and Vallinoto, M and Sampaio, I and Evangelista-Gomes, G}, title = {Molecular identification based on mtDNA analysis of commercial crustaceans in the coastal Amazon: exotic species, cryptic diversity, and implications for sustainable fisheries in northern Brazil.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19586}, pmid = {41112752}, issn = {2167-8359}, mesh = {Animals ; Brazil ; *Crustacea/genetics/classification ; *Fisheries ; *DNA, Mitochondrial/genetics/analysis ; Phylogeny ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Located around the Caeté River estuary, the municipality of Bragança is one of the primary fishing hubs in the region. Several high-value crustacean species are intensively harvested in this area and are commonly sold at open-air markets. However, fishery products are often labeled with generic trade names, which hinders accurate species identification and conceals the true diversity of the exploited species.<br><br>METHODS: Therefore, we conducted the molecular identification of crustacean species sold in Bragan&#xe7;a. Samples were collected during two periods: from February to August 2017, and from September 2021 to May 2022. A total of 137 samples were analyzed, including 120 obtained from markets and 17 collected from the wild. Specimens were first identified morphologically, and two regions of the cytochrome c oxidase subunit I (COI) gene were amplified for molecular identification. Genetic analyses included haplotype determination, Basic Local Alignment Search Tool (BLAST) comparisons, phylogenetic tree construction, and species delimitation approaches.<br><br>RESULTS: We obtained a dataset comprising 16 commercial names and 151 DNA sequences, including 38 sequences from region I (the barcode region) and 113 sequences from region II of the COI gene. A total of 15 crustacean species, belonging to seven genera and five families, were identified. Six of these species were classified as exotic, and three were recently described in the scientific literature. Additionally, we documented the occurrence of two distinct lineages of Penaeus monodon along the Brazilian coast. Molecular species delimitation tools effectively identified all sampled taxa and revealed underestimated levels of biodiversity due to the use of generic commercial names. This issue poses a potential threat to the long-term sustainability of fishery resources and commercial fishing in northern Brazil, as it leads to biased qualitative and quantitative assessments of fishery products.}, }
@article {pmid41112102, year = {2025}, author = {Rudresh, HS and Yathisha, NS and Vaishnavi, SL and Santosh Kumar, HS and Jogaiah, S and Sharathchandra, RG}, title = {A combination of morphological, biochemical and structural responses is required for desiccation tolerance in Selaginella repanda.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {31}, number = {9}, pages = {1575-1587}, pmid = {41112102}, issn = {0971-5894}, abstract = {The innate ability for desiccation tolerance in Selaginella repanda was determined by evaluating the physiological and biochemical modifications that occur during water loss and gain, in different stages namely, hydrated (H), desiccation (D), and rehydrated stages (R). Herbarium JCB and rbcl gene barcoding were used for its identification. In the desiccated stage, relative water content (RWC) was 8.3% which regained to 96.8% in R stage. Leaf water potential decreased to -3.8MPa in D stage. Scanning electron microscopic images shows significant modification of stomata and cell in D and R stages. Scanning electron microscopic images shows significant modification of stomata and cell in D and R stages. Total chlorophyll (0.9-fold) and carotenoids (0.7-fold) concentrations were found to be reduced during D stage, when compared to H stage. Concentration of anthocyanin (1.14-fold), proline (2.9-fold) and lipid peroxidation (1.9-fold) were found to be significantly high in D stage. Carbon dioxide exchange rate (- 0.6 µ mol m[-2] s[-1]) was negative during D stage. Also, activity of antioxidant enzymes such as superoxide dismutase (1.7-fold), catalase (2.57-fold) and peroxidase (5.5-fold) were found to be significantly increased in D stage. Sucrose concentration (4.7-fold) also increased during desiccation. The quantity of starch (0.5-fold) was lower in the D stage. In R stage, all biochemical parameters tested above were significantly similar to that in the H stage. S. repanda exhibits constitutive and inducible repair mechanism towards desiccation and can therefore serve as model to study desiccation in Selaginella species.}, }
@article {pmid41109425, year = {2025}, author = {Sheedy, A and Davinack, AA}, title = {Seasonal dynamics of Polydora infestation in eastern oysters (Crassostrea virginica) from a tidally restricted New England estuary.}, journal = {Journal of invertebrate pathology}, volume = {214}, number = {}, pages = {108472}, doi = {10.1016/j.jip.2025.108472}, pmid = {41109425}, issn = {1096-0805}, abstract = {Shell-boring polychaetes of the genus Polydora pose a significant threat to oyster aquaculture worldwide, yet little is known about their seasonal dynamics in tidally restricted estuaries. This study investigates the prevalence, intensity, and environmental covariates of Polydora websteri infestation in wild eastern oysters (Crassostrea virginica) over a 12-month period in the Herring River estuary (Cape Cod, Massachusetts), a system slated for tidal restoration. Oysters were collected monthly, and worms identified morphologically and by COI barcoding. Infestations were observed year-round, with prevalence and intensity lowest in late summer and peaking in fall-winter. Gravid females were only observed from April through August, indicating a seasonal reproductive window. The seasonal peak in visible infestation and pathology in colder months is therefore consistent with a lag between summer recruitment and subsequent shell damage. Using a Gaussian generalized linear model as a descriptive correlational tool, we observed a negative association between temperature and monthly mean intensity at this site and year; salinity and pH showed no detectable association. These associations are interpreted within the seasonal/lag context rather than as casual drivers. Overall, this work provides baseline data on seasonal Polydora dynamics in the Herring River estuary that will be essential for future, post-restoration assessments.}, }
@article {pmid41109409, year = {2025}, author = {Byamukama, D and Ndekezi, C and Omara, D and Nakyanzi, A and Natwijuka, F and Kato, F and Mugaba, S and Kimuda, MP and Kapaata, A and Nduati, E and Kaleebu, P and Balinda, SN}, title = {Validation of High-throughput Oxford Nanopore Technology for HIV-1 Transmitted/Founder Virus Identification.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108138}, doi = {10.1016/j.ijid.2025.108138}, pmid = {41109409}, issn = {1878-3511}, abstract = {HIV-1 transmitted/founder (T/F) viruses cause 80-90% of heterosexual transmissions, making their rapid identification vital for vaccine and cure development. Single-genome amplification (SGA) followed by Sanger sequencing is the gold standard for Transmitted/Founder detection, but low throughput and high cost limit its scalability. Here, we evaluated Oxford Nanopore Technology (ONT) as a high-throughput alternative. We sequenced 195 archived HIV-1 single genome amplicons (SGAs) from 20 acutely infected participants, encompassing both 3' and 5' genome halves. Libraries were prepared with end repair, native barcoding, and adapter ligation, then sequenced on a MinION MK1C device with R9.4 flow cells. Data processing included read, filtering, error correction, and haplotype reconstruction. T/F viruses were identified using Highlighter plots and by applying a criterion of intra-patient mean pairwise diversity <0.60%, together with phylogenetic clustering, with the sequence most closely related to the most recent common ancestor (MRCA) designated as the T/F virus. Phylogenetic analysis showed strong concordance between ONT and Sanger sequences, with 100% bootstrap support. ONT identified 35 of 39 T/F viruses detected by Sanger, achieving 89.70% sensitivity. Sequence similarity between ONT and Sanger derived T/Fs averaged of 99.81% (95% CI: 99.76-99.87%), ranging from 99.45-99.96%. These findings demonstrate ONT's promise as a reliable, high-throughput alternative for HIV-1 T/F identification. Advances such as the Dorado basecaller and Q20+ chemistry are expected to further improve ONT's accuracy, supporting its use in large-scale, resource-limited settings.}, }
@article {pmid41107736, year = {2025}, author = {Fan, YJ and Li, CG and Ma, C and He, M and Ma, JP and Luo, MR and Hodel, RGJ and Jabbour, F and Zhao, L and Yang, Q}, title = {Holistic approach for plant species circumscription integrating standard barcodes, chloroplast genomes, single-copy nuclear genes and micro-morphological data: a case study in Epimedium (Berberidaceae).}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {931}, pmid = {41107736}, issn = {1471-2164}, support = {32170381//National Natural Science Foundation of China/ ; 2025JC-YBQN-252//Natural Science Fundamental Research Plan of Shaanxi Province/ ; }, mesh = {*Epimedium/genetics/classification/anatomy &amp; histology ; *DNA Barcoding, Taxonomic/methods ; *Genome, Chloroplast ; Phylogeny ; Genes, Plant ; Cell Nucleus/genetics ; }, abstract = {BACKGROUND: Accurate plant species circumscription is fundamental to biodiversity conservation, medicinal resource development, and ecological research. Yet challenges such as sample incompleteness and reliance on limited molecular markers often hinder precise species circumscription. A single identification method-molecular or morphological-is in most cases not sufficient to accurately recognize plant species. Notably, single-copy nuclear genes, despite their critical importance in resolving species circumscription through higher evolutionary rates and biparental inheritance, remain underexplored in current research. A critical next step is developing nuclear genes as DNA barcodes. In some cases, micro-morphological characteristics mirror molecular evidence and confirm species identification. Epimedium (Berberidaceae), well known for its medical and horticultural significance, remains poorly understood taxonomically due to its phenotypic diversity. It is an ideal taxon to explore integrative plant species circumscription combining molecular and micro-morphological data.<br><br>RESULTS: Chloroplast genome structure analysis revealed that the variations near the IR/SC boundary, the unique trnQ-UUG gene rearrangement, and the repeat sequences in Epimedium hold significant evolutionary implications. It not only uncovered the conservation and specificity of genomic structures but also provided novel insights into the phylogeny and molecular evolution of this genus. We identified eight hypervariable regions in Epimedium species that emerged as strong candidates for potential DNA special barcodes. These regions and the whole chloroplast genome showed higher species discriminability compared to standard barcodes. Single-copy nuclear genes were more useful in species circumscription over chloroplast genomes. Furthermore, micro-morphological characteristics served as strong complementary evidence for species circumscription and could help distinguish species that were unresolved using only molecular or genomic analyses.<br><br>CONCLUSIONS: Using Epimedium as a case study, we propose a Multilayer Precision Species Circumscription Approach (MPSCA), a diagnostic framework that combines standard barcodes, chloroplast genome, single-copy nuclear genes, and micro-morphological data.}, }
@article {pmid41107347, year = {2025}, author = {Roy, L and Uranw, S and Rai, K and Cloots, K and Das, ML and Smitz, N and Van Bortel, W}, title = {Mapping the distribution of phlebotomine sand fly species with emphasis on Leishmania vectors in Nepal and exploring the potential of DNA barcoding for their identification.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {36356}, pmid = {41107347}, issn = {2045-2322}, support = {716228/40/70//Institute of Tropical Medicine, Belgium/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Nepal/epidemiology ; *Insect Vectors/genetics/parasitology/classification ; *Phlebotomus/genetics/classification/parasitology ; *Psychodidae/genetics/classification/parasitology ; Leishmaniasis, Visceral/transmission/parasitology/epidemiology ; *Leishmania ; Electron Transport Complex IV/genetics ; Phylogeny ; }, abstract = {Nepal is committed to eliminating visceral leishmaniasis as a public health problem by 2030. The scattered distribution of VL cases across wide geo-ecological regions, including areas previously considered unsuitable for the survival of vectors and the transmission of the pathogen, poses a major threat to Nepal's national VL elimination programme. Regular monitoring and accurate identification of sand fly species are essential for implementing tailored vector control interventions. Hence, this study aimed to update the distribution of sand fly species with a focus on Leishmania vectors and evaluate DNA barcoding as a complementary tool for their identification. Sand flies were collected from 43 districts with active VL cases across the country between 2017 and 2022. The mitochondrial COI gene was amplified for DNA barcoding analysis. The primary vector, Phlebotomus argentipes, was present in all except three districts. Potential vectors, Ph. (Adlerius) spp. and Ph. major, were found common in high-altitude regions. The species identification success rate of generated COI barcode sequences based on the "Best Close Match" was 97%, indicating high accuracy in delineating sand flies to the species level. The information on the distribution of phlebotomine sand flies and the potential use of DNA barcoding for their identification could be milestones for sand fly research and help to guide the vector control interventions in support of VL elimination in Nepal.}, }
@article {pmid41102527, year = {2025}, author = {Pei, Y and Forstmeier, W and Suh, A and Bambach, L and Borges, I and Low, GW and Dion-Côté, AM and Knief, U and Wolf, J and Kempenaers, B}, title = {Evolution of large polymorphic inversions in a panmictic songbird.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaf262}, pmid = {41102527}, issn = {1537-1719}, abstract = {Chromosomal inversions have long been appreciated as an important source of genetic diversity, local adaptation and speciation. However, selection pressures maintaining ancestral and derived alleles at high frequency over extended periods of time remain poorly characterized. Using genome-wide single-nucleotide polymorphism (SNP) markers and shared barcodes of linked-read sequences from twenty wild and seven captive zebra finches Taeniopygia guttata, we systematically scanned a high-quality zebra finch reference genome and identified all large polymorphic inversions that segregate at high minor allele frequencies. Apart from the known polymorphic inversions on chromosomes Tgu5, Tug11, Tgu13 and TguZ, we characterized two inversions on microchromosomes Tgu26 and Tgu27 and identified another eight putative inversions, located mostly on microchromosomes and ranging in size from 0.42 to 65.22Mb. Population genomic analyses show that most of the six bona fide inversions are complex, containing short nested inversions. The early inversions emerged an estimated 0.6-2.2 million years ago and segregate at relatively high frequencies in the wild (minor haplotype frequency range: 0.289-0.429). Based on fitness-related measures of about 5,000 captive zebra finches, we conclude that three of the inversion polymorphisms (Tgu11, Tgu27, and TguZ) may be maintained by net heterosis. In the youngest of the six inversions (Tgu13), the derived haplotype showed weak positive additive effects on various fitness components. In combination with previous discoveries, we provide a comprehensive overview of the genomic distribution and evolutionary dynamics of large polymorphic inversions in the panmictic zebra finch. Our findings highlight (1) that microchromosomes may harbor quite a few additional inversion polymorphisms, (2) that most of the inversions contain smaller nested or overlapping inversions, and (3) that inversions were most likely maintained by weak heterosis with small fitness effects requiring large sample sizes to be detected.}, }
@article {pmid41091119, year = {2025}, author = {Çubukçu, HC}, title = {The role of AI in pre-analytical phase - use cases.}, journal = {Clinical chemistry and laboratory medicine}, volume = {}, number = {}, pages = {}, pmid = {41091119}, issn = {1437-4331}, abstract = {The pre-analytical phase of laboratory testing, encompassing processes from test ordering to sample analysis, represents the most error-prone component of laboratory medicine, accounting for 68-98 % of laboratory mistakes. These errors compromise patient safety, increase healthcare costs, and disrupt operational efficiency. Artificial intelligence (AI) and machine learning (ML) technologies have emerged as promising solutions to address these challenges across multiple pre-analytical applications. This narrative review examines current AI research applications and commercial implementations across seven key pre-analytical domains: clot detection, wrong blood in tube (WBIT) error detection, sample dilution management, chemical manipulation detection in urine samples, serum quality assessment based on hemolysis/icterus/lipemia (HIL), test utilization optimization, and automated tube handling. Research studies demonstrate impressive performance, with neural networks achieving accuracies exceeding 95 % for clot detection, XGBoost models reaching 98 % accuracy for WBIT detection, and deep learning systems attaining AUCs above 0.94 for test recommendation systems. However, a significant translation gap persists between research prototypes and commercial deployment. Academic models excel at pattern recognition using curated datasets but face limitations including single-center validation, retrospective designs, and integration challenges. Commercial solutions prioritize deterministic controls, barcoding, and sensor-based approaches that ensure reliability and scalability, with limited explicit AI implementation. Successful clinical laboratory translation requires multicenter prospective validation, robust laboratory information system integration, regulatory compliance frameworks, and evaluation metrics focused on operational outcomes rather than solely statistical performance. As infrastructure and standards mature, strategic AI adoption in pre-analytical tasks offers measurable improvements in safety, efficiency, and cost-effectiveness.}, }
@article {pmid41091115, year = {2025}, author = {Bakhshinyan, D and Custers, S and Escudero, L and Suk, Y and Brown, KR and Patel, H and Adile, AA and Chokshi, C and Shaikh, MV and McKenna, D and Qazi, MA and Zhai, K and Tieu, D and Chan, K and Weetal, M and Venugopal, C and Moffat, J and Singh, S}, title = {Leveraging Medulloblastoma Clonal Dynamics to Overcome Treatment Resistance.}, journal = {Clinical cancer research : an official journal of the American Association for Cancer Research}, volume = {}, number = {}, pages = {}, doi = {10.1158/1078-0432.CCR-24-4010}, pmid = {41091115}, issn = {1557-3265}, abstract = {PURPOSE: Medulloblastoma (MB) is a common pediatric brain tumor with distinct molecular subgroups, of which, Group 3 MB is associated with increased recurrence, metastatic potential and poor patient outcomes. Small molecule inhibitors targeting BMI1 have been shown to be efficacious against several types of malignant tumors, including pediatric MB. While our previously published in vivo study provides a promising proof-of-concept for the therapeutic targeting of BMI1 in Group 3 MB with small molecule inhibitor, it is not sufficient to eradicate the tumour.<br><br>EXPERIMENTAL DESIGN: In this study, following preclinical validation of BMI1 inhibitor PTC-596, DNA barcoding technology was leveraged to profile in vivo clonal dynamics of Group 3 MB in response to the established chemoradiotherapy regimen alone and in combination with PTC-596. Following demonstration of a small number of treatment-refractory clones we sought to identify potential druggable molecular vulnerabilities by utilizing phosphoproteomic profiling and genome-wide CRISPR screening.<br><br>RESULTS: By comparing the changes in phosphorylation pattern of key signaling kinases post PTC-596 treatment with the list of sensitizer genes from in vitro genome-wide CRISPR/Cas9 screen and to the essential genes in human neural stem cells (hNSCs), we identified several context-specific regulators of mTOR, AKT and PLK1 pathways. Subsequently, targeting the PI3K pathway with Enzastaurin was shown to be most meanable to synergistic targeting alongside BMI1 inhibition.<br><br>CONCLUSION: This work provides the foundation for clinical validation of small-molecule inhibitors synergistic with PTC-596 to improve the durability of remissions and extend survival of patients with treatment-refractory Group 3 MB.}, }
@article {pmid41087879, year = {2025}, author = {Zhu, Z and Cheng, L and Pu, T and Liu, Y and Wang, J and Shang, M and Wang, J and Wang, Y and Duan, B}, title = {Development of molecular markers for marker-assisted breeding and quality evaluation of Aconitum carmichaelii cultivars.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1373}, pmid = {41087879}, issn = {1471-2229}, support = {202205AF150026//Yunnan academician expert workstation/ ; 202301BA070001-042//Special Basic Cooperative Research Programs of Yunnan Provincial Undergraduate Universities' Association/ ; }, abstract = {BACKGROUND: Aconitum carmichaelii (AC), a traditional Chinese medicinal herb, provides substantial economic benefits to the pharmaceutical industry and rural development. Its broad genetic diversity has led to multiple cultivars with distinct biological traits. However, accurately identifying these cultivars is challenging due to the morphological similarities, particularly at the seedling stage. Misidentifying cultivars or selecting inappropriate cultivation regions may lead to crop failure. Moreover, the chemical profiles of different cultivars remain insufficiently characterized. Therefore, there is an urgent need to develop rapid and accurate authentication methods and to clarify quality-related differences among AC cultivars.<br><br>RESULTS: We sequenced and analyzed the chloroplast (cp) genomes of 26 AC samples and measured the content of their major active compounds. The result revealed that the cp genomes were highly conserved, ranging from 155,880 to 155,891&#xa0;bp, and contained 42&#x2013;47 simple sequence repeats (SSRs), primarily mononucleotide repeats. Two DNA barcodes, trnT(GGU)-psbD 1F/1R and trnS(UGA)-psbZ 1F/1R, were identified as effective tools for differentiating between AC cultivars. Phylogenetic analyses clustered the 26 samples into three groups, Suggesting the presence of three distinct cultivars relevant to agricultural production. The divergence time of AC was estimated to be approximately 1.38 million years ago (Mya). Additionally, the total content of monoester alkaloids (benzoylaconitine, benzoylmesaconine, and benzoylhypacoitine) ranged from 0.07 to 0.12&#xa0;mg/g, while diester alkaloids (aconitine, meaconitine, and hypoaconitine) ranged from 1.22 to 1.82&#xa0;mg/g. Notably, the YFIII cultivars exhibited the highest levels of monoester alkaloids and lowest levels of diester alkaloids, indicating a potential safety advantage. Furthermore, 11 typical chromatographic peaks were identified through peak alignment and multi-point correction. Among them, the VIP values for P6, P8, and P9 were more significant than 1, suggesting that these peaks may serve as potential markers for quality control in AC cultivars.<br><br>CONCLUSIONS: Our findings highlight AC cultivars&#x2019; significant genetic and chemical diversity. The chloroplast markers trnT(GGU)-psbD 1F/1R and trnS(UGA)-psbZ 1F/1R are practical tools for the precise identification and selective breeding of AC. This genetic diversity likely contributes to variations in the plant&#x2019;s chemical composition. This study lays an important foundation for the sustainable utilization and conservation of AC genetic resources.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07289-w.}, }
@article {pmid41087882, year = {2025}, author = {Eminoğlu, A and İzmirli, &#x15e;G and Beriş, F&#x15e; and Dinçer, D and Yazıcı, K}, title = {SSR genotyping of 200 tea (Camellia sinensis) clones obtained by selection and DNA barcoding of 12 varietal registration candidates.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1381}, pmid = {41087882}, issn = {1471-2229}, support = {118G038//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; 118G038//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; 118G038//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; 118G038//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; 118G038//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; }, mesh = {*Camellia sinensis/genetics/classification ; *DNA Barcoding, Taxonomic ; *Microsatellite Repeats/genetics ; Genotype ; Genetic Variation ; Genotyping Techniques ; Polymorphism, Genetic ; }, abstract = {Genotype and cultivar identification is essential for conserving tea genetic diversity within plantation ecosystems and ensuring the sustainability of high-quality tea production. This study represents the first large-scale genetic characterization of 200 elite varietal candidate tea (Camellia sinensis) clones, which were pre-selected from 2,034 genotypes originating from the Eastern and Western Black Sea regions of Türkiye. Eight polymorphic simple sequence repeat (SSR) markers located near loci associated with catechin content, including epicatechin (EC), epicatechin gallate (ECG), epigallocatechin (EGC), and epigallocatechin gallate (EGCG), were employed. SSR profiles were generated for all 200 tea clones cultivated in control plots at the National Tea Gene Bank, and the resulting data were additionally used for DNA barcoding of 12 varietal candidate tea clones currently under registration. Among the evaluated markers, TM412 (EGC) exhibited the highest polymorphism information content (PIC = 0.8816), whereas TM376 (EC) showed the lowest (0.4321). Notably, TM412 (EGC) and TM399 (ECG) displayed high PIC values, indicating their strong discriminatory potential for Turkish tea genotypes. The findings indicate that Turkish tea germplasm possesses substantial genetic diversity, and some markers may be effectively utilized in variety registration and breeding efforts. This study presents the first comprehensive molecular characterization of tea genetic resources in Türkiye. It contributes to the long-term conservation of selected clones and supports the variety registration process through DNA barcoding and a QR code-based traceability system. The genetic dataset generated in this work contributed directly to the establishment of Türkiye's first and the world's fifth-largest tea gene pool in Rize Province, providing a valuable reference for strengthening tea genetic resource conservation and breeding programs at both national and global scales.}, }
@article {pmid41084989, year = {2025}, author = {Bonomo, M and Bronstein, O}, title = {Non-Invasive Underwater DNA Sampling Illuminates Red Sea Echinoderm Diversity.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70059}, doi = {10.1111/1755-0998.70059}, pmid = {41084989}, issn = {1755-0998}, support = {2407/20//Israel Science Foundation/ ; 1001808844//Israels Ministry of Regional Cooperation/ ; }, abstract = {Species-specific non-invasive underwater DNA sampling remains largely understudied for marine invertebrates despite its potential to revolutionise biodiversity assessment of vulnerable species or fragile ecosystems. Comprehensive species-specific DNA barcode databases are essential for accurate species identification and taxonomic assignment, particularly at a time of increasingly employed metabarcoding monitoring of marine biodiversity. We present an in situ swab-based protocol adapted for underwater collection of genetic material, using Red Sea echinoderms as a case study. We sampled 308 individuals from over 50 species across all five echinoderm classes using a newly designed underwater sampling kit applying sterile buccal swabs and an underwater sampling container. The novel sampling protocol was compared to traditional tissue-based DNA extractions and tested for preservation conditions (fixatives, temperatures and durations). DNA yield from swabs was lower than from traditional tissue biopsies, yet sufficient for all downstream applications. Overall PCR amplification success was 88% (240/274 echinoderm swabs), with a 94% sequencing success rate (202/214), and no significant difference in DNA integrity between swab and tissue methods. Phylogenetic analyses of 231 specimens revealed 37 clades, including 20 novel Red Sea lineages and provisional identifications of cryptic and rare species. Our results demonstrate that underwater swabbing is a rapid (< 1 min per sample), cost-effective, and non-destructive, suitable for generating high-quality genetic data under challenging field conditions. We propose this protocol as an alternative to traditional DNA sampling, providing an efficient approach for studying at-risk ecosystems and species while prioritising conservation and sustainability and facilitating large-scale genetic screening of wild populations.}, }
@article {pmid41083851, year = {2025}, author = {Zmitrovich, IV and Shabunin, DA and Bukharova, NV and Perelygin, VV}, title = {Calcipostia guttulata (Basidiomycota, Polyporales) in Russia.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {}, number = {}, pages = {}, pmid = {41083851}, issn = {1608-3105}, abstract = {The aim of this work was to summarize the data on the ecological, biological, and morphological features of Calcipostia guttulata (Polyporales, Basidiomycota) by using the original materials, revised herba-rium specimens, data on molecular barcoding of original collections, the available literature, and iconography and information stored on the GBIF portal. It was shown that C. guttulata is a widespread, but rare polypore in the Holarctic; is confined to the early stages of drying of coniferous stands, primarily spruce forests; and is a poorly studied headwood pathogen and a saprotroph that colonizes coniferous deadwood and, less often, fallen trees. The morphological diagnosis of C. guttulata was clarified. Its substrate spectrum, distribution, and relationships with insects, which are important for forest pathology, have been identified most fully to date. The conservation status of the species and the prospects for its use in biotechnology are discussed.}, }
@article {pmid41083475, year = {2025}, author = {Hadjiargyrou, SL and Rubin, M and Karkout, H and Hayes, S and Vasquez Taveras, AA and Brookes, BJ and King, MK and Khan, R and Nye, JA and Weisberg, SJ}, title = {Novel species-level database of fish embryos and larvae in New York offshore waters, 2021-2023.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1638}, pmid = {41083475}, issn = {2052-4463}, support = {MOU #900286-02//New York State Department of Environmental Conservation (DEC)/ ; MOU #900286-0//New York State Department of Environmental Conservation (DEC)/ ; }, mesh = {Animals ; *Fishes/embryology/classification/genetics ; New York ; Larva/classification ; Ecosystem ; DNA Barcoding, Taxonomic ; Embryo, Nonmammalian ; }, abstract = {Understanding the population dynamics of fish is vital to maintaining healthy ocean ecosystems and the human communities that depend on them. However, most fish population models lack crucial information about early life stages. Even when fish embryos and larvae (collectively, ichthyoplankton) are sampled, similar morphological features make species-level visual identification difficult, especially for embryos. So, although the Northeast US continental shelf is well-studied, existing ichthyoplankton datasets generally lack species-level information on embryos. Unlike visual methods, DNA barcoding can readily discriminate between morphologically indistinguishable specimens. Thus, our dataset of 2,294 DNA barcoded fish embryos and larvae, collected near New York (USA), contributes valuable insight into local ichthyoplankton assemblages. This dataset contains 50 unique species. Most have previously been documented in our region, but one was novel: we identified an embryo of Bathyanthias mexicanus, a species not known to inhabit or spawn in the sampled area. More broadly, this dataset can be used to address questions about fish habitat across life stages and to help ensure that local fisheries are sustainably managed.}, }
@article {pmid41083230, year = {2025}, author = {Caiafa, MV and Kaminsky, L and Healy, R and Sheffer, LP and Willis, CB and Deitz, K and Richter, BS and Lemmond, BR and Borland, D and Roy, BA and Dawson, HA and Delevich, CA and Conery, JS and Warner, D and Caboň, M and Karlsen-Ayala, E and Grupe, AC and Kraisitudomsook, N and Reynolds, NK and Drechsler-Santos, ER and Truong, C and Corrales, A and Mujic, AB and Kennedy, PG and Jusino, MA and Swenie, RA and Noffsinger, CR and Grootmyers, D and Matheny, PB and Wilson, AW and Smith, ME}, title = {Think globally, barcode locally: nine years of macrofungi sampling reveals extensive biodiversity at the ordway-swisher biological station, a subtropical site in Florida.}, journal = {Fungal biology}, volume = {129}, number = {7}, pages = {101643}, doi = {10.1016/j.funbio.2025.101643}, pmid = {41083230}, issn = {1878-6146}, mesh = {Florida ; *Biodiversity ; *DNA Barcoding, Taxonomic ; DNA, Fungal/genetics/chemistry ; *Fungi/classification/genetics/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics/chemistry ; Phylogeny ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Molecular Sequence Data ; }, abstract = {The Ordway-Swisher Biological Station (OSBS) is a 38-km[2] reserve owned by the University of Florida and is part of the National Ecological Observatory Network (NEON). The reserve contains several iconic Florida habitats, such as sandhill, mesic hammock, and scrubby flatwoods. While plants and animals have been extensively studied at OSBS, the fungi remain poorly known. Fungal inventories are critical to increase knowledge of both fungal diversity and species ranges, and thus to provide foundational data for a wide array of applications in ecology and resource management. Here, we present the results of a nine-year effort to collect, preserve, and DNA barcode the macrofungi at OSBS. This effort generated >1200 vouchered specimens and 984 ITS rDNA sequences, representing more than 546 species. Our sampling was dominated by Basidiomycota and revealed a high diversity of symbiotic ectomycorrhizal fungi, particularly species of Amanita, Cortinarius, and Russula. Sampling curves and both Chao1 and Jacknife1 richness estimators suggest that our DNA barcoding efforts captured only about half of the macrofungi species and that a more complete inventory would detect 897-1177 macrofungi species at OSBS. Our sampling found more species of macrofungi at OSBS than the known number of vertebrate animal species at the reserve and our estimates also suggest that there are likely more macrofungi species than plant species at OSBS. This study is the first comprehensive macrofungi inventory within a NEON site and highlights the importance of long-term monitoring to provide novel data on fungal diversity, community structure, conservation, biogeography, and taxonomy.}, }
@article {pmid41082500, year = {2025}, author = {Madhu, MK and Murarka, RK}, title = {Mechanistic Basis for GPCR Phosphorylation-Dependent Allosteric Signaling Specificity of β-Arrestin 1 and 2.}, journal = {Journal of chemical information and modeling}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jcim.5c01078}, pmid = {41082500}, issn = {1549-960X}, abstract = {β-Arrestins (βarr1 and βarr2) are key transducers of G protein-coupled receptor (GPCR) signaling, orchestrating both shared and isoform-specific intracellular pathways. Phosphorylation of the receptor C-terminal tail by GPCR kinases encodes regulatory "barcodes" that modulate β-arrestin conformations and interactions with downstream effectors. However, how distinct phosphorylation patterns shape β-arrestin structure and function remains poorly understood. In this study, we integrate all-atom molecular dynamics simulations with machine learning, including graph neural networks, to systematically characterize the barcode-specific conformational landscape of β-arrestins bound to the phosphorylated vasopressin receptor 2 tail (V2Rpp). We find that V2Rpp engages βarr1 more stably than βarr2, mediated by isoform-specific residue contacts that trigger distinct allosteric responses. These include differential interdomain rotations and rearrangements in key structural motifs, potentially facilitating selective effector protein engagement. Furthermore, we identify critical residue networks that transmit phosphorylation signals to effector-binding interfaces in a barcode- and isoform-specific manner. Notably, βarr1 exhibits stronger allosteric coupling between V2Rpp and c-edge loop 2 compared to βarr2, which is consistent with its enhanced membrane association. Together, these findings advance our understanding of the molecular mechanisms by which β-arrestins interpret GPCR phosphorylation signatures, offering a framework that could aid in the design of pathway-selective therapeutics.}, }
@article {pmid41081656, year = {2025}, author = {Kauer, J and Weinhold, N and Raab, MS}, title = {Acquired and Selected: Tracking Antigen Escape during T Cell-Redirecting Therapies in Multiple Myeloma.}, journal = {Blood cancer discovery}, volume = {}, number = {}, pages = {OF1-OF3}, doi = {10.1158/2643-3230.BCD-25-0328}, pmid = {41081656}, issn = {2643-3249}, abstract = {In this issue of Blood Cancer Discovery, Papadimitriou and colleagues implement a temporal workflow to monitor genomic antigen escape during BCMA- or GPRC5D-directed immunotherapy. Using chemotherapy-induced mutational signatures as barcodes, they provide evidence that these mutations are acquired during therapy rather than being preexisting in newly diagnosed patients. See related article by Papadimitriou et al., p. XX .}, }
@article {pmid41079571, year = {2025}, author = {Marin, IN and Palatov, DM}, title = {Niphargus Schiödte, 1849 (Crustacea, Amphipoda, Niphargidae) is a new component of the biotic community in the deep pebble beach habitats of the northern Black Sea region.}, journal = {ZooKeys}, volume = {1254}, number = {}, pages = {283-311}, pmid = {41079571}, issn = {1313-2989}, abstract = {A new species of the genus Niphargus Schiödte, 1849 (Crustacea: Amphipoda: Niphargidae) is described from the deep pebble beach interstitial habitats along the northern Black Sea coastline, revealing a new type of environment for this amphipod genus and providing new insight into the diversity of this unusual biotope. Niphargus primoricus sp. nov. belongs to "stygius-longicaudatus" species group corresponds to a distinct phylogenetic lineage, recently called "tarkhankuticus" ingroup (clade), which currently includes several species from the coastal areas of the Black Sea (Crimean Peninsula, southern Caucasus, and northern coast of the Republic of Türkiye [Turkey]). Molecular genetic analysis revealed that the speciation within this ingroup started in the Pliocene, approximately 5.76-3.6 Mya, and correlated with the Black Sea transgression. The divergence of the "tarkhankuticus" clade from the related European congeners probably occurred in the Late Miocene (~ 11-10 Mya), and is likely related to the separation of the Paratethys into different basins (Euxinian, Alpine and Pannonian). The new species has a wide distribution, currently inhabiting nearly 190 kilometers along the Black Sea coastline, from Gelendzhik to Khosta, and is characterized by a low level of genetic divergence between populations. The deep pebble interstitial coastal biotopes in the area are also inhabited by specific gammarid amphipods, for example, Dursogammarus dromaderus Marin &amp; Palatov, 2022 and Litorogammarus dursi Marin, Palatov &amp; Copilaş-Ciocianu, 2023 (Amphipoda: Gammaridae), whose biology has not been studied, and it is unknown how they spread along the coastline.}, }
@article {pmid41078471, year = {2025}, author = {Fang, Y and He, JY and van Achterberg, C and Zhu, JC and Chen, XX and Tang, P}, title = {New species of Phanerotomella (Hymenoptera, Braconidae, Cheloninae) based on morphological and molecular evidence.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e171754}, pmid = {41078471}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Phanerotomella Szépligeti, 1900 (Hymenoptera, Braconidae, Cheloninae, Phanerotomini), is restricted to the Old World, with no records from the Nearctic or Neotropical Regions. Reliably species-identified COI sequences are scarce for this genus in public databases, hindering comprehensive phylogenetic and DNA-barcoding analyses.<br><br>NEW INFORMATION: This study provides 29 COI sequences for this genus. Two species delimitation approaches, combined with morphological evidence, were employed to delimit species. The findings indicated the existence of 16 species, including one new species: P. nitidifascia Fang, He, van Achterberg, sp. nov. and one newly-recorded species: P. namkyensis Sigwalt, 1978. Additionally, we provide the first available COI sequence for the Chinese endemic genus Siniphanerotomella.}, }
@article {pmid41078469, year = {2025}, author = {Kang, Y and Lee, W}, title = {A new record of the genus Mollitrichosiphum Suenaga (Hemiptera, Aphididae, Greenideinae) from South Korea.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e157863}, pmid = {41078469}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Mollitrichosiphum Suenaga belongs to the subfamily Greenideinae, with 18 species hav been recorded worldwide.<br><br>NEW INFORMATION: The genus Mollitrichosiphum is a completely new record in South Korea. In 2024, Mollitrichosiphum (Metatrichosiphon) luchuanum (Takahashi, 1930) was collected on Meliosma myriantha located in Hawon-dong, Seogwipo-si, Jeju-do, South Korea (33.19590, 126.28340). Illustrations of apterous viviparous females and alate viviparous females, description, measurement, host plants and distributions are provided. In addition, DNA barcoding, based on a mitochondrial cytochrome c oxidase subunit I (COI) sequence and a mitochondiral cytochrome b (CytB) sequence are provided.}, }
@article {pmid41076928, year = {2025}, author = {Hampe, P and López-Villalba, &#xc1; and Inoue, M and Shchepin, ON and Woyzichovski, J and Popa, F and Schnittler, M}, title = {Nivicolous myxomycetes in the French Pyrenees - A biodiversity study aided by two molecular markers.}, journal = {Protist}, volume = {179}, number = {}, pages = {126130}, doi = {10.1016/j.protis.2025.126130}, pmid = {41076928}, issn = {1618-0941}, abstract = {We report a systematic survey for nivicolous myxomycetes (Amoebozoa, Myxomycetes) carried out between April 30 and May 6 in the French Pyrenees (Hautes-Pyrénées, 900-2000 m). The 738 specimens were barcoded for the nuclear small subunit ribosomal gene (nucSSU, 652, 88.3 % successful). Trichia alpina, the only bright-spored species found, was not sequenced. Additionally, a section of the translation elongation factor 1-alpha gene (EF1A) was successfully sequenced for 496 specimens (67.2 %). The nucSSU phylogeny showed 31 dark-spored species as genetically distinct, yet not always monophyletic lineages. Two species, Polyschismium fallax and P. peyerimhoffii, were grouped in one clade, although differing in barcode sequences. These separations were confirmed by EF1A in all cases except Didymium pseudodecipiens, where EF1A sequences could not be obtained. The resolution for the species pair P. fallax and P. peyerimhoffii increased, and for Polyschismium chailletii two distinct clades were found, indicating a cryptic species complex. Based on the molecular clades, we describe in detail the corresponding morphological differences in four taxa (Didymium dubium and Didymium pseudodecipiens; Polyschismium chailletii groups a and C). The study confirms the reliability of barcoding via nucSSU with an independent second marker and delivers a barcoded, quality-checked comprehensive data set for the Pyrenees.}, }
@article {pmid41073556, year = {2025}, author = {Wang, W and Yang, C and He, G and Zhao, W and Yang, J and Yang, Y}, title = {Complete cox 1 gene and ITS sequence of Hirudinaria manillensis and molecular evolution analysis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35511}, pmid = {41073556}, issn = {2045-2322}, mesh = {Animals ; *Evolution, Molecular ; *Leeches/genetics/classification ; Phylogeny ; *Cyclooxygenase 1/genetics ; Sequence Analysis, DNA ; Genetic Variation ; Open Reading Frames ; }, abstract = {Hirudinaria manillensis is an important blood-sucking medicinal leech widely distributed in Southeast Asia and southern China. It has been shown to treat cardiovascular and cerebrovascular diseases. Molecular identification technology has developed rapidly, and the results are accurate and stable, which can help us to obtain rich biological information of samples for genetic evolution analysis. This study designed 3 pairs of primers for complete cox 1 gene. After sequencing by PCR products and splicing by SeqMan software, the full-length sequence of cox 1 gene was obtained by annotation of open reading frame (ORFs) on MITOS2 platform. The cox 1 gene with a length of 1536nt was obtained, and the species was identified as Hirudinaria manillensis. The Hd value and FST value of cox 1 gene were 0.858 and 0.10938, which were higher than the Hd value of ITS (0.314) and the FST value close to 0. The nucleotide diversity and GST values of the two genes were very low, and the Tajima's D values of the neutral test were negative, without statistical significance. The genetic distance calculated by the Kimura-2 parameter method was very low. According to the biological information provided by the samples in this study, the population size of Hirudinaria manillensis in southern China was on the rise, but stable genetic diversity was not formed, and there was no obvious population differentiation and geographical isolation. This may be due to the mature artificial breeding technology in recent years, which enabled Hirudinaria manillensis to migrate from the traditional gathering places and breed in a large number in the new environment and migration site. At present, there are many molecular barcoding data of cox 1 gene in the NCBI database, but there is no complete cox 1 gene sequence as a reference, and the related ITS sequence information is more limited, indicating that there is still a lot of space for gene research of Hirudinaria manillensis.}, }
@article {pmid41020308, year = {2025}, author = {Goldberg, TL}, title = {Infestation of humans and non-human primates with Cordylobia rodhaini (Diptera: Calliphoridae) in a 'hotspot' of furuncular myiasis.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-7}, doi = {10.1017/S0031182025100875}, pmid = {41020308}, issn = {1469-8161}, abstract = {Lund's fly, Cordylobia rodhaini (Calliphoridae), is an African blowfly considered to be an uncommon cause of furuncular myiasis. Far less is known about C. rodhaini than about the more frequently reported tumbu fly, Cordylobia anthropophaga. From 2011 to 2020, fly larvae were collected and analysed from 11 independent infestations of wild non-human primates and 10 independent infestations of humans (including 1 from this author) in Kibale National Park, Uganda. All 21 larvae were identified morphologically and genetically as C. rodhaini. Larvae from non-human primates were on average 4·5 times larger than larvae from humans. Non-human primates had empty furuncles, indicating recent egress of mature third instar larvae and completion of the larval stage of the lifecycle; however, eastern chimpanzees (Pan troglodytes schweinfurthii) were photographed removing larvae from furuncles of grooming partners. A total of 4 closely related mitochondrial haplotypes were identified, 2 of which were shared by larvae from humans and non-human primates. Genetic variation within C. rodhaini from this single location was comparable to that within other calliphorid species. Non-human primates may play a larger role in the maintenance of C. rodhaini than previously known, and in certain forested locations C. rodhaini may be the predominant cause of furuncular myiasis. The sylvatic lifecycle of C. rodhaini may explain its differentiation from Cordylobia anthropophaga, which has a peridomestic lifecycle. In general, these findings shed new light on how myiasis-causing flies can adapt to different ecological settings and be regionally rare but locally abundant.}, }
@article {pmid41071924, year = {2025}, author = {de Kroon, RR and Kreulen, IAM and Davids, M and van Thiel, IAM and Admiraal, I and Verdoes, X and van Weissenbruch, MM and Niemarkt, H and de Jonge, WJ and de Meij, T and , }, title = {The gut as a source of infection for fungal pathogens: increased fecal Candida albicans precedes onset of Candida late-onset sepsis in very preterm infants.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf524}, pmid = {41071924}, issn = {1537-6613}, abstract = {BACKGROUND: The skin-to-blood route is traditionally considered the main pathway in Candida late-onset sepsis (LOS) development in preterm infants. However, emerging evidence suggests that the gut also serves as a source of infection. We aimed to characterize fecal mycobiota and microbiota profiles preceding onset of Candida LOS to assess the role of the preterm gut microbiome in disease development.<br><br>METHODS: In this multicenter, case-control study, very preterm infants (<30 weeks of gestation) with Candida LOS were included. Each case was matched to non-affected controls by gestational and postnatal age, hospital site, and/or cumulative antibiotic exposure prior to day of LOS onset (t=0). Fecal samples collected at t=0 and the five preceding days were analyzed using ITS1 and 16S RNA sequencing. Microbial amplicon yields, composition, and inter-kingdom correlations were assessed.<br><br>RESULTS: Of 2,397 screened infants, fecal samples were available for 8/19 infants with Candida LOS. In these 8 cases, the ITS/16S amplicon yield ratio was increased (p<0.001) and the relative abundance of fecal Candida albicans correlated positively with fungal amplicon yield (&#x3c1;=0.71, padj=0.005), suggesting increased absolute abundance up to five days before onset. Additionally, bacterial yields were significantly lower (p=0.02) and &#x3b1;-diversity was significantly decreased (p=0.012), compared to the controls.<br><br>CONCLUSIONS: Increased fecal C. albicans preceded Candida LOS onset, implicating the preterm gut as a potential source of infection. Reduced bacterial yields and diversity suggest ecological alterations that may facilitate Candida pathogenicity in the preterm gut. These findings support further research into gut-derived Candida LOS and potential for microbiota-targeted prevention strategies.}, }
@article {pmid41070223, year = {2025}, author = {Intharuangrung, N and Sirikul, C and Nimsamer, P and Wongsurawat, T and Saejia, A and Anukul, N}, title = {Concordance of an in-house 2-steps PCR-SSP and nanopore sequencing for HLA-B*57:01 and HLA-B*58:01 typing: a comparative study.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1649990}, pmid = {41070223}, issn = {1664-8021}, abstract = {This study reports an optimized in-house 2-step PCR-SSP assay for rapid, cost-effective detection of HLA-B*57:01 and HLA-B*58:01 in routine pharmacogenomics laboratory. This assay employs allele-specific primers positioned within exon 2-3 boundaries, validated in silico against common HLA-B alleles. Using 30 clinical DNA samples, our PCR workflow (<1 h) showed 100% concordance at 2-field resolution with Oxford Nanopore sequencing performed using ligation-based sequencing kit with PCR barcoding. Cohen's kappa was 1.00 with 95% CI. The turnaround time and reagent cost per sample were reduced to 1 h of hands-on PCR time and USD 7 per sample, respectively. These do not include DNA extraction or gel electrophoresis analysis. This 2-step PCR-SSP offers a robust alternative for pharmacogenomic screening in resource-limited settings for detecting the HLA-B*57:01 and HLA-B*58:01.}, }
@article {pmid41069873, year = {2025}, author = {Carvajal-Vallejos, FM and Gallo-Cardozo, F and Careaga, M and Campero, M}, title = {Weight-Length Ratio of Piranhas Serrasalmus (Characiformes, Serrasalmidae) in Bolivia: Relationships to Molecular Divergence and Maximum Size?.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e70970}, pmid = {41069873}, issn = {2045-7758}, abstract = {Weight-Length Relationships (WLRs) provide a basis for comparing life history strategies and morphological differentiation among fish species, potentially linking slope variations to evolutionary divergences in size and weight. This study presents the WLRs of nine Serrasalmus piranha species from the Amazon and La Plata basins in Bolivia, assessing whether WLRs slopes are influenced by phylogenetic relationships using a phylogenetic mixed model analysis on the mitochondrial DNA COI (barcoding) locus. All species demonstrated an exponential (power-type) growth pattern, with most showing positive allometric growth. The species showing the greatest differentiation in both WLRs and genetic variation was S. elongatus. We detected a strong phylogenetic signal in WLR slopes, though clustering techniques for WLRs slopes and molecular data revealed only partial concordance. We discuss how these concordances and discrepancies between WLRs and genetic data may reflect ancient and intermediate speciation events, shaped by habitat conditions and stochastic evolutionary processes. Such processes appear to influence swimming mechanisms and ecological niche navigation in these closely related Serrasalmus species.}, }
@article {pmid41068953, year = {2025}, author = {Ding, H and Torno, M and Vongphayloth, K and Ng, G and Tan, D and Sng, W and Ho, K and Randrianambinintsoa, FJ and Depaquit, J and Tan, CH}, title = {Hidden in plain sight: discovery of sand flies in Singapore and description of four species new to science.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {402}, pmid = {41068953}, issn = {1756-3305}, support = {xxxxxx//Ministry of Finance, Singapore/ ; }, mesh = {Animals ; Singapore ; Phylogeny ; *Psychodidae/classification/genetics/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; Cytochromes b/genetics ; *Insect Vectors/classification/anatomy &amp; histology/genetics ; Female ; Electron Transport Complex IV/genetics ; Male ; Phlebotomus/classification/genetics/anatomy &amp; histology ; Leishmaniasis/transmission ; }, abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are tiny, blood-sucking insects that are of significant public and veterinary health importance for their role in the transmission of Leishmania parasites, bacteria, and arboviruses. Although sand flies have been documented in most Southeast Asian countries, there are no published records confirming their presence in Singapore. Here, we present this fauna with descriptions of new species.<br><br>METHODS: Sand fly species identification was confirmed using an integrative taxonomic approach that combines morphological analysis with DNA barcoding of the mitochondrial cytochrome b (cytb) and cytochrome c oxidase subunit I (COI) genes.<br><br>RESULTS: We identified eight sand fly species, including four newly described species: Phlebotomus seowpohi n. sp., Sergentomyia leechingae n. sp., Sergentomyia gubleri n. sp., and Sergentomyia retrocalcarae n. sp. Phylogenetic analyses suggest that the new Phlebotomus species, belonging to subgenus Euphlebotomus, is closely related to Phlebotomus argentipes, an important vector of Leishmania donovani from the South Asian region.<br><br>CONCLUSIONS: The potential risk of leishmaniasis in Singapore is compounded by the recent detection of antibodies to Leishmania infantum in local free-roaming dogs. Therefore, continuous monitoring is essential to assess and manage the risk of disease agent transmission, support the development of an early warning system, and enable timely and targeted public health interventions. The findings of this study contribute to the global knowledge on sand flies and enhance our understanding of local fauna diversity and distribution.}, }
@article {pmid41068271, year = {2025}, author = {Ashour, EM and Ahmed, RA and Abass, NY}, title = {DNA barcoding and phylogenetic analysis to characterize biodiversity of some freshwater fish species in Lake Nasser and River Nile.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {35237}, pmid = {41068271}, issn = {2045-2322}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Phylogeny ; Lakes ; Rivers ; *Biodiversity ; Electron Transport Complex IV/genetics ; Fresh Water ; }, abstract = {The present study aims to provide an inventory of eight freshwater fish species that represent 6 families obtained from Lake Nasser and the River Nile using DNA barcoding, using analysis of cytochrome oxidase subunit I (COI) gene sequences. Fish samples were identified morphologically as Ctenopharyngodon idella, Oreochromis niloticus, Bagrus bajad, Sarotherodon galilaeus, Auchenoglanis occidentalis, Lates niloticus, Sardinella tawilis, and Coptodon zillii. COI gene was successfully amplified for using PCR, showing a readable fragment length of ~ 700 base pairs (bp). The obtained sequences were compared to GenBank and the Barcode of Life Data System (BOLD). The GenBank and BOLD resulted in a total of 6 fish samples finding their best hits with similarity scores ranging from 99.29 to 100%. The average AT content (53.12%) was higher than the average GC content (46.88%) in the studied fish species. The minimum genetic Kimura 2-parameter (K2P) distance between species was 0.089 and the maximum distance was 0.313. According to phylogenetic tree analysis, the majority of fish species were grouped into monophyletic units. The current study confirms that DNA barcoding is a useful method to identify the vast majority of fish species in Lake Nasser and the River Nile. However, the morphological identification remains crucial.}, }
@article {pmid41064596, year = {2025}, author = {Nazarov, S and Xu, Y and Jiang, LY and Qiao, GX}, title = {A new species and two new records of Indomasonaphis Verma, 1971 (Hemiptera, Aphididae) from China.}, journal = {ZooKeys}, volume = {1253}, number = {}, pages = {343-362}, pmid = {41064596}, issn = {1313-2989}, abstract = {Indomasonaphis Verma, 1971 is a small genus primarily distributed in the southern Himalayan region. The genus is morphologically characterized by a concave frons; sparse, long, thick, and blunt or capitate dorsal setae; long clavate siphunculi; spinulose tarsi; and conspicuously hairy cauda. Based on the examination of Chinese specimens, the genus Indomasonaphis is recorded for the first time in China. A new species, Indomasonaphis polygoni Qiao &amp; Xu, sp. nov. on Polygonum sp. is described here. Additionally, Indomasonaphis anaphalidis (Basu, 1964) and Indomasonaphis rumicis (Chakrabarti &amp; Raychaudhuri, 1975) are newly recorded here from China. DNA barcode sequences of two species in the genus, I. anaphalidis (Basu) and I. polygoni Qiao &amp; Xu, sp. nov. were obtained for the first time. Keys to the Chinese species in this genus have been constructed.}, }
@article {pmid41053549, year = {2025}, author = {Wang, J and Guo, X and Li, B and Zhang, C and Yi, Y and Tang, M and Tang, X}, title = {Molecular identification and phylogenetic analysis of Polygonatum Kingianum with different floral colors on the basis of chloroplast genomes.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1285}, pmid = {41053549}, issn = {1471-2229}, support = {32360330, 32360262//National Natural Science Foundation of China/ ; 32360330, 32360262//National Natural Science Foundation of China/ ; 32360330, 32360262//National Natural Science Foundation of China/ ; 32360330, 32360262//National Natural Science Foundation of China/ ; 32360330, 32360262//National Natural Science Foundation of China/ ; U1812401//The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; U1812401//The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; U1812401//The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; U1812401//The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; U1812401//The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; U1812401//The Joint Fund of the National Natural Science Foundation of China and the Karst Science Research Center of Guizhou Province/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianKeHeChengGuo [2022]010//Guizhou Provincial Program on Commercialization of Scientific and Technological Achievements/ ; QianJiaoJi[2023]004//Water-Fertilizer Coupling and Biodiversity Restoration in Karst Rocky Desertification/ ; QianJiaoJi[2023]004//Water-Fertilizer Coupling and Biodiversity Restoration in Karst Rocky Desertification/ ; 202308520101//China Scholarship Council/ ; }, abstract = {UNLABELLED: Polygonatum kingianum, a plant with both medicinal and edible properties, demonstrates considerable variation in perianth coloration, making its differentiation from related species through morphological characteristics particularly challenging. This variation has led to frequent substitution of P. kingianum with other Polygonatum species in commercial markets, thereby compromising product quality and posing risks to the safety and efficacy of clinical applications. This research reports the sequencing and assembly of chloroplast genomes from three P. kingianum phenotypes with distinct floral colors. The complete chloroplast genome sizes are 155,827 bp, 155,825 bp, and 155,792 bp in length, each including 86 Protein-Coding Genes (PCGs), 8 rRNA genes, and 38 tRNA genes. Phylogenetic analysis of chloroplast PCG sequences confirmed that the three color phenotypes are variants of P. kingianum, indicating that the white-flowered phenotype represents the ancestral trait. Comparative analysis of chloroplast genome structures among closely related species revealed no substantial differences in repeat composition or codon usage bias between the color phenotypes. The consistent IR boundary contraction/expansion patterns provided additional evidence for a highly conserved chloroplast genome structure. These distinct characteristics from other Polygonatum species substantiated that the three flower color phenotypes are phenotypic variations of P. kingianum. Furthermore, we identified hypervariable regions suitable for use as DNA barcodes to authenticate different flower-color phenotypes of P. kingianum and distinguish them from adulterant species.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07147-9.}, }
@article {pmid40667010, year = {2025}, author = {Michielsen, L and Prjibelski, AD and Foord, C and Hu, W and Jarroux, J and Hsu, J and Tomescu, AI and Hajirasouliha, I and Tilgner, HU}, title = {Spatial isoform sequencing at sub-micrometer single-cell resolution reveals novel patterns of spatial isoform variability in brain cell types.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.25.661563}, pmid = {40667010}, issn = {2692-8205}, support = {R35 GM152101/GM/NIGMS NIH HHS/United States ; U01 DA053625/DA/NIDA NIH HHS/United States ; T32 DA039080/DA/NIDA NIH HHS/United States ; RF1 MH121267/MH/NIMH NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; }, abstract = {Spatial long-read technologies are becoming increasingly common but lack nanometer- and therefore often single-cell resolution. This leaves the question unanswered of whether spatially variable isoforms represent spatial variability within one cell type or differences in cell-type composition between different regions. Here, we developed Spl-ISO-Seq2 (220nm spot size and 500nm resolution), and the accompanying software packages Spl-IsoQuant-2 and Spl-IsoFind, enabling long-read sequencing using 140 million barcodes compared to 80,000 previously. Applying this to the adult mouse brain, we compared spatial variability by examining (a) differential isoform abundance between known brain regions and (b) spatial isoform patterns that do not align with predefined regions. While the former revealed more spatial isoform differences, both approaches identified overlapping hits, e.g., Rps24 in oligodendrocytes. For Snap25, previously known to exhibit spatial isoform variation, we now show that this variability occurs in excitatory neurons. The second approach also uncovered patterns not captured by predefined-region comparisons, e.g., Tnnc1 in excitatory neurons. Furthermore, we show that a surprising number of spatial isoform signals is not driven by cell-type composition alone. Finally, we applied our software to public Visium HD 3 long-read data to demonstrate its applicability and strong reproducibility across protocols and biological replicates. Taken together, our experimental and analytical methods enrich spatial transcriptomics with a so-far elusive isoform view of spatial variation for individual cell types.}, }
@article {pmid41055246, year = {2025}, author = {Lussier, F and Moon, BU and Janta-Polczynski, M and Morocz, Y and Svahn, F and Shen, M and Lukic, L and Malic, L and Veres, T and Ng, A and Juncker, D}, title = {PiP-Plex: A Particle-in-Particle System for Multiplexed Quantification of Proteins Secreted by Single Cells.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e06398}, doi = {10.1002/adma.202506398}, pmid = {41055246}, issn = {1521-4095}, abstract = {Cell signaling is modulated by the secretion of various proteins, which can be used to infer a cell's phenotype. However, these proteins cannot be readily detected in multiplex by commonly used methods at the single-cell level. Here we present PiP-plex a particles-in-particle (PiPs) syst for multiplex protein secretion analysis by confocal microscopy. PiP-plex-comprises (i) fluorescence intensity barcoded microparticles (BMPs) co-entrapped with (ii) a single cell inside an alginate hydrogel particle. We found that PiPs maintained >90% cellular viability and allowed live cells retrieval. A seven-plex fluorescent barcoding and concomitant sandwich immunoassay in PiPs was developed with limits of detection ranging from 0.8 pg mL[-1] to 2 ng mL[-1] depending on the protein. PiP-plex assays were benchmarked with bulk immunoassays and found to rival or outperform them. Proteins secreted by single THP-1 cells upon exposure to lipopolysaccharid were measured by PiP-plex and varying cell responses detected, including a significant increase in MIP-1α, TNF-α, and IL-17A; MIP-1α and IL-17A were the most frequently secreted cytokines, while other cytokines were typically co-secreted. Using PiP-plex, we analyzed ≈750 THP-1 cells, showcasing its potential for characterizing cells and cell-based therapeutics for e.g. cancer immunotherapies.}, }
@article {pmid41054354, year = {2025}, author = {Palomo, JL and Rogel, JI and Moreno, MA and Joyce, AL}, title = {Low genetic diversity of Aedes albopictus (Diptera: Culicidae) in El Salvador based on mitochondrial COI sequences: evidence of a well-preserved ancestral lineage in the Americas.}, journal = {Journal of insect science (Online)}, volume = {25}, number = {5}, pages = {}, doi = {10.1093/jisesa/ieaf085}, pmid = {41054354}, issn = {1536-2442}, support = {//University of California Merced/ ; //Research Office of the University of El Salvador/ ; }, mesh = {Animals ; *Aedes/genetics ; *Genetic Variation ; El Salvador ; Phylogeny ; DNA, Mitochondrial/genetics ; Haplotypes ; Electron Transport Complex IV/genetics ; Americas ; }, abstract = {Aedes albopictus (Skuse) is an invasive mosquito species which has rapidly expanded across the Americas since the 1980s. This species has significant implications for public health. This study aimed to assess the genetic diversity and potential invasion routes of Ae. albopictus populations in El Salvador and throughout the Americas using the mitochondrial DNA (mtDNA) CO1 barcode. The mtDNA CO1 was sequenced from 52 samples from 5 departments in El Salvador. Analyses included the El Salvador populations, and an additional 205 GenBank sequences from the American continent and Asia, the region of origin. Haplotype and nucleotide diversity assessments, genetic differentiation, and phylogenetic clustering were performed. Genetic diversity in populations of Ae. albopictus from El Salvador and from most countries in America was generally low; El Salvador had 3 haplotypes. One exception was Colombia, where 12 haplotypes were detected. In the Americas, 22 haplotypes were found overall. Phylogenetic analyses grouped American samples into 2 major clusters, 1 centered around haplotype 19, which was the most abundant and widely distributed. El Salvador shared 2 haplotypes with North America. Ae. albopictus from Puerto Rico was genetically distinct from other groups and grouped together with Asian samples. The Asian outgroups were more diverse than samples from America. The analysis highlighted the presence of ancestral lineages in El Salvador and their role in early and complex colonization patterns of this species across the Americas, providing critical data for future management and control strategies against this invasive vector.}, }
@article {pmid41052572, year = {2025}, author = {Krücken, J and Diekmann, I and Andreotti, S and Bredtmann, CM and Mbedi, S and Sparmann, S and Schmidt, JS and de Almeida Borges, F and de Freitas, MG and Sallé, G and Hofer, H and Matthews, JB and Tzelos, T and Nielsen, MK and Kuzmina, TA and Samson Himmelstjerna, GV}, title = {Cytochrome c oxidase I deep amplicon sequencing for metabarcoding of equine strongyle communities: unexpectedly high Strongylus spp. prevalence in treated horses.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2025.09.007}, pmid = {41052572}, issn = {1879-0135}, abstract = {Equines are parasitized by complex communities of Strongylidae (Nematoda) comprising multi-species infections. Currently, Cyathostominae are most prevalent, while Strongylus species are only rarely detected. Since eggs and, in most cases, infective larvae cannot be differentiated to species level, except for Strongylus spp., species-specific knowledge of the pathology, epidemiology and ecology of these parasitic nematodes is limited. Reference sequence data for several cyathostomin species are limited or missing. Deep amplicon sequencing of internal transcribed spacer 2 (ITS-2) regions of nematodes has been used in equines previously, although barcoding studies demonstrated a better species resolution for the cytochrome c oxidase subunit I (COI) region. The present study introduces a nemabiome method based on sequencing of COI fragments. This method was applied to compare third stage larvae, representing strongyle communities, derived from regularly treated (RT) and never treated (NT) equine populations from Brazil, France (only RT), Germany, Ukraine, the UK, and the USA. Samples were predominantly from horses, but some were obtained from Przewalski's horses (Ukraine), donkeys (Germany, Ukraine) and kulans (Ukraine). Most sequence reads (87.7%) were identified to species level, but unclassified reads occurred more frequently in donkeys and kulans than horses. No obvious difference in species diversity and richness was observed between RT and NT equines. However, there were significant differences in species composition between the RT and NT groups. Strongylus spp. were more common in NT groups but also showed unexpectedly high abundances in RT horses. Cylicocyclus nassatus, Cylicostephanus longibursatus, and Cyathostomum catinatum were more abundant in RT groups, suggesting that strongyle communities in domestic equines may have been shaped by anthelmintic treatments during last decades. The decreased classification success for reads from non-caballine equines suggests that there are more strongyle species specific for this rarely-investigated group which requires additional efforts to improve the sequence database, particularly for these hosts.}, }
@article {pmid41052227, year = {2025}, author = {Shi, PQ and Feng, L and Huang, KC and Hu, JC and Feng, F and Xu, J}, title = {Two hymenopteran parasitoid species of the jackfruit borer Diaphania caesalis (Lepidoptera: Pyralidae) in China.}, journal = {Journal of insect science (Online)}, volume = {25}, number = {5}, pages = {}, doi = {10.1093/jisesa/ieaf079}, pmid = {41052227}, issn = {1536-2442}, support = {R19029//Guangdong Ocean University/ ; A24403//Guangdong Science and Technology Department/ ; 202305AF150146//Yunnan Province Science and Technology Talents and Platform Plan/ ; //Feng Feng Expert Workstation in Yunnan Province/ ; //Jackfruit Germplasm Resource Nursery of Guangdong province (Guangdong Ocean University)/ ; //Jackfruit Science and Technology Backyard in Yunnan's Hekou/ ; }, mesh = {Animals ; China ; *Moths/parasitology/growth &amp; development ; Pest Control, Biological ; *Wasps/physiology/classification/genetics/anatomy &amp; histology ; Host-Parasite Interactions ; Larva/parasitology/growth &amp; development ; DNA Barcoding, Taxonomic ; Artocarpus/growth &amp; development ; Female ; *Hymenoptera/physiology/classification ; }, abstract = {Jackfruit borer, Diaphania caesalis (Walker), is a major boring pest of Artocarpus plants (Moraceae). Biological control is considered an environmentally sustainable means of managing pests. However, parasitoids of D. caesalis in China are unknown. Here, we investigated the parasitoids of D. caesalis through field monitoring and surveys and identified them through morphological observation and DNA barcoding technology. Two hymenopteran parasitoid species, Dolichogenidea sp. and Eulophidae undet. sp., were identified on D. caesalis. The parasitism rate of Dolichogenidea sp. (21.0 ± 1.8%) was significantly higher than that of Eulophidae undet. sp. (3.8 ± 2.2%). The field incidence of Dolichogenidea sp. in the Artocarpus integer and Artocarpus heterophyllus orchards was 30.8 ± 2.5% and 22.3 ± 7.6%, respectively, but there was no significant difference. Overall, Dolichogenidea sp. was the dominant parasitoid of D. caesalis in China. Further research is needed to determine the species' identity, and their biological characteristics should be evaluated to determine their potential applications in biocontrol programs.}, }
@article {pmid41051286, year = {2025}, author = {Paladini, A and Carvalho, GS and Cabral-de-Mello, DC and Mariguela, TC and Domahovski, AC and Barão, KR}, title = {Shades of red: several lines of evidence reveal a pest of sugarcane as new species of Mahanarva (Hemiptera: Auchenorrhyncha: Cercopidae).}, journal = {Bulletin of entomological research}, volume = {}, number = {}, pages = {1-17}, doi = {10.1017/S0007485325100503}, pmid = {41051286}, issn = {1475-2670}, abstract = {Many species of spittlebugs (Auchenorrhyncha: Cercopidae) use sugarcane and other grasses as host plants, and when damage is extensive they are considered pests leading tom economic losses. Mahanarva fimbriolata and Mahanarva spectabilis are the most common in sugarcane and can be distinguished mainly by genital morphology. Recently, another morphotype of Mahanarva occurring in sugarcane fields that did not match the morphologies of either of these Mahanarva species mentioned above has been widely collected in Brazil, raising doubts on the identification of Mahanarva species using sugarcane. Accurate specimen identification is critical for sugarcane pest management, because misidentifications can lead to economic losses and inefficient control strategies. Thus, we combined morphology, geometric morphometrics, and molecular techniques to investigate the hypothesis that this morphotype could be considered a new species of Mahanarva. Morphological analyses included examination of male genitalia and tegminal colouration patterns. We also quantified hindwing shapes using geometric morphometrics; and performed a phylogenetic analysis using the mitochondrial COI gene. Morphological evidence distinguished the new morphotype through unique traits in male genitalia. Geometric morphometrics reliably separated species, with over 89% classification accuracy. Molecular analyses confirmed the morphotype as a distinct lineage closely related to M. fimbriolata and M. spectabilis. Thus, we describe M. diakantha sp. n., demonstrating the effectiveness of an integrative approach in resolving taxonomic challenges. Additionally, we provide formal diagnoses for M. fimbriolata and M. spectabilis. This work underscores the importance of precise taxonomy in agroecosystems, supporting sustainable pest management practices.}, }
@article {pmid41051238, year = {2025}, author = {Gencel, M and Gagné-Leroux, D and Serohijos, AWR}, title = {Doblin: Inferring dominant clonal lineages from high-resolution DNA barcoding time series.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf555}, pmid = {41051238}, issn = {1367-4811}, abstract = {MOTIVATION: The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population's ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms.<br><br>RESULTS: In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin's accuracy using lineage data from evolutionary simulations, showing that it recovers the clones' identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of E. coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin's versatility allows it to be applied to lineage time-series data across different experimental setups.<br><br>Doblin is available on CRAN (https://CRAN.R-project.org/package=doblin) and Github (https://github.com/dagagf/doblin).}, }
@article {pmid41049183, year = {2025}, author = {Fussy, A and Austoni, S and Winkelmann, T and Papenbrock, J}, title = {Comparative assessment of species identification methods for European Salicornia sources: a multifaceted approach employing morphology, nuclear DNA content, phylogenetic markers, RNA topology, and SSR fingerprinting.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1666009}, pmid = {41049183}, issn = {1664-462X}, abstract = {Accurate identification of Salicornia species is a fundamental prerequisite for their potential usability and domestication. This study utilized a multifaceted methodological approach integrating morphological, cytogenetic, and molecular techniques to identify species from available European Salicornia sources. The following methods were compared: nuclear DNA content analysis; application of marker-based DNA barcoding via four common Salicornia markers; investigations of RNA topologies of these marker sequences by predicting theoretical secondary structures; utilization of diagnostic single-nucleotide polymorphism (SNP) positions within the external transcribed spacer (ETS) marker sequences for European Salicornia taxa; comparison of three promising microsatellite (SSR) markers regarding their ability to differentiate Salicornia subspecies; and evaluation of morphological data on habitus and flower characteristics utilizing a Salicornia identification key. The results demonstrate that ETS marker analysis offers reliable and cost-effective species determination, with SNP comparisons being more user friendly than phylogenetic trees are, and microsatellite markers can be differentiated down to the subspecies level via fragment length differences. However, microsatellite analysis alone is not suitable for primary species identification. DNA content can provide a rough estimation of potential species and is already more reliable than morphological methods. The differentiation among species is crucial for creating transparency for farmers and consumers and for initiating breeding processes, particularly within the context of frequent misidentification.}, }
@article {pmid41047867, year = {2025}, author = {Fontes, JT and Mokhtar-Jamaï, K and Nchioua, Z and Durand, JD and Landi, M and Meira, J and Machado, L and Baali, A and Sobrino, I and Barri, I and Kouamé, E and Adepo-Gourène, BA and Diop, M and Kidé, NG and Wehye, AS and Sohou, Z and Carneiro, M and Martins, R and Soares, P and Costa, FO}, title = {Phylogeography of the widely distributed John Dory (Zeus faber, Actinopterygii: Zeiformes) reaffirms the prevalence of at least two deeply divergent clades.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70245}, pmid = {41047867}, issn = {1095-8649}, abstract = {The John Dory Zeus faber is a commercially exploited demersal fish species with a known distribution ranging from the Northeast Atlantic to parts of the Indian and Pacific oceans. A previous genetic survey using cytochrome c oxidase subunit I (COI) DNA barcodes suggested the presence of two geographically segregated taxonomic units within Z. faber. We revisit this hypothesis by expanding the number and geographic coverage of DNA barcodes, addressing a major data gap along parts of the Atlantic coast of Africa and conducting a comprehensive phylogeographic analysis. Our findings consolidated the existence of two highly divergent mitochondrial clades, Clade A and Clade B (mean K2P distance: 7.4%), with the transition zone between them located along the Atlantic coast of Morocco. Clade A exhibited no phylogeographic structure, with haplotypes shared between Northeast Atlantic and Mediterranean populations. Conversely, four geographically structured subclades (mean K2P distance: 0.9%) were detected within Clade B, extending south and eastward from Morocco to Japan and New Zealand. Historical demographic events driving allopatric divergence, along with oceanographic and environmental factors, likely shaped the current geographic distribution of the two clades. These findings not only prompt the need to re-evaluate the taxonomic status of Z. faber but also highlight the probable existence of multiple evolutionarily significant units (ESUs) that must be considered in the scope of stock assessment, fisheries management and conservation purposes.}, }
@article {pmid41045070, year = {2025}, author = {Stenbäck, JB and Schmidt, D and Noborg, U and Gustafsson, J and Norberg, P and Andersson, ME and Fu, MX and Harvala, H and Ringlander, J}, title = {Accurate and Cost-Efficient Whole Genome Sequencing of Hepatitis B Virus Using Nanopore.}, journal = {Journal of medical virology}, volume = {97}, number = {10}, pages = {e70630}, doi = {10.1002/jmv.70630}, pmid = {41045070}, issn = {1096-9071}, support = {//This study was funded by the Gothenburg Society of Medicine and the Sahlgrenska University Hospital./ ; }, mesh = {*Hepatitis B virus/genetics/isolation &amp; purification ; Humans ; *Whole Genome Sequencing/methods/economics ; *Genome, Viral ; DNA, Viral/genetics ; *Nanopores ; *High-Throughput Nucleotide Sequencing/methods/economics ; Hepatitis B/virology ; *Nanopore Sequencing/methods/economics ; Genotype ; }, abstract = {Deep sequencing of the whole hepatitis B virus genome increases the analytical resolution and has the potential to improve molecular epidemiology investigations. The aim of this study was to develop and evaluate the performance of such deep sequencing using the Nanopore technology. The method includes an initial PCR step to generate two overlapping amplicons that cover the whole relaxed circular HBV genome found in circulating viral particles and covalently closed circular DNA in infected hepatocytes, followed by sequencing using the Nanopore rapid barcoding kit that allows parallel analysis of several samples in one reaction. The libraries can be sequenced with the standard Nanopore flow cell on MiniIon or GridIon devices, as well as the Flongle. The performance of the method was evaluated by comparing Nanopore and Sanger sequences or qPCR results from 64 clinical samples. The Nanopore-derived consensus sequences were, on average, 99.9% similar to those from Sanger sequencing, and the full HBV genome was determined in samples with HBV DNA levels of approximately 3 log10 IU/mL with MagNA pure 96 extraction and < 2 log10 IU/mL using a high-volume manual extraction protocol on a subset of samples from patients with very low viral load (1.62-3.74 IU/mL). A perfect agreement with Sanger/qPCR-derived genotype was seen. The cost of sequencing per genome using the Nanopore method is low, ranging from 6 to 37 euros. We conclude that whole genome sequencing of HBV with Nanopore is well suited for genomic characterization, antiviral resistance mutation analysis, and genotyping of HBV in a routine laboratory setting.}, }
@article {pmid41044471, year = {2025}, author = {Afshan, NU and Ahmad, MA and Jabeen, M and Binyameen, S and Khalid, AN}, title = {New species and new records of genus Melampsora (Melampsoraceae) from Pakistan using electron microscopy and DNA barcoding techniques.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1310}, pmid = {41044471}, issn = {1471-2229}, abstract = {The genus Melampsora, known for its significant role as a plant pathogen, exhibits a rich species diversity. Current study reports Melampsora himalayensis sp. nov. as new species with M. ferrinii and M. populnea as new records from different regions (Fairy Meadows, Gilgit Baltistan; Khanspur, Khyber Pakhtunkhwa) of Pakistan, contributing to the knowledge of rust fungi diversity and distribution. Their placement within genus Melampsora was validated by comparative morpho-anatomical investigation. Detailed morphological characterization was employed using Scanning electron microscopy which provided features of spore morphology including their surface ornamentation. Additionally, molecular analysis was performed for species delimitation and to resolve phylogenetic relationships within genus Melampsora. Combined morpho-anatomical and phylogenetic data led to the discovery of previously unrecorded species, Melampsora ferrinii and M. populnea from Pakistan, including a novel taxon, Melampsora himalayensis sp. nov. This study provides information about taxonomy, host range and distribution of Melampsora in Pakistan.}, }
@article {pmid41044180, year = {2025}, author = {Warguła, J and Dmuchowska, W and Stec, D and Kaczmarek, &#x141;}, title = {Integrative taxonomy elucidates phylogenetic position of a clawless African eutardigrade (Tardigrada) supporting the erection of a new genus.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {34511}, pmid = {41044180}, issn = {2045-2322}, abstract = {In the presented study, we re-investigated the soil-dwelling clawless tardigrade species Apodibius nuntius (Binda, 1984) using an integrative taxonomic approach. Our analysis is based on detailed morphological comparisons between three populations from three different countries: Mozambique (type population), Australia and Uganda. The first two populations comprise historical specimens deposited in museum collections, whereas the third one is newly found and reported for the first time in this study. In addition to morphological analysis, we constructed a phylogenetic tree of Isohypsibioidea using two ribosomal gene fragments (18S rRNA and 28S rRNA). The obtained results enabled us to establish a new genus, Sinunguibius gen. nov., which is assigned to the family Hexapodibiidae. The new genus constitutes the second known genus within Eutardigrada characterized by a complete absence of claws. The main morphological chacter that differentiates the new genus from the also clawless genus Apodibius is the number of placoids in the pharynx. Our results suggest that the complete loss of claws is a convergent trait that occurs in at least two families: Doryphoribiidae and Hexapodibiidae. The inclusion of the new genus within the family Hexapodibiidae required a corresponding amendment to its family diagnosis.}, }
@article {pmid41042067, year = {2025}, author = {Lam, L and Watson, S and Ramaswamy, Y and Singh, G}, title = {High-Throughput Strategies for Streamlining Lipid Nanoparticle Development Pipeline.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e11551}, doi = {10.1002/advs.202511551}, pmid = {41042067}, issn = {2198-3844}, abstract = {Lipid nanoparticles (LNPs) have become clinically validated nanocarriers for nucleic acid delivery, enabling applications in mRNA vaccines and therapies for cancer, ocular, and infectious diseases. Identifying LNPs formulations with optimal physicochemical and pharmacokinetic properties using traditional low-throughput methods is resource-intensive and impractical for evaluating large libraries. Recent advances in automation, high-throughput platforms for lipid synthesis, characterization, and screening tools are transforming the landscape of LNP formulation. These strategies enable rapid multi-parametric generation and evaluation of hundreds to thousands of formulations across key properties such as size, charge, stability, biodistribution, cellular uptake, and intracellular trafficking. In parallel, advanced biomimetic models and in vivo multiplexed barcoding screening strategies provide deeper insights into tissue targeting and therapeutic delivery outcomes. This review provides an integrated framework that combines automation with high-throughput combinatorial synthesis, characterization, and in vitro/in vivo screening tools. In this development pipeline, performance benchmarks applied at each step systematically exclude suboptimal candidates, ensuring that only clinically viable LNP candidates advance. Future directions, including automation, high-throughput, and closed-loop machine learning guided design strategies, are further discussed to advance the development of next-generation LNP therapeutics and accelerate their translation from bench to bedside.}, }
@article {pmid41041654, year = {2025}, author = {Nakahama, N and Hirasawa, K and Kato, M and Watanabe, K and Kurata, S and Hayashi, M}, title = {Mitochondrial DNA 16S region and voucher specimen collection of Japanese aquatic Coleoptera and Hemiptera for environmental DNA metabarcoding analyses.}, journal = {ZooKeys}, volume = {1253}, number = {}, pages = {103-119}, pmid = {41041654}, issn = {1313-2989}, abstract = {Aquatic coleopteran and hemipteran insects primarily inhabit lentic waters, many of which are at risk of extinction due to development, agriculture, and invasive alien species. Environmental DNA (eDNA) analysis has recently emerged as a powerful tool for conducting comprehensive distribution surveys. The cytochrome c oxidase subunit I (COI) universal primers are conventionally used for DNA barcoding but they often result in non-specific amplification and frequent amplication failures. Primers in the mitochondrial DNA (mtDNA) 16S rRNA region that alleviate these issues have been developed and are considered helpful for eDNA analysis. It is necessary to accumulate reference sequences of the mtDNA 16S rRNA region in aquatic coleopteran and hemipteran insects. However, molecular identification at the genus or species level remains challenging, as only a few of these insect groups in Japan have registered reference DNA sequences for both the mtDNACOI and 16S rRNA. Therefore, we constructed a comprehensive dataset of the mtDNA 16S rRNA region for these insects distributed in Japan. As a result of this study, we were able to obtain partial sequences of the mtDNA 16S rRNA region from 140 coleopteran taxa (35.5% of Japanese aquatic species or subspecies) and 58 hemipteran taxa (45.3% of Japanese aquatic species or subspecies). These voucher specimens were deposited in four research institutions. The DNA sequence datasets are expected to significantly contribute as an essential database for eDNA analysis and other DNA metabarcoding studies.}, }
@article {pmid41041551, year = {2025}, author = {Zhang, N and Fu, Y and Mathew, D and Wang, M and Chen, X and Lin, K and Schaff, D and Shaffer, S and Pardoll, D and Jackson, C}, title = {Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-7510946/v1}, pmid = {41041551}, issn = {2693-5015}, abstract = {Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.}, }
@article {pmid41041396, year = {2025}, author = {Irawan, AD and Eguchi, K}, title = {Application of Invertebrate-Derived DNA Barcoding (iDNA) in Blood Sucking Leeches From West Sumatra: A Discovery of Blue-Eyed Litter Frog Leptobrachium waysapuntiense.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72235}, pmid = {41041396}, issn = {2045-7758}, abstract = {Indonesia is one of the world's most biodiversity-rich countries, including a wide variety of vertebrate and plant species. However, assessing biodiversity in tropical rainforests remains challenging itself. The use of conventional tools has commonly been employed for monitoring and research purposes. Invertebrate-derived DNA (iDNA), a subdiscipline of environmental DNA (eDNA), has emerged as a noninvasive tool that complements traditional methods for biodiversity assessment. It enables the detection of vertebrate species and the monitoring of their populations through molecular approaches. Utilizing abundant haematophagous leeches provides a promising approach to sample a broader range of host species within an area, as these leeches retain high-quality host DNA in their guts for extended periods. Using Sanger sequencing with five primer sets (16Scp, 16Sed, 12S, ND2, and RepCOI) designed to target broad taxonomic groups, 272 Haemadipsa spp. samples were successfully amplified, resulting in the identification of 17 unique vertebrate hosts, including mammals, amphibians, and reptiles. Within our 16Sed results, we noted that the primer sets could capture a broader range of taxa than originally targeted, encompassing both mammals and reptiles, thereby enhancing species richness detection. Notably, we present evidence of the first iDNA-based detection of the rare blue-eyed litter frog, Leptobrachium waysepuntiense, from western Sumatra. Therefore, this study suggests that the use of haematophagous leeches represents a promising approach for biodiversity monitoring in Indonesia. This method offers a complementary strategy that can be integrated with existing practices to strengthen conservation efforts.}, }
@article {pmid41040332, year = {2025}, author = {Ashok, Y and Bubb, KL and Oi, C and Gorjifard, S and Cuperus, JT and Queitsch, C and Fields, S}, title = {Dosa: A method to covalently barcode proteins for high throughput biochemistry.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.21.677650}, pmid = {41040332}, issn = {2692-8205}, abstract = {Deep mutational scanning couples a protein's activity to DNA sequencing for high throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like growth, as proxy for protein activity. Here, we covalently link variant proteins in vivo to an RNA barcode by fusing them to E. coli tRNA (m 5 U 54) methyltransferase TrmA (E358Q), which forms a covalent bond with a tRNA stem-loop. Following cell lysis, variant proteins are separated in vitro according to their biochemical properties and identified by their barcodes. We use this method, Dosa, to analyze a large pool of FLAG epitope variants for binding to an anti-FLAG antibody, to profile the cleavage preferences of variants of enteropeptidase and human rhinovirus 3C protease, and to measure the solubility of several hundred Aβ(1-42) variants. This method should be amenable to numerous biochemical assays with proteins produced in E. coli or mammalian cells.}, }
@article {pmid41040279, year = {2025}, author = {Park, SY and Sheridan, A and An, B and Jarvis, E and Lyudchik, J and Patton, W and Axup, JY and Chan, SW and Damstra, HGJ and Leible, D and Leung, KS and Magno, CA and Meeran, A and Michalska, JM and Rieger, F and Wang, C and Wu, M and Church, GM and Funke, J and Huffman, T and Leeper, KGC and Truckenbrodt, S and Winnubst, J and Kornfeld, JMR and Boyden, ES and Rodriques, SG and Payne, AC}, title = {Combinatorial protein barcodes enable self-correcting neuron tracing with nanoscale molecular context.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.26.678648}, pmid = {41040279}, issn = {2692-8205}, abstract = {Mapping nanoscale neuronal morphology with molecular annotations is critical for understanding healthy and dysfunctional brain circuits. Current methods are constrained by image segmentation errors and by sample defects (e.g., signal gaps, section loss). Genetic strategies promise to overcome these challenges by using easily distinguishable cell identity labels. However, multicolor approaches are spectrally limited in diversity, whereas nucleic acid barcoding lacks a cell-filling morphology signal for segmentation. Here, we introduce PRISM (Protein-barcode Reconstruction via Iterative Staining with Molecular annotations), a platform that integrates combinatorial delivery of antigenically distinct, cell-filling proteins with tissue expansion, multi-cycle imaging, barcode-augmented reconstruction, and molecular annotation. Protein barcodes increase label diversity by >750-fold over multicolor labeling and enable morphology reconstruction with intrinsic error correction. We acquired a ∼10 million μm [3] volume of mouse hippocampal area CA2/3, multiplexed across 23 barcode antigen and synaptic marker channels. By combining barcodes with shape information we achieve an 8x increase in automatic tracing accuracy of genetically labelled neurons. We demonstrate PRISM supports automatic proofreading across micron-scale spatial gaps and reconnects neurites across discontinuities spanning hundreds of microns. Using PRISM's molecular annotation capability, we map the distribution of synapses onto traced neural morphology, characterizing challenging synaptic structures such as thorny excrescences (TEs), and discovering a size correlation among spatially proximal TEs on the same dendrite. PRISM thus supports self-correcting neuron reconstruction with molecular context.}, }
@article {pmid41039089, year = {2025}, author = {Liu, Y and Vukic, M and Hannon, E and Mei, H and Walker, E and Sinke, L and ,  and Mill, J and Daxinger, L and Heijmans, BT}, title = {Identification of SENP7 and UTF1/VENTX as new loci influencing clustered protocadherin methylation across blood and brain using a genome-wide association study.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {41039089}, issn = {1476-5578}, support = {K013807//RCUK | Medical Research Council (MRC)/ ; W004984//RCUK | Medical Research Council (MRC)/ ; M008924//RCUK | Medical Research Council (MRC)/ ; }, abstract = {The epigenetic regulation of clustered protocadherin (cPCDH) genes is tightly linked to their function as specific cell surface barcodes for neural self-nonself discrimination. Differential cPCDH DNA methylation has been implicated in diverse neurological diseases as well as body weight, cancer and aging. However, the unique regulation of cPCDH methylation remains poorly understood. Therefore, we performed a genome-wide association study to evaluate the association of >7 million genetic variants with DNA methylation at 607 cPCDH CpGs measured in whole blood of 3777 individuals and validated findings in prefrontal cortex samples obtained from 523 brain donors. We observed concordant cPCDH methylation patterns in blood and prefrontal cortex, which switched between hypo-, intermediate and hypermethylation over short distances with the former overlapping with the promoter regions of each cPCDH member. Through methylation quantitative trait locus (meQTL) analysis in trans, we first confirmed the broad effect of the candidate gene SMCHD1 on cPCDH methylation in blood and then validated this effect in prefrontal cortex. Through a genome-wide analysis, we next identified the SENP7 and UTF1/VENTX loci to have widespread, subcluster-specific effects on cPCDH methylation in blood and brain. While SENP7 can indirectly affect DNA methylation through the deSUMOylation of the chromatin repressor KAP1, UTF1 and VENTX are two genes involved in embryonic development not previously implicated in epigenetic regulation. Our findings shed new light on the processes involved in cPCDH methylation that may underlie associations with neurological disease.}, }
@article {pmid41034732, year = {2025}, author = {Khezri, A and Branders, S and Bellankimath, AB and Ali, J and Chapagain, C and Asadi, F and Grabherr, MG and Ahmad, R}, title = {MysteryMaster: scraping the bottom of the barrel of barcoded Oxford nanopore reads.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {235}, pmid = {41034732}, issn = {1471-2105}, abstract = {BACKGROUND: The high error rate associated with Oxford Nanopore sequencing technology adversely affects demultiplexing. To improve demultiplexing and reduce unclassified reads from nanopore sequencing data, we developed MysteryMaster, a demultiplexer that utilizes the optimal sequence aligner, Cola.<br><br>RESULTS: When compared to Oxford Nanopore&#xb4;s Dorado and Guppy demultiplexing tools across three datasets of 37 diverse samples with established ground truth, we found that MysteryMaster accurately identifies a similar or greater percentage of reads among the different basecalling models: Fast, HAC, and SUP. MysteryMaster performs slightly better than the other tools on data that was basecalled using the Fast basecalled model, while its performance in HAC and SUP data is similar to Dorado's. MysteryMaster has a false positive rate of just 0.41% with default settings.<br><br>CONCLUSIONS: While MysteryMaster can function as a standalone demultiplexer tool, the sequential application of Dorado and MysteryMaster produced the best overall performance.}, }
@article {pmid41034246, year = {2025}, author = {Sánchez-Vendizú, P and Erkenswick, G and Reyes, J and Clinton, SL and Espejo, TS and Cáceres, G and Libke, Z and Arana, A and Mendoza-Silva, J and Tirapelle, C and Williams, S and Swamy, V and Martínez-Altamirano, J and Esteves, J and Barnuevo-Bullón, JP and Hernández-Mejía, J and Caffo, X and Mendevil Malpica, A and Salazar-Aragón, R and Gutiérrez-Jiménez, L and Stabile, J and Cuzmar, N and Paine, TD and Peralta-Aguilar, P and Inga-Díaz, G and Lescano, J and Viñas-Martínez, A and McElroy, ME and Coayla, D and Linares R, LM and Pilfold, NW and Sacco, AJ and Arakaki, M and Mena, JL and Tobler, MW and Salinas, L and Arana, C and Pacheco, V and Prost, S and Watsa, M}, title = {Decoding the Peruvian Amazon with in situ DNA barcoding of vertebrate and plant taxa.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1545}, pmid = {41034246}, issn = {2052-4463}, support = {9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9772//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9772//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 9776//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, mesh = {*DNA Barcoding, Taxonomic ; Peru ; Animals ; *Birds/genetics/classification ; *Mammals/genetics/classification ; *Vertebrates/genetics/classification ; *Plants/genetics/classification ; }, abstract = {Species extinctions in the tropics are accelerating, outpacing documentation efforts. Meanwhile, DNA barcoding is flourishing in the Global North, backed by extensive infrastructure, allowing non-taxonomic experts to identify species from nonlethal, minimally invasive, and environmental samples. However, hyper-diverse regions like Peru make up only 0.52% (n = 93,246) of the Barcode of Life Database (BOLD). To address this, we established three decentralized laboratories with low-cost, portable nanopore sequencers. From 2018-2023, we generated 1,858 barcodes in situ using six genetic markers for 1,097 vertebrates and 76 plants from existing and new biobanks. We present the first genetic barcodes for 30 mammal and 196 bird species from Peruvian specimens, increasing the number of Peruvian mammal and bird species in BOLD by 110% and 36.5% respectively. We also report the first records of the marsupial Marmosops ocellatus and the bat Sturnira lilium for Peru. This dataset represents an effort to go from fresh or museum-preserved samples to barcodes entirely in situ, avoiding the export of samples outside the country, and facilitating local capacity in molecular biodiversity research.}, }
@article {pmid41033544, year = {2025}, author = {Świątek, P and Gajda, &#x141; and Urbisz, AZ}, title = {Ovary organization and oogenesis in two species of cave-living clitellate annelids from the genus Delaya (Clitellata, Pelodrilidae).}, journal = {Developmental biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ydbio.2025.09.021}, pmid = {41033544}, issn = {1095-564X}, abstract = {Clitellate annelids (Clitellata) are hermaphrodites with gonads localized in specific segments in the anterior body part. Localization of gonads and the structure of the reproductive systems are considered conservative traits of clitellate evolution and are used as crucial features in their taxonomy and in phylogenetic considerations. The study aimed to present the ovary morphology, histology, and ultrastructure in two Delaya species. The genus Delaya groups poorly known cave-living clitellate annelids, and their ovary organization and oogenesis are entirely unknown. Moreover, their taxonomic status is under debate. According to recent molecular analyses, Delaya and two other genera form the family Pelodrilidae, closely related to earthworms. To enhance our understanding of these cave-living animals' reproductive biology and provide new characters that may aid in phylogenetic considerations, the light and electron microscopic techniques were used to study the organization of the ovaries and the course of oogenesis in two species: one from a cave in Greece (Delaya sp. GR) and the other from a cave in France (Delaya sp. FR). In both species studied, two pairs of ovaries are located in two consecutive segments - XII and XIII. Each ovary consists of 3-5 functional units. The ovarian units are polarized: their apical parts (attached to the septum) contain oogonia and early meiotic cells, while the broader distal ends contain growing oocytes and nurse cells. Initially, germline cells (oogonia and early meiotic cells) develop synchronously, forming syncytial cysts in which each cell is connected via a single ring canal to the central cytoplasm (cytophore). Then, during meiotic prophase (in diplotene), synchrony is lost, and it is likely that one cell per cyst begins accumulating nutrients and differentiating into an oocyte. As oocytes detach from the cyst and continue oogenesis as individual cells, the remaining cells stay interconnected, do not grow, and are regarded as nurse cells. Yolk absorption is not completed in the ovary; vitellogenic oocytes are transferred to the ovisacs, where they continue to accumulate nutrients. Ovisacs are paired, long, sac-like structures, extending through several body segments (XII-XV). Delaya produces mesolecithic eggs with prominent yolk spheres, lipid droplets, and glycogen granules. Only some minor differences were observed between the two studied species. The most notable difference concerns the cytophore shape and volume in cysts connecting nurse cells. In Delaya sp. FR, the cytophore is reticular and inconspicuous, whereas in Delaya sp. GR, the cytophore is more prominent and may contain nurse cell nuclei. The obtained results confirm that the formation of the germline cysts equipped with the cytophore is a conservative phase of oogenesis in clitellates. Morphological observations suggest that in Delaya, the clustering cells differentiate into two subpopulations: oocyte and nurse cells, which aligns with the reports presenting oogenesis in other clitellates. Considering the differences in ovary organization between Delaya and other clitellates, we propose to refer to these as "Delaya-type" ovaries. The main similarities and differences between "Delaya" ovaries and other clitellate annelids are discussed. It is suggested that the presence of cysts equipped with the reticular cytophore could be an apomorphy of Pelodrilidae, earthworms, and allied taxa. We also provide DNA barcode sequences for Delaya sp. FR to shed light on its taxonomic identity. Furthermore, the phylogenetic analysis that was conducted indicates that Delaya sp. FR occupies a basal position among its congeners for which molecular data are available.}, }
@article {pmid41030982, year = {2025}, author = {Chen, D and Isakova, A and Wan, ZJ and Wagner, MJ and Wu, Y and Zhao, BS}, title = {Connectome-seq: High-throughput Mapping of Neuronal Connectivity at Single-Synapse Resolution via Barcode Sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.13.638129}, pmid = {41030982}, issn = {2692-8205}, abstract = {Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods particularly limited in mapping long-distance circuits and preserving cell type information. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding, and parallel single-nucleus and single-synaptosome sequencing to map neuronal connectivity at single-synapse resolution. This AAV-based approach enables simultaneous capture of both synaptic connections and molecular identities of connected neurons. We validated this approach in the mouse pontocerebellar circuit, identifying both established projections and potentially novel synaptic partnerships. Through integrated analysis of connectivity and gene expression, we identified molecular markers enriched in connected neurons, suggesting potential determinants of circuit organization. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision and gene expression information, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states. This advance in connectivity mapping methodology opens new possibilities for understanding circuit organization in complex mammalian brains.}, }
@article {pmid41030583, year = {2025}, author = {Maroni, PJ and Weston, JNJ and Kitazato, H and Jamieson, AJ}, title = {Hadal Snailfishes (Teleostei: Liparidae) Extend Across Multiple Trenches: Molecular Insights and Implications for Taxonomic Nomenclature.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e71779}, pmid = {41030583}, issn = {2045-7758}, abstract = {The hadal zone, Earth's deepest oceanic region, is defined by distinct geological features and hosts a variety of endemic species, including the Liparidae Gill, 1861 (snailfishes). Ecological understanding of snailfishes dwelling at depths greater than 6000 m remains limited due to challenges in physical specimen collection and preservation. This study employs molecular tools to assess the phylogenetic relationships and distribution patterns of hadal snailfishes by analyzing three mitochondrial DNA markers (16S, Cyt-B, COI) and incorporates 20 new specimens from the Japan and Tonga trenches (Pacific Ocean) and the Diamantina Fracture Zone (Indian Ocean). The phylogenetic hypotheses and species delimitation assessments were tested among a framework of six taxonomic units -Pseudoliparis swirei Gerringer and Linley, 2017, Pseudoliparis belyaevi Andriashev and Pitruk, 1993, Notoliparis kermadecensis Nielsen, 1964, Notoliparis stewarti Stein, 2016, and Paraliparis selti Linley, Gerringer, and Canto-Hernández, 2022. The results revealed wider geographic distributions than previously thought, particularly for Notoliparis c.f. stewarti. Further, the molecular data support the hypothesis that Notoliparis Andriashev, 1975 should be treated as a subjective junior synonym of Pseudoliparis Andriashev, 1955. Our findings do emphasize the challenges and limitations of using DNA barcoding solely to distinguish closely related or recently diverged species. Together, this study advances the biogeographic understanding of hadal snailfishes and highlights the importance of expanding sampling efforts.}, }
@article {pmid41029546, year = {2025}, author = {Ma, D and Tian, Q and Wang, Y and Duan, H and Zhang, Y and Luo, Y and Li, L}, title = {Comparative chloroplast genome of six species in Hypoxidaceae from China: insights into phylogenetic relationships and molecular marker development.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1232}, pmid = {41029546}, issn = {1471-2229}, support = {NSFC 32060049//National Natural Science Foundation of China/ ; NSFC 32270225//National Natural Science Foundation of China,China/ ; }, mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; Genetic Markers ; China ; }, abstract = {BACKGROUND: The family Hypoxidaceae (order Asparagales) is a predominantly Southern Hemisphere lineage comprising approximately 11 genera and 200 species, many of which possess significant medicinal and ornamental value. Despite their economic importance, Hypoxidaceae has received limited research attention, leading to problematic identification of species and misuse of wild resources in traditional medicine markets. Taxonomically, the phylogenetic position of Hypoxidaceae and the intergeneric relationships within this family remain controversial and unresolved, particularly concerning the delimitation of Curculigo and Molineria. Previous studies based on morphological traits and molecular markers have yielded inconsistent results, highlighting the need for more robust genomic evidence. In angiosperms, complete chloroplast genomes have proven highly effective in resolving systematic uncertainties considering their conserved structure and high informational content. However, such genomic data remain scarce for Hypoxidaceae, limiting phylogenetic clarity. In this research, the complete chloroplast genomes of six species representing three key genera (Curculigo, Molineria, and Hypoxis) were sequenced and characterized for a comparative and phylogenetic analysis.<br><br>RESULTS: The chloroplast genomes of six species exhibited conserved quadripartite structures, measured 157,472&#xa0;bp to 158,550&#xa0;bp in length. The overall GC content of these genomes ranged between 37.3 and 37.5%. Gene annotations identified 132 genes, 19 duplicated in the inverted repeat regions, and had complete ndh gene. Comparative analysis of six complete chloroplast genomes revealed highly similarity, but they were varied in repeats sequence, codon usage bias, contractions and expansions in the IR region. Five molecular markers showed the highest degree of variability between the six cp genomes. Phylgenetic analysis based on cp genomic data confirmed that Hypoxidaceae was a monophyly, being a sister to Asteliaceae with higher supports than the previous research. Three main clades were recognized in Hypoxidaceae, including Curculigo clade, Hypoxis clade, and Pauridia-Empodium clade. And what's more, Curculigo clade could be divided into three subclades, containing Molineria subclade, Curculigo subclade, and Seychellean subclade, indicating significantly phylogenetic insights.<br><br>CONCLUSIONS: The complete cp genomes of six species of three representative genera from Hypoxidaceae were sequenced and analyzed in detail, including the general data on the genome length, repeat sequence, codon usage, IR expansion and contraction, structural comparison and divergence hotspot identification analyses, and phylogenetic analysis. A comparative analysis revealed that the cp genome was highly consistent of four Molineria species, but varied greatly at the generic level between Hypoxis, Curculigo, and Molineria, which could be used for generic delimitation. Five DNA barcodes (psbK-psbI, rpoB-trnC, ndhF-rpl32, ycf1, and trnE-trnT) were selected for authentication of Hypoxidaceae medicinal materials. Hypoxidaceae was a monophyletic lineage, containing three major clades, being a sister to Asteliaceae with stronger supports than before. The three main clades in Hypboxidaceae were re-confirmed as the three stable lineages for this family. In the Curculigo Clade, three subclades were identified with significant phylogenetic insights. The phylogenetic evidence presented here, combined with distinct chloroplast genome features, supports Molineria Subclade separated from Curuculigo Subclade, being a monophyletic group by transferring Sinocurculigo taishanica and two Borneo Curculigo species into Molineria. Further research should provide a better understanding of the intergeneric relationships among Hypoxidaceae, adding more genomic data with extensive samplings across the center distribution of Southern Hemisphere.}, }
@article {pmid41028562, year = {2025}, author = {Ren, J and Zeng, H and Huang, J and Tian, J and Wu, M and Shi, H and Sui, X and Wang, CK and Zhou, H and Tang, Z and Luo, S and Wang, X}, title = {Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {41028562}, issn = {1750-2799}, support = {Stanley center gift//Broad Institute | Stanley Center for Psychiatric Research, Broad Institute (Stanley Center)/ ; }, abstract = {Controlled gene expression programs have a crucial role in shaping cellular functions and activities. At the core of this process lies the RNA life cycle, ensuring protein products are synthesized in the right place at the right time. Here we detail an integrated protocol for imaging-based highly multiplexed in situ profiling of spatial transcriptome using antibody-based protein comapping (STARmap PLUS), spatial translatome mapping (RIBOmap) and spatiotemporal transcriptome mapping (TEMPOmap). These methods selectively convert targeted RNAs, ribosome-bound mRNAs or metabolically labeled RNAs to DNA amplicons with gene-unique barcodes, which are read out through in situ sequencing under a confocal microscope. Compared with other methods, they provide the analytical capacity to track the spatial and temporal dynamics of thousands of RNA species in intact cells and tissues. Our protocol can be readily performed in laboratories experienced in working with RNA and equipped with confocal microscopy instruments. The wet lab experiments in preparing the amplicon library take 2-3 d, followed by variable sequencing times depending on the sample size and target gene number. The spatially resolved single-cell profiles enable downstream analysis, including cell type classification, cell cycle identification and determination of RNA life cycle kinetic parameters through computational analysis guided by the established tutorials. This spatial omics toolkit will help users to better understand spatial and temporal RNA dynamics in heterogeneous cells and tissues.}, }
@article {pmid41028292, year = {2025}, author = {Sahu, A and Singh, M}, title = {First report of aberrant Mystus vittatus (Bloch, 1794) from wild population in the Gomti River, Uttar Pradesh, India, based on integrative approach: a new conservation concern.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {10}, pages = {1163}, pmid = {41028292}, issn = {1573-2959}, support = {FISHNBFGRSIL 2023001300260//ICAR-NBFGR, Lucknow, India/ ; }, abstract = {This present study documents first recorded abnormality in Mystus vittatus (Bloch 1794) from the Gomti River near Thauri, Sultanpur District, Uttar Pradesh, India. Collected fish specimens were identified using integrative taxonomy, combining morphological and molecular data (Sanger or dideoxy sequencing). Interestingly, both the morphologically abnormal M. vittatus (MYAB1) and normal (NKG44N) exhibited 0% genetic divergence based on analysis of COI datasets. Molecular result indicates that the reported deformity is not associated with mitochondrial genetic variation and may instead be attributed to environmental factors. Comparative assessment of normal and abnormal individuals revealed no significant differences in morphological characters, except for the complete absence of caudal fin in abnormal fish. The total weight and length of the abnormal specimen were recorded as 9.59 g and 7.17 cm, respectively. Radiographic (X-ray) imaging further exposed underlying vertebral fusion at the hypural region from the 23rd to 27th vertebrae. Recorded water parameters included temperature (28.2 ± 7.2 °C), dissolved oxygen (5.1 ± 0.4 mg/L), pH (7.7 ± 0.7), ammonia (0.39 ± 0.05 mg/L), salinity (0.41 ± 0.20 ppt), TDS (264 ± 31 mg/L), conductivity (930 ± 40 µS/cm), and transparency (22 ± 3 cm). These values indicate potential environmental stress that may have contributed to the reported abnormality. Potential etiological and environmental factors include chemical contaminants, microplastics (MPs), heavy metals, essential nutrient deficiencies, and genetic mutations during larval development. In riverine habitats and other water bodies, documented exposure to agricultural and urban pollutants could also be responsible, emerging as plausible drivers of observed abnormalities. Malformation of the caudal fin may be referred to as "saddleback syndrome," which is often attributed to physical injury or developmental disruption during early life stages. Additionally, any predatory attack on its caudal region during its early development stages could have resulted in physical and traumatic injury. Despite such predatory attack, suspected individual might have escaped, survived, and healed, albeit with severe and permanent deformity. This study underscores the utility of radiology as critical diagnostic tool for detecting sub-surface anatomical abnormalities in wild fish populations. Our findings highlight the urgent action for targeted water quality monitoring in the Gomti River to mitigate anthropogenic impacts on native aquatic genetic resources (AGR). Future research should include both temporal and spatial assessments of water quality with fish health, particularly focusing on skeletal and soft tissue abnormalities.}, }
@article {pmid41028017, year = {2025}, author = {Gutiérrez-Rodríguez, J and Zaldívar-Riverón, A and López-Estrada, EK and Barranco, P and García-París, M}, title = {DNA barcode reference library of bush-crickets (Orthoptera, Tettigoniidae) from the Iberian Peninsula.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33883}, pmid = {41028017}, issn = {2045-2322}, support = {FJC2018-035899-I//Juan de la Cierva-Formaci&#xf3;n, Ministerio de Ciencia e Innovaci&#xf3;n, Spain/ ; DOC_00668//Doctores Junta de Andaluc&#xed;a (FEDER EU/Consejer&#xed;a de Econom&#xed;a, Conocimiento, Empresas y Universidad, Junta de Andaluc&#xed;a)/ ; 58548//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; PID2019-110243GB-100/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n, Spain/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Spain ; *Gryllidae/genetics/classification ; *Gene Library ; Phylogeny ; *Orthoptera/genetics/classification ; Biodiversity ; }, abstract = {Curated DNA barcode reference libraries are crucial for advancing environmental DNA (eDNA) studies, monitoring biological invasions, reliable biodiversity assessments, accurate species identification, etc. However, DNA barcode databases remain highly incomplete for most invertebrate taxa. In this study, we present the most comprehensive reference library to date for the family Tettigoniidae (Orthoptera) from the Iberian Peninsula-the most species-rich orthopteran family globally, with over 8,000 valid species. We generated 402 new DNA barcodes from at least 121 tettigoniid species from the Iberian Peninsula and integrated these with 169 previously published sequences. The resulting dataset comprises 571 barcoded specimens, representing 49 genera and 123 species, including many recently described taxa. Notably, we provide DNA barcodes for at least 68 described species that previously lacked them. Our dataset covers 85% of the tettigoniid species in the Iberian Peninsula and approximately 25% of European bush-cricket species. Furthermore, our analyses show that most tettigoniid species (95%) can be reliably identified using DNA barcoding. However, mitochondrial introgression events were detected in several species of the subfamilies Bradyporinae and Tettigoniinae, highlighting the need for cautious application of this molecular identification tool.}, }
@article {pmid41026659, year = {2025}, author = {, }, title = {Correction: Pot-pollen DNA barcoding as a tool to determine the diversity of plant species visited by Ecuadorian stingless bees.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0333633}, doi = {10.1371/journal.pone.0333633}, pmid = {41026659}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323306.].}, }
@article {pmid41024994, year = {2025}, author = {Ross, EG and Piertney, SB and Sigwart, JD and Crook, NF and Moreau, A and Layton, KKS}, title = {A Comprehensive DNA Barcode Reference Library for the Macroinvertebrates of Scottish Seagrass Beds Using Oxford Nanopore Flongle Flowcells.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72219}, pmid = {41024994}, issn = {2045-7758}, abstract = {Oxford Nanopore Sequencing Technology (ONT) has emerged as a scalable method for generating DNA barcode reference libraries, capable of sequencing hundreds of DNA barcodes simultaneously using the portable, benchtop MinION sequencing device. In this study, we use ONT Flongle flowcells to produce DNA barcodes for 146 seagrass-associated marine invertebrate OTUs collected from four seagrass beds in Scotland, targeting COI and 18S V4 regions. We make use of degenerate and group-specific primer pairs to improve recovery and demonstrate how mapping ONT reads to pre-existing DNA barcodes can be used to reduce ambiguous basecalls and improve recovery of sequences from contaminated specimens. Overall, this study informs prospective users intending to carry out multimarker DNA barcoding projects using Oxford Nanopore Sequencing. Furthermore, we generated the first DNA barcode reference library for seagrass beds in Scotland to support future biomonitoring of these priority habitats.}, }
@article {pmid41024993, year = {2025}, author = {Nhlengethwa, N and Stewart, RD and Emami-Khoyi, A and Teske, PR and Csányi, S and Heltai, M and van der Bank, M}, title = {An eDNA Survey of Plant Biodiversity in a Local Dam Within South Africa's Largest City.}, journal = {Ecology and evolution}, volume = {15}, number = {10}, pages = {e72196}, pmid = {41024993}, issn = {2045-7758}, abstract = {Ecosystems within cities can play a crucial role in conserving local biodiversity amid rapidly expanding urban sprawl, but they face significant threats from anthropogenic activities and the introduction of alien invasive species (AIS). A comprehensive management plan is required to effectively preserve the biodiversity supported by urban ecosystems. However, the ecological information needed to establish, implement and monitor such plans is often incomplete. In this study, we assessed the application of eDNA metabarcoding in surveying plant biodiversity in an aquatic habitat by collecting water samples at five sites in an urban dam in the City of Johannesburg. Out of 1001 reconstructed Amplicon Sample Variants (ASVs), plant taxa were assigned to 47 unique taxonomic ranks at the family level, 42 unique ranks at the generic level and only 13 unique ranks at the species level (including three AIS). The remaining ASVs could only be identified at higher taxonomic ranks, indicating that no DNA barcodes have yet been generated for the putative species in question. Although this study provides a good overview of plant community structure, it also highlights a gap in the taxonomic coverage of South African plants on public DNA databases. To address this shortcoming, increased national DNA barcoding efforts are needed to expand current reference databases. This will be indispensable for the effective application of eDNA metabarcoding in studying South Africa's unique biodiversity.}, }
@article {pmid41023109, year = {2025}, author = {Macrina, L and Terraneo, TI and McFadden, CS and Chimienti, G and Marchese, F and Vimercati, S and Vicario, S and Reimer, JD and Purkis, SJ and Eweida, AA and Pieribone, V and Qurban, M and Duarte, CM and Rodrigue, M and van der Zwan, FM and Augustin, N and Westphal, H and Benzoni, F}, title = {The hidden diversity of Saudi Arabian Red Sea octocorals revealed through a morpho-molecular assessment across bathymetric and latitudinal gradients.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33651}, pmid = {41023109}, issn = {2045-2322}, mesh = {Saudi Arabia ; Indian Ocean ; *Biodiversity ; *Anthozoa/genetics/classification/anatomy &amp; histology ; Animals ; Phylogeny ; Genetic Variation ; Ecosystem ; DNA Barcoding, Taxonomic ; }, abstract = {Octocorals, a globally distributed class of Cnidaria, inhabit a wide range of environments, from cold to tropical waters and from shallow to deep-sea ecosystems. In the Red Sea, studies on octocoral diversity have mostly been focused on the Gulf of Aqaba and selected families or genera. While these studies have revealed a remarkable richness and diversity of shallow-water species, mesophotic and deep-sea octocoral research remains limited in the region, in particular along the Saudi Arabian coast. Here, we provide a first comprehensive assessment of this group's genetic diversity across the basin's bathymetric and latitudinal gradients. Following six Red Sea oceanographic expeditions and various biodiversity surveys conducted between 2020 to 2023, we analysed a collection of 728 octocoral specimens sampled along 13 degrees of latitude in the Saudi Arabian Red Sea, from shallow-water reefs to deep-sea habitats. We combined morphological identification and sequencing of mitochondrial barcode markers (mtMutS and COI) to delimit lineages. Our integrated results revealed the occurrence of 26 families and 56 genera in the basin from 3 to 859 m of depth. While the description of new species was beyond the scope of this work, here we provide a reference dataset for octocoral diversity from a biodiversity hotspot, as well as essential insights to inform biodiversity management and planning of conservation measures, particularly relevant for the rapidly developing Saudi Arabian Red Sea coast.}, }
@article {pmid41023068, year = {2025}, author = {Flitcroft, RL and Penaluna, BE and Hauck, LL and Munyon, JW and Capurso, JM}, title = {Multi-species eDNA as a screening tool to facilitate early detection and eradication of aquatic invasive species in large water bodies.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {33615}, pmid = {41023068}, issn = {2045-2322}, mesh = {*Introduced Species ; *DNA, Environmental/analysis/genetics ; Animals ; *Aquatic Organisms/genetics ; *Environmental Monitoring/methods ; Biodiversity ; Fishes/genetics ; Plants/genetics ; }, abstract = {Aquatic invasive species can devastate native biodiversity and human water infrastructure. Effective eradication relies on early detection. However, commonly used visual surveys are ineffective for detection of small populations of submerged invasive species in large water bodies. Here, we explored detection of invasive aquatic plants, animals (vertebrate and invertebrate), and pathogens using 10 environmental DNA (eDNA) water sampling events every two weeks between June and October, 2018, informing ideal sampling times for long-term early-detection monitoring. The highest number of species detections across taxa were found using 6 replicates in late August and early September. Detections varied by taxon, with the most detections for fishes, followed by invertebrates, amphibians, and submerged plants. All expected species were detected with eDNA except for three terrestrial and emergent riparian plants. Reservoirs had the most consistent presence of AIS, suggesting that those systems and aquatic communities may be susceptible to new invasions. AIS detections occurred across more sites and water bodies than had been previously documented which provided evidence of silent invasions by species such as crayfishes, mollusks, and plants. We offer a framework for interpreting management response to low-read counts from multispecies eDNA sampling that balances interpretation of results with the cost of management responses.}, }
@article {pmid41022899, year = {2025}, author = {Ceballos-Escalera, A and Llewellyn, T and Richards, J and Inward, D and Vogler, A}, title = {A Reference DNA Barcode Library for UK Fungi associated with Bark and Ambrosia Beetles.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1580}, pmid = {41022899}, issn = {2052-4463}, support = {Leverhulme Centre for the Holobiont//Leverhulme Trust/ ; Leverhulme Centre for the Holobiont//Leverhulme Trust/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; United Kingdom ; *Weevils/microbiology ; *Fungi/genetics/classification ; Biodiversity ; Gene Library ; *Coleoptera/microbiology ; Plant Bark ; Forests ; }, abstract = {Bark and ambrosia beetles are ecologically important and widespread forest organisms. While flying between host plants and tunnelling into bark, they vector a high diversity of plant and insect-associated fungi within and between forests. These fungal communities live under the bark and rarely produce visible spore-bearing structures, making them difficult to sample and identify at scale. By combining passive insect trapping across the United Kingdom with individual beetle metabarcoding, we generated a reference DNA barcode library for fungi associated with over 1000 beetles, representing 25 native weevil species in the subfamily Scolytinae (Curculionidae). Sampling sites span longitudinal and latitudinal gradients, multiple forest types, and both natural and plantation forests. We use state-of-the-art fungal ITS2 OTU clustering and identification, resulting in 5274 identified fungal OTUs. This fungal diversity data can be used alongside extensive site and sample metadata to explore geographic and ecological biodiversity patterns. As these associations can be highly invasive and damaging, this resource provides a baseline to understand current fungal communities and monitor future changes.}, }
@article {pmid41021029, year = {2025}, author = {He, Q and Sun, J and Huang, S}, title = {GPCR Phospho-Barcodes and Biased Signaling.}, journal = {Handbook of experimental pharmacology}, volume = {}, number = {}, pages = {}, pmid = {41021029}, issn = {0171-2004}, abstract = {G protein-coupled receptors (GPCRs), the largest family of membrane receptors in humans, primarily regulate diverse physiological and pathological processes through G protein- and arrestin-mediated signaling pathways, making them important drug targets. Notably, arrestins not only mediate GPCR desensitization and internalization but also regulate G protein-independent signal transduction. However, the mechanisms underlying arrestin-mediated biased signaling remain incompletely understood, posing significant challenges for developing targeted GPCR drugs with signaling bias. To address this knowledge gap, researchers have conducted systematic investigations and proposed innovative models, including the flute model, the polyproline sorting dock model, and the time order effects of GPCR phospho-barcodes to elucidate the dynamic processes driving biased signaling in arrestin activations. These key findings not only refine the theoretical framework of GPCR phosphorylation in biased signaling but also provide a solid foundation for developing biased drugs targeting the GPCR-arrestin pathway, offering new opportunities for precision therapeutics in diverse diseases.}, }
@article {pmid41020297, year = {2025}, author = {Chen, C and Zhan, T and Hu, L and Ding, M and Wu, X and Wang, H and Xu, B}, title = {Barcode-integrated cellulose based microfluidic system for intelligent point-of-care blood typing.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5lc00688k}, pmid = {41020297}, issn = {1473-0189}, abstract = {Accurate and rapid blood typing plays a critical role in life-saving clinical procedures such as blood transfusions and organ transplantation. Herein, we proposed a novel blood typing system (BloodStrips) that combines cellulose based microfluidics with universal barcode technology, achieving intelligent, rapid, and user-friendly blood type detection. The BloodStrips system employed heat transfer printing to create barcode patterns on hydrophobic cotton substrates and integrated cotton threads to construct hydrophilic channels. Meanwhile, the swinging elution method was harnessed to remove free red blood cells (RBCs) while retaining aggregated RBCs on the cotton threads, thereby resulting in creating a distinct white/red contrast at the macro level (white represents cotton thread, red represents bloodstain). The white/red barcodes with different combinations were used to represent various blood types. Based on this principle, we further developed a portable and automated blood tying chip called the BloodBar chip. It is worth noting that this device leverages a simple and straightforward smartphone scanning technique to decipher blood types, avoiding reading errors caused by ambient light intensity and personal bias. This work provides a universal and intelligent visual diagnostic platform for simple, rapid, and accurate blood typing, which may find wide applications in developing countries or resource-limited areas.}, }
@article {pmid41019179, year = {2025}, author = {Yıldırım, N and Gerçek, YC}, title = {Preliminary Characterization of Monofloral Helianthus annuus L. Bee Pollen Using Advanced Analytical Techniques: A Comparative Study With Polyfloral Pollen.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {10}, pages = {e71016}, pmid = {41019179}, issn = {2048-7177}, abstract = {In recent years, there has been an increased interest in the characterization of monofloral bee pollen of different botanical origins as it offers a more homogeneous and traceable component profile compared to polyfloral bee pollen. In this study, we aimed to verify the botanical origin of monofloral Helianthus annuus (sunflower) pollen and polyfloral bee pollen samples collected from the same geographical region and to evaluate their metabolomic profiles comparatively. The botanical origins of the pollen samples were confirmed by palynological analysis and DNA barcoding. Then, physicochemical, phytochemical, and advanced chromatographic analyses (LC-MS/MS) were performed to reveal the bioactive compound contents and nutrient profiles of the samples in detail. When the polyphenol profile was analyzed, the highest level of hyperoside (11,071.28 mg/kg) was detected in monofloral sunflower pollen and rutin (1287.16 mg/kg) in the polyfloral sample. The most dominant amino acid in both pollen types was proline, which was measured as 4652.08 mg/kg (monofloral) and 12,476.82 mg/kg (polyfloral), respectively. Moreover, both samples contained remarkable levels of folic acid (vitamin B9; 20.80 and 20.77 mg/kg). The results obtained from this study reveal that bee pollen derived from the widely cultivated sunflower plant also possesses remarkable potential for the development of functional foods and nutraceutical products. However, as the study was conducted solely with monofloral and polyfloral bee pollen samples collected from a single geographical region, it can be stated that the findings should be considered as part of a preliminary evaluation. Despite this limitation, the data obtained through comprehensive analytical methods provide a scientific basis for the functional applications of monofloral sunflower pollen with its biologically valuable components.}, }
@article {pmid41018503, year = {2025}, author = {Alqurashi, SI and Alqahtani, SM and Alghamdi, KMS and Sharawi, SE and Al-Solami, HM and Alghamdi, AG and Alyahya, HS and Al-Rashidi, HS and Mahyoub, JA}, title = {Molecular insights into Aedes aegypti (L.) populations and vector surveillance in the urban areas of Jeddah and Jizan, Saudi Arabia.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1638582}, pmid = {41018503}, issn = {2673-8600}, abstract = {INTRODUCTION: The Aedes aegypti constitutes the primary vector for dengue fever, yellow fever, chikungunya, Zika, West Nile, and encephalitis viruses, all of which have impacted One Health (human, animal, and environmental health) significantly. It has been distributed widely in urban settings in Saudi Arabia, particularly in cities like Jeddah and Jizan, a situation that underscores the urgent need for innovative and sustainable vector control strategies. Molecular tools, such as DNA barcoding using mitochondrial markers, have become essential for identifying mosquito species accurately and understanding their role in disease transmission. Such knowledge is vital for informing effective, climate-resilient public health interventions.<br><br>METHODS: This research focuses on identifying Aedes species in various regions of Saudi Arabia using polymerase chain reaction (PCR) and sequencing techniques, in order to evaluate the molecular diversity of these dengue vectors in Jeddah and Jizan. The study utilizes the cytochrome one oxidase (COI) gene as a molecular marker for phylogenetic analysis to compare the populations of Aedes species.<br><br>RESULTS: The findings reveal the presence of significant genetic variation among mosquito populations. In the Jeddah region, the Ae. aegypti types MN299016.1 and KU495081.1 match completely (100%) the respective populations found in Argentina and Australia, with 93.1% (27/29) and 6.9% (2/29) respectively. Meanwhile, the samples from the Jizan region are 100% and 99.6% similar to the Ae. aegypti types MN298998.1, MK300226.1, PP892777.1, and MF043259.1 found in Canada, Kenya, India, and England.<br><br>CONCLUSION: This study underscores the necessity of using molecular techniques in vector surveillance to mitigate the spread of Zoonotic and vector borne diseases in Saudi Arabia. Moreover, these efforts align with the objectives of the Saudi Vision 2030 by promoting environmentally responsive vector surveillance in Jeddah and Jizan, thereby supporting integrated approaches to public health and ecological sustainability.}, }
@article {pmid41017704, year = {2025}, author = {Methou, P and Johnson, SB and Sherrin, J and Shank, TM and Chen, C and Tunnicliffe, V}, title = {A Tale of Two Shrimps-Speciation and Demography of Two Sympatric Shrimp Species From Hydrothermal Vents.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e70119}, doi = {10.1111/mec.70119}, pmid = {41017704}, issn = {1365-294X}, support = {ANR-22-POCE-0007//ANR LIFEDEEPER/ ; ANR-17-EURE-0015//ANR ISBLUE/ ; //David and Lucile Packard Foundation/ ; }, abstract = {Hydrothermal vents can serve as natural laboratories to study speciation processes due to their fragmented distribution, often with geographic barriers between habitats. Two sympatric species of Rimicaris shrimps occur at vents on the Izu-Bonin-Mariana volcanic arc: Rimicaris loihi also occurs near Hawai'i and R. cambonae is present on the Tonga Arc. These two species biogeographically co-occur and are genetically similar, raising questions about their speciation mechanisms, how they maintain distinct species, and whether interbreeding occurs. Here, we used barcoding and shotgun sequencing to test their genetic isolation and investigate their speciation process. We also evaluated population demography over 10 years to assess population densities and sex ratios at vents. Our results supported R. cambonae and R. loihi as two distinct species despite sympatry throughout part of their range. We also observed regional-scale genetic structure among R. loihi populations from the Izu-Bonin-Mariana volcanic arc, despite high dispersal potential. Finally, we found concomitant variations of shrimp densities and genetic diversity following fluctuations in geological and venting activities over a decade. A combination of geological instability, ocean currents dynamics and sea-level changes might drive temporary isolation among these local populations. We suggest that similar factors, with longer isolation periods, may also have promoted speciation between the two Rimicaris species, whereas distinct life-history traits could strengthen and maintain reproductive barriers. Overall, we found that the two species with large geographic distributions had significant patterns of genetic partitioning on a volcanic arc; this scenario contrasts with those observed previously at vents from mid-ocean ridges or back-arc basin systems.}, }
@article {pmid41013878, year = {2025}, author = {Dopheide, A and Buckley, T}, title = {Optimising Extraction of DNA From Museum Insect Specimens.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70048}, doi = {10.1111/1755-0998.70048}, pmid = {41013878}, issn = {1755-0998}, abstract = {DNA technologies have many advantages for biomonitoring and biodiversity analyses, but these depend on the availability of relevant reference DNA barcodes. To be most useful, a DNA barcode should be linked to a taxonomic name, which can in turn be connected to ecological information. This linking can be achieved by DNA barcoding of taxonomically identified specimens. Museums are a promising source of such specimens, but the DNA in museum specimens is often degraded, necessitating carefully optimised DNA extraction methods. In this issue of Molecular Ecology Resources, Holmquist et al. (2025) present a DNA extraction protocol for museum insect specimens, using in-house formulated Solid Phase Reversible Immobilisation (SPRI) beads. The authors carried out several experiments with statistical evaluation to determine optimal DNA extraction parameters, before testing the protocol on a large and diverse pool of museum-held insect specimens. The result is a low-cost and effective DNA extraction protocol for diverse museum insect specimens.}, }
@article {pmid41013580, year = {2025}, author = {Licheri, M and Mwanga, M and Licheri, MF and Graaf-Rau, A and Sägesser, C and Bittel, P and Harder, T and Suter-Riniker, F and Kelly, JN and Dijkman, R}, title = {Optimized high-throughput whole-genome sequencing workflow for surveillance of influenza A virus.}, journal = {Genome medicine}, volume = {17}, number = {1}, pages = {103}, pmid = {41013580}, issn = {1756-994X}, support = {IZCOZ0_220329//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; IZCOZ0_220329//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; IZCOZ0_220329//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 2821ERA24//ICRAD/ ; 2821ERA24//ICRAD/ ; }, mesh = {*Influenza A virus/genetics ; Humans ; Animals ; *Whole Genome Sequencing/methods ; Workflow ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Swine ; Influenza, Human/virology ; Birds ; }, abstract = {Whole-genome sequencing (WGS) is essential for monitoring the genetic diversity of influenza A virus (IAV) across host species. We optimized a multisegment RT-PCR (mRT-PCR) protocol to enhance amplification of all eight IAV segments using modified RT and PCR conditions. Additionally, we introduced a dual-barcoding approach for the Oxford Nanopore platform, enabling high-throughput multiplexing without compromising sensitivity. The resulting workflow is robust, scalable, and effective for avian, swine, and human IAV samples, even at low viral loads. This approach strengthens genomic surveillance at the human-animal interface, supporting early detection, evolutionary monitoring, and rapid identification of IAV spillover events.}, }
@article {pmid41012048, year = {2025}, author = {Yin, W and Du, C and Zhang, X and Zhang, W and Wu, W and Fang, C and Xiao, X and Zhu, J and Yang, F and Zhang, M}, title = {DNA Barcoding Provides Taxonomic Clues for Identifying Five Endangered Phoebe Species in Southern China.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/plants14182895}, pmid = {41012048}, issn = {2223-7747}, support = {2024C03258//the Key Research and Development Program of Zhejiang Province/ ; 2022HK124//Research projects of the General Administration of Customs the People's Republic of China/ ; LTGC23C160001//Zhejiang Provincial Natural Science Foundation of China/ ; 2017YFF0210304//the National Key Research and Development Program of China/ ; 2022SJ052//the Zhejiang Provincial Science and Technology Program/ ; }, abstract = {Trees in the genus Phoebe of the Lauraceae family are commonly known as "Nanmu" in traditional Chinese culture. As they have offered highly valued timbers for construction, furniture, and coffins since the pre-Qin Dynasty, it is crucial to identify and protect these Phoebe species. However, the accuracy of Phoebe species identification is frequently hampered due to the limitations of traditional morphological and wood anatomy methods as the marker characteristics are very similar between the species, alongside the requirement for specialized expertise. Here, we use DNA barcoding technology for the rapid and accurate identification of five endangered Phoebe species in China, including Phoebe bournei, P. chekiangensis, P. hui, P. sheareri and P. zhennan. Four highly divergent regions (petA-psbJ-psbL-psbF-psbE, Ψycf1-ndhF, rpl32-trnL[UAG] and ycf1) were identified from a comparison of the 20 Phoebe plastomes downloaded from the database. Furthermore, phylogenetic analysis on 20 Phoebe species showed that rpl32-trnL[UAG] + ycf1, as well as rpl32-trnL[UAG] + ycf1 + Ψycf1-ndhF, effectively distinguished the fifteen Phoebe species. We further validated the usefulness of the core 2-locus barcode using wood and leaf samples from multiple sites for five target species. The study confirms the reliability of molecular diagnostics for five Phoebe species. It also establishes critical taxonomic protocols for conserving these endangered Nanmu species in southern China.}, }
@article {pmid41011285, year = {2025}, author = {Song, JH and Seo, YS and Kim, Y and Jeong, S and Yang, S and Choi, G and Kim, JS and Park, I}, title = {Integrative Study of Dipsaci Radix and Phlomidis Radix: Nomenclature, Morphology, DNA-Based Authentication, and Comparative Effects on Osteoclastogenesis.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {9}, pages = {}, doi = {10.3390/ph18091418}, pmid = {41011285}, issn = {1424-8247}, support = {RS-2023-00208589//National Research Foundation of Korea/ ; RS-2024-00445180//National Research Foundation of Korea/ ; RS2024-00444460//National Research Foundation of Korea/ ; KSN2511030//Korea Institute of Oriental Medicine/ ; }, abstract = {Background/Objectives: Dipsaci Radix (Dipsacus asper) and Phlomidis Radix (Phlomoides umbrosa) are both traditional medicines used in Korea and China for various bone-associated diseases. However, the two are misused due to similarities in name and appearance. Additionally, D. japonicus root frequently contaminates Dipsaci Radix in Korean herbal markets. Methods: We examined morphological plant traits and performed a DNA barcoding analysis using ITS2 and matK sequences to differentiate between these three species. The effects of root extracts on bone resorption and osteoclast differentiation, measured as tartrate-resistant acid phosphatase (TRAP)-positive cell formation, were evaluated using mouse (5 weeks male ICR mice) bone marrow-derived macrophages. Cytotoxicity assays were conducted to assess extract safety. Results: Phlomoides umbrosa is easily distinguished by its verticillaster inflorescences and 2-labiate corollas. Dipsacus asper and D. japonicus, which share globose inflorescences, are distinguishable by flower color and leaf lobation. The ITS2 and matK sequences clearly differentiated the three species, with haplotype analysis supporting their genetic distinctiveness, enabling robust species discrimination. All three extracts decreased osteoclastic bone resorption and inhibited TRAP-positive cell formations in a dose-dependent manner. Only the D. japonicus extract demonstrated toxicity. Conclusions: This integrative study provides the current scientific names of the original species and proposes their use in the Korean Herbal Pharmacopoeia. Moreover, a reasonable molecular method for authenticating medicinal materials is suggested. Dipsacus japonicus shows promise as an additional origin species in the Korean Pharmacopoeia. However, processing methods that reduce toxicity must be discovered.}, }
@article {pmid41009963, year = {2025}, author = {Chen, H and Zhang, J}, title = {Chloroplast Genome Evolution and Codon Usage In the Medicinal Plant Pothos chinensis (Araceae).}, journal = {Genes}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/genes16091017}, pmid = {41009963}, issn = {2073-4425}, support = {sszx077//Funding of Special Project for Applying for Master's Degree during the 14th Five-Year Plan of Anshan Normal University/ ; }, mesh = {*Genome, Chloroplast/genetics ; *Codon Usage/genetics ; *Plants, Medicinal/genetics ; *Evolution, Molecular ; Phylogeny ; *Araceae/genetics/classification ; Codon/genetics ; Chloroplasts/genetics ; }, abstract = {BACKGROUND/OBJECTIVES: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants' evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis.<br><br>METHODS: In this study, the chloroplast genome of the medicinal plant P. chinensis was newly obtained. Comparative analyses, DNA barcoding investigation, codon usage bias, and phylogenetic reconstruction were conducted to reveal the chloroplast genome characteristics of P. chinensis.<br><br>RESULTS: The length of the chloroplast genome of P. chinensis was 165,165 bp. A total of 134 genes were annotated, i.e., 90 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Compared to its sister group Anthurium andraeanum, the length of the large single-copy region (LSC) had been expanded, while the small single-copy region (SSC) had been contracted. Within P. chinensis and P. scandens there were no obvious differences in the length of LSC, SSC, and two inverted repeat regions. Based on Pi values, seven hypervariable regions of whole plastomes were identified. The analysis of codons showed that an average frequency of the 50 candidate genes was 35.30%, and these genes preferred A/U-ending codons. The average effective number of codon (ENC) value was 45.49, which indicated weak codon usage bias. ENCs had a highly significant positive correlation with GC3. Fourteen optimal codons had been identified, 11 of which ended with A/U. The results of the neutrality plot, ENC-plot, and PR2-plot analysis indicated that natural selection might have a significant impact on codon usage patterns.<br><br>CONCLUSIONS: Taken together, our study unraveled the codon usage patterns in P. chinensis and provided valuable genetic information for the genus Pothos.}, }
@article {pmid41009161, year = {2025}, author = {Rizzo, D and Downes, A and Zubieta, CG and Moriconi, M and Ranaldi, C and Palmigiano, B and Aronadio, A and Bartolini, L and Bolige, E and Garonna, AP and Russo, E}, title = {Development of an LNA-Based qPCR Assay for Detecting Toumeyella parvicornis (Cockerell, 1897) (Hemiptera: Coccidae) from Insect and Honeydew DNA.}, journal = {Insects}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/insects16090982}, pmid = {41009161}, issn = {2075-4450}, support = {000001--ALTRO_R-2022-F-PENNACCHIO_001_001//Campania Region-funded URCOFI project/ ; }, abstract = {The invasive sap-feeding pest Toumeyella parvicornis (pine tortoise scale) is rapidly spreading across Europe, threatening pine ecosystems, particularly in forest-urban areas of Italy. In this scenario, early detection and monitoring strategies are critical to prevent new outbreaks and mitigate impacts in infested regions. Current surveillance is challenged by the lack of rapid, sensitive tools for indirect detection of this cryptic, canopy-dwelling pest, despite advancements in molecular diagnostics and environmental DNA (eDNA). Here, we established a highly specific qPCR assay using LNA probe chemistry for detecting T. parvicornis DNA from both adult insects and their excreted honeydew. DNA was successfully isolated/quantified from all tested matrices. We recorded average Cq values of 20.9 for insect specimens and 30.3 for collected honeydew samples. Targeting the COI barcoding region, the assay demonstrated excellent specificity in both in silico and in vitro tests, showing no cross-reactivity to other pine-associated taxa. The limit of detection for DNA isolated from insect was 64 fg/µL. This is the first diagnostic protocol to use honeydew as a matrix for indirect detection of T. parvicornis. Optimized for routine application by Plant Health Services, this eDNA-based tool offers a valuable approach for future monitoring of sap-sucking hemipterans in multiple environments.}, }
@article {pmid41009156, year = {2025}, author = {Podeniene, V and Podenas, S and Butkauskas, D and Sneideris, D and Yum, JW and Ahn, NH and Kim, SY and Kim, J and Starkevich, P}, title = {Integrative Study of the Crane Fly Genus Brithura Edwards, 1916 (Diptera: Tipulidae) in East Asia: First Larval Descriptions of the Genus and Insights from Adult Morphology and DNA Barcoding.}, journal = {Insects}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/insects16090978}, pmid = {41009156}, issn = {2075-4450}, abstract = {Brithura Edwards, 1916 (Diptera: Tipulidae) is a small genus of crane flies currently comprising 16 described species distributed across the East Palaearctic and Oriental regions. Although the adults of this genus rank among the largest representatives of the family Tipulidae, their immature stages have remained undocumented until now. In this study, mitochondrial cytochrome c oxidase subunit I (COI) gene fragment sequences (DNA barcodes) of Brithura sancta Alexander, 1929 were analyzed using both recently collected adult specimens from the Republic of Korea and historical museum specimens from China (collected in 1933). These sequences were compared with COI data obtained from larvae collected in Republic of Korea. We present the first description, with detailed illustrations and ecological information, of the previously unknown final instar larva of Brithura, specifically for the East Palaearctic species B. sancta. Diagnostic larval characters for the genus are discussed. Additionally, a redescription and comprehensive morphological documentation of the adult male and female B. sancta, including habitus and genitalia, are provided. This study represents the first phylogenetic contribution to the taxonomy of Brithura larvae based on mitochondrial COI sequence data.}, }
@article {pmid41009153, year = {2025}, author = {Qian, X and Fu, Y and Ma, Y}, title = {A Review of the Genus Homidia (Collembola, Entomobryidae) in China Informed by COI DNA Barcoding, with the Description of Three New Species.}, journal = {Insects}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/insects16090974}, pmid = {41009153}, issn = {2075-4450}, abstract = {The genus Homidia contains 84 species of which 60 have been reported from China. The sequence of COI for ten Homidia species are provided and a neighbour-joining tree is presented. Three new species of Homidia are described from Chongqing Municipality, China. Homidia wuxiensis sp. nov. is characterised by its colour pattern and chaetotaxy of Abd. IV; Homidia pseudochroma sp. nov. by some expanded post-labial chaetae and chaetotaxy of dorsal head and Abd. II-IV and Homidia yangi sp. nov. by its colour pattern. Based on similarities in COI sequences and morphology, we designate Homidia linhaiensis (Shi, Pan &amp; Qi), as a junior synonym of Homidia tiantaiensis (Chen &amp; Li).}, }
@article {pmid41008247, year = {2025}, author = {Biltes, R and Villa, C and Costa, J and Mafra, I}, title = {Exploiting Marker Genes for Reliable Botanical Authentication of Bacopa monnieri Products.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/foods14183275}, pmid = {41008247}, issn = {2304-8158}, support = {PTDC/SAU-PUB/3803/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; UIDB/50006/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 2023.07644.CEECIND/CP2842/CT0011//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 2021.03583.CEECIND/CP1662/CT0012//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; 2021.03670.CEECIND/CP1662/CT0011//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Bacopa monnieri, commonly known as Brahmi, is a perennial herbaceous plant used in Ayurvedic medicine owing to its nootropic properties. The increased demand for bacopa-derived herbal/food products has motivated adulteration practices through plant substitution. This work is aimed at developing a new method for B. monnieri detection and quantification in herbal products. The chloroplast gene encoding the Ycf1 photosystem I assembly protein (Ycf1) and the nuclear gene coding for the flavonoid glucosyltransferase (Flag) were selected as candidate markers to develop a real-time PCR assay with EvaGreen dye for B. monnieri detection. Both markers were specific to the target species, with Ycf1 providing the best real-time PCR kinetics and highest sensitivity. Therefore, a new method targeting the Ycf1 barcode was developed, exhibiting high specificity and a sensitivity of 1 pg of bacopa DNA. Additionally, a calibration model was proposed using reference mixtures of B. monnieri in Ginkgo biloba with a linear dynamic range of 25-0.1% (w/w). The curve parameters of slope, PCR efficiency and correlation coefficient met the acceptance criteria. The method was successfully validated with blind mixtures and further applied to commercial herbal products, revealing an important level of adulteration in bacopa/Brahmi-labelled products (60%) due to absence of or reduction in bacopa content. In this work, the first quantitative real-time PCR method for the botanical authentication of B. monnieri in herbal products is proposed as a powerful tool, which can be used by quality control laboratories and regulatory authorities to ensure labelling compliance.}, }
@article {pmid41008229, year = {2025}, author = {Tsolakidou, MD and Nikoloudakis, N and Tisseyre, C and Knez, M and Barilli, E and Mattas, K and Katsiotis, A}, title = {DNA Barcoding for Tracing Biodiversity in Mixed Crop Food Products: A Proof of Concept Within the BioValue Project.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {18}, pages = {}, doi = {10.3390/foods14183256}, pmid = {41008229}, issn = {2304-8158}, support = {101000499//European Union's Horizon 2020 research and innovation program/ ; }, abstract = {In a world of rapidly globalizing food markets, biodiversity, authenticity, and the safety of food products have become a universal concern. DNA barcoding is a widely used molecular-based method that can identify biological material and is used for the traceability of both raw materials and ingredients in processed food. In the present study, contacted within the framework of the BioValue Horizon Project, which promotes the role of agrobiodiversity in sustainable food systems, DNA barcoding using the ITS and rbcL markers was employed as a proof-of-concept approach to reveal the biodiversity and authenticity of ten commercial plant-based products. Following successful DNA amplification and sequencing using six products as a proof-of-concept, a diverse range of plant genera and species were identified, verifying biodiversity. A strong correlation between ITS and rbcL-based markers was demonstrated, supporting their combined use for reliable species-level biodiversity assessment. Finally, heat map analysis of label contents and sequencing-based genera identification confirmed high concordance between label claims and sequencing results in most cases, though undeclared species and absent labeled taxa were also detected, highlighting potential mislabeling or cross-contamination.}, }
@article {pmid41007952, year = {2025}, author = {Gál, J and Kovács, G and Vincze, Z and Keve, G and Páll-Gergely, B and Bagyó, R and Fehér, E and Bali, K and Kaszab, E}, title = {The Red-Colored Oddball-A New Ladybird Spider with Unusual Coloring from Morocco, Eresus rubrocephalus sp. nov. (Araneae: Eresidae).}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {18}, pages = {}, doi = {10.3390/ani15182707}, pmid = {41007952}, issn = {2076-2615}, support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; }, abstract = {According to our current knowledge, the prothorax of male spiders belonging to the genus Eresus is covered with black hairs. However, during our collection activities in Morocco, we found male specimens showing habitus that can be clearly distinguished from the previously known species based on their pars cephalica of prosoma covered with distinct red hairs. Diagnostic drawings and digital photographs of male copulatory organs, alongside DNA and COI barcoding results, are also presented.}, }
@article {pmid41007276, year = {2025}, author = {Iacovelli, MV and Bellia, E and Caruso, M and Zaffuto, E and Crobe, V and Marrone, F and Mazzotti, S and Tinti, F}, title = {Integrated Taxonomy and Species Diversity of the Historical Chondrichthyan Collection of the Zoology Museum "Pietro Doderlein" at the University of Palermo (Italy).}, journal = {Biology}, volume = {14}, number = {9}, pages = {}, doi = {10.3390/biology14091129}, pmid = {41007276}, issn = {2079-7737}, abstract = {In the context of the progressive tendency to perceive a degraded environmental state as normal, due to the loss of memory of past ecological conditions (i.e., the Shifting Baseline Syndrome), natural history museum collections represent invaluable resources for studying long-term biodiversity shifts. This study deals with the taxonomic validation of the chondrichthyan species from the historical ichthyological collection assembled by Pietro Doderlein from 1863 to 1922 at the Museum of Zoology of the University of Palermo. The chondrichthyan specimens were digitally catalogued to meet current standards of museum documental identification. Biometric measurements were taken for each specimen, and an integrated analytical approach-combining morphology and ancient DNA analysis-was applied to assign species identities. The collection comprises 342 specimens associated with 76 valid codes. Of these, 288 specimens were identified to species level by morphology, revealing 58 discrepancies with the historical identifications. Sixteen specimens that could not be morphologically assigned were analyzed by DNA barcoding, resulting in eight additional species-level identifications. In total, 62 valid species belonging to 27 families were digitally catalogued according to ministerial guidelines. This taxonomic validation and cataloguing of the "P. Doderlein" chondrichthyan collection represent the first successful effort to bridge the gap in available data and tissue resources from Italian historical natural museums.}, }
@article {pmid41006299, year = {2025}, author = {Dimaquibo, AC and Jhuang, WC and Huang, WC and Encarnacion, AB and Villarao, MC and Yutuc, RV and Liao, TY}, title = {DNA Barcoding of Teleost Fishes from North Luzon, Philippines: A Dataset for Ichthyofaunal Diversity Assessment.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1571}, pmid = {41006299}, issn = {2052-4463}, mesh = {Philippines ; *DNA Barcoding, Taxonomic ; Animals ; *Fishes/genetics/classification ; *Biodiversity ; RNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; }, abstract = {Reliable identification of teleost fishes is essential for understanding their biology and conserving biodiversity. To support this, a comprehensive DNA barcode reference library was developed for Aurora, Cagayan, and Zambales, Luzon, Philippines. A total of 1,513 specimens were collected from 27 sampling sites, including fish markets, landing areas, and freshwater habitats, and analyzed using COI (707 sequences) and 12S rRNA gene (343 sequences) markers. The dataset identified 323 fish species across 187 genera, 83 families, and 37 orders, including nine newly recorded species for the Philippines and nine deep-sea species (>200 meters). Additionally, 29 newly barcoded taxa were deposited in GenBank, with sequences available for COI, 12S rRNA gene, or both. The expansion of the 12S rRNA gene sequence library enhances its utility as an alternative genetic tool, particularly for environmental DNA (eDNA) studies. This reference database serves as a valuable resource for species identification, biodiversity assessments, and sustainable fisheries management in North Luzon, Philippines.}, }
@article {pmid41005946, year = {2025}, author = {Gao, K and Chen, B}, title = {The application of advanced analytical techniques in ensuring quality, nutrition, and safety of cereal-based food.}, journal = {Advances in food and nutrition research}, volume = {117}, number = {}, pages = {265-302}, doi = {10.1016/bs.afnr.2025.07.005}, pmid = {41005946}, issn = {1043-4526}, mesh = {*Edible Grain/chemistry ; *Food Safety/methods ; *Nutritive Value ; *Food Analysis/methods ; Food Contamination/analysis ; Humans ; Food Quality ; }, abstract = {Cereals and cereal-based foods are fundamental to global nutrition, providing essential macronutrients and micronutrients that support food security. Ensuring their quality, nutrition, and safety is impacted by factors such as contamination, adulteration, and nutrient degradation during processing and storage. Advanced analytical techniques have emerged as powerful tools to address these challenges, offering innovative solutions for detecting contaminants, optimizing nutritional value, and ensuring food safety. This chapter explores the application of these techniques, including spectroscopy, chromatography, molecular biology, and omics technologies, in the cereal-based food systems. Spectroscopy and chromatography enable rapid and precise detection of chemical contaminants and adulterants, while molecular biology methods like PCR and DNA barcoding ensure product authenticity. Omics approaches, such as lipidomics, proteomics, and flavoromics, provide comprehensive insights into the molecular composition and functional properties of cereals, facilitating the development of high-quality, nutritious products. Emerging technologies, including nanotechnology and artificial intelligence, further enhance the efficiency and accuracy of cereal safety monitoring. By integrating these advanced methods, the cereal research field can address existing challenges, ensuring the production of safe, high-quality, and nutritious cereal-based foods to meet global dietary needs.}, }
@article {pmid41002353, year = {2025}, author = {Chen, Q and Xu, Y and Wu, JW and Yang, JM and Huang, CH}, title = {Decoding Molecular Network Dynamics in Cells: Advances in Multiplexed Live Imaging of Fluorescent Biosensors.}, journal = {Biosensors}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/bios15090614}, pmid = {41002353}, issn = {2079-6374}, support = {R01GM136711/GF/NIH HHS/United States ; P50CA098252/GF/NIH HHS/United States ; NA//Sol Goldman Pancreatic Cancer Research Center/ ; }, mesh = {*Biosensing Techniques/methods ; Humans ; Luminescent Proteins ; Signal Transduction ; }, abstract = {Genetically encoded fluorescent protein (FP)-based biosensors have revolutionized cell biology research by enabling real-time monitoring of molecular activities in live cells with exceptional spatial and temporal resolution. Multiplexed biosensing advances this capability by allowing the simultaneous tracking of multiple signaling pathways to uncover network interactions and dynamic coordination. However, challenges in spectral overlap limit broader implementation. Innovative strategies have been devised to address these challenges, including spectral separation through FP palette expansion and novel biosensor designs, temporal differentiation using photochromic or reversibly switching FPs, and spatial segregation of biosensors to specific subcellular regions or through cell barcoding techniques. Combining multiplexed biosensors with artificial intelligence-driven analysis holds great potential for uncovering cellular decision-making processes. Continued innovation in this field will deepen our understanding of molecular networks in cells, with implications for both fundamental biology and therapeutic development.}, }
@article {pmid41001831, year = {2025}, author = {de Jager, ML and Reiter, N and Wicks, M and Bohman, B and Holmes, GD and Phillips, RD}, title = {Sexually deceptive orchids with distinct flower morphologies elicit different behaviours from a shared pollinator.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcaf234}, pmid = {41001831}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Pollination by sexual deception is one of the most specialised pollination strategies among angiosperms, with co-occurring plant species often exploiting males of different insect species. We test if the morphologically divergent orchids Caladenia cardiochila and its sympatric Endangered congener C. lowanensis are dependent on the same thynnine wasp pollinator. We further investigate the role of floral traits on pollinator behaviour and evaluate potential hybridisation risk.<br><br>METHODS: Pollinator sharing was tested for with DNA barcoding. Pollinator behaviour was quantified and experimental floral dissections used to determine the site of sexual attractant release. We employed GC-MS to test for the presence of sugar on orchid labella, hand crosses to assess the impact of interspecific pollen transfer on seed viability, and population monitoring to quantify natural pollination success.<br><br>KEY RESULTS: We found that C. cardiochila and C. lowanensis both employ sexual deception of Phymatothynnus aff. nitidus wasps as pollination strategy. However, the behaviour they elicit differs with wasps attempting to mate with the insectiform labellum in C. cardiochila and the glandular sepal tips in C. lowanensis, which are the respective sources of sexual attractant. Unlike most sexually deceptive orchids, C. lowanensis secretes minute amounts of sugar from its labellum. While wasps interacted more frequently with the labellum in C. cardiochila, placing them closer to its reproductive structures, both species exhibited comparable pollination success and pollen transfer efficiency. Experimental crosses revealed that hybrid seed has high viability.<br><br>CONCLUSIONS: Sexual deception of the same pollinator by orchids varying in the location of sexual attractant and flower morphology highlights the considerable flexibility of this pollination strategy. Given their overlapping distributions and the viability of hybrid seed, pollinator sharing poses a hybridisation risk that needs to be considered in the management of wild C. lowanensis populations and future conservation translocations.}, }
@article {pmid41001662, year = {2025}, author = {Lekuti, AA and Li, VYC and Malekjahani, A and Ahmed, S and Mladjenovic, SM and Macduff, MGG and Chan, WCW}, title = {Designing Nanoparticle Surfaces with DNA Barcodes for Accurate In Vivo Quantification.}, journal = {JACS Au}, volume = {5}, number = {9}, pages = {4211-4223}, pmid = {41001662}, issn = {2691-3704}, abstract = {DNA barcoding is a common method for identifying the biodistribution of nanoparticles. DNA barcodes are typically encapsulated within nanoparticles to ensure accurate measurements by next-generation sequencing. This method limits the types of nanoparticles that can be screened. DNA can also be coated on nanoparticle surfaces. However, it is unclear whether surface-coated DNA can be used as barcodes because they can degrade, making the identification and quantification of nanoparticle designs challenging. Here, we developed strategies to reduce DNA degradation on nanoparticle surfaces, allowing surface-based DNA barcodes for biodistribution applications. We demonstrate that nanoparticle size, DNA density, and polymer length and density are essential design parameters for accurately identifying and quantifying nanoparticles in vivo. We found that chemical modification of DNA and shielding using neutral polymers reduce DNA degradation. We validated that surface barcoding can determine the in vivo distribution of nanoparticles. Our findings pave the way for the use of surface-based DNA barcodes for in vivo screening of nanoparticle formulations for targeted applications.}, }
@article {pmid41001006, year = {2025}, author = {Zhang, X and Zhang, L and Wang, E and Benton, S and Modolo, E and Maksimov, M and Shleizer-Burko, S and Gong, Q and Wang, C and Lamkin, M and Mendenhall, E and Gymrek, M and Goren, A}, title = {Systematic evaluation of the impact of promoter proximal short tandem repeats on expression.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.14.676153}, pmid = {41001006}, issn = {2692-8205}, abstract = {Genetic variation at thousands of short tandem repeats (STRs), which consist of consecutive repeated sequences of 1-6bp, has been statistically associated with gene expression and other molecular phenotypes in humans. However, the causality and regulatory mechanisms for most of these STRs remains unknown. Massively parallel reporter assays (MPRA) enable testing the regulatory activity of a large number of synthesized variants, but have not been applied to STRs due to experimental and computational challenges. Here, we optimized an MPRA framework based on random barcoding to study the impact of variation in repeat copy number on expression. We first performed an MPRA on sequences derived from 30,516 promoter-proximal STR loci along with up to 152bp of genomic context, testing 3-4 variants with differing repeat copy numbers for each locus in HEK293T cells. We identified 1,366 loci with significant associations between repeat copy number and expression, which were enriched for positive effect sizes (P=2.08e-110). We then designed a second MPRA in which we performed deeper perturbations, including systematic manipulation of the repeat unit sequence, orientation, and copy number, with 200-300 perturbations for each of the 300 loci with the strongest signals. Our results revealed that the repeat unit sequence is the primary driver of differences in the relationship between copy number and expression across loci, whereas orientation and flanking sequence have weaker effects, primarily for AT-rich repeat units. The high resolution of these perturbations enabled us to detect non-linear effects, most notably for AAAC/GTTT repeats, which emerge only beyond a certain copy number threshold. Finally, we observed that a subset of STRs in our library show expression levels that are tightly linked with predicted DNA secondary structure formation. We repeated our perturbation MPRA in HeLa S3 cells under wildtype and RNase H1 knockdown conditions, which, via reduction in RNase H1 activity, are expected to hinder resolution of R-loops. This demonstrated that associations between copy number and expression at G-quadruplex-forming CCCCG/CGGGG repeats are particularly sensitive to loss of RNase H1, providing support for an R-loop mediated mechanism for these repeats. Altogether, we establish STRs as a critical component of the non-coding regulatory grammar and provide a framework for understanding how this dynamic form of genetic variation shapes gene expression.}, }
@article {pmid41000875, year = {2025}, author = {Li, H and Chen, Y and Kaster, J and Dunne, M and Xiao, M and Li, L and Thomas, M and Promi, N and Fingerman, D and Brown, GS and Zheng, Q and Zhu, X and Reale, M and Patterson, A and Gao, L and Zhang, X and Jiang, S and Hu, T and Fang, H and Ren, J and Qi, C and Wang, L and Mou, H and Thacker, G and Salazar, ER and Villanueva, J and Raj, A and Hoon, DS and Bin, T and Madzo, J and Wei, Z and Auslander, N and Herlyn, M}, title = {Clonal dynamics shaped by diverse drug-tolerant persister states in melanoma resistance.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.16.676608}, pmid = {41000875}, issn = {2692-8205}, abstract = {Most advanced melanomas initially respond to targeted therapy but eventually relapse. Rather than acquiring new mutations, resistance is driven by drug-tolerant persister cells that enter a reversible drug-refractory state. We developed MeRLin, a high-resolution lineage tracing platform integrating cellular barcoding, single-cell transcriptomics, RNA fluorescence in situ hybridization (FISH), and computational analyses to track clonal and transcriptional dynamics in patient-derived melanoma models during prolonged therapy. Clonal dynamics revealed that persister subpopulations first responded to treatment but persisted and expanded during minimal residual disease, ultimately leading to tumor recurrence. Pre-treatment melanoma populations diversified into four conserved persister states characterized by stress-like, lipid metabolism, PI3K signaling, and extracellular matrix remodeling programs associated with adaptive resistance. Spatial transcriptomics showed the organization of these adaptive programs and a complex signaling network of autocrine and paracrine interactions among persister subpopulations. Barcoded RNA-FISH enabled spatial mapping of clonal identity and gene expression, revealing in situ co-localization of a dominant resistant clone with SLC2A1 expression. MeRLin provides a robust framework for dissecting cancer heterogeneity and identifying vulnerabilities in persister populations.}, }
@article {pmid41000852, year = {2025}, author = {Salla, M and Obermayer, B and Cotta, M and Friebel, E and Campo-Garcia, J and Charalambous, G and Bueno, RJ and Lieu, D and Dabek, P and Helmuth, A and Tellides, G and Assi, R and Bankov, K and Lodrini, M and Deubzer, H and Beule, D and Chung, H and Radbruch, H and Capper, D and Heppner, F and Starossom, SC and Lareau, CA and Liu, I and Ludwig, LS}, title = {Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.17.675534}, pmid = {41000852}, issn = {2692-8205}, abstract = {High-throughput clonal tracing of primary human samples relies on naturally occurring barcodes, such as somatic mitochondrial DNA (mtDNA) mutations detected via single-cell ATAC-seq (mtscATAC-seq). Fresh-frozen clinical specimens preserve tissue architecture but compromise cell integrity, thereby precluding their use in multi- omic approaches such as mitochondrial genotyping at single-cell resolution. Here, we introduce Cryo-mtscATAC-seq, a broadly applicable method for diverse pathophysiological contexts to isolate nuclei with their associated mitochondria ("CryoCells") from frozen samples for high-throughput clonal analysis. We applied Cryo-mtscATAC-seq to the neurodegenerated human brain, glioblastoma (GBM), pediatric neuroblastoma, and human aorta, and implemented mitobender, a computational tool to reduce ambient mtDNA in single-cell assays. Our approach revealed regional clonal gliogenesis and microglial expansions in amyotrophic lateral sclerosis (ALS), persistence of oligodendrocyte progenitor cell (OPC)-like clones in GBM recurrence, mtDNA depth heterogeneity after neuroblastoma chemotherapy, and oligoclonal proliferation of smooth muscle cells in human aorta. In conclusion, Cryo-mtscATAC-seq broadly extends mtDNA genotyping to archival frozen specimens across tissue types, opening new avenues for investigation of cell state- informed clonality in human health and disease.}, }
@article {pmid40997258, year = {2025}, author = {Prati, S and Reyes Camargo, AC and Jamonneau, T and Halima, IB and Sures, B}, title = {Seasonal exchange of microsporidian parasites between native and non-native pet-traded freshwater crustaceans: Is parasite spillover favored over spillback?.}, journal = {Parasite (Paris, France)}, volume = {32}, number = {}, pages = {61}, doi = {10.1051/parasite/2025053}, pmid = {40997258}, issn = {1776-1042}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Seasons ; *Microsporidia/isolation &amp; purification/physiology/classification ; France ; Fresh Water ; *Introduced Species ; *Decapoda/microbiology/parasitology ; Ecosystem ; Pets/parasitology ; *Crustacea/microbiology/parasitology ; Rivers ; *Microsporidiosis/epidemiology/veterinary/transmission ; Biodiversity ; }, abstract = {The introduction of non-native pet-traded species poses potential threats to global biodiversity, particularly in freshwater ecosystems. This study investigated the seasonal dynamics of microsporidian infections in an established feral population of cherry shrimp (Neocaridina davidi) and the coexisting populations of crustaceans, comprising both native and non-native species, inhabiting the thermal waters of the Fontcaude Park and the nearby Mosson River in southern France. Our aim was to assess the potential occurrence of spillover and/or spillback events between N. davidi and co-occurring crustaceans, as well as the influence of seasonal dynamics on these interactions. The prevalence and diversity of microsporidian parasites exhibited strong seasonal variations. Although parasites associated with the pet trade were not detected, we highlight the acquisition of native parasites by feral N. davidi, which seems to be a suitable alternative host for native host-generalist microsporidians. Our findings indicate that all prerogatives for spillback events to occur are met. Feral N. davidi may establish and survive year-round in European rivers with natural thermal regimes. Thus, human-mediated introductions can potentially alter parasite transmission dynamics in these ecosystems.}, }
@article {pmid40995013, year = {2025}, author = {D'Agostino, N and Fruggiero, I and Maisto, A and Taranto, F and Al-Kilani, MA and Al-Abdallat, AM}, title = {Exploring the plastome diversity of fifteen centuries-old olive trees (Oleae europaea L.) from Jordan: insights and implications for conservation.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1647776}, pmid = {40995013}, issn = {1664-462X}, abstract = {The olive tree (Olea europaea L.) holds exceptional ecological, cultural, and economic significance in the Mediterranean Basin. Understanding its genetic diversity is critical for conservation, breeding, and authentication of olive cultivars. While nuclear genome analyses have elucidated much of the species' genetic structure, chloroplast genome sequencing provides complementary insights, particularly in tracing maternal lineages, uncovering domestication pathways, and identifying cryptic genetic variation. In this study, we investigated the plastome diversity of fifteen centuries-old olive trees from Jordan through reference-guided assembly and comparative analysis using the FARGA cultivar plastome as a reference. Despite overall genomic conservation, nucleotide diversity analyses revealed several polymorphic hotspots-most notably within the psbM and ycf1 genes and the atpB-rbcL intergenic spacer. Structural variation, including simple sequence repeats and tandem repeats, highlighted intra-population diversity. One sample (TF - 3) exhibited heteroplasmy, suggesting a biological origin that warrants further investigation. Phylogenetic reconstruction grouped most samples within the Mediterranean E1 lineage, with TF - 3 and a few others forming distinct clusters. Comparisons with nuclear genotyping data demonstrated both congruence and divergence, emphasizing the value of a dual-genome approach. This study reinforces the utility of plastome sequencing in varietal identification, conservation genetics, and evolutionary studies, and contributes novel genomic resources for Jordanian olive germplasm.}, }
@article {pmid40994301, year = {2025}, author = {Sherwood, AR and Allsopp, KR and Alvarado, EA and Kosaki, RK and Paiano, MO and Rentsch, P and Spalding, HL and Wade, RM}, title = {Systematics and taxonomy of Codium (Bryopsidales, Chlorophyta) in the Hawaiian Islands: Description of six new species.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70091}, pmid = {40994301}, issn = {1529-8817}, support = {NFWF 0810.20.068602//National Fish &amp; Wildlife Foundation/ ; DEB-1754117//NSF Division of Environmental Biology (DEB)/ ; DEB-2242142//NSF Division of Environmental Biology (DEB)/ ; //National Oceanic and Atmospheric Administration (NOAA) Papah&#x101;naumoku&#x101;kea National Marine Sanctuary/ ; }, abstract = {The well-known Bryopsidalean genus Codium has a worldwide distribution and contains almost 150 species, with cryptic diversity confusing the actual number. In the Hawaiian Islands, 15 species have been previously recorded, with several of these described in the past several decades, largely from specimens collected from mesophotic coral ecosystems. We assessed the diversity of Codium in Hawai'i from both shallow and mesophotic habitats by employing DNA barcoding and phylogenetic analyses of partial rbcL and tufA gen plastid markers and morphological characterization. DNA sequence analyses supported 18 species of Hawaiian Codium (eight of which are considered endemic), which is a 20% increase in recognized species richness for this genus in Hawai'i. Ten previously reported species were confirmed or provisionally confirmed, six new species have been described (C. pikoii sp. nov., C. upohoae sp. nov., C. hakakaupilii sp. nov., C. kanepohihiae sp. nov., C. torulosum sp. nov., and C. iolekaae sp. nov.), and two new records have been reported (C. "geppiorium4" and C. taylorii). Twenty-eight percent of Hawaiian Codium clades were mesophotic only, and 22% were shallow only, while 50% of clades were known from both shallow and mesophotic depths. Recent emphasis on the systematics of Hawaiian mesophotic algae has sufficiently increased specimen numbers from this habitat to allow a more complete assessment of the genus in this location, making it one of the most thoroughly collected and studied marine algal genera from Hawai'i and an excellent model for future examination of both horizontal (i.e., spatial) and vertical (i.e., depth) distributional trends.}, }
@article {pmid40985397, year = {2025}, author = {McPherson, VJ and Gillings, MR and Ghaly, TM}, title = {Diverse, Cryptic, and Undescribed: Club and Coral Fungi in a Temperate Australian Forest.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, doi = {10.3390/jof11070502}, pmid = {40985397}, issn = {2309-608X}, abstract = {Fungi are the most poorly described kingdom of Eukarya. Fundamental questions about their species diversity, their distributions, and their biotic interactions remain largely unanswered, despite fungi playing important roles in the ecology and biogeochemistry of terrestrial ecosystems. To assess some of these data gaps, we intensively surveyed club and coral fungi in a temperate Australian forest in the Upper Lane Cove Valley, Sydney, Australia, over a period of two years. Specimens identified as Clavulinopsis, Ramaria, or Ramariopsis based on morphology were then assigned to operational taxonomic units (OTUs) using the criterion of 97% identity across the entire rDNA internal transcribed spacer (ITS) region. Based on this criterion and ITS-based phylogenies, we identified 80 OTUs in these genera of club and coral fungi within the survey area. Of these OTUs, only 11.25% could be assigned a species name based on BLASTn matches to full-length ITS sequences, suggesting that almost 90% of OTUs were novel taxa, or are yet to be represented in DNA databases. Specimens that were morphologically similar to well-known Northern Hemisphere species were shown to be distinct upon DNA sequencing. Accumulation curves suggest that our surveys only recovered about half of the species in the target genera, and seven times the effort would be required to sample to exhaustion. In summary, even in a small area of less than 100 km[2], there is evidence for multiple undescribed, cryptic, and undiscovered species. This highlights the fundamental work that remains to be completed in fungal taxonomy and biology.}, }
@article {pmid40984528, year = {2025}, author = {Li, B and Liu, L and Xu, L}, title = {Ultra-sensitive and wide-range temperature sensing utilizing a microbottle resonator coupled with fiber Mach-Zehnder interferometer.}, journal = {Optics express}, volume = {33}, number = {16}, pages = {33704-33714}, doi = {10.1364/OE.566867}, pmid = {40984528}, issn = {1094-4087}, abstract = {An ultra-sensitive and wide-range temperature detection method has been proposed based on coupling a microbottle resonator with a fiber Mach-Zehnder Interferometer (FMZI), which can change the small mode shift into a large intensity variation. We theoretically and experimentally investigated the sensing performance of this method. Through appropriately adjusting the length difference of FMZI, the microbottle resonant peaks and the FMZI peak move in opposite directions. Measuring the Fano dip depth gives a temperature sensitivity of up to 307.5 dB/°C and a temperature resolution of 4 × 10[-3] °C. Theoretical calculations demonstrate that the temperature detection limit can reach 4 × 10[-6] °C under an 80 dB Signal-to-Noise Ratio (SNR). Moreover, experiments have confirmed that by using the encoding method of universal commercial barcodes to record the changes in the resonant frequencies and intensities of the modes and by matching the proposed barcodes with the Bit Error Rate, temperature sensing with an almost unlimited range can be achieved. The proposed method makes it possible to achieve high sensitivity and a wide range of temperature sensing applications.}, }
@article {pmid40980947, year = {2025}, author = {Harms, D and McRae, J and Curran, M and Harvey, MS}, title = {Identifying refugia for invertebrate conservation in biodiversity hotspots: examples from a new genus of dragon pseudoscorpions (Pseudotyrannochthoniidae: Karrichthonius).}, journal = {Invertebrate systematics}, volume = {39}, number = {}, pages = {}, doi = {10.1071/IS25028}, pmid = {40980947}, issn = {1447-2600}, mesh = {Animals ; *Biodiversity ; Western Australia ; *Conservation of Natural Resources ; *Refugium ; *Odonata/classification/anatomy &amp; histology/genetics ; Species Specificity ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Conservation management in ancient landscapes has shifted in recent years from the protection of single species to the broader management of areas of high biodiversity. One of the landscapes that has most benefited from this shift is the south-west of Western Australia, an internationally recognised biodiversity hotspot and one of the oldest and most stable landscapes on Earth. Significant progress has been made in recent years to identify refugia in the south-west and prioritise them for invertebrate protection but more studies are still needed to assist practical conservation management. Here, we describe a new genus of pseudoscorpions from south-western Australia (Pseudoscorpiones: Pseudotyrannochthoniidae: Karrichthonius gen. nov.) that has speciated extensively within mesic refugia. Karrichthonius is endemic to the High Rainfall Province of the biodiversity hotspot and features often-localised populations in spatially isolated mesic habitats. Through a combination of DNA barcoding, morphological features and spatial mapping, we infer 12 species: Karrichthonius giganteus (Beier, 1971) comb. nov. , K. booraraensis , sp. nov. , K. buzattoi , sp. nov. , K. dalei , sp. nov. , K. farquhari , sp. nov. , K. heatherae , sp. nov. , K. leniae , sp. nov. , K. porongurupensis , sp. nov. , K. pyungurupensis , sp. nov ., K. rixi , sp. nov. , K. talyuberlupensis , sp. nov. and K. toolbrunupensis , sp. nov . All species are short-range endemics and occur in landforms that are either known refugia for invertebrate conservation or inferred here as potential refugia to be recognised and analysed further. By mapping species distributions and providing species diagnoses, we contribute to an understanding of invertebrate biodiversity in the south-west, and strengthen the concepts that are underlying conservation management practices in biodiversity hotspots. ZooBank: urn:lsid:zoobank.org:pub:EC51BFC7-0C8E-49D6-A704-DA59648B2325.}, }
@article {pmid40979753, year = {2025}, author = {Jeong, JH and Heo, UH and Lee, JY and Oh, JI and Song, YG and Kim, SY and Park, Y and Byun, BK}, title = {Two new species of the genus Acrolepiopsis Gaedike, 1970 (Lepidoptera, Glyphipterigidae) from Korea.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e163874}, pmid = {40979753}, issn = {1314-2828}, abstract = {BACKGROUND: The family Glyphipterigidae comprises small-sized moths with a wingspan ranging from 8 to 14 mm. This family is mainly distributed in the Palaearctic and Oriental Regions. In Korea, five species of the genus Acrolepiopsis Gaedike, 1970 have been recorded. However, species-level identification within this genus is often challenging due to high morphological similarity amongst species.<br><br>NEW INFORMATION: In this study, two new species of the genus Acrolepiopsis, A. quinquelobatae sp. nov. and A. koreana sp. nov., are described from Korea. Species delimitation is supported by COI gene analysis and morphological characteristics of genitalia, both of which reveal clear genetic divergence from other Acrolepiopsis species previously recorded in Korea. Photographs of adults and genitalia, along with information on host plants, are also provided.}, }
@article {pmid40978795, year = {2025}, author = {Qazi, IH and Yuan, T and Liu, X and Liu, J}, title = {Identification of Pseudocercospora mori as the causal agent of grey leaf spot disease in mulberry (Morus atropurpurea) from various localities in Guangdong Province, China.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1648690}, pmid = {40978795}, issn = {1664-462X}, abstract = {During periods of high temperature and humidity, mulberry trees become susceptible to fungal leaf spot disease, which can significantly reduce both the yield and quality of their leaves. In this study, we collected samples of mulberry leaf spot disease from six regions of Guangdong province of China. The disease samples were studied using traditional morphological methods, high-throughput sequencing technology, molecular phylogenetic analysis, and pathogenicity tests. The observed morphological features of the pathogen were consistent with those of Pseudocercospora. High-throughput sequencing results revealed the presence of multiple fungal species in the samples, with Pseudocercospora spp. comprising the highest proportion. The complete rDNA and mitochondrial genome sequences of Pseudocercospora spp. were assembled. Based on the sequencing data, primers were designed to amplify and sequence barcode gene regions, including ITS, Cyt b, and COI. Phylogenetic analyses consistently placed the pathogen within the family Mycosphaerellaceae. ITS-based identification confirmed the pathogen as a member of the genus Pseudocercospora, while the Cyt b and COI sequences indicated a relatively distant relationship with the closely related genus Cercospora, thereby supporting the morphological classification of the pathogen at the molecular level. In addition, pathogenicity validation identified Pseudocercospora mori as a primary causal pathogen of leaf spot disease in mulberry. PCR primers specifically designed based on the rDNA sequence of Pseudocercospora mori achieved a detection sensitivity as low as 3 × 10[-2] ng/μL. In conclusion, based on morphological and molecular phylogenetic evidence, we identified Pseudocercospora mori as the causal pathogen of mulberry leaf spot disease. This study provides useful data for practical management of mulberry leaf spot disease at the field level, aiding in the sustainable development of sericulture.}, }
@article {pmid40977149, year = {2025}, author = {Schneider, T and Vierstraete, A and Kosterin, OE and Ikemeyer, D and Hu, FS and Kompier, T and Dumont, HJ}, title = {Molecular phylogenetic analysis of the family Chlorogomphidae (Odonata, Anisoptera).}, journal = {Invertebrate systematics}, volume = {39}, number = {}, pages = {}, doi = {10.1071/IS25016}, pmid = {40977149}, issn = {1447-2600}, mesh = {*Phylogeny ; Animals ; *Odonata/classification/genetics ; Species Specificity ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; }, abstract = {Phylogenetic analysis of the family Chlorogomphidae was carried out using two nuclear markers, the ITS and histone H3-H4 regions, and a barcoding fragment of the mitochondrial COI gene, using sequences obtained in this study and adopted from GenBank. Their joint analysis was performed using StarBEAST software. In total, 36 (64%) of 56 species of all three genera currently recognised in this family were analysed. Our analysis showed Chlorogomphidae as a monotypic family containing the single speciose genus Chlorogomphus Selys, 1854. Chlorogomphus montanus Chao, 1999, syn. nov., is synonymised to Chlorogomphus nasutus Needham, 1930, Chlorogomphus urolobatus Chen, 1950, syn. nov., is synonymised to Chlorogomphus infuscatus Needham, 1930. The synonymy of Chlorogomphus suzukii Oguma, 1926 and Chlorogomphus tunti Needham, 1930 is confirmed. Some other potential synonyms are discussed. The phylogenetic trees reconstructed here showed that the species name C. nasutus Needham, 1930 actually refers to two (not three) different taxa. Thus, we suggest considering these two taxa as separate species, C. nasutus and C. satoi Asahina, 1995. ZooBank: urn:lsid:zoobank.org:pub:5188C826-AD51-4605-8B06-3C63DE80F1F0.}, }
@article {pmid40976471, year = {2025}, author = {Hornok, S and Keskin, A and Uspensky, I and Kontschán, J and Takács, N and Lesiczka, P and Warbroek, T and van den Bosch, TJM and Keve, G and Pitó, A and Sándor, AD}, title = {Updates on subgenus Ixodes in the Mediterranean region: validity of Ixodes festai Rondelli, 1926, reinstatement of Ixodes tatei , and a new species closely related to Ixodes gibbosus.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2025.09.002}, pmid = {40976471}, issn = {1879-0135}, abstract = {The southern part of Europe is one of the most species-rich regions from the point of view of the genus and subgenus Ixodes. However, numerous unresolved or questionably interpreted issues exist in the context of tick species indigenous to Mediterranean countries, such as the validity of Ixodes festai, synonymy of Ixodes tatei with Ixodes eldaricus (never tested molecularly) or the haplotype heterogeneity of Ixodes gibbosus. In this study, 21 specimens of six tick species from the subgenus Ixodes were compared morphologically with high resolution digital microscopy and also analyzed with molecular-phylogenetic methods based on two mitochondrial genetic markers. The nymphs of I. eldaricus and I. tatei showed differences in the morphology of the scutum and basis capituli. Both the nymph and the females of I. festai could be distinguished from those of I. eldaricus, I. ventalloi and I. acuminatus. A female tick resembled I. gibbosus but was also different from this species, based on its descriptions. Analysis of phylogenetic relationships confirmed with moderate to strong support that all six species examined in this study represent different taxa of the subgenus Ixodes, including a previously unknown sister species to I. gibbosus. The latter is recognized and described here as a new species, Ixodes paragibbosus Hornok and Kontschán, sp. nov. Based on findings of this study, the tick species I. tatei Arthur, 1959 should be resurrected and reestablished. Morphological and phylogenetic comparisons performed here (including the first barcoding sequences of I. eldaricus and I. festai) confirm that the latter is a valid species, distinct from both I. eldaricus and I. ventalloi. For the differential diagnosis of the above species, the results highlight the importance of observing (among other structures) the auriculae, the internal spur of coxa I and the hypostome.}, }
@article {pmid40970423, year = {2025}, author = {Castanon, CP and Hernandez, D and Khetrapal, AN and Hellberg, RS}, title = {Comparison of PCR-Based Methods for the Detection of Canned Tuna Species.}, journal = {Journal of food science}, volume = {90}, number = {9}, pages = {e70424}, doi = {10.1111/1750-3841.70424}, pmid = {40970423}, issn = {1750-3841}, support = {//Chapman University/ ; //National Science Foundation/ ; }, mesh = {Animals ; *Tuna/genetics/classification ; *Real-Time Polymerase Chain Reaction/methods ; *Food, Preserved/analysis ; *DNA Barcoding, Taxonomic/methods ; Multiplex Polymerase Chain Reaction/methods ; Species Specificity ; Food Contamination/analysis ; *Seafood/analysis ; DNA ; *Polymerase Chain Reaction/methods ; Food Labeling ; }, abstract = {Canned tuna is susceptible to mislabeling due to its high consumer demand, complex global supply chains, and range of prices. DNA barcoding of a short fragment of the mitochondrial control region (CR), termed the CR mini-barcode, has been established as an effective method for tuna species identification. However, the high level of DNA degradation in canned tuna products reduces the effectiveness of this method. Therefore, this study aimed to compare CR mini-barcoding to targeted (i.e., real-time or multiplex) PCR-based methods to determine the most effective approach for canned tuna species identification. DNA was extracted in duplicate from 24 canned tuna products labeled as albacore, skipjack, yellowfin, and light tuna. Each sample was analyzed with CR mini-barcoding, real-time PCR, and multiplex PCR. The top-performing targeted method also underwent sensitivity testing using binary species mixtures. Real-time PCR showed the highest species identification rate, with 100% of products detected, followed by CR mini-barcoding (33%) and multiplex PCR (29%). Real-time PCR also showed excellent sensitivity, detecting 0.1%-1% of the target species in fresh and heat-treated binary species mixtures. Multiplex PCR and real-time PCR showed similar effectiveness in terms of cost and time, with a price of US$6 per sample and a total time of 3-6 h when testing all targeted species. Although CR mini-barcoding required greater costs and time, it allowed for sequencing-based detection of a range of species in the products. In conclusion, a combination of real-time PCR and CR mini-barcoding is recommended to allow for rapid screening of target species along with sequencing-based confirmation. PRACTICAL APPLICATIONS: This research provides a practical recommendation regarding the use of genetic methods for detecting species in canned tuna. Implementation of the recommended methodology is expected to enhance consumer protection and help regulatory agencies enforce accurate labeling.}, }
@article {pmid40967690, year = {2025}, author = {Nagarajan, G and Kanagarajadurai, K and Pachaiyappan, K and Yadav, G}, title = {Identification and DNA barcoding of Tabanid flies in the pasture area of sheep at Mannavanur, Palani Hills, Tamil Nadu, India.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {64}, number = {}, pages = {101326}, doi = {10.1016/j.vprsr.2025.101326}, pmid = {40967690}, issn = {2405-9390}, mesh = {Animals ; *DNA Barcoding, Taxonomic/veterinary ; India ; *Diptera/genetics/classification/anatomy &amp; histology ; Sheep ; Electron Transport Complex IV/genetics ; *Sheep Diseases/parasitology ; Phylogeny ; }, abstract = {The present study was carried out to identify the tabanid flies creating annoyance to sheep in the grazing area of SRRC, Mannavanur by means of morphological keys and DNA barcoding targeting mitochondrial cytochrome c oxidase subunit I (COI) gene. Two different kinds of tabanid flies were caught from the pasture area by graziers during the months of May &amp; June 2021. With the help of Dept. of Agricultural Entomology, Centre for Plant Protection studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India and Zoological Survey of India, Kolkata, West Bengal, India, it was identified that Haematopota nathani (Cleg fly) and Tabanus subcinerascens (Horse fly) were the two dipteran tabanid flies causing annoyance and aching bite in sheep and shepherds. The total genomic DNA isolated from the flies were subjected to COI gene based PCR assay using the universal primer set and the resultant PCR amplified DNA fragments were cloned into E.coli based vector. The confirmed recombinant plasmids were subjected for gene sequencing protocol through outsourcing. Upon the BLAST analysis, the nucleotide sequences obtained from the flies identified by TNAU and ZSI, were having the highest identity with COI gene of Haematopota sp and Tabanus sp., respectively. The obtained nucleotide sequences were analysed using the standard bioinformatics tools. Small number of fly specimens and the analysis based on the partial nucleotide sequences of COI gene are the limitations. It was concluded that the documentation of H. nathani and T. subcinerascens as well as barcoding of both tabanid flies from Palani hills, Tamil Nadu, India, based on mitochondrial COI DNA marker had been carried out for the first time.}, }
@article {pmid40967208, year = {2025}, author = {Tai, H and Li, Q and Wang, J and Tan, J and Zhao, B and Lang, R and Petrof, BJ and Ding, J}, title = {Computational tracking of cell origins using CellSexID from single-cell transcriptomes.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101181}, doi = {10.1016/j.crmeth.2025.101181}, pmid = {40967208}, issn = {2667-2375}, abstract = {Cell tracking in chimeric models is essential yet challenging in developmental biology, regenerative medicine, and transplantation research. Current methods like fluorescent labeling and genetic barcoding are technically demanding, costly, and often impractical for dynamic tissues. We present CellSexID, a computational framework that uses sex as a surrogate marker for cell-origin inference. By training machine-learning models on single-cell transcriptomic data, CellSexID accurately predicts individual cell sex, enabling in silico distinction between donor and recipient cells in sex-mismatched settings. The model identifies minimal sex-linked gene sets through ensemble feature selection and has been validated using public datasets and experimental flow sorting, confirming biological relevance. We demonstrate CellSexID's applicability beyond chimeric models, including organ transplantation and sample demultiplexing. As a practical alternative to physical labeling, CellSexID facilitates precise cell tracking and supports diverse biomedical applications where mixed cellular populations need to be distinguished.}, }
@article {pmid40963787, year = {2025}, author = {Rossouw, L and Ngcobo, N and Clouse, K and Nattey, C and Technau, KG and Maskew, M}, title = {Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study.}, journal = {Discover health systems}, volume = {4}, number = {1}, pages = {115}, pmid = {40963787}, issn = {2731-7501}, abstract = {BACKGROUND: The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information.<br><br>METHODS: We explored an alternative method to examine patient files from a large administrative dataset in South Africa (the National Health Laboratory Services, or NHLS), by linking external data to the NHLS database using specimen barcodes associated with laboratory tests. This provides a deterministic way of performing data linkages without accessing demographic information. In this paper, we quantify the performance metrics of this approach.<br><br>RESULTS: The linkage of the large NHLS data to external hospital data using specimen barcodes achieved a 95% success. Out of the 1200 records in the validation sample, 87% were exact matches and 9% were matches with typographic correction. The remaining 5% were either complete mismatches or were due to duplicates in the administrative data.<br><br>CONCLUSIONS: The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective deterministic linkage tool that enable creation of large linked datasets without compromising confidentiality.}, }
@article {pmid40963001, year = {2025}, author = {Liu, S and Huang, J and Qu, L and Li, B and Yang, J}, title = {NAP-seq for full-length noncapped RNA sequencing.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {40963001}, issn = {1750-2799}, support = {32225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32430019//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370588//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The majority of the mammalian genome is transcribed into RNAs, most of which are noncapped RNAs (napRNAs) that not only regulate diverse biological processes through their functions as noncoding RNAs but also serve as processing products to delineate specific RNA biogenesis pathways. However, due to their heterogeneous lengths, diverse terminal modifications and complex secondary structures, identifying these napRNAs poses substantial challenges. Recently, we developed a napRNA sequencing technique (NAP-seq) to identify full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution. Here we describe the experimental design principles and detailed step-by-step procedures for discovering napRNAs across multiple cell types. The procedure includes T4 polynucleotide kinase pretreatment to standardize RNA termini, enabling comprehensive capture of modified napRNAs; size-selection followed by depletion of known high-abundance RNAs via RNase H to enrich long and low-abundance RNAs; and use of custom-designed adapters with random barcodes, permitting identification of full-length napRNAs at single-nucleotide resolution while minimizing PCR biases and adapter ligation inefficiencies. The use of thermally stable reverse transcriptase enzymes and nested reverse transcriptase primers ensures full-length cDNA synthesis across structured or modified RNA regions while minimizing mispriming artifacts. Libraries are sequenced in parallel using Oxford Nanopore (long-read) and Illumina (short-read) platforms, synergizing advantages of third-generation and next-generation sequencing technologies. The entire experimental procedure, from library preparation to deep sequencing and computational analysis, can be completed within 8 d. The NAP-seq approach enables researchers to discover novel classes of noncoding RNAs with regulatory functions and to investigate RNA biogenesis in various tissues and cell lines.}, }
@article {pmid40956667, year = {2025}, author = {Plaza, DF}, title = {Protocol for genomic surveillance of Plasmodium falciparum antigens using amplicon-based PacBio long-read sequencing.}, journal = {STAR protocols}, volume = {6}, number = {4}, pages = {104093}, doi = {10.1016/j.xpro.2025.104093}, pmid = {40956667}, issn = {2666-1667}, abstract = {Here, we present a protocol that identifies and classifies structurally diverse variants of msp1, msp2, glurp, and csp in Plasmodium falciparum using an amplicon-based long-read sequencing platform. We describe steps for PCR barcoding, PacBio circular consensus sequencing (CCS), in silico PCR-based size variant calling, and advanced data analysis in Galaxy. By resolving full-length sequences for each antigenic clone, this approach measures infection complexity, constructs isolate phylogenies, and supports vaccine design. For complete details on the use and execution of this protocol, please refer to Plaza et al.[1].}, }
@article {pmid40955360, year = {2025}, author = {Wacira, TN and Makonde, HM and Kamau, JN and Kibiti, CM}, title = {Identification and Antimicrobial Potential of Marine Sponges (Carteriospongia foliascens, Callyspongia fallax, and Paratetilla arcifera) from Kenyan Marine Waters.}, journal = {International journal of microbiology}, volume = {2025}, number = {}, pages = {4208163}, pmid = {40955360}, issn = {1687-918X}, abstract = {Emerging and re-emerging infectious diseases and pathogens present a significant global public health threat that has led researchers to focus on discovering new antimicrobial agents in order to address the challenge. Sponges are a promising source of marine natural products, which can be used as lead molecules for drug discovery. This study was aimed at identifying marine sponges through morphological and molecular techniques and evaluate the bioactivity potential of their organic crude extracts against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. Deoxyribonucleic acid (DNA) barcoding of the cytochrome c oxidase subunit I (COI) gene identified three genera of sponges (Carteriospongia, Callyspongia, and Paratetilla). Disk diffusion assay was used to determine the inhibition zone diameter (IZD) of the sponges' extracts. Minimum inhibitory concentrations (MICs) and the minimum bactericidal/fungicidal concentrations (MBCs/MFCs) of the most active sponge extracts were determined. The bioactive compounds were analyzed using gas chromatography-mass spectrometry (GC-MS). The dichloromethane extracts of Carteriospongia foliascens demonstrated the highest antifungal activity against C. albicans (31.33 ± 1.2 mg mL[-1]), surpassing the standard drug fluconazole (29.33 ± 1.5 mg mL[-1]). The MIC values for the sponge extracts ranged from 3.86 to 5.89 mg mL[-1], and the ethyl acetate extract of Callyspongia fallax had an MBC of 4.03 mg mL[-1] against S. aureus. GC-MS chromatogram identified 98 compounds across 41 classes in three sponge extracts. Notably, 9.2% of these compounds have been reported to exhibit antimicrobial activity against human pathogens. This study confirms that sponges are a source of useful biochemicals, which have potential for drug discovery. To the best of our knowledge, this is the first comprehensive study to report on the characterization of marine sponges from the Kenyan waters. Further research work to structurally elucidate and identify the most active bioactive compounds from the extracts of C. foliascens and C. fallax is recommended.}, }
@article {pmid40951674, year = {2025}, author = {Gan, J and Mi, X and Wang, C and Fan, L}, title = {Three new species of Theridiidae Sundevall, 1833 (Araneae) from Xizang, China.}, journal = {ZooKeys}, volume = {1251}, number = {}, pages = {1-15}, pmid = {40951674}, issn = {1313-2989}, abstract = {Three new species belonging to the spider family Theridiidae are described based on materials collected from Xizang Autonomous Region, Southwestern China: Moneta linzhi Gan, Mi &amp; Wang, sp. nov. (♀♂), M. yinae Gan, Mi &amp; Wang, sp. nov. (♀♂) and Phoroncidia cibagou Gan, Mi &amp; Wang, sp. nov. (♀♂). Diagnostic photos of the habitus and copulatory organs, and a distribution map are provided.}, }
@article {pmid40950469, year = {2025}, author = {Rueda, M and Gut, IG}, title = {ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.05.25335150}, pmid = {40950469}, abstract = {BACKGROUND: In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making integration, cohort selection, and downstream analysis cumbersome. While structured barcoding systems exist in large consortia (e.g., TCGA, GTEx) or domain-specific contexts (e.g., SPREC, GOLD), no unified, extensible framework currently spans both subjects and biosamples in a human- and machine-readable way.<br><br>METHODS: We developed ClarID, a domain-agnostic specification that supports two identifier formats: (i) a human-readable form (e.g., 'CNAG_Test-HomSap-00001-LIV-TUM-RNA-C22.0-TRT-P1W' that encodes key metadata such as project, species, subject_id, tissue, assay, disease, timepoint and duration (from that event); and (ii) a compact version named 'stub' (e.g., 'CT01001LTR0N401T1W') optimized for filenames, pipelines, and labeling.ClarID is implemented through an open-source command-line tool, ClarID-Tools, which processes tabular metadata files (CSV/TSV) and uses a YAML-based codebook to generate, decode, and validate identifiers, as well as to create and read QR codes. The tool supports bulk and single-sample processing and allows easy integration with institutional workflows.<br><br>RESULTS: To demonstrate ClarID's utility, we applied it to datasets from the Genomic Data Commons (GDC), generating interpretable identifiers for more than 113,000 clinical records (subjects) and 4,255 biospecimen records. All materials, including pre-processing scripts, input and encoded data, are publicly available and fully reproducible via the accompanying GitHub repository and Google Colab.<br><br>CONCLUSIONS: ClarID fills a critical gap between opaque accession numbers and rich metadata schemas by embedding key context directly into structured identifiers. It enhances traceability, facilitates downstream analysis, and remains adaptable to project-specific needs through a configurable codebook. The accompanying ClarID-Tools software is freely available, together with full documentation and reproducible pipelines, at https://github.com/CNAG-Biomedical-Informatics/clarid-tools .}, }
@article {pmid40950163, year = {2025}, author = {Fu, Y and Mathew, D and Wang, M and Chen, XE and Lin, KZ and Schaff, D and Shaffer, SM and Pardoll, DM and Jackson, C and Zhang, NR}, title = {Deciphering Cell Fate and Clonal Dynamics via Integrative Single-Cell Lineage Modeling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.09.01.673503}, pmid = {40950163}, issn = {2692-8205}, abstract = {Through natural or synthetic lineage barcodes, single-cell technologies now enable the joint measurement of molecular states and clonal identities, providing an unprecedented opportunity to study cell fate and dynamics. Yet, most computational methods for inferring cell development and differentiation rely exclusively on transcriptional similarity, overlooking the lineage information encoded by lineage barcodes. This limitation is exemplified by T cells, where subtle transcriptional differences mark divergent fates with distinct biological activity. Single-cell RNA and matched TCR sequencing is now ubiquitous in the analysis of clinical samples, where the TCR sequence provides an endogenous clonal barcode and could reveal clonal T cell responses. We present Clonotrace, a computational framework that jointly models gene expression and clonotype information to infer cell state transitions and fate biases with higher fidelity. While motivated by challenges in analyzing T cell populations, especially in the tumor microenvironment and immunotherapy settings, Clonotrace is broadly applicable to any lineage-barcoded single-cell dataset. Across diverse systems including T cells, hematopoietic differentiation, and cancer therapy resistance models, Clonotrace reveals differentiation hierarchies, distinguishes unipotent from multipotent states, and identifies candidate fate-determining genes driving lineage commitment.}, }
@article {pmid40947820, year = {2025}, author = {Prosser, SWJ and Floyd, RM and Thompson, KA and Monckton, SK and Hebert, PDN}, title = {BOLDistilled: Automated Construction of Comprehensive but Compact DNA Barcode Reference Libraries.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70043}, doi = {10.1111/1755-0998.70043}, pmid = {40947820}, issn = {1755-0998}, support = {MSI 42450//Canada Foundation for Innovation/ ; OGI-233//Genome Canada and Ontario Genomics/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; }, abstract = {Advances in DNA sequencing technology have stimulated the rapid uptake of protocols-such as eDNA analysis and metabarcoding-that infer the species composition of environmental samples from DNA sequences. DNA barcode reference libraries play a critical role in the interpretation of sequences gathered through such protocols, but many of these libraries lack a taxonomic consensus, include redundant records, do not support end-user analytical pipelines, and are not permanently archived. Furthermore, because DNA sequencers are outpacing Moore's Law and reference libraries are growing, the computational power required to assign sequences to source taxa is rapidly increasing. This paper introduces an algorithmic approach to construct DNA barcode reference libraries that addresses these issues. Hosted online, 'BOLDistilled' libraries are comprehensive but compact, because the algorithm distills genetic variation into a minimal set of records. We provide a BOLDistilled library for the barcode region of the cytochrome c oxidase 1 gene (COI) based on data in the Barcode of Life Data System (BOLD). It contains 1.7 M records versus the 15.7 M in the complete library, a compression that reduced the time required for sequence analysis of metabarcoded samples by ≥ 98% with no reduction in the accuracy of taxonomic placements. BOLDistilled libraries will be updated regularly, with current and previous versions available at https://boldsystems.org/data/boldistilled. By providing access to persistent, comprehensive, and high-quality reference data, these libraries strengthen the capacity of DNA-based identification systems to advance biodiversity science.}, }
@article {pmid40946051, year = {2025}, author = {Guo, Z and Fan, L and Ma, Y and Tian, K and Qiu, W and Wei, A and Fu, W and Chen, Y and Cui, Z and Wang, S and Zhan, C}, title = {Vascular endothelial cell-targeted mRNA delivery via synthetic lipid nanoparticles for venous thrombosis prevention.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {114147}, doi = {10.1016/j.jconrel.2025.114147}, pmid = {40946051}, issn = {1873-4995}, abstract = {Venous thromboembolism significantly contributes to the global disease burden. Anticoagulant and antiplatelet therapies are currently the treatment strategies. However, challenges remain due to hemorrhagic complications and the inability to resolve established thrombi. There is an urgent need for a new generation of antithrombotic agents. Given the fibrin specificity and rapid thrombus dissolution capacity of recombinant tissue plasminogen activator (TPA) protein, along with the significant advantages of mRNA therapeutics in protein replacement, we aim to develop an antithrombotic strategy through the targeted delivery of TPA mRNA to vascular endothelial cells using synthetic lipid nanoparticles (LNPs). A series of amino ionizable lipids were synthesized to create an LNP library, from which the LNP selectively targeting vascular endothelial cells (vtLNP) was selected by a DNA barcode labeling high-throughput screening method. The antithrombotic efficacy and safety of vtLNP loaded with TPA mRNA (vtLNP@TPA) were evaluated in a deep vein thrombosis (DVT) mouse model and normal ICR mice, respectively. The results revealed that vtLNP@TPA significantly prevented the occurrence and development of venous thrombosis. This study provides relevant experimental evidence for a novel antithrombotic therapy strategy for venous thrombosis using mRNA therapeutics.}, }
@article {pmid40945162, year = {2025}, author = {Koppala Narayana, SK and Kaira, P and Karthikeyan, M and Shanmugam, M and Sundharamoorthy, S and Andalil, R and Kallingil Gopi, D and Prakasam, R and Ramachandran, S and Arumugam, K}, title = {Integrating macro-microscopy, DNA barcoding and HPTLC for quality assessment of berberine containing botanicals traded as Maramanjal/Daruharidra.}, journal = {Journal of Ayurveda and integrative medicine}, volume = {16}, number = {5}, pages = {101192}, doi = {10.1016/j.jaim.2025.101192}, pmid = {40945162}, issn = {0975-9476}, abstract = {BACKGROUND: Daruharidra/Maramanjal is one of the most popular shrub used in Ayurveda, Siddha and other Indian medicinal systems. More than one botanical source is traded under this name, predominantly Berberis aristata and Coscinium fenestratum with an annual trade of 1000-2000 metric tonnes. The herbal drug trade is often reported with misidentification, adulteration and/or substitution issues due to morphological resemblance and confusion in vernacular names. This work aimed to integrate macro-microscopic, DNA marker strategies and phytochemical assay to differentiate Berberis aristata from its traded sources.<br><br>MATERIAL AND METHODS: Thirteen marketed samples and one authentic field sample from natural habitat were collected from various regions of the Indian market under the trade name Maramanjal/Daruharidra. The traditional identification methods included macro-microscopic and phytochemical screening by High-Performance Thin Layer Chromatography (HPTLC). Additionally, DNA barcode-based molecular identification and phylogenetic analysis were done using the ITS2 (Internal Transcribed Spacer 2) marker.<br><br>RESULTS: The macroscopic observations revealed 80 % ad-mixing of various allied botanicals in addition to accepted north Indian and south Indian sources such as B. aristata and C. fenestratum respectively. DNA barcoding enabled the identification of genuine and adulterated raw drugs from the collected samples. The HPTLC quantification revealed the presence of berberine in all 14 samples varying from 1.12 % to 26.33 %.<br><br>CONCLUSIONS: The macro-micro, HPTLC, and DNA barcoding helped in the identification of adulteration and substitution practices in this highly traded botanical drug. DNA barcoding can prove an effective tool for discovering the adulteration and substitution of Maramanjal/Daruharidra and this is its first report on the application of morphology, microscopy, phytochemical analysis, and DNA markers in differentiating these traded species.}, }
@article {pmid40944710, year = {2025}, author = {Dutta, N and Svensson, J and Saad, GA and Mello, M and Eklund, EA and Altinönder, I and Torstensson, P and Sayin, VI and Rohlin, A and Luche, H and Hallqvist, A and Raghavan, S}, title = {High baseline PD-1+ CD8 T Cells and TIGIT+ CD8 T Cells in circulation associated with response to PD-1 blockade in patients with non-small cell lung cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {10}, pages = {309}, pmid = {40944710}, issn = {1432-0851}, support = {21/1721//Cancerfonden/ ; }, abstract = {Blockade of PD-1 or its ligand PD-L1 with antibodies revolutionized treatment for stage III and IV non-small cell lung cancer (NSCLC) since FDA approval in 2015. However, resistance to PD-1/PD-L1 blockade remains a challenge, highlighting the need for biomarkers. This study analyzed 36 stage III and IV NSCLC patients, classified as responders or non-responders by iRECIST criteria. Peripheral blood mononuclear cells collected at baseline and post-treatment were examined for surface and intracellular markers via flow cytometry. CITE sequencing of CD8 T cells from three patients and plasma ctDNA analysis from 13 patients was performed using an ultrasensitive barcoding and next-generation sequencing method. Phenotypic analysis of CD8 T cells revealed higher TIGIT and PD-1 expression at baseline in responders compared to non-responders. Long-term responders (> 21 months) exhibited increased TCF-1[+]PD-1[+] CD8 T cell frequencies relative to shorter-term responders (> 15 months) and non-responders. CITE sequencing revealed intrinsic differences in immune regulation pathways between responders and non-responders. Finally, non-responders showed elevated and increasing ctDNA levels post-treatment, correlating with declining TCF-1[+]PD-1[+] CD8 T cells. Our data suggests combining CD8 T cell analysis with ctDNA dynamics could identify promising biomarkers for monitoring clinical response and treatment efficacy to PD-1/PD-L1 blockade in NSCLC.}, }
@article {pmid40944309, year = {2025}, author = {Parmar, DR and Johnston, NP and Dinka, MD and Szpila, K}, title = {Species delimitation of the Afrotropical and Palaearctic Calliphora Robineau-Desvoidy and discovery of two new species in Afrotropics.}, journal = {Medical and veterinary entomology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mve.70011}, pmid = {40944309}, issn = {1365-2915}, support = {2018/31/B/NZ8/02113//Polish National Science Centre/ ; 4-G046X5I//Australian Biological Resources Study/ ; }, abstract = {The blowflies (Calliphoridae) represent a significant portion of schizophoran fly diversity, comprising approximately 2000 known species. Among them, the genus Calliphora Robineau-Desvoidy is one of the largest, with over 100 species primarily distributed in the Holarctic Region and Australasia. Blowflies include several ubiquitous species and are primarily recognised for their medical and veterinary importance. In the Afrotropics, Calliphora was previously known from only two species: the native Calliphora croceipalpis Jaennicke and the introduced Calliphora vicina Robineau-Desvoidy. Two new distinctive species of Calliphora collected during recent fieldwork in Ethiopia are described using methods of integrative taxonomy. Calliphora teraramma sp. n. is characterised by peculiar male genitalia, with large cerci and a minute phallus. Calliphora mesay sp. n. is characterised by morphological and molecular traits, a close relative of the cosmopolitan C. vicina. In addition, we developed a cytochrome c oxidase subunit I (COI) barcode reference library for Palaearctic and Afrotropical Calliphora species, including 33 newly generated barcodes. Molecular species delimitation analyses using the software Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), implemented through the recently developed integrative platform Spart Explorer, largely support morphological species concepts.}, }
@article {pmid40943390, year = {2025}, author = {Baig, A and Akram, A and Lin, MK}, title = {Agarwood in the Modern Era: Integrating Biotechnology and Pharmacology for Sustainable Use.}, journal = {International journal of molecular sciences}, volume = {26}, number = {17}, pages = {}, doi = {10.3390/ijms26178468}, pmid = {40943390}, issn = {1422-0067}, support = {MOST 111-2320-B-039-023-MY3//National Science Council/ ; }, abstract = {Agarwood, valued for its resin, has long been used in perfumery, incense, and traditional medicine. Its resin is primarily derived from species of Aquilaria and is produced through a still-unknown process in response to biotic or abiotic stress. Concerns regarding agarwood's sustainability and conservation have emerged because of the substantial loss of natural resources due to overharvesting and illegal trade. To address these concerns, artificial techniques are being used to produce agarwood. The mechanism underlying agarwood production must be elucidated to enhance yield. The authentication of agarwood species is challenging because of morphological similarities between pure and hybrid Aquilaria species. Techniques such as DNA barcoding, molecular marker assessment, and metabolomics can ensure accurate identification, facilitating conservation. Artificial intelligence and machine learning can support this process by enabling rapid, automated identification on the basis of genetic and phytochemical data. Advances in resin induction methods (e.g., fungal inoculation) and chemical induction treatments are improving yield and quality. Endophytic fungi and bacteria promote resin production at minimal harm to the tree. Agarwood's pharmacological potential-antimicrobial, anti-inflammatory, and anticancer effects-has driven research into bioactive compounds such as sesquiterpenes and flavonoids for the development of novel drugs. This systematic review synthesized current evidence on species authentication, induction techniques, and pharmacological properties. The findings may guide future research aimed at ensuring sustainable use and enhancing the medicinal value of agarwood.}, }
@article {pmid40941119, year = {2025}, author = {Kim, KR and Kim, HJ and Bang, IC}, title = {Development of a Rapid and Cost-Effective Multiplex PCR Assay for the Simultaneous Identification of Three Commercially Important Sea Squirt Species (Halocynthia spp.).}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {17}, pages = {}, doi = {10.3390/foods14173003}, pmid = {40941119}, issn = {2304-8158}, support = {20200425-03//Ministry of Oceans and Fisheries Korea/ ; 2025//Soonchunhyang University Research Fund, Korea/ ; R2025046//National Institute of Fisheries Science, Korea/ ; }, abstract = {We developed and validated a rapid, cost-effective multiplex PCR assay targeting mitochondrial cytochrome c oxidase subunit I (COX1) to discriminate three commercially important sea-squirt species, Halocynthia roretzi, H. aurantium and H. hilgendorfi ritteri. Species-specific forward primers were designed from interspecific single-nucleotide polymorphisms within the barcode region and combined with a common reverse primer in a single reaction. Specificity was confirmed in all tested individuals (n = 7 per species) without cross-amplification. Sensitivity tests demonstrated consistent amplification down to 0.1 ng of template DNA, matching or surpassing detection limits reported for other food-authentication markers. Because the entire reaction including DNA extraction can be completed within three hours and requires only basic laboratory equipment, the method is well suited for quality control laboratories, border inspections and routine monitoring of processed products. The COX1 multiplex PCR set proposed here provides a reliable tool to enhance traceability, protect consumer choice, and support regulatory enforcement in the sea-squirt supply chain.}, }
@article {pmid40940606, year = {2025}, author = {Waghmode, MS and Sahoo, DK and Patil, NN and Abhyankar, PS and Gaikwad, DD and Shekh, S}, title = {Pseudomonas sp. MSW2-Mediated Biodegradation of Pharmaceutical Micropollutants: Experimental and In Silico Investigations.}, journal = {Current microbiology}, volume = {82}, number = {11}, pages = {499}, pmid = {40940606}, issn = {1432-0991}, abstract = {Environmental contamination from pharmaceutical and personal care products is a growing concern due to their widespread use. This study was aimed to investigate the biodegradation of acetaminophen and hydroxychloroquine alongside computational analysis (DFT calculations and molecular docking). The acetaminophen and hydroxychloroquine-tolerant strain was isolated from pharma industrial wastewater and identified as Pseudomonas sp. MSW 2 (GenBank: PP800223.1) based on morphological, biochemical, as well as DNA barcoding method. Based on the UV-VIS spectroscopy and HPLC data it was confirmed that Pseudomonas sp. MSW 2 degrades 1000 ppm of acetaminophen by 95% within 3 days and 50 ppm of hydroxychloroquine by 95% within 5 days, following first-order degradation kinetic models with rate constants of 0.65 d[-1] and 0.457 d[-1], respectively. Based on HRMS and [1]H NMR spectroscopy data, 1,4-benzoquinone and 7-chloro-4-quinolinamine were identified as degradative product of acetaminophen and hydroxychloroquine, respectively. The HOMO-LUMO energy gap (ΔEg) for acetaminophen,1,4 benzoquinone, hydroxychloroquine and 7-chloro-4-quinolinamine is 5.35 eV, 2.38 eV, 4.45 eV, and 4.55 eV, respectively. Data suggests that 1,4 benzoquinone has lower stability and higher reactivity compared to the acetaminophen. Whereas in case of hydroxychloroquine degradative product (7-chloro-4-quinolinamine), negligible changes were observed in the reactivity. Molecular docking simulations predicted a strong binding affinity (-26 kcal/mol) between acetaminophen and the amidase (PDB ID 2UXY) enzyme from P. aeruginosa, facilitated by hydrogen bonding. This study gives new insights in the bioremediation process, using the DFT calculations to theoretically document the reactivity and stability of pollutant as well as their biodegradative metabolites.}, }
@article {pmid40938793, year = {2025}, author = {Brock, AA and Duraivel, S and Jiang, J and Fischer, J and Greenberg, ZF and He, M and Angelini, TE and Schmittgen, TD}, title = {RNA Sequencing at Single Vesicle Resolution via 3D Printed Embedded Droplet Arrays.}, journal = {ACS applied materials &amp; interfaces}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsami.5c09959}, pmid = {40938793}, issn = {1944-8252}, abstract = {Single-cell RNA sequencing has transformed our understanding of cellular heterogeneity; however, comparable methods for studying individual extracellular vesicles (EVs) remain scarce. To address the heterogeneity of RNA cargo contained within EVs, we developed a platform that 3D prints droplet arrays that generate cDNA for sequencing single EVs. The printing method leverages the interfacial instability between a hydrocarbon-based support material and printed aqueous solutions, driving printed features to break up into controllable, homogeneous droplets of a desired size that become stably trapped in 3D space. We printed picoliter aqueous droplets of EVs, DNA barcoded oligonucleotide beads, and biochemicals and performed a variety of reactions within the organogel support medium including PCR and synthesis of poly(A)[+] RNA sequencing compatible cDNA. Printing conditions were optimized to ensure ideal droplet loading of individual barcoded beads and single EVs within each droplet. Following collection of aqueous cDNA material from the organogel, additional biochemical reactions were performed in tubes in order to generate sequencable RNA libraries. Individual CD9, CD63, and CD81 positive EVs contained a wide variety of poly(A)[+] RNAs including mRNA, mitochondrial RNA, and noncoding RNAs. Poly(A)[+] RNAs of individual 100 nm immunopurified THP-1 EVs were sequenced using the 3D printing method and identified 3689 unique barcodes with at least two corresponding reads of poly(A)[+] RNA per EV, and the average amount of poly(A)[+] RNA per EV was 3.32. The developed platform resolves EV poly(A)[+] RNA heterogeneity with potential implications for biomarker discovery and other clinical applications.}, }
@article {pmid40937516, year = {2025}, author = {Stefani, F and Laterrière, M and Abdellatif, L and Banchini, C and Mader Stevens, G and Séguin, S and Dadej, K and Koziol, L and Findlay, W and Dalpé, Y}, title = {The pitfalls of rDNA-based AMF identification: a comparative analysis of rDNA and protein-coding genes.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70557}, pmid = {40937516}, issn = {1469-8137}, support = {J-001012//Agriculture and Agri-Food Canada/ ; J-001315//Agriculture and Agri-Food Canada/ ; J-002272//Agriculture and Agri-Food Canada/ ; J-0161867//Agriculture and Agri-Food Canada/ ; J-002295//Agriculture and Agri-Food Canada/ ; }, abstract = {Intragenomic polymorphism of rDNA in arbuscular mycorrhizal fungi (AMF) has been largely overlooked in ecological and taxonomic studies, and the reliability of nuclear rDNA regions for species identification has not been comprehensively evaluated and compared with protein-coding genes. Analysis of rDNA copies from Rhizophagus irregularis strains revealed average intragenomic distances ranging from 0.08% (small subunit) to 6.9% (internal transcribed spacer 2 (ITS2)), with a maximum of 21.1% in ITS1 within strain DAOM 197198. Intragenomic rDNA polymorphisms are widespread throughout the AM fungal phylogeny, as confirmed by single nucleotide polymorphism density analysis and PacBio sequencing of 148 AM fungal cultures representing 44 species. All commonly targeted rDNA loci in ecological and taxonomic studies are polymorphic, with ITS and large subunit being the most variable, leading to paraphyletic clades and misleading phylogenetic interpretations among closely related species. No unique genetic distance threshold can be applied to identify AMF, because none of the examined protein-coding genes or partial rDNA had a barcode gap. However, indicative distance thresholds of 1% for glomalin, 1.1% for RPB1, and 1.7% for H[+]-ATPase provide guidance for species delimitation. This study characterizes the extent of intragenomic rDNA polymorphism in AMF, underscores the taxonomic challenges posed by highly variable loci, and describes a bioinformatics pipeline for recovering rDNA copies.}, }
@article {pmid40936965, year = {2025}, author = {Chen, HP and Huang, CL and Shiao, SF}, title = {A taxonomic revision of the genus Alexeter Förster (Hymenoptera, Ichneumonidae, Ctenopelmatinae, Mesoleiini) from Taiwan, with descriptions of six new species.}, journal = {ZooKeys}, volume = {1250}, number = {}, pages = {315-358}, pmid = {40936965}, issn = {1313-2989}, abstract = {The genus Alexeter Förster, 1869 is first recorded from Taiwan. One previously described species, A. shakojiensis Uchida, 1930, is newly recorded from Taiwan. Six new species, A. flavomaculatus sp. nov., A. hsiaoae sp. nov., A. mediolobus sp. nov., A. monticola sp. nov., A. pseudozangicus sp. nov., and A. rufispeculus sp. nov., are described and can be distinguished from their congeners primarily based on color pattern, mandibular teeth, propodeal carinae, fore wing length and venation, ocellar and first metasomal tergite measurements, and flagellomere counts. Illustrations of the male genitalia and a diagnostic key to the Taiwanese Alexeter species are provided. DNA-based species delimitations are provided as supporting evidence for four new species. In a COI-based phylogeny sampling 31 operative taxonomic units of Alexeter and similar genera, the genus Alexeter was not resolved as a monophyletic group. Additionally, the COI barcode showed limitations in distinguishing some Alexeter morphospecies, indicating the need for further evaluation of COI-based species delimitation in this genus.}, }
@article {pmid40934910, year = {2025}, author = {Guo, W and Chen, Z and Li, X and Huang, J and Hu, Q and Gu, J}, title = {scTrace+: Enhancing cell fate inference by integrating the lineage-tracing and multi-faceted transcriptomic similarity information.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101398}, doi = {10.1016/j.cels.2025.101398}, pmid = {40934910}, issn = {2405-4720}, abstract = {Deciphering the cell state dynamics is crucial for understanding biological processes. Single-cell lineage-tracing technologies provide an effective way to track single-cell lineages by heritable DNA barcodes, but the high missing rates of lineage barcodes and the intra-clonal heterogeneity bring great challenges to dissecting the mechanisms of cell fate decision. Here, we systematically evaluate the features of single-cell lineage-tracing data and then develop an algorithm, scTrace+, to enhance the cell dynamic traces by incorporating multi-faceted transcriptomic similarities into lineage relationships via a kernelized probabilistic matrix factorization model. We assess its feasibility and performance by conducting ablation and benchmarking experiments on multiple real datasets and show that scTrace+ can accurately predict the fates of cells. Further, scTrace+ effectively identifies some important driver genes implicated in cellular fate decisions of diverse biological processes, such as cell differentiation or tumor drug responses. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid40933667, year = {2024}, author = {Cheng, HJ and Bellini, BC and Janssens, F and Nakamori, T and Chang, CH}, title = {The Cryptic Diversity of the Terrestrial Microarthropods, Ptenothrix Börner (Collembola: Dicyrtomidae) from Taiwan: New Species Plus the Lectotype Designation for Ptenothrix denticulata (Folsom, 1899).}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e42}, doi = {10.6620/ZS.2024.63-42}, pmid = {40933667}, issn = {1810-522X}, abstract = {This is the first taxonomic study of Collembola in Taiwan integrating morphological and molecular evidence to investigate the Taiwanese species in the genus Ptenothrix Börner. We discovered that specimens previously identified as Ptenothrix denticulata (Folsom, 1899) actually consist of several cryptic species, of which we described two species new to science. Our data revealed that, although these species are remarkably similar to each other, they can be distinguished by color patterns, chaetotaxic characters and DNA barcoding (COI). We also designated one of the syntypes of Ptenothrix denticulata (Folsom, 1899) as its lectotype, and treated Dicyrtoma denticulata (Salmon 1964) as a synonym of Ptenothrix denticulata (Salmon 1964) (syn. nov.). Lastly, our study suggests that the diversity of Collembola in Taiwan is still poorly understood, with a high potential for new studies focusing on these microarthropods.}, }
@article {pmid40933665, year = {2024}, author = {Jiang, GC and Yang, CH and Wakabayashi, K and Chan, TY}, title = {An Integrated Taxonomy Approach Identified the Final Stage of Giant Phyllosoma of Parribacus antarcticus (Lund, 1793) (Crustacea: Decapoda: Scyllaridae) from Taiwan Waters.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e56}, doi = {10.6620/ZS.2024.63-56}, pmid = {40933665}, issn = {1810-522X}, abstract = {A bizarre marine planktonic organism giant phyllosoma with a body length of 79 mm was collected off Taiwanese waters for the first time. The specimen is positively identified as Parribacus antarcticus (Lund, 1793) by DNA barcoding, representing the largest and the first final stage giant phyllosoma with identification confirmed. The characteristics of the phyllosoma from Taiwan is described and illustrated in detail. As morphometric ratios previously proposed for identifying phyllosomae of Parribacus failed to assign correctly the species of the Taiwanese specimen, there is still no reliable morphological character for separating these giant phyllosomae. A key to the different phyllosoma stages of P. antarcticus is provided.}, }
@article {pmid40933664, year = {2024}, author = {Fuke, Y}, title = {Commentary: Integrative Taxonomy Reveals Freshwater Shrimp Diversity (Decapoda: Atyidae: Neocaridina) from Kyushu and Southern Honshu of Japan, with a Discussion on Introduced Species.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e53}, doi = {10.6620/ZS.2024.63-53.}, pmid = {40933664}, issn = {1810-522X}, abstract = {Shih et al. (2024) reported on the detection of Neocaridina species in Japan and their morphological characteristics in Zoological Studies. Eleven taxa were identified based on mitochondrial DNA (mtDNA) analysis and morphological examination. Among these, they identified two taxa that formed sister groups: N. denticulata and N. davidi, which are primarily found in Japan and China. In this commentary, I argue that both species are actually N. davidi. This conclusion was previously drawn by Onuki and Fuke (2022) based on their examination of genome-wide SNPs, mtDNA, and morphological data. The doubts raised about this identification represent a serious issue in terms of conservation, as N. denticulata is a native species, whereas N. davidi is considered an invasive alien species in Japan. Two likely reasons for this misidentification are the oversight of previous studies and the inability to account for the effects of interspecific and intraspecific hybridization. Inaccurate or unsubstantiated identifications pose significant challenges to taxonomy and conservation, underscoring the need for research grounded in reliable methods and well-characterized specimens.}, }
@article {pmid40932095, year = {2025}, author = {Del Sambro, L and Ali, A and Normanno, G and Capozzi, L and Castellana, S and Di Taranto, P and Petruzzi, F and Belluscio, D and Parisi, A and Bianco, A}, title = {A retail market survey on fish fraud from Southern Italy using DNA barcoding.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2025.13376}, pmid = {40932095}, issn = {2239-7132}, abstract = {Consumption of seafood, which includes both wild and aquaculture products, has increased several-fold during the last 50 years. Species substitution, in which low-value fish are replaced with high-value fish, is one of the prominent phenomena happening in the international seafood trade and the leading cause of fraud in the fishery sector, leading to both economic and health concerns. In this study, DNA barcoding was employed to identify 78 fishery product samples collected from markets and supermarkets located in the Apulia region (Southern Italy) at the genus or species level. Non-compliance between the species detected and the species declared in the label was detected in 5 (6.41%) samples. This study highlights the need for further investigations regarding the traceability and assessment of food product authentication. Indeed, accurate taxonomic assignment and a robust traceability system are essential tools for tackling food adulteration problems, providing transparency, and protecting food safety.}, }
@article {pmid40931279, year = {2025}, author = {Sarmento, FRP and Duarte, T and Teixeira, ACP and Salles, FF}, title = {Decoding Tupiperla illiesi Froehlich 1998 (Plecoptera: Gripopterygidae): Insights into Morphological Variation and Molecular Species Delimitation.}, journal = {Neotropical entomology}, volume = {54}, number = {1}, pages = {96}, pmid = {40931279}, issn = {1678-8052}, support = {309666/2019-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; APQ 05461-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; APQ-01591-23//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; RESOL-2022-788-APN-DIR#CONICET//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; }, abstract = {This study addresses historical uncertainties regarding morphological variation in the paraprocts of Tupiperla illiesi, a stonefly with a complex taxonomic history. We tested whether these variations represent phenotypic plasticity or distinct species using integrative taxonomy. Adult gripopterygids were collected from Estação Biológica de Boracéia utilizing Malaise and light traps. The morphology of the specimens was analyzed in accordance with existing literature, and selected individuals underwent DNA extraction, amplification, and sequencing of the cytochrome c oxidase subunit I (COI) barcode region. Molecular distances were estimated using the Kimura 2-parameter model, and clustering was determined using Neighbor-Joining and Bayesian methods. Species delimitation was further refined using the SPdel pipeline. The combined analysis of COI sequence and morphological differences in the paraprocts led to the identification of distinct morphotypes within T. illiesi, resulting in the description of a new species, Tupiperla tucum sp. nov.}, }
@article {pmid40931062, year = {2025}, author = {Gabbutt, C and Duran-Ferrer, M and Grant, HE and Mallo, D and Nadeu, F and Househam, J and Villamor, N and Müller, M and Heath, S and Raineri, E and Krali, O and Nordlund, J and Zenz, T and Gut, IG and Campo, E and Lopez-Guillermo, A and Fitzgibbon, J and Barnes, CP and Shibata, D and Martin-Subero, JI and Graham, TA}, title = {Fluctuating DNA methylation tracks cancer evolution at clinical scale.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40931062}, issn = {1476-4687}, abstract = {Cancer development and response to treatment are evolutionary processes[1,2], but characterizing evolutionary dynamics at a clinically meaningful scale has remained challenging[3]. Here we develop a new methodology called EVOFLUx, based on natural DNA methylation barcodes fluctuating over time[4], that quantitatively infers evolutionary dynamics using only a bulk tumour methylation profile as input. We apply EVOFLUx to 1,976 well-characterized lymphoid cancer samples spanning a broad spectrum of diseases and show that initial tumour growth rate, malignancy age and epimutation rates vary by orders of magnitude across disease types. We measure that subclonal selection occurs only infrequently within bulk samples and detect occasional examples of multiple independent primary tumours. Clinically, we observe faster initial tumour growth in more aggressive disease subtypes, and that evolutionary histories are strong independent prognostic factors in two series of chronic lymphocytic leukaemia. Using EVOFLUx for phylogenetic analyses of aggressive Richter-transformed chronic lymphocytic leukaemia samples detected that the seed of the transformed clone existed decades before presentation. Orthogonal verification of EVOFLUx inferences is provided using additional genetic data, including long-read nanopore sequencing, and clinical variables. Collectively, we show how widely available, low-cost bulk DNA methylation data precisely measure cancer evolutionary dynamics, and provides new insights into cancer biology and clinical behaviour.}, }
@article {pmid40930527, year = {2025}, author = {van der Toorn, W and Naarmann-de Vries, IS and Liu-Wei, W and Dieterich, C and von Kleist, M}, title = {WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing.}, journal = {Nucleic acids research}, volume = {53}, number = {17}, pages = {}, doi = {10.1093/nar/gkaf873}, pmid = {40930527}, issn = {1362-4962}, support = {//European Union's Horizon 2020/ ; 955974//MarieSklowska-Curie Actions Innovative Training Networks/ ; 01KI2016//German Ministry for Science and Education/ ; 390685689//Deutsche Forschungsgemeinschaft/ ; 439669440 TRR319 RMaP TP B01//German RMaP consortium/ ; //Robert Koch Institute/ ; }, mesh = {*RNA, Transfer/genetics/chemistry ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopores ; *Software ; }, abstract = {Transfer RNA (tRNA) plays an essential role in protein translation, and tRNA modifications are important to their function. Recently, nanopore direct RNA sequencing (dRNA-seq) has shown promising results in the detection of complex tRNA modifications. However, its wider adoption in the tRNA field has been limited by a lack of (de)multiplexing solutions. Here, we present WarpDemuX-tRNA: an extension to the WarpDemuX method specifically optimized for multiplexed nanopore tRNA sequencing. Using consensus-based signal analysis using (soft) dynamic time warping and barycenter averaging, our approach improves barcode feature generation and achieves more robust barcode identification. WarpDemuX-tRNA outperforms the original method and achieves 99% precision and 95% recovery for four barcodes, while reducing computational complexity and runtime to 6 min per one million reads. WarpDemuX-tRNA is an open-source and free-to-use solution to high-throughput nanopore tRNA sequencing, facilitating more accessible, cost-effective, and high-throughput studies of tRNA modifications and their regulatory mechanisms.}, }
@article {pmid40927319, year = {2025}, author = {Sadyrova, M and Martin, E and Ramsey, P and Bullington, L}, title = {Mock Plant Communities and a Large Mammal Case Study Reveal ITS2 Primer Bias Against Graminoids.}, journal = {Ecology and evolution}, volume = {15}, number = {9}, pages = {e72102}, pmid = {40927319}, issn = {2045-7758}, abstract = {DNA fecal metabarcoding has revolutionized the field of herbivore diet analyses, offering deeper insight into plant-herbivore interactions and more reliable ecological inferences. However, due to PCR amplification bias, primer selection has a major impact on the validity of these inferences and insights. Using two pooling approaches on four mock communities and a case study examining diets of four large mammalian herbivores (LMH), we evaluated the efficacy of two primer pairs targeting the internal transcribed spacer 2 (ITS2) region: the widely used ITS-S2F/ITS4 pair and the UniPlant F/R pair, designed specifically for DNA metabarcoding. Both primer pairs consistently underrepresented graminoids, where > 40% of graminoid species did not amplify in vitro. However, the UniPlant F/R primer pair more accurately amplified mock plant communities, whereas the ITS-S2F/ITS4 pair underestimated graminoid relative abundance by at least twofold more than UniPlant F/R primers. Furthermore, in the LMH case study, UniPlant F/R primers identified graminoids as the dominant plant group for at least one LMH, indicating diet niche partitioning, while ITS-S2F/ITS4 primers largely failed to amplify graminoid DNA, potentially overestimating LMH diet overlap. Our findings underscore the importance of incorporating mock community analyses into DNA metabarcoding protocols to identify and mitigate primer bias, thereby enhancing the accuracy of ecological conclusions and supporting more effective conservation and management decisions.}, }
@article {pmid40926684, year = {2025}, author = {Tian, S and Li, Y and Yao, J and Huan, C and Zhang, W and Li, S and Zhang, Z and Guo, Z and Yang, Q and Li, C and Li, C and Li, J and Zhou, L}, title = {A barcode-specific immobilization interface for microfluidics-assisted uniform spatially barcoded microarray analysis.}, journal = {The Analyst}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5an00534e}, pmid = {40926684}, issn = {1364-5528}, abstract = {Microfluidics-assisted spatially barcoded microarray technology offers a high-throughput, low-cost approach towards spatial transcriptomic profiling. A uniform barcoded microarray is crucial for spatially unbiased mRNA analysis. However, non-specific adsorption of barcoding reagents in microchannels occurs during liquid transport, causing non-uniform barcoding in the chip's functional regions. The uneven microarray further leads to biased transcriptome capture. Herein, we develop a barcode-specific immobilization (BarSI) interface with both anti-adsorption properties and biological activity for the development of uniform spatially barcoded microarray chips. We immobilize DNA probes in straight and serpentine microchannels with coefficients of variation (CV) of 2.3% and 3.2%. Based on the orthogonal barcoding system, we developed spatially barcoded microarray chips with an overall fluorescence intensity CV of 8.47 ± 1.26%, compared with the CV of 20.91 ± 2.84% of microarrays developed on conventional amino glass slides. Using the uniform spatially barcoded microarray chip, we achieved spatially unbiased detection of mouse liver mRNA with an absolute value of Moran's I below 0.05. We present an economical and accessible method for manufacturing uniform spatially barcoded microarray chips, introducing a novel strategy for unbiased transcriptome analysis.}, }
@article {pmid40926494, year = {2025}, author = {Lee, M and Kanturski, M and Lee, S}, title = {Unveiling host plant associations and cryptic genetic diversity of Miyalachnus sorini (Aphididae: Lachninae) on cherry trees in South Korea.}, journal = {Bulletin of entomological research}, volume = {}, number = {}, pages = {1-10}, doi = {10.1017/S0007485325100400}, pmid = {40926494}, issn = {1475-2670}, abstract = {This study presents the first record of Miyalachnus sorini Kanturski &amp; Lee, 2024 (Aphididae: Lachninae) in South Korea, thereby extending its known distribution beyond Japan and identifying a new host plant, Prunus sargentii (Rosaceae). We describe diagnostic morphological traits across multiple life stages and compare them with those of Japanese populations. Comparative analyses with Japanese populations demonstrated consistent morphological differentiation, notably elevated ratios of the ultimate rostral segment to antennal segments across multiple morphs in the Korean population, indicating potential ecological adaptation. DNA barcoding using the mitochondrial cytochrome c oxidase I gene revealed low intraspecific divergence (average 0.2%) and interspecific divergence (average 10.5%) between Miyalachnus sp. and M. sorini. Haplotype analysis was performed to investigate the relationship between host plants and cryptic genetic diversity. These findings enhance our understanding of the morphological and genetic diversity of M. sorini and underscore the importance of monitoring its spread for informed pest management strategies.}, }
@article {pmid40925998, year = {2025}, author = {Qi, Z and Xue, S and Chen, J and Zhao, W and Johnson, K and Wen, X and Charles Richard, JL and Lin, P and Zhong, S}, title = {Genome-wide mapping of RNA-protein associations through sequencing.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40925998}, issn = {1546-1696}, support = {R01GM138852//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; UH3CA256960//Center for Strategic Scientific Initiatives, National Cancer Institute (NCI Center for Strategic Scientific Initiatives)/ ; R01HD107206//U.S. Department of Health &amp; Human Services | NIH | NICHD | National Center for Medical Rehabilitation Research (NCMRR)/ ; DP1DK126138//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, abstract = {RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing. We apply PRIM-seq to two human cell lines and construct a human RNA-protein association network (HuRPA), encompassing >350,000 associations involving ~7,000 RNAs and ~11,000 proteins, including 2,610 proteins that each interact with at least 10 distinct RNAs. We experimentally validate the tumorigenesis-associated lincRNA LINC00339, the RNA with the highest number of protein associations in HuRPA, as a protein-associated RNA. We further validate the RNA-associating abilities of chromatin-conformation regulators SMC1A, SMC3 and RAD21, as well as the metabolic enzyme PHGDH. PRIM-seq enables systematic discovery and prioritization of RNA-binding proteins and their targets without gene- or protein-specific reagents.}, }
@article {pmid40923893, year = {2025}, author = {Reyes Gamas, K and Seamons, TR and Dysart, MJ and Fang, L and Chappell, J and Stadler, LB and Silberg, JJ}, title = {Controlling the Taxonomic Composition of Biological Information Storage in 16S rRNA.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00313}, pmid = {40923893}, issn = {2161-5063}, abstract = {Microbes can be programmed to record participation in gene transfer by coding biological-recording devices into mobile DNA. Upon DNA uptake, these devices transcribe a catalytic RNA (cat-RNA) that binds to conserved sequences within ribosomal RNAs (rRNAs) and perform a trans-splicing reaction that adds a barcode to the rRNAs. Existing cat-RNA designs were generated to be broad-host range, providing no control over the organisms that were barcoded. To achieve control over the organisms barcoded by cat-RNA, we created a program called Ribodesigner that uses input sets of rRNA sequences to create designs with varying specificities. We show how this algorithm can be used to identify designs that enable kingdom-wide barcoding, or selective barcoding of specific taxonomic groups within a kingdom. We use Ribodesigner to create cat-RNA designs that target Pseudomonadales while avoiding Enterobacterales, and we compare the performance of one design to a cat-RNA that was previously found to be broad host range. When conjugated into a mixture of Escherichia coli and Pseudomonas putida, the new design presents increased selectivity compared to a broad host range cat-RNA. Ribodesigner is expected to aid in developing cat-RNAs that store information within user-defined sets of microbes in environmental communities for gene transfer studies.}, }
@article {pmid40922982, year = {2025}, author = {Beers, D and Leygonie, J}, title = {The fiber of persistent homology for trees.}, journal = {Journal of applied and computational topology}, volume = {9}, number = {3}, pages = {22}, pmid = {40922982}, issn = {2367-1734}, abstract = {Consider the space of continuous functions on a geometric tree X whose persistent homology gives rise to a finite generic barcode D. We show that there are exactly as many path connected components in this space as there are merge trees whose barcode is D. We find that each component is homotopy equivalent to a configuration space on X with specialised constraints encoded by the merge tree. For barcodes D with either one or two intervals, our method also allows us to compute the homotopy type of this space of functions.}, }
@article {pmid40919462, year = {2025}, author = {Huang, M and Lawes, MJ and Zhou, W and Wei, F}, title = {Integrating hotspot dynamics and centers of diversity: a review of Indo-Australian Archipelago biogeographic evolution and conservation.}, journal = {Marine life science &amp; technology}, volume = {7}, number = {3}, pages = {420-433}, pmid = {40919462}, issn = {2662-1746}, abstract = {The Indo-Australian Archipelago (IAA) is the world's preeminent marine biodiversity hotspot, distinguished by its exceptional species richness in tropical shallow waters. This biodiversity has spurred extensive research into its evolutionary and biogeographic origins. Two prominent theoretical frameworks dominate explanations for the IAA's biodiversity: the "centers-of hypotheses" and the "hopping hotspot hypothesis". The "centers-of hypotheses" posits that specific regions serve as key sources of IAA biodiversity, either through the accumulation and overlap of species from external areas or via elevated rates of local speciation. In contrast, the "hopping hotspot hypothesis" asserts that biodiversity hotspots are dynamic, shifting across geological timescales in response to tectonic and environmental changes. This review synthesizes these contrasting perspectives into an integrated framework, the "Dynamic Centers Hypothesis," which proposes that as biodiversity hotspots migrate over time, the IAA's role in generating and sustaining biodiversity has evolved, with varying contributions from different sources dominating distinct historical phases. By synthesizing the evidence for both hypotheses and incorporating recent findings, including fossil and phylogeography data, we propose the "Dynamic Centers Hypothesis" as a comprehensive and unifying explanation for the IAA's biodiversity. The review further explores biogeographic delineation, aligning tropical marine realms with the IAA's evolutionary trajectory, from its Tethyan roots to its modern Indo-West Pacific dominance. Looking forward, advances in DNA barcoding and genomics are uncovering vast cryptic diversity, revolutionizing our comprehension of IAA phylogeographic history. These discoveries underscore the imperative for a multidimensional conservation framework, integrating phylogenetic, and functional diversity, to preserve this biodiversity hotspot amid escalating global change.}, }
@article {pmid40917261, year = {2025}, author = {Egg, S and Lopes-Lima, M and Bayerl, H and Froufe, E and Stoeckle, BC and Kuehn, R and Geist, J}, title = {The Impact of Glacial Disturbance History Upon the Genetic Diversity of Unio crassus and Unio nanus in Europe and Implications for Conservation.}, journal = {Ecology and evolution}, volume = {15}, number = {9}, pages = {e72113}, pmid = {40917261}, issn = {2045-7758}, abstract = {Historically, the thick-shelled river mussel (Unio crassus agg. complex) was considered a single, widespread species across Europe. However, recent phylogenetic taxonomic revisions have delineated 12 species from this complex, including Unio crassus (s. str. Philipsson in Retzius, 1788) and Unio nanus (Lamarck, 1819 stat. rev.), which exhibit substantial range overlap and broad European distributions. Understanding their fine-scale genetic diversity, population structure, and potential for recent or ancient hybridization is critical for effective conservation planning. This study investigated the genetic diversity and structure of U. crassus and U. nanus across Europe, examining the influence of glacial disturbance history and host-fish associations. Using mitochondrial (COI) and nuclear (microsatellite) markers on 60 populations, we revealed a discordance between mitochondrial and nuclear structuring, suggesting ancient introgression. Crucially, no evidence of recent hybridization was detected between U. crassus and U. nanus. We found significantly higher nuclear genetic diversity in U. crassus compared to U. nanus. Our findings indicate an older Black Sea-Caspian Sea divergence and ancient introgression between U. nanus and U. crassus, as well as distinct postglacial colonization routes: a Western route for U. nanus and an Eastern route for U. crassus, converging in a secondary contact zone. Our results highlight the strong influence of host-fish associations and glacial history in shaping the genetic patterns of these mussels, underscoring the need to incorporate intraspecific genetic diversity into conservation strategies. As shell morphology proved unreliable for species identification, we recommend DNA barcoding for reliable species recognition and suggest further research into host-fish preferences to improve conservation efforts.}, }
@article {pmid40915726, year = {2025}, author = {Zhou, Z and Mao, D and Chen, G and Feng, C and Zhu, X}, title = {Research progress of DNA barcoding in precision medicine and molecular diagnosis- A review.}, journal = {Analytica chimica acta}, volume = {1373}, number = {}, pages = {344492}, doi = {10.1016/j.aca.2025.344492}, pmid = {40915726}, issn = {1873-4324}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Precision Medicine ; Humans ; *Molecular Diagnostic Techniques ; *DNA/genetics ; Animals ; }, abstract = {BACKGROUND: A DNA barcode is a short DNA fragment used to classify and identify specific organisms, taking advantage of the specificity and diversity inherent in biological molecules. Since Herbert introduced the concept in 2003, DNA barcoding has been increasingly used in precision medicine and related fields, including species identification and environmental monitoring, over the past few decades. Although numerous molecular diagnostic techniques have emerged, many face notable obstacles such as sensitivity to handling conditions, high expenses, and limitations in accuracy. To overcome these issues, researchers have progressively integrated DNA barcoding with various molecular biology methods.<br><br>RESULTS: This review examines different types of DNA barcodes and their applications in precision medicine, emphasizing their clear benefits over conventional species identification approaches, particularly in terms of biocompatibility, specificity, and the precision of molecular detection.<br><br>SIGNIFICANCE AND NOVELTY: Being the first comprehensive overview of DNA barcoding technology, this review addresses a critical knowledge gap in cross-platform methodological integration. Innovations in DNA barcoding can greatly improve the detection efficiency of biomolecules and cellular components. Furthermore, DNA barcoding holds strong potential for wider use in clinical medicine, diagnostic testing, and immunology, especially in personalized medicine and rapid pathogen detection.}, }
@article {pmid40915677, year = {2025}, author = {Costa, FF and Lustosa, BPR and Perico, CP and Belmonte-Lopes, R and Carvalho, JLVR and Razzolini, EL and Santos, GDD and Lima, BJFS and Souza-Motta, CM and Raittz, RT and Song, Y and Selbmann, L and de Hoog, GS and Meis, J and Vicente, VA}, title = {In silico search reveals the association of lichens with black yeast-like fungi in the order Chaetothyriales.}, journal = {Fungal biology}, volume = {129}, number = {6}, pages = {101618}, doi = {10.1016/j.funbio.2025.101618}, pmid = {40915677}, issn = {1878-6146}, mesh = {*Lichens/microbiology/classification ; *Ascomycota/genetics/classification/isolation &amp; purification/physiology ; Metagenomics ; Symbiosis ; Phylogeny ; Computer Simulation ; Metagenome ; }, abstract = {Lichens exemplify a unique symbiotic relationship between fungi and algae or cyanobacteria, where fungi (mycobionts) provide structural support, while algae or cyanobacteria (photobionts) provide nutrients. Recent discoveries in the order Chaetothyriales have led to the description of several lichenicolous species, underscoring an intricate relationship of some black yeast-like fungi with lichens. The present study aims to investigate public metagenomic data of lichens available in the SRA database, covering a total of 2888 samples. The analysis incorporated 122 molecular marker sequences (barcodes and padlock probes) previously documented in the literature for species classified within Chaetothyriales. Additionally, 11 novel barcodes for species recently identified in lichens of the genera Cladophialophora and Paracladophialophora are described. The selected metagenomes were then compared with molecular marker sequences using local BLASTn (v2.6.0+), considering only alignments with a coverage cut-off and 100 % identity (perfect match). Reads from each sample were retrieved from the SRA as a multifasta file and analyzed with the SWeeP method for vector-based, alignment-free sequence analysis. The analysis identified fungi that are known as environmental inhabitants and, occasionally, opportunistic pathogens of vertebrates, including species in the genera Cladophialophora, Cyphellophora, and Exophiala. These species were distributed across 11 BioProjects from various locations around the world. The findings of this study corroborate extant knowledge concerning fungal colonization in diverse extremophilic environments, including deserts, tundra, and rocky surfaces.}, }
@article {pmid40914237, year = {2025}, author = {Jeon, J and Lee, DY and An, SB and Ryu, J and Jeong, JU and Roh, IS and Choi, KS}, title = {Hiding in plain sight: Uncovering the hidden diversity of Culicoides spp. (Diptera: Ceratopogonidae) in the Republic of Korea using DNA barcoding data.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107821}, doi = {10.1016/j.actatropica.2025.107821}, pmid = {40914237}, issn = {1873-6254}, abstract = {Culicoides spp. (Diptera: Ceratopogonidae) are vectors of livestock diseases, including bluetongue, Akabane, and African horse sickness. Accurate species identification is a crucial first step in effective vector management. However, morphological identification of the genus Culicoides is challenging due to their small size (<2.5 mm) and considerable intraspecific morphological variability. Additionally, there is a notable lack of molecular studies to support the identification process. This study aimed to use DNA barcoding data (Cytochrome c oxidase subunit 1) to accurately identify Culicoides species in the Republic of Korea (ROK) and to elucidate intra- and interspecies relationships. Samples were collected from livestock farms across various regions of the ROK between 2022 and 2024. DNA barcoding sequences were analysed, and species delimitation was conducted using split methods (ABGD, ASAP, bPTP, GMYC) to investigate the potential presence of cryptic species. A total of 24 morphospecies were identified, among which five (Culicoides circumbasalis, Culicoides circumscriptus, Culicoides erairai, Culicoides kibunensis, and Culicoides sumatrae) formed two or more molecular operational taxonomic units, suggesting the potential existence of cryptic species. In addition to compiling existing literature, we updated the checklist of Culicoides species in the ROK, identifying three species (C. circumbasalis, C. thurmanae, and C. verbosus) that had not been previously documented in the ROK. The findings of this study provide a foundation for the precise identification of Culicoides species in East Asia and contribute to the development of effective control programs aimed at managing livestock disease outbreaks.}, }
@article {pmid40911100, year = {2025}, author = {Tiwari, N and Shilpi, K and James, SW and Yadav, S}, title = {Integrative taxonomy uncovers four novel species of Drawida Michaelsen, 1900 (Clitellata: Moniligastridae) revealing untapped earthworm diversity in India.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {869}, pmid = {40911100}, issn = {1573-4978}, support = {CRG/2022/001908.//Anusandhan National Research Foundation/ ; }, mesh = {Animals ; *Oligochaeta/classification/genetics ; India ; Phylogeny ; Biodiversity ; Ecosystem ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: The earthworm fauna of India remains inadequately documented, despite its pivotal ecological importance, and there is a pressing need to address this gap. Recognizing this lack of comprehensive documentation, the present study was undertaken to explore and characterize the diversity in previously under-surveyed regions. During systematic surveys in Madhya Pradesh (Central India) and Manipur (North-Eastern India), four novel species of the genus Drawida Michaelsen, 1900 were discovered: D. gouri Tiwari &amp; Yadav sp. nov., D. heingangensis Tiwari &amp; Yadav sp. nov., D. leibiensis Tiwari &amp; Yadav sp. nov., and D. laichingensis Tiwari &amp; Yadav sp. nov.<br><br>MATERIALS AND METHODS: Specimens were collected from diverse habitats in Madhya Pradesh and Manipur, including the campus of Dr. Harisingh Gour Vishwavidyalaya, paddy fields along the Imphal River, and the Yangoupokpi-Lokchao Wildlife Sanctuary. Detailed morphological analyses focused on pigmentation patterns, genital marking glands, and spermathecal structures. Mitochondrial Cytochrome COxidase subunit I (COI) barcoding was employed to validate species boundaries and confirm their taxonomic distinctness.<br><br>CONCLUSION: D. gouri belongs to the primitive willsi species group, characterized by distinct pigmentation and prostate-like genital marking glands. D. heingangensis is assigned to the glandless group and possesses a thin-walled sac formed by the ental part of the spermathecal atria. D. leibiensis and D. laichingensis, also members of the glandless group, exhibit digitiform spermathecal atria. These findings reveal the considerable yet under-documented diversity of India's earthworm fauna and highlight the urgent need for intensified surveys employing integrative taxonomic approaches.}, }
@article {pmid40909566, year = {2025}, author = {Joshy, DM and Yi, SV}, title = {Expanding canonical cortical cell type markers in the era of single-cell transcriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.08.26.672469}, pmid = {40909566}, issn = {2692-8205}, abstract = {Cell type markers have been instrumental to physiological and molecular investigation of the human brain and remain essential for annotating cell type clusters in single-cell expression data and for targeted validation studies. However, expression of canonical markers in the target cell type (which we termed as the expression 'fidelity') as well as expression in unrelated cell types (which we termed as the 'background expression') across cortical regions remains poorly characterized. Using nearly 500,000 high-quality single-nucleus profiles from 19 studies, we quantified marker fidelity, revealing substantial regional variability. We developed a statistical framework that aggregates annotated barcodes into pseudo-bulk profiles, applied rigorous performance metrics, and identified markers with improved fidelity, reduced background, and consistent expression across regions. This approach extended the canonical marker set for six major brain cell types and yielded superior subtype-specific markers. The resulting marker lists, and a user-friendly analysis interface, provide a valuable resource for cell type annotation and validation in neurological research.}, }
@article {pmid40909179, year = {2024}, author = {Ponpinij, S and Hasin, S and Kaewgrajang, T and Voraphab, I and Nipitwattanaphon, M}, title = {Morphological and Molecular Identification of Fungus-growing Termites (Isoptera, Termitidae, Macrotermitinae) in Thailand.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e52}, pmid = {40909179}, issn = {1810-522X}, abstract = {Fungus-growing termites (FGTs) play ecologically important roles as both decomposers and producers of termite mushrooms. However, they are difficult to research due to a lack of an updated identification key and the inability to locate type specimens. Molecular identification may be helpful, but this requires database information that is lacking for many species found in Thailand. In addition, some researchers use the cytochrome oxidase subunit I (COI) gene as a barcoding gene, but others use cytochrome oxidase subunit II (COII). Thus, we offer detailed descriptions of nine FGT species commonly found in Thailand, together with the DNA sequences of both the COI and COII genes. The descriptions include those of both major and minor soldiers. The DNA sequences of the two genes confirm the morphological identifications. Our data will aid future FGT identification and facilitate research on the biodiversity, conservation, and sustainable use of FGTs and termite mushrooms.}, }
@article {pmid40909118, year = {2025}, author = {Park, J and Yagi, S and Hirowatari, T}, title = {Taxonomic study of the genus Erechthias (Lepidoptera, Tineidae) from the Ogasawara Islands, with two new records and four new species.}, journal = {ZooKeys}, volume = {1250}, number = {}, pages = {13-48}, pmid = {40909118}, issn = {1313-2989}, abstract = {This study reviewed the genus Erechthias Meyrick, 1880 on the Ogasawara Islands, Japan with regards to eight recognized species, two of which were known (E. itoi Moriuti &amp; Kadohara, 1994 and E. zebrina (Butler, 1881)), two of which are newly recorded (E. minuscula (Walsingham, 1897) and E. atririvis (Meyrick, 1931)), and four of which are new species (E. mirabilis sp. nov., E. oculus sp. nov., E. flavimacula sp. nov., and E. nidumicola sp. nov.). Photographs of adult specimens and of their genitalia as well as illustrations of wing venation are provided. A preliminary phylogenetic tree based on mitochondrial DNA (the partial COI region, DNA barcode region) includes seven Erechthias species. Furthermore, haplotype networks were also constructed using DNA barcode regions for three species distributed across three or more island groups (Mukojima Islands, Chichijima Islands, Hahajima Islands, and other Islands). All examined E. flavimacula sp. nov. and E. nidumicola sp. nov. had unique haplotypes and were divided into three units corresponding to the group of islands.}, }
@article {pmid40909117, year = {2025}, author = {Sruoga, V and Kaila, L and Laine, E}, title = {First male description of Urodeta longa Sruoga &amp; Kaila, 2019 from Thailand with identification keys to Asian species of Urodeta Stainton, 1869 (Lepidoptera, Elachistidae, Elachistinae).}, journal = {ZooKeys}, volume = {1250}, number = {}, pages = {1-12}, pmid = {40909117}, issn = {1313-2989}, abstract = {A male of the little-known species Urodeta longa Sruoga &amp; Kaila, 2019 is described for the first time based on material collected in northern Thailand. The species is diagnosed based on characters found in the habitus and genitalia, which are illustrated in detail. Conspecificity of male and female specimens is confirmed by DNA barcodes. Identification keys to all known Asian species of the genus Urodeta Stainton, 1869, based on male and female genitalia, are provided. Exceptionally high intra-generic barcode divergence among Urodeta species is reported.}, }
@article {pmid40908939, year = {2025}, author = {Sato, JJ and Kosakaie, R and Kado, K and Yamaguchi, Y}, title = {Fecal DNA Metabarcoding Analyses Imply Seasonally Opportunistic Feeding by the Japanese Marten, Martes melampus (Mammalia: Carnivora), in Southwestern Honshu Island, Japan.}, journal = {Zoological science}, volume = {42}, number = {4}, pages = {}, doi = {10.2108/zs250005}, pmid = {40908939}, issn = {0289-0003}, mesh = {Animals ; *Mustelidae/physiology ; *DNA Barcoding, Taxonomic ; *Feces/chemistry ; Japan ; Seasons ; *Feeding Behavior/physiology ; Diet/veterinary ; }, abstract = {An understanding of the food web in forest ecosystems is essential to ensuring that society lives in harmony with nature; however, this can be challenging in areas mainly composed of forest environments, such as in the Japanese Archipelago. Examining fecal samples collected from the forest edge can aid in determining the ecological roles of host species. In this study, a DNA barcoding method using original primers was applied to identify the carnivoran host species from fecal samples. DNA metabarcoding using ITS2 and COI markers was then conducted to elucidate the plant and invertebrate diets of the Japanese marten, Martes melampus (Carnivora, Mustelidae). The dietary analyses revealed that M. melampus consumed a diverse array of plants and animals. Most of the consumed plant species were fresh fruits, reflecting the fruiting season of the detected plants. This implies a role for M. melampus in seed dispersal and thus in forest maintenance. Considering the activity seasons, we also found that various adult-stage insects (beetles, cicadas, sphinx moths, and grasshoppers) contributed to the marten's diet, together with invertebrates (earthworms, etc.), which are easily digested and therefore difficult to detect through traditional methods. Although the COI marker used was designed for invertebrate species, one bird species, the brown-eared bulbul, Microscelis amaurotis, was found to make up a small part of the winter to early spring diet. These results show that, while M. melampus mainly consumes seasonal fruits, it can adapt its diet in response to environmental changes, such as by including invertebrates and small vertebrates.}, }
@article {pmid40907964, year = {2025}, author = {Egizi, A and Bezhani, F and Jordan, RA and Price, DC}, title = {Parasitism of a US traveler by a nymphal Amblyomma tapirellum Dunn, 1933 (Ixodida: Ixodidae) and review of exotic tick interceptions on humans in the United States.}, journal = {Journal of medical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jme/tjaf109}, pmid = {40907964}, issn = {1938-2928}, support = {NE2443//USDA-NIFA Multistate/ ; }, abstract = {A resident of Monmouth County, New Jersey, United States removed an engorged nymphal tick after returning from travel to Costa Rica. The tick was identified by cox1 barcoding as Amblyomma tapirellum Dunn, 1933, a Central American species whose immature stages are undescribed. This species is associated with wet, tropical forests, and most host records come from Baird's tapirs (Tapirus bairdii), though feeding on other mammalian orders and on humans has been observed. To date, no human pathogens have been detected in A. tapirellum, although very few specimens have been tested. The A. tapirellum reported here was screened for Rickettsia spp. via qPCR and additionally for bacterial pathogens via 16S amplicon sequencing, and no pathogens were detected. However, we report the presence of a Coxiella-like endosymbiont, common among -Amblyomma spp. We also briefly review 29 published records comprising 14 exotic hard tick species removed from US travelers returning from abroad, most commonly Amblyomma spp. from Africa. Due to the near-worldwide distribution of ticks and tick-borne disease as well as the growing frequency of international tourism, travelers are urged to prevent tick bites and physicians are encouraged to be mindful not only of native tick-borne diseases but potential exposure to exotic tick-borne diseases. There is also a need to improve identification resources for ixodids and for existing resources to be made more accessible.}, }
@article {pmid40906971, year = {2025}, author = {Papadimitriou, M and Ahn, S and Diamond, BT and Lee, H and McIntyre, JB and Truger, M and Durante, MA and Ziccheddu, B and Osz, K and Landgren, O and Rasche, L and Bahlis, NJ and Neri, P and Maura, F}, title = {Timing genomic antigen loss in multiple myeloma treated with T-cell redirecting immunotherapies.}, journal = {Blood cancer discovery}, volume = {}, number = {}, pages = {}, doi = {10.1158/2643-3230.BCD-25-0005}, pmid = {40906971}, issn = {2643-3249}, abstract = {Genomic antigen loss is a recurring mechanism of resistance to chimeric antigen receptor T-cell (CAR-T) and T-cell engagers (TCE) in relapsed/refractory multiple myeloma (RRMM). Yet, it remains unclear whether these events are acquired under treatment or merely selected from pre-existing, undetectable clones. By leveraging chemotherapy mutational signatures as temporal barcodes within whole genome sequencing data, we could time genomic antigen escape in 4 out of 11 RRMM patients. In all cases, the biallelic loss was driven by genomic events acquired after exposure to BCMA- and GPRC5D-targeted CAR-T/TCE, and not present at baseline. Longitudinal digital PCR analysis corroborated that resistance mutations were undetectable at therapy initiation but emerged preceding relapse. Among 752 newly diagnosed patients only 2.7% and 9% had monoallelic inactivation of TNFRSF17 and GPRC5D, respectively, with no biallelic loss. Our findings suggest limited utility of mutational screening prior to CAR-T/TCE, while underscoring the importance of dynamic surveillance during therapy.}, }
@article {pmid40905664, year = {2025}, author = {Thielecke, L and Nattamai, K and Hassan, A and Glauche, I and Geiger, H and Cornils, K}, title = {The impact of donor and recipient age on post-transplantation clonality in murine haematopoiesis.}, journal = {Stem cells (Dayton, Ohio)}, volume = {}, number = {}, pages = {}, doi = {10.1093/stmcls/sxaf059}, pmid = {40905664}, issn = {1549-4918}, abstract = {The sustained production of blood and immune cells is driven by a pool of hematopoietic stem cells (HSCs) and their offspring. Due to the intrinsic heterogeneity of HSCs, the composition of emergent clones changes over time, leading to a reduced clonality in aging mice and humans. Theoretical analyses suggest that clonal conversion rates and clonal complexity depend not only on HSC heterogeneity, but also on additional stress conditions. These insights are particularly relevant in the context of stem cell transplantations, which still remain the only curative option for many hematologic diseases, increasingly considered viable for elderly individuals. However, age-related clonal changes post-transplantation are not well understood. To address this, we conducted a barcode-based assessment of clonality to investigate post-transplantation changes in both homo- and hetero-chronic settings, combined with low- and high-intensity pre-conditioned recipients. A robust and polyclonal engraftment was observed across all groups, but with distinct differences in barcode diversity. In particular, transplanted aged HSCs showed no changes in clonality, regardless of recipient age or pre-conditioning. Young HSCs transplanted into severely pre-conditioned old hosts as well as under reduced pre-conditioning, allowed for full lymphoid reconstitution, but showed substantial differences in clonality. Also, myeloid lineage bias, a hallmark of aged HSCs, was confirmed at a clonal level across all experimental groups. Overall, we found that aged HSCs generally maintain clonal diversity similar to young HSCs, but notable differences emerge under hetero-chronic conditions and varying pre-conditioning regimens. These findings challenge current paradigms and underscore the complex interactions between aging and transplantation conditions.}, }
@article {pmid40905625, year = {2025}, author = {Trull, A and Worthey, EA and Ianov, L}, title = {Scnanoseq: an nf-core pipeline for oxford nanopore single-cell RNA-sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf487}, pmid = {40905625}, issn = {1367-4811}, abstract = {MOTIVATION: Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge.<br><br>RESULTS: Here we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and transcript-level quantification. The scnanoseq pipeline is implemented using Nextflow and is built upon the nf-core framework, enabling portability across computational environments, scalability and reproducibility of results across pipeline runs. The nf-core/scnanoseq workflow follows best practices for analyzing single-cell and single-nuclei data, performing barcode detection and correction, genome and transcriptome read alignment, unique molecular identifier deduplication, gene and transcript quantification, and extensive quality control reporting.<br><br>AVAILABILITY: The source code, and detailed documentation are freely available at https://github.com/nf-core/scnanoseq and https://nf-co.re/scnanoseq under the MIT License. Documentation for the version of nf-core/scnanoseq used for this paper, including default parameters and descriptions of output files are available at https://nf-co.re/scnanoseq/1.1.0.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40904667, year = {2025}, author = {Goren, M and Feldstein-Farkash, T}, title = {A new Pseudophoxinus species (Teleostei, Cypriniformes, Leuciscidae) from the upper Jordan River basin (Israel) with comments on the status of a few other congeneric species.}, journal = {ZooKeys}, volume = {1249}, number = {}, pages = {303-315}, pmid = {40904667}, issn = {1313-2989}, abstract = {A taxonomic reassessment of Pseudophoxinus populations in the upper Jordan River basin has revealed that specimens previously identified as Pseudophoxinus kervillei actually represent an undescribed species. In addition, earlier taxonomic revisions have shown that P. kervillei is a junior synonym of P. libani and should no longer be regarded as a valid species. In this study, we formally describe the newly recognized species as Pseudophoxinus galilaeus sp. nov. Pseudophoxinus galilaeus sp. nov. is characterized by 39-44 scales along the mid-lateral row, 13-17 pored lateral line scales, and 20-23 predorsal scales. It has 4-5 gill rakers on the lower arch of the first gill, with two being notably short. The species possesses 33-34 vertebrae; its dorsal fin originates at vertebrae 12 or 13, and its anal fin commonly originates at vertebra 19, occasionally extending to vertebra 20 or 21. Pseudophoxinus galilaeus sp. nov. inhabits ponds, lakes, and rivers with slow to moderate currents. A unique DNA barcoding signature (mtDNA COI) revealed that it differs from any other previously bar-coded Pseudophoxinus species. In phylogenetic analyses, it clustered with the Pseudophoxinus species from neighboring countries in the Levant region, suggesting a common ancestor for these species. This analysis shows that sequences of P. kervillei from Turkey differ from P. libani from Lebanon and Syria. Further morphological examination is needed to determine the status of the species.}, }
@article {pmid40902006, year = {2025}, author = {Zhou, X and Feng, R and Ding, N and Cao, W and Liu, Y and Zhou, S and Deng, Y}, title = {Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.}, journal = {Nucleic acids research}, volume = {53}, number = {16}, pages = {}, doi = {10.1093/nar/gkaf863}, pmid = {40902006}, issn = {1362-4962}, support = {2024YFA0918000//National Key R&amp;D Program of China/ ; BK20220089//Distinguished Young Scholars of Jiangsu Province/ ; BE2022322//Key R&amp;D Project of Jiangsu Province/ ; 22378170//National Natural Science Foundation of China/ ; 22478156//National Natural Science Foundation of China/ ; 2022SP-T16-B//"Pilot Plan" Internet of Things Special Project/ ; }, mesh = {*Promoter Regions, Genetic ; *Escherichia coli/genetics ; *Deep Learning ; Gene Expression Regulation, Bacterial ; Gene Library ; }, abstract = {Core promoters are essential regulatory elements that control transcription initiation, but accurately predicting and designing their strength remains challenging due to complex sequence-function relationships and the limited generalizability of existing AI-based approaches. To address this, we developed a modular platform integrating rational library design, predictive modelling, and generative optimization into a closed-loop workflow for end-to-end core promoter engineering. Conserved and spacer region of core promoters exert distinct effects on transcriptional strength, with the former driving large-scale variation and the latter enabling finer gradation. Based on this insight, Mutation-Barcoding-Reverse Sequencing approach was used and constructed a synthetic promoter library comprising 112 955 variants with minimal redundancy and a 16 226-fold expression range. A Transformer-based model trained on this dataset achieved a Pearson correlation of 0.87 with experimentally measured promoter strengths. When combined with a conditional diffusion model, the system enabled de novo generation of promoter sequences with defined strengths, achieving a design-to-measurement correlation of 0.95 and maintaining high accuracy (R = 0.93) across varied sequence contexts. The designed promoters consistently preserved their intended strength gradients, demonstrating robust plug-and-play functionality. This work establishes a scalable and extensible platform (www.yudenglab.com) for deep learning-guided programmable design of Escherichia coli core promoters, enabling precise transcriptional control.}, }
@article {pmid40901798, year = {2025}, author = {Bertrand, G and Levallois, O and Santesteban, CG and Nogues, N and Renac, V}, title = {Non-invasive fetal HPA genotyping by UMI-NGS: a robust method for antenatal diagnosis including 48 fetal DNA markers.}, journal = {Blood transfusion = Trasfusione del sangue}, volume = {}, number = {}, pages = {}, doi = {10.2450/BloodTransfus.1070}, pmid = {40901798}, issn = {2385-2070}, abstract = {BACKGROUND: Non-invasive fetal HPA typing is a valuable tool to identify the pregnancies at risk of fetal and neonatal alloimmune thrombocytopenia (FNAIT). Different approaches have been developed, mainly based on real-time PCR and droplet digital-PCR. Those methods have a limited ability to multiplex and require replicates due to the contamination risk. Moreover, in order to exclude false-negative results caused by insufficient cell-free fetal DNA, the presence of fetal DNA is usually assessed with a single epigenetic marker whereas large single-nucleotide variant (SNV) panels are now available to more accurately measure the sample's fetal fraction.<br><br>MATERIALS AND METHODS: We developed an innovative method for the simultaneous genotyping of HPA-1, -2, -3, -4, -5, -6, -9 and 15, in combination with a panel of 48 SNV markers, based on cell-free DNA target-enrichment with specific probes. An improved accuracy using NGS sequencing was reached with the Unique Molecular Identifiers (UMIs); these molecular barcodes are short sequences used to uniquely tag each molecule in a sample library.<br><br>RESULTS: 81 plasma samples were collected from French and Spanish pregnant women, from 10 to 40 weeks of gestation ([wg]; 4 samples <12 wg; 38 samples 13-24 wg; 39 samples >24 wg). The panel of 48 SNVs allowed a precise quantification of fetal DNA (range: 1.1%-16.1%). All samples but one gave concordant results with the confirmed HPA genotypes. One sample was discordant for HPA-2 and HPA-3, due to false negative cffDNA results for these two loci. However, a low amount of fetal fraction in that sample was effectively alerted by the SNV markers results.<br><br>DISCUSSION: In our experience, 16 samples can be simultaneously sequenced and analyzed in a 72 hours assay. UMIs NGS sequencing of HPA and SNV markers constitutes a robust and sensitive method for non-invasive fetal HPA genotyping.}, }
@article {pmid40901553, year = {2025}, author = {Wei, F and Lin, Y and Tang, D and Liang, Y and Qin, S}, title = {Comparative analysis of complete chloroplast genomes of Flemingia prostrata and Flemingia macrophylla, two commonly used medicinal plants in southern China.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1591427}, doi = {10.3389/fpls.2025.1591427}, pmid = {40901553}, issn = {1664-462X}, abstract = {Flemingia prostrata and Flemingia macrophylla, belonging to the genus Flemingia, are ethnomedicinal plants that contain valuable medicinal and nutritional compounds. However, their medicinal materials are frequently confused in the Chinese medicinal materials market. Moreover, molecular genomic resources for this genus remain limited, which hinders phylogenetic studies. In this study, the complete chloroplast (cp) genomes of F. macrophylla and F. prostrata were sequenced to enable genome comparison and phylogenetic analysis. Both cp genomes exhibited typical quadripartite structures, with genome sizes of 152,937 bp for F. macrophylla and 153,033 bp for F. prostrata. Each genome consisted of a large single copy (LSC) region (83,594 and 83,701 bp, respectively), a small single copy (SSC) region (17,773 and 17,776 bp, respectively), and two inverted repeats (IR) regions (50,570 and 51,556 bp, respectively). A total of 129 genes were annotated in each cp genome, including 8 ribosomal RNAs, 83 protein-coding genes, and 37 transfer RNAs. Comparative analysis revealed that although the overall genome structure, codon usage bias, simple sequence repeats (SSRs), and dispersed repetitive sequences were relatively conserved between the two cp genomes, certain genomic variations were present. Specifically, 286 SNPs and 104 indels were identified, and psaJ-rps18 showed the highest variability and could serve as potential DNA barcode regions. Furthermore, phylogenetic analysis supported a close evolutionary relationship between the genus Flemingia and Cajanus. Divergence time estimation suggested that F. macrophylla and F. prostrata diverged approximately 0.26 million years ago (Mya). Finally, we successfully distinguished the two species using SSR markers. This study lays the foundation for enriching the molecular data and phylogenetic insights of this genus, as well as for the safe application of its medicinal materials.}, }
@article {pmid40900687, year = {2024}, author = {Chou, TK and Huang, WC and Jhuang, WC and Liao, TY}, title = {Checklist and DNA Barcoding of the Scorpaenidae (Teleostei: Scorpaeniformes) in Taiwan.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e37}, pmid = {40900687}, issn = {1810-522X}, abstract = {Species of the family Scorpaenidae are easily misidentified due to their similar appearances, a result of camouflaging to their surroundings. In recent years, many species from this family have been described, and generic placements of some species have been revised. Previously, there were 80 species belonging to 29 genera of the Scorpaenidae recorded in Taiwanese waters. However, their taxonomy has not been revised for decades. It is necessary to update the checklist of the Scorpaenidae occurring in Taiwanese waters based on updated morphological and molecular data. In the present study, we revised the Taiwanese scorpaenids based on 296 specimens and updated the checklist, amounting to a total of 85 species of 29 genera, of which Sebastapistes mauritiana (Cuvier) is a new record, and three species from the genera Phenacoscorpius, Scorpaenopsis, and Sebastapistes are unable to be identified to any species. Using molecular analysis, we conducted the first comprehensive DNA barcoding study of the Scorpaenidae from Taiwanese waters based on a partial cytochrome c oxidase I (COI) gene of 655 bps. A total of 118 COI sequences were generated from voucher specimens of 66 species (28 genera) identified based on morphological characters. The COI sequences of Parascorpaena maculipinnis, Scorpaena pepo, and Scorpaenopsis orientalis are new to online databases. According to the Kimura-2 Parameter (K2P) genetic distance, the mean interspecific variation (15.61%) was distinctly greater than the mean intraspecific variation (0.22%), suggesting a barcoding gap. The maximum likelihood tree showed that all lineages were supported by high bootstrap values.}, }
@article {pmid40898047, year = {2025}, author = {Hu, Y and Wang, S and Xu, Z and Yan, S and Ali, M and Li, Z and Shao, J}, title = {Chloroplast genome comparison and taxonomic reassessment of Polygonatum sensu Lato (Asparagaceae): implications for molecular marker development in traditional medicinal plants.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {796}, pmid = {40898047}, issn = {1471-2164}, support = {32070370//National Natural Science Foundation of China/ ; }, abstract = {The Polygonati Rhizoma have generated significant market attention for their medicinal and culinary applications. However, morphological similarities and ambiguous species boundaries complicate the identification of genera and species, thereby impeding product development and utilization within Polygonatum sensu lato. Despite the widespread application of the chloroplast genome for taxonomic boundary revisions for Polygonatum s.l., a critical gap persist regarding their genomic applicability and the lack of standardized pipelines for developing species-specific molecular markers capable of rapid discrimination among species. This study aims to assess the effectiveness of chloroplast genomes in clarifying the current taxonomic status of the genera and species of Polygonatum s.l., and develop a reliable process for rapid identification of designated species from other species. A total of 21 chloroplast genomes were sequenced and assembled, and subsequent analyses included phylogenetic inference, multiple molecular species delimitation methods, and an automated screening framework were employed for subsequent analysis. Comparative analyses revealed relatively conserved chloroplast genomes, with notable variation limited primarily to the length of IR and LSC regions. By integrating multiple delimitation methods, the chloroplast genome validated 82.46% of the current classifications of Polygonatum s.l., demonstrating strong support (90.63%) for species represented by multiple sequences, yet only moderate support (70%) for those with single-sequence representation. Additionally, this study established and validated a scalable molecular marker development framework, spanning from identification of species-specific SNPs/InDels to the design of high-resolution molecular markers, illustrated through case studies involving Heteropolygonatum and three medicinally significant Polygonatum species.}, }
@article {pmid40897784, year = {2025}, author = {Fantozzi, D and Sferra, G and Trupiano, D and Scippa, GS}, title = {Design and application of species-specific primers to Quercus cerris roots' identification in urban forests.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32298}, pmid = {40897784}, issn = {2045-2322}, support = {Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; }, abstract = {Accurate species identification, the first crucial step for effective root studies, is a time-demanding, experience-based and error-prone process. Molecular methods are therefore needed to ensure this process, especially in urban settings where root sampling is challenging. Here, we developed a novel molecular method for root identification in complex environments. Specifically, we focused on detecting Quercus cerris-a species common in European cities and non-urban areas and used in afforestation-from bulk root samples, including those collected non-invasively. To achieve this, we conducted the first comprehensive analysis of candidate DNA regions to discriminate among Quercus species. Among the candidate sequences tested, ITS and ITS2 showed the highest discriminatory power compared to commonly used barcodes such as matK, psbA-trnH, rbcL, rpoC1, trnL-trnF. Based on this results, we designed specific primers to target ITS and ITS2 and we developed a PCR-based protocol capable of reliability and specificity detecting Q. cerris within mixed Quercus root samples. This method was then successfully applied to root bulk samples collected via excavation and non-invasive soil coring in the urban area of Campobasso (central Italy), with results validated through traditional identification techniques. The outcome is a novel, rapid, low-cost, and non-invasive molecular approach for monitoring Q. cerris roots. More broadly, this tool enable in situ root identification and mapping which support the study of root functioning and dynamics in ecosystems and is particularly valuable in challenging urban environments.}, }
@article {pmid40895702, year = {2025}, author = {Hayashi, E and Amemiya, T and Tomita, T}, title = {Pitfalls of a Drug-Dispensing Audit Support System.}, journal = {Cureus}, volume = {17}, number = {8}, pages = {e89200}, doi = {10.7759/cureus.89200}, pmid = {40895702}, issn = {2168-8184}, abstract = {Dispensing audit support systems that authenticate pharmaceuticals via barcodes have been introduced into clinical practice to prevent dispensing errors, yet they occasionally generate false warnings, complicating clinical usage. This study sought to identify drugs prone to weight-error false warnings in the C-correct II[®] dispensing audit support system and to clarify its operational problems. We investigated the drugs that caused false weight-error warnings in the system, confirming that such errors did occur. Furthermore, the drugs causing weight errors tended to be significantly heavier than those that did not. Accurately identifying and addressing such operational issues within dispensing audit support systems will minimize the risk of dispensing errors and ultimately enhance medical safety.}, }
@article {pmid40895230, year = {2025}, author = {Mwamula, AO and Bae, CH and Kim, YS and Lee, DW}, title = {Description of a New Cryptic Rhabditid, Parasitorhabditis paraterebrana n. sp. (Nematoda: Rhabditidae), with Remarks on Two Known Species from Korea.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250027}, doi = {10.2478/jofnem-2025-0027}, pmid = {40895230}, issn = {0022-300X}, abstract = {A new cryptic species of the genus Parasitorhabditis isolated from the bark of a dead pine tree was characterized using morphological features, morphometrics, and DNA barcodes. Parasitorhabditis paraterebrana n. sp. is characterized by its stoma 20-24 μm in depth; tips of prorhabdions not bent inwards; metarhabdions with two subventral, and two subdorsal teeth; corpus longer than postcorpus; hemizonid 15.0-26.5 μm posterior to excretory pore; vulva-anus distance 21.5-31.5 μm, ca equal to or slightly less than vulval body diameter; rectum distinctly longer than anal body diameter; female tail cupola-shaped, conoid posteriorly, with an extended spike; male with slender spicules, nearly straight to minimally curved towards a nearly acute to a bluntly rounded tip; and bursa with 10 pairs of bursal rays, with a 2 + 3 + 2 + 3 typical pattern. It differs from the morphologically similar P. terebrana by the non-bent tips of prorhabdions, the corpus being longer than postcorpus, the bursal rays' pattern, and a more cupola-shaped tail in female and DNA barcodes. The DNA phylogenies using the 18S rRNA, 28S rRNA and COI gene markers showed well-supported sister relations of Parasitorhabditis paraterebrana n. sp. with P. terebrana and P. obtusa.}, }
@article {pmid40894274, year = {2025}, author = {Wu, C and Tao, Z and Wang, Y and Luo, Y}, title = {The revision and phylogenetic position of Hippasa bifasciata Buchar, 1997 (Araneae, Lycosidae).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e166495}, doi = {10.3897/BDJ.13.e166495}, pmid = {40894274}, issn = {1314-2828}, abstract = {BACKGROUND: Hogna Simon, 1885 is the second-largest genus in the family Lycosidae after Pardosa C. L. Koch, 1847 (517 species), including 232 species so far. This genus has a cosmopolitan distribution spanning multiple continents. However, only four species (Hogna rubetra (Schenkel, 1963), Hogna trunca Yin, Bao &amp; Zhang, 1996, Hogna jiafui Peng, Yin, Zhang &amp; Kim, 1997 and Hogna arborea Lo, Wei &amp; Cheng, 2023) have been recorded in China.<br><br>NEW INFORMATION: A new combination, Hogna bifasciata (Buchar, 1997), comb. nov. (from Yunnan and Sichuan Provinces in south-western China), is proposed with both morphological and molecular evidence. Detailed morphological descriptions, photographs, scanning electron micrographs and a distribution map are provided. This species is distinguished from congeners by the unique structure of the female epigyne and its somatic pattern. Molecular phylogenetic analyses suggest H. bifasciata (Buchar, 1997) and all analysed Hogna species cluster together within the subfamily Lycosinae and the species is sister to the group, including Hogna frondicola Emerton, 1885, Hogna carolinensis Walckenaer, 1805 and Hogna crispipes L. Koch, 1877.}, }
@article {pmid40892906, year = {2025}, author = {Holmes, KE and Ferreri, LM and Elie, B and Ganti, K and Lee, CY and VanInsberghe, D and Lowen, AC}, title = {Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.}, journal = {PLoS biology}, volume = {23}, number = {9}, pages = {e3003352}, doi = {10.1371/journal.pbio.3003352}, pmid = {40892906}, issn = {1545-7885}, abstract = {For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Since genetic diversity represents adaptive potential, such losses of diversity are thought to limit the opportunity for viral populations to undergo antigenic change and other adaptive processes. Thus, a detailed picture of evolutionary dynamics during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. To advance this understanding, we used a barcoded virus library and a guinea pig model of transmission to decipher where in the transmission process influenza A virus populations lose diversity. In inoculated guinea pigs, we show that a high level of viral barcode diversity is maintained. Within-host continuity in the barcodes detected across time furthermore indicates that stochastic effects are not pronounced within the inoculated hosts. Importantly, in both aerosol-exposed and direct contact animals, we observed many barcodes at the earliest time point(s) positive for infectious virus, indicating robust transfer of diversity through the environment. This high viral diversity is short-lived, however, with a sharp decline seen 1-2 days after initiation of infection. Although major losses of diversity at transmission are well described for influenza A virus, our data indicate that events that occur following viral transfer and during the earliest stages of natural infection have a central role in this process. This finding suggests that host factors, such as immune effectors, may have greater opportunity to impose selection during influenza A virus transmission than previously recognized.}, }
@article {pmid40892738, year = {2025}, author = {Peiris, MALM and Nanayakkara, D and Silva, C and Abeysundara, SP and Wijesinghe, P}, title = {Barcode high-resolution melting (Bar-HRM) analysis to authenticate true cinnamon (Cinnamomum verum) from its adulterants and contaminants.}, journal = {PloS one}, volume = {20}, number = {9}, pages = {e0328808}, pmid = {40892738}, issn = {1932-6203}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Cinnamomum zeylanicum/genetics/classification ; DNA, Plant/genetics ; *Food Contamination/analysis ; *Cinnamomum/genetics ; }, abstract = {Sri Lankan cinnamon, widely known as true cinnamon (Cinnamomum verum), is a world-renowned commodity. With the high market demand, many incidents have reported adulteration of true cinnamon with other cinnamon species such as Cinnamomum aromaticum, Cinnamomum burmanni, and Cinnamomum loureiroi. Moreover, the contamination of cinnamon products with fungi (Aspergillus flavus) has also significantly negatively impacted the cinnamon export market. Morphological and chemical detection of adulterations has limitations, benchmarking the necessity for precise and effective new detection methods. The current study reports gene-specific novel molecular markers that can be used in Barcode High-Resolution Melting (Bar-HRM) analysis to distinguish C. verum from other substitutes. Six barcode regions (rbcL, trnH-psbA, matK, ITS2, trnL, trnL-trnF) were analyzed. The results demonstrate that trnH-psbA can effectively discriminate all selected cinnamon species from one another. Novel markers were designed to target the diagnostic nucleotide variations found within the designated barcode regions. Commercial cinnamon products and authentic samples of C. verum were used to validate the assay, and the DNA extraction protocol was optimized to ensure the acquisition of high-quality DNA. Bar-HRM was performed with the novel markers, and the four major cinnamon species in the international market were successfully distinguished. The spiked-in A. flavus DNA was also detected in a cinnamon admixture. Hence, these Bar-HRM conditions with the novel gene-specific markers can serve as an economical, efficient, and promising assay to detect the authenticity and purity of cinnamon samples.}, }
@article {pmid40890382, year = {2025}, author = {Goulpeau, A and Hedde, M and Ganault, P and Lapied, E and Maggia, ME and Marcon, E and Decaëns, T}, title = {Biotic interactions and environmental filtering both determine earthworm alpha and beta diversity in tropical rainforests.}, journal = {Oecologia}, volume = {207}, number = {9}, pages = {151}, pmid = {40890382}, issn = {1432-1939}, support = {ANR-10-LABX-25-01//ANR/ ; ANR-10-LABX-41//ANR/ ; Our Planet Reviewed//Mus&#xe9;um National d'Histoire Naturelle/ ; CFREF-2015-00004//Canadian Center for DNA Barcoding/ ; BC-Wormbank APEGE 2013//CNRS/ ; }, mesh = {Animals ; *Oligochaeta ; *Biodiversity ; *Rainforest ; Ecosystem ; French Guiana ; Soil ; Tropical Climate ; }, abstract = {Understanding the relative importance of biotic interactions, multiple environmental drivers, and neutral processes in shaping community diversity and composition is a central question for both theoretical and applied ecology. We analysed a dataset describing 125 earthworm communities sampled in 10 localities in French Guiana. DNA barcodes were used to delimit operational taxonomic units (OTUs) that we considered as species surrogates to avoid the taxonomic deficit and calculate community-scale species richness and pair-wise Sørensen beta-diversity. We used log-ratio and generalised linear models to highlight the effects of biotic interactions and environment as drivers of alpha diversity, and generalised dissimilarity models to figure out the relative contribution of space and environment to beta-diversity at different spatial extents. Community-scale alpha diversity was mainly explained by habitat filtering (soil texture) and interspecific competition that limit the number of locally co-existing species. Beta diversity between pairs of communities was mainly explained by distance when comparing communities in similar habitats, by topography and available soil phosphorus when comparing communities in different habitats, and by distance, elevation and climate when comparing all possible pairs of communities. While community composition is determined locally by neutral processes and environmental filtering, biogeographic processes linked to dispersal limitation and adaptation to local environment are the most influential on a regional scale. This highlights the complex interplay of dispersal limitation, biotic interactions and environmental filtering during the process of community assembly.}, }
@article {pmid40890121, year = {2025}, author = {Gao, M and Barile, M and Chabra, S and Haltalli, M and Calderbank, EF and Chao, Y and Zheng, W and Wilson, NK and Laurenti, E and Göttgens, B and Huang, Y}, title = {CLADES: a hybrid NeuralODE-Gillespie approach for unveiling clonal cell fate and differentiation dynamics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {8174}, pmid = {40890121}, issn = {2041-1723}, support = {62222217//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Cell Differentiation/genetics ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Clone Cells/cytology ; Algorithms ; Animals ; Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Mice ; Stochastic Processes ; }, abstract = {Recent lineage tracing based single-cell techniques (LT-scSeq), e.g., the Lineage And RNA RecoverY (LARRY) barcoding system, have enabled clonally resolved interpretation of differentiation trajectories. However, the heterogeneity of clone-specific kinetics remains understudied, both quantitatively and in terms of interpretability, thus limiting the power of barcoding systems to unravel how heterogeneous stem cell clones drive the overall cell population dynamics. Here, we present CLADES, a NeuralODE-based framework to faithfully estimate the clone and population-specific kinetics from both newly generated and publicly available LARRY LT-scSeq data. By incorporating a stochastic simulation algorithm (SSA) and differential expression gene (DEGs) analysis, CLADES yields the summary of cell division dynamics across differentiation time-courses and reconstructs the lineage tree of the progenitor cells in a quantitative way. Moreover, clone-level behaviors can be grouped into characteristic types by pooling individual clones into meta-clones for analyses at various resolutions. Finally, we show that meta-clone specific cellular behaviors identified by CLADES originate from hematopoietic stem and progenitor cells in distinct transcriptional states. In conclusion, we report a scalable approach to robustly quantify clone-specific differentiation kinetics of cellular populations for time-series systems with static barcoding designs.}, }
@article {pmid40887508, year = {2025}, author = {Wongsuwan, P and Tansawat, R and Khaoiam, P and Rattanakrajang, P and Phokham, B and Uthairangsee, A and Picheansoonthon, C and Sukrong, S}, title = {Integrating untargeted volatile metabolomics and molecular evidence supporting chemotaxonomy in Kaempferia species for more effective identification.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32020}, pmid = {40887508}, issn = {2045-2322}, support = {GCUGR1125671060D//The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund)/ ; GCUGR1125671060D//The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund)/ ; }, mesh = {*Metabolomics/methods ; *Zingiberaceae/metabolism/classification/genetics/chemistry ; Gas Chromatography-Mass Spectrometry ; Phylogeny ; *Oils, Volatile ; *Volatile Organic Compounds/metabolism/analysis ; DNA Barcoding, Taxonomic ; }, abstract = {Kaempferia L., a medicinal genus of Zingiberaceae family, is widely distributed from India to Southeast Asia and is rich in terpenoids, flavonoids, phenolics, and volatile oils. Recently, it has gained attention for its diverse biological activities, including antioxidant, anticancer, analgesic, anti-inflammatory, and anti-tuberculosis effects. However, several Kaempferia species complexes exhibit similar morphological characteristics, making identification and classification challenging. This study integrates morphology, molecular phylogeny, and phytochemistry to identify and distinguish Kaempferia species. Phylogenetic relationships were reconstructed using four DNA barcoding markers: one nuclear region (ITS) and three chloroplast markers (matK, rbcL, and psbA-trnH). Untargeted metabolomic analysis using SPME-GC-MS, combined with multivariate statistical analyses, was employed to resolve species relationships and display volatile profiles among 15 Kaempferia species from two subgenera. A total of 217 metabolites were identified by the SPME-GC-MS technique. Variable Importance in Projection (VIP ≥ 1.5) analysis indicated 30 key metabolites, primarily sesquiterpenes, as specific chemotaxonomic markers. This study provides a comprehensive chemical profile of Kaempferia species and highlights metabolomic differences among them. Our findings emphasize the importance of integrating morphological, molecular, and phytochemical approaches for precise identification of closely related species, particularly within Kaempferia. This chemotaxonomic research also provides further applications for species authentication in pharmaceuticals and medicine.}, }
@article {pmid40887478, year = {2025}, author = {Luce, JJ and Reardon-Lochbaum, CA and Cadinu, P and Xu, RJ and Aceves-Salvador, J and Semizoglou, E and Wong, B and Lopez, I and Cantor, AB and Renthal, W and Moffitt, JR}, title = {Protocol optimization improves the performance of multiplexed RNA imaging.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {32030}, pmid = {40887478}, issn = {2045-2322}, support = {5T32HL007574/HL/NHLBI NIH HHS/United States ; R01HL159106/HL/NHLBI NIH HHS/United States ; R01HL159106/HL/NHLBI NIH HHS/United States ; U19NS130617/NS/NINDS NIH HHS/United States ; U19NS130617/NS/NINDS NIH HHS/United States ; R01GM143277/GM/NIGMS NIH HHS/United States ; }, mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA/genetics/analysis ; Humans ; Animals ; *Single Molecule Imaging/methods ; }, abstract = {Spatial transcriptomics has emerged as a powerful tool to define the cellular structure of diverse tissues. One such method is multiplexed error robust fluorescence in situ hybridization (MERFISH). MERFISH identifies RNAs with error tolerant optical barcodes generated through sequential rounds of single-molecule fluorescence in situ hybridization (smFISH). MERFISH performance depends on a variety of protocol choices, yet their effect on performance has yet to be systematically examined. Here we explore a variety of properties to identify optimal choices for probe design, hybridization, buffer storage, and buffer composition. In each case, we introduce protocol modifications that can improve performance, and we show that, collectively, these modified protocols can improve MERFISH quality in both cell culture and tissue samples. As RNA FISH-based methods are used in many different contexts, we anticipate that the optimization experiments we present here may provide empirical design guidance for a broad range of methods.}, }
@article {pmid40883593, year = {2025}, author = {Nama, S and Shanmughan, A and Akter, S and K, AW and Bhushan, S and Ramteke, K and Deshmukhe, G and Jaiswar, AK and Kumar, AP and Nayak, BB}, title = {DNA barcoding reveals the temporal variation of ichthyoplankton assemblages and their relationship with environmental variables in a tropical mangrove estuary.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {9}, pages = {1060}, doi = {10.1007/s10661-025-14473-w}, pmid = {40883593}, issn = {1573-2959}, mesh = {*Estuaries ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Environmental Monitoring ; Animals ; Seasons ; *Wetlands ; Plankton ; *Zooplankton/classification/genetics ; Fishes/classification ; }, abstract = {Seasonal ichthyoplankton dynamics and their relationship with environmental parameters were studied in the Karanja mangrove estuary from January 2022 to March 2023 to determine ichthyoplankton biodiversity. Twenty-four ichthyoplankton species from 16 families and 3 orders were identified using morphological characteristics and DNA barcoding methods. The most dominant family was Mugilidae, contributing 20% of the total ichthyoplankton assemblage, followed by Engraulidae (12%). The maximum abundance of ichthyoplankton was recorded during the monsoon seasons, indicating that Karanja estuary can be a spawning ground for Mugil cephalus, Osteomugil perusii, Stolephorus insularis, Thryssa hamiltonii, Escualosa thoracata, Terapon jarbua, and Dendrophysa russelii. Redundancy analysis (RDA) and biotic-environmental (BIO-ENV) analysis revealed that water temperature, salinity, dissolved oxygen, nitrate, and transparency were the prevailing environmental factors affecting seasonal variation of ichthyoplankton in the estuary. The Shannon-Wiener index (index = 2.54), Margalef index (index = 2.60), and Pielou's index (index = 0.95) indicate diverse ichthyoplankton dynamics in the estuary. This is the first report of ichthyoplankton biodiversity from the Karanja estuary using integrated taxonomy, with the first-time documentation of Tridentiger barbatus and Scombrops sp. in the region. These findings provide valuable insights into the intricate interactions between environmental factors, food plankton, and ichthyoplankton assemblages, which will be crucial for biodiversity inventories, effective management, and sustainability of resources.}, }
@article {pmid40883345, year = {2025}, author = {Shah, HK and Fathima, PA and Gupta, B and Rahi, M and Saini, P}, title = {Molecular identification of wild caught phlebotomine sand flies (Diptera, Psychodidae) by mitochondrial DNA barcoding in India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31950}, pmid = {40883345}, issn = {2045-2322}, support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; India ; Phylogeny ; *Psychodidae/genetics/classification ; Electron Transport Complex IV/genetics ; *DNA, Mitochondrial/genetics ; }, abstract = {Sand flies are medically important insects with diverse distributions and roles in pathogen transmission. Globally, over a thousand species have been documented, with Indian sand fly fauna currently comprising 71 species. Traditional morphological identification faces challenges due to specimen damage and the presence of cryptic species. This study utilizes DNA barcoding of the mitochondrial marker, cytochrome c oxidase subunit I (COI) to enhance accurate identification of Indian sand flies. A total of 10,456 sand flies, representing 31 species, were collected from 26 districts across six Indian states between 2018 and 2024. Legs from voucher specimens were used to generate ~ 720 bp COI sequences, which were analyzed phylogenetically. In total, 169 COI sequences were generated. A common 570 bp region was selected for final analysis. The gene showed an AT-rich composition with a GC content of 34.8%. Maximum likelihood phylogenetic analysis, supported by ABGD and ASAP species delimitation methods, confirmed the majority of morphological identifications. Species delimitation analyses using ABGD, ASAP, and bPTP grouped the specimens into 32, 34, and 68 clusters, respectively, with bPTP showing evidence of over splitting. Despite this, COI-based classification proved effective in delineating species boundaries and serves as a reliable tool for the DNA barcoding of sand fly species.}, }
@article {pmid40881467, year = {2025}, author = {Dadykin, IA and Pereboev, DD}, title = {Revision of Lathonurarectirostris (O.F. Müller, 1785) (Anomopoda, Macrothricidae) leads to translocation of East Asian populations to a separate species, Lathonurabekkerae sp. nov.}, journal = {ZooKeys}, volume = {1249}, number = {}, pages = {147-192}, doi = {10.3897/zookeys.1249.154922}, pmid = {40881467}, issn = {1313-2989}, abstract = {The family Macrothricidae (Branchiopoda: Anomopoda) remains one of the least studied groups of water fleas (Cladocera). One of macrothricids with an unclear phylogenetic status is Lathonura Lilljeborg, 1853 comprising a single universally accepted valid species, L.rectirostris (O.F. Müller, 1785). Despite its wide distribution in the Northern Hemisphere, no studies were conducted to prove conspecificity of L.rectirostris from different regions and properly describe its gamogenetic stages. Here, the morphological and genetic diversity of Lathonura in the Holarctic is revised. Our results show that in East Eurasia and Alaska a separate species of the genus occurs, L.bekkerae sp. nov., which differs from L.rectirostris s. str. by the posteroventral valve armature, structure of antenna I, and ephippium ornamentation. Mitochondrial DNA barcoding supports separation of L.bekkerae sp. nov. and reveals a deeply divergent clade of L.rectirostris s. l. in Canada, for which parthenogenetic females are morphologically indistinct from those of L.rectirostris s. str. Lathonura distribution fits well to the known patterns of Anomopoda biogeography. Males of Lathonura possess two additional setae at antenna II basipodite, P1 with a subdistal lobe lacking setae, P1 IDL with a hook and an additional seta, and an unmodified postabdomen. As noted in some previous studies, Lathonura likely represents a phylogenetic lineage distinct from the subfamily Macrothricinae, differing from most macrothricines by the absence of Fryer's fork at P1 inner endite anterior setae and presence of P1 accessory seta. However, the phylogenetic position of the genus and its diversity in South Eurasia, Africa, and North America requires further studies.}, }
@article {pmid40880439, year = {2025}, author = {Stein, F and Gailing, O}, title = {Identification of BOLD engine deficiencies and suggestions for improvement based on a curated Tachina (Diptera) record set.}, journal = {PloS one}, volume = {20}, number = {8}, pages = {e0331216}, doi = {10.1371/journal.pone.0331216}, pmid = {40880439}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Diptera/genetics/classification ; Algorithms ; }, abstract = {The increasing number of Barcode of Life Database (BOLD) records per species and genus leads to contradictory species assignments within Barcode Index Numbers (BINs), serving as identifiers for the BOLD ID engine. To examine these issues, we analyzed a dataset comprising original and curated BOLD records for the genus Tachina (Insecta: Tachinidae), based on a previous publication. This dataset included both published and private records. We were able to assess the performance of the BOLD engine's species determination algorithm, Refined Single Linkage (RESL), and compare it to Assemble Species by Automatic Partitioning (ASAP). Additionally, we investigated the usage of BINs by the BOLD v4 ID engine. Our analysis confirmed that BOLD queries primarily rely on BINs for species identification, although some cases deviated from this pattern, resulting in species matches inconsistent with the assigned BIN species. ASAP was found to be superior to RESL due to RESL's adherence to the concept of the DNA barcoding gap. Moreover, we found that taxonomic misassignments, inconsistencies in BIN formation, and missing metadata also contribute significantly to unreliable identifications. These problems appear to stem from both algorithmic limitations and deficiencies in submission and post-submission processes. Moreover, we noted that the default mode of the BOLD v4 ID engine integrates both private and published data, leading to public records based solely on COI-based identifications. However, this issue may now be mitigated, as the BOLD v5 ID engine default mode exclusively employs published data. To enhance BOLD's reliability, we propose improvements to submission and post-submission processes. Without such amendments, the accumulation of contradictory species assignments within BINs will continue to rise and the reliability of specimen identification by BOLD will decrease.}, }
@article {pmid40877266, year = {2025}, author = {Le, TTM and Jin, L and Wang, RJ and Deng, YF and Yan, HF and Ge, XJ}, title = {A DNA barcode reference library of native seed plants in the Guangdong-Hong Kong-Macao Greater Bay Area.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1505}, pmid = {40877266}, issn = {2052-4463}, mesh = {*DNA Barcoding, Taxonomic ; China ; *Seeds/genetics ; Biodiversity ; *Plants/genetics/classification ; Ecosystem ; }, abstract = {The Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is a critical region in the Pearl River Delta along the South China coast and has a remarkably diverse seed plant species. However, factors such as rapid urbanization and climate change are increasingly impacting the resilience of the Greater Bay Area's ecosystems. While morphology identification has many drawbacks such as slow process, incorrect identifications, and unreliable for distinguishing species at the growth stage; DNA barcoding has become a valuable tool in plant taxonomy by effectively overcoming many limitations of traditional methods. In this study, we constructed a comprehensive DNA barcoding database for native seed plants in the GBA using three barcodes (matK, rbcL, and ITS2). A total of 2864 native species from 1117 genera and 192 families were represented, of which 695 individuals from 516 species that were newly generated. This study enhances sustainable management and accurate identification of species, facilitates research on plant evolution and ecology, and supporting biodiversity monitoring and conservation efforts within the Greater Bay Area.}, }
@article {pmid40875882, year = {2025}, author = {Chen, A and Lan, F and Ding, Y and Tian, R and Zheng, W and Wu, Q and Zhang, P and Fang, X and Yang, C}, title = {In Situ MicroRNA Profiling of Single Tumor Extracellular Vesicles for Precise Prostate Cancer Diagnosis.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.5c02902}, pmid = {40875882}, issn = {1520-6882}, abstract = {MicroRNAs (miRNAs) packaged within extracellular vesicles (EV) exhibit remarkable stability in circulation and reflect the genetic and epigenetic characteristics of their parent cells, making them promising biomarkers for cancer diagnosis. However, the intrinsic heterogeneity of EV populations and the low abundance of miRNAs in early stage cancer pose a challenge in the sensitive detection of miRNAs in tumor-cell-derived EV (TEV). Herein, we present a one-pot strategy named miR-nSTEV for specific recognition and in situ miRNA profiling of TEV at the single-particle level for precise prostate cancer (PCa) diagnosis. Utilizing dual-surface protein recognition (CD63 and EpCAM) and orthogonal DNA barcoding-based fusion between the identified TEV and DNA-tagged liposome encapsulating variant miRNA probes (Tag-Lipo probes), our approach enables selective isolation and precise miRNA analysis of individual TEVs by nanoflow cytometry (nFCM). By integrating dual-protein sorting, DNA-directed fusion, and nFCM detection into one platform, miR-nSTEV effectively eliminates interference from free nucleic acids and RNases, significantly enhancing the detection fidelity. As a proof of concept, we profiled six PCa-associated miRNAs (miR-153, miR-183, miR-18A, miR-181, miR-429, and miR-940) in both cell culture medium and clinical plasma samples. The miR-nSTEV assay demonstrated superior diagnostic performance, achieving 100% accuracy in distinguishing PCa patients from healthy donors (HD), outperforming conventional RT-qPCR while simplifying the workflow. Overall, miR-nSTEV offers a robust, sensitive, and noninvasive tool for real-time TEV miRNA analysis, paving the way for early detection and precision diagnostics in PCa patients.}, }
@article {pmid40874976, year = {2025}, author = {Jiang, F and Yan, L and Jing, X and Chen, G and Wang, Y and Zhao, C and Huang, Y}, title = {Insights into traditional Chinese medicine: molecular identification of black-spotted tokay gecko, Gekko reevesii, and related species used as counterfeits based on mitochondrial 16S rRNA gene sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/24701394.2025.2550967}, pmid = {40874976}, issn = {2470-1408}, abstract = {Authentication of traditional Chinese medicine (TCM) is challenging due to DNA degradation in Chinese medicinal materials, which are usually processed and stored dry. The standard DNA barcoding length (648 bp) or longer are difficult to amplify, which makes it difficult to identify adulterants in Chinese medicinal materials. In this study, we used the mitochondrial 16S rRNA gene (< 200bp) as a barcode to differentiate black-spotted tokay geckoes (Gekko reevesii) from the related species used as counterfeits. We collected 63 specimens from 17 species of G. reevesii and their counterfeits, and each specimen generated a 189 bp 16S rRNA gene sequence. The average uncorrected p-distances within genuine G. reevesii was 0.9%, while the average uncorrected p-distances between G. reevesii and their counterfeits was 6.3% (at a minimum). According to phylogenetic analysis and genetic distances, the genuine G. reevesii samples collected in this study constitute a monophyly that can be distinguished from its counterfeits in TCM formulations, including G. gecko (red-spotted tokay geckos), which have very similar morphology. Thus, the short 16S rRNA barcode provides an effective tool for distinguishing G. reevesii from its counterfeits, ensuring the safety and efficacy of clinical medications containing components from G. reevesii in TCM.}, }
@article {pmid40872302, year = {2025}, author = {Wisely, SM and Torhorst, CW and Botero-Cañola, S and Atsma, H and Burkett-Cadena, ND and Reeves, LE}, title = {Evaluation of Mosquito Blood Meals as a Tool for Wildlife Pathogen Surveillance.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {8}, pages = {}, doi = {10.3390/pathogens14080792}, pmid = {40872302}, issn = {2076-0817}, support = {7004318//United States Department of Agriculture/ ; }, mesh = {Animals ; *Animals, Wild/virology/blood ; *Culicidae/virology/physiology ; Swine ; Deer/blood/virology ; Florida ; Turkeys/blood ; DNA Barcoding, Taxonomic ; }, abstract = {Mosquito blood meals provide a biological sample of host blood which can then be used in downstream applications including host-pathogen detection. We conducted DNA barcoding to identify the host species of blood meals from 4557 blood engorged mosquitoes collected in south central Florida, USA. We identified 314 blood meals from invasive wild pigs, 219 wild turkey blood meals, and 1046 white-tailed deer blood meals. From a subset of these host blood meals, we used molecular assays to detect the nucleic acids of Torque teno sus virus 1 (TTSuV1) in wild pig blood meals, Lymphoproliferative virus (LPDV) in wild turkey blood meals, and bluetongue virus (BTV) in white-tailed deer blood meals. None of these wildlife pathogens are transmitted by mosquitoes, but viral nucleic acids circulate in the peripheral blood of host species during or post infection. Prevalence of TTSuV1 in wild pig blood meals was 34%; in wild turkey blood meals the prevalence of LPDV was 2.7%, and BTV prevalence in blood meals of white-tailed deer was 3.6%. These prevalence values were similar to estimates obtained from peripheral blood collected directly from these hosts in Florida. Our analysis suggests that mosquito blood meals are a valuable sampling tool for the detection of wildlife pathogens. We suggest that this type of exogenous xenosurveillance, using mosquitoes to infer information about the vertebrate host, is distinct from endogenous xenosurveillance in which the goal is to understand the role of the arthropod in vectoring a pathogen.}, }
@article {pmid40870646, year = {2025}, author = {Ma, S and Dai, L and Lv, H and Wei, Y and Zhang, X}, title = {Discobola Osten Sacken, 1865 (Diptera, Limoniidae) in China: Taxonomic Review, Updated Distribution, and DNA Barcoding.}, journal = {Insects}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/insects16080845}, pmid = {40870646}, issn = {2075-4450}, support = {32470481//the National Natural Science Foundation of China/ ; }, abstract = {The genus Discobola Osten Sacken, 1865 from China is taxonomically reviewed using an integrative approach that combines detailed morphological examination and molecular analysis. Discobola parvispinula (Alexander, 1947), a species widely distributed across the Palaearctic region, is newly recorded from China. Updated distributional data are presented for species known from China: D. annulata (Linnaeus, 1758), D. armorica (Alexander, 1942), D. margarita Alexander, 1924, and D. taivanella (Alexander, 1930). Detailed redescriptions and illustrations, including intraspecific morphological variation, are provided for these species. An identification key to Chinese Discobola species is also presented. Geographical analysis reveals a higher species richness in southern China and the Qinghai-Tibet region, with a progressive decline toward northern and northwestern China. The first DNA barcode reference library for Chinese Discobola is established, comprising 15 mt COI sequences from five species. These sequences, analyzed alongside an additional 101 mt COI sequences from Discobola species in other countries, show that intraspecific divergence within the genus remains below 7.4%, while interspecific divergence ranges from 7.6% to 17.7%. These findings provide important insights into the taxonomy, species delimitation, and biogeography of Discobola in China, contributing to a more comprehensive understanding of Discobola diversity across the region.}, }
@article {pmid40870559, year = {2025}, author = {Nedeljković, Z and Mengual, X and Ricarte, A}, title = {Revision of the North African Hoverflies of the Genus Xanthogramma Schiner, 1861 (Diptera: Syrphidae), with Description of a New Species.}, journal = {Insects}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/insects16080758}, pmid = {40870559}, issn = {2075-4450}, support = {PGC2018-095851-A-C65//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; Fauna y aves marinas exp P2C4I1.S000A2//Tragsatec/ ; }, abstract = {North Africa has a poorly and unevenly known hoverfly fauna. Xanthogramma Schiner, 1861 (Syrphinae, Syrphini) is represented in this territory by some scattered records of four species, Xanthogramma dives (Rondani, 1857), Xanthogramma evanescens Becker &amp; Stein, 1913 (endemic to North Africa), Xanthogramma marginale (Loew, 1854), and Xanthogramma pedissequum (Harris, 1776). After examination of old Xanthogramma material collected in Tanger, Morocco, from the 'Museo Nacional de Ciencias Naturales, Madrid, Spain (MNCN)', specimens with distinctive morphology were spotted and found to be different from a syntype of X. evanescens collected in the same locality. Consequently, we revised all the available material of Xanthogramma from North Africa, characterised a new species, proposed a lectotype for X. evanescens, and provided an identification key to the North African species of this genus. The new species is also found in Tunisia and differs from X. evanescens in facial width, colour of the thoracic pleura, length of mesonotum hairs, wing pollinosity, and shape of the yellow maculae on tergum 2.}, }
@article {pmid40869309, year = {2025}, author = {Zhang, Z and Liu, C and Gong, J and Su, C and Liu, Z and Li, J and Zhang, H}, title = {Distinct Phosphorylation Patterns of AT1R by Biased Ligands and GRK Subtypes.}, journal = {International journal of molecular sciences}, volume = {26}, number = {16}, pages = {}, doi = {10.3390/ijms26167988}, pmid = {40869309}, issn = {1422-0067}, mesh = {Phosphorylation ; *Receptor, Angiotensin, Type 1/metabolism/genetics/chemistry ; Humans ; Ligands ; HEK293 Cells ; Angiotensin II/metabolism/pharmacology ; *G-Protein-Coupled Receptor Kinases/metabolism ; Signal Transduction ; Amino Acid Motifs ; Mutation ; }, abstract = {G protein-coupled receptors (GPCRs) transmit through G proteins upon agonist activation, followed by phosphorylation by GPCR kinases (GRKs) to initiate β-arrestin signaling. However, the molecular mechanisms underlying GPCR signaling regulation by distinct agonists, GRK subtypes, and phosphorylation patterns remain poorly understood. The angiotensin II (AngII) type 1 receptor (AT1R), a prototypical GPCR, serves as an ideal model for studying biased ligands and signaling. Here, we investigated the wild-type (WT) AT1R and mutants of three potential phosphorylation motifs at its C-terminus (Motif I: S326/S328/S331, Motif II: T332/S335/T336/S338, and Motif III: S346/S347/S348/T349) using unbiased agonist AngII, β-arrestin-biased agonist TRV026, and G protein-biased agonist TRV056, along with GRK2/3/5/6 subtypes. We employed phosphorylation assays, β-arrestin pull-down experiments, molecular dynamics simulations, and AlphaFold3 predictions to dissect these mechanisms. Our results reveal that GRK2-mediated AT1R phosphorylation is abolished by mutations in Motifs I and II, with Motif II exhibiting a more pronounced effect. This phosphorylation was enhanced by Gβγ subunits. In contrast, GRK3-mediated phosphorylation remained unaffected by any mutations. GRK5 specifically phosphorylated Motif II, while GRK6 phosphorylated Motif II with the unbiased agonist AngII and both Motifs I and II with biased agonists TRV026 and TRV056. Notably, Motif II mutations reduced β-arrestin1/2 recruitment by GRK5/6 but not GRK2/3. Molecular dynamics simulations demonstrated that Motif II phosphorylation minimized steric hindrance, facilitating stable β-arrestin interactions, whereas Motif I phosphorylation increased intramolecular contacts that potentially impede recruitment. AlphaFold3 models provided detailed insights into the interactions between Motif II and β-arrestin1/2. Collectively, our findings elucidate diverse AT1R phosphorylation patterns driven by different agonists and GRK subtypes, offering a framework for developing signaling-biased AT1R therapeutics by decoding GRK-specific phosphorylation barcodes.}, }
@article {pmid40868840, year = {2025}, author = {Tian, C and Li, J and Zhang, Y and Zhang, J and Gao, X and Yin, X and Yang, L and Feng, H}, title = {Involvement of Gonolabis distincta in the Control of Root Maggots in Garlic Fields.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/life15081192}, pmid = {40868840}, issn = {2075-1729}, support = {232103810016//Scientific and technological breakthrough foundation of Henan Province/ ; :254000510002//Project of Central Plains scholars/ ; }, abstract = {Garlic root maggots are the main pest of garlic in Qi County, Henan Province, China, which has become an important factor restricting the development of the garlic industry. Earwigs play an important role in controlling root maggots because of their similar ecological niches. In this study, through DNA barcoding and morphological identification, the following root maggots and main earwigs species from Qi County were quickly identified: Delia platura (Meigen), Bradysia odoriphaga Yang et Zhang, Delia antiqua (Meigen), Muscina angustifrons (Loew), Lucilia sericata (Meigan), and the main species of earwigs was Gonolabis marginalis (Dohrn). D. platura was the dominant species and accounted for 98% among all garlic root maggots. The predation ability for each stage of G. distincta on the larvae and pupae of D. platura showed that G. distincta at different developmental stages preyed on both the the larvae and the entire pupae of D. platura. Among them, female adults had the strongest predation ability and the largest daily predation on first instar larvae of gray D. platura (71.25 ± 0.66). First instar nymphs of G. distincta also had a certain predation ability with the daily predation of first instar larvae being (1.85 ± 0.13). The predation ability of G. distincta at different instars on the larvae of the same instar of D. platura increased with the increasing of the instar. For the first to second instar larvae of D. platura, the female adult of G. distincta had the strongest predation ability, followed by the male adult of G. distincta, and then the fifth instar nymph of G. distincta. There was no significant difference in the predation ability between the male and female adults of G. distincta, but the adults' predation capacities were significantly higher than that of the fifth instar nymph of G. distincta. The capacity of the fifth instar nymph of G. distincta was significantly higher than the fourth instar nymph of G. distincta, the fourth instar nymph of G. distincta was significantly higher than the first to third instar nymphs, and there was no significant difference in the predation amount among the first to third instar nymphs. The predation selection experiment indicated that the fifth instar nymphs and the male and female adults of G. distincta showed a positive preference for the first to third instar larvae of D. platura and a negative preference for the pupae of D. platura. Our study provided a preliminary scientific basis for green prevention and control of garlic root maggot.}, }
@article {pmid40867097, year = {2025}, author = {Ye, J and Yu, L and Wang, YJ and Li, XX and Sun, YQ and Zheng, ST}, title = {Giant 3d-4f Heterometallic Polyoxoniobates of {Na2Zn29Ln12Nb122}, {Zn10Eu8Nb60}, and {Zn16Ln8Nb88} with Photonic Barcodes.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e06482}, doi = {10.1002/smll.202506482}, pmid = {40867097}, issn = {1613-6829}, support = {22171046//NSF of China/ ; 2024J01234//Natural Science Foundation of Fujian Province/ ; }, abstract = {The integration of the rich electronic properties of 3d-4f heterometallic clusters with rigid and diamagnetic polyoxometalates is of great interest and is expected to yield novel materials with enhanced properties due to synergistic effects. For the first time, the study succeeds in introducing fluorescent Zn-Ln heterometallic clusters into polyoxoniobates (PONbs), forming a family of rare giant heterometallic PONbs with various architectures, including 78-metal {Zn10Eu8Nb60}, 112-metal {Zn16Ln8Nb88} (Ln = La, Y), and 165-metal {Na2Zn29Ln12Nb122} (Ln = Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho). These heterometallic PONbs exhibit many appealing structural features and unique building blocks. Particularly, they are the largest 3d-4f heterometallic PONbs and also the PONbs incorporating the largest number of 3d-4f metal ions and the highest-nuclearity 3d-4f clusters known to date. Furthermore, the combination of PONbs and Zn-Ln clusters renders these new-type heterometallic PONbs multicolor luminescent characteristics and high fluorescence quantum yields, making them promising candidate cluster molecules for responsive photonic barcodes.}, }
@article {pmid40867047, year = {2025}, author = {Ocari, T and Zin, EA and Tekinsoy, M and Van Meter, T and Desrosiers, M and Cammarota, C and Dalkara, D and Nemoto, T and Ferrari, U}, title = {Optimal sequencing depth for measuring the concentrations of molecular barcodes.}, journal = {Nucleic acids research}, volume = {53}, number = {16}, pages = {}, doi = {10.1093/nar/gkaf793}, pmid = {40867047}, issn = {1362-4962}, support = {ANR-10-LABX-65//Agence Nationale de la Recherches/ ; ANR-18-IAHU-01//Agence Nationale de la Recherches/ ; 863214 - NEUROPA//H2020 European Research Council/ ; I-D&#xe9;mo//Bpifrance/ ; REGE-NETHER 639888//Union Nationale des Aveugles et D&#xe9;ficients Visuels/ ; 22K17994//Japan Society for the Promotion of Science/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods/standards ; Gene Library ; *DNA Barcoding, Taxonomic/methods ; *Sequence Analysis, DNA/methods ; Humans ; Polymerase Chain Reaction ; DNA ; }, abstract = {In combinatorial genetic engineering experiments, next-generation sequencing (NGS) allows for measuring the concentrations of barcoded or mutated genes within highly diverse libraries. When designing and interpreting these experiments, sequencing depths are thus important parameters to take into account. Service providers follow established guidelines to determine NGS depth depending on the type of experiment, such as RNA sequencing or whole genome sequencing. However, guidelines specifically tailored for measuring barcode concentrations have not yet reached an accepted consensus. To address this issue, we combine the analysis of NGS datasets from barcoded libraries with a mathematical model taking into account the polymerase chain reaction amplification in library preparation. We demonstrate on several datasets that noise in the NGS counts increases with the sequencing depth; consequently, beyond certain limits, deeper sequencing does not improve the precision of measuring barcode concentrations. We propose, as rule of thumb, that the optimal sequencing depth should be about ten times the initial amount of barcoded DNA molecules before any amplification step.}, }
@article {pmid40866952, year = {2025}, author = {Broche, J and Kelemen, O and Sekar, A and Schütz, L and Muyas, F and Forschner, A and Schroeder, C and Ossowski, S}, title = {GeneBits: ultra-sensitive tumour-informed ctDNA monitoring of treatment response and relapse in cancer patients.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {964}, pmid = {40866952}, issn = {1479-5876}, abstract = {BACKGROUND: Circulating tumour DNA (ctDNA) in liquid biopsies has emerged as a powerful biomarker in cancer patients. Its relative abundance in cell-free DNA serves as a proxy for the overall tumour burden. Here we present GeneBits, a method for cancer therapy monitoring and relapse detection. GeneBits employs tumour-informed enrichment panels targeting 20-100 somatic single-nucleotide variants (SNVs) in plasma-derived DNA, combined with ultra-deep sequencing and unique molecular barcoding. In conjunction with the newly developed computational method umiVar, GeneBits enables accurate detection of molecular residual disease and early relapse identification.<br><br>RESULTS: To assess the performance of GeneBits and umiVar, we conducted benchmarking experiments using three different commercial cell-free DNA reference standards. These standards were tested with targeted next-generation sequencing (NGS) workflows from both IDT and Twist, allowing us to evaluate the consistency and accuracy of our approach across different oligo-enrichment strategies. GeneBits achieved comparable depth of coverage across all target sites, demonstrating robust performance independent of the enrichment kit used. For duplex reads with &#x2265; 4x UMI-family size, umiVar achieved exceptionally low error rates, ranging from 7.4&#xd7;10[-7]&#xa0;to 7.5&#xd7;10[-5]. Even when including mixed consensus reads (duplex &amp; simplex), error rates remained low, between 6.1&#xd7;10[-6]&#xa0;and 9&#xd7;10[-5]. Furthermore, umiVar enabled variant detection at a limit of detection as low as 0.0017%, with no false positive calls in mutation-free reference samples. In a reanalysed melanoma cohort, variant allele frequency kinetics closely mirrored imaging results, confirming the clinical relevance of our method.<br><br>CONCLUSION: GeneBits and umiVar enable highly accurate therapy and relapse monitoring in plasma as well as identification of molecular residual disease within four weeks of tumour surgery or biopsy. By leveraging small, tumour-informed sequencing panels, GeneBits provides a targeted, cost-effective, and scalable approach for ctDNA-based cancer monitoring. The benchmarking experiments using multiple commercial cell-free DNA reference standards confirmed the high sensitivity and specificity of GeneBits and umiVar, making them valuable tools for precision oncology. UmiVar is available at https://github.com/imgag/umiVar .}, }
@article {pmid40865182, year = {2025}, author = {Song, ZT and Sun, KY and Hou, L and Wu, JJ and Hu, WT and Zhou, S and Zhang, CY and Song, J and Lan, HB and Wei, F and Feng, CP}, title = {3D printable phase change information storage label films for dynamic and multi-level anti-counterfeiting.}, journal = {Journal of colloid and interface science}, volume = {701}, number = {}, pages = {138694}, doi = {10.1016/j.jcis.2025.138694}, pmid = {40865182}, issn = {1095-7103}, abstract = {Anti-counterfeiting technology demands continuous innovation to address escalating global counterfeiting challenges. This study introduces 3D printable phase change information storage label films for dynamic, multi-level anti-counterfeiting applications. Utilizing extrusion-based 3D printing, customizable anti-counterfeiting labels with complex encrypted information such as barcodes and QR codes were fabricated. These labels leverage the thermal responsiveness of phase change materials (PCMs) to reveal hidden information under infrared thermography at specific temperature and specific duration, while remaining concealed at ambient or elevated temperatures. Notably, a multi-level encryption strategy is achieved by integrating PCMs with distinct phase transition temperatures (30 °C and 53 °C), enabling sequential decryption of information at different temperature intervals. This approach significantly enhances anti-counterfeiting complexity and security. The work demonstrates the potential of PCM-based 3D printing for high-capacity information storage and adaptable anti-counterfeiting solutions, offering a versatile platform for diverse industrial applications.}, }
@article {pmid40864172, year = {2025}, author = {Wade, RM and Ogushi, R and Gabrielson, PW and Hind, KR and Hughey, JR and Lindstrom, SC and Miller, KA and Martone, PT}, title = {Type-assisted taxonomy and biogeography of Corallina (Corallinales, Rhodophyta) in the eastern Pacific: Corallina americana sp. nov., C. bathybentha, C. hommersandiorum sp. nov., and C. saundersii sp. nov.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70078}, pmid = {40864172}, issn = {1529-8817}, support = {//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; //Hakai Institute/ ; }, abstract = {The articulated coralline genus Corallina is common in temperate rocky ecosystems and provides settlement substrate and refugia for other organisms. However, our ability to understand species-specific traits and interactions has been confounded by overlapping morphological characteristics among species. DNA sequences from type specimens and recently collected specimens have begun to address these issues by clarifying phylogenetic species boundaries and geographic distributions. We sequenced an rbcL gene barcode from a paratype specimen of Corallina bathybentha (type locality: 0.5 miles south of the west end of Anacapa Is., California, United States) and have provided an updated description. Three cryptic species have been described: C. hommersandiorum and C. saundersii are endemic to the northeastern Pacific, whereas C. americana is anti-tropical in the eastern Pacific. Haplotype network analyses using the COI locus suggested that C. americana naturally dispersed from North to South America; it was not likely a recent or human-mediated introduction. To explore species boundaries, stepwise discriminant models were used to analyze morphological and ecological traits and were visualized in canonical multidimensional plots. Every species overlapped in canonical space with at least one other species, further illustrating that morphological identifications of Corallina species are challenging and unreliable. This work completes the taxonomic study of the currently known diversity of Corallina in the northeast Pacific for which we have access to type specimens. Given that this region is likely the center of origin and home to three-quarters of the known Corallina species, these taxonomic studies, including this one, make a significant contribution to our understanding of coralline diversity.}, }
@article {pmid40864133, year = {2025}, author = {Barretto, M and Olson, A and Alemayehu, D and Clausnitzer, R and Haas-Stapleton, EJ}, title = {Barcoding Quantitative PCR Assay to Distinguish Between Aedes aegypti and Aedes sierrensis.}, journal = {Tropical medicine and infectious disease}, volume = {10}, number = {8}, pages = {}, pmid = {40864133}, issn = {2414-6366}, support = {FY2024.6503//Alameda County Mosquito Abatement District/ ; }, abstract = {The accurate identification of mosquito species is critical for effective mosquito surveillance and control, especially when presented with morphologically similar species like Aedes aegypti and Aedes sierrensis. Damaged specimens and morphologically similar life stages such as eggs and larvae make it difficult to distinguish Aedes aegypti from Aedes sierrensis using microscopy and taxonomic keys. To address this, the AegySierr.ID-qPCR assay, a multiplex quantitative PCR assay that utilizes single-nucleotide polymorphisms within the mitochondrial cytochrome oxidase subunit I gene, was developed to distinguish between these two species. The assay was tested on DNA extracted from the eggs, larvae, and adults of both species, as well as from environmental DNA (eDNA) collected from natural mosquito reproduction sites. It demonstrated a high diagnostic accuracy across multiple life stages, with a sensitivity exceeding 95% for most groups and specificity exceeding 90%, except for field-collected adult Ae. sierrensis (75%). For eDNA samples, the assay achieved 100% sensitivity and 94% specificity for samples classified as Ae. sierrensis and 91% sensitivity and 86% specificity for Ae. aegypti. A two-graph receiver operating characteristic analysis was also used as an alternate method with which to establish Ct thresholds for interpreting results from unknown samples. The AegySierr.ID-qPCR assay enables the rapid and sensitive identification of Ae. aegypti and Ae. sierrensis from specimens and eDNA, and may be of use in mosquito surveillance programs.}, }
@article {pmid40860682, year = {2025}, author = {Bakmaz, D and Sönmez, S and Korkmaz, EM}, title = {Evaluating COI and ITS2 dual barcoding for molecular delimitation and taxonomic insights in Arenosetella Wilson, 1932 (Harpacticoida: Ectinosomatidae) along Turkish Coasts.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19870}, pmid = {40860682}, issn = {2167-8359}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Turkey ; Phylogeny ; *Copepoda/genetics/classification ; Haplotypes ; Genetic Variation ; *DNA, Ribosomal Spacer/genetics ; }, abstract = {BACKGROUND: Accurate species delimitation is essential in morphologically conservative taxa such as harpacticoid copepods, in which cryptic diversity may go unnoticed without molecular data. The genus Arenosetella, common along the Turkish coastline, comprises two species: Arenosetella germanica and A. lanceorostrata, with overlapping ranges and subtle morphological differences. This study aimed to assess species boundaries and uncover potential hidden diversity within Arenosetella using the dual-marker DNA barcoding approach.<br><br>METHODS: Specimens of Arenosetella were collected from the Mediterranean, Aegean, and Black Sea coasts of T&#xfc;rkiye. Nuclear DNA from a total of 46 individuals were amplified and sequenced for both mitochondrial cytochrome oxidase I (COI) and nuclear internal transcribed spacer 2 (ITS2) markers. COI sequences were analysed for haplotype diversity, phylogenetic relationship, and species delimitations. ITS2 sequences were subjected to evaluation with regard to nucleotide diversity, secondary structure, and compensatory base changes (CBCs), using both sequence- and structure-based approaches. The concatenated dataset and species tree reconstruction (StarBEAST2) were employed to test gene tree-species tree congruence.<br><br>RESULTS: The COI analyses revealed a high level of haplotype diversity (21 haplotypes) and the presence of three molecular operational taxonomic units (MOTUs) within A. germanica and one MOTU within A. lanceorostrata, consistent with the geographic distribution patterns. ITS2 sequences exhibited relatively more conservation with nine haplotypes. These sequences revealed informative structural variation, including CBCs among candidate species. The species delimitation approaches reliably supported the identification of four to seven MOTUs, which corresponded to geographic populations. The analyses of the concatenated dataset supported four well-supported candidate species, and yielded congruent species trees, with high posterior probabilities. Morphological comparisons among MOTUs revealed subtle differences in female P5 structure and anal somite ornamentation among A. germanica lineages, while A. lanceorostrata MOTUs were morphologically indistinguishable.<br><br>CONCLUSION: This study provides the first integrative application of COI and ITS2 barcoding in Arenosetella and within Harpacticoida overall, combining DNA sequences and structure, and morphological data for species delimitation. The results demonstrate that COI is effective for detecting geographic differentiation and haplotype diversity, whereas ITS2 contributes structural resolution and potential markers of reproductive isolation through CBCs. These findings suggest the presence of a species complex within A. germanica and confirm the distinct status of A. lanceorostrata. Dual-marker barcoding, particularly incorporating ITS2 secondary structure, represents a valuable tool for taxonomic studies in morphologically conservative copepod groups.}, }
@article {pmid40860566, year = {2025}, author = {Arnau, V and Ortiz-Maiques, A and Valero-Tebar, J and Mora-Quilis, L and Kurmauskaite, V and Campos Dopazo, L and Domingo-Calap, P and Džunková, M}, title = {CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf134}, pmid = {40860566}, issn = {2730-6151}, abstract = {Split-and-pool barcoding generates thousands of unique barcode strings through sequential ligations in 96-well plates, making single-cell omics more accessible, thus advancing microbial ecology, particularly in studies of bacterial interactions with plasmids and bacteriophages. While the wet-lab aspects of the split-and-pool barcoding are well-documented, no universally applicable bioinformatic tool exists for demultiplexing single cells barcoded with this approach. We present CleanBar (https://github.com/tbcgit/cleanbar), a flexible tool for demultiplexing reads tagged with sequentially ligated barcodes, accommodating variations in barcode positions and linker lengths while preventing misclassification of natural barcode-like sequences and handling diverse ligation errors. It also provides statistics useful for optimizing laboratory procedures. We demonstrate CleanBar's performance with the Atrandi platform for microbial single-cell genomics, coupled with PacBio sequencing, to reach a cell throughput comparable with traditional bulk metagenomics, but overcoming its limitations in studying phage-bacteria interactions. In four Klebsiella strains infected with their corresponding phages and a control phage, the single-cell genomics revealed infection heterogeneity and enabled phage copy number estimation per cell. By combining efficiency, adaptability, and precision, CleanBar, when applied to the Atrandi split-and-pool barcoding platform and PacBio sequencing, serves as a powerful high-throughput tool for advancing microbial single-cell genomics and understanding microbial ecology and evolution.}, }
@article {pmid40860319, year = {2025}, author = {Moser, M and Vasilița, C and Haas-Renninger, M and Pirvu, E and Haas, M and Krogmann, L}, title = {German Barcode of Life reveals unexpected diversity of Ceraphronoidea (Hymenoptera).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e159561}, pmid = {40860319}, issn = {1314-2828}, abstract = {Insect populations still experience marked declines globally, contributing to the ongoing biodiversity crisis. Counteracting these declines requires sound taxonomic and ecological knowledge on all levels of biodiversity, from genes to species to ecosystems. The superfamily Ceraphronoidea (Hymenoptera) has remained relatively obscure due to complex challenges in exploring its diversity and ecological roles. Despite their ecological importance as parasitoids or hyperparasitoids, these wasps are under-represented in scientific exploration and conservation. In a case study within the German Barcode of Life (GBOL) Dark Taxa project, we aim to bridge this knowledge gap through a comprehensive taxonomic investigation covering 2,136 specimens of Ceraphronoidea across 18 locations in the putatively well-studied State of Baden-Württemberg (south-western Germany). Our study identifies a surprising species richness of at least 193 conjectural species, based on COI-barcoding clusters, extrapolates key species richness estimators for the German ceraphronoid fauna and records a species new to the German fauna: Creatorspissicornis (Hellén, 1966). By setting a foundational benchmark for Ceraphronoidea biodiversity, our research advocates for the inclusion of dark taxa in broader insect biodiversity assessments, contributing meaningfully to the discourse on conservation priorities and strategies.}, }
@article {pmid40857085, year = {2025}, author = {Mamane-Logsdon, A and Zane, I and Chong, JS and Chou, OHI and Huang, J and Rawal, M and Gillman, AC and Wongwiwat, W and Saleban, M and Donovan-Banfield, I and Matthews, DA and White, RE}, title = {A direct RNA-seq-based EBV latency transcriptome offers insights into the biogenesis of EBV gene products.}, journal = {The Journal of general virology}, volume = {106}, number = {8}, pages = {}, doi = {10.1099/jgv.0.002134}, pmid = {40857085}, issn = {1465-2099}, mesh = {*Herpesvirus 4, Human/genetics/physiology ; Humans ; *Virus Latency/genetics ; *Transcriptome ; Epstein-Barr Virus Nuclear Antigens/genetics ; RNA-Seq ; *Viral Proteins/genetics/biosynthesis ; Epstein-Barr Virus Infections/virology ; Gene Expression Regulation, Viral ; B-Lymphocytes/virology ; Cell Line ; Alternative Splicing ; Promoter Regions, Genetic ; RNA, Viral/genetics ; MicroRNAs/genetics ; }, abstract = {Epstein-Barr virus (EBV) ubiquitously infects humans, establishing lifelong persistence in B cells. In vitro, EBV-infected B cells can establish a lymphoblastoid cell line (LCL). EBV's transcripts in LCLs (latency III) produce six nuclear proteins [EBV nuclear antigens (EBNAs)], two latency membrane proteins (LMPs) and various microRNAs and putative long non-coding RNAs [BamHI A rightward transcripts (BARTs)]. The BART and EBNA transcription units are characterized by extensive alternative splicing. We generated LCLs with B95-8 EBV-BACs, including one engineered with 'barcodes' in the first and last repeat of internal repeat 1 (IR1), and analysed their EBV transcriptomes using long-read nanopore direct RNA-seq. Our pipeline ensures appropriate mapping of the W promoter (Wp) 5' exon and corrects W1-W2 exon counts that misalign to IR1. This suggests that splicing across IR1 largely includes all W exons and that Wp-derived transcripts more frequently encode the EBNA-LP start codon than Cp transcripts. Analysis identified a short variant of exon W2 and a novel polyadenylation site before EBNA2, provided insights into BHRF1 miRNA processing and suggested co-ordination between polyadenylation and splice site usage, although improved read depth and integrity are required to confirm this. The BAC region disrupts the integrity of BART transcripts through premature polyadenylation and cryptic splice sites in the hygromycin expression cassette. Finally, a few transcripts extended across established gene boundaries, running from EBNA to BART to LMP2 gene regions, sometimes including novel exons between EBNA1 and the BART promoter. We have produced an EBV annotation based on these findings to help others better characterize EBV transcriptomes in the future.}, }
@article {pmid40854923, year = {2025}, author = {Intharuksa, A and Prasertwitayakij, N and Yanaso, S and Phrutivorapongkul, A and Charoensup, W and Thongkhao, K and Sasaki, Y and Wongcharoen, W}, title = {Uncovering the poisonous aconitine containing plants in homemade herbal liquor using a convergent approach.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {31286}, pmid = {40854923}, issn = {2045-2322}, abstract = {Human exposure to toxic plants is a global concern, with numerous reported cases of accidental poisoning. In this study, a patient experienced poisoning after inadvertently consuming an herbal preparation preserved in alcohol. The patient exhibited characteristic electrocardiogram abnormalities, prompting further investigation into the toxic plant responsible. A relative provided the suspected herbal sample for identification. Symptomatic treatment was administered, successfully stabilizing the patient. Given the suspicion of aconitine toxicity-despite the absence of naturally occurring Aconitum species in Thailand-a multi-approach methodology was employed to identify the plant source. Macroscopic and microscopic analyses were performed to characterize the morphological and histological features of the specimens. Organoleptic assessment revealed blackish-brown, shrunken surfaces with longitudinal wrinkles and a pale alcoholic-like odor. Microscopic examination identified three major structural layers: metaderm and cortex, vascular tissues, and a parenchyma-rich central pith, consistent with Aconitum storage roots. Chemical identification using thin-layer chromatography (TLC) compared the patient samples (SX1 and SX2) with standard aconitine and Aconitum crude drugs (AC1-AC5). The TLC chromatograms confirmed the presence of aconitine in SX1 and SX2, as evidenced by matching Rf values and characteristic color reactions. Further molecular analysis utilizing DNA barcoding targeted the trnH-psbA region to determine the genetic origin of the specimens. PCR successfully amplified DNA from SX1, SX2, and Aconitum reference samples, generating approximately 150 bp amplicons. BLAST analysis revealed a 99.07% sequence identity with Aconitum species, and phylogenetic analysis clustered the patient specimens with authenticated Aconitum species. Given that Aconitum, Delphinium, and Consolida species are not naturally distributed in Thailand, this case highlights the risks associated with imported medicinal plants containing aconitine. The integration of macroscopic, microscopic, chemical, and molecular techniques provided definitive identification of the toxic plant material. These findings underscore the importance of public health initiatives to raise awareness of aconitine poisoning and the need for regulatory measures to ensure the safe use of medicinal plants.}, }
@article {pmid40854664, year = {2025}, author = {Azzam, CR and Rizk, MS and Mostafa, SSM and Arafa, RA and Al-Nabawi, MS and Morsi, NAA and Nasr El-Din, MM and Taher, EH and Khaled, KA}, title = {Characterization of two novel chia (Salvia hispanica L.) white and black genotypes via DNA barcoding, physiological, and agronomic traits.}, journal = {Journal, genetic engineering &amp; biotechnology}, volume = {23}, number = {3}, pages = {100545}, doi = {10.1016/j.jgeb.2025.100545}, pmid = {40854664}, issn = {2090-5920}, abstract = {BACKGROUND: Chia (Salvia hispanica L.) is recognized for its nutritional value and health-promoting compounds, including flavonoids.<br><br>AIM: This study utilized DNA barcoding to identify and differentiate two novel chia genotypes, CACH-W and CACH-B, providing insights for breeding programs and genetic resource conservation (CA refers to the developer and CH refer to Chia).<br><br>METHODS: DNA was extracted from controlled samples and analyzed using five barcode markers: trnH-psbA, matK, rpoC1, rbcL, and ITS. Genetic diversity was evaluated through phylogenetic analysis with appropriate bioinformatics tools.<br><br>RESULTS: DNA barcoding using five markers (trnH-psbA, matK, rpoC1, rbcL, and ITS) successfully amplified sequences of 930&#xa0;bp, 1520&#xa0;bp, 2295&#xa0;bp, 1910&#xa0;bp, and 1630&#xa0;bp, respectively. Among them, rbcL, rpoC1, and ITS effectively differentiated the two genotypes, and phylogenetic analysis confirmed their genetic identity and relationship with existing (Salvia hispanica L.) sequences. Functional analyses highlighted the conserved roles of key genes, including rbcL (carbon fixation), rpoC1 (chloroplast transcription), and matK (RNA splicing). The white genotype (CACH-W) outperformed the black genotype (CACH-B) in germination, physiological, and agronomic traits, achieving a higher seedling vigor index (11.68 vs. 8.51), longer radicle (6.94&#xa0;cm vs. 5.02&#xa0;cm), and greater total phenolic content (31.92&#xa0;mg/g vs. 28.95&#xa0;mg/g). Agronomically, CACH-W showed superior plant height, spike weight, and seed yield (1003.83&#xa0;kg/feddan vs. 606.46&#xa0;kg/feddan), making it a promising candidate for cultivation and breeding.<br><br>CONCLUSION: This study demonstrates the effectiveness of certain plastome gene sequences in identifying and distinguishing chia varieties, offering a reliable tool for breeding, quality control, and germplasm conservation. The white genotype (CACH-W) outperformed the black genotype (CACH-B) in germination, physiological, and agronomic traits, achieving a higher seedling vigor index, longer radicle, and greater total phenolic content. Agronomically, CACH-W showed superior plant height, spike weight, and seed yield, making it a promising candidate for cultivation and breeding. The results also support the integration of marker-assisted selection for developing chia varieties with improved traits, enhancing their commercial and agricultural value.}, }
@article {pmid40851185, year = {2025}, author = {Shastay, A and Bertagnoli, S}, title = {Difficult-to-scan barcodes on intravenous bags need to be escalated.}, journal = {Nursing}, volume = {55}, number = {9}, pages = {55}, doi = {10.1097/NSG.0000000000000258}, pmid = {40851185}, issn = {1538-8689}, }
@article {pmid40850985, year = {2025}, author = {Asaf, S and Williams, YA and Lubna,  and Riethoven, JM and Eslamieh, J and Al-Rawahi, A and Al-Harrasi, A and Khan, AL}, title = {Plastome structure, evolution and diversity of Frankincense-producing Boswellia genus.}, journal = {Functional &amp; integrative genomics}, volume = {25}, number = {1}, pages = {172}, pmid = {40850985}, issn = {1438-7948}, mesh = {*Boswellia/genetics/classification ; *Genome, Plastid ; *Evolution, Molecular ; Phylogeny ; Genetic Variation ; }, abstract = {The genus Boswellia is famous for its commercially important frankincense production. Additionally, it has unique ecological and taxonomic importance. However, the Boswellia species often face natural hybridization, and the lack of genomic datasets frequently contributes to taxonomic uncertainties. Here, we sequenced and analyzed the complete plastid genomes (plastomes) of six Boswellia species (B. carteri, B. bullata, B. dioscoridis, B. elongata, B. serrata, B. frereana, and a hybrid variant of B. sacra (B. sacra var. supersacra). The genome size of Boswellia plastomes is between 159,189 bp and 160,743 bp, displaying a typical structure with large single-copy (LSC; 86,811-88,054), small single-copy (SSC; 26,666-26,763), and inverted repeat (IR; 26,544-26,763) regions. The IR regions (~ 25,000 bp) are highly conserved across species, contributing to the stability of the plastome structure. Our study identified consistent gene content, typical of angiosperms, and showed that the IR boundaries remained unchanged across species. The simple sequence repeats revealed a range between 43 and 52 across the plastomes, with B. sacra exhibiting the highest count. We detected long, repetitive sequences that could serve as useful genetic markers for species differentiation. Nucleotide diversity analysis highlighted significant gene variations (matK, rbcL, rpl14, and rpoC2). The results showed substantial genetic divergence in regions (rpl14, matK, and rpoC2), demonstrating distinct variations among species. In evolutionary history, the B. carteri diverged around 4.2 million years ago (mya), while B. sacra and B. serrata separated by approximately 7.0 mya. The phylogenomic analysis supported the distinction between B. carteri and B. sacra, challenging prior claims that these are synonymous. These findings contribute to a deeper understanding of species boundaries within Boswellia and offer valuable resources for future DNA barcoding efforts.}, }
@article {pmid40849035, year = {2025}, author = {Banerjee, N and Mazumdar, SM and Bellis, G and Mazumdar, A}, title = {New species, country records, DNA barcoding and host blood meal analysis of some Indian species of Culicoides Latreille subgenus Trithecoides Wirth and Hubert (Diptera: Ceratopogonidae).}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107798}, doi = {10.1016/j.actatropica.2025.107798}, pmid = {40849035}, issn = {1873-6254}, abstract = {Light trap collections from four states in India revealed the presence of four species belonging to Culicoides (Trithecoides). Included were a new species from the macfiei group, Culicoides tenebrus sp. nov., which is diagnosed with a dark mid-knee and a yellow scutum featuring a dark anterior quarter, two new country records for India: Culicoides paraflavescens Wirth and Hubert, 1959, and Culicoides laoensis Howarth, 1985, and some variants of the widely distributed species Culicoides palpifer Das Gupta and Ghosh, 1956. Collections contained blood-fed specimens of each of these species, and host blood meal analysis using 16S rRNA revealed that all specimens had fed on cattle. DNA barcodes obtained from some specimens of these species were analysed along with other species from Culicoides (Trithecoides), and a phylogenetic tree based on these sequences supported the status of each of these species. Considerable variation was observed within C. palpifer both in morphology and DNA barcodes, suggesting that this species requires some taxonomic revision. The apparent preference of these four species for cattle hosts suggests that studies into their vector potential are warranted; however, the status of the species of Trithecoides requires clarification before any vector potential studies.}, }
@article {pmid40847262, year = {2025}, author = {Stern, N and Milstein, D and Bollous, M and Morov, AR}, title = {Comparative performance of eDNA and conventional capture-based monitoring approaches to detect riverine fish assemblages.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {9}, pages = {1036}, pmid = {40847262}, issn = {1573-2959}, mesh = {Animals ; *Environmental Monitoring/methods ; *Fishes/classification ; *DNA, Environmental/analysis ; Biodiversity ; Rivers/chemistry ; DNA Barcoding, Taxonomic ; Israel ; Ecosystem ; Fresh Water ; }, abstract = {Monitoring biodiversity constitutes a fundamental element in assessing the ecological status of sensitive and vulnerable habitats such as inland freshwater bodies. Although conventional capture-based methodologies in fish monitoring are still widely used, the development of alternative strategies is being vigorously pursued. The use of environmental DNA (eDNA) to detect species' presence is now a standard practice in aquatic ecology and is generating considerable attention within the scientific community. Here, we present the first eDNA metabarcoding study of the Israeli freshwater ecosystems, aiming to detect and compare fish assemblages of previously surveyed sites. Four riverine systems with different characteristics and known fish fauna were sampled, in parallel to the preparation of a complete 12S rRNA barcode reference library for the Israeli freshwater ichthyofauna. In total, 25 fish species belonging to 15 families were detected from 63 water samples using 12S eDNA metabarcoding. Comparisons with previous capture-based data have shown that eDNA surveys provided better species coverage, including the first documentation of two non-indigenous species and regardless of water characteristics or volume of filtered water. Lastly, we explain and discuss discrepancies in false-negative and false-positive results between the two methods.}, }
@article {pmid40846697, year = {2025}, author = {Brunet, L and Alexandre, D and Lee, J and Blanquer-Rosselló, MDM and Bracquemond, D and Guernet, A and Chhouri, H and Goupil, M and Kherrouche, Z and Arabo, A and Mancini, M and Cartier, D and Yao, S and Godefroy, D and Dehedin, J and Li, JR and Duparc, C and Jamme, P and Vinchent, A and Bérard, C and Tulasne, D and Arena, S and Bardelli, A and Cheng, C and Cho, BC and Wurtz, O and Coulouarn, C and Maraver, A and Aaronson, SA and Cortot, AB and Anouar, Y and Grumolato, L}, title = {Prolonging lung cancer response to EGFR inhibition by targeting the selective advantage of resistant cells.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {7853}, pmid = {40846697}, issn = {2041-1723}, support = {PLBIO 2017-159//Institut National Du Cancer (French National Cancer Institute)/ ; METROPOLIS-158530//Agence Nationale de la Recherche (French National Research Agency)/ ; PJA20161205119//Fondation ARC pour la Recherche sur le Cancer (ARC Foundation for Cancer Research)/ ; }, mesh = {Humans ; *Drug Resistance, Neoplasm/drug effects/genetics ; *Lung Neoplasms/drug therapy/pathology/genetics/metabolism ; ErbB Receptors/antagonists &amp; inhibitors/metabolism/genetics ; Sorafenib/pharmacology ; Animals ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/genetics/metabolism ; *Protein Kinase Inhibitors/pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; Cell Line, Tumor ; Mice ; STAT3 Transcription Factor/metabolism ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism/genetics ; Phosphorylation/drug effects ; Female ; Mice, Nude ; }, abstract = {Non-small cell lung cancers (NSCLCs) treated with tyrosine kinase inhibitors (TKIs) of the epidermal growth factor receptor (EGFR) almost invariably relapse in the long term, due to the emergence of subpopulations of resistant cells. Through a DNA barcoding approach, we show that the clinically approved drug sorafenib specifically abolishes the selective advantage of EGFR-TKI-resistant cells, while preserving the response of EGFR-TKI-sensitive cells. Sorafenib is active against multiple mechanisms of resistance/tolerance to EGFR-TKIs and its effects depend on early inhibition of MAPK-interacting kinase (MKNK) activity and signal transducer and activator of transcription 3 (STAT3) phosphorylation, and later down-regulation of MCL1 and EGFR. Using different xenograft and allograft models, we show that the sorafenib-EGFR-TKI combination can delay tumor growth and promote the recruitment of inflammatory cells. Together, our findings indicate that sorafenib can prolong the response to EGFR-TKIs by targeting NSCLC capacity to adapt to treatment through the emergence of resistant cells.}, }
@article {pmid40845955, year = {2025}, author = {McPhail, BA and Tomusiak, S and Veinot, H and Dodds, N and Hanington, PC}, title = {Reclaimed wetlands support rich trematode and host diversity: Findings from a four-year survey.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2025.08.006}, pmid = {40845955}, issn = {1879-0135}, abstract = {Snail hosts play a central role in structuring trematode communities. To test how snail hosts shape parasite diversity in central Alberta, we built upon a previous snail-trematode survey conducted at six lakes in central Alberta from 2013-2015 that uncovered 79 trematode species. However, analyses suggested that additional species remained to be uncovered. To build on this baseline, we conducted further snail-trematode collections from 2019 to 2022 at eight reclaimed wetland sites in various stages of reclamation, along with one established lake in Alberta. Across the nine sites, we collected 22,397 snails, of which 1,981 were infected with digenetic trematodes. We also documented broader biodiversity at these sites using traditional survey techniques. Through DNA barcoding, we identified 74 trematode species infecting five snail species. Among these were 23 trematode species not previously reported in central Alberta and nine provisionally-named lineages with no matches to species in publicly available databases. In addition, we observed several previously unreported snail-trematode interactions. While trematode richness did not vary significantly with the wetland reclamation stage, host identity did influence richness: Physa gyrina hosted significantly more trematode species than Planorbella trivolvis. When combined with data from the earlier survey, sample completeness analyses indicate that we captured 100% of the dominant species and 99% of the typical species, but only 63% of the overall species diversity in central Alberta. These findings underscore that trematode diversity in central Alberta remains incompletely characterized and highlight the continued value of long-term and host-inclusive sampling efforts.}, }
@article {pmid40844265, year = {2025}, author = {Bogaerts, B and Maex, M and Commans, F and Goeders, N and Van den Bossche, A and De Keersmaecker, SCJ and Roosens, NHC and Ceyssens, P-J and Mattheus, W and Vanneste, K}, title = {Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0041025}, doi = {10.1128/jcm.00410-25}, pmid = {40844265}, issn = {1098-660X}, abstract = {UNLABELLED: Core-genome multi-locus sequence typing (cgMLST) is a well-established and standardized method for genomics-based cluster detection and phylogenomic analysis of bacteria. The reduced error rate of Oxford Nanopore Technologies (ONT) R10 sequencing has prompted many laboratories to explore incorporating this technology into their activities. However, conflicting reports exist on the performance of ONT R10 sequencing for cgMLST analysis. This study evaluates the suitability of ONT R10 data for cgMLST allele calling and cluster detection for bacterial outbreak investigation. ONT and Illumina sequencing data were generated for 24 Neisseria meningitidis and 24 Salmonella enterica isolates. For ONT, both the rapid barcoding kit (RBK) and the rapid PCR barcoding kit (RPB) were used. The percentage of loci called in the ONT-only assemblies was very high for both species. However, the proportion of mismatched alleles to the hybrid assemblies was substantially higher for the Neisseria ONT-only assemblies with the RBK kit, resulting in incorrect cluster assignments. The large majority of these mismatched alleles were due to incorrect base calls at methylated positions, which did not affect the ONT data generated using the RPB kit or any of the Salmonella ONT-only assemblies. In conclusion, ONT R10 sequencing shows great potential as a viable method for cgMLST analysis, but methylation-related errors can affect performance for certain species and strains. When properly corrected for, ONT R10 had the same performance for cgMLST analysis as Illumina, and both could be used interchangeably. These results support the integration of ONT R10 sequencing into routine public health and clinical workflows.<br><br>IMPORTANCE: This study evaluates the suitability of Oxford Nanopore Technologies R10 sequencing for core-genome multi-locus sequence typing (cgMLST), a widely used method in (clinical) outbreak investigation and bacterial strain tracking. We have sequenced 24 Neisseria meningitidis and 24 Salmonella enterica strains, including confirmed outbreak cases, using Illumina and ONT R10 sequencing to evaluate the performance for cgMLST analysis. We used a PCR-based and native barcoding protocol for the ONT sequencing, which enabled us to demonstrate a substantial species-dependent impact of methylation-related errors on the performance. However, we demonstrate that when these errors are properly addressed, ONT R10 can be used for accurate cgMLST-based clustering, including integration with strains sequenced using Illumina. Our findings support the use of ONT R10 as an alternative to Illumina sequencing for cgMLST analysis in routine public health practice.}, }
@article {pmid40844238, year = {2025}, author = {Wang, C and Zheng, J and Xiong, Z and Yin, W and Zhao, Y and Wu, H and Liang, S and Zhang, L and Yao, C and Deng, Z and Liu, Y and Song, Q and Zhou, G and Zou, B}, title = {Voltage-Programmed Sequential Fluorescence Encoding (VPSFE) Enables Multiplexed In Situ Proteo-Imaging with Electric-Field Turing Patterns.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202511629}, doi = {10.1002/anie.202511629}, pmid = {40844238}, issn = {1521-3773}, support = {82404581//National Natural Science Foundation of China/ ; 82173780//National Natural Science Foundation of China/ ; BE2023843//Jiangsu Province Key R&amp;D Program Social Development Project/ ; BK20241591//Natural Science Foundation of Jiangsu Province/ ; S202510316086//National Innovation and Entrepreneurship Training Program for Undergraduate/ ; S202510316087//National Innovation and Entrepreneurship Training Program for Undergraduate/ ; 3322400176//National Innovation and Entrepreneurship Training Program for Undergraduate/ ; }, abstract = {DNA barcode-based immunolabeling has revolutionized single-cell protein profiling. However, conventional multiplexed imaging methods are hindered by laborious probe exchange procedures involving buffer washing-based probe removal and prolonged hybridization cycles (requiring tens of minutes to 1.5 h per cycle), which limit throughput, specificity, and universality. Here, we introduce an electrophoresis-based in situ probe removal method that achieves high-specificity iterative probe imaging without washing steps, utilizing 2-min low-voltage electrophoresis for excess probes removal and 3-min high-voltage electrophoresis for hybridized probes dissociation. The robustness was validated through 19 rounds of cyclic electrophoresis, 10 rounds of repetitive imaging, and simultaneous processing of 14 probes (µM-level) across five rounds of multiprobe exchange, demonstrating exceptional specificity and efficiency. Applied to sequential color coding-based multiplexed imaging, this approach establishes voltage-programmed sequential fluorescence encoding (VPSFE), enabling multiplexed imaging of epithelial-mesenchymal transition (EMT)-related proteins. Furthermore, we developed a VPSFE-based Turing pattern coding strategy for multiplexed detection that requires only a single multicolor probe hybridization step. Using three voltage conditions and three fluorescence channels, this system generates 27 unique fluorescence Turing patterns to encode 27 distinct targets. This electric-field Turing pattern coding strategy represents a novel probe exchange-free approach for rapid, universal, and highly specific multiplexed in situ imaging.}, }
@article {pmid40844198, year = {2025}, author = {Feng, Y and Xu, Q and Ouyang, C and Wei, Y and Gan, Z and Liu, Y and Yu, L and Xiao, Y}, title = {Dual-Enhanced Lanthanide MOF-Based Fluorescent Bio-Barcode via Conformational Regulation for Ultrasensitive Detection of DNA Epigenetic Biomarker.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e04246}, doi = {10.1002/smll.202504246}, pmid = {40844198}, issn = {1613-6829}, support = {82273895//National Natural Science Foundation of China/ ; 82304440//National Natural Science Foundation of China/ ; 82073811//National Natural Science Foundation of China/ ; }, abstract = {Aberrant epigenetic modifications (EMs) serve as critical biomarkers but remain challenging to detect due to their low abundance in biological samples. A lanthanide metal-organic framework (Ln-MOF) bio-barcode method integrating the dual actions of ultrahigh DNA loading density and anion-π interaction-driven fluorescence enhancement for the ultrasensitive detection of EMs, such as 5-formylcytosine (5fC), is developed. The system employs streptavidin-functionalized magnetic beads to selectively capture biotinylated 5fC-modified nucleic acids, which then capture Er-organic framework probes (UiO-66 (Er)) tagged with thousands of quenched fluorescent oligonucleotides (FAM-ODN). After magnetic separation, phosphate-induced desorption restores the fluorescence of oligonucleotides, signaling the presence of 5fC. Subsequently, free phosphate, functioning as both a strong base and an anion, further amplifies fluorescence by altering the conformation of FAM molecules. This dual-action mechanism combines high nucleic acid loading capacity of Ln-MOF and conformation-regulated fluorescence enhancement enables the fluorescent bio-barcode to achieve a detection limit of 0.0225% content. The detection results of 5fC in cellular and thyroid cancer tissue samples confirm global 5fC downregulation as a robust epigenetic hallmark of cancer. The enzyme- and amplification-free design ensures robustness and cost-efficiency, while modular probe architecture enables adaptation to diverse low-abundance targets, from epigenetic modifications to protein biomarkers.}, }
@article {pmid40836224, year = {2025}, author = {Xu, J and Zheng, W and Ou, X and He, H and Yang, C and Guo, L and Xiao, C and Jiang, W and Shu, G and Zhou, T}, title = {Identification and functional analysis of novel precursor genes in cyclic peptide biosynthesis in Pseudostellaria heterophylla.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1103}, pmid = {40836224}, issn = {1471-2229}, abstract = {BACKGROUND: Pseudostellaria heterophylla, a member of the Caryophyllaceae family, is widely used in traditional Chinese medicine due to its bioactive cyclic peptides (CPs) with immunomodulatory functions. Caryophyllaceae- like CPs, one of the largest types plant-derived CPs, typically consist of 5–12 amino acids and are derived from ribosomally synthesized peptide precursors. The diversity of CPs arises from variations in their core peptide sequences. However, the precursor genes responsible for Caryophyllaceae-like CPs biosynthesis in P. heterophylla remain largely uncharacterized.<br><br>RESULTS: In this study, barcoding PCR combined with high-throughput sequencing was used to efficiently genotype precursor genes encoding CPs in P. heterophylla. This approach enabled the identification of known and novel precursor genes, including prePhHB_1, prePhHB_2, prePhPE and prePhPN. The core peptide regions showed high variability, while the leader and follower regions were relatively conserved, with a few nucleotide mutations. Tissue-specific expression analysis revealed that prePhHB was predominantly expressed in the phloem and fibrous roots, while prePhPE was specifically expressed in the xylem. prePhPN exhibited low expression level and was mainly detected in the phloem and stem. Moreover, the expression of these precursor genes was responsive to abscisic acid and nitrogen stress. RNA in situ hybridization revealed that prePhPE transcripts were primarily localized in the xylem and phellem of the roots. Transient co-expression in Nicotiana benthamiana indicated that prePhPE is involved in the biosynthesis of Pseudostellarin E (PE).<br><br>CONCLUSIONS: Barcoding PCR combined with high-throughput sequencing provides an effective strategy for investigating CP precursor genes, including those with low expression. The results reveal conserved features in CP precursor genes and highlight a previously unrecognized mechanism contributing to CP diversity. The prePhPE gene was identified as the precursor gene of PE, which accumulates mainly in the xylem of P. heterophylla roots. prePhPN may be a precursor gene for a novel CP.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-06972-2.}, }
@article {pmid40833964, year = {2025}, author = {Wisitrassameewong, K and Adamčík, S and Adamčíková, K and Tang, SM and Tangthirasunun, N and Chuankid, B and Raspé, O}, title = {Russula orientalovirescens sp. nov., a common Southeast Asian edible fungus is different from the European look-alike R. virescens.}, journal = {PloS one}, volume = {20}, number = {8}, pages = {e0322545}, doi = {10.1371/journal.pone.0322545}, pmid = {40833964}, issn = {1932-6203}, mesh = {Phylogeny ; *Basidiomycota/genetics/classification ; Asia, Southeastern ; DNA, Fungal/genetics ; Europe ; }, abstract = {Green-cracking Russulas are edible fungi that are widely consumed and traded in Southeast Asia. Asian collections of this morphotype were frequently identified as R. virescens in local literature. Multilocus phylogenetic analyses of ITS nrDNA, rpb2 and tef1 regions presented in this study strongly supported that the majority of green cracking Russula collections from Southeast Asia represent a species different from European R. virescens and these collections are described here as R. orientalovirescens sp. nova. Analysis of ITS barcoding region confirmed that published sequence data from China, Laos and Myanmar reported this species as R. virescens. In addition, this analysis showed that the species is widely distributed in Southeast Asia from Malayan Peninsula to Japan, preferring areas with dry season, and is associated with coniferous and deciduous trees as well as heterotrophic plants. Morphological analyses and detailed comparison with recent collections of R. virescens showed that R. orientalovirescens differs from the latter by larger spores and shorter and more abundant pileocystidia. Green-cracking Russula species with distinctly areolate pileus formed a monophyletic lineage where our new species is grouped with Asian R. viridirubrolimbata, European R. virescens and North American R. parvovirescens. Few publicly available ITS sequences from Southeast Asia clustered with either European or North American species suggesting that the phylogenetic lineage of green-cracking Russulas urgently require further attention.}, }
@article {pmid40833555, year = {2025}, author = {Hurwitz, SN}, title = {Mapping Hematopoietic Fate after Transplantation.}, journal = {Stem cell reviews and reports}, volume = {}, number = {}, pages = {}, pmid = {40833555}, issn = {2629-3277}, abstract = {Hematopoietic stem and progenitor cells (HSPCs) form the foundation of lifelong blood cell production and immune function. Understanding their fate, including how they differentiate, self-renew, and respond to environmental cues has long been a cornerstone of stem cell biology and regenerative medicine. This knowledge is especially vital in the context of therapeutic hematopoietic stem and progenitor cell transplantation, where the diverse behavior of transplanted HSPCs directly impacts patient outcomes. Advances in single-cell omics, lineage barcoding, and in situ tracking now allow us to directly trace the developmental trajectories and clonal contributions of individual HSPCs. These tools are reshaping our understanding of hematopoiesis not as a rigid hierarchy but as a dynamic and adaptive system. This review highlights key technologies that enable fate mapping of HSPCs, integrates insights into clonal behavior during both transplantation and native hematopoiesis, and discusses how these findings are likely to inform future diagnostic and therapeutic strategies. CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40832237, year = {2025}, author = {Aleksandrovic, E and Fross, SR and Golomb, SM and Liu, X and Zhao, Z and Das, NM and Reese, TC and Ma, W and Lopez, J and Stack, MS and Zhao, M and Zhang, S}, title = {Temporal Clonal Tracing and Functional Perturbation Reveal Niche-Adaptive and Tumor-Intrinsic IFNγ Dependencies Driving Ovarian Cancer Metastasis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.08.13.669778}, pmid = {40832237}, issn = {2692-8205}, abstract = {Metastasis is an emergent continuum, driven by evolving reciprocal adaptations between continuously disseminating tumor cells (DTCs) and the specialized metastatic niches of distant organs. The interplay between intrinsic and niche-driven mechanisms that enables DTCs to survive and home to distant organs remains incompletely understood. Here, using MetTag, a single-cell barcoding and transcriptome profiling approach with time-stamped BC.IDs, we mapped temporal, clonal dynamics of DTCs and the immune cell landscape across ovarian cancer metastatic niches. Deep sequencing of barcodes revealed preferred enrichment of early-disseminated clones across metastatic niches. Mechanistically, single-cell RNA sequencing (scRNA-seq) coupled with velocity analyses in ascites and metastasis-bearing omentums uncovered an emergent, distinct interferon-gamma (IFNγ) centric transcriptional trajectory, enriched among early seeding clones. Moreover, in vivo CRISPR/Cas9 screening of metastatic niche-specific signatures demonstrated that genes belonging to the ascites IFNγ signature, including Marco, Gbp2b, and Slfn1, are functionally important for peritoneal metastasis. Knockout of IFNγ receptor 1 (Ifngr1) in tumor cells significantly reduced metastatic burden and extended survival, underscoring the importance of tumor cell intrinsic IFNγ signaling in ovarian cancer metastasis. Furthermore, we identified that the tumor intrinsic IFNγ response and ascites-derived tumor-associated macrophages (TAMs) protect cancer cells from anoikis-mediated death within the IFNγ-rich ascites environment. Our study resolves temporal dynamics of disseminating tumor cells and highlights an ascites-driven, IFNγ program as a necessary pro-metastatic adaptation in the ovarian metastasis cascade.}, }
@article {pmid40830572, year = {2025}, author = {Foyt, D and Brown, D and Zhou, S and Moser, B and Zhu, Q and Gartner, ZJ and Huang, B}, title = {HybriSeq: probe-based device-free single-cell RNA profiling.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1250}, pmid = {40830572}, issn = {2399-3642}, support = {R01DK127421//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; CRI5054//Cancer Research Institute (CRI)/ ; }, abstract = {We have developed the HybriSeq method for single-cell RNA profiling, which utilizes in situ hybridization of multiple probes for targeted transcripts, followed by split-pool barcoding and sequencing analysis of the probes. We have shown that HybriSeq can achieve high sensitivity for RNA detection with multiple probes and profile entire transcripts without an end bias. The utility of HybriSeq is demonstrated in characterizing cell-to-cell heterogeneities of a panel of 196 genes in peripheral blood mononuclear cells and the detection of missed annotations of transcripts.}, }
@article {pmid40830305, year = {2025}, author = {Maetens, H and Mukungilwa, PN and Kasangaki, A and Boom, AF and Nshimiyumuremyi, T and Munyandamutsa, PS and Clausnitzer, V and Vranken, N and Snoeks, J and Van Steenberge, M}, title = {An ichthyological borderland: The fishfauna of Nyungwe National Park and surroundings (Rwanda, East Africa).}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70185}, pmid = {40830305}, issn = {1095-8649}, support = {B2/202/P1/KEAFish//Belgian Science Policy Office/ ; 1128222N//Fonds Wetenschappelijk Onderzoek/ ; //Volkswagen Foundation/ ; }, abstract = {Nyungwe National Park (NP) is a mountainous region situated in the southwestern part of Rwanda on Congo-Nile watershed. In spite of the high biodiversity in primates, birds and plants, no fish were reported to occur in the park, probably because of the cold temperatures of the rivers. An expedition in 2022 examined the fish diversity within the Nyungwe NP and its buffer zones. Additional sampling was performed in the main river draining the park into Lake Kivu: the Kamiranzovu. Three hundred and twenty specimens belonging to 13 species were collected. Specimens were collected only in the western part of the park, draining towards the Congo basin. The diversity within the park proper was limited to two putative species within the complex of Amphilius cf. kivuensis, which were caught on either side of the Kivu-Rusizi watershed. In contrast, a higher fish diversity, including one clariid species and two species of Enteromius, was observed in the rivers at a lower altitude of the buffer zone. However, the highest species diversity was found near the mouth of Kamiranzovu River, including 11 species, of which 4 were non-native: the guppy Poecilia reticulata, Astatotilapia burtoni, the blue-spotted tilapia Oreochromis leucosticus and the Egyptian mouth-brooder Pseudocrenilabrus multicolor.}, }
@article {pmid40827881, year = {2025}, author = {Guan, W and Liu, S and Chen, Y and Chu, C and Peng, G and Wang, J and Weng, Q and Fu, Y and Li, J}, title = {HPVPool-Seq: a genotype-guided pooling strategy for cost-effective next-generation sequencing detection of HPV integration in cervical samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0139925}, doi = {10.1128/spectrum.01399-25}, pmid = {40827881}, issn = {2165-0497}, abstract = {UNLABELLED: Integration of high-risk human papillomavirus (hrHPV) DNA is a critical event in carcinogenesis and a promising biomarker for risk stratification. However, the high cost of next-generation sequencing (NGS) limits its widespread clinical adoption. We developed HPVPool-Seq, an innovative pooling strategy that leverages the inherent diversity of HPV genotypes as natural barcodes, enabling cost-effective, scalable integration detection. Samples were pooled based on qPCR-derived HPV genotypes and viral loads prior to targeted NGS and bioinformatic decoding. A web-based automation tool was implemented to streamline pooling and decoding workflows. In a proof-of-concept study of 175 clinical specimens, HPVPool-Seq achieved 77.1% exact genotype concordance and 97.1% combined sensitivity compared with qPCR. Cost simulations demonstrated a 60% reduction in per-sample sequencing expenses. Self-correcting capability through targeted retesting further enhanced reliability. HPVPool-Seq offers a novel, traceable, and economically viable solution for high-throughput HPV integration profiling, balancing cost, scalability, and clinical precision. This strategy sets a new framework for molecular screening in HPV-associated cancers.<br><br>IMPORTANCE: Accurate detection of high-risk HPV integration is critical for identifying individuals at true risk of progression to malignancy. However, the high cost of next-generation sequencing (NGS) has limited its widespread clinical application. Here, we propose HPVPool-Seq, a novel pooling-based sequencing strategy that uses HPV genotypes as intrinsic barcodes to guide sample pooling without compromising detection sensitivity. This method dramatically reduces sequencing costs while maintaining genotype-level traceability and offers a built-in mechanism for selective retesting of discordant cases. By addressing both technical and economic barriers, our approach provides a scalable, clinically applicable solution for HPV integration profiling in large cohorts, with important implications for precision screening, triage, and epidemiological surveillance.}, }
@article {pmid40827760, year = {2025}, author = {Dhami, MK and Matheson, P and Bird, S and Walker, L and Hohaia, H and McGaughran, A}, title = {Revisiting Genetic Data Stewardship Practices in Aotearoa New Zealand: A Call to Action on Integrating Māori Data Sovereignty.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70021}, doi = {10.1111/1755-0998.70021}, pmid = {40827760}, issn = {1755-0998}, support = {2223-44-010//New Zealand Biological Heritage National Science Challenge/ ; }, abstract = {Genetic data, including environmental DNA (eDNA), are regularly used to monitor escalating biodiversity concerns globally. In Aotearoa New Zealand, biodiversity is unique and cherished-many species are taonga (treasured) and cared for by kaitiaki (guardians with customary responsibilities), specifically mana whenua with custodial rights (Māori; the Indigenous people of New Zealand). Discussions are currently underway regarding the development of a reference DNA barcode database for biodiversity in Aotearoa New Zealand to improve outcomes for biosecurity surveillance and biodiversity assessment. A priority of these discussions is that the database development and eventual implementation accords with Te Tiriti o Waitangi (The Treaty of Waitangi). Here, we evaluate current practices for storing genetic data from samples collected in Aotearoa New Zealand by examining two major public data repositories-the National Centre for Biotechnology Information (NCBI) GenBank and the Barcode of Life Data System (BOLD). We find that current database practices limit opportunities for Māori data sovereignty, with DNA from many taonga species uploaded to public repositories with no associated restrictions or guidelines over use. This is an important finding that will help shape the development of a future DNA reference database for Aotearoa New Zealand that integrates the rights and interests of Indigenous communities.}, }
@article {pmid40827628, year = {2025}, author = {von der Heyden, S}, title = {'It's not much, but it's honest work': The status of environmental DNA analyses of fish biodiversity in southern Africa.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70187}, pmid = {40827628}, issn = {1095-8649}, support = {SRUG2204041792//National Research Foundation/ ; }, abstract = {Environmental DNA (eDNA) biodiversity surveys have the power to transform the detection of species in natural environments, which is crucial for the conservation and management of freshwater, estuarine and marine environments. Globally, eDNA-based analyses have increased significantly, with fishes being the most widely studied aquatic organisms. However, the extent of work and the current status of eDNA-based surveys for southern Africa are unclear. A literature search for studies with a focus on fishes was carried out for Botswana, Namibia, Mozambique, South Africa and Zimbabwe and retrieved 16 papers. Most of these were from South Africa (n = 14), with one paper each from Botswana and Mozambique. No papers were found for Namibia and Zimbabwe. Eleven papers utilized metabarcoding to detect fish communities, whereas four utilized species-specific primers to detect rare (e.g., coelacanth, pipefishes, endangered and vulnerable freshwater fishes) or invasive (silver carp) species and one consisted of a diet study. There were five papers from freshwater and 11 studies applying eDNA-based surveys in estuaries or marine systems. A scan of some of the technical aspects of the eDNA workflow (biological replication filtration, inclusion of negative controls, primer choice and technical replication) showed a wide range of approaches, highlighting the need for standardization of the eDNA workflow and the reporting of its data. Unsurprisingly, one of the largest challenges remains the lack of referenced barcodes, which limits the ability to determine species distributions and associated ecological inferences. Building on the exciting work highlighted here and to fully realize the power of eDNA will require increasing collaborations across all aspects of the eDNA workflow. Further, exploring pathways for the meaningful integration of data derived from eDNA surveys to support conservation and management decisions, not only for fishes but also for all the incredible biodiversity of southern Africa, is crucial.}, }
@article {pmid40806250, year = {2025}, author = {Dang, Z and Wu, Q and Zhou, Y and Wang, L and Liu, Y and Yang, C and Liu, M and Xie, Q and Chen, C and Ma, S and Shan, B}, title = {Comparative Transcriptomic Analysis for Identification of Environmental-Responsive Genes in Seven Species of Threadfin Breams (Nemipterus).}, journal = {International journal of molecular sciences}, volume = {26}, number = {15}, pages = {}, pmid = {40806250}, issn = {1422-0067}, support = {NO. 42206109//National Natural Science Foundation of China/ ; Modern fishery cooperation between China and neighboring countries around the South China Sea//Asia Cooperation Fund Project/ ; NO.2023TD93//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {Members of the genus Nemipterus are economically important fish species distributed in the tropical and subtropical Indo-West Pacific region. The majority of species in this genus inhabit waters with sandy-muddy substrates on the continental shelf, although different species are found at slightly varying water depths. In this study, we sequenced seven species within the genus Nemipterus after identifying the specimens using complementary morphological analysis and DNA barcoding. Each species yielded over 40,000,000 clean reads, totaling over 300,000,000 clean reads across the seven species. A total of 276,389 unigenes were obtained after de novo assembly and a total of 168,010 (60.79%) unigenes were annotated in the protein database. The comprehensive functional annotation based on the KOG, GO, and KEGG databases revealed that these unigenes are mainly associated with numerous physiological, metabolic, and molecular processes, and that the seven species exhibit similarity in these aspects. By constructing a phylogenetic tree and conducting divergence time analysis, we found that N. bathybius and N. virgatus diverged most recently, approximately during the Neogene Period (14.9 Mya). Compared with other species, N. bathybius and N. virgatus are distributed in deeper water layers. Therefore, we conducted selection pressure analysis using these two species as the foreground branches and identified several environmental-responsive genes. The results indicate that genes such as aqp1, arrdc3, ISP2, Hip, ndufa1, ndufa3, pcyt1a, ctsk, col6a2, casp2 exhibit faster evolutionary rates during long-term adaptation to deep-water environments. Specifically, these genes are considered to be associated with adaptation to aquatic osmoregulation, temperature fluctuations, and skeletal development. This comprehensive analysis provides valuable insights into the evolutionary biology and environmental adaptability of threadfin breams, contributing to the conservation and sustainable management of these species.}, }
@article {pmid39677764, year = {2024}, author = {Cho, S and Moon, W and Martino, N and Yun, SH}, title = {Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677764}, issn = {2692-8205}, support = {R01 EB033155/EB/NIBIB NIH HHS/United States ; R01 EB034687/EB/NIBIB NIH HHS/United States ; }, abstract = {Laser particles (LPs) emitting narrowband spectra across wide spectral ranges are highly promising for high-multiplex optical barcoding. Here, we present LPs based on indium phosphide (InP) nanodisks, operating in the near-infrared wavelength range of 740-970 nm. Utilizing low-order whispering gallery resonance modes in size-tuned nanodisks, we achieved an ultrawide color palette with 27% bandwidth utilization and nanometer-scale linewidth. The minimum laser size was 430 nm in air and 560 nm within the cytoplasm, operating at mode order 4 or 5. We further demonstrated spectral detection of laser peaks with high signal-to-background ratios in highly-scattering media, including 1-cm-thick chicken breast tissue and blood vessels in live mice.}, }
@article {pmid39416107, year = {2024}, author = {Chen, J and Nilsen, ED and Chitboonthavisuk, C and Mo, CY and Raman, S}, title = {Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416107}, issn = {2692-8205}, support = {R21 AI156785/AI/NIAID NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; }, abstract = {Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.}, }
@article {pmid39203446, year = {2024}, author = {Darienko, T and Rad-Menéndez, C and Pröschold, T}, title = {The New Genus Caulinema Revealed New Insights into the Generic Relationship of the Order Ulotrichales (Ulvophyceae, Chlorophyta).}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203446}, issn = {2076-2607}, support = {P 34416-B//FWF Austrian Science Fund/ ; }, abstract = {Traditionally, the order Ulotrichales comprised green algae of an unbranched, uniseriate, filamentous morphology. However, since the establishment of ultrastructural features, the circumscription of this order has dramatically changed. Some genera and species have been excluded from this order and others with different morphologies (sarcinoid, branched filaments or even parenchymatous taxa) have been included. Phylogenetic analyses have confirmed the monophyly of this order, but its differentiation from the Ulvales and Acrosiphoniales remains difficult because of the lack of synapomorphies at every level (morphology, molecular signatures). To demonstrate the difficulties of placement into genera and orders, we investigated two sarcinoid taxa with the absence of zoospore formation. SSU and ITS rDNA tree topology and the ITS-2/CBC approach revealed that both strains SAG 2661 and CCAP 312/1 belong to Ulosarcina terrestrica and the newly erected genus Caulinema, respectively. The species conception using this approach was evaluated by sequencing the plastid-coding gene tufA, a commonly used barcode marker for green algae. All three molecular markers resulted in similar topologies at the generic and species levels, which is consistent with the ITS-2/CBC approach and tufA for barcoding. The reevaluation of the ultrastructural features revealed that the presence of organic scales on the surfaces of motile cells is characteristic for the order Ulotrichales and can be used for separation from the closely related orders. As a consequence of our study, we propose the new genus Caulinema for strain CCAP 312/1.}, }
@article {pmid38002986, year = {2023}, author = {Gao, T and Shi, Y and Xiao, J}, title = {Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae).}, journal = {Genes}, volume = {14}, number = {11}, pages = {}, pmid = {38002986}, issn = {2073-4425}, support = {41976083//National Natural Science Foundation of China/ ; 41776171//National Natural Science Foundation of China/ ; 2021C0204//the Province Key Research and Development Program of Zhejiang/ ; }, mesh = {Animals ; Phylogeny ; Thailand ; *Fishes/genetics ; *Perciformes/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.}, }
@article {pmid36123605, year = {2022}, author = {Maes, T and De Corte, Z and Vangestel, C and Virgilio, M and Smitz, N and Djuikwo-Teukeng, FF and Papadaki, MI and Huyse, T}, title = {Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia).}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {328}, pmid = {36123605}, issn = {1756-3305}, support = {1S86319N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; *Bulinus/parasitology ; *Gastropoda/genetics ; Genetics, Population ; Humans ; Phylogeny ; Schistosoma haematobium/genetics ; }, abstract = {BACKGROUND: Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17-150 km) and inter-regional (1000-5400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively.<br><br>METHODS: Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus.<br><br>RESULTS: A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission.<br><br>CONCLUSIONS: HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission.}, }
@article {pmid36080967, year = {2022}, author = {Khan, G and Hegge, A and Gemeinholzer, B}, title = {Development and Testing of the A1 Volumetric Air Sampler, an Automatic Pollen Trap Suitable for Long-Term Monitoring of eDNA Pollen Diversity.}, journal = {Sensors (Basel, Switzerland)}, volume = {22}, number = {17}, pages = {}, pmid = {36080967}, issn = {1424-8220}, support = {01LC19031//Federal Ministry of Education and Research/ ; }, mesh = {*Air Pollutants/analysis ; Biodiversity ; *Environmental Monitoring/methods ; Humans ; Pollen/chemistry ; }, abstract = {Airborne pollen surveys provide information on various aspects of biodiversity and human health monitoring. Such surveys are typically conducted using the Burkard Multi-Vial Cyclone Sampler, but have to be technically optimized for eDNA barcoding. We here developed and tested a new airborne pollen trap, especially suitable for autonomous eDNA-metabarcoding analyses, called the A1 volumetric air sampler. The trap can sample pollen in 24 different tubes with flexible intervals, allowing it to operate independently in the field for a certain amount of time. We compared the efficiency of the new A1 volumetric air sampler with another automated volumetric spore trap, the Burkard Multi-Vial Cyclone Sampler, which features shorter and fewer sampling intervals to evaluate the comparability of ambient pollen concentrations. In a sterile laboratory environment, we compared trap performances between the automated volumetric air samplers by using pure dry pollen of three species-Fagus sylvatica, Helianthus annuus and Zea mays-which differ both by exine ornamentation and pollen size. The traps had a standard suction flow rate of 16.5 L/min, and we counted the inhaled pollen microscopically after a predefined time interval. Our results showed that though we put three different pollen types in the same container, both the traps inhaled all the pollens in a statistically significant manner irrespective of their size. We found that, on average, both traps inhaled equal an number of pollens for each species. We did not detect any cross-contamination between tubes. We concluded that the A1 volumetric air sampler has the potential to be used for longer and more flexible sampling intervals in the wild, suitable for autonomous monitoring of eDNA pollen diversity.}, }
@article {pmid34646477, year = {2021}, author = {Hurtado, G and Mayer, G and Mabry, KE}, title = {Does urbanization ameliorate the effect of endoparasite infection in kangaroo rats?.}, journal = {Ecology and evolution}, volume = {11}, number = {19}, pages = {13390-13400}, pmid = {34646477}, issn = {2045-7758}, support = {R25 GM061222/GM/NIGMS NIH HHS/United States ; }, abstract = {Urban development can fragment and degrade remnant habitat. Such habitat alterations can have profound impacts on wildlife, including effects on population density, parasite infection status, parasite prevalence, and body condition. We investigated the influence of urbanization on populations of Merriam's kangaroo rat (Dipodomys merriami) and their parasites. We predicted that urban development would lead to reduced abundance, increased parasite prevalence in urban populations, increased probability of parasite infection for individual animals, and decreased body condition of kangaroo rats in urban versus wildland areas. We live trapped kangaroo rats at 5 urban and 5 wildland sites in and around Las Cruces, NM, USA from 2013 to 2015, collected fecal samples from 209 kangaroo rats, and detected endoparasites using fecal flotation and molecular barcoding. Seven parasite species were detected, although only two parasitic worms, Mastophorus dipodomis and Pterygodermatites dipodomis, occurred frequently enough to allow for statistical analysis. We found no effects of urbanization on population density or probability of parasite infection. However, wildland animals infected with P. dipodomis had lower body condition scores than infected animals in urban areas or uninfected animals in either habitat. Our results suggest that urban environments may buffer Merriam's kangaroo rats from the detrimental impacts to body condition that P. dipodomis infections can cause.}, }
@article {pmid29115074, year = {2017}, author = {Cho, YC and Lee, SH and Cho, YH and Choy, YB}, title = {Adapter-based Safety Injection System for Prevention of Wrong Route and Wrong Patient Medication Errors.}, journal = {Journal of Korean medical science}, volume = {32}, number = {12}, pages = {1938-1946}, pmid = {29115074}, issn = {1598-6357}, mesh = {Catheters ; Equipment Design ; Humans ; Injections/instrumentation/*methods ; Medication Errors/*prevention &amp; control ; Printing, Three-Dimensional ; }, abstract = {Wrong-route or -patient medication errors due to human mistakes have been considered difficult to resolve in clinical settings. In this study, we suggest a safety injection system that can help to prevent an injection when a mismatch exists between the drug and route or patient. For this, we prepared two distinct adapters with key and keyhole patterns specifically assigned to a pair of drug and route or patient. When connected to a syringe tip and its counterpart, a catheter injection-port, respectively, the adapters allowed for a seamless connection only with their matching patterns. In this study, each of the adapters possessed a specific key and keyhole pattern at one end and the other end was shaped to be a universal fit for syringe tips or catheter injection-ports in clinical use. With the scheme proposed herein, we could generate 27,000 patterns, depending on the location and shape of the key tooth in the adapters. With a rapid prototyping technique, multiple distinct pairs of adapters could be prepared in a relatively short period of time and thus, we envision that a specific adapter pair can be produced on-site after patient hospitalization, much like patient identification barcodes.}, }
@article {pmid40823546, year = {2025}, author = {Rodríguez-Flores, PC and Bracken-Grissom, HD and Lemaitre, R and Felder, DL and Nizinski, MS}, title = {A new squat lobster (Crustacea, Decapoda, Munidopsidae) from the western Atlantic with redescription of Munidopsisexpansa Benedict, 1902 and several range extensions.}, journal = {ZooKeys}, volume = {1248}, number = {}, pages = {321-340}, pmid = {40823546}, issn = {1313-2989}, abstract = {The western Atlantic Ocean harbors a rich fauna of deep-sea squat lobsters that have been intensively studied during the last two centuries. We revise material recently collected by trawls, ROV and submersibles on several expeditions in the Gulf of Mexico and the Caribbean Sea. Using an integrative taxonomy approach, we describe Munidopsismessingi sp. nov. and redescribe M.expansa Benedict, 1902, the latter species known only from a few records. Additionally, we report a new record of M.turgida Rodríguez-Flores, Macpherson &amp; Machordom, 2018 for the Gulf of Mexico. This rare species was previously known from only the holotype, collected in the Guadeloupe Islands, Caribbean Sea. We apply micro-CT scanning in the course of morphological illustrations and report barcode data as available.}, }
@article {pmid40823049, year = {2025}, author = {Zaman, M and Faraz, A and Azad, R and Khan, IA and Faheem, B and Rafiq, N and Khan, A and Shilin, T and ALmunqedhi, BM and Ali, HM}, title = {Updating the Systematic Status of Genus Heterotermes (Rhinotermitidae: Isoptera: Blattodea) by Combining Morphometric Analysis, Distribution Mapping, and DNA Barcoding Approaches.}, journal = {Ecology and evolution}, volume = {15}, number = {8}, pages = {e71993}, pmid = {40823049}, issn = {2045-7758}, abstract = {Termites are eusocial insects, found widely in the tropics of the world. They are known as serious pests to agriculture, forestry, and structures, but they also act as key ecological engineers in the wild. We assessed termites diversity in three districts (Buner, Swabi and Haripur), which belong to various agro-ecological regions of Khyber Pakhtunkhwa (Pakistan; Oriental region). Sampling was done either by breaking visible mud galleries or by using modified NIFA termaps. Fourteen characters/indices were assessed for species morphometrics and Principal Component Analysis (PCA), and DNA was extracted from the identified soldier caste in each sample for MtDNA COII barcoding. An identification key and distribution map were made for Heterotermes gretudae (MZ018116.1) and Heterotermes indicola (MZ055400.1). H. gretudae is a true species endemic to India but is recorded in Pakistan for the first time (Buner and Swabi districts) on new feeding host substrates, while H. indicola has a new locality record. PCA analysis (74.9% variation) and MtDNA COII barcoding (Maximum Likelihood analyses) were used to validate the species. Novel COII sequences were submitted to the GenBank.}, }
@article {pmid40822413, year = {2025}, author = {Kim, S and Sohn, J and Lee, M and Kim, H}, title = {First records of the genera Aclitus and Protaphidius (Hymenoptera, Braconidae, Aphidiinae) from South Korea.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e161563}, pmid = {40822413}, issn = {1314-2828}, abstract = {BACKGROUND: The aphidiine genera Aclitus Förster, 1863 and Protaphidius Ashmead, 1900 (Hymenoptera, Braconidae, Aphidiinae) each contain only a few species worldwide. In this study, we report the first records of Aclitus and Protaphidius from Korea, based on specimens of Aclitussappaphis Takada &amp; Shiga, 1974 and Protaphidiusnawaii (Ashmead, 1906).<br><br>NEW INFORMATION: We provide detailed morphological characters, diagnostic characters, and photographic documentation for both species. A new host record, Hamamelistesbetulinus (de Horv&#xe1;th, 1896), of Aclitussappaphis is provided. To support species identification and future phylogenetic studies, mitochondrial (COI, COII, ND1, Cytb) and nuclear (28SD2, EF1A1, Wingless) gene sequences for both species are also provided.}, }
@article {pmid40817273, year = {2025}, author = {Kaifu, K and Han, YS and Shiraishi, H}, title = {Global consumption of threatened freshwater eels revealed by integrating DNA barcoding, production data, and trade statistics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {29968}, pmid = {40817273}, issn = {2045-2322}, support = {JP22H00371//Japan Society for the Promotion of Science/ ; NSTC 111-2313-B-002-016-MY3//National Science and Technology Council/ ; }, abstract = {Fisheries resources depend on natural ecosystems, yet their sustainable management is often limited by uneven regional capacities and the pressures of international trade. High demand from certain regions can lead to overexploitation in others, highlighting the need to understand global consumption patterns of key aquatic species. This study introduces an integrated approach that combines DNA barcoding of freshwater eel (Anguilla spp.) products collected from end markets in 11 countries/regions with global production and trade statistics. We estimate that over 99% of eels consumed worldwide belong to three IUCN-listed threatened species: the American eel, Japanese eel, and European eel. Consumption was heavily concentrated in East Asia-particularly China, Japan, and South Korea-where supply volumes far exceed those of other regions. Our approach yields the most comprehensive quantitative global estimate to date of eel species composition in consumption, offering essential insights for the conservation and sustainable management of this highly exploited group.}, }
@article {pmid40816522, year = {2025}, author = {Meng, XQ and Xu, XL and Gao, Y and Deng, SL}, title = {Establishment of CRISPR/Cas9 lineage tracking technology for pig embryos.}, journal = {Molecular and cellular probes}, volume = {}, number = {}, pages = {102046}, doi = {10.1016/j.mcp.2025.102046}, pmid = {40816522}, issn = {1096-1194}, abstract = {Understanding tissue development in pigs is critical for biomedical research and genetic engineering, particularly for modeling human disease. However, tracing developmental origins and reconstructing lineage trees for pig cells remains a significant challenge. Here, we present a high-resolution lineage tracing system that combines molecular barcoding with single-cell transcriptomics in pigs. Our system combines two key components: DNA barcodes (three CRISPR/Cas9 target sites and an 8-base pair intBC) integrated into the genome via piggyBac transposition, and a constitutive Cas9-EGFP cassette stably integrated at the Rosa26 locus using CRISPR/Cas12a. By combining lineage barcodes with single-cell RNA sequencing (scRNA-seq), we constructed an evolutionary lineage recorder that captures distinct cell states across developmental or differentiation trajectories. This system provides an essential tool for the subsequent construction of complete porcine cell fate maps. Our work provides a tool for studying porcine developmental biology, but also helps to optimize regenerative medicine strategies and improve the design of genetically engineered animal models.}, }
@article {pmid40815071, year = {2025}, author = {Silva, RGD and Teixeira, AAM and Chaves, RECRF and Ribeiro, SC and Ferreira, RR and Vasconcellos, A and Almeida, WO}, title = {Integrative taxonomy of Raillietiella gigliolii Hett, 1924 (Pentastomida: Raillietiellidae) - molecular and morphological evidence from Neotropical Amphisbaenians.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e94}, doi = {10.1017/S0022149X25100655}, pmid = {40815071}, issn = {1475-2697}, support = {BMD-0008-02422.01.18/24//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PVS-0215-00125.01.00/23//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; BP5-0197-00161.01.00/22)//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 308534/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 309820/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.929233/2023-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 88887.950422/2024-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {This study provides a comprehensive analysis of the morphology and genetics of Raillietiella gigliolii, an endoparasitic pentastomid found in amphisbaenians. The research was based on specimens deposited in the Universidade Regional do Cariri (URCA), as well as newly collected individuals from the Brazilian Caatinga. Detailed morphological descriptions were carried out, including measurements of the hooks, cephalothorax, tail, buccal cadre, and the copulatory spicule in males. In parallel, the first molecular characterisation of this species was performed, targeting the mitochondrial COI gene (barcode region). All specimens exhibited consistent morphotypes, particularly in the shape of the hooks, with no observable variation between males and females, nor between individuals parasitising different hosts (Amphisbaena alba and A. vermicularis). Molecular analyses revealed a well-supported monophyletic clade, with no detectable genetic divergence among individuals, confirming both the morphological stability and genetic delimitation of the species. These findings support the recognition of R. gigliolii as a clearly delineated species, currently restricted to amphisbaenians, which does not exhibit significant morphological variability, in contrast to other congeners.}, }
@article {pmid40813494, year = {2025}, author = {Yan, R and Zeng, Y and Chen, C and Rab, A and Li, H and Ullah, R and Islam, M and Cui, Y and Liu, M and Tian, X}, title = {Molecular evolution of chloroplast genome in Triumfetta (Grewioideae, Malvaceae).}, journal = {Planta}, volume = {262}, number = {4}, pages = {82}, pmid = {40813494}, issn = {1432-2048}, support = {2060302//The Ability Establishment of Sustainable Use for Valuable Chinese Medicine Resources/ ; }, abstract = {This study provides insights into the chloroplast genome evolution of Triumfetta, identifies polymorphic loci for molecular marker development, and offers preliminary phylogenomic evidence on the evolutionary relationships within the genus. The genus Triumfetta Plum. ex L. (Grewioideae, Malvaceae) is a pantropical group comprising approximately 177 species. Despite its diversity, its chloroplast (cp) genomics remain unstudied. To investigate evolutionary dynamics and phylogenetic relationships within Triumfetta, complete cp genomes of eight species were de novo assembled and compared with two publicly available genomes. These cp genomes were 160,075 to 160,604 base pairs (bp) long and consisted of a large single-copy region (89,006-89,386 bp), a small single-copy region (20,142-20,266 bp), and a pair of inverted repeats (IRa and IRb, 25,440-25,498 bp), encoding 112 unique genes (78 protein-coding, 30 transfer RNA, and 4 ribosomal RNA). Comparative analyses showed high similarity in GC content, IR contraction/expansion, codon usage, substitution patterns, and repeat structures. An inversion was identified in the LSC region of Triumfetta tomentosa, reversing six genes: trnC, petN, psbM, trnD, trnY, and trnE, without gene loss. Six genes (psbK, rpl20, rpl23, rps16, rps7, and ycf2) showed signatures of positive selection, suggesting potential roles in adaptation. Ten polymorphic loci were identified across intergenic and coding regions, including trnR-atpA, rpl33-rps18, ccsA-ndhD, clpP, rpl22, and ycf1, representing useful markers for DNA barcoding and population genetics. Phylogenetic analysis revealed Triumfetta is monophyletic and closely related to Corchorus L. Triumfetta species formed two distinct clades, reflecting a clear biogeographic divergence: one comprising African and Asian species, and the other consisting exclusively of Australian species. This study provides the first insights into cp genome variation and phylogenetic relationships in Triumfetta, offering resources for further phylogenetic, barcoding, and conservation research.}, }
@article {pmid40813104, year = {2025}, author = {Chou, WC and Canchola, A and Zhang, F and Lin, Z}, title = {Machine Learning and Artificial Intelligence in Nanomedicine.}, journal = {Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology}, volume = {17}, number = {4}, pages = {e70027}, pmid = {40813104}, issn = {1939-0041}, support = {R01 EB031022/EB/NIBIB NIH HHS/United States ; R03 EB035643/EB/NIBIB NIH HHS/United States ; R01EB031022/EB/NIBIB NIH HHS/United States ; R03EB035643/EB/NIBIB NIH HHS/United States ; }, abstract = {Nanomedicine harnesses nanoscale materials, such as lipid, polymeric, and inorganic nanoparticles, to deliver diagnostic or therapeutic agents for cancer, infectious disease, and neurological disorders, among others. However, translating promising nanoparticle designs into clinically approved products remains a challenge. Factors such as particle size, surface chemistry, and payload interactions must be optimized, and preclinical results often fail to predict human efficacy. In recent years, artificial intelligence (AI) and machine learning (ML) have emerged as transformative tools to address these hurdles at every stage of nanomedicine development. By rapidly screening extensive libraries and extracting structure-function relationships, AI-driven models can rationalize nanoparticle formulation, predict biodistribution, and guide optimal design. Techniques like high-throughput DNA barcoding and automated liquid handling facilitate robust, large-scale data collection, feeding into computational pipelines that expedite discovery while reducing reliance on resource-intensive trial-and-error experiments. AI-based platforms also enable improved modeling of protein corona formation, which profoundly affects nanoparticle immunogenicity and cellular uptake. Despite these advances, challenges persist in data standardization, model generalizability, and establishing a clear regulatory framework since no dedicated U.S. Food and Drug Administration (FDA) guidance addresses the intersection of AI and nanomedicine. Overcoming these limitations requires harmonized data sharing, rigorous in vivo validation, and clear ethical and regulatory guidelines. This review summarizes the rapidly evolving landscape of AI in nanomedicine, highlighting key successes in design and preclinical prediction, as well as persistent obstacles to full-scale clinical integration. By illuminating these dynamics, we aim to chart a more efficient path forward in developing next-generation nanomedicine.}, }
@article {pmid40809554, year = {2025}, author = {Zhang, J and Xing, Y and Yu, H and Li, S}, title = {Six new species of the spider genus Clubiona Latreille, 1804 (Araneae, Clubionidae) from subtropical forests of Sichuan Province, China.}, journal = {ZooKeys}, volume = {1248}, number = {}, pages = {61-91}, pmid = {40809554}, issn = {1313-2989}, abstract = {Six new species, belonging to three species groups of Clubiona Latreille, 1804 are described from both males and females: C.huntianling Yu &amp; Li, sp. nov., C.rouqiu Yu &amp; Li, sp. nov. and C.yinyangjian Yu &amp; Li, sp. nov. from the corticalis group; C.huojianqiang Yu &amp; Li, sp. nov. and C.qiankunquan Yu &amp; Li, sp. nov. from the trivialis group; C.nezha Yu &amp; Li, sp. nov. from the zilla group. These species are currently known to occur only in subtropical forests, Sichuan, China. The DNA barcodes of all species were obtained for species delimitation, matching of sexes and future use.}, }
@article {pmid40809552, year = {2025}, author = {Fang, Y and van Achterberg, C and Tang, P and Chen, XX}, title = {Revision of genus Zele Curtis (Hymenoptera, Braconidae, Euphorinae) from China, with description of nineteen new species.}, journal = {ZooKeys}, volume = {1248}, number = {}, pages = {125-208}, pmid = {40809552}, issn = {1313-2989}, abstract = {Zele Curtis is a braconid parasitoid wasp genus within the subfamily Euphorinae (Hymenoptera, Braconidae), consisting of only 30 species worldwide. The Chinese species of the genus Zele are revised and 29 species are now recognised, including 19 species new to science: Z.aquilus Fang, van Achterberg &amp; Chen, sp. nov., Z.carinatus Fang, van Achterberg &amp; Chen, sp. nov., Z.confusus Fang, van Achterberg &amp; Chen, sp. nov., Z.cristatus Fang, van Achterberg &amp; Chen, sp. nov., Z.curvatus Fang, van Achterberg &amp; Chen, sp. nov., Z.curvinervis Fang, van Achterberg &amp; Chen, sp. nov., Z.densipunctatus Fang, van Achterberg &amp; Chen, sp. nov., Z.extensus Fang, van Achterberg &amp; Chen, sp. nov., Z.fulgidus Fang, van Achterberg &amp; Chen, sp. nov., Z.fuscatus Fang, van Achterberg &amp; Chen, sp. nov., Z.impolitus Fang, van Achterberg &amp; Chen, sp. nov., Z.inclinator Fang, van Achterberg &amp; Chen, sp. nov., Z.irregularis Fang, van Achterberg &amp; Chen, sp. nov., Z.petiolatus Fang, van Achterberg &amp; Chen, sp. nov., Z.rugulosus Fang, van Achterberg &amp; Chen, sp. nov., Z.sculpticoxis Fang, van Achterberg &amp; Chen, sp. nov., Z.shaanxiensis Fang, van Achterberg &amp; Chen, sp. nov., Z.syntomus Fang, van Achterberg &amp; Chen, sp. nov., and Z.vacatus Fang, van Achterberg &amp; Chen, sp. nov. 31 barcode region sequences of mitochondrial cytochrome c oxidase I (COI) from the genus Zele were obtained and combined with 102 sequences from BOLD. They were used to validate new species and to get an indication of similarity among species. Three species are reinstated: Zeleperonatus (Shestakov, 1940), Z.romani (Fahringer, 1929), and Z.rufulus (Thomson, 1895). In addition, an identification key for the Zele species recorded in China (plus one expected species) is provided.}, }
@article {pmid40809550, year = {2025}, author = {Gallardo Salamanca, ML&#xc1; and Asorey, C and Macpherson, E}, title = {A new species of Galathea (Decapoda, Galatheidae) from the seamounts of the Easter Island area (Southeast Pacific Ocean Ridge) associated with a sea urchin.}, journal = {ZooKeys}, volume = {1248}, number = {}, pages = {111-123}, pmid = {40809550}, issn = {1313-2989}, abstract = {Galatheatukitukimea sp. nov. is described from the seamounts near Rapa Nui (Easter Island) and represents the first record of the genus for this region of the Pacific Ocean and for Chilean territory. The new species belongs to the group of species having the carapace with median protogastric and cardiac spines. G.tukitukimea has always been observed associated with the sea urchin Stereocidarisnascaensis. This potential mimicry-based association is uncommon in squat lobsters, which warrants further study.}, }
@article {pmid40809456, year = {2025}, author = {Guo, Y and Zhang, L and Zhao, X and Xu, C and Li, Y and Gao, Z and Ou, G and Chen, P and Zheng, W and Pei, H and Liu, X and Liu, BF and Li, Y}, title = {Toti-N-glycan Recognition Enables Universal Multiplexed Single-Nucleus RNA Sequencing.}, journal = {Research (Washington, D.C.)}, volume = {8}, number = {}, pages = {0678}, pmid = {40809456}, issn = {2639-5274}, abstract = {Sample barcoding-based multiplex single-cell and single-nucleus sequencing (sc/sn-seq) offers substantial advantages by reducing costs, minimizing batch effects, and identifying artifacts, thereby advancing biological and biomedical research. Despite these benefits, universal sample barcoding has been hindered by challenges such as inhomogeneous expression of tagged biomolecules, limited tagging affinity, and insufficient genetic insertion. To overcome these limitations, we developed Toti-N-Seq, a universal sample multiplex method, by tagging Toti-N-glycan on cell surfaces or nuclear membranes via our engineered streptavidin-Fbs1 GYR variant fusion protein, which could be used not only for sc-seq but also for sn-seq. Instead of targeting lipids or proteins, we focused on targeting the ubiquitous N-glycans found on any species with accessible membranes, which minimizes the exchange between barcoded samples and avoids biased barcoding. Our technology can be broadly applied to multiple species and nearly all eukaryotic cell types, with an overall classification accuracy of 0.969 for sc-seq and of 0.987 for sn-seq. As a demonstration with clinical human peripheral blood mononuclear cells, our Toti-N-Seq achieved rapid one-step sample preparation (<3 min) for easily scaling up while keeping high fidelity of sample ratios, removing artifacts, and detecting rare cell populations (~0.5%). Consequently, we offer a versatile platform suitable for various cell types and applications.}, }
@article {pmid40808602, year = {2025}, author = {Grigoryeva, MA and Khrenova, MG and Zvereva, MI}, title = {NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency.}, journal = {Journal of bioinformatics and computational biology}, volume = {23}, number = {4}, pages = {2550011}, doi = {10.1142/S0219720025500118}, pmid = {40808602}, issn = {1757-6334}, abstract = {In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation.}, }
@article {pmid40808235, year = {2025}, author = {Hansen, ML and Kordatos, KIT and Nørgaard, JK and Peter Bredal Jørgensen, J and Strube, ML and Schostag, MD and Yang, L and Jelsbak, L}, title = {Genetic Memory Devices to Detect Specialized Metabolites in Plant and Soil Microbiomes.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00073}, pmid = {40808235}, issn = {2161-5063}, abstract = {Root-associated microbiomes significantly influence plant growth and resilience through intricate chemical dialogues mediated by plant- and microbe-derived specialized metabolites. These metabolites play pivotal roles in shaping the assembly, dynamics, and ecological functions of soil microbiomes. Despite advances in in vitro and DNA sequencing studies, a comprehensive understanding of in situ chemical signaling within plant and soil microbiomes remains elusive due to experimental constraints. To address this gap, we developed and tuned a set of five whole-cell biosensors in Escherichia coli for spatiotemporal, nondisruptive detection of biologically relevant specialized metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, tetracycline, salicylic acid, and naringenin. Four of these biosensors were successfully adapted to the soil-compatible Pseudomonas putida KT2440 Δall-Φ strain. Additionally, the four sensors were shown to respond to their cognate ligand in a nonsterile soil extract medium containing a diverse microbiome extracted from soil. By employing genetic memory devices with DNA barcodes for readouts, our approach provides a scalable platform for sensing additional specialized metabolites in the future. This work demonstrates the potential of biosensor technologies to unravel the complex chemical interactions driving soil microbiome ecology, with implications for sustainable agricultural practices.}, }
@article {pmid40806377, year = {2025}, author = {Ghosh, M and Bayat, AH and Pearse, DD}, title = {Small Extracellular Vesicles in Neurodegenerative Disease: Emerging Roles in Pathogenesis, Biomarker Discovery, and Therapy.}, journal = {International journal of molecular sciences}, volume = {26}, number = {15}, pages = {}, pmid = {40806377}, issn = {1422-0067}, abstract = {Neurodegenerative diseases (NDDs) such as Alzheimer's, Parkinson's, ALS, and Huntington's pose a growing global challenge due to their complex pathobiology and aging demographics. Once considered as cellular debris, small extracellular vesicles (sEVs) are now recognized as active mediators of intercellular signaling in NDD progression. These nanovesicles (~30-150 nm), capable of crossing the blood-brain barrier, carry pathological proteins, RNAs, and lipids, facilitating the spread of toxic species like Aβ, tau, TDP-43, and α-synuclein. sEVs are increasingly recognized as valuable diagnostic tools, outperforming traditional CSF biomarkers in early detection and disease monitoring. On the therapeutic front, engineered sEVs offer a promising platform for CNS-targeted delivery of siRNAs, CRISPR tools, and neuroprotective agents, demonstrating efficacy in preclinical models. However, translational hurdles persist, including standardization, scalability, and regulatory alignment. Promising solutions are emerging, such as CRISPR-based barcoding, which enables high-resolution tracking of vesicle biodistribution; AI-guided analytics to enhance quality control; and coordinated regulatory efforts by the FDA, EMA, and ISEV aimed at unifying identity and purity criteria under forthcoming Minimal Information for Studies of Extracellular Vesicles (MISEV) guidelines. This review critically examines the mechanistic roles, diagnostic potential, and therapeutic applications of sEVs in NDDs, and outlines key strategies for clinical translation.}, }
@article {pmid40806300, year = {2025}, author = {Thongkhao, K and Intharuksa, A and Phrutivorapongkul, A}, title = {Unveiling Adulteration in Herbal Markets: MassARRAY iPLEX Assay for Accurate Identification of Plumbago indica L.}, journal = {International journal of molecular sciences}, volume = {26}, number = {15}, pages = {}, pmid = {40806300}, issn = {1422-0067}, abstract = {The root of Plumbago indica L. is commercially available in herbal markets in both crude and powdered forms. P. indica root is a key ingredient in numerous polyherbal formulations. However, P. indica has two closely related species, P. zeylanica L. and P. auriculata Lam. Since only P. indica is traditionally used in Thai polyherbal products, adulteration with other species could potentially compromise the therapeutic efficacy and overall effectiveness of these formulations. To address this issue, a MassARRAY iPLEX assay was developed to accurately identify and differentiate P. indica from its closely related species. Five single nucleotide polymorphism (SNP) sites-positions 18, 112, 577, 623, and 652-within the internal transcribed spacer (ITS) region were selected as genetic markers for species identification. The assay demonstrated high accuracy in identifying P. indica and was capable of detecting the species at DNA concentrations as low as 0.01 ng/µL. Additionally, the assay successfully identified P. zeylanica in commercial crude drug samples, highlighting potential instances of adulteration. Furthermore, it was able to distinguish P. indica in mixed samples containing P. indica, along with either P. zeylanica or P. auriculata. The developed MassARRAY iPLEX assay proves to be a reliable and effective molecular tool for authenticating P. indica raw materials. Its application holds significant potential for ensuring the integrity of herbal products by preventing misidentification and adulteration.}, }
@article {pmid40805713, year = {2025}, author = {Amin, A and Park, S}, title = {Harnessing Molecular Phylogeny and Chemometrics for Taxonomic Validation of Korean Aromatic Plants: Integrating Genomics with Practical Applications.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {15}, pages = {}, pmid = {40805713}, issn = {2223-7747}, abstract = {Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts.}, }
@article {pmid40805682, year = {2025}, author = {Romadanova, NV and Altayeva, NA and Zemtsova, AS and Artimovich, NA and Shevtsov, AB and Kakimzhanova, A and Nurtaza, A and Tolegen, AB and Kushnarenko, SV and Bettoni, JC}, title = {Geobotanical Study, DNA Barcoding, and Simple Sequence Repeat (SSR) Marker Analysis to Determine the Population Structure and Genetic Diversity of Rare and Endangered Prunus armeniaca L.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {15}, pages = {}, pmid = {40805682}, issn = {2223-7747}, support = {project 0123&#x420;&#x41a;01118//Ministry of Science and Higher Education of Kazakhstan Republic/ ; }, abstract = {The ongoing genetic erosion of natural Prunus armeniaca populations in their native habitats underscores the urgent need for targeted conservation and restoration strategies. This study provides the first comprehensive characterization of P. armeniaca populations in the Almaty region of Kazakhstan, integrating morphological descriptors (46 parameters), molecular markers, geobotanical, and remote sensing analyses. Geobotanical and remote sensing analyses enhanced understanding of accession distribution, geological features, and ecosystem health across sites, while also revealing their vulnerability to various biotic and abiotic threats. Of 111 morphologically classified accessions, 54 were analyzed with 13 simple sequence repeat (SSR) markers and four DNA barcoding regions. Our findings demonstrate the necessity of integrated morphological and molecular analyses to differentiate closely related accessions. Genetic analysis identified 11 distinct populations with high heterozygosity and substantial genetic variability. Eight populations exhibited 100% polymorphism, indicating their potential as sources of adaptive genetic diversity. Cluster analysis grouped populations into three geographic clusters, suggesting limited gene flow across Gorges (features of a mountainous landscape) and greater connectivity within them. These findings underscore the need for site-specific conservation strategies, especially for genetically distinct, isolated populations with unique allelic profiles. This study provides a valuable foundation for prioritizing conservation targets, confirming genetic redundancies, and preserving genetic uniqueness to enhance the efficiency and effectiveness of the future conservation and use of P. armeniaca genetic resources in the region.}, }
@article {pmid40801815, year = {2025}, author = {Taylor, KE and Saunders, GW}, title = {Assessment of rhodolith-forming species diversity in British Columbia uncovers novel cryptic diversity in the genera Boreolithothamnion and Rhodolithia gen. nov. (Florideophyceae, Rhodophyta) and the occurrence of hybrid rhodoliths.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70066}, pmid = {40801815}, issn = {1529-8817}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Northeast Algal Society Development Committee/ ; //New Brunswick Innovation Foundation/ ; //Canada Foundation for Innovation/ ; }, abstract = {Rhodolith collections in British Columbia have historically been limited, and published regional species diversity data are poor. The acquisition of recent collections, notably from rhodolith beds in Haida Gwaii, provided an opportunity to assess diversity in these waters. The DNA barcode markers COI-5P, rbcL-3P, and psbA were used to identify unique genetic groups, which were then placed into a phylogenetic context with other coralline algae and subsequently observed anatomically. These analyses uncovered six rhodolith-forming species: two known, viz. Boreolithothamnion phymatodeum and Boreolithothamnion soriferum; a species provisionally called Boreolithothamnion sp. 1heterocladum; and three novel species described here, viz. Boreolithothamion astragaloi sp. nov., Boreolithothamnion tanuense sp. nov., and Rhodolithia gracilis gen. et. sp. nov., which comprises three varieties. Of particular interest, sequences of the ITS rDNA region showed the variety Rhodolithia gracilis var. gracilis × ramosa var. nov. to be a hybrid of the other two varieties: Rhodolithia gracilis var. gracilis var. nov. and Rhodolithia gracilis var. ramosa var. nov. Although understanding the full extent of BC rhodolith beds will require additional sampling, these findings indicate that rhodoliths are widespread and diverse in British Columbia.}, }
@article {pmid40800620, year = {2025}, author = {Partanen, V and Dekić Rozman, S and Karkman, A and Muurinen, J and Hiltunen, T and Virta, M}, title = {Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf113}, pmid = {40800620}, issn = {2730-6151}, abstract = {One of the most important knowledge gaps in the antimicrobial resistance crisis is the lack of understanding regarding how genes spread from their environmental origins to bacteria pathogenic to humans. In this study our aim was to create a system that allows the conduction of experiments in laboratory settings that mimic the complexity of natural communities with multiple resistance genes and mobile genetic elements circulating at the same time. Here we report a new sequence-based barcode system that allows simultaneous tracking of the spread of antimicrobial resistance genes from multiple genetic origins. We tested this concept with an experiment in which we added an antimicrobial resistance gene to different genetic environments in alive and dead donors and let the gene spread naturally in an artificial microbial community under different environmental conditions to provide examples of factors that can be investigated. We used emulsion, paired-isolation, and concatenation polymerase chain reaction to detect the new gene carriers and metagenomic analysis to see changes in the genetic environment. We observed the genes moving and were able to recognise the barcode from the gene sequences, thus validating the idea of barcode use. We also saw that temperature and gene origin had effects on the number of new host species. Our results confirmed that our system worked and can be further developed for more complicated experiments.}, }
@article {pmid40799287, year = {2025}, author = {Choi, H and Favret, C and Lee, S}, title = {First record of the tropical aphid Schoutedeniaralumensis (Hemiptera, Aphididae) from Cambodia, with a re-description of the oviparous females and DNA barcoding.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e159374}, pmid = {40799287}, issn = {1314-2828}, abstract = {BACKGROUND: Schoutedenia Rübsaamen, 1905 (Hemiptera, Aphididae, Greenideinae) is a small aphid genus associated with woody Euphorbiaceae and Phyllanthaceae. Of its two recognised species, Schoutedeniaralumensis Rübsaamen, 1905 is widely distributed across Southeast Asia, India, Africa and along the eastern coast of Australia. Taxonomic difficulties arise from subtle morphological differences and an unusual life cycle in which all morphs may occur simultaneously. Moreover, the oviparous female remains inadequately described, limiting reliable identification and comparative analyses.<br><br>NEW INFORMATION: Schoutedeniaralumensis is newly recorded from Cambodia on Phyllanthus sp. (Phyllanthaceae). The poorly-known morphology of oviparous females is re-described with live photographs, biometric measurements and photomicrographic illustrations. Additionally, DNA barcoding, based on mitochondrial cytochrome c oxidase (COI) sequences, was performed on the Cambodian specimen and compared with available sequences, including one of S.emblica. Additionally, we propose the synonymisation of S.emblica under S.ralumensis as a conspecific variant. These findings expand the known distribution of S.ralumensis and contribute to a better understanding of aphid diversity in Cambodia.}, }
@article {pmid40796904, year = {2025}, author = {Nowak, KH and Hartop, E and Prus-Frankowska, M and Buczek, M and Kolasa, MR and Roslin, T and Ovaskainen, O and Łukasik, P}, title = {What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {186}, pmid = {40796904}, issn = {2049-2618}, support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; 856506//Horizon 2020/ ; 336212//Research Council of Finland/ ; PPN/PPO/2018/1/00015//Narodowa Agencja Wymiany Akademickiej/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in 'dark taxa'-hyperdiverse yet understudied clades.<br><br>RESULTS: Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities. It combines four methodological innovations: (1) To establish a host taxonomic framework, we sequenced amplicons of the host marker gene (COI) and reconstructed barcodes alongside microbiota characterisation using 16S-V4 rRNA bacterial gene amplicons. (2) To assess microbiota abundance, we incorporated spike-in-based quantification. (3) To improve the phylogenetic resolution for the dominant endosymbiont, Wolbachia, we analysed bycatch data from the COI amplicon sequencing. (4) To investigate the primary drivers of host-microbe associations in massive multi-dimensional datasets, we performed Hierarchical Modelling of Species Communities (HMSC). Applying this approach to 1842 wild-caught scuttle flies (Diptera: Phoridae) from northern Sweden, we organised them into 480 genotypes and 186 species and gained unprecedented insights into their microbiota. We found orders-of-magnitude differences in bacterial abundance and massive within-population variation in microbiota composition. Patterns and drivers differed among microbial functional categories: the distribution and abundance of facultative endosymbionts (Wolbachia, Rickettsia, Spiroplasma) were shaped by host species, genotype, and sex. In contrast, many other bacterial taxa were broadly distributed across species and sites.<br><br>CONCLUSIONS: This study highlights facultative endosymbionts as key players in insect microbiota and reveals striking variations in distributional patterns of microbial clades. It also demonstrates the power of integrative sequencing approaches in uncovering the ecological complexity and significance of symbiotic microorganisms in multi-species natural communities. Video Abstract.}, }
@article {pmid40796813, year = {2025}, author = {Shehata, DHM and El-Mahdy, MM and Ibrahim, M and El Araby, MMI and El-Akkad, SS and Ellmouni, FY}, title = {Analytical assessment of physical characteristics, metabolic processes, and molecular investigations of selected wheat (Triticum spp.) cultivars.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1067}, pmid = {40796813}, issn = {1471-2229}, abstract = {BACKGROUND: Wheat, a primary cereal crop, is crucial in addressing global food security. Understanding genetic diversity and conserving wheat germplasm is essential for developing cultivars resilient to climate change. This study investigates grain quality, nutritional profiles, and genetic diversity across a selection of Egyptian and internationally sourced wheat cultivars. Physical and chemical analyses were conducted to assess grain/flour quality, hardness, and micronutrient content. Genetic diversity was evaluated using protein profiling, SCoT markers, and rbcL chloroplast DNA barcoding, chosen for its highly conserved nature and proven utility in plant species identification and phylogenetic analysis, making it a reliable marker for assessing genetic relationships among wheat cultivars. The findings from this study revealed distinct patterns of genetic variation and highlight valuable traits within the germplasm, providing crucial information for developing wheat cultivars adapted to diverse climatic conditions.<br><br>RESULTS: Physical and biochemical analyses revealed that two Egyptian cultivars, Sohag 5 and Misr 1, exhibited superior quality and nutritional value among the nine evaluated wheat cultivars. Both showed favorable physical properties (e.g., grain weight, falling number, gluten content). Sohag 5 was notably rich in carbohydrates, protein content, and essential minerals (zinc, calcium, magnesium), while Misr 1 also maintained healthy carbohydrate and gluten levels. Genetic diversity analysis, employing SDS-PAGE protein profiling and SCoT markers, effectively differentiated the wheat cultivars. These molecular markers consistently grouped the cultivars, generally distinguished between bread wheat and durum wheat varieties, and provided insights into the genetic relationships between Egyptian and imported lines. While the specific clustering patterns varied between marker types, particularly with rbcL sequences providing a distinct grouping since the rbcL chloroplast gene exhibited limited resolution for differentiating closely related cultivars. The combined genetic data confirmed significant diversity within the germplasm. Overall, the analysis identified two primary genetic groups among the cultivars, with Group I comprising seven diverse cultivars and Group II containing two distinct cultivars (Benisuif 6 and Sohag 5).<br><br>CONCLUSIONS: Overall, the investigated Egyptian wheat cultivars demonstrated competitive or superior performance in standard physical and nutritional parameters compared to the imported varieties, with Sohag 5 and Misr 1 notably excelling in grain quality and micronutrient content. The genetic diversity analysis, incorporating protein profiling, SCoT markers, and rbcL chloroplast DNA barcoding, effectively characterized the genetic landscape of the cultivars. A key finding was the consistent genetic distinction of specific Egyptian cultivars, notably Sohag 5 and Benisuif 6, which clustered uniquely, aligning with their classification as durum wheat varieties. This revealed genetic relationships, alongside the identified superior traits (e.g., in Sohag 5), provides valuable insights that can be strategically utilized in breeding programs to develop new wheat cultivars with enhanced quality and adaptability to diverse climatic conditions.}, }
@article {pmid40796554, year = {2025}, author = {Okkelman, IA and Zhou, H and Borisov, SM and Debruyne, AC and Lefebvre, AEYT and Leomil Zoccoler, M and Chen, L and Devriendt, B and Dmitriev, RI}, title = {Visualizing the internalization and biological impact of nanoplastics in live intestinal organoids by Fluorescence Lifetime Imaging Microscopy (FLIM).}, journal = {Light, science &amp; applications}, volume = {14}, number = {1}, pages = {272}, pmid = {40796554}, issn = {2047-7538}, support = {101073507//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101073507//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {Increased micro- and nanoplastic (MNP) pollution poses significant health risks, yet the mechanisms of their accumulation and effects on absorptive tissues remain poorly understood. Addressing this knowledge gap requires tractable models coupled to dynamic live cell imaging methods, enabling multi-parameter single cell analysis. We report a new method combining adult stem cell-derived small intestinal organoid cultures with live fluorescence lifetime imaging microscopy (FLIM) to study MNP interactions with gut epithelium. To facilitate this, we optimized live imaging of porcine and mouse small intestinal organoids with an 'apical-out' topology. Subsequently, we produced a set of pristine MNPs based on PMMA and PS (<200 nm, doped with deep-red fluorescent dye) and evaluated their interaction with organoids displaying controlled epithelial polarity. We found that nanoparticles interacted differently with apical and basal membranes of the organoids and showed a species-specific pattern of cellular uptake. Using a phasor analysis approach, we demonstrate improved sensitivity of FLIM over conventional intensity-based microscopy. The resulting 'fluorescence lifetime barcoding' enabled distinguishing of different types of MNP and their interaction sites within organoids. Finally, we studied short (1 day)- and long (3 day)-term exposure effects of PMMA and PS-based MNPs on mitochondrial function, total cell energy budget and epithelial inflammation. We found that even pristine MNPs could disrupt chemokine production and mitochondrial membrane potential in intestinal epithelial cells. The presented FLIM approach will advance the study of MNP toxicity, their biological impacts on gastrointestinal tissue and enable the tracing of other fluorescent nanoparticles in live organoid and 3D ex vivo systems.}, }
@article {pmid40794723, year = {2025}, author = {Muffett, KM and Labonté, JM and Miglietta, MP}, title = {Florida Keys Cassiopea host benthos-like external microbiomes and a gut dominated by Vibrio, Endozoicomonas and Mycoplasma.}, journal = {PloS one}, volume = {20}, number = {8}, pages = {e0330180}, pmid = {40794723}, issn = {1932-6203}, mesh = {Animals ; Florida ; RNA, Ribosomal, 16S/genetics ; *Mycoplasma/genetics/isolation &amp; purification/classification ; *Vibrio/genetics/isolation &amp; purification ; *Scyphozoa/microbiology ; *Microbiota ; Phylogeny ; *Gastrointestinal Microbiome ; Symbiosis ; }, abstract = {Interactions with microbial communities fundamentally shape metazoans' physiology, development, and health across marine ecosystems. This is especially true in zooxanthellate (symbiotic algae-containing) cnidarians. In photosymbiotic anthozoans (e.g., shallow water anemones and corals), the key members of the associated microbiota are increasingly well studied, however there is limited data on photosymbiotic scyphozoans (true jellyfish). Using 16S rRNA barcoding, we sampled the internal and external mucus of the zooxanthellate Upside-Down Jellyfish, Cassiopea xamachana during August throughout eight sites covering the full length of the Florida Keys. We find that across sites, these medusae have low-diversity internal microbiomes distinct from the communities of their external surfaces and their environment. These internal communities are dominated by only three taxa: Endozoicomonas cf. atrinae, an uncultured novel Mycoplasma, and Vibrio cf. coralliilyticus. In addition, we find that Cassiopea bell mucosal samples were high diversity and conform largely to the communities of surrounding sediment with the addition of Endozoicomonas cf. atrinae. The microbial taxa we identify associated with wild Florida Keys Cassiopea bear a strong resemblance to those found within photosymbiotic anthozoans, increasing the known links in ecological position between these groups.}, }
@article {pmid40792566, year = {2025}, author = {Mehdizadeh, M and Omidi, A and Morya, S and Abideen, Z}, title = {Combating saffron fraud: a systematic review of adulteration practices, detection technologies, recommendations and challenges.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/10408398.2025.2544767}, pmid = {40792566}, issn = {1549-7852}, abstract = {Saffron, the world's most valuable spice, faces pervasive threats from food fraud, compromising its authenticity, economic value, and consumer safety. This systematic review synthesizes evidence from 23 studies to evaluate the prevalence, methods, impacts, and detection strategies of saffron adulteration. Following PRISMA guidelines, peer-reviewed articles from PubMed, Scopus, and ScienceDirect (2015-2025) were analyzed. Findings reveal that 20-30% of commercial saffron is adulterated globally, though with significant regional disparities (e.g., 3.5% in regulated EU markets vs. 60% in India), driven by economic incentives and regulatory gaps. Common fraudulent practices include substitution with safflower, marigold, or turmeric; dilution with extraneous plant materials; and the addition of hazardous synthetic dyes such as Sudan compounds and auramine-O. Advanced detection technologies including DNA barcoding, spectroscopy, hyperspectral imaging, and machine learning demonstrate high accuracy but face barriers in cost, accessibility, and real-world applicability. Health risks, such as exposure to carcinogenic dyes, and economic losses for legitimate producers underscore the urgency of addressing supply chain vulnerabilities. The review highlights fragmented regulatory frameworks and emphasizes the need for harmonized ISO standards, blockchain-enabled traceability, and consumer education to combat fraud. Emerging portable tools, such as smartphone-based spectroscopy and AI-driven platforms, offer promising solutions for on-site authentication.}, }
@article {pmid40792429, year = {2025}, author = {Zhou, P and Mills, CB and Dong, ZM and Barber, BR and Beronja, S}, title = {Barcoded Orthotopic Patient-Derived Head &amp; Neck Squamous Cell Carcinoma Model Demonstrating Clonal Stability and Maintenance of Cancer Driver Mutational Landscape.}, journal = {Cancer medicine}, volume = {14}, number = {15}, pages = {e71137}, pmid = {40792429}, issn = {2045-7634}, support = {//Fred Hutchinson Cancer Research Center/ ; //Dick and Loraine Burger Pilot Funding/ ; //AAO-HNSF Resident Research Grant/ ; }, mesh = {Humans ; Animals ; Mice ; *Squamous Cell Carcinoma of Head and Neck/genetics/pathology ; *Head and Neck Neoplasms/genetics/pathology ; *Mutation ; Disease Models, Animal ; Female ; Xenograft Model Antitumor Assays ; Mice, SCID ; Exome Sequencing ; Male ; *DNA Barcoding, Taxonomic ; }, abstract = {OBJECTIVE: To illustrate a new barcoded orthotopic patient-derived xenograft (PDX) mouse model where one can investigate phenotypic effects of single-cell level gene manipulation in a pooled format. To address some concerns of current PDX mouse models of head and neck squamous cell carcinoma (HNSCC): (1) genomic evolution with passage by generating high-purity cancer cells, which can also be utilized for other downstream applications, including cell culture-based studies, and (2) cost-effectiveness of current PDX models.<br><br>METHODS: Two-millimeter tumor cubes from nine patients were implanted into immunodeficient mouse flanks subcutaneously. Purified tumor cells were obtained from subcutaneous xenografts. Various numbers of purified tumor cells were then injected into the lingual tissue of immunodeficient mice, and the lowest amount of cells needed to achieve a 100% orthotopic engraftment rate were identified. Clonal stability was tested using a lentiviral barcoding system. The orthotopic PDXs' genetic landscapes were characterized using whole exome sequencing.<br><br>RESULTS: This approach yielded an overall engraftment rate of 88.9%. The purification process increased cancer cell purity from 34% to 92%. Lingual injection of 100,000 purified tumor cells achieved a 100% orthotopic engraftment rate from purified subcutaneous PDX tumor cells while maintaining clonal and genetic stability.<br><br>CONCLUSION: Our study presents a barcoded orthotopic patient-derived xenograft model for head and neck squamous cell carcinoma with clonal stability. This model provides a way to study phenotypic effects of single cell level gene manipulation in a pooled format. The method can be adapted for in&#xa0;vitro work as well.}, }
@article {pmid40792070, year = {2025}, author = {Lyu, H and Li, Y and Wu, S and Fu, L and Liang, X and Liu, E}, title = {Editorial: Expanding insights into structure, function, and disorder of genome by the power of artificial intelligence in bioinformatics.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1649410}, doi = {10.3389/fgene.2025.1649410}, pmid = {40792070}, issn = {1664-8021}, }
@article {pmid40791109, year = {2025}, author = {Yuan, H and Han, J and Yang, M and Chen, S and Pang, X}, title = {DNA Metabarcoding: Current Applications and Challenges.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c06002}, pmid = {40791109}, issn = {1520-5118}, abstract = {DNA metabarcoding is a versatile approach that combines high-throughput sequencing (HTS) with DNA barcoding and enables the simultaneous identification of multiple species in complex DNA samples. With the rapid development of high-throughput sequencing (HTS), DNA meta-barcoding has been widely applied in many fields. This review summarizes the current state of research on DNA metabarcoding, focusing on recent advances in its application in several major fields. DNA metabarcoding can effectively analyze community biodiversity and contribute significantly to the foundation of ecological research. In terms of food safety, it can detect food-derived ingredients to ensure the accuracy of food labeling and prevent adulteration. It can reveal the dietary analysis of animals and provide a scientific foundation for biodiversity protection. It can also identify species in trace samples and help solve crimes in forensic research. Additionally, the challenges ahead and potential developments in DNA meta-barcoding are considered. This review provides comprehensive information about DNA metabarcoding and its multifaceted applications, which could facilitate interdisciplinary communication and improve methodological standardization.}, }
@article {pmid40787725, year = {2025}, author = {Puillandre, N and Zuccon, D and Abdelkrim, J and Lemarcis, T and Ratti, C and Van Weddingen, M and Zaharias, P and Farhat, S}, title = {The CODEX Approach: High-Throughput Sequencing of the Cox-1 Barcode Fragment in Neogastropods (Mollusca, Gastropoda).}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70031}, doi = {10.1111/1755-0998.70031}, pmid = {40787725}, issn = {1755-0998}, support = {865101//H2020 European Research Council/ ; }, abstract = {DNA barcoding traditionally relies on Sanger sequencing but faces limitations with degraded samples. High-throughput sequencing (HTS) offers a cost-effective alternative, enabling rapid barcode generation for extensive datasets. The advantage of HTS is its ability to employ multiplexing strategies, allowing thousands of samples to be processed simultaneously in a single sequencing run. This study presents the CODEX approach, a double-indexed HTS method designed to sequence overlapping cox-1 barcode fragments, suitable for samples with degraded DNA. The approach was applied to neogastropods, a diverse lineage of marine molluscs, using specimens (both recently collected and relatively older) from the Muséum national d'Histoire naturelle (MNHN) collections. The pipeline was used to process 15,076 samples, yielding 10,905 cleaned and assembled sequences, achieving a success rate of 72.33%. The CODEX method demonstrated advantages over Sanger sequencing by enabling the recovery of barcodes from samples previously deemed unsuitable, with significantly reduced costs (€0.5 per sequence vs. €4.5). Notably, DNA quality and sequencing success were strongly correlated with collection date, emphasising the impact of preservation methods and storage conditions. Sequencing success rates varied among families but were not correlated with phylogenetic relationships or specimen size, indicating the robustness of the primers designed for neogastropods. This study highlights the efficiency of the CODEX approach for large-scale DNA barcoding projects, especially when handling degraded samples. The CODEX pipeline and associated resources are publicly accessible, offering a scalable solution for molecular systematics and beyond.}, }
@article {pmid40787158, year = {2025}, author = {Juhász, A and Makaula, P and Cunningham, LJ and Archer, J and Cowlishaw, R and Jones, S and LaCourse, JE and Kayuni, SA and Musaya, J and Stothard, JR}, title = {Notes on the threadworm Strongyloides fuelleborni (Nematoda: Strongyloididae) in vervet monkeys (Chlorocebus pygerythrus) and zoonotic strongyloidiasis in southern Malawi.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {28}, number = {}, pages = {101121}, pmid = {40787158}, issn = {2213-2244}, abstract = {We sought to ascertain whether zoonotic strongyloidiasis occurred in vervet monkeys (Chlorocebus pygerythrus), a non-human primate (NHP) species becoming increasingly common in Southern Malawi. Faecal collection took place in four locations: Nyala Park, a private wildlife reserve adjacent to a sugarcane plantation in Chikwawa District, and three public locations, each near tourist lodges in Mangochi District. Our sampling took place during July 2023, when 32 faecal samples were inspected with parasitological methods. After faecal culture, threadworm larvae were noted in both districts that were confirmed by molecular identification methods as Strongyloides fuelleborni, a first report for Malawi. Given the close spatial proximity of vervets with people, our findings affirm prior disease surveillance concerns of local zoonotic potential. We therefore encourage future targeted helminthological surveys for better local monitoring of strongyloidiasis in NHPs and people.}, }
@article {pmid40785988, year = {2025}, author = {Neuhaus, J and de Wilt, ME and Rossel, S and Brix, S and Etter, RJ and Jennings, RM and Linse, K and Martínez Arbizu, P and Schwentner, M and Peters, J}, title = {High Connectivity at Abyssal Depths: Genomic and Proteomic Insights Into Population Structure of the Pan-Atlantic Deep-Sea Bivalve Ledella ultima (E. A. Smith, 1885).}, journal = {Ecology and evolution}, volume = {15}, number = {8}, pages = {e71903}, pmid = {40785988}, issn = {2045-7758}, abstract = {Phylogeographic analyses have advanced our understanding of evolutionary processes in the deep sea, yet patterns of genetic variation and population divergence at abyssal depths remain poorly understood. The bivalve Ledella ultima is one of the most abundant protobranchs in the abyssal Atlantic, making it a valuable model organism for studying phylogeographic patterns and population connectivity. However, evidence for sex-specific heteroplasmic mtDNA challenges the assessment of genetic structure using mitochondrial markers alone. To address this, we used mtDNA (COI, 16S), single-nucleotide polymorphisms (SNPs) from 2b-RAD, and proteomic profiles to examine the population structure of L. ultima across seven Atlantic basins spanning over 10,000 km in latitude. Five mitochondrial lineages with a lack of geographic structure were consistently identified by COI and 16S. Conversely, SNP and proteomic data did not mirror these findings, denoting that heteroplasmic mtDNA inflates intraspecific genetic divergence in this gonochoric species. Despite the SNP data revealing overall low genetic divergence, subtle genetic structure was detected by admixture analyses supporting two source populations: one in the north and central Atlantic, and a second in the south Atlantic, with moderate admixture in the Brazil and Cape basins. Proteomic fingerprinting revealed two basin-separated groups with patterns distinct from the nuclear data, suggesting environmentally driven shifts in protein expression. Our findings underscore the value of integrating nuclear genomic and proteomic tools to decipher population connectivity at abyssal depths, where minimal genetic differentiation necessitates fine-scale analyses.}, }
@article {pmid40785415, year = {2025}, author = {Williamson, R and Dusek, N and Lopez-Echartea, E and Ramsett, MKT and Geddes, BA}, title = {Evaluation of Engineering Potential in Undomesticated Microbes With VECTOR.}, journal = {Microbial biotechnology}, volume = {18}, number = {8}, pages = {e70215}, pmid = {40785415}, issn = {1751-7915}, support = {//Richard and Linda Offerdahl Faculty Fellowship/ ; FF-NIA21-0000000061m//Foundation for Food and Agriculture Research/ ; }, mesh = {*Genetic Vectors ; Plasmids/genetics ; *Bacteria/genetics ; *Genetic Engineering/methods ; Green Fluorescent Proteins/genetics/analysis ; }, abstract = {Genetic engineering research has predominantly focused on well-characterised organisms like Escherichia coli and Bacillus subtilis, with methods that often fail to translate to other microorganisms. This limitation presents a significant challenge, particularly given the increasing isolation of large microbial collections through high-throughput culturomics. In response, we developed a scalable, high-throughput pipeline to evaluate the engineerability of diverse microbial community members we named VECTOR (Versatile Engineering and Characterisation of Transferable Origins and Resistance). We utilised a library of vectors with the Bacterial Expression Vector Archive (BEVA) architecture that included combinations of three antibiotic resistance genes and three broad host-range origins of replication (pBBR1, RK2 and RSF1010) or the restricted host-range R6K with an integrative mariner transposon. We tagged each vector with green fluorescent protein and a unique nucleotide barcode. The resulting plasmids were delivered en masse to libraries of undomesticated microbes from plant microbiomes in workflows designed to evaluate their ability to be engineered. Utilising OD600 and relative fluorescence measurements, we were able to monitor genetic cargo transfer in real time, indicating successfully engineered strains. Next-generation sequencing of plasmid molecular barcodes allowed us to identify specific vector architectures that worked well in particular bacterial strains from a large community. Modifications to the procedure facilitated isolation of engineered microbes.}, }
@article {pmid40783800, year = {2025}, author = {Urumarudappa, SKJ and Bommuluri, V and J, S and Chaturvedi, S and Mittal, AK and Zhang, Y and Chang, P and Swanson, G}, title = {Authentication Methods for Phytochemicals (Botanicals) in Plant Extracts and Dietary Supplements.}, journal = {Journal of dietary supplements}, volume = {}, number = {}, pages = {1-42}, doi = {10.1080/19390211.2025.2538487}, pmid = {40783800}, issn = {1939-022X}, abstract = {Demand for high-quality and standardized phytochemicals (botanicals) and plant extracts if rising in both the food and dietary supplement industries. Ensuring the authenticity of the plant raw materials used in botanical and dietary supplement manufacturing is an important step before processing raw materials. However, authenticating phytochemicals (botanicals) are challenging due to their unique characteristics, including geographical location, seasonal variations, environmental conditions, and plant diversity. These factors cause variability in properties, making consistent authentication methods difficult to establish. The current review is centered on the utilization of multisource and qualitative methods for authenticating the identity of botanical and food ingredients. This review highlights the integral role of various botanicals and plant extracts authentication methods such as micro/macroscopy, chromatography, and spectroscopy technology, including DNA-based approaches. Further summarizing the current state of knowledge and importance its potential contributions to the field of botanical ingredient authentication system. This study also highlights the plants used in dietary supplement categories of weight management, memory enhancement and blood sugar regulation and their adulteration/admixture. Furthermore, discusses considerations for selecting appropriate methods and optimization steps in the implementation and standardization of botanical and plant extract authentication. In addition, we discussed the challenges and opportunities associated with the implementation and standardization of botanical and plant extracts authentication system. The future of botanical authentication will be shaped by advances in molecular diagnostics such as targeted DNA barcoding, Next-Generation Sequencing (NGS), and chemometric integration with spectroscopic techniques which are set to greatly enhance accuracy, traceability, and global compliance in botanical product safety and quality.}, }
@article {pmid40781841, year = {2025}, author = {Li, CJ and Jiang, YZ and Li, DZ and Wu, QZ}, title = {Test Species Discrimination in Codonopsis (Campanulaceae) Using Genome Skimming Data.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70025}, doi = {10.1111/1755-0998.70025}, pmid = {40781841}, issn = {1755-0998}, support = {BS202211//Shenyang Normal University Ph.D., Introduced Talents Scientific Research Project Startup Fund/ ; JYTQN2023418//Liaoning Provincial Department of Education University Fundamental Research Project/ ; XDB31000000//Chinese Academy of Sciences/ ; 2024-BS-104//Liaoning Provincial Doctoral Research Startup Fund/ ; }, abstract = {To overcome the limitations of conventional barcoding loci, plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequences recovered from genome skimming, proposed as 'super-barcodes' have been suggested as candidates for delimitating recently diverged species or complex plant groups. DNA super-barcodes must be further assessed for their effectiveness in other diverse plant groups. This research focused on the genus Codonopsis, a medicinally significant yet taxonomically complex group characterised by morphological similarity and high phenotypic plasticity in response to environmental conditions. We analysed standard DNA barcodes and super-barcodes across 81 individuals from 36 of the 42 species of Codonopsis from Asia. Our work provides a comprehensive DNA barcode library for Codonopsis species identification. Our findings demonstrated that super-barcodes significantly improved the phylogenetic resolution and the discriminatory power compared to standard DNA barcodes. Since mitochondrial sequence variation is generally low in plant species, few studies have assessed its effectiveness as super-barcodes. We screened the mitochondrial protein-coding sequences (CDS) using genome skimming and evaluated the identification capacity of their combination. Unexpectedly, the discriminatory power of mitochondrial DNA with high nucleotide variation was comparable to that of the concatenated plastid CDS. However, the organelle genome cannot wholly determine the species boundaries of Codonopsis, which might be related to their rapid evolutionary radiation, ILS, hybridisation and strong natural selection. Future multi-locus nuclear markers will likely be developed in plants for additional discriminatory power. Our study provides new knowledge and insights into species discrimination of recently evolved Codonopsis taxa in a biodiversity hotspot.}, }
@article {pmid40777731, year = {2025}, author = {Shao, KT and Ko, HL and Chiu, YC and Huang, HK and Chen, YF and Chang, YW}, title = {Establishing a COI DNA barcoding reference database for Taiwanese coastal fish species from egg and larvae specimens.}, journal = {ZooKeys}, volume = {1247}, number = {}, pages = {207-216}, pmid = {40777731}, issn = {1313-2989}, abstract = {Fish eggs and larval stages are essential components of marine ecosystems and play important roles in sustaining marine food webs. However, the egg and larval stages often lack distinct diagnostic characteristics, making it challenging to identify species solely based on their morphology. In this study, we applied a DNA barcoding approach targeting the cytochrome c oxidase subunit I gene to establish a comprehensive reference for fish eggs and larval material in coastal waters off Taiwan. A total of 7602 records of fish eggs and larvae were collected from marine coastal waters surrounding Taiwan between 2004 and 2023 and identified using a DNA barcoding approach. By comparing our newly generated DNA barcoding sequences with records from public reference databases, we identified 1112 different fish taxa encompassing 24 orders, 158 families, 500 genera, and 844 fish species. This DNA barcoding referencing effort will facilitate future studies on the early life stages of Taiwanese coastal marine fish communities. In addition, it will also provide an important baseline for the development of new methods, such as eDNA and DNA metabarcoding diet analysis. This database provides comprehensive spatial and temporal distribution data of fish eggs and larvae in the waters surrounding Taiwan, contributing to a better understanding of fish spawning seasons, spawning grounds, and resource fluctuations. This database enhances the accuracy of species identification and serves as a scientific foundation for biodiversity conservation and fishery resource management.}, }
@article {pmid40777057, year = {2025}, author = {Peñaherrera, E and Sarmiento-Pacurucu, J and Santos-Ordóñez, E and Kachatryan, A and Cuzco, N and Vanegas, D and Calle-López, J and Villao-Uzho, L and Heyden, YV and Wilches, I and León-Tamariz, F}, title = {Desmodium molliculum (Kunth) DC., an Andean medicinal plant: DNA barcoding and HPLC fingerprint for species discrimination and evaluation of its pharmacological potential.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1612556}, pmid = {40777057}, issn = {1664-462X}, abstract = {In the Ecuadorian traditional medicine, two species of the Desmodium genus, D. adscendens and D. molliculum, are used interchangeably for the treatment of various ailments, particularly those related to inflammatory processes, wound healing, stomach ulcers and liver disorders. Despite the extensive knowledge and characterization of D. adscendens, there is limited information regarding D. molliculum. This highlights the necessity for the development of analytical tools that facilitate the differentiation between these two species and the characterization of the latter. The tools were developed and evaluated at two distinct levels: genetically, using the DNA barcoding technique, and analytically, using chromatographic fingerprinting. Additionally, the antioxidant potential of the samples was evaluated through the establishment of the RACI index, based on various in vitro evaluation techniques. De novo genetic DNA barcodes were obtained for D. molliculum and the phylogenetic analysis separated them from those obtained from D. adscendens, demonstrating that the trnH-psbA, matK, and ITS1 markers are the most effective for differentiating between the species. Additionally, the antioxidant potential of D. molliculum was found to be higher than that of D. adscendens. The apigenin 8-C-glucoside (vitexin), together with tannic and chlorogenic acids have been pointed by HPLC fingerprinting analysis as responsible for this pharmacological activity.}, }
@article {pmid40776713, year = {2025}, author = {Cassim, N and Buthelezi, EP and Sarang, S and Moodly, S and Hans, L and Coetzee, LM}, title = {Assessing laboratory specimen losses for the city of Johannesburg, South Africa.}, journal = {African journal of primary health care &amp; family medicine}, volume = {17}, number = {1}, pages = {e1-e8}, pmid = {40776713}, issn = {2071-2936}, mesh = {South Africa ; Humans ; Retrospective Studies ; *Specimen Handling/standards ; Primary Health Care ; *Clinical Laboratory Information Systems ; *Laboratories ; }, abstract = {BACKGROUND: Specimen losses across the pathology value chain (PVC) result in missed diagnostic opportunities. It is difficult to fully assess these due to the current paper-based systems, with tracking of specimens only possible on the laboratory information system (LIS).<br><br>AIM: &#xa0;This study aimed to assess specimen losses using the paper-based register.<br><br>SETTING: &#xa0;Randomly selected Primary health care (PHC) facilities, City of Johannesburg, South Africa.<br><br>METHODS: &#xa0;The retrospective descriptive study design was used to scan 1,000 barcodes from facilities in sub-districts A to G. Data was limited to barcodes from the request form and excluded surveillance testing. Matching data from the laboratory repository was extracted. PVC losses were assessed by determining the percentage of scanned barcodes that had a registered, tested, reviewed and/or rejected date. The analysis was stratified according to sub-district, health facility type and test code.<br><br>RESULTS: &#xa0;The dataset analysed included 33 867 barcodes with 121 697 test codes, equating to 3.59 tests per barcode. Matching registered, tested and reviewed dates were detected for 33 107 (97.76%) barcodes. In total, a rejection for one or more test codes was detected for 1,961 barcodes (5.79%). At the sub-district level, between 95.95% (D) and 98.90% (E) of barcodes were reviewed. The rejection rate ranged from 3.27% (F) to 10.93% (D). For community health centres and clinics, 97.37% and 97.97% of the barcodes had a matching reviewed date.<br><br>CONCLUSION: &#xa0;PVC losses reported were 4.05%, excluding rejections (5.79%), with slightly higher levels noted at the sub-district level. Contribution: The continuous audit of PVC losses is recommended.}, }
@article {pmid40776180, year = {2025}, author = {Nguyen, HN and Madanian, S and Nguyen, M and Merry, A and Parry, D}, title = {Digital Transformation of Medication Identification: Technological Evolution.}, journal = {Studies in health technology and informatics}, volume = {329}, number = {}, pages = {1684-1685}, doi = {10.3233/SHTI251163}, pmid = {40776180}, issn = {1879-8365}, mesh = {*Medication Errors/prevention &amp; control ; Humans ; *Radio Frequency Identification Device ; *Electronic Data Processing ; }, abstract = {Medication errors pose a significant health challenge, contributing to thousands of deaths annually. This systematic review explores the technological evolution of medication identification: Barcode/Quick Response (QR) Code systems, Radio Frequency Identification (RFID)/Near-Field Communication (NFC), and Computer Vision, used to reduce errors and enhance patient safety. 140 articles from different databases were reviewed to compare their strengths, limitations, and applications. While barcodes offer cost-effective scanning, they require line-of-sight, RFID/NFC provide robust data retrieval yet faces high costs, and Computer Vision excels in flexibility despite computational demands. Combining these technologies could optimize safety.}, }
@article {pmid40775874, year = {2025}, author = {Konishi, S and Tanaka, Y and Sugimoto, K and Wada, S and Okada, K and Takeda, T}, title = {GS1 and RFID Integration for Enhanced Medical Device Traceability in Catheterisation Laboratories.}, journal = {Studies in health technology and informatics}, volume = {329}, number = {}, pages = {332-336}, doi = {10.3233/SHTI250856}, pmid = {40775874}, issn = {1879-8365}, mesh = {*Radio Frequency Identification Device/methods ; *Cardiac Catheterization/instrumentation ; Humans ; Systems Integration ; }, abstract = {This study presents a novel system that integrates GS1 barcodes and radio frequency identification (RFID) technology with the objective of enhancing the medical device traceability in catheterization laboratories. The necessity for precise tracking of medical devices, particularly in the context of cardiovascular procedures is underscored by the occurrence of sporadic product recalls. Despite the existence of traceability systems, no solution has effectively combined GS1 and RFID technologies to ensure precise tracking throughout the clinical process. In this study, an apparatus for reading and collecting RFID tags was developed and integrated with the radiology information system and medical device master database. The medical devices delivered to the hospital were linked to RFID tags by means of scanning the GS1 barcodes on their packaging. During the catheterization procedures, the tags of each medical device used were scanned to record the usage in real-time. The new system has already been employed in more than 500 catheterization procedures. In an analysis of 16 percutaneous coronary intervention procedures, the system demonstrated high accuracy in capturing the chronological order of device usage, with a mean Kendall's rank correlation coefficient of 0.95±0.12. While some discrepancies were observed when non-stock devices were used, the system demonstrated an overall robust reliability. The system, which combines GS1 and RFID technologies, enabled real-time recording of medical devices used in catheterization laboratories, thereby enhancing the traceability of medical devices. Potential future applications include the use of generative artificial intelligence to draft preliminary percutaneous coronary intervention reports, enable real-time detection of complications by comparing device usage patterns with an operator's past cases, and support retrospective analyses for educational and procedural improvements.}, }
@article {pmid40775323, year = {2025}, author = {Mahgoub, YA and Mahmoud, HA and El-Sebakhy, NA and Abdallah, II}, title = {Unravelling Artemisia species genetic variation via DNA barcoding, ISSR and RAPD with the development of eco-specific SCAR markers.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1034}, pmid = {40775323}, issn = {1471-2229}, mesh = {*Artemisia/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Random Amplified Polymorphic DNA Technique ; *Genetic Variation ; Phylogeny ; Genetic Markers ; *Microsatellite Repeats/genetics ; DNA, Plant/genetics ; Species Specificity ; }, abstract = {BACKGROUND: Genus Artemisia is one of the largest and most globally spread genera, comprising more than 500 species known for their phytochemical diversity and therapeutic properties. This necessitates the accurate authentication and differentiation of its species. Traditional morphological, microscopical and metabolic profiling methods are often insufficient for reliable discrimination. The aim of this study is the authentication and assessment of the genetic diversity of wild Egyptian Artemisia species; A. herba-alba, A. monosperma, A. judaica and cultivated A. annua using a combined molecular approach of DNA barcoding, ISSR, RAPD, and the development of eco-specific SCAR markers.<br><br>RESULTS: DNA barcoding targeting both nuclear (ITS2) and plastid (psbA-trnH) spacers revealed that ITS2 is recommended over psbA-trnH as the discriminatory barcode of choice since it accurately identified all species with >&#x2009;99% identity and phylogenetic clustering with greater genetic distances. ISSR fingerprinting with five primers generated 41 polymorphic bands (100% polymorphism) and displayed genetic diversity among the species. However, the morphologically and chemically similar A. herba-alba and A. judaica remained partly undifferentiated. Therefore, RAPD profiling was implemented as a complementary technique for better and reliable discrimination. RAPD profiling with 27 primers generated 212 bands (99.5% polymorphic). RAPD primers OPA-10 and OPK-07 showed superior differentiation of the Artemisia species, while primers OPG-07, OPB-20, OPS-12 and OPD-15 failed to discriminate between the studied species. The reproducible RAPD banding profiles generated by OPG-02, OPG-04, OPA-09 and OPD-15 primers were targeted for the development of species-specific SCAR markers by isolating, cloning, and sequencing the distinct RAPD bands specific for each species. These putative SCAR markers were assessed and validated confirming the identity of the studied species.<br><br>CONCLUSIONS: An integrated molecular approach combining ITS2 barcoding, ISSR, RAPD, and RAPD-derived SCAR markers offered a reliable strategy for the authentication and discrimination of Artemisia species based on their genetic profiles. It is worth mentioning that this is the first report of eco-specific SCAR markers for the Egyptian Artemisia species. The developed SCAR markers allow rapid species identification for quality control of medicinal plants, complementing conventional methods and overcoming their limitations. This provides a reproducible, cost-effective strategy for large-scale authentication of medicinal plants.}, }
@article {pmid40775299, year = {2025}, author = {Arias, T and Moreno, JS and Reyes, S and Almario, ML and Serna-Sánchez, A and Iturralde, GA and Valencia, J and Baquero, L and Zuluaga, A}, title = {Plastome phylogenomics of the diverse neotropical orchid genus Lepanthes with emphasis on subgenus Marsipanthes (Pleurothallidinae: Orchidaceae).}, journal = {BMC ecology and evolution}, volume = {25}, number = {1}, pages = {79}, pmid = {40775299}, issn = {2730-7182}, mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; *Genome, Chloroplast ; *Genome, Plastid ; }, abstract = {Well-resolved phylogenetic relationships within the diverse Neotropical orchid genus Lepanthes are presented based on a genome skimming approach that yielded nine newly sequenced chloroplast genomes. We complemented this with 17-86 plastome coding genes for 26 species retrieved from GenBank, alongside amplified matK and rITS regions. The Lepanthes plastomes (157,185-158,260 bp, 37.15% GC content) contained 136 annotated genes, including 86 protein-coding, 42 tRNA, and 8 rRNA genes. We identified six hypervariable regions, including parts of the ycf1 gene, as potential DNA barcodes. Phylogenetic analyses revealed that Carl Luer's subgeneric classifications are non-monophyletic, a finding confirmed by PCA of continuous morphological traits, reflecting significant morphological homoplasy. Six major clades were identified, though resolution for the phylogenetic backbone remains unresolved at two nodes. Subgenus Marsipanthes is not monophyletic as currently circumscribed, with two subclades recovered in distinct positions within the phylogeny. An early-diverging lineage, comprising species restricted to the eastern Andean slopes from southern Colombia to Peru, includes members of both Marsipanthes and Lepanthes. A derived clade, consisting of species from both subgenera, confined to the Chocó biogeographic region, forms an unresolved polytomy. Although only a subset of Lepanthes diversity was sampled, this study captures significant taxonomic, geographic, and morphological variation. It provides foundational insights into the genu's evolutionary history, along with tools and hypotheses that can be expanded upon in future research to further refine our understanding of its biogeographic history.}, }
@article {pmid40774373, year = {2025}, author = {Iwaki, T and Sasaki, M and Waki, T and Kurozumi, T}, title = {An unidentified species of Leucochloridium (Trematoda: Leucochloridiidae) found in an Amber snail (Succinea lauta) from Chiba Prefecture, Honshu, Japan.}, journal = {Parasitology international}, volume = {}, number = {}, pages = {103137}, doi = {10.1016/j.parint.2025.103137}, pmid = {40774373}, issn = {1873-0329}, abstract = {Leucochloridium spp. are intriguing parasites due to their colorful, pulsating larval broodsacs in amber snails' eyestalks. The unusual appearance is believed to mimic caterpillars to attract insectivorous birds. Sporocysts of Leucochloridium sp. were discovered in an amber snail (Succinea lauta) in Chiba, located in the central region of Honshu, Japan. The broodsacs displayed a distinctive pattern, characterized by large dark brown spots, bands of the same color at the anterior end, and light brown vertical stripes running through them. Phylogenetic analyses were conducted based on DNA sequences of the nuclear 28S ribosomal RNA gene (28S rDNA) and the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). Although the 28S rDNA sequence of the present species was closely related to that of Leucochloridium problematicum from North America, morphological differences in the broodsacs suggest that it is likely a distinctive species. A ML tree based on the cox1 sequences indicated that the Leucochloridium species analyzed in this study and L. subtilis form a clade separate from other Leucochloridium species in Europe and Asia. However, the p-distance between the cox1 sequences of the present species and L. subtilis was 0.24, supporting their distinction at the species level. Although definitive identification of Leucochloridium sp. was not achieved in this study, the DNA barcodes generated here and in related research may facilitate future direction and identification of adult Leucochloridium sp. in birds residing in or migrating through Japan.}, }
@article {pmid40772542, year = {2025}, author = {Reddy, S and Wacker, K and Fahmy, M and Hekkala, E and Bates, JM and Goodman, SM and Hackett, SJ and Raherilalao, MJ and Maddox, JD}, title = {VoronaGasyCodes: A Public Database of Mitochondrial Barcodes for Malagasy Birds.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70027}, doi = {10.1111/1755-0998.70027}, pmid = {40772542}, issn = {1755-0998}, abstract = {Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate-derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures.}, }
@article {pmid40772462, year = {2025}, author = {Ogiso-Tanaka, E and Ito, MA and Shimada, D}, title = {Nondestructive DNA extraction from specimens and bulk samples preserved in DESS solution for DNA barcoding.}, journal = {BioTechniques}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/07366205.2025.2542023}, pmid = {40772462}, issn = {1940-9818}, abstract = {DNA barcoding of small organisms often requires significant damage or destroy specimens. To address this, the development of nondestructive DNA extraction methods that maintain specimen morphology is crucial. Here, we present a protocol using the supernatant of DESS preservation solution (20% DMSO, 250 mM EDTA, saturated NaCl), which conserve both the morphological characteristics and DNA of biological samples long-term. This method successfully conducted nondestructive barcoding of nematodes preserved in DESS and stored 10 years at room temperature. The protocol also applies to bulk environmental samples, where sediment and seagrass collected in the field are immediately preserved in DESS. This enables the subsequent isolation and individual nondestructive barcoding of meiofauna and diatoms from the preserved environmental samples in the laboratory.}, }
@article {pmid40771425, year = {2025}, author = {Jeffet, J and Hadad, B and Froim, S and Kaboub, K and Rabinowitz, KM and Deek, J and Margalit, S and Dotan, I and Bahabad, A and Ebenstein, Y}, title = {DeepQR: single-molecule QR codes for optical gene-expression analysis.}, journal = {Nanophotonics (Berlin, Germany)}, volume = {14}, number = {15}, pages = {2549-2561}, pmid = {40771425}, issn = {2192-8614}, abstract = {Optical imaging and single-molecule imaging, in particular, utilize fluorescent tags in order to differentiate observed species by color. The degree of color multiplexing is dependent on the available spectral detection window and the ability to distinguish between fluorophores of different colors within this window. Consequently, most single-molecule imaging techniques rely on two to four colors for multiplexing. DeepQR combines compact spectral imaging with deep learning to enable 4 color acquisition with only 3 spectral detection windows. It allows rapid high-throughput acquisition and decoding of hundreds of unique single-molecule color combinations applied here to tag native RNA targets. We validate our method with clinical samples analyzed with the NanoString gene-expression inflammation panel side by side with the commercially available NanoString nCounter system. We demonstrate high concordance with "gold-standard" filter-based imaging and over a four-fold decrease in acquisition time by applying a single snapshot to record four-color barcodes. The new approach paves the path for extreme single-molecule multiplexing.}, }
@article {pmid40770058, year = {2025}, author = {Khosrowshahli, R and Kheiri, F and Asilian Bidgoli, A and Tizhoosh, HR and Makrehchi, M and Rahnamayan, S}, title = {Enhancing image retrieval through optimal barcode representation.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {28847}, pmid = {40770058}, issn = {2045-2322}, abstract = {Data binary encoding has proven to be a versatile tool for optimizing data processing and memory efficiency in various machine learning applications. This includes deep barcoding, generating barcodes from deep learning feature extraction for image retrieval of similar cases among millions of indexed images. Despite the recent advancement in barcode generation methods, converting high-dimensional feature vectors (e.g., deep features) to compact and discriminative binary barcodes is still an urgent necessity and remains an unresolved problem. Difference-based binarization of features is one of the most efficient binarization methods, transforming continuous feature vectors into binary sequences and capturing trend information. However, the performance of this method is highly dependent on the ordering of the input features, leading to a significant combinatorial challenge. This research addresses this problem by optimizing feature sequences based on retrieval performance metrics. Our approach identifies optimal feature orderings, leading to substantial improvements in retrieval effectiveness compared to arbitrary or default orderings. We assess the performance of the proposed approach in various medical and non-medical image retrieval tasks. This evaluation includes medical images from The Cancer Genome Atlas (TCGA), a comprehensive publicly available dataset, as well as COVID-19 Chest X-rays dataset. In addition, we evaluate the proposed approach on non-medical benchmark image datasets, such as CIFAR-10, CIFAR-100, and Fashion-MNIST. Our findings demonstrate the importance of optimizing binary barcode representation to significantly enhance accuracy for fast image retrieval across a wide range of applications, highlighting the applicability and potential of barcodes in various domains.}, }
@article {pmid40766630, year = {2025}, author = {Semwal, A and Morrison, J and Beddows, I and Palmer, T and Majewski, MF and Jang, HJ and Johnson, BK and Shen, H}, title = {Tranquillyzer: A Flexible Neural Network Framework for Structural Annotation and Demultiplexing of Long-Read Transcriptomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40766630}, issn = {2692-8205}, support = {UM1 DA058219/DA/NIDA NIH HHS/United States ; }, abstract = {Long-read single-cell RNA sequencing using platforms such as Oxford Nanopore Technologies (ONT) enables full-length transcriptome profiling at single-cell resolution. However, high sequencing error rates, diverse library architectures, and increasing dataset scale introduce major challenges for accurately identifying cell barcodes (CBCs) and unique molecular identifiers (UMIs) - key prerequisites for reliable demultiplexing and deduplication, respectively. Existing pipelines rely on hard-coded heuristics or local transition rules that cannot fully capture this broader structural context and often fail to robustly interpret reads with indel-induced shifts, truncated segments, or non-canonical element ordering. We introduce Tranquillyzer (TRANscript QUantification In Long reads-anaLYZER), a flexible, architecture-aware deep learning framework for processing long-read single-cell RNA-seq data. Tranquillyzer employs a hybrid neural network architecture and a global, context-aware design, and enables precise identification of structural elements - even when elements are shifted, partially degraded, or repeated due to sequencing noise or library construction variability. In addition to supporting established single-cell protocols, Tranquillyzer accommodates custom library formats through rapid, one-time model training on user-defined label schemas, typically completed within a few hours on standard GPUs. Additional features such as scalability across large datasets and comprehensive visualization capabilities further position Tranquillyzer as a flexible and scalable framework solution for processing long-read single-cell transcriptomic datasets.}, }
@article {pmid40766425, year = {2025}, author = {Chambwe, N and Kennedy, SR and Kohrn, BF and Lazarchuk, P and Leutert, M and Qin, G and Tercan, B and Sanchez-Contreras, M and Tang, W and Graber, JJ and Paddison, PJ and Villén, J and Shmulevich, I and Monnat, RJ}, title = {Cellular heterogeneity and therapeutic response profiling of human IDH+ glioma stem cell cultures.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40766425}, issn = {2692-8205}, support = {R35 GM153370/GM/NIGMS NIH HHS/United States ; P01 CA077852/CA/NCI NIH HHS/United States ; R35 GM152061/GM/NIGMS NIH HHS/United States ; R21 CA259780/CA/NCI NIH HHS/United States ; R35 GM133428/GM/NIGMS NIH HHS/United States ; R21 HG011229/HG/NHGRI NIH HHS/United States ; }, abstract = {Glioblastoma stem cell (GSC) cultures are initiated from glioblastoma (GBM) surgical resection tissue. They can capture and propagate key GBM primary tumor molecular and cellular features. We have deeply characterized four isocitrate dehydrogenase (IDH)-expressing (or IDH+) GSC cultures from unrelated adults to serve as cellular models for the majority of adult primary GBM. We demonstrate that GSC cultures can be continuously propagated in defined, serum-free media and 5% oxygen without requiring specialized growth substrates; have well-defined genomic and mtDNA variants and gene/protein expression profiles; and highly reproducible dose-survival curves when treated with the GBM standard-of-care therapies of ionizing radiation (IR) and temozolomide (TMZ). We also illustrate how expressed lentiviral barcodes, mtDNA variants and single cell gene expression profiling can be used to define and track cellular heterogeneity over 40 days after IR treatment. These well-characterized IDH+ GSC cultures can support many high throughput in vitro assay formats, including xenograft, organoid and other GBM disease modeling protocols. They should prove a useful resource to better understand GBM biology, and to identify new and more effective GBM therapies and treatment regimens.}, }
@article {pmid40765263, year = {2025}, author = {You, L and Zhang, J and Deng, Y and Shi, X and Liu, C and Zhong, L and Ye, Z and Zhang, Z and Peng, X and Zhou, C and Cao, Z and Li, C and Hu, H and Zheng, L and Zhang, Y}, title = {Multi-Omics Analyses Reveal Metabolic Regulatory Networks in Salinity and Drought Adaptation of Basil QF, a Chinese Cultivar.}, journal = {Physiologia plantarum}, volume = {177}, number = {4}, pages = {e70437}, doi = {10.1111/ppl.70437}, pmid = {40765263}, issn = {1399-3054}, support = {HBMUPI202104//Hubei University of Medicine/ ; 2022BMXKQT4//Hubei University of Medicine/ ; 32200680//National Nature Science Foundation of China/ ; 2060302//Key Project at Central Government Level/ ; T2023016//Science Research Program of Hubei Provincial Department of Education/ ; //Young Top-Notch Talent Cultivation Program of Hubei Province/ ; 222102110380//Science and Technology Development Programs of Henan Province/ ; //the Joint supported by Hubei Provincial Natural Science Foundation and Shiyan-of China [2025AFD172, 2025AFD179, 2025AFD205]/ ; }, mesh = {Droughts ; *Ocimum basilicum/genetics/physiology/metabolism ; Salinity ; Adaptation, Physiological ; Gene Expression Regulation, Plant ; *Metabolic Networks and Pathways ; Stress, Physiological ; Metabolomics ; Plant Leaves/physiology ; China ; Plant Roots/physiology ; Multiomics ; }, abstract = {The Ocimum genus, valued for its culinary, medicinal, and aromatic uses, is often cultivated in regions affected by drought and salinity. This study investigates the adaptive responses of QingFeng (QF), a newly identified basil cultivar locally known as vegetable "jingjie" in China, to high salinity and drought stress. DNA barcoding, mucilaginous seed analysis, flow cytometry, and karyotyping confirmed QF's identity, revealing a chromosome number of 2n = 76 and a 1C genome size of 2962 ± 36 Mb. Phenotyping, transcriptomic and metabolomic profiling, and hormone monitoring showed drought primarily suppressed leaf growth, while salinity inhibited root elongation. Notably, convergent and divergent responses to salinity and drought were observed, including stress-specific remodeling of core metabolic pathways such as the GS-GOGAT cycle, photorespiration, TCA cycle, and pyrimidine metabolism. Secondary metabolite profiling further demonstrated stress-specific patterns in the accumulation of flavonoids and alkaloids. These findings provide a theoretical foundation for deciphering abiotic stress adaptation mechanisms in basil and offering practical approaches to enhance local cultivation of the QingFeng cultivar.}, }
@article {pmid40763587, year = {2025}, author = {Azirakhmet, Z and Shchepin, O and Inoue, M and Kussainova, A and Bersimbaev, R and Schnittler, M}, title = {First records of nivicolous myxomycetes (Amoebozoa) from Kazakhstan.}, journal = {European journal of protistology}, volume = {100}, number = {}, pages = {126161}, doi = {10.1016/j.ejop.2025.126161}, pmid = {40763587}, issn = {1618-0429}, abstract = {We present the first survey of nivicolous myxomycetes (plasmodial slime molds, Amoebozoa) conducted in Kazakhstan, specifically from the Ile-Alatau mountain range near Almaty. A total of 82 specimens were collected, and 16 species were identified using a comparative morphological approach. Except for Didymium dubium, all identified species represent first records for Kazakhstan. DNA barcoding confirmed the morphology-based identification of 70 specimens, revealing 26 distinct barcode sequence variants. Among these, nine 18S rDNA barcode variants were novel and have not been previously reported in the GenBank database.}, }
@article {pmid40761132, year = {2025}, author = {Bu, A and Wu, G and Hu, L}, title = {Revealing the Heterogeneity of Extracellular Vesicles: From Population to Single Particle Level.}, journal = {Proteomics}, volume = {}, number = {}, pages = {}, doi = {10.1002/pmic.70024}, pmid = {40761132}, issn = {1615-9861}, support = {22374056//National Natural Science Foundation China/ ; 22374056//National Natural Science Foundation China/ ; 22374056//National Natural Science Foundation China/ ; }, abstract = {Extracellular vesicles (EVs) are secreted by cells and enclosed within lipid bilayers. These vesicles contain diverse biomolecular components, including proteins, nucleic acids, lipids, and metabolites. They serve critical roles in intercellular communication and regulate multiple physiological and pathological processes, such as immune modulation, angiogenesis, and tumorigenesis and metastasis. Notably, EVs exhibit marked heterogeneity in both physical characteristics and biomolecular composition. This article will systematically characterize the multidimensional heterogeneity of EVs at the population level through comprehensive analysis of their biogenesis origins, size distribution, surface protein, surface glycan chains, and surface lipid. Conventional population-level analyzes yield averaged molecular profiles that obscure subtype-specific functional correlations, thereby limiting mechanistic insights into EV subpopulation biology. To further understand EV heterogeneity, it is necessary to enhance our understanding about molecular characteristics of EVs from the population to the single particle level. Current single EVs analysis techniques mainly include super-resolution microscopy (SRM), atomic force microscopy (AFM), nanoparticle tracking Analysis (NTA), flow cytometry (FCM), surface enhanced Raman spectroscopy (SERS), mass spectrometry (MS), and proximity barcoding assay (PBA). In this review, we systematically examine population-level EV heterogeneity; evaluate single-particle detection methodologies; and discuss emerging technologies (e.g., click chemistry, Olink proteomics, and molecular imprinting) for resolving single EV heterogeneity.}, }
@article {pmid40758964, year = {2025}, author = {Molina, L and Williams, G and de Errasti, A and Hadziabdic, D and Pildain, MB}, title = {Diversity of fungi cultured from galleries and bodies of ambrosia beetles (Gnathotrupes spp.) and carpenter moths (Chilecomadia valdiviana) in lenga (Nothofagus pumilio) forests in Patagonia.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/00275514.2025.2522019}, pmid = {40758964}, issn = {1557-2536}, abstract = {Wood-boring insects play an important role in turnover of trees and biomass in temperate forests and interact with a functionally diverse mycobiome. However, the diversity and dynamics of ambrosia beetles, other wood-boring insects, and their fungi remain relatively poorly understood in the forests of temperate South America. Baseline knowledge of insect and fungal diversity is therefore needed to provide a foundation for understanding the potential future dynamics of these critically important ecosystems in the context of global change. This study aimed to document fungal diversity that could be obtained in culture from larvae, adults, and galleries of ambrosia beetles (Gnathotrupes spp.) and a carpenter moth (Chilecomadia valdiviana) from lenga (Nothofagus pumilio) in northwest Patagonia, Argentina. Long molecular barcodes from fungal cultures isolated from galleries, larvae, and adult insects were obtained using nanopore sequencing. Fungal assemblages associated with Gnathotrupes spp. (32 unique taxa) and C. valdiviana (17 unique taxa) differed in structure and composition but shared 11 distinct taxa. Differences were found between fungal assemblages associated with C. valdiviana gut tracts and galleries. Fungal assemblages found in galleries and insect bodies of Gnathotrupes varied among species, seasons, and health conditions of the host crown. Our results also showed that the ophiostomatoid fungi Raffaelea spp. and yeast Cyberlindnera sp. were commonly found with Gnathotrupes spp. whereas Ambrosiozyma angophorae and Oidiodendron sp. were found with C. valdiviana. Species of the blue stain fungi Ophiostoma patagonicum, O. nothofagi, an unidentified Sporothrix sp. and Huntiella decorticans were found with both beetles and moths, and O. patagonicum was the most frequently isolated species. This is the first comprehensive study of microbiota isolated from Gnathotrupes spp. and C. valdiviana.}, }
@article {pmid40758764, year = {2025}, author = {Edge, RJ and Marriott, AE and Keen, M and Xie, T and Crittenden, EP and Dawson, CA and Wilkinson, MC and Wüster, W and Casewell, NR and Ainsworth, S and Menzies, SK}, title = {Preclinical evaluation of the neutralising efficacy of three antivenoms against the venoms of the recently taxonomically partitioned E. ocellatus and E. romani.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {8}, pages = {e0013371}, pmid = {40758764}, issn = {1935-2735}, mesh = {Animals ; *Antivenins/pharmacology ; Mice ; *Viperidae/classification ; *Viper Venoms/antagonists &amp; inhibitors/toxicity ; *Snake Bites/drug therapy ; Male ; Female ; }, abstract = {Snakebite is a significant public health concern in Africa, with the viperid species Echis ocellatus being responsible for the majority of snakebite deaths in West Africa. Recently E. ocellatus underwent taxonomic revision and was split into two species, E. ocellatus sensu stricto and E. romani, leading to questions regarding differences in venom bioactivities and the efficacy of antivenoms indicated for treatment of 'E. ocellatus' envenoming against the two redefined species. Using a range of in vitro assays we compared the toxin activities of the two species and the venom-neutralising efficacy of three antivenoms (EchiTAbG, SAIMR Echis and Echiven) raised against 'E. ocellatus'. We then used murine preclinical assays to compare the in vivo efficacy of these antivenoms against E. romani and E. ocellatus s. str venoms. Mitochondrial barcoding of snake skins and venom revealed that E. romani, and not E. ocellatus, is used in the manufacture of several antivenoms raised against 'E. ocellatus'. There were also a number of differences in specific toxin activity between the venoms of the two species in the three in vitro assays utilised in this study.; E. ocellatus (Ghana) had the strongest phospholipase A2 (PLA2) activity, followed by weak PLA2 activity for E. romani (Cameroon) and insignificant activity by E. romani (Nigeria). E. ocellatus (Ghana) and E. romani (Nigeria) demonstrated comparable snake venom metalloproteinase activity, whilst E. romani (Cameroon) had reduced, albeit still significant, activity in comparison. However no differences were observed in a plasma clotting assay measuring coagulopathy between the venoms and localities. Venoms from E. ocellatus (Ghana) and E. romani (Cameroon and Nigeria) were all recognised comparably by the three antivenoms, and there were only modest differences between antivenoms in neutralising the various in vitro toxin effects. In murine preclinical assays, each antivenom could neutralise the lethal effects of E. romani (Nigeria), but differences were seen in their comparative potency when the same antivenom doses were tested against E. romani (Cameroon) and E. ocellatus (Ghana). In these comparative potency assays, all three antivenoms were unable to confer 100% survival when tested against E. romani (Cameroon), but SAIMR Echis provided the best protection with 80% survival. When tested against E. ocellatus (Ghana), the comparative doses of SAIMR Echis and Echiven provided 100% protection whereas EchiTAbG failed to prevent lethality beyond three hours. This represents the first detailed analysis of differences between E. ocellatus and E. romani venom bioactivities and the efficacy of existing antivenoms against these two species. Our findings demonstrate that EchiTAbG, SAIMR Echis and Echiven antivenoms are preclinically efficacious against the lethal effects of E. ocellatus and E. romani venom across a number of localities.}, }
@article {pmid40758432, year = {2025}, author = {Baker, SS and Carmona-Galindo, V and Hoque, M and Ali Edriss, F and Alrayyashi, A and Al-Shaghdari, A and Al-Wakeel, A and Ali, N and Alkuhali, A and Allen, A and Bangurah, S and Bazoun, W and Benford, H and Doss, D and Eady, A and Dourra, M and Guirgis, H and Hamade, I and Hamo, R and Jamal Iddin, J and Jarbo, J and Kawtharani, S and Kunnummyalil, K and Markos, B and Nistor, R and Obeid, H and Sema, R and Shelton, S and Riachi, L and Rodriguez, J and Saahir, T and Sareini, S and Scheys, C and Sterling, X and Vosbigian, G}, title = {Advancing Integrative Pollinator Biology Education with Course-based Undergraduate Research Experiences.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf145}, pmid = {40758432}, issn = {1557-7023}, abstract = {The next generation of pollination researchers faces unprecedented environmental change during the Anthropocene and must develop cross-disciplinary research skill sets. Course-based Undergraduate Research Experience (CURE) pedagogy is one instructional approach that can expose students to integrative biology research while introducing them to technologies that will become increasingly important in pollination system studies. CUREs offer additional advantages, including the potential of crowdsourcing research and strategies that can increase retention of underrepresented minorities in science, technology, engineering, and mathematics (STEM). In this perspective, we present CUREs that utilize pollinator research as exemplars of how undergraduates can gain experience with integrative research approaches while providing valuable data on the effects of human activity on pollination systems. At the University of Detroit Mercy, a metabarcoding CURE was developed that utilized nanopore sequencing technology to evaluate pollen profiles in urban apiaries. Another CURE involving the solitary leafcutter bee, Megachile rotundata, is being used to evaluate pollinator habitat restoration efforts in an urban park. The instructional approach involved students integrating classical field biology research techniques with DNA barcoding to determine the success of the restoration efforts. Another example is Bee the CURE, a curriculum at Pima Community College, where students conduct barcoding experiments by uploading bee DNA sequences to a barcoding database. This CURE uses a place-based pedagogy, which has been shown to have a positive impact on Hispanic students' perceptions of STEM. These examples demonstrate that pollinator-centered CUREs can integrate multiple approaches and technologies, contribute to scientific knowledge, and can be successfully implemented in diverse institutions. To expand its impact, the pollinator research community should collaborate to develop scalable programs that train future integrative biologists in emerging technologies, such as high-throughput DNA sequencing, DNA barcoding, and advanced computational methods.}, }
@article {pmid40758411, year = {2025}, author = {Li, W and Chen, X and Wen, N and Chen, Z and Yang, W and Guo, W and Zhang, Q and Wang, Z and Zhai, X and Qiu, L and Tan, W}, title = {Precision Mapping of Direct Membrane Protein Interactions via Binding-Induced DNA Barcode Transfer Labeling.}, journal = {Nano letters}, volume = {25}, number = {32}, pages = {12360-12368}, doi = {10.1021/acs.nanolett.5c03014}, pmid = {40758411}, issn = {1530-6992}, abstract = {Cell-cell communication is governed by dynamic membrane protein interactions. Precise tracking of direct protein binding and its functional outcomes across cellular engagements is essential for decoding complex biological processes. While proximity-based labeling techniques convert transient interactions into stable signals, they often fail to distinguish direct binding from nonspecific associations. In this work, we developed a binding-induced labeling strategy for 1:1 DNA barcode transfer between interacting proteins at the cellular interface. Using the PD1/PD-L1 immune checkpoint as a model, we designed functionalized aptamer probes targeting PD-L1 on cancer cells, which upon PD1/PD-L1 binding were covalently transferred to PD1 on T cells via click chemistry. By incorporating barcoded primer sequences and programmable DNA signal amplification, we achieved sensitive and sequential tracking of individual PD1/PD-L1 binding events across multiple cellular interactions. Furthermore, with the integration of single-cell transcriptional profiling, this platform revealed the progressive impact of iterative PD1/PD-L1 binding on T-cell reprogramming.}, }
@article {pmid40757888, year = {2025}, author = {Berkem, R and Özyol Atkaya, T}, title = {[Are Ureaplasma Species Being Disregarded in Urinary Tract Infections?].}, journal = {Mikrobiyoloji bulteni}, volume = {59}, number = {3}, pages = {292-306}, doi = {10.5578/mb.20250326}, pmid = {40757888}, issn = {0374-9096}, mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/epidemiology ; *Ureaplasma Infections/microbiology/diagnosis/epidemiology ; *Ureaplasma/isolation &amp; purification/genetics/classification ; Female ; Real-Time Polymerase Chain Reaction ; Ureaplasma urealyticum/isolation &amp; purification/genetics ; Male ; Adult ; Middle Aged ; }, abstract = {Ureaplasma parvum ve Ureaplasma urealyticum, üriner ve genital sistemde kolonize olabilmekte ve çeşitli enfeksiyonlara neden olmaktadır. Bu etkenler, zor üreme özellikleri nedeniyle rutin laboratuvar tanı yöntemleriyle tanımlanamamaktadır. Bu nedenle toplumdaki insidansı, direnç özellikleri ve klinikte neden oldukları enfeksiyonlarla ilgili daha ayrıntılı çalışmalara ihtiyaç duyulmaktadır. Bu çalışmada üriner sistem enfeksiyonu şüphesi olan hastalarda üreaplazmaların varlığının gösterilmesi amaçlanmıştır. Hedefleri arasında U.urealyticum ve U.parvum olan ticari gerçek zamanlı kantitatif polimeraz zincir reaksiyon [real-time quantitative polymerase chain reaction (Rt-qPCR)] panel kiti kullanılmış ve PCR sonuçlarının doğruluğu sekans analiziyle gösterilmiştir. Üriner sistem enfeksiyonu şüphesiyle laboratuvara gönderilen 603 orta akım idrar örneği, idrar yolu enfeksiyonları qPCR panel kiti (Bioeksen, Türkiye) ile çalışılmıştır. U.urealyticum ve/veya U.parvum pozitif bulunan 195 örneğin, örnek miktarı yeterli olan 130 adedine, -20 °C'de saklanmalarının ardından MinION™ (Oxford Nanopore Technologies®, Birleşik Krallık) sisteminde rapid barcoding kit (SQK-RBK110.96) (Oxford Nanopore Technologies®, Birleşik Krallık) ile üretici firma önerilerine uygun olarak yeni nesil dizileme [next generation sequencing (NGS)] analizi yapılmıştır. qPCR ile pozitif bulunan 195 (%32.33) örneğin; 138 (%70.76)'inde U.parvum, 46 (%23.58)'sında U.urealyticum, 11 (%5.64)'inde U.urealyticum ve U.parvum birlikte bulunmuştur. qPCR pozitifliği bulunan 195 örneğin; örnek miktarı yeterli olan 130'una NGS ile sekans analizi çalışılmıştır. Bu 130 örneğin 17'sinde elektroforezde pozitif bant (amplifikasyon ürünü) ve beş örnekte yeterli sekans (< 10 coverage) verisi elde edilememiştir. Dolayısıyla 22 örnekte sekans analiz sonucu elde edilememiş, 108 örnekte ise elde edilmiştir. Yüz sekiz örneğin; 102 (%94.44)'sinde qPCR ve NGS sonuçları uyumlu, altısında (%5.56) ise uyumsuz bulunmuştur. Uyumsuz altı örneğin biri qPCR ile U.urealyticum olarak tanımlanırken, sekans analizinde U.parvum olarak tanımlanmış, diğer beş örnekte qPCR'de birlikte bulunan U.urealyticum ve U.parvum'dan sadece biri NGS ile gösterilebilmiş diğeri gösterilememiştir; beş örneğin üçünde sekans analiziyle sadece U.parvum, ikisinde ise sadece U.urealyticum gösterilebilmiştir. Çalışmada orta akım idrar örneklerinde %32.33 oranında U.parvum ve/veya U.urealyticum pozitifliği bulunmuştur. Bu çalışmada, yüksek pozitiflik oranları nedeniyle bu mikroorganizmaların olası bir üriner sistem enfeksiyonu etkeni olabileceğine ve göz ardı edilmemeleri gerektiğine dikkat çekilmek istenmiştir.}, }
@article {pmid40757278, year = {2025}, author = {Kossatz, P and Mezhov, A and Andresen, E and Prinz, C and Schmidt, W and Resch-Genger, U}, title = {Assessing the Applicability of Lanthanide-Based Upconverting Nanoparticles for Optically Monitoring Cement Hydration and Tagging Building Materials.}, journal = {ACS omega}, volume = {10}, number = {29}, pages = {31587-31599}, pmid = {40757278}, issn = {2470-1343}, abstract = {Chemically stable, lanthanide-based photon upconversion micro- and nanoparticles (UCNPs) with their characteristic multicolor emission bands in the ultraviolet (UV), visible (vis), near-infrared (NIR), and short-wave infrared (SWIR) are promising optical reporters and barcoding tags. To assess the applicability of UCNPs for the monitoring of early stage cement hydration processes and as authentication tags for cementitious materials, we screened the evolution of the luminescence of self-made core-only NaYF4:Yb,Er UCNPs and commercial μm-sized Y2O2S:Yb,Er particles during the first stages of cement hydration, which largely determines the future properties of the hardened material. Parameters explored from the UCNP side included particle size, morphology, surface chemistry or coating, luminescence properties, and concentration in different cement mixtures. From the cement side, the influence of the mineral composition of the cement matrix was representatively examined for ordinary Portland cement (OPC) and its constituents tricalcium aluminate (C3A), tricalcium silicate (C3S), and gypsum at different water to cement ratios. Based on reflection and luminescence measurements, enabling online monitoring, which were complemented by XRD and isothermal heat-flow calorimetric measurements to determine whether the incorporation of these particles could impair cement hydration processes, well suited lanthanide particle reporters could be identified as well as application conditions. In addition, thereby the reporter influence on cement hydration kinetics could be minimized while still preserving a high level of information content. The best performance for the luminescence probing of changes during early stage cement hydration processes was observed for 25 nm-sized oleate (OA)-coated UCNPs added in a concentration of 0.1 wt %. Higher UCNP amounts of 1.0 wt % delayed cement hydration processes size- and surface coating-specifically in the first 24 h. Subsequent luminescence stability screening studies performed over a period of about one year support the applicability of UCNPs as optical authentication tags for construction materials.}, }
@article {pmid40756339, year = {2025}, author = {Jang, EY and Yang, SB and Chun, J and Kwack, KH and Kang, SW and Lee, JH and Moon, JH}, title = {Single-cell RNA sequencing using split-pool barcoding reveals transcriptional heterogeneity in Porphyromonas gingivalis with implications for periodontal pathogenesis.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2540827}, pmid = {40756339}, issn = {2000-2297}, abstract = {BACKGROUND: Porphyromonas gingivalis is a keystone pathogen in periodontitis, associated with dysbiosis and chronic inflammation. While its virulence mechanisms are well characterized, its transcriptional heterogeneity at the single-cell level remains unexplored.<br><br>MATERIALS AND METHODS: We applied split-pool barcoding-based single-cell RNA sequencing to profile gene expression in 1,942 individual P. gingivalis W83 cells cultured under anaerobic conditions. Clustering and differential expression analyses were conducted to identify distinct transcriptional subpopulations.<br><br>RESULTS: We identified six transcriptionally distinct clusters, with the two largest accounting for 72.7% of the population. Minor clusters exhibited signatures related to stress responses, metabolism, membrane transport, and DNA regulation. Sub-clustering of major populations revealed rare subgroups, including one enriched for genes involved in iron acquisition, proteolysis, and transport.<br><br>CONCLUSIONS: This study presents the first single-cell transcriptomic map of P. gingivalis, revealing rare but functionally significant subpopulations. Such diversity may support bacterial adaptability, virulence, and immune evasion, informing future strategies for targeted periodontal therapy.}, }
@article {pmid40755798, year = {2025}, author = {Carletti, M and Viñuela Rodríguez, N and Rossetti, G and Rossi, V and Tan, BGP and Reimer, JD}, title = {The tip of the iceberg: extraordinarily high diversity while examining two infralittoral nematode communities on Okinawa-jima Island, Japan, using morphology and DNA barcoding.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19757}, pmid = {40755798}, issn = {2167-8359}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Japan ; *Nematoda/genetics/classification/anatomy &amp; histology ; *Biodiversity ; Islands ; Ecosystem ; Coral Reefs ; Geologic Sediments/parasitology ; Phylogeny ; }, abstract = {BACKGROUND: Nematodes are among the most diverse and abundant metazoans in aquatic habitats, contributing significantly to global biodiversity. Despite their abundance and importance, the presumed number of undescribed species is high and their diversity is often underestimated.<br><br>METHODS: In this research, sediment samples were collected from three microhabitats (bare sand, seagrass, coral) in two sites around Okinawa-jima Island in subtropical southern Japan. Nematode specimens were obtained by filtering the sediment and were then used to determine meiofaunal assemblages with morphology and molecular methods at the two sites and to compare them with environmental variables.<br><br>RESULTS: The results showed an overwhelmingly high biodiversity of nematofauna with both methods. The morphological identification of free-living nematodes was partly supported by molecular analyses, with the results varying more regarding less common taxa. The discrepancies between different methods may be due to low success of DNA amplifications, high nucleotide variability, and overestimation of congeneric specimens. We observed that coral reef habitats clearly differed from nearby sand and seagrass beds in terms of nematode genus-level assemblages. We identified at least 10 orders and 38 genera of nematodes from our samples that only span two different sites, and it is highly likely these samples include undescribed taxa. Our results strongly suggest that coral reefs and neighboring areas are hot-spots for nematode diversity, at least around Okinawa-jima Island if not also in other coral reef regions.}, }
@article {pmid40755785, year = {2025}, author = {Abuassaf, RA and Al-Jamal, FF and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD}, title = {Evaluating the antibacterial properties of deep-sea sponges Dactylospongia elegants, Stelletta fibrosa, and Haliclona manglaris from the Jordanian Gulf of Aqaba.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19735}, pmid = {40755785}, issn = {2167-8359}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Microbial Sensitivity Tests ; *Porifera/chemistry/genetics ; *Gram-Positive Bacteria/drug effects ; *Haliclona/chemistry ; *Gram-Negative Bacteria/drug effects ; Tandem Mass Spectrometry ; }, abstract = {Marine sponges are known for their rich variety of secondary metabolites, many of which show potential for pharmaceutical applications. In this study, three deep-sea sponge species-Stelletta fibrosa, Dactylospongia elegans, and Haliclona manglaris-were identified using DNA barcoding, and their ethanolic extracts were tested for antibacterial activity. The extracts were evaluated against Gram-positive (e.g., Bacillus pumilus, Staphylococcus aureus, Staphylococcus epidermidis, and methicillin-resistant Staphylococcus aureus, MRSA) and Gram-negative bacteria (e.g., Escherichia coli and Klebsiella aerogenes) using the agar well diffusion method. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were also determined. Among the extracts, D. elegans exhibited the most potent antibacterial activity, with inhibition zones ranging from six to 21 mm against gram-positive bacteria and low MIC/MBC values from 0.25 to three mg/ml. Liquid chromatography-mass spectrometry (LC-MS/MS) analysis of D. elegans revealed the presence of bioactive compounds such as gallic acid, caffeic acid, bolinaquinone, dactyloquinone, and others, which are known for their antimicrobial properties. These findings suggest that D. elegans has promising antibacterial properties that could be valuable in combating antimicrobial resistance.}, }
@article {pmid40755128, year = {2025}, author = {Mat Jaafar, TNA and Seah, YG and Imamura, H and Motomura, H and Matsunuma, M}, title = {Rogadius azizahae, a new flathead (Perciformes: Platycephalidae) from the South China Sea.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70135}, pmid = {40755128}, issn = {1095-8649}, support = {20H03311//UMT/SRG/2023/55435; JSPS KAKENHI/ ; 21H03651//UMT/SRG/2023/55435; JSPS KAKENHI/ ; 23K20304//UMT/SRG/2023/55435; JSPS KAKENHI/ ; 24K02087//UMT/SRG/2023/55435; JSPS KAKENHI/ ; JPJSCCB20200009//JSPS Core-to-Core CREPSUM/ ; }, abstract = {A new flathead Rogadius azizahae (Platycephalidae) is described on the basis of five specimens [102.5-107.8 mm standard length (SL)] collected off the east coast of the Malay Peninsula, southern South China Sea. The new species is morphologically similar to Rogadius mcgroutheri Imamura, 2007, known from the Coral Sea off eastern Australia and New Caledonia, the two species sharing most diagnostic characters, including a minute, weakly developed antrorse spine on the preopercle [vs. a long, stout antrorse spine present in Rogadius asper (Cuvier in Cuvier &amp; Valenciennes, 1829), Rogadius fehlmanni Knapp, 2012, and Rogadius pristiger (Cuvier in Cuvier &amp; Valenciennes, 1829)]; usually a single preocular spine [vs. 2-4 in R. fehlmanni and 2-5 in Rogadius welanderi (Schultz in Schultz et al., 1966)]; no accessory spines along the preocular spine base [vs. present in R. fehlmanni and Rogadius serratus (Cuvier in Cuvier &amp; Valenciennes, 1829)]; and no longitudinal black band on the caudal fin (vs. present in Rogadius patriciae Knapp, 1987). The new species can also be distinguished from R. mcgroutheri by having 11 dorsal-fin soft rays [vs. 11 or 12, modally 12 (25 of 30 specimens) in the latter]; 7 lower gill rakers [vs. 5-7, modally 6 (21 of 30)]; the caudal fin brown basally, broadly whitish (semitranslucent) anteriorly and almost entirely brown on the posterior half (vs. ca. 4 irregular variously sized vertical rows of black blotches); the pelvic fin with ca. 6-8 rows of narrow, wavy black bands or dotted lines (vs. largely brownish, with no defined bands or spots); a relatively large orbit, its diameter 12.4-12.8 (mean 12.6)% SL [vs. 11.4-12.3 (11.7)% SL in 100-110 mm SL specimens]; and relatively narrow interorbital region, its width 1.3-1.5 (mean 1.4)% SL [vs. 1.7-2.2 (1.9)% SL]. DNA barcoding also indicated distinct divergence (14.3-14.4% uncorrected p-distance) between the new species and R. mcgroutheri. A revised key to species of Rogadius is provided.}, }
@article {pmid40753185, year = {2025}, author = {Li, L and Yang, W and Liu, Q and Jiang, X and Wu, K and Fang, L and Li, M and Zeng, S and Li, S}, title = {Comparative analysis of 18 chloroplast genomes reveals genomic diversity and evolutionary dynamics in subtribe Malaxidinae (Orchidaceae).}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {1013}, pmid = {40753185}, issn = {1471-2229}, support = {32070224//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Chloroplast/genetics ; *Orchidaceae/genetics/classification ; Phylogeny ; *Genetic Variation ; *Evolution, Molecular ; }, abstract = {BACKGROUND: The subtribe Malaxidinae encompasses diverse species, many of which possess remarkable medicinal properties that have been employed in traditional Chinese medicine for centuries. Although recent advancements have improved our understanding of the backbone phylogeny of Malaxidinae, clarifying the complex intergeneric relationships remains challenging, largely owing to limited genomic data. To address this gap and further investigate the genetic diversity and evolutionary patterns within this subtribe, we sequenced and assembled complete chloroplast (cp.) genomes from sixteen Malaxidinae species. These newly acquired genomic resources, combined with two previously published cp. genomes from closely related species, were incorporated into a comprehensive comparative genomic and phylogenomic analysis.<br><br>RESULTS: The complete cp. genomes of all 18 Malaxidinae species were analyzed, revealing lengths ranging from 143,062&#xa0;bp to 158,785&#xa0;bp. Each genome contains 123-133 genes, including 74-86 protein-coding genes, 38 tRNA genes, 8 rRNA genes and 1-8 pseudogenes. The chloroplast genomes of Malaxidinae species exhibit significant structural diversity, with particularly pronounced variations observed in the ndhF and ycf1 genes located at the IR/SSC boundary regions. In certain species, the SSC regions showed substantial size reduction, ranging from 10,224 to 15,582&#xa0;bp. Notable variability in both gene loss and truncation patterns was observed in the ndh gene family across these species, accompanied by diverse modifications affecting the length, position, and pseudogenization of the ycf1 gene. Furthermore, our study identified genomic inversions and rearrangements occurring in both the LSC and SSC regions of specific species. The detection of abundant long dispersed repeats and SSRs provides valuable molecular markers for evaluating both intrageneric and interspecific polymorphism as well as genetic diversity patterns. Through codon usage bias analysis, we established that natural selection serves as the predominant evolutionary force shaping codon usage patterns in most Malaxidinae species. Detailed sequence alignment of the chloroplast genome revealed that structural variants are primarily concentrated within single-copy regions. Ten highly variable cpDNA markers were chosen as mutational hotspots, with the potential for development as DNA barcodes for Malaxidinae species. Our phylogenomic analysis clearly resolved the Malaxidinae into three well-supported major clades. Clade I comprises species of Liparis s.s., Malaxis, and Oberonioides. Clade II includes species of Crepidium, Dienia, Diteilis and Empusa. Clade III consists of species from the genera Blepharoglossum, Cestichis, Oberonia, Platystyliparis and Stichorkis.<br><br>CONCLUSION: This research provides valuable insights into the unique characteristics of the chloroplast genome in Malaxidinae orchids, significantly advancing our comprehension of their evolutionary mechanisms and phylogenetic architecture. The acquired genomic data establish a crucial foundation to advance medical resources and aid in species differentiation.}, }
@article {pmid40747441, year = {2025}, author = {Li, L and Lu, Z and Liu, Z and Liang, C and Wang, J and Wang, Y}, title = {Dataset of the complete mitogenomes of the mushroom corals Fungiidae.}, journal = {Data in brief}, volume = {61}, number = {}, pages = {111857}, pmid = {40747441}, issn = {2352-3409}, abstract = {Twenty-four mitogenomes of the mushroom corals (Fungiidae), representing 18 species from 12 genera, were sequenced and annotated. These mitogenomes exhibit high similarity, each containing the same 13 protein-coding genes (PCGs) and two rRNA genes as other scleractinian corals. Compared to the genes, the intergenic regions (IGRs) are more diverse. Interestingly, minisatellite sequences were identified in the IGRs between COX1 and trnM (IGR [COX1] [-] [trnM]) and between ND4 and rrnS (IGR [ND4] [-] [rrnS]) of most Fungiidae mitogenomes. Primarily due to the existence of minisatellites in IGR [COX1] [-] [trnM] , the length of Fungiidae mitogenomes varies from 16,292 to 17,399 bp. Similar to the phylogenetic tree based on partial COI sequences, Bayesian phylogenetic trees constructed using 13 PCGs, IGR [COX1] [-] [trnM] and IGR [ND4] [-] [rrnS] divide Fungiidae into four distinct clades. However, the latter three trees provide a higher resolution of genus- and species-level evolutionary relationships. This mitogenome dataset will be valuable for better understanding the phylogeny of Fungiidae. The diverse IGRs in these mitogenomes may serve as a useful resource for developing Fungiidae DNA barcodes, while the identified minisatellites can facilitate studies on the population biology of Fungiidae.}, }
@article {pmid40746709, year = {2025}, author = {Crous, PW and Catcheside, DEA and Catcheside, PS and Alfenas, AC and Alfenas, RF and Barreto, RW and Lebel, T and Balashov, S and Broadbridge, J and Jurjević, &#x17d; and De la Peña-Lastra, S and Hoffmann, R and Mateos, A and Riebesehl, J and Shivas, RG and Soliz Santander, FF and Tan, YP and Altés, A and Bandini, D and Carriconde, F and Cazabonne, J and Czachura, P and Gryta, H and Eyssartier, G and Larsson, E and Pereira, OL and Rigueiro-Rodríguez, A and Wingfield, MJ and Ahmad, W and Bibi, S and Denman, S and Esteve-Raventós, F and Hussain, S and Illescas, T and Luangsa-Ard, JJ and Möller, L and Mombert, A and Noisripoom, W and Olariaga, I and Pancorbo, F and Paz, A and Piątek, M and Polman-Short, C and Suárez, E and Afshan, NS and Ali, H and Arzanlou, M and Ayer, F and Barratt, J and Bellanger, JM and Bidaud, A and Bishop-Hurley, SL and Bohm, M and Bose, T and Campo, E and Chau, NB and Çolak, &#xd6;F and Cordeiro, TRL and Cruz, MO and Custódio, FA and Couceiro, A and Darmostuk, V and Dearnaley, JDW and de Azevedo Santiago, ALCM and de Freitas, LWS and Yáñez-Morales, MJ and Domnauer, C and Dentinger, B and Dhileepan, K and De Souza, JT and Dovana, F and Eberhardt, U and Eisvand, P and Erhard, A and Fachada, V and García-Martín, A and Groenewald, M and Hammerbacher, A and Harms, K and Haroon, S and Haqnawaz, M and Henriques, S and Hernández, AJ and Jacobus, LM and Jaen-Contreras, D and Jangsantear, P and Kaygusuz, O and Knoppersen, R and Kumar, TKA and Lynch, MJ and Mahiques, R and Maraia, GL and Marbach, PAS and Mehrabi-Koushki, M and Miller, PR and Mongkolsamrit, S and Moreau, PA and Oberlies, NH and Oliveira, JA and Orlovich, D and Pérez-Méndez, AS and Pinto, A and Raja, HA and Ramírez, GH and Raphael, B and Rodrigues, A and Rodrigues, H and Ramos, DO and Safi, A and Sarwar, S and Saar, I and Sánchez, RM and Santana, JS and Scrace, J and Sales, LS and Silva, LNP and Stryjak-Bogacka, M and Tacconi, A and Thanh, VN and Thomas, A and Thuy, NT and Toome, M and Valdez-Carrazco, JM and van Vuuren, NI and Vasey, J and Vauras, J and Vila-Viçosa, C and Villarreal, M and Visagie, CM and Vizzini, A and Whiteside, EJ and Groenewald, JZ}, title = {Fungal Planet description sheets: 1781-1866.}, journal = {Persoonia}, volume = {54}, number = {}, pages = {327-587}, pmid = {40746709}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Septoria reinamora on leaf spots of Mutisia spinosa. Australia, Cortinarius albofolliculus on mossy soil, Cortinarius descensoriformis among leaf litter, Cortinarius kaki among leaf litter, Cortinarius lissosporus in leaf litter, Cortinarius malogranatus in leaf litter, Cortinarius meletlac on soil in mixed forest, Cortinarius sebosioides in long decayed wood litter, Helicogermslita australiensis as an endophyte from healthy leaves of Archontophoenix cunninghamiana, Puccinia clemensiorum on culms of Eleocharis ochrostachys, Puccinia geethae on leaves of Cyperus brevifolius, Puccinia marjaniae on leaves of Nymphoides indica, Puccinia scleriae-rugosae on leaves of Scleria rugosa. Brazil, Dactylaria calliandrae on living leaf of Calliandra tweediei, Mucor cerradoensis from soil, Musicillium palmae on living leaves of unidentified palm species, Neodendryphiella agapanthi from stalks of Agapanthus praecox, Parafusicladium riodejaneiroanum on living leaves of native bamboo, Parapenidiella melastomatis on living leaves of unidentified Melastomataceae, Pararamichloridium ouropretoense on living leaves of unidentified Poaceae, Pentagonomyces endophyticus (incl. Pentagonomyces gen. nov.) as endophytic from roots of Musa acuminata, Polyschema endophytica from healthy roots of coffee plant, Purimyces endophyticus as root endophyte of Cattleya locatellii, Ramularia rhododendri on living leaves of Rhododendron sp., Staphylotrichum soli from soil, Trichoderma sexdentis from leaves inside a nest of the leaf-cutting ant Atta sexdens rubropilosa, Wiesneriomyces soli from soil. France, Cosmospora nemaniae on dead or effete stromata of Nemania cf. colliculosa, Inocybe alnobetulae in subalpine green alder stands, Stylonectria hygrophila on dead twigs of Betula pubescens. Germany, Coniochaeta corticalis from bark humus, Coniochaeta fermentaria from fermentation residues from biogas plants, Coniochaeta fibricola from softwood fibres, Coniochaeta weberae from bark humus, Inocybe canicularis on calcareous to more acidic soil with conifers. Iceland, Inocybe islandica associated with Dryas octopetala. India, Vishniacozyma indica on dead twigs. Iran, Botryotrichum lycii on rotten leaf of Lycium depressum. Italy, Cuphophyllus dolomiticus among Salix retusa, Salix reticulata and Dryas octopetala, Inocybe subentolomospora on moss with the presence of Alnus incana, Populus nigra and Salix spp. Malaysia, Catenulostroma pellitae on leaf spots of Eucalyptus pellita. Mexico, Colletotrichum mexicanus from fruit of Persea americana cv. Hass. New Caledonia (France), Cortinarius caeloculus, Cortinarius luteigemellus and Cortinarius perpensus on soil under Nothofagus aequilateralis. New Zealand, Cytospora braithwaitei on branch of Malus domestica. Pakistan, Callistosporium khalidii on humus soil, Entoloma lilacinum on litter in conifer forest, Laccaria decolorans on litter in broad-leaved subtropical forest. Poland, Pseudoneoconiothyrium modrzynanum from resin of Larix decidua ssp. polonica, Tuberculiforma enigmatica isolated from sooty mould community on Quercus robur leaves. Portugal, Clavulus hemisphaericus (incl. Clavulus gen. nov.) on mossy slopes and under Laurus leaf litter, Entoloma daegae on sandy, granitic soil, Hygrocybe aurantiocitrina under laurel forest, Hygrocybe sanguineolutea gregarious in laurel forest, Hygrocybe vulcanica on mossy areas of laurel forest areas, Pachyphlodes algarvensis on sandy soil under Cistus salvifolius, Quercus suber and Pinus pinea. South Africa, Amycosphaerella podalyriae on leaf of Podalyria calyptrata, Erythrobasidium eucalypti from the gut of Gonipterus sp., Letendraea goniomae on leaves of Gonioma kamassi, Pezicula brabeji and Sphaerulina brabeji on twigs of Brabejum stellatifolium, Stachybotrys conicosiae on dead flower head of Conicosia elongata, Talaromyces ignescens from soil. Spain, Cortinarius phaeobrunneus on soil under Quercus ilex and Q. faginea, Inocybe pini-halepensis among grass and fallen leaves of Pinus halepensis, Inocybe subporcorum in sandy soils under Quercus ilex subsp. ballota and Pinus pinaster, Mycena morenoi on dead leaves of Betula pubescens and Salix atrocinerea, Pachyphlodes iberica on clayey and loamy soil under Quercus ilex and Quercus rotundifolia, Ramariopsis coronata in laurel forest. Switzerland, Inocybe minata in a bog on very wet acidic soil with Salix spp. and Betula spp. Thailand, Hypocrella khonsanitii on scale insects (Coccidae), Petchiella hymenopterorum on hymenopteran pupae in the nest (Hymenoptera). Trinidad and Tobago, Neodevriesia maravalensis from office swab. Türkiye, Russula anatolica under Quercus vulcanica. UK, Paracylindrosporium dactylorhizae (incl. Paracylindrosporium gen. nov.) on leaf spots of Dactylorhiza sp., Niesslia hepworthiae and Niesslia libertiae on living leaves of Libertia grandiflora. Ukraine, Lichenohendersonia cetrariae on thallus of terricolous Cetraria aculeata. USA, Atromagnispora indianensis (incl. Atromagnispora gen. nov.) on submerged wood in a freshwater stream, Cytospora michiganensis from utility room (settle plate), Exophiala aeris from air (settle plate), Hongoboletus americanus from mixed pine-hardwood forest, Lorrainsmithia pennsylvanica from bedroom, air, Superstratomyces massachusettsanus from lyse buffer. Vietnam, Aspergillus halopiscium on dry marine anchovy Stolephorus commersonnii. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Catcheside DEA, Catcheside PS, Alfenas AC, Alfenas RF, Barreto RW, Lebel T, Balashov S, Broadbridge J, Jurjević Ž, De la Peña-Lastra S, Hoffmann R, Mateos A, Riebesehl J, Shivas RG, Soliz Santander FF, Tan YP, Altés A, Bandini D, Carriconde F, Cazabonne J, Czachura P, Gryta H, Eyssartier G, Larsson E, Pereira OL, Rigueiro-Rodríguez A, Wingfield MJ, Ahmad W, Bibi S, Denman S, Esteve-Raventós F, Hussain S, Illescas T, Luangsa-ard JJ, Möller L, Mombert A, Noisripoom W, Olariaga I, Pancorbo F, Paz A, Piątek M, Polman-Short C, Suárez E, Afshan NS, Ali H, Arzanlou M, Ayer F, Barratt J, Bellanger J-M, Bidaud A, Bishop-Hurley SL, Bohm M, Bose T, Campo E, Chau NB, Çolak ÖF, Cordeiro TRL, Cruz MO, Custódio FA, Couceiro A, Darmostuk V, Dearnaley JDW, de Azevedo Santiago ALCM, de Freitas LWS, de J Yáñez-Morales M, Domnauer C, Dentinger B, Dhileepan K, De Souza JT, Dovana F, Eberhardt U, Eisvand P, Erhard A, Fachada V, García-Martín A, Groenewald M, Hammerbacher A, Harms K, Haroon S, Haqnawaz M, Henriques S, Hernández AJ, Jacobus LM, Jaen-Contreras D, Jangsantear P, Kaygusuz O, Knoppersen R, Kumar TKA, Lynch MJ, Mahiques R, Maraia GL, Marbach PAS, Mehrabi-Koushki M, Miller PR, Mongkolsamrit S, Moreau P-A, Oberlies NH, Oliveira JA, Orlovich D, Pérez-Méndez AS, Pinto A, Raja HA, Ramírez GH, Raphael B, Rodrigues A, Rodrigues H, Ramos DO, Safi A, Sarwar S, Saar I, Sánchez RM, Santana JS, Scrace J, Sales LS, Silva LNP, Stryjak-Bogacka M, Tacconi A, Thanh VN, Thomas A, Thuy NT, Toome M, Valdez-Carrazco JM, van Vuuren NI, Vasey J, Vauras J, Vila-Viçosa C, Villarreal M, Visagie CM, Vizzini A, Whiteside EJ, Groenewald JZ. (2025). Fungal Planet description sheets: 1781-1866. Persoonia 54: 327-587. doi: 10.3114/persoonia.2025.54.10.}, }
@article {pmid40746704, year = {2025}, author = {Xie, ML and Dima, B and Wang, K and Phukhamsakda, C and Li, Y and Qi, LL and Li, GJ and Liu, TZ and Jia, PS and Wang, Q and Song, LR and Wei, TZ and Li, Y}, title = {Taxonomy and phylogeny of Cortinarius sect. Anomali in China.}, journal = {Persoonia}, volume = {54}, number = {}, pages = {225-263}, pmid = {40746704}, issn = {0031-5850}, abstract = {Cortinarius section Anomali is a species-rich group that occurs worldwide, particularly in Europe and North America. The overlapping morphological and microscopical characteristics of Anomali species pose significant challenges for species identification. Therefore, the focus of this study was to clarify the taxonomy and phylogeny of section Anomali in China. A total of 229 specimens of section Anomali were collected in China over the past two decades. The present study, based on a combination of extensive morphological investigations and molecular methods, reports 22 Anomali species. Eleven of them are recognized as new to science and formally described here as C. albocyaneoides, C. campanianomalus, C. microalbocyaneus, C. neocaninus, C. qilianensis, C. robustianomalus, C. rufolilacinus, C. subalbocyaneus, C. subanomalus, C. xizangensis, and C. vernalianomalus, respectively. Cortinarius albocyaneus, C. azureovelatus, C. caninus, C. kranabetteri, C. lepidopus, and C. perrotensis are reported in China for the first time. In addition, the occurrence of C. cinnamomeolilacinus, C. epsomiensis, C. subclackamasensis, C. tabularis, and C. tropicus in China is confirmed. Descriptions, accompanied by illustrations of morphological characters of the Chinese Anomali species, and comparisons with closely related taxa are provided. The present study reports Cortinarius section Anomali in China or Asia, clarifying taxonomy and conducting phylogeny analyses based on nrITS, nrLSU, rpb1 and rpb2 sequences. We compare the Anomali species from China with those in Europe and North America, enriching the species and sequences of sect. Anomali. In addition, the ornamentation of basidiospores was studied using scanning electron microscopy. Citation: Xie ML, Dima B, Wang K, Phukhamsakda C, Li Y, Qi LL, Li GJ, Liu TZ, Jia PS, Wang Q, Song LR, Wei TZ, Li Y (2025). Taxonomy and phylogeny of Cortinarius sect. Anomali in China. Persoonia 54: 225-263. doi: 10.3114/persoonia.2025.54.07.}, }
@article {pmid40744379, year = {2025}, author = {Joseph, L and Murugesan, M and Jayarajan, J and Poojary, A and Ramasamy, J and Agarwal, V}, title = {Gap assessment in implementation of Biomedical Waste Management in Health Care Facilities: Nationwide survey in India.}, journal = {Indian journal of medical microbiology}, volume = {57}, number = {}, pages = {100947}, doi = {10.1016/j.ijmmb.2025.100947}, pmid = {40744379}, issn = {1998-3646}, abstract = {BACKGROUND: Biomedical Waste (BMW) management presents significant challenges globally. Despite the establishment of BMW management rules in India and their subsequent amendments, compliance gaps persist. To address these, the Consortium of Accredited Health Care Organizations (CAHO) conducted a nationwide survey aimed to identify gaps in the implementation of the BMW rules in India.<br><br>METHODS: The survey was designed by CAHO in collaboration with experts across India. A validated tool with 144 questions captured information on BMW management practices across India. A purposive sampling technique was conducted via online survey tool from July to September 2023. Compliance among healthcare facilities (HCFs) was analyzed, and geographical maps were created.<br><br>RESULTS: A total of 267 HCFs responded to the survey with 178 (67&#xa0;%) were accredited. Among them, 51&#xa0;% of the HCFs directly discarded the needles in the sharps container and 49&#xa0;% cut the needles before disposal. In 50&#xa0;% of HCFs blue bins with blue covers were used. Around 115 (43&#xa0;%) only used dedicated tags to secure the BMW and 58&#xa0;% fully implemented barcoding. Autoclaving of laboratory waste was done in 211 HCFs (79&#xa0;%). Dedicated temporary storage areas were found in 245 (92&#xa0;%) HCFs. Mercury filled devices were still in use in 75 (28&#xa0;%) of the HCFs.<br><br>CONCLUSION: The survey provides valuable insights into the BMW management practices, gaps and areas of improvement in India. The most notable variations evidenced are sharps disposal practices, usage of blue bins, disposal of pharmaceutical waste and continued use of mercury devices.}, }
@article {pmid40743803, year = {2025}, author = {Philpott, DE and Villacorta-Rath, C and DiBattista, JD and Rasheed, MA and Waltham, NJ and Smith, TM and York, PH}, title = {From nets to barcodes: Selecting suitable methods for assessing fish and prawn assemblages in seagrass meadows.}, journal = {Marine environmental research}, volume = {211}, number = {}, pages = {107395}, doi = {10.1016/j.marenvres.2025.107395}, pmid = {40743803}, issn = {1879-0291}, abstract = {Seagrass meadows are vital coastal ecosystems that support fish and prawn assemblages, providing essential resources such as food and refuge. They are especially important as nursery habitats for ecologically and economically important juvenile fish and prawns. However, seagrass ecosystems are declining globally due to their vulnerability to both natural disturbances and anthropogenic impacts. Effective monitoring and management strategies are therefore essential to ensure their conservation and ecological functionality. This review synthesises literature on methods for sampling fish and prawns in seagrass habitats, grouping them into three categories: capture, sensory, and molecular approaches. Capture methods, including beam trawls and seine nets, provide valuable biological data, but are extractive and can be destructive to the surrounding habitat. Sensory methods such as baited remote underwater video systems (BRUVs) and hydroacoustic techniques, offer a non-destructive alternative, but can be negatively influenced by environmental conditions such as turbidity and habitat complexity that are common in seagrass meadows. Molecular approaches, particularly environmental DNA (eDNA) metabarcoding, present a highly sensitive and non-invasive alternative approach, but challenges remain in quantifying species abundance and demographics. To guide method selection, we propose a structured framework of questions and visualisations to assist researchers in selecting the most appropriate sampling methods based on their specific research objectives. Given the biases and limitation of these methods individually, we suggest integrating multiple methods to enhance assessments of marine communities in seagrass habitats. Future research should focus on refining these methodologies to improve the accuracy of biodiversity monitoring in seagrass meadows, whilst minimising environmental impacts.}, }
@article {pmid40738429, year = {2025}, author = {Chakraborty, R and Kannan, SP and Afrose, N and Narayanasamy, D}, title = {Tumor microenvironment expressed enzymes (Matrix metalloproteinases, cathepsins, urokinase-type plasminogen activator) triggered polymersomes for liquid biopsy and cancer diagnostics: A review.}, journal = {International journal of biological macromolecules}, volume = {321}, number = {Pt 2}, pages = {146375}, doi = {10.1016/j.ijbiomac.2025.146375}, pmid = {40738429}, issn = {1879-0003}, abstract = {Enzyme-triggered polymersomes have emerged as a transformative platform in liquid biopsy and cancer diagnostics, enabling high-accuracy biomarker detection through precise enzymatic responsiveness. This review comprehensively examines the rational design, synthesis, and functionalization strategies of enzyme-responsive polymersomes, which undergo programmed structural changes in the presence of tumor microenvironment-associated enzymes such as matrix metalloproteinases (MMPs), cathepsins, and urokinase-type plasminogen activator (uPA). Key advances in polymer chemistry, including block copolymer self-assembly, stimuli-responsive linker integration, and surface ligand conjugation, have been critical in tailoring polymer specificity, enzymatic sensitivity, and biocompatibility. These engineered nanocarriers exploit the overexpression of tumor-associated proteases and lipases to selectively release DNA stains, fluorescent probes, contrast agents, and molecular barcodes, facilitating ultrasensitive detection of circulating tumor cells (CTCs), extracellular vesicles (EVs), and cell-free nucleic acids (cfNAs) in liquid biopsies. Recent innovations in enzyme-triggered cargo release mechanisms, CRISPR-integrated biosensing, and machine learning-enhanced biomarker analysis have further amplified diagnostic precision. Additionally, multifunctional polymersomes bridge diagnostics and therapy, serving as potent theranostic agents. By integrating advanced material synthesis with enzymatic targeting, these systems offer minimally invasive, real-time monitoring and personalized cancer detection. This review highlights current breakthroughs and future directions in enzyme-responsive nanotechnology, underscoring its potential to revolutionize precision oncology.}, }
@article {pmid40737112, year = {2025}, author = {Lancioni, GE and Alberti, G and Filippini, C and Abbinante, F and Singh, NN and O'Reilly, MF and Sigafoos, J}, title = {Technology and instructions to help people with blindness and intellectual disability manage indoor travel: a case series study.}, journal = {Disability and rehabilitation. Assistive technology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/17483107.2025.2541039}, pmid = {40737112}, issn = {1748-3115}, abstract = {PURPOSE: We evaluated a new technology system designed to help eight people with blindness and intellectual disability navigate indoor routes 70- to 140-meter long.<br><br>METHODS: The technology system entailed (a) a smartphone linked to two barcode readers that the participants wore, (b) barcodes printed on A-4 sheets of paper and displayed along the travel routes, and (c) a mini speaker. The technology system was set to provide verbal instructions at specific points of the travel routes to guide the participants to the destinations (to help them complete the scheduled traveling trials correctly). Each participant was exposed to an ABAB design in which A and B represented baseline phases (without system) and intervention phases (with system), respectively.<br><br>RESULTS: During the first baseline phase, the participants did not complete any traveling trial correctly (i.e., without research assistants' guidance). During the first intervention phase, the participants' percentage of traveling trials completed correctly increased to 83-97. The percentage declined during the second baseline phase and increased again (to 93-98) during the second intervention phase.<br><br>CONCLUSIONS: The findings suggest that the new system providing verbal instructions at specific points of the travel routes can help people with blindness and intellectual disability reach their scheduled destinations.}, }
@article {pmid40735452, year = {2025}, author = {Feka-Homsy, P and L'Huillier, AG and Monod, L and Monin, E and Guinand, N and Schwob, JM}, title = {Cochliomyia hominivorax aural myiasis in a 7-year-old traveler.}, journal = {IDCases}, volume = {41}, number = {}, pages = {e02327}, pmid = {40735452}, issn = {2214-2509}, abstract = {•This is a very rare case of aural Cochliomyia hominivorax diagnosed in a pediatric-traveler outside endemic area.•Unlike common travelers' myiasis, Cochliomyia hominivorax can be invasive and destructive.•Cytochrome-C oxidase-I (COI) DNA-barcoding may be a useful tool for diagnosing rare parasitosis.}, }
@article {pmid40735391, year = {2025}, author = {Loyola, DC and Placko, A and Fessl, B and McNew, SM}, title = {Novel microfilariae detected in Galápagos passerines.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {28}, number = {}, pages = {101115}, pmid = {40735391}, issn = {2213-2244}, abstract = {Emerging parasites pose a serious risk to the health and survival of wild animal populations, particularly on islands where species often lack prior exposure and evolved defenses. We present the first report of a novel microfilaria infection found in blood from six species of Galápagos passerines in the coastal zone of Santa Cruz Island. Across 13 months, spanning two wet seasons and one dry season, 294 individuals were sampled and evaluated for microfilarial presence through microscopy and/or polymerase chain reaction. We barcoded the mitochondrial Cytochrome c oxidase I (COI) gene to tentatively place this microfilaria in the genus Eufilaria. We found host species level variation in infection, with certain species, like the vegetarian finch (Platyspiza crassirostris) and the common cactus finch (G eospiza . scandens) having very high prevalence, while others, like the Galápagos mockingbird (Mimus parvulus) and small tree finch (Camarhynchus parvulus) showing significantly lower prevalence. We investigated leukocyte counts, H/L ratios and body condition to evaluate the potential effects of infection on birds and found no relationship between infection status and these health indices. We also tested to see if seasonality could predict the infection trends found in our data and found a relationship with monthly rainfall, where more rain predicts higher microfilarial prevalence. Although we cannot confirm exactly when this parasite established in the Galápagos, our study highlights the importance of continued disease surveillance in endemic systems and underscores the need for species-level COI barcodes to improve microfilaria identification and phylogenetics.}, }
@article {pmid40734901, year = {2025}, author = {Liu, J and Zang, E and Tian, Y and Li, X and Xin, T and Zeng, L and Xu, L and Xiao, P}, title = {Applications and challenges of DNA barcoding in rapid radiation groups: Rhodiola (Crassulaceae) as a case study.}, journal = {Chinese herbal medicines}, volume = {17}, number = {3}, pages = {555-561}, pmid = {40734901}, issn = {2589-3610}, abstract = {OBJECTIVE: Rhodiolae Crenulatae Radix et Rhizoma (Hongjingtian in Chinese, RCRR), the roots and rhizomes of Rhodiola crenulata and its application in the medicinal market is very chaotic. In this study, DNA barcoding database and identification engine of Rhodiola species were established, decoction pieces from the medicinal market were identified, and the application and challenges of DNA barcoding in the rapid radiation of Rhodiola species were analyzed. This study provides reference for the protection, rational development, and utilization of endangered resources within Rhodiola species.<br><br>METHODS: A total of 50 original plant samples from 20 species of the genus Rhodiola from Hebei, Xinjiang, Tibet, Jilin, and other major production areas were collected. Theses samples cover the typical distribution area (Qinghai-Tibetan Platea) of Rhodiola species and other scattered alpine regions (Changbai Mountain, Taibai Mountain, Lushan Mountain, etc.), it encompasses all Rhodiola species with thick rhizomes in China. ITS2 and psbA-trnH barcode of Rhodiola database (BORD) were established and an identification engine named Rhodiola-IDE was developed. The stability and accuracy of the standard DNA barcoding database were evaluated using two datasets. Rhodiola-IDE identified 31 decoction pieces of RCRR from the medicinal material market.<br><br>RESULTS: The BORD containing 1 532 sequences of 88 Rhodiola species has been established, and the identification efficiency results showed good accuracy and stability. According to the Chinese Pharmacopoeia (2020 edition), 23 samples (74.2%) were identified as authentic R. crenulata, while the rest of the marketed varieties were R. kirilowii, R. dumulosa, and R. fastigiata. The product label "Larger flower, Hongjingtian" was identified as R. crenulata. Samples labeled as "Smaller flower, Hongjingtian" were identified as R. crenulata, R. kirilowii, and R. fastigiata.<br><br>CONCLUSION: ITS2 and psbA-trnH barcodes can identify monophyletic groups represented by R. crenulata. However, for non-monophyletic species, it is necessary to collect as many samples as possible and combine them with multiple markers for joint identification. This study discussed the application and challenges of DNA barcodes in Rhodiola under rapid radiation conditions, providing a scientific basis for the rational development and utilization of Rhodiola varieties.}, }
@article {pmid40733470, year = {2025}, author = {Amin, A and Park, S}, title = {Chemotaxonomy, an Efficient Tool for Medicinal Plant Identification: Current Trends and Limitations.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {14}, pages = {}, pmid = {40733470}, issn = {2223-7747}, abstract = {This review highlights the critical role of chemotaxonomy in the identification, authentication, and discovery of bioactive compounds in medicinal plants. By analyzing secondary metabolites using techniques like UV spectroscopy, FTIR, HPLC, GC-MS, NMR, LC-MS-Qtof, and MALDI-TOF MS, chemotaxonomy ensures accurate plant identification, supporting the safe and effective use of plants in herbal medicine. Key secondary metabolites used in chemotaxonomic identification include alkaloids, flavonoids, terpenoids, phenolics, tannins, and plant peptides. Chemotaxonomy also facilitates the discovery of novel compounds with therapeutic potential, contributing to drug development. The integration of chemotaxonomy with genomics and proteomics allows a deeper understanding of plant biosynthesis and the mechanisms behind bioactive compound production. However, challenges due to variability in metabolite profiles and the lack of standardized methods remain, and future research should focus on developing global databases, improving standardization, and incorporating artificial intelligence and machine learning to enhance plant identification and bioactive compound discovery. The integration of chemotaxonomy with personalized medicine offers the potential to tailor plant-based therapies to individual genetic profiles, advancing targeted treatments. This review underscores chemotaxonomy's importance in bridging traditional knowledge and modern science, offering sustainable solutions for medicinal plant use and drug development.}, }
@article {pmid40732093, year = {2025}, author = {Frolova, MS and Kiselev, SS and Panyukov, VV and Ozoline, ON}, title = {Phylogroup Homeostasis of Escherichia coli in the Human Gut Reflects the Physiological State of the Host.}, journal = {Microorganisms}, volume = {13}, number = {7}, pages = {}, pmid = {40732093}, issn = {2076-2607}, support = {24-14-00433//Russian Science Foundation/ ; }, abstract = {The advent of alignment-free k-mer barcoding has revolutionized taxonomic analysis, enabling bacterial identification at phylogroup resolution within natural communities. We applied this approach to characterize Escherichia coli intraspecific diversity in human gut microbiomes using publicly available datasets representing diverse human physiological states. By estimating the relative abundance of eight E. coli phylogroups defined by their 18-mer markers in 558 fecal samples, we compared their distribution between gut microbiomes of healthy individuals, patients with chronic bowel diseases and volunteers subjected to various external interventions. Across all datasets, phylogroups exhibited bidirectional abundance shifts in response to host physiological changes, indicating an inherent bimodality in their adaptive strategies. Correlation analysis of phylogroup persistence revealed positive intraspecific connectivity networks and dependence of their patterns on both acute interventions like antibiotic or probiotic treatment and chronic bowel disorders. Along with predominantly negative correlations with Bacteroides, we observed a transition from positive to negative associations with Prevotella in Prevotella-rich microbiomes. Several interspecific correlations individually established by E. coli phylogroups with dominant taxa suggest their potential role in shaping intraspecific networks. Machine learning techniques statistically confirmed an ability of phylogroup patterns to discriminate the physiological state of the host and virtual diagnostic assays opened a way to optimize intraspecific phylotyping for medical applications.}, }
@article {pmid40730955, year = {2025}, author = {Castellanos, NL and Gunawardana, DN and McCarthy, B and Sathish, P and George, S and Li, D}, title = {Mitochondrial genome of Bactrocera fruit flies (Tephritidae: Dacini): features, structure, and significance for diagnosis.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {700}, pmid = {40730955}, issn = {1471-2164}, support = {406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; 406793//Operational Research programme of the Ministry for Primary Industries (MPI), New Zealand/ ; }, mesh = {Animals ; *Tephritidae/genetics/classification ; *Genome, Mitochondrial ; Phylogeny ; }, abstract = {BACKGROUND: True fruit flies (Diptera: Tephritidae) are among the most destructive pests of fruit and vegetables worldwide and are on the top of quarantine pest lists. To respond effectively to a fruit fly invasion, we need to identify the species rapidly and reliably to understand its biological features and guide response decisions. Molecular techniques have been used to improve the diagnostic ability circumventing many difficulties of morphological identification. However, the commonly used Cytochrome Oxidase I (COI) gene lacks sufficient variation to distinguish species within Bactrocera species complexes. Here we conducted mitochondrial genome sequencing to identify additional genetic markers that could aid diagnosis of Bactrocera fruit fly species.<br><br>RESULTS: We assembled 82 complete mitochondrial genomes from 16 Bactrocera species, including 13 species for which no mitochondrial genome data were previously available, as well as one species each from Dacus aneuvittatus, Dirioxa pornia and Zeugodacus gracilis. Phylogenetic analysis of the Tephritidae family confirmed the monophyly of the Bactrocera genus but could not properly resolve species within species complexes. Comparative mitochondrial genome analysis revealed that intergenic spacer and NADH dehydrogenase genes, specifically ND2 and ND6, harbour enough variations for new specific real-time PCR assays. Based on these findings, six TaqMan-based real-time PCR assays targeting ND2, COI, and CO3 genes were successfully designed and assessed for their specificity and sensitivity in detecting Bactrocera curvipennis, a member of the B. tryoni complex. Of these, one real-time PCR assay targeting the ND2 gene proved to be the most specific and sensitive. It detects B. curvipennis specifically at the level of 1 copy/&#xb5;L of target DNA.<br><br>CONCLUSIONS: Mitochondrial sequence analysis and comparative studies indicate that mitochondrial genomes offer valuable genetic markers for accurate diagnosis of Bactrocera fruit flies. The successful development of the B. curvipennis real-time PCR assay highlights the importance of having additional genetic markers to advance the molecular diagnostics in economically important Bactrocera species.}, }
@article {pmid40730843, year = {2025}, author = {Li, N and Tang, TT and Gu, M and Fu, YQ and Qian, WW and Ma, NN and Shen, AR and Zhu, T and Huo, RB and Zhang, T and Xie, JF and Zhang, L and Liu, BC and Lv, LL}, title = {Single urinary extracellular vesicle proteomics identifies complement receptor CD35 as a biomarker for sepsis-associated acute kidney injury.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6960}, pmid = {40730843}, issn = {2041-1723}, mesh = {Humans ; Biomarkers/urine ; *Extracellular Vesicles/metabolism ; *Acute Kidney Injury/urine/diagnosis/etiology ; Male ; Proteomics/methods ; Female ; Middle Aged ; *Sepsis/complications/urine ; *Receptors, Complement 3b/metabolism ; Aged ; Prospective Studies ; Podocytes/metabolism/pathology ; Adult ; ROC Curve ; }, abstract = {Sepsis-associated acute kidney injury (SA-AKI) portends severe health burden due to significant morbidity and mortality, while early diagnosis remains challenging. In this study, proximity-dependent barcoding assay (PBA) is established to profile the surface proteome of single urinary extracellular vesicle (uEV). Principle uEV clusters with unique function and origination are profiled in SA-AKI in a screening cohort. Complement receptor CD35 on single uEV (CD35-uEV) displays high diagnostic accuracy for SA-AKI (AUC-ROC 0.89 in validation cohort, n = 134). Besides, CD35-uEV enables identification of subclinical AKI (AUC-ROC 0.84 in prospective cohort, n = 72). Moreover, CD35-uEV correlates closely with AKI severity which also predicts persistent AKI (AUC-ROC 0.77), mortality risks (AUC-ROC 0.70) and progression to AKD (AUC-ROC 0.66). Multi-omics profiling reveals that CD35-uEV are predominantly released from injured podocytes exhibiting diminished CD35 expression. Overall, this study identifies a single uEV biomarker related to injured podocyte for early diagnosis and risk stratification of SA-AKI.}, }
@article {pmid40728500, year = {2025}, author = {Li, T and Gu, Z and Zhou, G}, title = {Next-Generation Barcoding for Single-Cell Omics.}, journal = {Analytical chemistry}, volume = {97}, number = {31}, pages = {16708-16713}, doi = {10.1021/acs.analchem.5c03587}, pmid = {40728500}, issn = {1520-6882}, mesh = {*Single-Cell Analysis/methods ; Humans ; }, abstract = {The ability to uniquely label and track individual cells at scale has become foundational to single-cell omics. Conventional barcoding strategies, ranging from plate-based combinatorial indexing to droplet microfluidics-based indexing, have enabled the rise of high-throughput single-cell profiling. However, these approaches each face trade-offs in throughput, cost, compatibility with complex biochemical workflows, or accessibility to nonspecialist laboratories. This perspective surveys the principles, benefits, and limitations of current barcoding methods and introduces emerging enzymatic and computational methods that may redefine how we uniquely index the cellular content, opening the door to simpler, more scalable, and more accessible single-cell analysis pipelines.}, }
@article {pmid40727006, year = {2024}, author = {Abidin, DHZ and Nor, SAM and Seah, YG and Ali, MS and Jamaluddin, JAF and Rahim, MA and A, B and Zulkifly, NS and Tan, MP and Zain, KM and Jaafar, TNAM}, title = {An Odyssey of Integrative Taxonomy Unveils Marine Fish Diversity, New Records and Cryptic Species in Malaysian Waters.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e30}, pmid = {40727006}, issn = {1810-522X}, abstract = {This study elucidates the species diversity of marine fishes in the Exclusive Economic Zone (EEZ) of Peninsular Malaysia (PM) using an integrative approach combining DNA barcoding and morphological identification. Our focus was on demersal surveys conducted on the east coast of PM in the South China Sea. We re-evaluated the diversity of 475 specimens across 93 putative species (92 barcoded morphospecies), from 16 orders and 41 families, including two IUCN vulnerable species. A total of two species - Saurida isarankurai and Oxyurichthys auchenolepis - are presented as new record, and three species - Nemipterus balinensoides, Gymnothorax reevesii and Synodus hoshinonis - as the first specimen-based records in Malaysian waters. Cytochrome c oxidase subunit I (COI) sequence analyses delineated 95 consensus Molecular Operational Taxonomic Units (MOTUs), exceeding morphological diversity. Interestingly, the barcode analysis revealed several MOTUs delimited within one morphologically identified fish species, with both intraspecific and interspecific genetic divergences exceeding 2%, indicating substantial intraspecific genetic divergence within species groups or the existence of morphologically cryptic species within our dataset. These findings highlight the complexity of species delimitation and the value of genetic methods. Our study provides valuable insights into marine fish diversity from the east coast of Peninsular Malaysia and enhances our understanding of genetic diversity, distribution, and conservation needs of ecosystems through DNA barcoding. By integrating DNA barcoding with morphology, we present a comprehensive framework for future research to develop conservation and management strategies for Malaysia's marine biodiversity. The expansion of the genetic barcode database generated in this study will facilitate future molecular taxonomy research.}, }
@article {pmid40725352, year = {2025}, author = {Zhou, H and Yang, D and Li, X}, title = {Integrated Taxonomy Discovers Four New Species of Grypoctonus Speiser, 1928 (Diptera: Asilidae) from China.}, journal = {Insects}, volume = {16}, number = {7}, pages = {}, pmid = {40725352}, issn = {2075-4450}, abstract = {The genus Grypoctonus Speiser, 1928 (Diptera: Asilidae) is a fuzzy-looking assassin fly, and adults have only been observed in autumn and winter. Currently containing four described species, this genus is readily distinguished from other Chinese asilids by the presence of two r-m crossveins. Through integrative taxonomic analysis of over 200 specimens from multiple Chinese provinces, we combined morphological assessment with DNA barcoding and four species delimitation methods (ABGD, ASAP, mPTP, and GMYC). Four species are newly described: G. aureussp. nov., G. sagittatussp. nov., G. solariussp. nov., and G. yongshanisp. nov. (the latter described solely from morphological examination of historical specimens). Genetic analyses revealed distinct barcoding gaps, with an interspecific distance of 1.38-7.07% versus an intraspecific distance of no more than 0.92%. We revised the generic diagnosis, provided a distribution map, and a revised key to all known species of Grypoctonus.}, }
@article {pmid40725306, year = {2025}, author = {Xu, HF and Lv, MY and Zhao, Y and Zhang, ZC and Liu, Z and Lin, XL}, title = {Cryptic Diversity and Climatic Niche Divergence of Brillia Kieffer (Diptera: Chironomidae): Insights from a Global DNA Barcode Dataset.}, journal = {Insects}, volume = {16}, number = {7}, pages = {}, pmid = {40725306}, issn = {2075-4450}, support = {12111300000018001-14//Innovative Research Project on the laboratory of Geo-Specimens Study and Testing at the Geological Museum of China/ ; 41502021//National Natural Science Foundation of China/ ; 31900344//National Natural Science Foundation of China/ ; 12110600000018003910//Ministry of Natural Resources' High-Level Scientific and Technological Innovation Talent Cultivation Program/ ; 2024HK157//Scientific Research Projects of the General Administration of Customs, China/ ; }, abstract = {Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed Brillia (Diptera: Chironomidae). We analyzed cytochrome c oxidase subunit I (COI) sequences of 241 specimens belonging to 13 Brillia species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes. Our integrated approach included genetic distance analysis, haplotype network construction, and ecological niche modeling. The results revealed remarkable cryptic diversity, with sequences clustering into 30 Barcode Index Numbers and 158 unique haplotypes, most being region-specific. Notably, East Asian and North American populations showed complete genetic distinctness, suggesting long-term isolation. Environmental factors, particularly temperature and precipitation gradients, were identified as key drivers of this diversification. The study also corrected several misidentifications in existing databases. These findings significantly advance our understanding of Brillia diversity and provide a reliable molecular tool for freshwater ecosystem monitoring, with important implications for biodiversity conservation and environmental assessment.}, }
@article {pmid40725296, year = {2025}, author = {Jia, N and Ding, X and Xie, D and Chen, H and Chi, D and Yu, J}, title = {First Record of Dioryctria simplicella (Lepidoptera: Pyralidae) in China: Morphology, Molecular Identification, and Phylogenetic Position.}, journal = {Insects}, volume = {16}, number = {7}, pages = {}, pmid = {40725296}, issn = {2075-4450}, support = {2022YFD140100//National Key R&amp;D Program of China/ ; 2023ZX02B05//Key R&amp;D Program of Heilongjiang Province/ ; }, abstract = {Dioryctria Zeller, 1846 (Lepidoptera: Pyralidae) is a significant genus whose species primarily infest coniferous trees and are predominantly distributed across the Northern Hemisphere. To date, 17 species within this genus have been recorded in China. This study reports the discovery of Dioryctria simplicella (Heinemann, 1863) in China. During field surveys in forests of Heilongjiang Province, D. simplicella was observed infesting the cones and trunks of Pinus sylvestris var. mongolica Litv. as larvae. Comprehensive morphological descriptions and diagnostic characteristics of the adult, larva, pupa, and egg stages of D. simplicella are provided herein to facilitate accurate species identification within the genus. Molecular phylogenetic analysis based on mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding sequences was conducted to assess the phylogenetic position of D. simplicella within Dioryctria. These results strongly support its species identity and clarify its phylogenetic relationships with congeners. This discovery not only expands the known diversity of Lepidoptera in China but also provides new data supporting taxonomic and phylogenetic studies of the genus Dioryctria.}, }
@article {pmid40725170, year = {2025}, author = {Samarina, LS and Koninskaya, NG and Shkhalakhova, RM and Simonyan, TA and Tsaturyan, GA and Shurkina, ES and Kulyan, RV and Omarova, ZM and Tutberidze, TV and Ryndin, AV and Orlov, YL}, title = {The Potential of Universal Primers for Barcoding of Subtropical Crops: Actinidia, Feijoa, Citrus, and Tea.}, journal = {International journal of molecular sciences}, volume = {26}, number = {14}, pages = {}, pmid = {40725170}, issn = {1422-0067}, mesh = {*Actinidia/genetics/classification ; *Citrus/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *Crops, Agricultural/genetics/classification ; *Tea/genetics ; Phylogeny ; }, abstract = {The molecular identification of valuable genotypes is an important problem of germplasm management. In this study, we evaluated the potential of 11 universal primer pairs for the DNA barcoding of locally derived cultivars of subtropical crops (actinidia, feijoa, citrus, and tea). A total of 47 accessions (elite cultivars, forms, and breeding lines) of these four genera were included in the study. The efficiency of the following universal primers was assessed using Sanger sequencing: ITS-p5/ITS-u4, ITS-p5/ITS-u2, ITS-p3/ITS-u4, 23S,4.5S&amp;5S, 16S, petB/petD, rpl23/rpl2.l, rpl2 intron, rpoC1 intron, trnK intron, and trnE-UUC/trnT-GUU. Among these primers, trnE-UUC/trnT-GUU showed greater intraspecific polymorphisms, while rpl2 intron and 16S displayed the lowest polymorphism levels in all crops. In addition, the 23S,4.5S &amp; 5S, and rpoC1 intron were efficient for intraspecific analysis of tea and actinidia species. Using five efficient chloroplast primers, a total of 22/6 SNPs/InDels were observed in tea accessions, 45/17 SNPs/InDels in actinidia, 23/3 SNPs/InDels in mandarins, and 5/4 SNPs/InDels in feijoa. These results will be useful for the further development of DNA barcodes of related accessions.}, }
@article {pmid40725055, year = {2025}, author = {Samarina, LS and Koninskaya, NG and Shkhalakhova, RM and Simonyan, TA and Kuzmina, DO}, title = {DNA-Barcoding for Cultivar Identification and Intraspecific Diversity Analysis of Agricultural Crops.}, journal = {International journal of molecular sciences}, volume = {26}, number = {14}, pages = {}, pmid = {40725055}, issn = {1422-0067}, mesh = {*Crops, Agricultural/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Genetic Variation ; DNA, Plant/genetics ; Computational Biology/methods ; }, abstract = {DNA barcoding of intraspecific diversity of agricultural crops is important to develop the genetic passports of valuable genotypes and cultivars. The advantage of DNA-barcoding as compared to traditional genotyping of cultivars is that the procedure can be unified and applied for the broad range of accessions. This not only makes it cost efficient, but also allows to develop open access genetic databases to accumulate information of the world's germplasm collections of different crops. In this regard, the aim of the review was to analyze the latest research in this field, including the selection of loci, universal primers, strategies of amplicons analysis, bioinformatic tools, and the development of databases. We reviewed the advantages and disadvantages of each strategy with the focus of cultivars identification. The data indicates that following chloroplast loci are the most prominent for the intraspecific diversity analysis: (trnE-UUC/trnT-GUU, rpl23/rpl2.l, psbA-trnH, trnL-trnF, trnK, rpoC1, ycf1-a, rpl32-trnL, trnH-psbA and matK). We suggest that the combination of three or four of these loci can be a sufficient DNA barcode for cultivar-level identification. This combination has to be selected for each crop. Advantages and disadvantages of different approaches of amplicons analysis are discussed. The bioinformatic tools and databases for the plant barcoding are reviewed. This review will be useful for selecting appropriate strategies for barcoding of intraspecific diversity of agricultural crops to develop genetic passports of valuable cultivars in germplasm collections worldwide.}, }
@article {pmid40722035, year = {2025}, author = {Andrianiaina, AF and Andry, S and Kettenburg, G and Ranaivoson, HC and Lacoste, V and Dussart, P and Heraud, JM and Laverty, TM and Guth, S and Young, KI and Andrianarimisa, A and Brook, CE}, title = {Diversity and seasonality of ectoparasite burden on two species of Madagascar fruit bat, Eidolon dupreanum and Rousettus madagascariensis.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {302}, pmid = {40722035}, issn = {1756-3305}, support = {R01 AI129822/AI/NIAID NIH HHS/United States ; 102825//National Geographic Society/ ; 1R01AI129822-01/NH/NIH HHS/United States ; EC-64015R-20//National Geographic Society/ ; }, mesh = {Animals ; *Chiroptera/parasitology/classification ; Madagascar/epidemiology ; *Ectoparasitic Infestations/veterinary/epidemiology/parasitology ; Seasons ; DNA Barcoding, Taxonomic ; *Diptera/classification/genetics/physiology ; Female ; Male ; Biodiversity ; Phylogeny ; Mites/genetics/classification ; }, abstract = {BACKGROUND: Bats are important reservoir hosts for a variety of pathogens, some of which are transmitted by ectoparasite vectors including mites, fleas, lice, ticks, and bat flies (families Nycteribiidae and Streblidae). All these ectoparasite taxa are known to parasitize two endemic fruit bats of Madagascar, Eidolon dupreanum and Rousettus madagascariensis. We aimed to describe the diversity of ectoparasite infestation for both bat species through morphological observation and DNA barcoding and elucidate ecological and climatic correlates of seasonal nycteribiid parasitism of these hosts.<br><br>METHODS: Eidolon dupreanum and R. madagascariensis fruit bats were live-captured in northern and central-eastern Madagascar periodically from 2013 to 2020. Ectoparasites on all captured bats were counted and identified in the field and then collected into ethanol. Field identification of a subset of samples was confirmed via microscopy and DNA barcoding of the cytochrome C oxidase subunit 1 (COI) and 18S genes. The seasonal abundance of nycteribiid bat flies on both host bats was analyzed using generalized additive models, and the role of climate in driving this seasonality was assessed via cross-correlation analysis combined with generalized linear models. Phylogenetic trees were generated to compare COI and 18S sequences of Madagascar nycteribiid and streblid bat flies with available reference sequences from GenBank.<br><br>RESULTS: Ectoparasites corresponding to four broad taxa (mites, ticks, fleas, and bat flies) were recovered from 628 of 873 E. dupreanum (71.9%) and 831 of 862 R. madagascariensis (96.4%). Eidolon dupreanum were most commonly parasitized by Cyclopodia dubia nycteribiids and R. madagascariensis by Eucampsipoda madagascariensis nycteribiids and Megastrebla wenzeli streblids. We observed significant seasonality in nycteribiid abundance on both bat hosts, which varied by bat sex and was positively correlated with lagged temperature, precipitation, and humidity variables. Barcoding sequences recovered for all three bat fly species grouped with previously reported sequences, confirming morphological species identification. Our study contributes the first DNA barcodes of any kind reported for M. wenzeli and the first 18S barcodes for C. dubia.<br><br>CONCLUSIONS: This study explores the diversity and abundance of ectoparasite burdens in two Malagasy fruit bat species, highlighting the importance of seasonal ecology and the influence of climate variables on parasitism, which correlates with resource availability.}, }
@article {pmid40722002, year = {2025}, author = {Jordan, S and Pothier, JF and de Maayer, P and Broders, K and Kvitko, BH and Coutinho, TA and Smits, THM}, title = {Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {456}, pmid = {40722002}, issn = {1471-2180}, support = {310030L_204333//Swiss National Science Foundation (SNSF)- South-African National Research Foundation (NRF) Lead Agency project/ ; 2019-51181-30013//USDA NIFA SCRI/ ; }, mesh = {*Enterobacter/genetics/classification/isolation &amp; purification ; *Polymerase Chain Reaction/methods ; *DNA Primers/genetics ; DNA, Bacterial/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates.<br><br>RESULTS: Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110&#xa0;bp and at 370&#xa0;bp, while strains only displaying the 110&#xa0;bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification.<br><br>CONCLUSIONS: The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.}, }
@article {pmid40720603, year = {2025}, author = {Tran, HL and Zheng, W and Issadore, DA and Im, H and Cho, YK and Zhang, Y and Liu, D and Liu, Y and Li, B and Liu, F and Wong, DTW and Sun, J and Qian, K and He, M and Wan, M and Zeng, Y and Cheng, K and Huang, TJ and Chiu, DT and Lee, LP and Zheng, L and Godwin, AK and Kalluri, R and Soper, SA and Hu, TY}, title = {Extracellular Vesicles for Clinical Diagnostics: From Bulk Measurements to Single-Vesicle Analysis.}, journal = {ACS nano}, volume = {19}, number = {31}, pages = {28021-28109}, pmid = {40720603}, issn = {1936-086X}, support = {R01 AI177986/AI/NIAID NIH HHS/United States ; R01 AI174964/AI/NIAID NIH HHS/United States ; U01 CA252965/CA/NCI NIH HHS/United States ; R01 AI179714/AI/NIAID NIH HHS/United States ; R01 AI175618/AI/NIAID NIH HHS/United States ; R01 HD103511/HD/NICHD NIH HHS/United States ; R21 NS130542/NS/NINDS NIH HHS/United States ; R01 AI144168/AI/NIAID NIH HHS/United States ; R01 HD090927/HD/NICHD NIH HHS/United States ; R01 AI173021/AI/NIAID NIH HHS/United States ; }, mesh = {*Extracellular Vesicles/chemistry/metabolism ; Humans ; Biomarkers/analysis/metabolism ; Animals ; }, abstract = {Extracellular vesicles (EVs) play a crucial role in intercellular communication, signaling pathways, and disease pathogenesis by transporting biomolecules such as DNA, RNA, proteins, and lipids derived from their cells of origin, and they have demonstrated substantial potential in clinical applications. Their clinical significance underscores the need for sensitive methods to fully harness their diagnostic potential. In this comprehensive review, we explore EV heterogeneity related to biogenesis, structure, content, origin, sample type, and function roles; the use of EVs as disease biomarkers; and the evolving landscape of EV measurement for clinical diagnostics, highlighting the progression from bulk measurement to single vesicle analysis. This review covers emerging technologies such as single-particle tracking microscopy, single-vesicle RNA sequencing, and various nanopore-, nanoplasmonic-, immuno-digital droplet-, microfluidic-, and nanomaterial-based techniques. Unlike traditional bulk analysis methods, these methods contribute uniquely to EV characterization. Techniques like droplet-based single EV-counting enzyme-linked immunosorbent assays (ELISA), proximity-dependent barcoding assays, and surface-enhanced Raman spectroscopy further enhance our ability to precisely identify biomarkers, detect diseases earlier, and significantly improve clinical outcomes. These innovations provide access to intricate molecular details that expand our understanding of EV composition, with profound diagnostic implications. This review also examines key research challenges in the field, including the complexities of sample analysis, technique sensitivity and specificity, the level of detail provided by analytical methods, and practical applications, and we identify directions for future research. This review underscores the value of advanced EV analysis methods, which contribute to deep insights into EV-mediated pathological diversity and enhanced clinical diagnostics.}, }
@article {pmid40720372, year = {2025}, author = {Delocado, ED and Banzon, VRH and Sanchez, EGS}, title = {A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {221}, pages = {}, doi = {10.3791/68323}, pmid = {40720372}, issn = {1940-087X}, mesh = {*Coleoptera/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; Philippines ; }, abstract = {Biodiversity decline is transpiring at rates unimaginable, yet biodiversity monitoring is hampered by a plethora of factors, including the incomplete inventory of baseline diversity and the dwindling population of skilled taxonomists. Bridging this impediment in species inventory of "dark taxa", or hyperdiverse groups often understudied in taxonomy, is particularly crucial in the tropics facing insurmountable environmental pressures. While morphology-based alpha-taxonomy remains the gold standard in species identification, DNA-based methods have been showing tremendous potential in accelerating species delineation and discovery. Here, we describe a concoction pipeline for generating molecular operational taxonomic units (MOTUs) involving six molecular species delimitation approaches implemented on two highly inconspicuous beetle genera, namely Byrrhinus Motschulsky, 1858 of family Limnichidae and Anacaena Thomson, 1859 of family Hydrophilidae, from the Philippines. As this protocol focuses on processing DNA barcodes and given that these genetic data can be obtained either by sequencing or by downloading from online databases, the starting point for the protocol described here are the DNA sequences. Given the COI barcodes, the pipeline utilizes a combination of three threshold-based molecular species delimitation approaches, namely TaxonDNA, K2P, and ASAP, which use sequence alignment as input data. Additionally, the pipeline proceeds with three coalescent-based approaches, namely PTP-ML, PTP-BI, and mPTP, which require a tree file as input data. Some approaches entail the use of web servers, while others utilize local software. With the selection of algorithmic methods presented, MOTUs can be identified, whether by consensus or by majority. Remarkably, this pipeline delineated almost conspicuous beetle species from the Philippines, even those documented from the same or adjacent localities.}, }
@article {pmid40717983, year = {2025}, author = {Li, X and Zhang, Y and Song, M and Xu, N and Qu, L and Li, H and Wang, Y and Duan, B and Zhang, Z}, title = {Molecular identification and phylogenetic analysis of confusing Tetrastigma species based on DNA barcoding and chloroplast genome.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1607947}, pmid = {40717983}, issn = {1663-9812}, abstract = {BACKGROUND: Tetrastigma plants are widely utilized in traditional medicine (such as Tetrastigma. obtectum and Tetrastigma. serrulatum, two important commonly medicinal plants), primarily for their properties in promoting blood circulation, strengthening bones and tendons, and so on. However, the high diversity of species differentiation poses a challenge in accurately identifying the various Tetrastigma species without specialized taxonomic knowledge.<br><br>MATERIALS AND METHODS: To screen the candidate barcode sequences of Tetrastigma species, we first report the complete chloroplasts (CP) genomes of T. obtectum and T. serrulatum obtained via high throughput Illumina sequencing and compare them with fourteen previously sequenced species. Furthermore, we collected fresh leaf samples from T. obtectum and T. serrulatum (totally 37 samples) and evaluated the discriminatory efficacy of the nuclear DNA Internal Transcribed Spacer 2 (ITS2) fragment through comparative analysis of sequence variations and secondary structures. Finally, to analyze the phylogenetic position of Tetrastigma species, we constructed a Maximum Likelihood (ML) phylogenetic tree using CP genome sequences of 46 species from seven genera within the Vitaceae family.<br><br>RESULTS AND DISCUSSION: The CP genomes of Tetrastigma exhibited a typical circular tetramerous structure, including a large single-copy region (LSC) (87,381-88,979&#xa0;bp), a small single-copy region (SSC) (18,649-19,339&#xa0;bp), and a pair of inverted repeats (IRa and IRb) (26,288-26,934&#xa0;bp). The guanine-cytosine content of the CP genomes is 37.35%-37.62%. The codon usage shows a significant preference for end with A/T. Then, the results of nucleotide diversity analysis showed that ten polymorphic hotspots (psbM-trnD-GUC, ndhF-rpl32, trnS-GCU-trnG-UCC, ycf1, rpl32-trnL-UAG, trnS-UGA-psbZ, psbE-petL, matK-rps16, rpl16, and rpl22) could be the candidate DNA marker suitable for Tetrastigma species. Furthermore, our results demonstrate that the ITS2 sequence could effectively discriminate T. obtectum and T. serrulatum, whereas the secondary structure cannot, proving that ITS2 can be used as an efficient barcode fragment to accurately identify the two species. The aim of this study was not only to determine the identification efficiency of the CP genome and ITS2 for T. obtectum and T. serrulatum but also to clarify the phylogenetic relationship and screen the candidate DNA marker suitable for Tetrastigma species, provide valuable data support for further accurate identification of the Tetrastigma genus.}, }
@article {pmid40709241, year = {2024}, author = {Cheng, SJ and Hsu, YC}, title = {Use of DNA Barcode Sequences for Distinguishing the Three Species in the Arctic Warbler (Phylloscopus borealis) Species Complex.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e33}, pmid = {40709241}, issn = {1810-522X}, abstract = {he Arctic warbler (Phylloscopus borealis) species complex is commonly present in the Palearctic region. By 2014, the three bird subspecies were split into three species, Arctic warbler (P. borealis), Japanese leaf warbler (P. xanthodryas), and Kamchatka leaf warbler (P. examinandus), based on different breeding areas and distinct vocalizations. However, their similar coloration and body size make it difficult to distinguish these species in the nonbreeding season. Taiwan is located in the potential migration routes of the Arctic warbler species complex; however, no confirmed record of P. xanthodryas and P. examinandus exists. In this study, we compared the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences of samples from breeding sites during the breeding season and confirmed that the three species could be distinguished based on CO1 gene sequences. We also examined the species of the Arctic warbler species complex samples collected from eastern Taiwan. For the first time, we confirmed that all three species visited Taiwan during migration season. In the Taiwanese samples, no clear distinction could be made between species based on plumage coloration and size, indicating that these traits are not reliable for species identification. Reassessment of the CO1 gene sequences of the three species deposited in the Barcode of Life Data System revealed that the taxonomic status needs to be updated for 31.8% of the samples.}, }
@article {pmid40708897, year = {2025}, author = {Taberer, TR}, title = {On the identity of the type species of Parasa (Lepidoptera: Limacodidae): investigations into the Nearctic Parasa chloris and related taxa.}, journal = {Annals of the Entomological Society of America}, volume = {118}, number = {4}, pages = {276-289}, pmid = {40708897}, issn = {0013-8746}, abstract = {The pantropical Limacodid genus Parasa Moore [1860] comprises a charismatic group of moths, whose adults display green banding on the forewing while the larvae are often brightly colored, possessing stinging hairs. Three previously unidentified syntypes of the type species Parasa chloris (Herrich-Schäffer [1854]) were identified in the National Museum of Natural History, Smithsonian Institution, USA, having passed through several collections over the past ca. 180 years. Described from specimens with a vague provenance, the true type locality was unveiled utilizing COI barcoding of the lectotype designated herein, together with other barcoded specimens from North and Central America, morphological observations in adults and male genitalia, as well as distribution records from museum specimens and the citizen science database iNaturalist. Results suggest the type locality of P. chloris as north-eastern USA, likely from the southern states. In addition, the nomenclatural history of P. chloris is here discussed in detail, and its synonyms are clarified with regard the morphologically-similar, sympatric species Parasa indetermina (Griffith and Pidgeon, 1832 nec Boisduval), and Limacodes viridus Reakirt (1864) syn. rev. is here revived as a synonym of the latter. Taxonomic remarks are also made regarding species closely related to P. chloris (Parasa minima (Schaus, 1892), Parasa huachuca Dyar (1905) stat. nov., Parasa cuernavaca Dyar (1907) stat. rev., and Parasa maysi Schaus (1920)), resulting from COI barcoding, and morphological examinations of all primary type and additional material. This research represents the first step in delimiting Parasa in preparation for future taxonomic work testing the monophyly of this widespread genus.}, }
@article {pmid40708374, year = {2025}, author = {Lozano-Sardaneta, YN and Huerta, H and Benítez-Guzmán, A and Cervantes-Torres, JB and Contreras-Ramos, A}, title = {Appearance may be deceiving: Mexican sand flies (Diptera: Psychodidae: Phlebotominae) embrace a high diversity of cryptic species.}, journal = {Journal of insect science (Online)}, volume = {25}, number = {4}, pages = {}, pmid = {40708374}, issn = {1536-2442}, support = {//Biodiversidad de Diptera y Neuropteroidea de la Reserva de la Bi&#xf3;sfera Tehuac&#xe1;n-Cuicatl&#xe1;n con herramientas novedosas/ ; }, mesh = {Animals ; *Psychodidae/classification/genetics ; Mexico ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {Phlebotomine sand flies stand out for their role in vector-borne diseases, having taxonomic priority in aspects of public health. Traditional identification based on morphology involves some limitations that have been corrected with the implementation of complementary methodologies such as cytochrome c oxidase subunit I barcoding and recently mass spectrometry. In Mexico, nearly 38% of sand fly species count with a molecular characterization, but additional information is still necessary for improving sand fly species delimitation. We carried out a molecular species delimitation study of sand flies distributed in the Mexican Transition Zone, between the Nearctic and Neotropical regions, with newly generated cytochrome c oxidase subunit I barcodes, and the first protein profiles created. Compelling evidence showed putative new taxa emerge from Micropygomyia aff. durani (Vargas &amp; Diaz-Nájera) and Pintomyia Series serrana Barretto, and several cryptic species be contained within the genera Micropygomyia and Psathyromyia, which could be of biological and epidemiological interest. However, for some taxa an exhaustive taxonomic revision at the morphological and molecular levels is recommended, especially for sand flies of wide distribution in the New World.}, }
@article {pmid40708054, year = {2025}, author = {Bunchom, N and Saijuntha, W and Tantrawatpan, C and Maleewong, W and Valencia, J and Agatsuma, T and Bounavong, V and Buchy, P and Iwagami, M}, title = {Micro-scale genetic structure and genetic variation of Neotricula aperta (Gastropoda: Pomatiopsidae), the intermediate host of Schistosoma mekongi (Digenea: Schistosomatidae) in Champasak Province, Laos.}, journal = {Tropical medicine and health}, volume = {53}, number = {1}, pages = {97}, pmid = {40708054}, issn = {1348-8945}, support = {No. N42A670561//National Research Council of Thailand (NRCT) through the High-Potential Research Team Grant Program/ ; No. JP24jm0110028; 2022-2028//Japan International Cooperation Agency (JICA) and the Japan Agency for Medical Research and Development (AMED) through the SATREPS project, titled "Project for Malaria and Neglected Parasitic Diseases Control and Elimination using Advanced Research Technique, Communication Tools, and Eco-Health Education"/ ; }, abstract = {BACKGROUND: Neotricula aperta, a freshwater snail found in the Mekong River, serves as the intermediate host of the blood fluke Schistosoma mekongi, the causative agent of schistosomiasis mekongi in Cambodia and Laos. Understanding the genetic diversity, population structure of this snail in relation to its geographical distribution is crucial for a comprehensive understanding of disease transmission. In this study, we investigated the genetic diversity, and genetic structure of N. aperta in Champasak Province, Laos.<br><br>METHODS: A total of 80 N. aperta snails were collected from 13 various localities across five villages in Khong and Mounlapamok districts in Champasak Province, Laos in May 2024. Species of snails were initially identified based on morphology and subsequently confirmed by DNA barcoding. Molecular analyses were conducted using specific primers to amplify two mitochondrial DNA genes, namely cytochrome c oxidase subunit 1 (cox1) and 16S ribosomal RNA (16S rRNA), in order to assess the genetic diversity of N. aperta populations.<br><br>RESULTS: Based on cox1 sequences, the overall haplotype diversity was 0.996, while the overall nucleotide diversity was 0.049. For the 16S rRNA marker, the overall haplotype diversity was 0.911, and the overall nucleotide diversity was 0.015. Analysis of molecular variance (AMOVA) confirmed significant genetic differentiation (P-value&#x2009;<&#x2009;0.05) among populations at different spatial scales, including villages, catchments, and countries. This genetic structure likely reflects limited gene flow among snail populations, potentially due to geographical barriers. Although local environmental factors may also contribute to differentiation, the current genetic data are insufficient to distinguish between geographic isolation and adaptive divergence. Further ecological and functional investigations will be needed to determine whether adaptive processes are influencing population structure.<br><br>CONCLUSIONS: The genetic divergence of N. aperta observed in this study indicates a high level of genetic differentiation both among and within populations. This pattern suggests that N. aperta is possibly undergoing localized adaptation or that barriers to gene flow, such as physical, ecological, or behavioral factors, are promoting the accumulation of genetic differences. Micro-scale genetic structuring within populations may be driven by microhabitats or small-scale ecological gradients, while limited dispersal, localized mating preferences, or other behavioral traits may contribute to differentiation among populations.}, }
@article {pmid40707727, year = {2025}, author = {Lim, H and Jun, S and Kim, T and Lee, JH and Bang, D}, title = {Correcting errors in PCR-derived libraries for rare allele detection by reconstructing parental and daughter strand information.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {1098}, pmid = {40707727}, issn = {2399-3642}, support = {2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; 2021R1A2C2008490//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Polymerase Chain Reaction/methods ; Humans ; *Alleles ; *Gene Library ; Mutation ; *Circulating Tumor DNA/genetics ; }, abstract = {Molecular barcoding methods enable high-sensitivity detection of circulating tumor DNA that is rarely present in liquid biopsy samples. Many methods involve ligation of molecular barcodes to DNA prior to hybridization capture, enabling recovery of starting molecules. Development of polymerase chain reaction (PCR)-based methods could facilitate more cost- and labor- effective detection; however, tracking molecular identity can be difficult, as new barcodes overwrite old barcodes in each cycle. Here, we present a sensitive genotyping method based on a peer-to-peer network-derived identifier for error reduction in amplicon sequencing (SPIDER-seq) and enable molecular identity tracking with PCR-derived libraries using overwritten barcodes. SPIDER-seq detected mutations at frequences as low as 0.125% after only two consecutive general PCR cycles and systematically analyzed the error pattern in the peer-to-peer network. Our method could facilitate the rapid detection of mutations associated with various cancers.}, }
@article {pmid40705799, year = {2025}, author = {Wacira, TN and Makonde, HM and Kamau, JN and Aura, CM and Kibiti, CM}, title = {Characterization and bioactivity potential of marine sponges (Biemna fistulosa, Callyspongia diffusa, and Haliclona fascigera) from Kenyan coastal waters.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0325642}, pmid = {40705799}, issn = {1932-6203}, mesh = {Animals ; *Porifera/chemistry/genetics ; Microbial Sensitivity Tests ; Kenya ; *Haliclona/chemistry/genetics ; Anti-Bacterial Agents/pharmacology ; Pseudomonas aeruginosa/drug effects ; Escherichia coli/drug effects ; Candida albicans/drug effects ; Gas Chromatography-Mass Spectrometry ; Staphylococcus aureus/drug effects ; *Anti-Infective Agents/pharmacology ; Humans ; }, abstract = {Sponges have been reported as a rich source of bioactive compounds, which could potentially be developed into lead compounds for pharmaceutical use. The present study aimed to identify sponges and assess the biological activity of their extracts against human disease-causing organisms, including Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans. Morphological characterization and DNA barcoding of the cytochrome c oxidase subunit I (COI) gene characterized three sponge species (Biemna fistulosa, Callyspongia diffusa and Haliclona fascigera). The Kirby-Bauer test assessed the antimicrobial activity of the extracts, and the inhibition zone diameters (IZD) were measured. The extracts were further subjected to minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) tests to determine the antibiotic susceptibility. The Gas Chromatography-Mass Spectrometry (GC-MS) was used to identify and quantify the organic compounds in the sponges' extracts. The methanolic extract of B. fistulosa (28.00 ± 3.5 mm) and H. fascigera. (28.33 ± 3.8 mm) exhibited a broad spectrum of antibacterial activity against E. coli, surpassing the positive control (27.67 ± 0.9 mm). The inhibitory activity of ethyl acetate extract of the C. diffusa (29.33 ± 2.4 mm) against P. aeruginosa was observed to be higher compared to the standard antibiotic streptomycin (26.67 ± 0.7 mm). The methanolic extract of H. fascigera demonstrated the lowest MIC (0.53 ± 0.0 mg mL-1) compared to the streptomycin drug (1.36 ± 0.0 mg mL-1), and showed an MBC of 1.25 mg mL-1 against E. coli. The GC-MS chromatogram data analysis identified 114 distinct compounds categorized into 39 classes across three sponge extracts: 11.4% of these compounds demonstrated documented antimicrobial activity against human pathogens. This study corroborates sponges as a promising source of bioactive compounds, which are valuable leads for drug discovery and development. Future research must explore their mechanisms, molecular-level toxicity, and lead optimization to enhance drug development.}, }
@article {pmid40703786, year = {2025}, author = {Kim, S and Sohn, J and Kim, H}, title = {Three new species and a new record of the genus Lipolexis (Hymenoptera, Braconidae, Aphidiinae) from South Korea.}, journal = {ZooKeys}, volume = {1245}, number = {}, pages = {323-342}, pmid = {40703786}, issn = {1313-2989}, abstract = {The genus Lipolexis Förster, 1863 consists of 11 species worldwide, with two species previously recorded in South Korea. In this study, three new species: L.depressiceps S. Kim &amp; H. Kim, sp. nov., L.sulcata S. Kim &amp; H. Kim, sp. nov., and L.longipetiolata S. Kim &amp; H. Kim, sp. nov. with an unrecorded species, L.peregrina, Tomanović &amp; Kocić, 2020, are described and reported with photographs, mitochondrial cytochrome c oxidase subunit I (COI) data (barcode region), and a gene tree.}, }
@article {pmid40703784, year = {2025}, author = {Wägele, H and Raubold, LM and Papu, A and Undap, N and Yonow, N}, title = {On two new Phyllidia species (Gastropoda, Nudibranchia, Doridina) and some histology from the Coral Triangle.}, journal = {ZooKeys}, volume = {1245}, number = {}, pages = {1-18}, pmid = {40703784}, issn = {1313-2989}, abstract = {Two new species of Phyllidia from North Sulawesi, Indonesia, Phyllidiafontjei sp. nov. and Phyllidiaovata sp. nov., are described based on morphology and molecular barcoding of CO1 and/or 16S. Both species are rare and distinctive and can be easily recognised by their colouration. Additionally, histological sections were made of the holotype of Phyllidiafontjei sp. nov. and a similarly sized Phyllidiaocellata and these morphologies are compared with the only other detailed histological examination of the Mediterranean Phyllidiaflava.}, }
@article {pmid40702707, year = {2025}, author = {Fu, Y and Youness, M and Virzì, A and Song, X and Tubeeckx, MRL and De Keulenaer, GW and Heidbuchel, H and Segers, VFM and Sipido, KR and Thienpont, B and Roderick, HL}, title = {Benchmarking of computational demultiplexing methods for single-nucleus RNA sequencing data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {4}, pages = {}, pmid = {40702707}, issn = {1477-4054}, support = {20-VLIR-iBOF-027//BOF/ ; C14/21/093//KU Leuven/ ; //China Scholarship Council/ ; G0C7319N//FWO, Research Foundation - Flanders/ ; }, mesh = {Humans ; *Software ; Benchmarking ; *Sequence Analysis, RNA/methods ; *Computational Biology/methods ; Polymorphism, Single Nucleotide ; *Cell Nucleus/genetics ; *Single-Cell Analysis/methods ; }, abstract = {Single-nucleus RNA sequencing (snRNA-Seq) has transformed our understanding of complex tissues, providing insights into cellular composition and heterogeneity in gene expression between cells, and their alterations in development and disease. High costs however constrain the number of samples analysed. Sample pooling and their demultiplexing following sequencing based on prior labelling with antibodies or lipid anchors conjugated to DNA barcodes (cell hashing and MULTI-seq), or using genetic differences between samples, provides a solution. However, there remains no comprehensive evaluation of these demultiplexing tools to guide selection between them. Here, we benchmark the leading software (Vireo, Souporcell, Freemuxlet, scSplit) used for sample demultiplexing using genetic variants. We further compared obtaining genetic variants from SNP array analysis of gDNA and from sample-matched bulk-RNA-Seq data, identified using three different variant calling tools (BCFtools, cellSNP, FreeBayes). Demultiplexing performance was evaluated on simulated multiplexed datasets comprising two, four, and six samples with doublet percentages between 0% and 30%, and validated against demultiplexing using sex-linked genes. Software implementation and execution were evaluated by run speed, robustness, scalability, and usability. Our results show that all tools excluding scSplit provide high recall and precision with an accuracy of 80%-85%. Vireo achieved the best accuracy. Demultiplexing tools were differentially affected by the variant calling tool with which it was paired. For all tools, accuracy decreased with the increasing percentage of doublets. Deployment of demultiplexing during analysis of pooled real-world 10x RNA-Seq data from the human heart and from different species is shown, as are advantages for doublet detection and removal.}, }
@article {pmid40702435, year = {2025}, author = {Dong, LN and Liu, ZF and Xu, WB and Yang, JB and Kidner, CA and Hughes, M and Yan, HF and Wang, H and Li, DZ}, title = {Identification of herbal medicine species of Lysimachia L. (Primulaceae) in Southern China using genome skimming.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {953}, pmid = {40702435}, issn = {1471-2229}, support = {2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; 2017-LSFGBOWS-02//Large-scale Scientific Facilities of the Chinese Academy of Sciences/ ; }, mesh = {China ; *DNA Barcoding, Taxonomic/methods ; *Primulaceae/genetics/classification ; *Plants, Medicinal/genetics/classification ; *Genome, Plant ; Phylogeny ; DNA, Plant/genetics ; Herbal Medicine ; Sequence Analysis, DNA ; Lysimachia ; }, abstract = {BACKGROUND: The accurate identification of herbal medicine is a prerequisite for safe and effective use. DNA barcoding has been widely used for the identification of herbal medicine. However, choosing and refining a suitable barcode is complex in plants. The genus Lysimachia includes over 180 species and is widely used as herbal medicine in China and elsewhere. Species identification within this genus based on morphological, microscopic, or chemical characters is often challenging. In this study, 44 accessions representing 17 putative species of Lysimachia from southern China were sequenced using genome skimming. Whole plastome and nrDNA sequences were successfully recovered from these data. Combining 13 published plastomes of Lysimachia, the discrimination power of standard barcodes, along with plastome and hypervariable sequences from the plastome were compared across 57 plastomes from 22 putative species.<br><br>RESULTS: Standard barcodes have limitation in providing accurate species level identification; however, they can facilitate the rapid classification of unknown samples at the generic level. The plastomes exhibit a highly degree of conservation in the structure and gene content, yet they successfully identify all studied taxa. Five highly variable loci from plastomes were identified: petN-psbM, ycf1, rpl22, trnK-rps16, and ndhC-trnV. While these regions improved the discrimination power compared to standard barcodes, they still could not yield accurate identification of all taxa studied. However, when combined with ITS, ycf1 provides 100% successful species identification.<br><br>CONCLUSIONS: We recommend that the use of whole plastome and the combination of ycf1&#x2009;+&#x2009;ITS as accurate and effective barcodes for species identification in Lysimachia. This study also highlights the potential for effective use of genome skimming data.}, }
@article {pmid40700316, year = {2025}, author = {Stoeva, D and Gencheva, D and Radoslavov, G and Hristov, P and Yordanova, R and Beev, G}, title = {Novel DNA Barcoding and Multiplex PCR Strategy for the Molecular Identification and Mycotoxin Gene Detection of Fusarium spp. in Maize from Bulgaria.}, journal = {Methods and protocols}, volume = {8}, number = {4}, pages = {}, pmid = {40700316}, issn = {2409-9279}, support = {AF3/24//Trakia University/ ; }, abstract = {Fusarium spp. represent a critical threat to maize production and food safety due to their mycotoxin production. This study introduces a refined molecular identification protocol integrating four genomic regions-ITS1, IGS, TEF-1α, and β-TUB-for robust species differentiation of Fusarium spp. isolates from post-harvest maize in Bulgaria. The protocol enhances species resolution, especially for closely related taxa within the Fusarium fujikuroi species complex (FFSC). A newly optimized multiplex PCR strategy was developed using three primer sets, each designed to co-amplify a specific pair of toxigenic genes: fum6/fum8, tri5/tri6, and tri5/zea2. Although all five genes were analyzed, they were detected through separate two-target reactions, not in a single multiplex tube. Among 17 identified isolates, F. proliferatum (52.9%) dominated, followed by F. verticillioides, F. oxysporum, F. fujikuroi, and F. subglutinans. All isolates harbored at least one toxin biosynthesis gene, with 18% co-harboring genes for both fumonisins and zearalenone. This dual-protocol approach enhances diagnostic precision and supports targeted mycotoxin risk management strategies.}, }
@article {pmid40699425, year = {2025}, author = {Al Hayek, S and Praité, A and Lambert, JM and Bender, S and Delpy, L}, title = {5'RACE Method for RNA-Based Sequencing of the Mouse Immunoglobulin Repertoire.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2962}, number = {}, pages = {103-119}, pmid = {40699425}, issn = {1940-6029}, mesh = {Animals ; Mice ; *High-Throughput Nucleotide Sequencing/methods ; B-Lymphocytes/immunology/metabolism ; *Immunoglobulins/genetics ; Immunoglobulin Heavy Chains/genetics ; *Sequence Analysis, RNA/methods ; DNA, Complementary/genetics ; *RNA/genetics/isolation &amp; purification ; Spleen/cytology ; }, abstract = {This chapter outlines a detailed methodology for high-throughput sequencing of the immunoglobulin (Ig) repertoire from mouse RNA samples. We describe RNA extraction from splenic B cells, followed by the conversion into cDNA using the 5'RACE (Rapid Amplification of cDNA Ends) technique and PCR amplification of the Ig heavy and light chain repertoire. The amplified products are prepared using specific primers for Illumina next-generation sequencing (NGS) and unique molecular identifiers (UMI) as molecular barcodes. The protocol includes stringent quality control steps to ensure the integrity of RNA and the accuracy of amplification. We describe the amplification of Ighm and all Ighg subclasses, for Ig heavy chains and for the predominant Igκ light chain isotype. RNA-based 5'RACE-RepSeq proves very useful to analyze the diversity and clonality of Ig repertoire, as well as somatic hypermutations, providing insights into the adaptive immune response. This method enables the high-throughput characterization of the mouse Ig repertoire in immunological contexts.}, }
@article {pmid40698406, year = {2025}, author = {Alpsoy, L and Tieu, S and Dehestanizad, S and Brandstetter, T and Rühe, J}, title = {Hydrogel beads for enhanced nucleic acid analysis in complex fluid matrices.}, journal = {Lab on a chip}, volume = {25}, number = {17}, pages = {4422-4435}, doi = {10.1039/d5lc00447k}, pmid = {40698406}, issn = {1473-0189}, abstract = {We present a functionalized hydrogel bead platform designed to capture cell-free DNA (cfDNA), which is released from tumor cells into the bloodstream, and the use of this cfDNA as a biomarker for cancer detection. Hydrogel beads with covalently incorporated probes (HBP) are generated via photo-cross-linking in a two-phase microfluidic system. The precursor solutions from which the beads are generated are comprised of a photoreactive copolymer, magnetic nanoparticles, Cy3-labelled oligonucleotides serving as a barcode for bead identification, and a specific probe designed to bind the target DNA. From these solutions, droplets are generated in the microfluidic system and photocross-linked through C, H-insertion cross-linking (CHic). As a demonstration case, the hydrogel beads are used to detect a mutation (c.1633G>A) in MCF-7 cells, which is known to promote breast cancer progression by activating oncogenic signalling pathways. The HBPs were successfully employed to detect a fluorescently labelled mutation sequence (92 bp) in phosphate-buffered saline (PBS), serum, and whole blood using a fluorescent reader, followed by amplification through polymerase chain reaction (PCR). The sensitivity of the cfDNA detection method described here demonstrates a detection limit as low as 0.36 ng mL[-1], which is lower than any other detection limit in the literature so far. The sensitivity of the hydrogel bead platform can be further significantly increased. This is because beads containing the captured DNA can be subjected directly to PCR for the amplification of the target sequence, eliminating the need for any additional purification steps. The simplicity of production, modification, and functionalization of the hydrogel beads, coupled with their high sensitivity in detecting cfDNA, makes this platform a promising approach for diagnosing a range of diseases.}, }
@article {pmid40698045, year = {2025}, author = {Kamani, J and Irene, S and Yakubu, AR and Bwala, FH and Nahum-Biala, Y and Nnabuife, EH and Budaye, J and Harrus, S and Schaer, J}, title = {Vector Abundance and Genetic Diversity of Anopheles Mosquitoes Collected in a Laboratory-Office Complex in Vom, Nigeria: Implications for Vector Control.}, journal = {Public health challenges}, volume = {4}, number = {3}, pages = {e70079}, pmid = {40698045}, issn = {2769-2450}, abstract = {Malaria remains a significant threat in high-burden high-impact (HBHI) countries despite substantial investments in disease control. This highlights the need for more comprehensive and inclusive strategies to meet national and international targets. Although agricultural and poorly maintained environments are known for mosquito breeding, workplaces are rarely considered in conventional malaria control measures. In this pilot investigation, we assessed the presence of Anopheles spp. in a laboratory-office complex in Vom, Nigeria, to assess workplace malaria risk and its implications for control strategies. We conducted molecular barcoding on 74 Anopheles specimens targeting the mitochondrial cytochrome oxidase I gene (cox1). Our analyses identified Anopheles funestus (n = 29; 54.6%), Anopheles gambiae sensu lato (n = 17; 32.1%), and Anopheles rufipes (n = 6; 11.3%). Haplotype network analyses revealed 12, 8, and 6 distinct haplotypes for A. funestus, A. gambiae, and A. rufipes, respectively. Genetic divergence estimates for cox1 sequences were ≤0.011% for A. funestus, ≤0.007% for A. gambiae, and ≤0.018% for A. rufipes. The detection of genetically diverse Anopheles vector species in an office setting underscores the potential risk of workplace malaria transmission. This pilot study provides initial evidence that workplace environments can harbor genetically diverse malaria vectors and should be considered in future surveillance and control strategies. We recommend subnational tailoring (SNT) of intervention strategies to incorporate workplace environments and public places into malaria control efforts.}, }
@article {pmid40697875, year = {2025}, author = {Xiang, R and Hu, J and Chuluunbat, J and Wu, F and Qin, B and Zhang, X and Jiang, R}, title = {Comparative chloroplast genomes and phylogenetic analysis of the Phlegmariurus (Lycopodiaceae) from China and neighboring regions.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1543431}, pmid = {40697875}, issn = {1664-462X}, abstract = {The lycophyte genus Phlegmariurus (Herter) Holub (Huperzioideae, Lycopodiaceae) is ecologically and pharmaceutically significant, notably as a natural source of Huperzine A-a promising therapeutic candidate for Alzheimer's disease. Despite its medicinal potential, taxonomic ambiguities on species delimitation and infrageneric classification have impeded conservation and sustainable utilization efforts. Here, we assembled 40 Phlegmariurus complete chloroplast genomes, including all taxa from China, most of which were reported for the first time. Our results revealed the conserved quadripartite architectures and little variation in genome size and GC content in the genus. Comparative analyses on genome sequences identified seven hypervariable loci as prospective DNA barcodes for species discrimination. The phylogenetic toopologies reconstructed from nuclear ribosomal DNA and chloroplast genome data consistently resolved four monophyletic clades, further validated by SNP-based discriminant analysis of principal components. They are well corresponding to the four sections' classification on Chinese taxa (sect. Squarrosurus, sect. Phlegmariurus, sect. Fargesiani, sect. Hamiltoniani). Notably, nuclear and chloroplast data congruently yielded a sister relationship between sect. Squarrosurus and sect. Phlegmariurus. However, the phylogenetic positions of sect. Fargesiani and sect. Hamiltoniani conflicted across different datasets. The diversification of the Chinese Phlegmariurus was traced back to the Oligocene (ca. 26.04 Ma). The comprehensive genetic resources generated herein provide a foundation for future research on species identification, population genomics and genetic diversity preservation in this medicinally significant vital genus.}, }
@article {pmid40694563, year = {2025}, author = {Kar, O and Mukherjee, A and Mukherjee, K and Pramanik, D and Naskar, A and Banerjee, D}, title = {Molecular identification and genetic variations of forensically significant blow flies (Diptera: Calliphoridae) from Eastern India using DNA barcoding.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0327039}, pmid = {40694563}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Calliphoridae/genetics/classification ; India ; Electron Transport Complex IV/genetics ; *Genetic Variation ; *Forensic Entomology/methods ; Phylogeny ; *Diptera/genetics/classification ; Species Specificity ; }, abstract = {Flies, especially those from the Calliphoridae family, play a crucial role in decomposition and are the first to colonize a cadaver. Firstly, accurate species identification is a prerequisite for entomological evidence-based calculation of postmortem interval (PMI). While morphological criteria for identifying the species of adult blow flies exist, there are either absent or inadequate keys for younger stages. In all phases of blow fly development, molecular identification offers a quick and accurate procedure. It is widely known that mitochondrial cytochrome oxidase subunit I has the capacity for molecular identification but is ineffective in certain species. This study was conducted to assess the effectiveness of the cytochrome oxidase 1 gene in the identification of seventeen different species of calliphorid flies involving four genera, Calliphora, Chrysomya, Lucilia, and Hemipyrellia. In West Bengal, 2,977 blow fly specimens were gathered from four distinct geo-climatic zones. COI barcodes were able to confirm morphological identification through low K2P intraspecific genetic divergences (0% to 1%) and moderate to high K2P interspecific genetic divergences (0.39% to 12.29%). The Neighbour-Joining (NJ) analysis demonstrated well-supported reciprocal monophyly among the species. The species grouping was in agreement with morphological and molecular identifications. The four delimitation methods, BIN, ASAP, PTP, and GMYC, used for species identification produced similar results and facilitated the proper identification of species. Therefore, it can be concluded that COI barcodes are a highly successful alternative for the molecular identification of blow flies, facilitating forensic cases and biodiversity research in India.}, }
@article {pmid40694500, year = {2025}, author = {Zhong, S and Wang, R and Gao, X and Guo, Q and Lin, R and Luo, M}, title = {Modular DNA barcoding of nanobodies enables multiplexed in situ protein imaging and high-throughput biomolecule detection.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, pmid = {40694500}, issn = {2050-084X}, support = {32322032//National Natural Science Foundation of China/ ; 2022ZD0206700//China Brain Initiative/ ; 20230484303//Beijing Nova Program/ ; 2021ZD0202803//China Brain Initiative/ ; Research Unit of Medical Neurobiology 2019RU003//Chinese Academy of Medical Sciences/ ; }, mesh = {Animals ; *Single-Domain Antibodies/genetics ; Mice ; *SARS-CoV-2/immunology/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Humans ; COVID-19/diagnosis ; Brain ; Immunoglobulin G ; High-Throughput Nucleotide Sequencing ; High-Throughput Screening Assays/methods ; }, abstract = {Current immunodetection methods using antibody-DNA conjugates enable multiplexed target detection through orthogonal DNA barcodes, but existing conjugation approaches are labor-intensive and often compromise antibody function. Here, we present a modular, site-specific, and cost-efficient DNA tagging strategy - multiplexed and modular barcoding of antibodies (MaMBA). Utilizing nanobodies as modular adaptors, MaMBA enables direct site-specific labeling of off-the-shelf IgG antibodies with a one-component design. We first applied MaMBA to develop the MaMBA-assisted immunosignal hybridization chain reaction (misHCR) method for highly multiplexed in situ protein imaging via orthogonal HCR. Its cleavable variant, misHCR[n], achieves simultaneous visualization of 12 different targets within the same mouse brain sections through iterative probe use. We further extended the cleavable MaMBA to develop the barcode-linked immunosorbent assay (BLISA) for multiplexed and high-throughput biomolecule detections. By combining BLISA with next-generation sequencing, we successfully measured SARS-CoV-2 IgG and hepatitis B virus (HBV)-associated antigens in a large number of human serum samples. Additionally, we demonstrated a small-scale drug screen by using BLISA to simultaneously detect eight protein targets. In conclusion, MaMBA offers a highly modular and easily adaptable approach for antibody DNA barcoding, which can be broadly applied in basic research and clinical diagnostics.}, }
@article {pmid40693379, year = {2025}, author = {Choi, W and Moestopo, WP and Gu, S and Lee, T and Yoo, JH and Xia, X and Armstrong, MR}, title = {Helical Photonic Metamaterials for Encrypted Chiral Holograms.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e07931}, doi = {10.1002/advs.202507931}, pmid = {40693379}, issn = {2198-3844}, support = {DE-AC52-07NA27344//Lawrence Livermore National Laboratory/ ; 22-ERD-056//LLNL Laboratory Directed Research and Development/ ; 24-LW-035//LLNL Laboratory Directed Research and Development/ ; }, abstract = {Helical structures are among the most quintessential three-dimensional (3D) forms that exhibit mirror asymmetry, a hallmark of chirality. Various structural parameters of helices directly linked to chiroptical properties highlight their importance as essential optical metamaterials for polarization-resolved sensors, imaging, and spectroscopies. However, such function-defining properties remain incompletely understood due to fabrication challenges and the lack of a relationship between structure and optical properties. Here, helical structures are analyzed parametrically, and correlations are established that are applicable to the design of chiral helical optical metamaterials. By systematically varying independent parameters-such as from single-turn to five-turn helices and from small major radii to larger ones optimized to fit the unit cell-the underlying relationships with ellipticty are revealed. In addition to theoretical modeling, the findings are experimentally validated using 3D printing and terahertz spectroscopy. The results demonstrate that optimized helical structures are mechanically tunable and exhibit unprecedented optical properties, including broadband and high-magnitude ellipticity spectra. Being embedded in soft elastomers, helical arrays can serve as soft, stretchable optical-mechanical sensors and holograms containing encoded information, such as barcodes and quick response (QR) codes. Chiral QR codes are realized using pixelated single helices with different handedness, demonstrating their potential as advanced encryption/decryption systems for security applications and chiral metaholograms.}, }
@article {pmid40692849, year = {2025}, author = {Rowe, CE and Ahyong, ST and Figueira, WF and Burghardt, I and Keable, SJ}, title = {Identification of Cassiopea sp. in Lake Macquarie, Australia and revision of the taxonomic status of Cassiopea maremetens Gershwin, Zeidler &amp; Davie, 2010 (Cnidaria: Scyphozoa: Cassiopeidae).}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19669}, pmid = {40692849}, issn = {2167-8359}, mesh = {Animals ; *Scyphozoa/genetics/classification/anatomy &amp; histology ; Lakes ; Phylogeny ; Australia ; Queensland ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {Scyphozoans of the genus Cassiopea are notable for their unusual benthic habit of lying upside-down with their exumbrella resting on the substrate and oral arms facing upwards resulting in their common name "upside-down jellyfish". Cassiopea includes species that have been historically confused because of taxonomic ambiguity. Additionally, some species are considered to be invasive, which can have significant economic and environmental consequences by impacting fisheries, tourism, and trophic structures. In temperate southeastern Australia, Cassiopea medusae were first reported in temperate Wallis Lake and Lake Illawarra in 2016, and then Lake Macquarie in 2017, though historically these jellyfish have a more northern tropical distribution in Queensland, eastern Australia. Owing to the invasive potential of Cassiopea, correct species identification is crucial for future management. To address this knowledge gap, this study used genetic comparison through the cytochrome c oxidase subunit I (COI) barcoding gene and morphometric analysis, together with revision of type and topotype material of Cassiopea maremetens Gershwin, Zeidler &amp; Davie, 2010, an incompletely known nominal species from Queensland, to investigate the identity of Cassiopea occurring in Lake Macquarie. The morphometric analysis was also used to identify key features that distinguish the Lake Macquarie species from a second species, designated Cassiopea sp.3, that is also expanding its range southwards in eastern Australia, and which may be sympatric in some areas. The results of this study show the species occurring in Lake Macquarie is Cassiopea xamachana Bigelow, 1892, originally described from Jamaica and subsequently widely reported from the Western Atlantic and the Indo-West Pacific. Additionally, we demonstrate that Cassiopea maremetens, is a junior synonym of C. xamachana. Morphological characters that can be most readily used to distinguish mature specimens of C. xamachana from C. sp.3, which has an overlapping distribution on the Australian east coast, are: (1) the number of large appendages on the oral disc, which is much higher in Cassiopea sp.3 (at least 1 but up to 14) vs. a maximum of two in C. xamachana; (2) the oral arm branching pattern, which is usually alternating for C. xamachana, but a combination of alternating, bifurcating and pinnate for Cassiopea sp.3; (3) the length of the large appendage on the oral arm, which is proportionally longer relative to the bell diameter in C. xamachana.}, }
@article {pmid40692202, year = {2025}, author = {Ansai, E and Sekine, H and Munakata, K and Sase, T and Sasaki, M and Nitta, M and Suzuki, S and Abe, T and Takano, T and Fukumori, H and Nakatsubata, Y and Suzuki, M and Waki, T}, title = {Life cycles of trematodes infecting six species of intertidal gastropods in Japan.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e83}, doi = {10.1017/S0022149X25100485}, pmid = {40692202}, issn = {1475-2697}, mesh = {Animals ; Japan ; *Trematoda/classification/genetics/isolation &amp; purification/growth &amp; development/anatomy &amp; histology ; *Gastropoda/parasitology ; *Life Cycle Stages ; Phylogeny ; *Snails/parasitology ; DNA, Helminth/genetics/chemistry ; Metacercariae ; }, abstract = {A variety of larvae and parthenitae of trematodes have been detected in gastropods in the intertidal zone in Japan. However, because of the difficulty associated with the morphological identification of these stages, they have rarely been identified to the species or higher taxonomic levels. In this study, trematodes of these stages were sampled from intertidal gastropods in the Japanese coastal regions and were identified to the species, genus, or family levels morphologically and molecularly to elucidate or predict their life cycles. Investigation of 17 gastropod species (682 individuals in total) from 14 localities led to the detection of trematodes in 47 individuals belonging to six snail species. The infected gastropods were morphologically identified as Nipponacmea fuscoviridis, Monodonta confusa, Trochus sacellum, Batillaria attramentaria, Littorina brevicula, and Purpuradusta gracilis. Our molecular analyses revealed that sporocysts, rediae, and metacercariae from the gastropods were divided into 14 species belonging to nine families: Philophthalmidae, Fellodistomidae, Gymnophallidae, Lepocreadiidae, Heterophyidae, Opisthorchiidae, Notocotylidae, Microphallidae, and Opecoelidae. These trematodes were thought to use fishes, octopuses, seabirds, and marine mammals as their definitive hosts. Marine organisms such as jellyfishes, crustaceans, and fishes are also thought to act as the second intermediate and paratenic hosts of few present trematode species. As for the other trematode species, DNA barcodes of trematodes from various marine organisms will also illuminate the life cycles in future.}, }
@article {pmid40689223, year = {2025}, author = {Adamčíková, K and Kiran, M and Caboň, M and Matheny, BP and Sánchez-García, M and Arnolds, E and Caboňová, M and Corriol, G and Dima, B and Friebes, G and Griffith, GW and Grootmyers, D and Harries, D and Karich, A and Mešić, A and Mihaljevič, M and Moreau, PA and Pošta, A and Shapkin, V and Tkalčec, Z and Vizzini, A and Vondrovicová, L and Adamčík, S and Jančovičová, S}, title = {A phylogenetic and morphological study of the genus Dermoloma (Agaricales, Tricholomataceae) in Europe and North America exposes inefficiency of opportunistic species descriptions.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e157337}, pmid = {40689223}, issn = {2210-6340}, abstract = {Dermoloma is traditionally known as a small genus of agarics classified in the family Tricholomataceae. This study implemented a multilocus phylogeny of six DNA regions to recognize phylogenetic species within the genus. The species concept is reinforced by observations of well-defined morphological characters enhanced by long term sampling effort in Europe and North America. Thirty European Dermoloma species are described, including 16 new species from Europe and three from North American. These species are classified into two subgenera morphologically distinguished by spores with positive or negative amyloid reaction. A new genus Neodermoloma is introduced for the Dermoloma-like species N.campestre. Localized or continental-scale species endemicity was confirmed based on studied material, but more inclusive phylogenetic clustering supported a mixture of North American species among the European clades. Of the 22 names validly published from Europe prior to this study, 11 could be assigned to well-defined Dermoloma species recognized here. Of the remaining 11 names, two were considered representing Dermoloma species not recorded since their description, and nine were established as later synonyms of other species. Morphological studies of Dermoloma are challenging due to the relatively low number of characters suitable for identification of species. The majority of morphological characters showed continuous variation with high overlap throughout the genus. For this reason, species identification requires an awareness of morphological variability within species, and multiple distinguishing characters need to be combined, and furthermore, often a barcode sequence is needed for a certain identification. Stable isotope analysis in Dermoloma of δ[13]C and δ[15]N revealed an ecological signature similar to known CHEGD fungi, i.e. Clavariaceae and Hygrocybe s.l. This indicates that Dermoloma species are biotrophic but neither ectomycorrhizal nor saprotrophic and may form mutualistic root endophytic associations with vascular plants.}, }
@article {pmid40689039, year = {2025}, author = {Platzgummer, K and Kniha, E and Dvorak, V and Halada, P and Walochnik, J and Vomackova Kykalova, B and Hanusniakova, I and Farkas, R and Volf, P and Trájer, AJ}, title = {Updating the distribution of sand flies in Hungary with implications on their biology and ecology.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {8}, number = {}, pages = {100293}, pmid = {40689039}, issn = {2667-114X}, abstract = {In Europe, sand flies (Diptera: Psychodidae: Phlebotominae) are characteristic Mediterranean fauna, though some species expand their range further north. However, the sand fly fauna of Central Europe remains underreported, particularly in Hungary where recent data is lacking due to limited and outdated entomological surveys. To address this gap, a series of sand fly surveys were conducted in Hungary, with significant findings from two trapping efforts in 2017 and 2024. In 2017, only a single female Phlebotomus papatasi was trapped in northern Hungary, which marks one of the northernmost records of the species. In 2024, a more extensive and geographically wider survey recorded 264 sand flies at 34 sites, including three species: Ph. mascittii, Ph. neglectus, and Ph. papatasi. Sand flies were found across diverse environmental settings, including urban, agricultural, and natural habitats. Particularly, the previously rare presence of Ph. mascittii at rural sites (natural rock formations) was reported. Analysis of historical and current data revealed the presence of four sand fly species in Central and South Transdanubia, with evidence suggesting potential range expansion. Blood meal analysis of engorged females identified a variety of domestic and wild host species, but no Leishmania or Phlebovirus infections were detected. Habitat modelling and linear discriminant analysis indicated substantial climate suitability across Southeast Europe, with most positive sand fly observations observed in discontinuous urban fabric CORINE Land Cover classes. This study offers important insights into the ecology, distribution, and climatic preferences of sand flies in Hungary and provides crucial baseline data to monitor potential future spread.}, }
@article {pmid40688177, year = {2025}, author = {Piasecki, W and Boxshall, GA and Panicz, R and Eljasik, P}, title = {New identification traits of Tracheliastes maculatus (Copepoda: Lernaeopodidae), a parasite of bream, Abramis brama (Cyprinidae).}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {27}, number = {}, pages = {101108}, pmid = {40688177}, issn = {2213-2244}, abstract = {The parasitic copepod Tracheliastes maculatus Kollar, 1835, infects the freshwater bream, Abramis brama, a key species in European freshwater ecosystems. Despite its widespread occurrence and potential to cause skin hemorrhages, scale erosion and perforation, and fish mortality, species-level identification within the genus Tracheliastes has been problematic due to insufficient diagnostic traits. This study refines identification criteria by integrating morphological and genetic approaches. We present the first DNA barcode (COI gene sequence) for Tracheliastes maculaus, providing a molecular basis for taxonomic clarification. Additionally, scanning electron microscopy (SEM) reveals novel morphological details, including the number and distribution pattern of secondary denticles on endopodal Claw 1 of the antenna and structural differences in endopodal and exopodal side denticles of the antenna, both of which, may serve as new diagnostic features within the genus. Furthermore, we regard Tracheliastes mourkii as a nomen nudum because it was not morphologically diagnosed, and no museum specimen is extant. These findings improve species discrimination and set a benchmark for future taxonomic revisions of Tracheliastes, facilitating more precise ecological and parasitological assessments. A mini-review of the genus is also provided.}, }
@article {pmid40687770, year = {2025}, author = {Mwesige, R and Maosa, J and Couvreur, M and Bert, W}, title = {Morphological and Molecular Characterization of Hoplolaimus tuberosus n. sp. (Nematoda: Hoplolaimidae) Associated with Potato in Uganda.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250025}, pmid = {40687770}, issn = {0022-300X}, abstract = {The new nematode species Hoplolaimus tuberosus n. sp., isolated from potato rhizosphere in Budwale sub-county, Mbale district, Eastern Uganda, is characterized based on light and scanning electron microscopy alongside four molecular markers. Females of H. tuberosus n. sp. are moderately large (1.2-1.6 mm) and exhibit distinctive morphological features, including an offset lip region with 4-5 lip annuli, a basal lip annule divided into 10-12 irregular blocks, a robust stylet (45-50 μm), a variable lateral field, characterized by one incisure (zigzag longitudinal line formed by anastomoses) anteriorly and posteriorly, and 2-3 irregular, incomplete striae at mid-body, a secretory-excretory pore positioned anterior to the hemizonid, 6 gland nuclei, and a hemispherical to bluntly rounded tail with 8-10 annuli. Males are slightly smaller at 1.0-1.3 mm, have a basal lip annule divided into 2-4 blocks and relatively long spicules (46-58 μm). Phylogenetic analyses of COI mtDNA, ITS-rRNA, 18S-rRNA and D2D3 of 28S-rRNA demonstrated a close relation of the new species with morphologically similar species (Hoplolaimus columbus, Hoplolaimus indicus, Hoplolaimus seinhorsti, Hoplolaimus dubius and Hoplolaimus pararobustus) yet H. tuberosus n. sp. had in all analyses a distinct phylogenetic position. The population density of 50-75 H. tuberosus n. sp. per 100 ml of soil, combined with the polyphagous nature of related Hoplolaimus species, suggests that this new species could pose a significant pest threat to potato crops, warranting further pathogenicity studies.}, }
@article {pmid40687555, year = {2025}, author = {Naji, SS and Mahmood, MA and Hussein, HM and Mahmood, AA and Baker, HS}, title = {The Effect of Quercus robur Bark on Oral Candidiasis Caused by Candida albicans and Candida glabrata Isolated from a Pediatric Oral Infection as Comparison to Azole Antifungal.}, journal = {Clinical, cosmetic and investigational dentistry}, volume = {17}, number = {}, pages = {285-292}, pmid = {40687555}, issn = {1179-1357}, abstract = {BACKGROUND: The original diversity of Quercus rubra L. (oak) is in eastern America and then distributed to European districts. Oral candidiasis is the most common fungal infection among humans. Azole antifungal drugs can be used to treat Candida infection. Candida albicans and Candida glabrata have emerged as the most common pathogenic yeasts in cases of oral candidiasis.<br><br>AIM OF THE STUDY: This study aimed to explore the genotype Candida spp. and evaluate the antifungal activity of hot water extract of oak bark against C. albicans and C. glabrata as an alternative pharmacotherapy compared to azole antifungal agents.<br><br>MATERIALS AND METHODS: The sample was isolated from an 8-year-old child with aggressive oral candidiasis and identified by culturing on sabouraud dextrose agar (SDA) CHROMagar. Genotyping of Candida spp. was performed using the internal transcribed spacer (ITS) region. Standard discs of the antifungal's fluconazole, itraconazole, ketoconazole 10&#x2009;mg/L for each, amphotericin 100, nystatin 50&#x2009;mg/L, and hot water oak bark extract were administered to C. albicans and C. glabrata in vitro.<br><br>RESULTS: Genotyping of Candida spp. showed that 98% of oral candidiasis cases were C. glabrata which had an 870 bp genotype, while 2% were C. albicans which had a 550 bp genotype based on ITS barcoding region size. The findings that the oak bark extract had high antifungal activity against C. glabrata showed an inhibition zone diameter of 3.067 mm compared to high resistance to antifungals.<br><br>CONCLUSION: Oak extract is considered a successful alternative for the treatment of oral candidiasis infections by antifungals such as azole and nystatin in children.}, }
@article {pmid40687156, year = {2025}, author = {Zhang, J and Du, Q and Dai, Y and Yu, H}, title = {Re-description of Clubionahuaban (Araneae, Clubionidae), with the first description of the female.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e157384}, pmid = {40687156}, issn = {1314-2828}, abstract = {BACKGROUND: Clubionahuaban Xin, Zhang, Li, Zeng &amp; Yu, 2020, one of the members of the Clubionatrivialis group, was described, based on two male types from Xiangzhigou Scenic Spot, Guyang City, Guizhou Province, China.<br><br>NEW INFORMATION: Recently, new material of sac spiders has been collected from southwest China, including the type locality. The males were identified as C.huaban, based on comparison with the holotype. On the basis of the morphological characters and DNA barcoding, we credibly matched the females and males together as C.huaban. Therefore, C.huaban is re-described, based on new material and the female is described and illustrated for the first time.}, }
@article {pmid40685845, year = {2025}, author = {Araujo, GS and Sampaio, CLS and Rocha, LA and Leite, CEF}, title = {Integrative taxonomy reveals a new species of the soapfish genus Rypticus (Teleostei: Grammistidae) from the eastern Atlantic Ocean.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70132}, pmid = {40685845}, issn = {1095-8649}, support = {#2023/12231-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; PROTAX #443302/2020//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; #4-22-0314//Lakeside Foundation/ ; //Hope for Reefs/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Alagoas/ ; //Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; #7937-05//National Geographic Society/ ; }, abstract = {A new species of the soapfish genus Rypticus is described based on 14 specimens from the eastern Atlantic Ocean. The new species was previously misidentified as the greater soapfish, R. saponaceus, due to their similar appearance. However, it differs from R. saponaceus in several key characteristics, including a comparatively shorter head, snout and upper jaw, and a deeper body. Molecular data, obtained from the mitochondrial cytochrome oxidase I gene, strongly suggest the monophyly of the new species and support its description as new.}, }
@article {pmid40685410, year = {2025}, author = {Pikalo, J and Sychra, O and Peña-Espinoza, M and Galat, M and Unterköfler, MS and Heddergott, M and Glawischnig, W and Fuehrer, HP}, title = {Chewing lice (Phthiraptera) on a wild Golden eagle (Aquila chrysaetos) and a zoo-kept Eurasian griffon vulture (Gyps fulvus) in Tyrol, Austria.}, journal = {Parasitology research}, volume = {124}, number = {7}, pages = {85}, pmid = {40685410}, issn = {1432-1955}, mesh = {Animals ; Austria ; *Lice Infestations/veterinary/parasitology ; *Bird Diseases/parasitology ; *Eagles/parasitology ; *Falconiformes/parasitology ; Animals, Zoo/parasitology ; *Phthiraptera/classification/anatomy &amp; histology ; Male ; DNA Barcoding, Taxonomic ; }, abstract = {Chewing lice (Phthiraptera) are obligate and permanent ectoparasites commonly found on birds. The life cycle of these insects is completed on the body of the host and therefore many are host specific. This is the first report of chewing lice on a wild Golden eagle (Aquila chrysaetos) and a zoo-kept Eurasian griffon vulture (Gyps fulvus) in Tyrol, Austria. Three different species of chewing lice were identified: Craspedorrhynchus aquilinus was found on Aquila chrysaetos and Colpocephalum turbinatum and Falcolipeurus quadripustulatus were found on Gyps fulvus. The lice were identified morphologically and by barcoding. Chewing lice (Phthiraptera) of eagles, vultures, and other Accipitriformes are understudied, and further research is needed.}, }
@article {pmid40685354, year = {2025}, author = {Kapustová, A and Kulich Fialová, M and Svobodová, M and Brzoňová, J}, title = {Combining blood meal analysis and parasite detection yields a more comprehensive understanding of insect host feeding patterns.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {288}, pmid = {40685354}, issn = {1756-3305}, support = {598120//Grant Agency of Charles University/ ; CA22108//WIMANET-COST Action/ ; UNCE/24/SCI/011//Charles University Research Centre program/ ; }, mesh = {Animals ; *Feeding Behavior ; Czech Republic ; *Ceratopogonidae/parasitology/physiology ; Host-Parasite Interactions ; Haemosporida/isolation &amp; purification/genetics ; Female ; *Mosquito Vectors/parasitology/physiology ; *Culicidae/parasitology/physiology ; Trypanosoma/isolation &amp; purification/genetics ; *Insect Vectors/parasitology/physiology ; Polymerase Chain Reaction ; *Blood/parasitology ; }, abstract = {BACKGROUND: Traditionally, blood meal analysis has been the primary method used to assess feeding patterns of insects. In contrast, parasite detection is commonly applied to monitor parasite circulation and prevalence in vectors, but rarely to study host feeding patterns. Our study aimed to test whether broad-target screening for haemosporidian and trypanosome parasites could complement blood barcoding by revealing additional host associations. We hypothesised that combining both methods would provide a more comprehensive understanding of vector feeding behaviour than either method alone. In addition to evaluating the two methods, we also analysed the vector species composition and their abundance, providing important faunistic and prevalence data that contribute to the broader understanding of local vector-parasite dynamics.<br><br>METHODS: Mosquitoes and biting midges were trapped over a 5-year period at three localities in Czechia. Blood-fed individuals underwent blood meal barcoding analysis. In parallel, parasite detection was conducted using nested polymerase chain reaction (PCR) and gut dissection techniques.<br><br>RESULTS: A total of 10,152 mosquitoes were collected, with Culex pipiens (66%) and Aedes vexans (18%) being the predominant species. In addition, 1701 biting midges, primarily Culicoides pictipennis (61%) and C. festivipennis (12%), were captured. Among the collected samples, 281 mosquitoes (3%) and 52 biting midges (3%) were blood-fed. Parasites were detected in 468 mosquito pools (5%, 341 trypanosomes, 127 haemosporidians) and 21 midge pools (1%, 8 trypanosomes, 13 haemosporidians). Blood meal barcoding of engorged Aedes, Anopheles, Culiseta, and Mansonia samples revealed only mammalian hosts; however, parasite detection indicated previous feeding on birds. Culex displayed stronger ornithophily according to parasite detection, although blood meal analysis showed a more opportunistic behaviour, with the detection of avian, mammalian and even amphibian blood. Avian parasites were detected in five Culicoides species (Culicoides alazanicus, C. festivipennis, C. kibunensis, C. nubeculosus and C. pictipennis) while human blood was detected only in C. pictipennis. Overall, four Haemoproteus lineages and 15 Plasmodium lineages were identified, 11 of which were new records for Czechia and 4 were newly described.<br><br>CONCLUSIONS: Integrating blood meal analysis with parasite detection provides a more comprehensive understanding of insect feeding patterns and vector-host dynamics. Blood meal analysis remains the gold standard for identifying recent host interactions, offering direct and often species-level evidence of feeding events. In addition, parasite detection extends the window of detectability beyond the digestion of host blood and can reveal additional or otherwise-overlooked host associations. Together, these complementary approaches increase the likelihood of detecting interactions with a broader range of hosts, including humans, who might be missed by parasite screening alone.}, }
@article {pmid40683866, year = {2025}, author = {Fu, Y and Kim, H and Roy, S and Huang, S and Adams, JI and Grimes, SM and Lau, BT and Sathe, A and Ji, HP and Zhang, NR}, title = {Single cell and spatial alternative splicing analysis with Nanopore long read sequencing.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6654}, pmid = {40683866}, issn = {2041-1723}, support = {R33CA247700//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35HG011292-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01CA217875//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {*Alternative Splicing/genetics ; *Single-Cell Analysis/methods ; Humans ; *Nanopore Sequencing/methods ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Protein Isoforms/genetics ; }, abstract = {Long-read sequencing boosts alternative splicing analysis but faces technical and computational barriers in single-cell and spatial settings. High Nanopore error rates compromise cell barcode and UMI recovery, while read truncation and misalignment undermine isoform quantification. Downstream, a statistical framework to assess splicing variation within and between cells or spatial spots is lacking. We introduce Longcell, a statistical and computational pipeline for isoform quantification from single-cell and spatially barcoded Nanopore long reads. Longcell efficiently recovers cell barcodes and UMIs, corrects sequencing errors, and models splicing diversity within and between cells or spots. Applied across multiple datasets, Longcell allows accurate identification of spatial isoform switching. Longcell also reveals widespread high intra-cell isoform heterogeneity for highly expressed genes. Finally, on a perturbation experiment for 9 splicing factors, Longcell identifies regulatory targets that are validated by targeted sequencing.}, }
@article {pmid40682185, year = {2025}, author = {Barazandeh, M and Gaikani, HK and Pattanshetti, R and Ogbede, JU and Sinha, S and Moore, R and Carr, CE and Giaever, G and Nislow, C}, title = {Bar-seq: A robust, platform-agnostic method for massively parallel cell-based screens.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkaf166}, pmid = {40682185}, issn = {2160-1836}, abstract = {Bar-seq (barcode sequencing) is a high-throughput method originally developed for systematically identifying gene-drug interactions and genetic dependencies in yeast using pooled deletion mutant libraries. This approach enables high-resolution profiling of large mutant libraries over time, across diverse experimental conditions, providing relative fitness values for each individual within the population. As the technology for enumerating barcodes has evolved, we have continued to incorporate improvements to the method. Here, we present an optimized Bar-seq workflow adaptable to multiple sequencing platforms, including instruments from Illumina, MGI, Element, and Oxford Nanopore. We highlight the advantages and limitations of each approach to aid in experimental design decisions. We introduce refinements in barcode amplification, sequencing strategies, and data analysis to enhance accuracy and scalability while making adoption as straightforward as possible.}, }
@article {pmid40681695, year = {2025}, author = {Ali, MA and Gowda, NR and Allam, MA and Fayed, SA}, title = {Conservation of Verbascum sinaiticum Benth using innovative tissue culture technique and DNA barcoding.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {26075}, pmid = {40681695}, issn = {2045-2322}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Verbascum/genetics/growth &amp; development ; *Tissue Culture Techniques/methods ; Plant Shoots/growth &amp; development/genetics ; Culture Media ; Plants, Medicinal/genetics/growth &amp; development ; *Conservation of Natural Resources/methods ; }, abstract = {Egypt has diverse medicinal plants, many of which are endangered because of environmental and human pressures. Verbascum sinaiticum Benth (V. sinaiticum) is a medicinal plant from the Scrophulariaceae family and a locally rare species endemic to Sinai. This study introduces an innovative in vitro regeneration protocol for V. sinaiticum, developed for the first time using optimized tissue culture techniques. Additionally, the incorporation of molecular identification by DNA barcoding and biochemical profiling (via HPLC and SDS-PAGE) presents a complete strategy to conservation and genetic documentation, to support future biotechnological applications. An efficient in vitro regeneration system for V. sinaiticum was established using tissue culture techniques. The study investigated the effects of three different shoot induction media on growth, The first medium was BA medium, a combination of 0.5 mg L[- 1] benzyl adenine (BA), 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine was added to the initial medium. The second medium was MD medium supplemented with 3 mg L[- 1] BA, 0.2 mg L[- 1] naphthaleneacetic acid (NAA), 10 mg L[- 1] thiamine HCl, 1 mg L[- 1] nicotinic acid, and 1 mg L[- 1] pyridoxine. The third medium was AB medium formulated with 1 mg L[- 1] Adenine sulfate, 1 mg L[- 1] benzyl adenine, 10 mg L[- 1] thiamine HCl, 1 mg L[- 1] nicotinic acid, and 1 mg L[- 1] pyridoxine, and three media for rooting, The first medium was IB medium supplemented with 0.4 mg L[- 1] indol butyric acid, 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine. The second medium was IA medium containing 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine. The third medium was NA media formulated with 0.4 mg L[- 1] naphthaleneacetic acid, 5 mg L[- 1] thiamine HCl, 0.5 mg L[- 1] nicotinic acid, and 0.5 mg L[- 1] pyridoxine. All media were prepared using Murashige and Skoog (MS) basal salts 4.4 g L[- 1] supplemented with 30 g L[- 1] sucrose, and solidified with 2.8 g L[- 1] gelrite. Various propagation protocols were tested based on the availability of plant materials. We have devised flexible methods for large-scale micropropagation that offer a sustainable and quick production strategy, even in the face of resource constraints. The surface sterilization technique was refined, resulting in up to 75% contamination-free cultures. The highest germination rate was observed with 20% Clorox for 15-20 min, but extended exposure (25-30 min) resulted in decreased germination.HPLC analysis revealed that the ethanolic extract had the highest quantities of rutin (19.07 µg/mL) and vanillin (6.29 µg/mL), while the aqueous extract had the highest levels of gallic acid (7.02 µg/mL) and chlorogenic acid (6.02 µg/mL). SDS-PAGE examination revealed five protein bands ranging in molecular weight from 240 kDa to 28 kDa. This study introduces an innovation and preservation strategy for V. sinaiticum, a locally rare species in Egypt. DNA barcoding was used for molecular authentication, and the acquired sequence was matched to GenBank database sequences using the BLAST tool.}, }
@article {pmid40679848, year = {2025}, author = {Vereecke, N and Yoon, TB and Luo, TL and Corey, BW and Lebreton, F and Mc Gann, PT and Dekker, JP}, title = {An open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.}, journal = {Journal of clinical microbiology}, volume = {63}, number = {8}, pages = {e0066425}, pmid = {40679848}, issn = {1098-660X}, support = {//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/ ; //U.S. Department of Defense/ ; }, abstract = {UNLABELLED: In this work, we present an optimized nanopore long-read only sequencing workflow for epidemiologic analysis of clonal outbreaks built with open-source tools. A set of unrelated clinical Pseudomonas aeruginosa isolates (n = 10) was chosen for workflow optimization, and sequencing libraries were prepared using a modified rapid barcoding strategy that incorporates temperature ramps to improve performance for high-GC content genomes. Sequencing data were used to benchmark the performance of the dorado suite (v0.9.1), including its basecaller, pre-assembly read error correction, and post-assembly polishing algorithms. All long-read assemblies and core genome multilocus sequence typing (cgMLST) were performed with Flye and pyMLST, respectively. Results were compared with a standard reference Illumina short-read approach, and discordant positions were determined at the core and whole-genome levels. Optimal performance was found with dorado sup@v5.0.0 basecalling with the inclusion of dorado error correction and dorado polish with its bacterial model. This workflow was then validated with four retrospective hospital outbreak isolate sets, including Klebsiella pneumoniae (n = 12), P. aeruginosa (n = 11), Enterococcus faecium (n = 10), and Staphylococcus aureus (n = 10). The nanopore-only assemblies obtained from the optimized pipeline demonstrated fully concordant cgMLST-based minimum spanning trees compared to the Illumina short-read reference. At the whole-genome level, high concordance was also observed, with as few as two discordant positions per genome compared to short-read assemblies. This optimized library preparation and open-source computational workflow enables nanopore-only clonality and outbreak analysis with performance comparable to that of Illumina short-read sequencing and will contribute critically to hospital infection control.<br><br>IMPORTANCE: For the past decade, bacterial whole-genome sequencing has been performed using high-accuracy short-read sequencing. More recently, long-read sequencing with Oxford Nanopore Technologies (ONT) instruments has emerged as a potential alternative based on multiple advantages, including lower costs, portability, and speed. However, this platform has suffered from basecall error rates that were too high for many applications in clinical microbiology, including outbreak tracing. With the release of new flow cell chemistries and basecall algorithms, the accuracy has improved dramatically, making this approach feasible for outbreak investigations. In this work, we optimize a streamlined nanopore-only workflow for epidemiologic analysis of bacterial pathogens. The workflow was validated with isolates from four previously identified clinical outbreaks with varying GC content and demonstrated fully concordant cgMLST clustering as compared to short-read references. This workflow will facilitate the broader implementation of ONT-only genomes and cgMLST analysis to assist in hospital outbreaks worldwide.}, }
@article {pmid40679398, year = {2025}, author = {Goldstein, I and Hale, JJ and Ehrenreich, IM}, title = {Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyaf136}, pmid = {40679398}, issn = {1943-2631}, abstract = {Global epistasis is a phenomenon in which the effects of genetic perturbations depend on the fitness of the individuals in which they occur. In populations with natural genetic variation, global epistasis arises from interactions between perturbations and polymorphic loci that are mediated by fitness. To investigate the prevalence and characteristics of loci involved in these interactions in the budding yeast Saccharomyces cerevisiae, we used combinatorial DNA barcode sequencing to measure the fitness of 169 cross progeny (segregants) subjected to 8,126 CRISPRi perturbations across two environments. Global epistasis was evident in these data, with more fit segregants within each environment exhibiting greater sensitivity to genetic perturbations than less fit segregants. We dissected the genetic basis of this global epistasis by scanning the genome for loci whose effects covary with CRISPRi-induced reductions in population fitness. This approach identified 58 loci that interact with fitness, most of which exhibited larger effects in the absence of genetic perturbations. In aggregate, these loci explained the observed global epistasis in each environment and demonstrated that the loci contributing to global epistasis largely overlap with those influencing fitness in unperturbed conditions.}, }
@article {pmid40677748, year = {2025}, author = {Bae, S}, title = {Validation of improved cytochrome c oxidase I (COI) primers for comprehensive biodiversity assessment of ascidians.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19671}, pmid = {40677748}, issn = {2167-8359}, mesh = {Animals ; *Urochordata/genetics/classification/enzymology ; *Biodiversity ; *Electron Transport Complex IV/genetics ; *DNA Primers/genetics ; Polymerase Chain Reaction ; *DNA Barcoding, Taxonomic/methods ; }, abstract = {Reliable molecular tools are needed for effective biodiversity assessment of marine organisms. These tools can be used in ascidians species, which are one of the most invasive taxa worldwide and morphologically difficult to identify. This study aimed to redesign and improve ascidian-specific primers and validate the new primer pair (AscCOI2) for comprehensive biodiversity assessment. To design an optimized primer, 3,948 COI sequences from 273 ascidian species were used as a dataset. The AscCOI2 pair was developed through strategic modifications to the binding site and validated using in silico and in vitro approaches. Analysis of penalty scores showed the improved efficiency of the redesigned AscCOI2 pair, with ascidians scoring less than 150 points for both forward and reverse primers and the non-target groups maintaining a score above 480. Primer-binding analysis results showed a significant improvement in amplification success rate from 47.99% to 82.42% at the species level. In vitro validation using conventional polymerase chain reaction (PCR) confirmed the successful amplification of six ascidian species and failure for a non- ascidian taxon. Barcoding gap analysis showed a clear gap of 0.015 between intraspecific and interspecific genetic distances. The species detection capability of the redesigned AscCOI2 pair greatly improved, and the high taxonomic specificity of ascidians is maintained. Overall, this study demonstrates that the AscCOI2 pair is an effective tool for both metabarcoding and mini-barcode applications in biodiversity assessment and molecular systematics research of ascidians.}, }
@article {pmid40677746, year = {2025}, author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D}, title = {Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19674}, pmid = {40677746}, issn = {2167-8359}, mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Pacific Ocean ; Animals ; *Aquatic Organisms/genetics/classification ; Biodiversity ; Electron Transport Complex IV/genetics ; *Databases, Nucleic Acid/standards ; *Databases, Genetic ; }, abstract = {DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding.}, }
@article {pmid40677014, year = {2025}, author = {Li, H and Cai, Y and Zhang, L and Hu, E and Yang, J and Guo, H and Cui, Y and Chen, B and Qian, G}, title = {Anisotropic Excitation-Modulated Multi-Color Three-photon Excited Luminescence in Ln-MOF Heterostructure.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e09590}, doi = {10.1002/adma.202509590}, pmid = {40677014}, issn = {1521-4095}, support = {52402206//National Natural Science Foundation of China/ ; 52302200//National Natural Science Foundation of China/ ; 52025131//National Natural Science Foundation of China/ ; LQN25E020013//Natural Science Foundation of Zhejiang Province/ ; LQ23E020004//Natural Science Foundation of Zhejiang Province/ ; 2024-3-029//Key Projects of Jinhua Science and Technology Bureau/ ; }, abstract = {Multi-photon excited luminescence (MPEL) modulation is of great application value for optoelectronics, especially MPEL with the characteristics of multi-color emission and optical anisotropy. However, it still suffers from the obstacles in highly-integrating and orientedly-assembly of various MPEL units. Herein, a hierarchical assembly-in situ doping strategy is proposed to establish a novel lanthanide-graded metal-organic framework based heterostructure. Well-designed ligand and Ln[3+] ions are respectively selected as the MPEL energy donor and acceptor units (MEDU and MEAU). Through utilizing the effective energy transfer between them, the as-obtained triblock heterostructure displays multi-dimensional three-photon excited luminescence (3PEL) modulation, where the emission band and intensity can be switched by manipulating excited regions and excitation polarization based on a single pump source. This is attributed to the precise integration and orientation of photonic units. As a result, the heterostructure exhibits multi-color 3PEL with a record-high MPEL color gamut (>30% of sRGB area) in MOFs and high degree of linear polarization values (max ≈88.6%). Such anisotropic 3PEL modulation shows promising potential in nonlinear optical switches, programmable logic gates, and multi-level optical barcodes. These findings open up an intriguing way to develop up-conversion luminescent materials with functions on demand toward photonic modulation.}, }
@article {pmid40676502, year = {2025}, author = {Univaso, L and Peña, F and Román-Figueroa, C and Paneque, M}, title = {The rps15-rpl32 intergenic locus is a phylogeographic marker for Latin American Zea mays landrace varieties and subspecies.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {672}, pmid = {40676502}, issn = {1471-2164}, support = {40035912-0/2022//FIC &#xd1;UBLE/ ; }, mesh = {*Zea mays/genetics/classification ; Phylogeography ; Genetic Markers ; Latin America ; Phylogeny ; *Ribosomal Proteins/genetics ; *DNA, Intergenic/genetics ; *Plant Proteins/genetics ; Genetic Loci ; }, abstract = {BACKGROUND: Maize (Zea mays L.) has a deep cultural significance in Latin America, with traditional and native varieties cultivated for millennia. Approximately 220 maize races have been identified in the region. These races have adapted to the diverse environmental conditions, resulting in a considerable diversity of varieties. Although DNA barcoding is widely used for species identification, distinguishing between varieties within a species remains challenging in plants, owing to the conserved nature of standard barcoding loci. Intragenic marker combinations are often used to address this limitation. However, they remain insufficient for variety-level resolution. Therefore, we developed a pipeline to identify robust markers that can distinguish maize varieties based on their phylogeographic origins.<br><br>RESULTS: In this study, the small single-copy (SSC) region of the chloroplast genome exhibited the highest mutation rate per nucleotide. Furthermore, the intergenic regions rps15-rpl32 and ndhD-ndhF exhibited the highest mutation rates in the SSC. Comparatively, the coding genes in this region were more conserved. The rps15-rpl32 locus demonstrated improved resolution for phylogeographic analysis when concatenated with a short genetic anchor sequence. This marker accurately identified the geographic origin of maize samples. Overall, it was the most informative marker despite its relatively low SNP and InDel frequency and moderate divergence levels. Contrastingly, the ndhF-ndhD locus exhibited higher mutation rates but failed to effectively resolve phylogenetic relationships.<br><br>CONCLUSIONS: Our findings demonstrate that concatenated loci can accurately identify the geographic origin of Zea mays varieties and subspecies and elucidate their relationships. Moreover, the superior performance of rps15-rpl32 in the delineation of phylogenetic relationships among regional genomes shows its potential application as a marker for distinguishing closely related varieties and subspecies. This locus can facilitate the streamlined validation of Zea mays varieties for regional authenticity.}, }
@article {pmid40675575, year = {2025}, author = {Ortega-Morales, AI and Rodríguez-Rojas, JJ and Fernández-Santos, NA and Medrano-Santillana, M and Ayala-Sulca, YO and Arque-Chunga, W and Colos-Galindo, P and Ortega-Morales, NB and López-Hernández, I and Rodríguez-Pérez, MA}, title = {THE PRESENCE OF AEDES HENDERSONI IN MEXICO.}, journal = {Journal of the American Mosquito Control Association}, volume = {}, number = {}, pages = {}, doi = {10.2987/25-7223}, pmid = {40675575}, issn = {1943-6270}, abstract = {The mosquito species commonly named Henderson American pointy mosquito, Aedes hendersoni, was found during a routine mosquito vector surveillance from 2020 to 2023 in diverse collection sites with conserved forested vegetation at the Eco-Parks Rincón de la Silla and El Salto in Nuevo León, northeastern Mexico. Collected specimens were labeled, mounted, and identified using taxonomic keys. Further confirmation of Ae. hendersoni was performed by deoxyribonucleic acid (DNA) barcoding and cytochrome oxidase-I (COI) sequences served to confirm the identity of Ae. hendersoni by comparison with other sequences of species with Triseriatus group and Protomacleaya subgenus of Aedes. Voucher specimens were curated and are available in 2 Mexican collection repositories and COI sequences were deposited in the NCBI GenBank with accession number MG242473.1. Hence, the presence of Ae. hendersoni in México is documented for the first time. Now, geographic occurrence of this species is from Canada throughout United States to northeastern México. With this new record, there are the 4 mosquito species in the Triseriatus group [Aedes: (Protomacleaya)] and 252 species in México.}, }
@article {pmid40672196, year = {2025}, author = {Simonson, AW and Chao, MC and Hood, LE and Donlan, RA and Hopkins, F and Chase, MR and Vickers, AJ and Callendrello, A and Klein, E and Borish, HJ and Malin, M and Maiello, P and Scanga, CA and Lin, PL and Fortune, SM and Flynn, JL}, title = {Protection against reinfection with Mycobacterium tuberculosis extends across heterologous Mtb lineages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40672196}, issn = {2692-8205}, support = {75N93019C00071/AI/NIAID NIH HHS/United States ; T32 AI060525/AI/NIAID NIH HHS/United States ; T32 AI089443/AI/NIAID NIH HHS/United States ; }, abstract = {Immunological memory elicited either through previous or ongoing M. tuberculosis (Mtb) infection provides a critical mechanism by which hosts protect against re-infection and disease progression upon Mtb re-exposure. Conversely, the uneven competition between distinct Mtb strains suggest certain bacterial clades have enhanced ability to spread across communities and circulate globally, potentially by evading memory responses gained by prior infection with genomically different strains. To address whether memory responses induced by one strain can protect against a genetically distinct strain, we conducted a heterologous reinfection study in cynomolgus macaques involving primary infection by a Lineage 4 Erdman Mtb strain and subsequent re-challenge by a Lineage 2 strain, HT-L2. Recent epidemiologic studies have shown that the clade to which HT-L2 belongs has been spreading successfully over the last decade in Lima, Peru. Here, through microbiologic, PET-CT imaging and sequencing of Mtb genomic barcodes, we show that reinfected animals developed fewer lung lesions and controlled both pulmonary and disseminated forms of infection better than naïve animals without prior exposure to Mtb. Our data support that protection against reinfection is not limited by Mtb lineage, providing optimism that vaccines can be effective across populations and geographic locations.}, }
@article {pmid40671796, year = {2025}, author = {Picker, L and Keele, B and Okoye, A and Immonen, T and Varco-Merth, B and Duell, D and Nkoy, C and Goodwin, W and Hoffmeister, S and Kose, E and Conchas, A and Goodman, C and Fennessey, C and Macairan, A and Bosche, W and Fast, R and Homick, C and Hull, M and Oswald, K and Shoemaker, R and Silipino, L and Welker, J and Smedley, J and Labriola, C and Axthelm, M and Estes, J and Barouch, D and Lifson, J}, title = {Identification of initial sites of SIV rebound after treatment cessation.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {40671796}, issn = {2693-5015}, support = {P51 OD011092/OD/NIH HHS/United States ; UM1 AI164560/AI/NIAID NIH HHS/United States ; }, abstract = {Antiretroviral therapy (ART) suspends HIV replication, but virus persists and rebounds after ART discontinuation. Although much is known about the persistent viral population, the tissue origin(s) and the earliest viral dynamics of post-ART viral rebound remain obscure. Here, using barcoded SIVmac239 in rhesus macaques (RMs) and extensive necropsy tissue sampling on ART and early post ART, we defined the spectrum of low-level barcode-specific viral RNA expression in tissues during ART and then assessed initial clonal rebound by identifying barcodes in individual tissues that exceeded this distribution limit ("outliers"). Eight such outlier barcodes were identified in 4 of 11 aviremic (<1 copy/mL) post-ART RM, with 16 additional outliers in 5 of 6 post-ART RM with low viremia (5-30 copies/ml). Nine of these 16 barcodes were also identified in rebound viremia, confirming specific tissues as rebound origin sites. An RM with post-ART viremia of 4700 copies/mL showed 8 outlier barcodes that ranged from a single site to anatomically discontinuous, multi-site spread. Among all identified outlier barcodes, 27 were determined to reflect rebound origins, of which 96% were in the gastrointestinal (GI) tract (26%) or GI-tract-draining lymphoid tissues (70%). These results indicate that distinct tissue sites differentially restrict/promote post-ART viral rebound, with potential therapeutic implications for interventions designed to prevent or control these events.}, }
@article {pmid40671503, year = {2025}, author = {Shamie, I and Bliss-Moreau, M and Lee, JC and Mathieu, R and Hoffman, HM and Geng, B and Lewis, NE and Zhu, YP and Croker, BA}, title = {Comparative single-cell lineage bias in human and murine hematopoietic stem cells.}, journal = {Haematologica}, volume = {}, number = {}, pages = {}, doi = {10.3324/haematol.2025.287897}, pmid = {40671503}, issn = {1592-8721}, abstract = {The commitment of hematopoietic stem cells (HSC) to myeloid, erythroid, and lymphoid lineages is influenced by microenvironmental cues, and governed by cell-intrinsic and epigenetic characteristics that are unique to the HSC population. To investigate the nature of lineage commitment bias in human HSC, mitochondrial single cell (sc) ATAC-Sequencing (mtscATAC-Seq) was used to identify somatic mutations in mitochondrial DNA to act as natural genetic barcodes for tracking the ex vivo differentiation potential of HSC to mature cells. Clonal lineages of human CD34+ cells and their mature progeny were normally distributed across the hematopoietic lineage tree without evidence of significant skewing. To investigate commitment bias in vivo, mice were transplanted with limited numbers of long-term HSC (LT-HSC). Variation in the ratio of myeloid and lymphoid cells between donors, although suggestive of a skewed output, was not altered by increasing numbers of LT-HSC. These data suggest that the variation in myeloid and lymphoid engraftment is a stochastic process dominated by the irradiated recipient niche with minor contributions from the cell-intrinsic lineage bias of LT-HSC.}, }
@article {pmid40668962, year = {2025}, author = {Montenegro, C and Ibiapino, A and Nascimento, T and da Costa, AF and Brasileiro-Vidal, AC and Pedrosa-Harand, A}, title = {Cytogenomic and phylogenomic evidence for new infrageneric relationships in Macroptilium (Benth.) beans.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcaf151}, pmid = {40668962}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Macroptilium (Benth.) Urb. is native to regions from North to South America. Phylogenetic analyses place it close to Phaseolus L. beans, however, its infrageneric division into two sections is not well supported. Despite its chromosomal number stability (2n = 22), interspecific rDNA loci variation enabled species differentiation, suggesting that a cytogenomic approach might be valuable for inferring species relationships and genome evolution.<br><br>METHODS: Here, we (1) characterized nine Macroptilium species through oligonucleotide-based chromosome painting and barcoding (Oligo-FISH); (2) generated genome skimming data for six species and used it to investigate their repeatome dynamics, and (3) performed phylogenomic reconstruction using complete plastomes.<br><br>KEY RESULTS: Oligo-FISH data unveiled de novo translocations between chromosomes 2 and 6, and 3 and 11 in species from proposed groups II and III, respectively, in disagreement with the currently proposed phylogenetic hypothesis. Our phylogenomic (plastid) and repeatome (nuclear) analyses supported groups II and III as clades, with clade-specific satDNA families. Group I was paraphyletic and resembled the Ancestral Phaseolinae Karyotype.<br><br>CONCLUSIONS: We demonstrated the efficiency of different cytogenomic approaches to characterize Macroptilium species, providing insights into its genomic evolution and indicating the need for a systematic re-evaluation of the genus. These findings also support the power of these approaches to solve phylogenetic relationships even in groups with chromosome number stability and recent diversification.}, }
@article {pmid40668245, year = {2025}, author = {Tan, Y and Ma, Z and Hua, X and Tian, H and Zhao, P and Dai, C and Zhang, R and Sun, G and Gleason, ML and Liu, F and Liang, X}, title = {Genome Comparison Reveals a High-Resolution DNA Marker for Phylogenetic Discrimination Within the Colletotrichum gloeosporioides Species Complex.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-07-24-0239-SC}, pmid = {40668245}, issn = {0031-949X}, abstract = {The Colletotrichum gloeosporioides species complex (CGSC), comprising more than 50 closely-related species, constitutes a globally significant phytopathogenic group. Current species delimitation within this complex predominantly relies on multi-locus phylogeny, an approach that is time-consuming and technically demanding. To address these limitations, we screened for novel high-resolution markers by performing comparative analyses of public CGSC genomes. Candidate loci being universally present across CGSC, showing clock-like evolutionary rate and rapid sequence divergence were further evaluated based on characteristics of DNA barcoding gap, gene tree-species tree concordance, and phylogenetic topological support. This multi-criteria screening pipeline identified a 3,111-bp locus (M28), which encodes a PMS1 homolog in the DNA mismatch repair pathway with good potential. In phylogenetic reconstruction using 103 representative isolates spanning 41 validated CGSC species, single-locus M28 phylogeny showed high topological congruence with genome-based phylogeny, and demonstrated good species-level discrimination capacity except for very shallow phylogenetic nodes. Consequently, a degenerate primer pair targeting the M28 locus was designed, which demonstrated high PCR amplification efficiency. Together, this study establishes M28 as an efficient species discrimination barcode for cost-effective, high-throughput species diversity assessments‌ in CGSC.}, }
@article {pmid40667186, year = {2025}, author = {Wu, JW and Yang, JM and Wang, S and Chen, Y and Huang, CH}, title = {Cell barcoding with tandem fluorescent proteins enables high-throughput signaling dynamics analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.17.660155}, pmid = {40667186}, issn = {2692-8205}, support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; S10 OD016374/OD/NIH HHS/United States ; S10 OD023548/OD/NIH HHS/United States ; }, abstract = {Cell barcodes are essential for a wide array of experimental applications, including lineage tracing, genetic screening, and single-cell analysis. An optimal barcode library would provide high diversity, live-cell compatible identification, and simple readout. In this work, we introduce single chain tandem fluorescent protein (sctFP) barcodes, constructed by linking different fluorescent proteins (FPs) into a single polypeptide chain with varied copy numbers. We found that the fluorescence signal intensity ratio at different wavelengths can reliably differentiate sctFPs generated using cnidarian FPs, but not prokaryotic FPs that require exogenous cofactors. The sctFPs enable the multiplexing of genetically encoded fluorescent biosensors, enhancing current biosensor multiplexing methods through a simplified imaging and analysis pipeline that support high-throughput applications. Their robust spectral profiles are compatible with a broad range of biosensor types. Using sctFPs, we demonstrate simultaneous tracking of various signaling activities with biosensors of different spectral properties. Together, this strategy provides a robust and scalable method for barcoding cells across diverse experimental contexts.}, }
@article {pmid40666854, year = {2025}, author = {White, JA and Lu, C and Ombelets, L and Cai, L}, title = {Untangling overlapping barcodes in spatial genomics data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40666854}, issn = {2692-8205}, support = {DP1 NS131408/NS/NINDS NIH HHS/United States ; }, abstract = {Difficulty in resolving spatially overlapping barcodes is a major bottleneck for imaging-based spatial genomics methods. Here, we present an approach for untangling overlapping barcodes by using strong encoding and global optimization to reduce spurious solutions resulting from recombinations of barcodes. We demonstrate experimentally that cellular regions with average local densities of 127 barcodes per µm [2] can be decoded with an estimated FDR of less than 4%, enabling a new type of super-resolution microscopy by coding.}, }
@article {pmid40666714, year = {2025}, author = {Bastug, K and Umar, U and Olson, B and Slusher, T and Faulk, C and Okolo, M and Oguche, S and Thielen, BK}, title = {Utilization of Oxford Nanopore Technology for human infectious disease detection and surveillance in Africa: a scoping review.}, journal = {Access microbiology}, volume = {7}, number = {7}, pages = {}, pmid = {40666714}, issn = {2516-8290}, abstract = {Background. Nanopore-based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost-effective and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high- and low-resource settings. This scoping review (SR) aimed to (1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, (2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa and (3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases. Methods. This SR followed the Joanna Briggs Institute Reviewer's Manual framework for SRs. English language studies published from 1 January 2008 to 30 April 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL and the Cochrane Library. The protocol was publicly available on the Open Science Framework Bastug et al. (Nanopore Sequencing for Infectious Diseases Surveillance and Diagnostics in Africa: a Scoping Review 2024) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel. Results. One thousand one hundred sixty-two studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analysed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African country and 11% in a non-African country, while 32% did not specify the location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious disease outbreak, 25 of which studied severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline, and five studies published the per-specimen cost. Conclusions. ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Most studies used ONT for genomic surveillance of pathogens or antimicrobial resistance genes, while only one study used ONT directly for a real-time clinical application. A small number of studies described a short interval between specimen collection and sequence result, supporting that clinical applications are possible. There is a need for improved reporting of ONT methodology including pipeline timelines, cost, use of barcoding, flow cell models and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low-resource settings.}, }
@article {pmid40666688, year = {2025}, author = {Cramer, ERA and Chen, KC and Johnsen, A}, title = {Overwintering and Resident Birds in Qatar: Explorations With DNA Barcoding.}, journal = {Ecology and evolution}, volume = {15}, number = {7}, pages = {e71817}, pmid = {40666688}, issn = {2045-7758}, abstract = {Genetic research is unevenly distributed across the globe, with most research done in temperate zones. To better understand the birdlife in an under-represented, arid subtropical country, Qatar, we blood sampled birds and salvaged tissue from dead birds, then sequenced a mitochondrial marker (cytochrome c oxidase subunit I, COI, the "DNA barcoding" gene). We chose the DNA barcoding gene because it has previously proven useful for preliminary explorations of evolutionary history. We obtained DNA barcodes for 115 birds (34 species, 12 orders). Our data suggest that the existing DNA barcode reference library, built largely from sampling in the Americas, Europe, and east Asia, is generally sufficient for species identification in Qatar. Based on DNA barcode similarity, Qatar provides overwintering habitat to some species with apparent strong migratory connectivity and others with weaker migratory connectivity. Among locally breeding species, we found no evidence of hybridization between House Sparrows Passer domesticus (n = 16 males) and Spanish Sparrows P. hispaniolensis (n = 14 males), breeding simultaneously and in the same habitats, although in other locations of range overlap, habitat segregation and timing of breeding are hypothesized to be the primary reproductive barrier between them. Our results highlight the benefits of expanding the geographic range of genetic and ecological research.}, }
@article {pmid40665108, year = {2025}, author = {Thuwanut, P and Sirayapiwat, P and Roytrakul, S and Tuntiviriyapun, P and Suebthawinkul, C and Panyawongudom, N and Sereepapong, W}, title = {Peptidomic and Proteomic Signatures in Human Blood Serum, Follicular Fluid and Spent Media: A Study of Embryo Development Competency after In Vitro Fertilization.}, journal = {Reproductive sciences (Thousand Oaks, Calif.)}, volume = {32}, number = {8}, pages = {2654-2668}, pmid = {40665108}, issn = {1933-7205}, support = {RA65/026//Ratchadapisek Somphote Endowment Fund/ ; }, abstract = {This research aimed to investigate peptide barcodes and proteomic profiles in blood serum, follicular fluid, and spent media from infertile patients, focusing on their potential to retrieve good-quality embryo during in vitro fertilization (IVF). Biological samples were collected from 30 participants, equally comprising individuals who retrieved mature oocyte and developed or did not develop to good-quality blastocyst. Analysis of peptide barcodes and proteomic profiles was conducted using MALDI-TOF MS and nano-LC-ESI MS/MS. Subsequently, data peptide mass peak patterns, proteins and protein interaction networks were generated. Primary results in participants with good embryo development competency indicated that 448 of 1,792 peptide mass peaks were up-regulated in blood serum, 76 of 1,793 peptides in follicular fluid, and 51 of 1,610 peptides in spent media (fold-change ≥ 1.0, P < 0.05). Up-regulated proteins including angiomotin in blood serum, capping protein and janus kinase in follicular fluid were identified (edge confidence scores > 0.90). Additionally, spent media showed unique protein network involving ATP-dependent RNA helicase DDX19A and ankyrin repeat proteins via ubiquitin C protein (edge confidence score > 0.80). In conclusion, identified peptide barcodes and protein interaction networks in this study may offer novel insights into molecular mechanisms underlying embryo development competency after IVF treatment.}, }
@article {pmid40664616, year = {2025}, author = {Fu, Q and Li, Y and Lv, Y and Ye, T and Liu, X and He, C and Liu, X and Lu, Z and Shi, P}, title = {Fluorescent DNA-Polymer Enables Signal Amplification and Precise Protein Localization in Immunofluorescence Imaging.}, journal = {Analytical chemistry}, volume = {97}, number = {29}, pages = {15844-15854}, doi = {10.1021/acs.analchem.5c02025}, pmid = {40664616}, issn = {1520-6882}, mesh = {*DNA/chemistry ; Humans ; *Fluorescent Dyes/chemistry ; *Polymers/chemistry ; *Optical Imaging/methods ; Microscopy, Fluorescence ; }, abstract = {The DNA-barcoding method has revolutionized immunofluorescence imaging, offering a transformative approach to protein visualization and analysis. However, achieving effective signal amplification while maintaining precise target localization remains a critical challenge. In this study, we developed fluorescent DNA-polymer conjugates through enzyme-catalysis-mediated reversible addition-fragmentation chain transfer polymerization, enabling the attachment of multiple fluorescent molecules to a single DNA strand. Utilizing a straightforward one-step DNA complementation process, DNA-polymers facilitate in situ signal amplification without the need for complex DNA nanostructures. Unlike DNA self-assembly-based amplification techniques, this approach minimizes positional deviations caused by bulky DNA structures, thereby significantly enhancing the protein localization accuracy. We validated the precision of DNA-polymers in protein localization using stochastic optical reconstruction microscopy and demonstrated their signal amplification and multiplexed imaging capabilities in expansion microscopy and peripheral blood leukocyte analysis. This versatile platform enables a broad range of fluorescence imaging applications, including signal amplification, multiplexed protein imaging, and super-resolution imaging, positioning DNA-polymers as a powerful tool with immense potential to advance diverse areas of biological research.}, }
@article {pmid40663320, year = {2025}, author = {Matysiak, SM and Hellmuth, K}, title = {DNA-Encoded Peptide Library Synthesis and Applications, a Mini-Review.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2934}, number = {}, pages = {13-23}, pmid = {40663320}, issn = {1940-6029}, mesh = {*Peptide Library ; *DNA/chemistry/genetics ; Drug Discovery/methods ; Combinatorial Chemistry Techniques/methods ; Small Molecule Libraries/chemistry ; *Peptides/chemistry/chemical synthesis ; Humans ; Nucleic Acid Hybridization ; }, abstract = {DNA-encoded chemical libraries (DECLs) are an innovative technology that combines molecular biology and combinatorial chemistry to create and screen vast libraries of small molecules and peptides. DECLs, including DNA-encoded peptide libraries (DEPLs), leverage DNA as a molecular barcode, enabling the identification of binders through affinity selection and sequencing. Advanced techniques, such as DNA-encoded self-assembled chemical libraries (DESACLs), enhance library diversity by using DNA hybridization and self-assembly to produce dual pharmacophores, significantly advancing fragment-based drug discovery.The modular nature of DESACLs allows for dynamic assembly and combinatorial expansion, generating libraries with millions of combinations. This approach supports drug discovery by targeting complex biological interactions, such as protein-protein interfaces and provides a platform for molecular diagnostics.}, }
@article {pmid40661123, year = {2025}, author = {LaGreca, S and Crouch, U and Paul, A and Thomas, J and Thompson, J and Shaw, C and Cubeta, MA and Braun, U and Bradshaw, M}, title = {Hidden treasures of herbaria - even small collections contain a wealth of diversity: the powdery mildews of the North Carolina State Larry F. Grand Mycological Herbarium.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e156231}, pmid = {40661123}, issn = {2210-6340}, abstract = {The occurrence of cryptic species is well documented in fungi but the extent of their diversity is not fully understood. This study assessed the fungal diversity within a part of the Larry F. Grand Mycological Herbarium (NCSLG), a small, well-maintained collection at North Carolina State University, with a focus on the powdery mildew fungi (Erysiphaceae). Erysiphaceae were selected due to their economic impact as plant pathogens and availability of extensive DNA sequence data for multiple barcode loci. Our research objectives included determining the number of phylogenetic species compared with those identified morphologically, and to identify undescribed species. We generated sequence data for 220 of the 299 powdery mildew specimens (73% success rate) in the herbarium, which represented 60 species in 10 genera, collected from 134 host plant species. Our analyses revealed that ~83% (183/220) of the sequenced specimens had identifications that were incorrect and/or outdated based on current genus/species concepts. Additionally, four new species are described: Erysipheamphicarpaeicola, E.ulmi-alatae, E.quercus-virginianae, and Takamatsuellagrandii. A specimen deposited at NCSLG is designated as an epitype for Phyllactinialiriodendri, and a species of Phyllactinia identified on Carpinuscaroliniana, as well as multiple species infecting Quercus spp., likely represent additional undescribed species that require more data. This research highlights the critical role of herbarium collections in uncovering fungal biodiversity, and underscores the importance of preserving these valuable resources, particularly with the growing trend to discard herbaria due to financial and space constraints.}, }
@article {pmid40660617, year = {2025}, author = {Mendonça, MB and Peixoto, LAW and Chamon, CC and Akama, A and de Santana, CD}, title = {Molecular phylogeny reveals a new species of ghost electric knifefish Porotergus Ellis 1912 (Gymnotiformes: Apteronotidae), from the Amazon basin.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70085}, pmid = {40660617}, issn = {1095-8649}, support = {FAPESP #2016/19075-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; FAPESP#2018/05084-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; CNPq#168395/2022-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; FAPESPA#2023/158693//Funda&#xe7;&#xe3;o Amaz&#xf4;nia de Amparo a Estudos e Pesquisas/ ; #0118003100//Financiadora de Estudos e Projetos/ ; PPBio3570//Programa de Pesquisa em Biodiversidade/ ; }, abstract = {A new species of ghost electric knifefish, Porotergus sambaibensis sp. nov., is described from the Javaés River, a tributary of the Araguaia River in Brazil. The new species was assigned to the genus Porotergus as the closest relative to Porotergus gimbeli through maximum likelihood reconstruction of a concatenated multilocus dataset. Additionally, the origin of adductor mandibulae, pars stegalis in P. sambaibensis sp. nov. provided further evidence to support the molecular hypothesis. External and internal anatomical characters diagnosed the new species. DNA barcode data were used to test species monophyly and its genetic divergence from other species in the clade. Porotergus sambaibensis sp. nov. is distinguished from its closely related species by the colour pattern of the trunk, dark brown; the lower count of total anal-fin rays, 146-160; the higher number of teeth rows on the dentary, two; the presence of premaxilla teeth; two prominent foramina on dorsal portion of hyomandibula and its distribution pattern; and the second basibranchial, unossified. The genetic divergence between the new species and its relatives ranged from 3.7% in P. gimbeli to 10.3% in Porotergus duende. The species was categorised as deficient data (DD) based on the International Union for Conservation of Nature (IUCN) criteria.}, }
@article {pmid40659347, year = {2025}, author = {Dykman, LN and Davis, DB and Blend, CK}, title = {NEOLEBOURIA MULLINEAUXAE N. SP. (TREMATODA: DIGENEA) AND ANOTHER OPECOELID FROM DEEP-SEA HYDROTHERMAL VENT FIELDS OFF CENTRAL AMERICA AND PAPUA NEW GUINEA, WITH SPECIES KEYS AND A COMPARISON TO MESOBATHYLEBOURIA.}, journal = {The Journal of parasitology}, volume = {111}, number = {4}, pages = {451-478}, doi = {10.1645/24-113}, pmid = {40659347}, issn = {1937-2345}, mesh = {Animals ; *Trematoda/classification/anatomy &amp; histology/genetics/ultrastructure ; *Fish Diseases/parasitology/epidemiology ; *Trematode Infections/veterinary/parasitology/epidemiology ; Hydrothermal Vents/parasitology ; Papua New Guinea/epidemiology ; *Perciformes/parasitology ; Pacific Ocean ; Microscopy, Electron, Scanning/veterinary ; Intestines/parasitology ; RNA, Ribosomal, 28S/genetics ; }, abstract = {Neolebouria mullineauxae n. sp. (Digenea: Opecoelidae), exhibiting remarkable morphological variation (i.e., 2 distinctive morphotypes), is described from the intestine of the zoarcid eelpout or pink vent fish, Thermarces cerberus, collected from deep-sea hydrothermal vent fields along the East Pacific Rise (EPR) off the west coast of Central America. It can be distinguished from its congeners by having a unique diagnostic combination of features including a small body and gonads that are smaller relative to body size, a prebifurcal genital pore, a cirrus pouch that extends posteriorly as far as the posterior margin of the ventral sucker while the anterior margin of the latter is either close to or overlaps the intestinal bifurcation, confluent vitelline fields within the posttesticular space, and vitelline follicles and eggs that are not as dense and few to moderate in number, respectively. This report introduces a new family (Zoarcidae) and genus (Thermarces) of fish infected by the genus Neolebouria, a new host record in that this is the first taxonomic description of a digenetic trematode from T. cerberus; a new geographic locality for Neolebouria (sensu stricto)-the East Pacific Ocean off the coast of Central America-and a life cycle of the new species within the hydrothermal vent biome is postulated, including the sporocyst stage which utilizes the glass limpet, Eulepetopsis vitrea, as a first intermediate host. Two immature digeneans (cf. Opecoelidae) are described herein, collected from vent fields off Papua New Guinea, and represent a new host record in that this is the first report of a digenetic trematode from the zoarcid eelpout, Pyrolycus manusanus. Based on molecular analysis of the 28S gene, N. mullineauxae n. sp. was 99.92% (1,218/1,219 base pairs [bp]) similar to Neolebouria georgiensis. It was genetically closer to a previously described vent digenean, Buticulotrema thermichthysi, than to Mesobathylebouria lanceolata, despite the new species sharing morphological characteristics with the genus Mesobathylebouria. The 2 distinctive morphotypes of N. mullineauxae n. sp. were genetically identical in the 28S and ITS2 barcoding regions, supporting their identity as a single species. Given the similarity of N. mullineauxae n. sp. to members of Mesobathylebouria morphologically and ecologically, a thorough comparison of both genera is presented, as well as new keys to species, and a plea offered for a more efficacious diagnostic suite of morphological characters to distinguish both genera.}, }
@article {pmid40657759, year = {2025}, author = {Monge, M and Giovanetti, SM and Ravishankar, A and Sadhu, MJ}, title = {Highly replicated experiments studying complex genotypes using nested DNA barcodes.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkaf146}, pmid = {40657759}, issn = {2160-1836}, support = {//Intramural Research Program of the National Human Genome Research Institute/ ; 1ZIAHG200401/GF/NIH HHS/United States ; }, abstract = {Many biological experiments involve studying the differences caused by genetic modifications, including genotypes composed of modifications at more than 1 locus. However, as the genotypes increase in number and complexity, it becomes a major challenge to independently generate and track the necessary number of biological replicate samples. A major development in genetic studies of large numbers of genotypes has been the use of barcode tracking. Inspired by such high-throughput studies, we developed a barcode-based method to track large numbers of independent replicates of a small number of combinatorial genotypes in a pooled format, enabling robust detection of subtle phenotypic differences. To construct a plasmid library of combinatorial genotypes, we utilized a nested serial cloning process to combine gene variants of interest that have associated DNA barcodes. The final plasmids each contain variants of multiple genes of interest, and a combined barcode that specifies the genotype of all the genes while also encoding a random sequence for tracking individual replicates. Sequencing of the pool of barcodes by next-generation sequencing allows the whole population to be studied in a single flask, enabling a high degree of replication even for complex genotypes. Using this approach, we tested the functionality of combinations of yeast, human, and null orthologs of the nucleotide excision repair factor I (NEF-1) complex and found that yeast cells expressing all 3 yeast NEF-1 subunits had superior growth in DNA-damaging conditions. We also assessed the sensitivity of our method by simulating downsampling of barcodes across different degrees of phenotypic differentiation. Our results demonstrate the utility of NICR (nested identification combined with replication) barcodes for high-throughput combinatorial genetic screens and provide a scalable framework for exploring complex genotype-phenotype relationships.}, }
@article {pmid40652458, year = {2025}, author = {Benton, N and Krokovsky, L and Gasparotto, A and Hunter, FF}, title = {New record of Psorophora howardii (Diptera: Culicidae) in Southern Ontario, Canada.}, journal = {Journal of medical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jme/tjaf096}, pmid = {40652458}, issn = {1938-2928}, abstract = {Psorophora howardii Coquillett is a large floodwater mosquito native to much of the tropical and subtropical regions of the Americas, including the southern United States, several Caribbean Islands, and portions of Central and South America. Although it is recognized as a nuisance species, substantial gaps exist in the known range of Ps. howardii. In September 2024, multiple adults (2 males and 4 females) of Ps. howardii were collected at 2 different locations in Windsor-Essex County, Ontario, Canada. Specimens were collected during routine West Nile virus mosquito surveillance using CDC miniature light traps, using UV light and CO2, and a BG-Sentinel trap. Morphological identifications were confirmed using DNA barcoding (cytochrome oxidase I gene). This constitutes the first official record of Ps. howardii in Canada and is the northernmost record for the species (~42°N latitude). The detection of Ps. howardii at 2 locations, separated by 26 km, suggests established populations are present in southern Ontario, Canada. This discovery highlights the need for continued mosquito surveillance to monitor the northward expansion of mosquito species.}, }
@article {pmid40649794, year = {2025}, author = {Leng, Z and Pang, Z and He, Z and Gao, Q}, title = {Comparative Analysis of Chloroplast Genomes of 19 Saxifraga Species, Mostly from the European Alps.}, journal = {International journal of molecular sciences}, volume = {26}, number = {13}, pages = {}, pmid = {40649794}, issn = {1422-0067}, support = {2023-SF-A5//Qinghai Provincial Science and Technology Major Project/ ; xbzg-zdsys-202203//the Chinese Academy of Sciences (CAS) International Innovation Team/ ; }, mesh = {*Genome, Chloroplast ; Phylogeny ; *Saxifragaceae/genetics/classification ; Chloroplasts/genetics ; Evolution, Molecular ; Europe ; Microsatellite Repeats ; }, abstract = {Complete chloroplast genome sequences are widely used in the analyses of phylogenetic relationships among angiosperms. As a species-rich genus, species diversity centers of Saxifraga L. include mountainous regions of Eurasia, such as the Alps and the Qinghai-Tibetan Plateau (QTP) sensu lato. However, to date, datasets of chloroplast genomes of Saxifraga have been concentrated on the QTP species; those from European Alps are largely unavailable, which hinders comprehensively comparative and evolutionary analyses of chloroplast genomes in this genus. Here, complete chloroplast genomes of 19 Saxifraga species were de novo sequenced, assembled and annotated, and of these 15 species from Alps were reported for the first time. Subsequent comparative analysis and phylogenetic reconstruction were also conducted. Chloroplast genome length of the 19 Saxifraga species range from 149,217 bp to 152,282 bp with a typical quadripartite structure. All individual chloroplast genome included in this study contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs. The IR boundaries keep relatively conserved with minor expansion in S. consanguinea. mVISTA analysis and identification of polymorphic loci for molecular markers shows that six intergenic regions (ndhC-trnV, psbE-petL, rpl32-trnL, rps16-trnQ, trnF-ndhJ, trnS-trnG) can be selected as the potential DNA barcodes. A total of 1204 SSRs, 433 tandem repeats and 534 Large sequence repeats were identified in the 19 Saxifraga chloroplast genomes. The codon usage analysis revealed that Saxifraga chloroplast genome codon prefers to end in A/T. Phylogenetic reconstruction of 33 species (31 Saxifraga species included) based on 75 common protein coding genes received high bootstrap support values for nearly all identified nodes, and revealed a tree topology similar to previous studies.}, }
@article {pmid40645994, year = {2025}, author = {Christodoulou, M and Derycke, S and Beentjes, KK and Hillewaert, H and Laakmann, S and Lundin, K and Kamyab, E and Khodami, S and Maes, S and Reiss, H and Uhlir, C and Van den Bulcke, L and Van der Hoorn, B and De Backer, A and Arbizu, PM}, title = {A taxonomically reliable DNA barcode reference library for North Sea macrobenthos.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {1198}, pmid = {40645994}, issn = {2052-4463}, support = {GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; GEANS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; }, mesh = {*DNA Barcoding, Taxonomic ; North Sea ; Animals ; *Gene Library ; *Aquatic Organisms/genetics/classification ; Ecosystem ; Environmental Monitoring ; }, abstract = {EU directives (e.g. MSFD, Habitats Directive), along with OSPAR guidelines, mandate sustainable marine resource management across national borders. Benthic organisms are crucial for assessing marine ecosystem health, but their morphological identification is time-consuming and costly. High-throughput sequencing, particularly DNA metabarcoding, offers an alternative. However, DNA-based monitoring requires substantial investment in high-quality DNA reference libraries. The GEANS project (Genetic Tools for Ecosystem Health Assessment in the North Sea Region) aimed to develop efficient DNA-based tools for benthic biomonitoring. GEANS created a curated DNA reference library (COI) for species relevant to North Sea macrobenthos monitoring, using new sequences, non-public barcode sequences, and mined sequences from GenBank and BOLD. The library, stored in a dedicated BOLD project with photographs and metadata, includes DNA barcodes for 4005 specimens from 715 species, representing over 29% of North Sea macrobenthos species. Arthropoda is the most represented, while Bryozoa and Annelida have the lowest coverage. This DNA library is expected to facilitate fast, cost-effective environmental health assessments in the North Sea for public authorities and academics.}, }
@article {pmid40644439, year = {2025}, author = {Bibi, R and Qasmi, N and Rashid, S}, title = {Cysteine pattern barcoding-based dataset filtration enhances the machine learning-assisted interpretation of Conus venom peptide therapeutics.}, journal = {PloS one}, volume = {20}, number = {7}, pages = {e0327578}, pmid = {40644439}, issn = {1932-6203}, mesh = {*Conus Snail/chemistry ; Animals ; *Machine Learning ; *Cysteine/chemistry ; *Peptides/chemistry/therapeutic use ; *Mollusk Venoms/chemistry ; Conotoxins/chemistry ; Amino Acid Sequence ; }, abstract = {Crude cone snail venom is a rich source of bioactive compounds with significant therapeutic potential. In this study, we conducted a comprehensive analysis of 5,985 cone snail peptides across 82 Conus species to identify unique cysteine (Cys) patterns and associated frameworks. The classification of these Cys patterns, based on conserved framework combinations, enabled the generation of species-level pattern barcodes. These barcodes were then evaluated to assess the species correlations of individual sequences. By analyzing 151 known Conus peptide PDB files, we computed Cys disulfide linkages to assess overall stability profiles. Incorporating barcode data allowed us to filter the dataset and prepare it for machine learning (ML) processing. Random Forest (RF) modeling, a supervised learning technique, was used to predict the therapeutic potential of venom peptides. Feature extraction was based on known venom-derived approved peptide-based drugs. The dataset was split into a 70:30 train-test ratio. A total of 6,430 peptides (5,985 from cone snails and 445 from other venomous species) were used to evaluate model prediction capability. The proposed model achieved ideal accuracy (90.48%) in peptide therapeutic classification. Subsequent model outputs underwent further structural and binding pattern analysis against known targets, revealing significant similarities between the binding patterns of approved and novel peptides. The model's performance could be further enhanced by incorporating additional datasets and optimizing feature selection, potentially broadening its applicability to larger peptide datasets. Overall, this study underscores the potential of ML in advancing pharmacological research on diverse venom peptides.}, }
@article {pmid40643763, year = {2025}, author = {Naqvi, SAH and Abbas, A and Hasnain, A and Bilal, Z and Hakim, F and Shabbir, M and Amin, A and Iqbal, MU}, title = {Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.}, journal = {Archives of microbiology}, volume = {207}, number = {9}, pages = {192}, pmid = {40643763}, issn = {1432-072X}, mesh = {*Fungi/genetics/classification/isolation &amp; purification ; *Machine Learning ; *Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; Mycoses/microbiology/diagnosis ; Humans ; Genome, Fungal ; DNA, Fungal/genetics ; }, abstract = {The study of fungal genetics has undergone transformative advancements in recent decades, profoundly reshaping our understanding of fungal diversity, evolution, and pathogenesis. This review synthesizes cutting-edge molecular techniques revolutionizing fungal diagnostics, with a focus on DNA fingerprinting, next-generation sequencing (NGS), and third-generation sequencing (TGS), alongside their applications in species identification, phylogenetic reconstruction, and disease management. We critically evaluated the utility of molecular markers such as the Internal Transcribed Spacer (ITS), Large Subunit (LSU), and protein-coding genes (e.g., RPB1, RPB2, TEF1-α), which have emerged as indispensable tools for resolving taxonomic ambiguities and cryptic species complexes. While ITS remains the gold standard for fungal barcoding due to its high interspecific variability, multi-locus strategies integrating loci like β-tubulin and CaM enhance resolution in challenging genera such as Aspergillus, Fusarium, and Penicillium. The review underscores the limitations of traditional morphology-based taxonomy, particularly its inability to address cryptic speciation or non-reproductive fungal phases. Advances in NGS platforms (e.g., Illumina, PacBio, Oxford Nanopore) have overcome these barriers, enabling high-throughput genomic analyses that reveal unprecedented fungal diversity in environmental and clinical samples. TGS technologies, with their long-read capabilities (> 10 kb), now facilitate the assembly of complex genomes, identification of structural variants, and exploration of horizontal gene transfer events, offering new insights into fungal adaptation and pathogenicity. Despite these breakthroughs, challenges persist in resolving intragenomic variation, reconciling gene tree discordance, and standardizing workflows for large-scale fungal population studies. The integration of multi-omics approaches (transcriptomics, proteomics, metabolomics) and machine learning algorithms promises to address these gaps, enabling predictive modeling of antifungal resistance and host-pathogen interactions. Collaborative efforts among mycologists, clinicians, and bioinformaticians are critical to harmonizing data sharing, refining diagnostic pipelines, and translating genomic insights into precision therapies. Fungal-related diseases pose escalating threats to global agriculture, healthcare, and ecosystem stability. Climate change further exacerbates pathogen spread and antifungal resistance, necessitating innovative management strategies. Emerging tools such as CRISPR-based diagnostics, portable sequencers (MinION), and synthetic biology platforms hold promise for real-time pathogen surveillance and engineered biocontrol solutions. By bridging genomic innovation with interdisciplinary collaboration, this review charts a roadmap for advancing fungal diagnostics, enhancing taxonomic clarity, and mitigating the socio-economic impacts of fungal diseases in an era of rapid environmental change.}, }
@article {pmid40642435, year = {2025}, author = {Oliver, PG and Garzia, M and Paulay, G and Salvi, D}, title = {On the species identity of a tropical oyster (Bivalvia, Ostreidae, Dendostrea) invading the eastern Mediterranean Sea.}, journal = {ZooKeys}, volume = {1243}, number = {}, pages = {207-224}, pmid = {40642435}, issn = {1313-2989}, abstract = {Molecular and morphological data suggest that the Mediterranean populations of the non-indigenous genus Dendostrea are part of a single clade. This clade includes oysters from Rodrigues but is distinct from oysters from Hawaii and Mauritius. Based on morphology and sequence data, the Hawaiian and Mauritian oysters can be referred to as Dendostreasandvichensis Sowerby, 1871. The Mediterranean/Rodrigues clade, although morphologically very similar to D.sandvichensis, is significantly genetically distant from it and from D.frons and D.folium. As a result, the Mediterranean/Rodrigues clade cannot be assigned to any currently accepted nominal species. However, the statuses of the junior synonyms of D.sandvichensis are based on morphology and are therefore reconsidered with the result that D.crenulifera Sowerby, 1871 is shown to be morphologically very similar to the Mediterranean/Rodrigues clade. Given that the type locality of D.crenulifera is the Red Sea, and that Mediterranean populations are considered tropical invaders, D.crenulifera is a likely candidate name. However, without supporting sequence data from the type locality in the Red Sea, we conservatively conclude that the most appropriate name for the Mediterranean/Rodrigues clade is Dendostreacf.crenulifera (Sowerby, 1871).}, }
@article {pmid40642432, year = {2025}, author = {Xu, Y and Chen, J and Kholmatov, BR and Jiang, LY and Qiao, GX}, title = {Amphicercidus (Hemiptera, Aphidinae, Macrosiphini) species in China: two synonyms and two new records.}, journal = {ZooKeys}, volume = {1243}, number = {}, pages = {29-49}, pmid = {40642432}, issn = {1313-2989}, abstract = {Amphicercidus Oestlund, 1923 is distinguished from other aphid genera by a body in life heavily covered with white wax powder, antennal segment III rather long and with numerous secondary rhinaria, body dorsal setae long and pointed, the second hind tarsal segment longer than the ultimate rostral segment, siphunculi as long stout cylinders, and cauda broad and short. Based on the examination of Chinese specimens, two species were found to be synonyms of Amphicercidusjaponicus (Hori, 1927): Amphicercidusforsythiae Zhang, Zhong &amp; Zhang, 1992, syn. nov. and Amphicercidussinilonicericola Zhang, 1980, syn. nov. Additionally, Amphicerciduspulverulens (Gillette, 1911) and Amphicercidustuberculatus David, Narayanan &amp; Rajasingh, 1971 are reported here as new records for China. Additionally, Lonicera (Caprifoliaceae) is a new host plant record for Amphicerciduspulverulens. The DNA barcodes for A.japonicus, A.pulverulens and A.tuberculatus have been obtained, with the barcodes of A.pulverulens and A.tuberculatus being acquired for the first time. Keys to Chinese species in this genus are presented.}, }
@article {pmid40642430, year = {2025}, author = {Muñoz, I and Clark, PF and Cuesta, JA}, title = {The systematic status of Afropisasanctaehelenae (Chace, 1966) (Decapoda, Brachyura, Majoidea, Epialtidae): morphological and molecular evidence.}, journal = {ZooKeys}, volume = {1243}, number = {}, pages = {225-240}, pmid = {40642430}, issn = {1313-2989}, abstract = {Afropisasanctaehelenae (Chace, 1966) was originally described from three specimens collected from Saint Helena Island, South Atlantic, and assigned to Pisa Leach, 1814. It is a poorly known species, and until now, no new records have been reported. Recently, this species was transferred to a new genus, Afropisa Muñoz, García-Raso, González, Lopes, dos Santos &amp; Cuesta, 2023, based exclusively on morphology. Nearly 60 years on from the original description, another eight specimens of A.sanctaehelenae have been made available for further study and sequencing. Mitochondrial 16S rRNA and cytochrome c oxidase subunit I sequences confirm the assignment of this Chace species to Afropisa. Photographs of the male holotype and female paratype confirmed the presence of additional characters; consequently, the present work provides a redescription of this species.}, }
@article {pmid40642429, year = {2025}, author = {Reemer, M and Mengual, X}, title = {Revision of the Neotropical species of the hoverfly genus Serichlamys Curran, 1925 (Diptera, Syrphidae, Microdontinae).}, journal = {ZooKeys}, volume = {1243}, number = {}, pages = {51-106}, pmid = {40642429}, issn = {1313-2989}, abstract = {The Neotropical species of the hoverfly genus Serichlamys Curran, 1925 are revised. A total number of 14 Neotropical species are recognized, two of which were previously described, namely S.mitis (Curran, 1940) and S.mus (Curran, 1936). The other 12 species are here described for the first time: S.boti Reemer, sp. nov., S.chloraspis Reemer, sp. nov., S.melamitis Reemer, sp. nov., S.mellimitis Reemer, sp. nov., S.pallitarsis Reemer &amp; Mengual, sp. nov., S.serpentiphallus Reemer, sp. nov., S.simpliciphallus Reemer, sp. nov., S.spathulata Reemer, sp. nov., S.trigonoides Reemer, sp. nov., S.varicaudata Reemer &amp; Mengual, sp. nov., S.vexilliphallus Reemer &amp; Mengual, sp. nov., and S.xanthocnemia Reemer, sp. nov. An identification key is provided including all the recognised species. The distribution of the genus in the Neotropical region is shown to be disjunct, with one group of species in the northwest of the South American landmass and another group in southeastern Brazil.}, }
@article {pmid40642427, year = {2025}, author = {Qiao, CH and Xu, YQ and Wang, HS}, title = {A new genus of Orgyiini (Lepidoptera, Erebidae, Lymantriinae) from China, with description of a new species.}, journal = {ZooKeys}, volume = {1243}, number = {}, pages = {131-142}, pmid = {40642427}, issn = {1313-2989}, abstract = {A new genus, Cyclomacula Qiao &amp; Wang, gen. nov., is established to accommodate a new species and three new combinations from China: C.medogensis Qiao &amp; Wang, sp. nov., C.glaucinoptera (Collenette, 1934), comb. nov., C.dudgeoni (Swinhoe, 1907), comb. nov. and C.flavimacula (Moore, 1865), comb. nov. Images of adults and genitalia of all currently recognized Cyclomacula species are provided, with illustrations of wing venation of the type species in the new genus. A key to species of the genus is presented, along with DNA barcode data.}, }
@article {pmid40638508, year = {2025}, author = {Cardoso, SF and Pinheiro, IC and Kikuti, LAO and Yoshikawa, AAG and Pitaluga, AN and Rona, LDP}, title = {Expanded range of Haemagogus leucocelaenus in yellow fever hotspots: new findings from Santa Catarina State, southern Brazil.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {120}, number = {}, pages = {e240240}, pmid = {40638508}, issn = {1678-8060}, mesh = {Brazil ; Animals ; Yellow Fever/transmission ; *Mosquito Vectors/classification/genetics/anatomy &amp; histology ; Polymerase Chain Reaction ; *Culicidae/classification/genetics/anatomy &amp; histology ; Female ; Electron Transport Complex IV/genetics ; Male ; Phylogeny ; *Animal Distribution ; }, abstract = {BACKGROUND: The Haemagogus genus includes nine mosquito species reported in Brazil, each with distinct distribution patterns. Haemagogus leucocelaenus, a major yellow fever vector, is widely distributed throughout the country, while Haemagogus leucophoebus, a morphologically similar species, has only been identified in Acre State.<br><br>OBJECTIVES: This study evaluated the presence of Haemagogus species in southern Brazil by comparing their morphological and molecular characteristics.<br><br>METHODS: Mosquitoes were collected from five municipalities in southern Santa Catarina State, Brazil. Each specimen was identified morphologically and photographed. Genomic DNA was extracted, and a Cytochrome C Oxidase Subunit I (COI) gene fragment was amplified using polymerase chain reaction (PCR). The positive amplicons were sequenced for molecular identification.<br><br>FINDINGS: New records of Hg. leucocelaenus were found in Santa Rosa de Lima, Rio Fortuna, Bra&#xe7;o do Norte, S&#xe3;o Martinho, and Pedras Grandes, located at the southern edge of the Atlantic Forest. This study expands the known distribution of Hg. leucocelaenus, the only Haemagogus species identified in the area, with 91 specimens collected. Although some specimens exhibited morphological variations that might lead to misidentification as Hg. leucophoebus, molecular identification confirmed that all were Hg. leucocelaenus.<br><br>MAIN CONCLUSIONS: This study is the first to report Hg. leucocelaenus in Santa Catarina, Brazil, and provides DNA barcoding sequences from southern Brazil. This method offers a reliable alternative for species identification, especially when combined with morphological analysis. Further molecular studies are needed to determine whether the morphological variations observed indicate intraspecific differences.}, }
@article {pmid40638159, year = {2025}, author = {Sekiguchi, S and Kohtsuka, H and Kakui, K}, title = {First Record of the Deep-Sea Sea Spider Bathypallenopsis californica (Arthropoda: Pycnogonida) from the Northwestern Pacific, with a Note on an Attached Crinoid.}, journal = {Zoological science}, volume = {42}, number = {3}, pages = {335-341}, doi = {10.2108/zs250004}, pmid = {40638159}, issn = {0289-0003}, mesh = {Animals ; Male ; Pacific Ocean ; Animal Distribution ; *Arthropods/anatomy &amp; histology/genetics/classification ; Phylogeny ; *Spiders/anatomy &amp; histology ; Electron Transport Complex IV/genetics ; }, abstract = {We report the first record of the pallenopsid pycnogonid species Bathypallenopsis californica (Schimkewitsch, 1893) from the northwestern Pacific. Based on one male specimen collected from 1987-2007 m depth off the southeastern coast of Hokkaido, Japan, we redescribe the species and present its cytochrome c oxidase subunit I (COI) sequence for use in future DNA barcoding. We found a cystidean-stage crinoid on the leg-1 femur of the sea spider, representing the first record of a cystidean found on a sea spider. BLAST searches for COI and 28S sequences revealed that the crinoid was Florometra asperrima (Clark, 1907).}, }
@article {pmid40636447, year = {2025}, author = {Heng, X and Li, F and Xie, D and Wang, A and Liu, C and Yang, Y}, title = {Species diversity of oysters (Mollusca, Bivalvia) in the intertidal zone of Hainan Island revealed by DNA barcoding analysis.}, journal = {ZooKeys}, volume = {1241}, number = {}, pages = {247-260}, pmid = {40636447}, issn = {1313-2989}, abstract = {The family Ostreidae (Mollusca, Bivalvia) is an important component of marine ecosystems. The unique location and marine environment of Hainan Island provide diverse habitats for oysters. However, in recent years, oyster resources of Hainan Island have been under severe threats due to environmental pollution and habitat destruction. To better protect and utilize these biological resources, this study conducted systematic identification of naturally distributed oysters on Hainan Island using DNA barcoding technology. The results revealed the presence of 17 lineages, belonging to 14 species of oysters. The interspecies genetic distances for the COI gene sequences ranged from 10.09% to 31.72%, with notable DNA barcode gaps observed between intra- and interspecies. Additionally, the interspecies genetic distances for the 28S rRNA gene sequences varied between 0.24% and 14.03%. The DNA barcoding analysis indicated the existence of cryptic lineages within Saccostreacuccullata (Born, 1778). Furthermore, the study highlighted that Saccostreamalabonensis (Faustino, 1932) is the most prevalent and dominant species along the Hainan Island coastline, attributed to its ability to adapt to a wide range of salinity levels. When comparing the species diversity of oysters between the western and eastern coasts of Hainan Island, it was found to be higher on the western coast. This disparity is likely influenced by geographical factors and human activities. Specifically, the western coast, situated in the Beibu Gulf, benefits from relatively stable water quality and numerous river inflows, providing abundant phytoplankton and optimal growth conditions for oyster larvae. Conversely, the eastern coast experiences frequent human activities, such as aquaculture and tourism, which may contribute to the decline in species diversity in this region. Overall, this study enhances our understanding of the species diversity of oysters on Hainan Island and provides scientific evidence that is crucial for the development, protection, and sustainable utilization of these valuable oyster resources.}, }
@article {pmid40634378, year = {2025}, author = {Pizzigalli, C and Regalla, A and Palmeirim, AF and Palma, L and Lopes-Lima, M and Razgour, O and Godinho, R and Intipe, WA and Brito, JC}, title = {Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24703}, pmid = {40634378}, issn = {2045-2322}, support = {2020.05054.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; FCT - InBIO Program&#xe1;tico FUI 2020-2023 (UIDP/50027/2020)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECINSTLA/00020/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.07926. CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECINST/00014/2018/CP1512/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; Projects GW_ICE-01, GW_CIB_02 and 03//Elephant Crisis Fund (Save the Elephants/Wildlife Conservation Network)/ ; }, mesh = {*Alligators and Crocodiles/genetics/physiology/classification ; Animals ; Guinea-Bissau ; *Conservation of Natural Resources ; *Biodiversity ; Ecosystem ; }, abstract = {Challenges in freshwater organism conservation in West Africa are worsened by significant knowledge gaps, even for charismatic species like crocodiles. This study addresses these gaps by assessing crocodile diversity, distribution, and conservation threats in Guinea-Bissau, where existing data is outdated. We used visual surveys, inquiries, molecular barcoding, camera trapping, and bibliographic reviews to investigate crocodile populations. Notably, we found evidence suggesting the Nile crocodile (Crocodylus niloticus), previously thought extinct in West Africa since about 200 years, may persist in Guinea-Bissau's Cacheu region. We also confirmed the presence of the West African crocodile (Crocodylus suchus) in major river basins and coastal lagoons, including the Bijagós Archipelago, and the West African dwarf crocodile (Osteolaemus cf. tetraspis) in the southern mainland and the Bijagós Archipelago. Habitat loss and deliberate killings were identified as major threats. Standardized surveys and genetic sampling are essential to assess population size, connectivity, and genetic diversity, informing evolutionary studies and conservation planning. Conservation efforts should prioritize habitat protection through community-managed reserves and restoration initiatives. Additionally, engaging local communities to raise awareness and develop conflict mitigation strategies is crucial, particularly in areas with human-crocodile interactions.}, }
@article {pmid40633110, year = {2025}, author = {Cheng, W and Zeng, W and Fan, J and Li, J and Wu, Y and Chen, Y and Yang, X and Wang, K and Huang, J}, title = {Molecular Encoded Beads with DNA Duplex Programming Fluorophore-Quencher Distance for Multiplexed Detection.}, journal = {Analytical chemistry}, volume = {97}, number = {28}, pages = {15199-15207}, doi = {10.1021/acs.analchem.5c01774}, pmid = {40633110}, issn = {1520-6882}, mesh = {*Fluorescent Dyes/chemistry ; *DNA/analysis/chemistry ; Fluorescence Resonance Energy Transfer ; Flow Cytometry ; Microspheres ; }, abstract = {Currently, the leading-edge bead encoding technique adopts the dye-doped strategy, which requires the construction of an encoded bead library in advance and is limited by strict material and technical barriers. Here, we report a simple, versatile, and plug-and-play bead encoding strategy, which uses bead surface DNA encoding instead of a dye-doped strategy. This is a fluorophore-quencher (F-Q) distance encoded strategy through the different Q-labeled positions at the DNA duplex, thereby changing the FRET efficiency. The strategy can simultaneously realize target capture and encoding on a bead surface, which greatly simplifies the process and reduces detection costs. In this work, we encoded 9-plex barcodes through the strategy and decoded them by 2-channel fluorescence flow cytometry. It is a modular technique that enables seamless integration with additional signal amplifier units. Herein, we constructed three kinds of multiplexed nucleic acid detection models, including "direct capture", "capture and then amplify", and "amplify and then capture", that enrich the encoding toolbox for bead-based multiplexed detection.}, }
@article {pmid40632720, year = {2025}, author = {Shumba, K and Bor, J and Nattey, C and Gareta, D and Lauren, E and Macleod, W and Fox, MP and Puren, A and Mlisana, K and Onoya, D}, title = {Record linkage without patient identifiers: Proof of concept using data from South Africa's national HIV program.}, journal = {PLOS global public health}, volume = {5}, number = {7}, pages = {e0004835}, pmid = {40632720}, issn = {2767-3375}, support = {R01 AI152149/AI/NIAID NIH HHS/United States ; }, abstract = {Linkage between health databases typically requires patient identifiers such as names and personal identification numbers. We developed and validated a record linkage strategy to combine administrative health databases without identifiers for South Africa's public sector HIV program. We linked CD4 counts and HIV viral loads from South Africa's TIER.Net with the National Health Laboratory Service (NHLS) database for patients receiving care between 2015-2019 in Ekurhuleni District (Gauteng Province). Linkage variables were result value, specimen collection date, facility of collection, year and month of birth, and sex. We used three matching strategies: exact matching on exact values of all variables, caliper matching allowing a ± 5 day window on result date, and specimen barcode matching using unique specimen identifiers. A sequential linkage approach applied specimen barcode, followed by exact, and then caliper matching. Exact and caliper matching were validated using barcodes (available for 34% of records in TIER.Net) as a "gold standard". Performance measures were sensitivity, positive predictive value (PPV), share of patients linked, and percent increase in data points. We attempted to link 2,017,290 laboratory test results from TIER.Net (523,558 unique patients) with 2,414,059 NHLS test results. Exact matching achieved 69.0% sensitivity and 95.1% PPV. Caliper matching achieved 75% sensitivity and 94.5% PPV. Sequential linkage matched 41.9% using specimen barcodes, 51.3% through exact matching, and 6.8% through caliper matching, for 71.9% (95% CI: 71.9, 72.0) of test results matched overall, with 96.8% (95% CI: 96.7, 97.1) PPV and 85.9% (95% CI: 85.7, 85.9) sensitivity. This linked 86.0% (95% CI: 85.9, 86.1) of TIER.Net patients to the NHLS (N = 1,450,087), increasing laboratory results in TIER.Net by 62.6%. Linkage of TIER.Net and NHLS without patient identifiers attained high accuracy and yield without compromising privacy. The integrated cohort provides a more complete laboratory test history and supports more accurate HIV program indicator estimates.}, }
@article {pmid40631198, year = {2025}, author = {Villegas, NK and Tran, MH and Keller, A and Plesa, C}, title = {BAR-CAT: Targeted Recovery of Synthetic Genes via Barcode-Directed CRISPR-dCas9 Enrichment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.06.27.658158}, pmid = {40631198}, issn = {2692-8205}, abstract = {Modern gene-synthesis platforms let us probe protein function and genome biology at unprecedented scale. Yet in large, diverse gene libraries the proportion of error-free constructs decreases with length due to the propagation of oligo synthesis errors. To rescue these rare, error-free molecules we developed BAR-CAT (Barcode-Assisted Retrieval CRISPR-Activated Targeting), an in-vitro enrichment method that couples unique PAM-adjacent 20-nt barcodes to each library member and uses multiplexed dCas9-sgRNA complexes to fish out the barcodes corresponding to perfect assemblies. After a single 15-min reaction and optimized wash regime (BAR-CAT v1.0), three low-abundance targets in a 300, 000-member test library were enriched 600-fold, greatly reducing downstream requirements. When applied to 384x and 1, 536x member DropSynth gene libraries, BAR-CAT retrieved up to 122-fold enrichment for 12 targets and revealed practical limits imposed by sgRNA competition and library complexity, which now guide ongoing protocol scaling. By eliminating laborious clone-by-clone validation and working directly on plasmid libraries, BAR-CAT provides a versatile platform for recovering perfect synthetic genes, subsetting large libraries, and ultimately lowering the cost of functional genomics at scale.}, }
@article {pmid40630932, year = {2025}, author = {Zajac, N and Zhang, Q and Bratus-Neuenschwander, A and Qi, W and Bolck, HA and Karakulak, T and Oltra, TC and Moch, H and Kahraman, A and Rehrauer, H}, title = {Comparison of single-cell long-read and short-read transcriptome sequencing via cDNA molecule matching: quality evaluation of the MAS-ISO-seq approach.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {3}, pages = {lqaf089}, pmid = {40630932}, issn = {2631-9268}, mesh = {*DNA, Complementary/genetics ; *Single-Cell Analysis/methods ; Humans ; *Transcriptome ; *Gene Expression Profiling/methods ; *Sequence Analysis, RNA/methods ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Single-cell RNA sequencing is used for profiling gene expression differences between cells. It can be performed with short reads, which provide high-throughput and high-quality information at the gene level, or with long reads, which provide isoform resolution via preserving full-length transcripts. It is, however, unclear how comparable the data is between the two methods. We investigate the types of bias introduced at the library preparation and the bioinformatic processing steps on the transcripts recovered from long- and short-read sequencing, and the effects of filtering, enabled by sequencing of full-length transcripts, on gene expression. For each sample, we sequenced the same 10x Genomics 3' complementary DNA (cDNA) using Illumina short reads and Pacific Biosciences long reads and cross-compared each molecule matched through cell barcode and unique molecular identifier. We find that both methods render highly comparable results and recover a large proportion of cells and transcripts. However, platform-dependent cDNA library processing and data analysis steps introduce biases. Short-read sequencing provided higher sequencing depth, but long-read sequencing allowed for retaining transcripts shorter than 500 bp and for removal of degraded cDNA contaminated by template switching oligos. Filtering of artefacts, identifiable only from full-length transcripts, reduces gene count correlation between the two methods.}, }
@article {pmid40630502, year = {2025}, author = {Meleshko, D and Yang, R and Maharjan, S and Danko, DC and Korobeynikov, A and Hajirasouliha, I}, title = {Blackbird: structural variant detection using synthetic and low-coverage long-reads.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf151}, pmid = {40630502}, issn = {2635-0041}, support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: Recent benchmarks show that most structural variations, especially within 50-10,000 bp range cannot be resolved with short-read sequencing, but long-read structural variant callers perform better on the same datasets. However, high-coverage long-read sequencing is costly and requires substantial input DNA. Reducing coverage lowers cost but significantly impacts the performance of existing structural variation (SV) callers. Synthetic long-read technologies offer long-range information at lower cost, but leveraging them for SVs under 50 kbp remains challenging.<br><br>RESULTS: We propose a novel hybrid alignment- and local-assembly-based algorithm, Blackbird, that uses synthetic long reads and low-coverage long reads to improve structural variant detection. Instead of relying on whole-genome assembly, Blackbird uses a sliding window approach and synthetic long-read barcode information to assemble local segments, integrating long reads to improve structural variant detection accuracy. We evaluated Blackbird on real human genome datasets. On the HG002 Genome in a Bottle (GIAB) benchmark, Blackbird in hybrid mode demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5 &#xd7; coverage to achieve F1-scores (0.835 and 0.808 for deletions and insertions) similar to PBSV and Sniffles2 using 10 &#xd7; PacBio Hi-Fi long-read coverage.<br><br>Blackbird is available at https://github.com/1dayac/Blackbird.}, }
@article {pmid40628719, year = {2025}, author = {Gencel, M and Cofino, GM and Hui, C and Sahaf, Z and Gauthier, L and Matta, C and Gagné-Leroux, D and Tsang, DKL and Philpott, DP and Ramathan, S and Menendez, A and Bershtein, S and Serohijos, AWR}, title = {Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {6314}, pmid = {40628719}, issn = {2041-1723}, support = {PG-408523//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; RGPIN-2016-06566//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; CRC-2022-00138//Canada Research Chairs (Chaires de recherche du Canada)/ ; 89967//National Research Foundation (NRF)/ ; }, mesh = {Animals ; *Escherichia coli/genetics/physiology/drug effects ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Microbial Interactions ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; }, abstract = {A microbiome's composition, stability, and response to perturbations are governed by its community interaction matrix, typically quantified through pairwise competition. However, in natural environments, microbes encounter multispecies interactions, complex conditions, and unculturable members. Moreover, evolutionary and ecological processes occur on overlapping timescales, making intra-species clonal diversity a critical but poorly understood factor influencing community interactions. Here, we present Dynamic Covariance Mapping (DCM), a general approach to infer microbiome interaction matrices from abundance time-series data. By combining DCM with high-resolution chromosomal barcoding, we quantify inter- and intra-species interactions during E. coli colonization in the mouse gut under three contexts: germ-free, antibiotic-perturbed, and innate microbiota. We identify distinct temporal phases in susceptible communities: (1) destabilization upon E. coli invasion, (2) partial recolonization of native bacteria, and (3) a quasi-steady state where E. coli sub-lineages coexist with resident microbes. These phases are shaped by specific interactions between E. coli clones and community members, emphasizing the dynamic and lineage-specific nature of microbial networks. Our results reveal how ecological and evolutionary dynamics jointly shape microbiome structure over time. The DCM framework provides a scalable method to dissect complex community interactions and is broadly applicable to bacterial ecosystems both in vitro and in situ.}, }
@article {pmid40628201, year = {2025}, author = {Saberi-Pirooz, R and Aghamir, F and Ahmadzadeh, F}, title = {Assessing the response of two soil engineering groups to reforestation in the Hyrcanian forests.}, journal = {Journal of environmental management}, volume = {391}, number = {}, pages = {126410}, doi = {10.1016/j.jenvman.2025.126410}, pmid = {40628201}, issn = {1095-8630}, mesh = {*Forests ; Animals ; *Ants ; Biodiversity ; Oligochaeta ; *Soil ; *Conservation of Natural Resources ; Ecosystem ; }, abstract = {Many forest ecosystems are becoming more vulnerable due to human activities and the considerable effects of forest exploitation. Furthermore, forest management practices often overlook the importance of biodiversity, focusing primarily on timber production and economic gain. The Hyrcanian forests, in particular, face significant challenges due to a combination of factors such as deforestation, climate change, and invasive species. This study aims to explore the impact of reforestation on the diversity, abundance, and community structure of two key groups of soil engineers: earthworms and ants. These groups were chosen due to findings from a previous study indicating their higher abundance in this region. Additionally, it aims to determine which of these groups is more significantly impacted. The study was conducted in both natural and planted forests across three locations in the central region of these forests. Samples were collected from 72 quadrats and 48 transects. A total of 251 samples were collected for earthworms and 410 samples for ants. Then, the samples were sorted into morphological operational taxonomic units (MorphOTUs) based on morphological characteristics. DNA barcoding studies were performed using the cytochrome c oxidase subunit 1 (COI) gene to determine the molecular OTUs. After that, the difference in OUT richness, abundance and composition between natural and planted forests was investigated using statistical analysis. In the current research, 16 and 19 OTUs were recognized for earthworms and ants, respectively. The results indicated that ant abundance was significantly higher in natural forests (n = 263) compared to planted forests (n = 147). However, the difference in earthworm numbers was negligible (n = 125 in natural and n = 126 in planted forests). The community compositions of both groups did not show significant differences between these forests. The difference between ants and earthworm abundance indicates that ants play a key role as pioneer species in the colonization process, followed by other groups (earthworms) that have settled in the planted forests. The study emphasizes the significance of a genetic approach to understanding the biodiversity of both groups. We believe that integrating both groups will improve the effectiveness of bioindicators in these areas. It is crucial to recognize the biodiversity of soil invertebrates for monitoring natural forests and developing effective reforestation policies, which are essential for fostering resilient ecosystems.}, }
@article {pmid40627868, year = {2025}, author = {Moreno-Torres, K and Prieto, C and Pyrcz, TW}, title = {Single-Locus species delimitation of Pronophilina butterflies (Nymphalidae: Satyrini) in the Colombian Andes: Congruence between morphology and MOTUs.}, journal = {Genome}, volume = {}, number = {}, pages = {}, doi = {10.1139/gen-2025-0041}, pmid = {40627868}, issn = {1480-3321}, abstract = {The subtribe Pronophilina (Nymphalidae: Satyrinae: Satyrini) is one of the most diverse subtribes within the Lepidoptera. In Colombia, these butterflies are distributed throughout the Andes, where they play a key role in montane ecosystems and exhibit high levels of endemism. Despite their complex genital morphology, species within the same genus often exhibit highly similar wing patterns, complicating taxonomic identification. In this study, we analyzed the concordance between DNA barcode-based species delimitation and morphological identifications using 334 cytochrome c oxidase subunit I (COI) barcodes from 94 a priori identified morphospecies in Colombia. We applied four molecular species delimitation methods (ABGD, RESL, PTP, and ASAP), delimitating between 98-108 molecular operational taxonomic units (MOTUs). Overall, the methods showed high consistency, with high congruence between morphological and molecular delimitations (81%). Additionally, 96.8% of the morphospecies exhibited a barcode gap, indicating clear genetic differentiation. However, we found some inconsistencies, including six cases of species merging and 12 cases of species splitting. Our findings underscore the utility of DNA barcoding for species delimitation in Pronophilina, while highlighting the need for integrative approaches to resolve taxonomic uncertainties in this diverse group.}, }
@article {pmid40624534, year = {2025}, author = {Ma, J and Jin, W and Rong, L and Gao, Z and Hazrat, Z and Shakhawat, HM and Long, F and Zhang, Z and Huang, J and Lu, X and Jin, G and Zhou, Z}, title = {IT-scC&amp;T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {196}, pmid = {40624534}, issn = {1474-760X}, support = {T13-602/21N//University Grants Committee/ ; KJ012019517//High-level Hospital Construction Project of Guangdong Provincial People's Hospital/ ; 2021B1515130004//Guangdong-Dongguan Joint Research Scheme Guangdong-Hong Kong-Macau Program/ ; JCYJ20210324 114408024//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; }, mesh = {*Single-Cell Analysis/methods ; Animals ; Mice ; Chromatin/metabolism ; *DNA/metabolism ; Female ; Transcription Factors/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Mammary Glands, Animal/metabolism ; Histone Code ; }, abstract = {Single-cell profiling protein-chromatin interactions is often constrained by complex workflows, high cost, or dependence on specialized equipment. We present indexed tagmentation-based single-cell CUT&amp;Tag-sequencing (IT-scC&amp;T-seq), a modular, plate-based strategy using three-round combinatorial barcoding. IT-scC&amp;T-seq robustly profiles histone modifications and transcription factors with high specificity and throughput, supporting simultaneous analysis of multiple samples and epitopes. Notably, it enables sensitive single-cell mapping of lamina-associated domains, low-abundance chromatin features previously difficult to resolve. Applied to adult mouse mammary gland, the method reveals cell-type-specific chromatin landscapes and lineage-regulatory dynamics. Together, IT-scC&amp;T-seq provides a scalable, cost-effective, and broadly accessible approach for high-resolution chromatin profiling.}, }
@article {pmid40624060, year = {2025}, author = {Maurya, S and Sukhramani, G and Lee, C and Jo, S and Kim, J and Jeong, EJ and Zamora, NA and Garcia, R and Zhang, Z and Choi, S and Choudhary, RK and Kim, SY}, title = {Comparative plastome evaluation, phylogenomic analysis, and DNA signatures of medicinally important malvaceous genera and their adulterants.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {24285}, pmid = {40624060}, issn = {2045-2322}, support = {313-5661-6703/2K23/1//CSIR/ ; IF210309//DST-INSPIRE/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; }, mesh = {Phylogeny ; *DNA, Plant/genetics ; *Plants, Medicinal/genetics/classification ; DNA Barcoding, Taxonomic ; Drug Contamination ; Microsatellite Repeats ; India ; }, abstract = {The Bala group of plants, classified under the Malvaceae family, is acknowledged in the Ayurvedic Pharmacopoeia of India and is well-known for its medicinal uses, especially in boosting vitality and addressing neurological and cardiovascular conditions. The key genera of this group, such as Sida and Abutilon, are highly valued in traditional medicine; however, the efficacy of herbal formulations is frequently compromised by adulterants from morphologically similar genera like Malvastrum and Malva. To address this critical challenge, our study focuses on plastome sequencing of various Bala group taxa and their adulterants, aiming to delineate DNA signatures for key species and provide a robust strategy against adulteration. Comprehensive analyses of plastomes from Sida, Abutilon, Malvastrum, and Malva reveal distinct indels, simple sequence repeats (SSRs), and tandem repeats across coding and non-coding regions, as well as potential DNA barcodes within specific intergenic regions. Investigations into gene composition, genetic variations, and nucleotide diversity further elucidate phylogenetic relationships within the Malveae tribe. Phylogenomic analyses clarify the placement of the Bala group and its adulterants, offering robust insights into their evolutionary context. This study underscores the utility of plastome-based approaches in safeguarding the authenticity of Bala group herbal drugs and highlights the broader implications for quality assurance in traditional medicine.}, }
@article {pmid40623487, year = {2025}, author = {Chotelersak, K and Machida, R and Thipaksorn, A and Samung, Y and Ruangsittichai, J}, title = {Mitochondrial COI barcoding of Pulicidae fleas and ultrastructural differentiation of the cat flea by scanning electron microscopy.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {133}, number = {}, pages = {105793}, doi = {10.1016/j.meegid.2025.105793}, pmid = {40623487}, issn = {1567-7257}, mesh = {Animals ; Microscopy, Electron, Scanning ; Phylogeny ; *Siphonaptera/genetics/classification/ultrastructure ; Cats ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Female ; Thailand ; }, abstract = {Fleas are widespread ectoparasites found across the globe-even in polar regions-and exhibit low host specificity, allowing them to infest both humans and animals, including birds. They feed on the blood of their hosts and serve as vectors for various infectious diseases, particularly in tropical and subtropical regions. In this study, the COI barcodes and ultrastructural characteristics using scanning electron microscopy (SEM) were performed to confirm classical morphological identification of cat flea taxonomic levels. Four species of medically important Pulicidae fleas were collected from hosts in various provinces of Thailand and identified based on their distinctive morphological characteristics: Xenopsylla cheopis, Echidnophaga gallinacea, Ctenocephalides felis and Ctenocephalides orientis. Phylogenetic analyses and calculated sequence distance based on mitochondrial COI barcodes were performed. The four species clearly formed monophyletic groups with low intraspecific distance (0 % -0.24 %) and high interspecific distance (4.60 % -21.26 %). Ctenocephalides felis and C. orientis were separated at the closely related level and separated into distinct clusters, with a sequence distance of 8.42 %. and C. orientis has shown closely genetic relationship with C. canis (4.60 %). Scanning electron microscopy (SEM) revealed ultrastructural characteristics that clearly differentiate C. felis and C. orientis, including differences in head shape and minute bristles on the dorsal end of the antennal fossa. Specifically, C. felis frons are elongated and pointed anteriorly, whereas C. orientis frons are short and rounded anteriorly. Additionally, the C. orientis female has 3-4-minute bristles at the dorsal end of the antennal fossa, while this structure is absent in the C. felis female but present and numerous (with 13-18 bristles) in all males of the genus Ctenocephalides. Fleas were identified, and their sex or ambiguous structures were determined using a stereoscope or low-power binocular microscope. DNA barcoding and ultrastructural analysis using SEM for differentiation of structures of taxonomic significance are useful for subspecies/species identification.}, }
@article {pmid40622985, year = {2025}, author = {Oladipo, SO and Everett, A and Durand, JD and Adelakun, KM and Dieudonne, WP and Maame, A and Nneji, IC and Ayoola, AO and Atofarati, OT and Kachi, JB and Nneji, LM}, title = {Morphology, DNA Barcoding and Range Extension of a Poorly Known Freshwater Stingray Fontitrygon garouaensis Stauch &amp; Blanc, 1962 from Nigerian Inland Water.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf125}, pmid = {40622985}, issn = {1557-7023}, abstract = {Increasingly sophisticated taxonomic tools have enhanced our understanding of species diversity and phylogenetic relationships in elasmobranchs. Nevertheless, ichthyologists continue to face challenges in resolving the taxonomic placement and authentication of some taxa, particularly those originally described based on morphology. The recently described genus Fontitrygon comprises several Atlantic dasyatid stingrays whose phylogenetic positions have remained unresolved due to the lack of molecular data. In this study, we employed an integrative taxonomic approach to identify and determine the phylogenetic position of the understudied Fontitrygon garouaensis from Nigeria. Specimens were collected from freshwater ecosystems along the Jebba and Lokoja stretches of the River Niger in Nigeria. Comparative morphological analysis distinguished F. garouaensis from other Fontitrygon species by the presence of a depressed central spine shaft with flanges extending along either side, a flattened oval disc, an obtuse snout, a whip-like tail bearing a sting, a broad and elongated snout, small pelvic fins, and radially arranged pectoral fins. Additionally, morphological measurements of the newly collected F. garouaensis were consistent with those of the syntype and holotype, confirming species identification. Phylogenetic analyses based on mitochondrial Cytochrome c Oxidase Subunit I (COI) gene sequences recovered Fontitrygon as a monophyletic lineage and identified F. garouaensis as the sister taxon to F. margarita and F. margaritella. This study provides an integrative taxonomic assessment of F. garouaensis, clarifying its species identity and confirming the presence of F. garouaensis from the upstream of the Jebba stretch of the River Niger. We, therefore, propose an update to its IUCN geographic range.}, }
@article {pmid40622584, year = {2025}, author = {Chen, X and Han, S and Zhao, D and Li, Z}, title = {Intraductal Injection of Adenoviruses to Perform Lineage Tracing in the Mammary Gland.}, journal = {Journal of mammary gland biology and neoplasia}, volume = {30}, number = {1}, pages = {10}, pmid = {40622584}, issn = {1573-7039}, support = {R01 CA222560/CA/NCI NIH HHS/United States ; SG-0062-10//Harvard Stem Cell Institute/ ; R01 CA222560/NH/NIH HHS/United States ; W81XWH-15-1-0100//U.S. Department of Defense/ ; }, mesh = {Animals ; Female ; *Cell Lineage ; *Adenoviridae/genetics ; Humans ; *Mammary Glands, Animal/pathology/metabolism/virology/cytology ; Mice ; *Mammary Glands, Human/pathology ; *Breast Neoplasms/pathology/genetics ; Integrases/genetics ; Epithelial Cells/metabolism ; Cell Differentiation ; }, abstract = {Lineage tracing is a fundamental tool in developmental biology and cancer research, providing critical insights into cell fate decisions, tissue homeostasis and tumor initiation. The mammary gland is a highly dynamic organ with a complex cellular hierarchy, making it an ideal system for lineage-tracing studies. Classic approaches, such as tamoxifen-inducible CreER/loxP recombination, have significantly advanced our understanding of mammary epithelial cell (MEC) differentiation, homeostasis, and transformation. However, these methods have limitations, including potential effects of tamoxifen on estrogen signaling, low mammary gland specificity, and the requirement for transgenic model creation and mouse breeding. Adenovirus-Cre (Ad-Cre)-based lineage tracing has emerged as a powerful alternative, enabling rapid and organ-specific recombination. This review provides a comprehensive evaluation of the Ad-Cre approach in mammary gland biology, comparing its efficiency, specificity, and technical advantages over the CreER-based method. We discuss applications of Ad-Cre intraductal injection-based lineage tracing in mapping MEC fates, identifying the cellular origins of breast cancer, and modeling tumor progression. Additionally, we highlight its ability to induce genetic marking at a clonal level, facilitating precise investigations into MEC plasticity and tumor cell heterogeneity. Despite its advantages, Ad-Cre lineage tracing also presents challenges, such as low cell-targeting efficiency and potential effect on the mammary gland immune microenvironment. Future advancements, including the integration of CRISPR-based barcoding, may further enhance its utility for high-resolution fate mapping. By summarizing recent advancements and comparative analyses, this review underscores the significance of Ad-Cre lineage tracing as a versatile and powerful tool in mammary gland biology and breast cancer research.}, }
@article {pmid40621477, year = {2025}, author = {Hayal, TB and Mulla, AA and Allan, DSJ and Duncan, BB and Joshi, S and Hong, SG and Basar, R and Rezvani, K and Childs, RW and Wu, C and Dunbar, CE}, title = {Optimization of lentiviral delivery of barcoded anti-CD20 chimeric antigen receptors into rhesus macaque and human natural killer cells.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {33}, number = {2}, pages = {101473}, pmid = {40621477}, issn = {2329-0501}, abstract = {Natural killer (NK) cells are pivotal in immunosurveillance and hold great potential for immunotherapy due to their ability to target malignant cells. Their low risk of causing graft-versus-host disease (GvHD) post-allogenic transplantation underscores their potential as an off-the shelf cellular therapy tool. Advances in genetic engineering focus on improving NK targeting, persistence, and fitness. However, NK cells pose challenges for lentiviral transduction, which are clinically relevant and safe. In this study, we identified Poloxamer 407 (P407) as a novel transduction enhancer for rhesus macaque (RM) and human NK cells. We found that P407 significantly improved transduction efficiency, achieving up to 60% in expanded RM NK cells, without compromising cell viability or functionality. Additionally, P407 facilitated the expression of anti-CD20 chimeric antigen receptors (CARs) with or without interleukin (IL)-15. In a xenograft mouse model, CAR-IL15 NK cells demonstrated superior anti-tumor activity, and maintained higher clonal diversity tracked by genetic barcoding compared to CAR-NK cells lacking IL-15 in vivo. Additionally, in human NK cells, P407 combined with the TBK1/IKKε inhibitor, BX795, further improved lentivirus-mediated transduction. This study is the first to engineer NK cells from a clinically relevant rhesus macaque model in an adaptive cell therapy context and highlights P407's potential as a transduction enhancer.}, }
@article {pmid40621193, year = {2025}, author = {Imran Hossain, NM and Jony, ME and Emon, SR and Sifat, NI and Rahman, MA and Shomrat, MGM and Jony, MMA}, title = {University Student's Knowledge, Practices, and Perceptions of Food Packaging Labels in Bangladesh: A Cross-Sectional Study.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {7}, pages = {e70567}, pmid = {40621193}, issn = {2048-7177}, abstract = {Food packaging labels play a crucial role in ensuring consumer safety and aiding informed decision-making. However, in Bangladesh, limited research exists on students' understanding and use of food packaging labels. This cross-sectional study assessed the knowledge, practices, and consumer preferences of food labeling among 397 students from various public and private universities across Bangladesh. A self-administered questionnaire, developed based on food safety regulations, was used for data collection. The study employed convenience sampling, and data analysis was conducted using SPSS 27.0, including descriptive statistics, Chi-square tests, and Spearman's rho correlation to evaluate relationships between knowledge and practices. The study found that 74.8% of students had adequate knowledge of food labeling, with high awareness of "Expiry Date" and "Nutritional Information," but limited understanding of "Batch Number" and "Packaging Symbols". Only 44.3% demonstrated good labeling practices, with gaps in checking "Best Before" dates, allergen content, and barcodes. Gender and residential background significantly influenced knowledge and practices (p < 0.001), with females and urban students performing better. A significant positive correlation (r s = 0.524, p < 0.01) indicated that higher knowledge led to better practices. Consumer preferences emphasized food protection, quality, and sustainability, with Kraft/Carton as the preferred packaging material. Although students possess sufficient knowledge, their labeling practices remain lacking, highlighting the need for targeted educational initiatives and policy measures to address this gap and encourage more informed food choices.}, }
@article {pmid40619368, year = {2025}, author = {Luo, J and Zheng, X and Xin, Q and Liu, M and Zhang, J and Chen, W and Chen, C and Zhang, C and Wan, G and Xia, C and Lu, J}, title = {Glycyrrhiza plastid paternal inheritance and a new DNA barcode provide new strategies for molecular identification of three medicinal licorice hybrid complexes.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {885}, pmid = {40619368}, issn = {1471-2229}, support = {31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The widespread hybridization and introgression of Glycyrrhiza L. medicinal plants (Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., and Glycyrrhiza glabra L.) complicate their classification and identification, thereby hindering the effective utilization of medicinal resources. Therefore, this study aimed to develop an efficient identification system to distinguish the three medicinal Glycyrrhiza species and their hybrid complexes.<br><br>RESULTS: Through morphological analysis of 345 samples from natural hybrid zones of three medicinal Glycyrrhiza species, this study identified five representative hybrid morphological phenotypes from hybrid complexes with interspecific mosaic characteristics, providing a morphological foundation for identifying hybrid complexes. However, it still has significant limitations to rely solely on morphological traits to determine the parental origins of hybrid complexes. To address this, high-throughput sequencing of parents and progeny from artificial reciprocal cross-experiments was performed, generating eight chloroplast genomes and identifying a plastid paternal inheritance mode, Glycyrrhiza, through comparative analysis of variation sites. Additionally, the DNA barcode ndhA was screened from hypervariable regions within 12 chloroplast genomes to distinguish between the three medicinal Glycyrrhiza species. Using these findings, a new identification system incorporating ndhA, ITS, and trnH-psbA was developed to identify parents and introgression types in 52 samples. It efficiently and accurately identified the three medicinal Glycyrrhiza species and their interspecific hybridization introgression types, achieving a species resolution of 98.08%, which surpassed the two older systems (ITS&#x2009;+&#x2009;trnH-psbA&#x2009;+&#x2009;rbcL&#x2009;+&#x2009;matK and ITS&#x2009;+&#x2009;trnH-psbA&#x2009;+&#x2009;rbcL&#x2009;+&#x2009;matK&#x2009;+&#x2009;trnV-ndhC) and represents the best currently available identification method. Furthermore, phylogenetic trees were constructed using chloroplast genomes, and the new system revealed that their paternal lineage influenced the position of the hybrid complexes in the phylogenetic tree.<br><br>CONCLUSIONS: In summary, this study resolved the parent origin, species identification, and phylogenetic relationships of Glycyrrhiza hybrid complexes through morphological observations, plastid inheritance mode, high-resolution chloroplast barcode ndhA, and a novel molecular identification system. These findings enhance our understanding of hybrid complexes, facilitating the optimized utilization of resources while ensuring the medicinal material&#x2019;s origin.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-06819-w.}, }
@article {pmid40616113, year = {2025}, author = {Ramdini, C and Calvez, E and Houy, O and Gréaux, C and Dollin, C and Pocquet, N and Almeras, L and Sonor, F and Déliscar-Jourdan, G and Vega-Rúa, A}, title = {First report of Aedes albopictus in Saint Barthélemy (French West Indies) confirmed by morphological, molecular and MALDI-TOF mass spectrometry approaches.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {258}, pmid = {40616113}, issn = {1756-3305}, support = {"Une sant&#xe9;" 2021-2027//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil Regional/ ; "Une sant&#xe9;" 2021-2027//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil Regional/ ; "Une sant&#xe9;" 2021-2027//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil Regional/ ; ARS/DSS/N&#xb0;2023-08//Collaboration convention Regional Health Agency and Institut Pasteur Guadeloupe/ ; }, mesh = {Animals ; *Aedes/genetics/anatomy &amp; histology/classification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Mosquito Vectors/anatomy &amp; histology/genetics/classification ; Guadeloupe ; Electron Transport Complex IV/genetics ; Introduced Species ; Female ; }, abstract = {Aedes albopictus is a mosquito vector of arboviruses that is native to southeast Asia. However, this invasive species has spread worldwide. It arrived in the Caribbean in 1993, but had never been recorded in the French Territories of the Americas. We report here the first detection of Aedes albopictus in Saint Barthélemy, Guadeloupe confirmed by morphological criteria, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), and cytochrome c oxidase 1 (cox1) gene barcoding. The presence of this invasive mosquito species in Saint Barthélemy, an island with daily aerial or maritime connections to the French Departments of the Americas, raises concerns about the risk of its introduction into these territories, as well as into other Caribbean countries. It also emphasizes the urgent need to locally reinforce vector surveillance and control measures to prevent the further spread of this mosquito vector.}, }
@article {pmid40615598, year = {2025}, author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J}, title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {23957}, pmid = {40615598}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; }, abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.}, }
@article {pmid40614237, year = {2025}, author = {Zhao, Y and Chen, X and Zhou, T and Zhang, R and Zhao, F and Zhang, X}, title = {Complete chloroplast genome sequence and phylogenetic analysis of Symphytum officinale.}, journal = {Genetics and molecular biology}, volume = {48}, number = {2}, pages = {e20240258}, pmid = {40614237}, issn = {1415-4757}, abstract = {Symphytum officinale is a perennial herb belonging to the Boraginaceae. Here, we sequenced the complete chloroplast (cp) genomes of S. officinale using Illumina sequencing technology. The results revealed that the cp genome is 148,149 bp in length and exhibits a typical quadripartite structure, with a pair of inverted repeat regions (IR) comprising 27,001 bp, a large single-copy (LSC) region comprising 77,366 bp, and a small single-copy (SSC) region comprising 16,781 bp. The sequence contained 133 unique genes, including 86 protein-coding genes, 37 transfer RNAs, eight ribosomal RNAs, and two pseudogenes. Six tandem, 42 dispersed, and 38 simple sequence repeats were identified. Sequence divergence analysis across 21 Boraginaceae species revealed that the most divergent regions, potentially serving as specific DNA barcodes, were found in non-coding spacers. A comparative analysis of the IR/SC boundary regions of the 21 Boraginaceae species revealed IR expansion events in S. officinale. Phylogenetic analysis based on 63 protein-coding genes demonstrated that S. officinale was closely related to Nonea vesicaria. This represents the first cp genome sequenced in Symphytum, and our results provide valuable genetic information for future population and phylogenetic studies of Boraginaceae.}, }
@article {pmid40612707, year = {2025}, author = {Barratt, JLN and Jacobson, D and Pierre-Louis, E and Bajic, M and Kelley, J and Patel, DS and Goldman, I and Zhou, Z and Shi, YP and Ridpath, A and Mace, K and Carlson, C and Sutcliffe, A and Butler, Q and Morrison, A and Stanek, D and Tomson, K and Blackmore, C and Cannons, A and Rollo, S and Wang, C and Tuladhar, R and Clemons, B and Madison-Antenucci, S and Mergen, K and White, J and Antwi, M and Rothfeldt, L and Lazenby, K and Hedges, S and Shray, JN and Courtney, A and Boyanton, B and Qvarnstrom, Y and Freeman, M and Raphael, BH}, title = {Genetic characterization of Plasmodium vivax linked to autochthonous malaria transmission in the US (2023) using Illumina AmpliSeq technology: a genetic epidemiology study.}, journal = {Lancet regional health. Americas}, volume = {48}, number = {}, pages = {101159}, pmid = {40612707}, issn = {2667-193X}, abstract = {BACKGROUND: Malaria is a mosquito borne disease caused by parasites of the genus Plasmodium. In 2023, the United States (US) experienced nine cases of autochthonous Plasmodium vivax malaria transmission; seven in Florida, one in Texas, and another in Arkansas. These were the first autochthonous cases since 2003 when a cluster was identified in Florida. The aim of this study was to genetically characterize the implicated P. vivax isolates in order to complement epidemiologic investigations of these cases.<br><br>METHODS: A custom Illumina AmpliSeq sequencing panel capturing 495 amplicons was designed. This panel was used to ascertain whether these 2023 cases were related, and assess if they were associated with a single or separate introduction events. Sequence data were hierarchically clustered and a Na&#xef;ve Bayes classification approach was used to assign genotypes to a probable geographic origin based on 113 'geo-informative' SNPs captured by the panel. Genotypes associated with the 2023 Arkansas, Texas, and Florida cases were clustered alongside those sequenced from archived blood samples from the 2003 Florida case-patients, a set of reference strains, and other travel-associated specimens. Microsatellite analysis was performed on a subset of samples from these autochthonous cases to complement the AmpliSeq analysis.<br><br>FINDINGS: The 2023 autochthonous Florida cases were genetically linked as were the 2003 Florida cases. The 2023 and 2003 Florida clusters were genetically distinct, and the two Florida clusters were distinct from the 2023 Texas and Arkansas cases, which were also distinct from each other. These genotypes classified to the Central or South American region using the Na&#xef;ve Bayes classifier, including those from the 2003 cluster.<br><br>INTERPRETATION: These data support that at least three distinct P. vivax introduction events in the US in 2023, involving parasites possessing genetic signatures consistent with Central or South America.<br><br>FUNDING: This work was supported by the National Center for Emerging and Zoonotic Infectious Diseases at the US Centers for Disease Control and Prevention.}, }
@article {pmid40608992, year = {2025}, author = {Fedosov, A and Bouchet, P and Dekkers, A and Gori, S and Huang, SI and Kantor, Y and Lemarcis, T and Marrow, M and Ratti, C and Rosenberg, G and Salisbury, R and Zvonareva, S and Puillandre, N}, title = {The phylogeny and systematics of the Costellariidae (Caenogastropoda: Turbinelloidea) revisited.}, journal = {Invertebrate systematics}, volume = {39}, number = {}, pages = {}, doi = {10.1071/IS24101}, pmid = {40608992}, issn = {1447-2600}, mesh = {Animals ; *Phylogeny ; *Gastropoda/classification/genetics/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; }, abstract = {The marine neogastropod family Costellariidae constitutes a large radiation encompassing 647 living species, widely distributed in tropical seas, with their highest diversity in the Central Indo-Pacific. The systematics of the family has undergone profound changes in the mid-2010s, when relationships within Costellariidae were critically revised based on molecular (multilocus) data from 80 species. Whereas four new genera were described, and two more transferred to Costellariidae from Ptychatractidae, relationships of some key lineages could not be resolved due to the incomplete taxonomic and geographic coverage. In the present study we combine an analysis of an extensive DNA-barcoding dataset with phylogenomics to propose a robust new phylogenetic hypothesis and revise the genus-level systematics of the family. Species delimitation was performed for a Cox1 dataset of 1475 specimens, which revealed 221 secondary species hypotheses (SSHs). The phylogeny was reconstructed from a 1003 loci dataset for 70 species representing all but two of the revealed major costellariid lineages. Maximum likelihood (ML) and Bayesian inference (BI) arrived at nearly identical topologies with full support for all backbone nodes but one, providing a robust framework for a new classification. We treat Turricostellaria as a synonym of Tosapusia. Further, based on a re-evaluation of the identity of the type species of Pusia , we conclude that the name should be applied to a Caribbean lineage, previously treated as a part of Vexillum . Consequently, the Indo-Pacific species of Pusia (Pusia) are here reassigned to a new genus Eupusia , and two other subgenera, Ebenomitra and Vexillena , are raised to full genera. Eight further new genera are described based on phylogenomics: Bathythala , Canaripusia and Caribbonus from the Caribbean in deep water, Pilgrivexillum , Pacifilux , Ponderiola and Cernohorskyola from the Central and southern Indo-Pacific, and Kilburniola from the south-western Indian Ocean. From a total of 25 SSHs corresponding to undescribed species, 23 are described herein in the genera Austromitra (1), Bathythala (1), Canaripusia (1), Caribbonus (3), Costapex (4), Eupusia (1), Kilburniola (1), Pilgrivexillum (1), Pusia (2), Thala (1), Tosapusia (1) and Vexillum (6). ZooBank: urn:lsid:zoobank.org:pub:0791EF1F-7F77-4F02-A447-40798388C7FE.}, }
@article {pmid40605520, year = {2025}, author = {Gallhammer, F and Grimm, J and Reier, S and Sefc, KM}, title = {Prevalence and diversity of Acanthocephala in stream-dwelling amphipods (Gammarus fossarum) around an urban area in the eastern Alpine foothills.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1017/S0031182025100449}, pmid = {40605520}, issn = {1469-8161}, abstract = {Population dynamics of aquatic parasites respond to factors like host availability, habitat age and quality. Amphipods are intermediate hosts for Acanthocephala, a widespread group of parasitic worms. Acanthocephalan infections of amphipods can easily be detected, and the widespread occurrence of amphipods makes their infection status an attractive potential proxy for the ecological status of their aquatic environment, including stressors introduced by urbanization. This study investigated the prevalence and the species-level and genetic diversity of Acanthocephala in the stream amphipod Gammarus fossarum. The study streams cross forested, agricultural and urban landscapes in the eastern foothills of the European Alps. Parasite prevalence ranged from 0% to 8.8% and increased towards downstream reaches independent of surrounding land use. Oxford Nanopore Technology was used to sequence the mitochondrial cytochrome oxidase I barcoding locus to identify parasite species and assess their genetic diversity. The majority of the parasites were Pomphorhynchus tereticollis, which use fish as definitive hosts. Despite their relative abundance in the studied streams, their genetic diversity was low and the most common haplotype was found at all sampling sites, which might indicate population expansion. Amphipods also hosted P. laevis and Polymorphus sp. type 1, the first evidence of this cryptic species within Polymorphus cf. minutus in Austria. Genetic diversity was high in Polymorphus sp. type 1, possibly reflecting a large effective population size due to gene flow maintained by the avian final hosts. The low and downstream-biased prevalence suggests that definitive hosts may be a limiting factor for Acanthocephala populations in small streams.}, }
@article {pmid40605502, year = {2025}, author = {Kuitunen, S and Laakkonen, L and Janhunen, K and Kvarnström, K and Linden-Lahti, C}, title = {Facilitators and Barriers Associated With the Use of Barcode Technologies in Drug Preparation and Administration in Hospital Settings-A Narrative Review of Qualitative Studies.}, journal = {Journal of patient safety}, volume = {}, number = {}, pages = {}, doi = {10.1097/PTS.0000000000001381}, pmid = {40605502}, issn = {1549-8425}, abstract = {OBJECTIVES: Barcode technologies are commonly used in hospital settings to improve medication safety. However, the implementation of these systems poses several challenges. This narrative review aims to synthesize qualitative studies exploring the facilitators and barriers associated with using barcode technologies in clinical environments.<br><br>METHODS: This review is grounded in the theory of systems-based risk management. A comprehensive literature search was conducted in November 2022 across 3 databases: CINAHL; MEDLINE (Ovid); and Scopus. Two independent reviewers utilized a predetermined SPIDER (Sample; Phenomenon of Interest; Design; Evaluation; Research type) tool for article selection by using Covidence software. The qualitative data from the selected studies were systematically summarized.<br><br>RESULTS: The search found 197 articles, of which 11 studies from 6 countries met the inclusion criteria. All included studies identified barriers, while 7 studies also highlighted facilitators. Seven common themes emerged as facilitators and barriers: efficacy; implementation; leadership; medication safety; process; technology; and user experience. Three themes-materials; system design; and work environment-were exclusively associated with barriers. Workarounds, such as bypassing barcoding, omitting process steps, and unauthorized process steps, were reported in 8 studies as responses to the barriers.<br><br>CONCLUSIONS: This review underscores the complexity of implementing and maintaining high-leverage, technology-based systemic defenses in clinical practice. The findings provide a foundation for the improvement of the safety and usability of barcode technologies in hospital settings. Future research should focus on developing and testing interventions that address the identified barriers and enhance the facilitators to optimize the use of barcode systems.}, }
@article {pmid40605267, year = {2025}, author = {Calegari, BB and Freyhof, J and Waldock, C and Wegscheider, B and Josi, D and Rüber, L and Seehausen, O}, title = {Two new species of stone loaches of the genus Barbatula (Cypriniformes: Nemacheilidae) from Europe with a neotype designation of B. barbatula (Teleostei: Nemacheilidae).}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70108}, pmid = {40605267}, issn = {1095-8649}, support = {//Kanton Bern/ ; //Wyss Academy for Nature/ ; //Swiss Federal Office of the Environmental/ ; }, abstract = {Ten species of Barbatula are recognised in Europe, west of the Urals: B. barbatula, B. caucasica, B. hispanica, B. leoparda, B. pironae, B. quignardi, B. sturanyi, B. taurica, B. vardarensis and B. zetensis, with B. caucasica and B. taurica formerly considered subspecies of B. barbatula. A comprehensive dataset of the DNA barcoding gene coI recovered four major clades within Europe: three in Eastern Europe including B. caucasica, B. pironae, B. sturanyi, B. taurica, B. vardarensis and B. zetensis, and one in Western Europe including B. barbatula, B. hispanica and B. leoparda. The results further indicated several genetic lineages, representing potentially new species. Recent surveys in Switzerland revealed two new species of Barbatula, within the Western clade, which are herein described. Barbatula fluvicola, a new species, inhabits streams and rivers in the upper and middle Rhine drainage in Switzerland and Germany, as well as the upper Danube drainage in Germany and Austria. Barbatula ommata, a new species, is mostly confined to lakes of the Aare-Rhine system. The two new species overlap geographically in Switzerland, where they occupy different habitats. Morphological differences, species delimitation analyses, phylogenetic reconstruction and genetic distances based on the coI gene corroborates the recognition of the two new species. To stabilise the nomenclatural status and the consequent use of the nomen B. barbatula, we are herein designating an unambiguously identifiable neotype from the Lez River population, previously recognised as B. quignardi, to clarify the identity of the nominal species Cobitis barbatula Linnaeus, 1758.}, }
@article {pmid40601148, year = {2025}, author = {Martínez-Moreno, JM and Llamas-Urbano, A and Barbarroja, N and Pérez-Sánchez, C}, title = {Proteomics by qPCR Using the Proximity Extension Assay (PEA).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2929}, number = {}, pages = {129-142}, pmid = {40601148}, issn = {1940-6029}, mesh = {*Proteomics/methods ; Humans ; *Real-Time Polymerase Chain Reaction/methods ; Software ; Immunoassay/methods ; }, abstract = {The Proximity Extension Assay (PEA) is an innovative technology developed by Olink Proteomics that has revolutionized proteomics research. This method enables the simultaneous detection of hundreds of proteins using a minimal sample volume (1 microliter), combining the specificity of antibody-based immunoassays with the sensitivity of quantitative PCR (qPCR). The PEA process relies on the binding of two antibodies, each conjugated with unique DNA sequences, to a target protein. Upon proximity, these DNA sequences hybridize, forming a molecular barcode that is subsequently amplified by PCR, ensuring high specificity and minimizing cross-reactivity-an issue commonly encountered in multiplexed immunoassays. This chapter provides a detailed overview of the technical and methodological aspects of PEA, including the incubation, extension, amplification, and detection steps, as well as the quality control measures implemented in the Olink[®] NPX Signature software for data analysis. This technology has been applied in more than 2000 peer-reviewed studies, demonstrating its potential for biomarker discovery in diagnostics, prognostics, and personalized medicine across various diseases. The integration of PEA into biomedical research continues to enhance the precision and reproducibility of proteomics studies.}, }
@article {pmid40597261, year = {2025}, author = {Usmani, S and Gebhardt, ME and Simubali, L and Saili, K and Hamwata, W and Chilusu, H and Muleba, M and McMeniman, CJ and Martin, AC and Moss, WJ and Norris, DE and Ali, RLMN}, title = {Phylogenetic taxonomy of the Zambian Anopheles coustani group using a mitogenomics approach.}, journal = {Malaria journal}, volume = {24}, number = {1}, pages = {203}, pmid = {40597261}, issn = {1475-2875}, support = {T32 AI138953/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; T32AI138953/NH/NIH HHS/United States ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; }, mesh = {Animals ; *Anopheles/classification/genetics ; *Phylogeny ; *Genome, Mitochondrial ; Zambia ; *Mosquito Vectors/classification/genetics ; }, abstract = {BACKGROUND: Mosquito species belonging to the Anopheles coustani group have been implicated in driving residual malaria transmission in sub-Saharan Africa and are regarded as an established primary vector in Madagascar. The morphological identification of mosquitoes in this group is challenging due to similarity of features and their molecular confirmation is difficult due to a paucity of reference sequence data representing all members of the group. Conventional molecular barcoding with the cytochrome oxidase I (COI) gene and the internal transcribed spacer 2 (ITS2) region targets is limited in their discrimination and conclusive identification of members of species complexes. In contrast, complete mitochondrial genomes (mitogenomes) have demonstrated much improved power over barcodes to be useful in rectifying taxonomic discrepancies in Culicidae. The goal of this study was to characterize the phylogenetic taxonomy of Zambian members of the An. coustani group by generating and then using complete mitochondrial genomes for phylogenetic rectification.<br><br>METHODS: A genome skimming approach was utilized via shallow shotgun sequencing on individual mosquito specimens to generate sequence reads for mitogenome assembly. Bayesian inferred phylogenies and molecular dating estimations were perfomed on the concatenated protein coding genes using the Bayesian Evolutionary Analysis by Sampling Trees 2 (BEAST 2) platform. Divergence estimates were calibrated for members of the An. coustani group based on published calucations for Anopheles-Aedes.<br><br>RESULTS: This study generated 17 new complete mitogenomes which were comprable to reference An. coustani mitogenomes in the GenBank repository by having 13 protein coding, 22 transfer RNA and 2 ribosomal RNA genes, with an average length of 15,400&#xa0;bp and AT content of 78.3%. Bayesian inference using the concatenated protein coding genes from the generated and publicly available mitogenomes yielded six clades: one for each of the four taxa targeted in this study, the GenBank references, and a currently unknown species. Divergence times estimated that the An. coustani group separated from the Anopheles gambiae complex approximately 110 million years ago (MYA), and members within the complex diverged at times points ranging from&#x2009;~&#x2009;34 MYA to as recent as&#x2009;~&#x2009;7 MYA.<br><br>CONCLUSIONS: These findings demonstrate the value of mitochondrial genomes in differentiating cryptic taxa and help to confirm morphological identities of An. coustani sensu stricto, Anopheles paludis, Anopheles zeimanni and Anopheles tenebrosus. Divergence estimates within the An. coustani group are similar when compared to species with morphologically distinct features. These analyses also highlight the likely presence of other cryptic An. coustani group members circulating in Zambia.}, }
@article {pmid40596413, year = {2025}, author = {Wilcken, CF and da Mota, TA and de Oliveira, CH and de Carvalho, VR and Benso, LA and Gabia, JA and Wilcken, SRS and Furtado, EL and Schiff, NM and de Camargo, MB and Ribeiro, MF}, title = {Sirex obesus (Hymenoptera: Siricidae) as invasive pest in pine plantations in Brazil.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22522}, pmid = {40596413}, issn = {2045-2322}, mesh = {Animals ; Brazil ; *Pinus/parasitology ; *Hymenoptera/genetics/classification/physiology ; *Introduced Species ; Female ; DNA Barcoding, Taxonomic ; Male ; }, abstract = {The genus Sirex (Hymenoptera: Siricidae) consists of 29 species including the Sirex Woodwasp, Sirex noctilio, which is the main insect pest of pine plantations in the Southern Hemisphere including Brazil. In 2023, a species of Sirex similar to S. noctilio was discovered in Southeastern Brazil infesting pine plantations and causing tree mortality of up to 40%. We definitively identified this species as Sirex obesus based on both morphological characters and DNA barcodes. It is a species indigenous to the Southwestern United States and Northern and Central Mexico with little information available regarding its biology and control. This is the first record of S. obesus in Brazil and the first record of the species outside of North America. We document details about S. obesus occurrence in Brazil, describe preliminary damage caused in pine plantations and provide a partial list of natural enemies.}, }
@article {pmid40595485, year = {2025}, author = {Li, J and Crown, A and Ney, P and Yekhanin, S and Partap, A and Shirole, A and Jiang, H and Russ, S and Gordon, M and Aroh, A and Nivala, J and Badam, A and Ranganathan, V and Strauss, K and Chandra, R and Chen, YJ}, title = {Hybridization-encoded DNA tags with paper-based readout for anti-forgery raw material tracking.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5832}, pmid = {40595485}, issn = {2041-1723}, mesh = {*DNA/genetics/chemistry ; *Paper ; *Nucleic Acid Hybridization/methods ; Cell Phone ; *Product Labeling/methods ; Radio Frequency Identification Device/methods ; }, abstract = {Tracking and tracing raw materials is crucial for securing global supply chains. Conventional methods like barcodes and Radio Frequency Identification (RFID) tags are effective but fall short in ensuring raw material traceability and anti-counterfeiting. This work introduces DNA as a powerful tool for source tracking, leveraging its invisibility, safety, and seamless product integration. We present DNATags-engineered DNA mixtures enabling product labeling with error tolerance-readable in the field via paper tickets that fluoresce under a mobile phone and filter device. Additionally, DNATrack employs DNA Hybridization Encoding (HyEn) for enhanced anti-forgery security. Although current costs are higher ($2-$4 per read and write), declining DNA synthesis costs, along with DNA's unique advantages, make this approach a promising solution for future supply chain management.}, }
@article {pmid40595213, year = {2025}, author = {Cannet, A and Chane, CS and Histace, A and Akhoundi, M and Romain, O and Jacob, P and Sereno, D and Souchaud, M and Bousses, P and Sereno, D}, title = {Application of wings interferential patterns (WIPs) and deep learning (DL) to classify some Culex. spp (Culicidae) of medical or veterinary importance.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {21548}, pmid = {40595213}, issn = {2045-2322}, mesh = {Animals ; *Deep Learning ; *Wings, Animal/anatomy &amp; histology ; *Culex/classification/anatomy &amp; histology ; Neural Networks, Computer ; }, abstract = {In this paper, we test the possibility of using Wing Interference Patterns (WIPs) and deep learning (DL) for the identification of Culex mosquitoes species to evaluate the extent to which a generic method could be developed for surveying Dipteran insects of major importance to human health. Previous applications of WIPs and DL have successfully demonstrated their utility in identifying Anopheles, Aedes, sandflies, and tsetse flies, providing the rationale for extending this approach to Culex. Accurate identification of these mosquitoes is crucial for vector-borne disease control, yet traditional methods remain labor-intensive and are often hindered by cryptic species or damaged samples. To address these challenges, we applied WIPs, generated by thin-film interference on wing membranes, in combination with convolutional neural networks (CNNs) for species classification. Our results achieved over [Formula: see text] genus-level accuracy and up to [Formula: see text] species-level accuracy. Nonetheless, challenges with underrepresented species emphasize the need for larger datasets and complementary techniques such as molecular barcoding. This study highlights the potential of WIPs and DL to enhance mosquito identification and contribute to scalable tools for broader surveys of health-relevant Dipteran insects.}, }
@article {pmid40595196, year = {2025}, author = {Sraphet, S and Javadi, B}, title = {Exploring genetic diversity and genomic insights of Bacillus subtilis isolates from cassava rhizosphere using molecular barcoding and whole genome sequencing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {22708}, pmid = {40595196}, issn = {2045-2322}, support = {&#xe07;&#xe1b;11773/2566//Suan Sunandha Rajabhat University/ ; }, mesh = {*Bacillus subtilis/genetics/isolation &amp; purification/classification ; *Manihot/microbiology ; *Rhizosphere ; *DNA Barcoding, Taxonomic/methods ; *Genetic Variation ; Phylogeny ; *Genome, Bacterial ; Whole Genome Sequencing/methods ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Genomics/methods ; }, abstract = {Bacillus subtilis plays a significant role in both agriculture and industry. It is commonly isolated from agricultural environments, particularly various soil types. This study aimed to investigate DNA barcoding and whole-genome sequencing of B. subtilis strains, focusing on those specific to the cassava rhizosphere. Genetic identification and diversity of B. subtilis strains isolated from the rhizosphere of the Piroon 2 cassava cultivar were initially characterized using 16 S rDNA, a molecular marker for species-level identification. To explore strain-specific biodiversity within B. subtilis, repetitive DNA elements-specifically extragenic palindromic and BOX sequences-were analyzed across the genomes of the isolated strains. These repetitive sequences revealed two main structural patterns, providing clear and distinct genomic fingerprints for biodiversity analysis. The results showed that both REP and BOX sequences were highly conserved within specific regions of the B. subtilis genome, resulting in reliable and reproducible DNA patterns suitable for whole-genome phylogenetic analysis. While the 16 S rDNA approach showed a high sequence similarity among the B. subtilis strains (99.98%), whole-genome analysis using repetitive sequences allowed for clearer differentiation, with phylogenetic distances exceeding 97%. Whole-genome sequencing of the elite strain BsPr8 was performed using the Illumina MiSeq platform. The sequencing results yielded 56 contigs, with an average GC content of 43.67% and a total genome size of approximately 4,050 Kbp. Genome annotation identified 3,575 proteins with functional assignments, including 1,055 enzymes classified by Enzyme Commission numbers. The PATRIC database further annotated 3,937 genus-specific protein families. Additionally, 45 genes homologous to known antibiotic resistance genes were identified within the BsPr8 genome. These findings have important implications for sustainable agricultural practices and cassava cultivation. By elucidating the genetic diversity and genomic characteristics of B. subtilis strains, this study facilitates the identification of beneficial traits-such as plant growth promotion, pathogen suppression, and improved nutrient uptake. These strains hold potential for development as biofertilizers or biopesticides, offering an environmentally friendly alternative to conventional chemical inputs.}, }
@article {pmid40594022, year = {2025}, author = {Liu, Y and Xie, Y and Wang, Y and Zong, Y and Liu, Y and Li, C and Dong, J}, title = {The development and application of mini-barcodes from mitochondrial DNA for identifying medicinal leeches from traditional medicines.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20444}, pmid = {40594022}, issn = {2045-2322}, support = {31801957//National Natural Science Foundation of China/ ; 32100334//National Natural Science Foundation of China/ ; BK20181471//Natural Science Foundation of Jiangsu Province, China/ ; BK20210897//Natural Science Foundation of Jiangsu Province, China/ ; D2020009//Scientific Research Foundation for the Talents by Xuzhou Medical University/ ; }, mesh = {Animals ; *Leeches/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Mitochondrial/genetics ; Phylogeny ; Medicine, Chinese Traditional ; }, abstract = {Species-specific efficacy necessitates accurate identification of medicinal leeches, but standard DNA barcoding often fails with degraded DNA from traditional medicines. This deficiency highlights the need for mini-barcoding. This study aimed to develop and validate mini-barcode markers for three Chinese Pharmacopoeia-listed leech species: Whitmania pigra, Whitmania acranulata and Hirudo nipponia. Four novel mini-barcode primer sets (ND1F1/R1, 12SF1/R1, 16SF1/R1 and COX1F1/R1) were developed and validated using seven morphologically identified specimens and subsequently tested on 16 commercial leech products. DNA extractions were performed using both single-tube and column purification kits, with the latter yielding superior DNA quality and meeting the requirements for following PCR amplification. The PCR results confirmed the validation of four candidate mini-barcodes targeting specific genetic regions, which produced results in 13 out of 16 commercial leech products. Mini-barcode sequences from morphologically identified W. pigra specimens exhibit > 95% identity to the complete ND1, 12S rDNA, 16S rDNA, and COX1 sequences (EU304459), whereas sequences from H. nipponia and W. acranulata show < 85% identity, and among leech-derived products only the proprietary Chinese medicine Maxuekang exhibits lower identity. Both the optimal partition of ASAP and phylogenetic tree identified three distinct groups correlating with the morphological species: W. pigra, W. acranulata, and H. nipponia. Mislabeled species have been uncovered in proprietary Chinese medicine, notably the claimed Hirudo nipponia, which was replaced by W. pigra. The results highlight the value of mini-barcodes in enhancing product quality control and offer a reliable method for accurate species identification in traditional and commercial leech-based medicines. This advance supports safer and more effective utilization of medicinal leeches and advocates for their integration into regulatory standards.}, }
@article {pmid40593543, year = {2025}, author = {Yang, L and Liu, F and Hahm, H and Okuda, T and Li, X and Zhang, Y and Kalyanaraman, V and Heitmeier, MR and Samineni, VK}, title = {Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5557}, pmid = {40593543}, issn = {2041-1723}, support = {R01DK139386//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 DA056829/DA/NIDA NIH HHS/United States ; R01 DK139386/DK/NIDDK NIH HHS/United States ; R01DK140445//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01DA056829//U.S. Department of Health &amp; Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; R01 DK140445/DK/NIDDK NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; R01DK128475//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01 DK128475/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Neurons/metabolism/cytology ; Female ; Mice ; Single-Cell Analysis/methods ; Dependovirus/genetics ; Mice, Inbred C57BL ; Brain/metabolism/cytology ; Epigenesis, Genetic ; }, abstract = {Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons in female mice. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.}, }
@article {pmid40593007, year = {2025}, author = {Liang, Z and Chen, X and Xie, Y and He, F and Zhang, L and Zhu, X and Lu, T}, title = {An integrated widely targeted metabolomics and network pharmacology study of Persicaria runcinata var. Sinensis against arthritis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20499}, pmid = {40593007}, issn = {2045-2322}, support = {QKHJC-ZK[2021]-YB156//Guizhou Province Science and Technology Department Support Plan/ ; 24141900201//Project of Shanghai Science and Technology Commission/ ; gzwkj 2021-245//Science and Technology Foundation of Health Commission of Guizhou Province/ ; }, mesh = {*Metabolomics/methods ; *Network Pharmacology/methods ; Animals ; Phylogeny ; *Arthritis/drug therapy/metabolism ; *Plant Extracts/pharmacology/chemistry ; Tandem Mass Spectrometry ; DNA Barcoding, Taxonomic ; Chromatography, High Pressure Liquid ; }, abstract = {The present study aimed to investigate the material basis of Persicaria runcinata var. sinensis (Hemsl.) Bo Li using widely targeted metabolomics and network pharmacology techniques. Efforts were also made to establish a DNA barcode for P. runcinata var. sinensis. Widely targeted metabolomics technique of Ultra performance liquid chromatography-mass spectrometry(UPLC-MS/MS) was employed to detect and analyze the metabolites in P. runcinata var. sinensis. Network pharmacology was used to screen and analyze metabolites with high content and pharmacological effects. DNA extraction, Polymerase chain reaction(PCR) amplification, sequence alignment, and phylogenetic tree construction were performed to establish the DNA barcode. A total of 716 metabolites were detected in Miao ethnomedicine P. runcinata var. sinensis, with key targets, enriched functions, and pathways identified using network pharmacology. The DNA sequence for the ITS2 primer of P. runcinata var. sinensis was determined and a phylogenetic tree was generated. Metabolite enrichment in P. runcinata var. sinensis revealed potential therapeutic compounds for arthritis. The study's approach provided theoretical support for understanding the substance basis and therapeutic effects of P. runcinata var. sinensis. Additionally, the high homology level with various Polygonum species provided the foundation for molecular identification in ethnomedicine.}, }
@article {pmid40590343, year = {2025}, author = {Gao, Y and Liu, J and Huang, S and Du, N and Zhang, G and Li, Y}, title = {Recent advances in DNA-encoded libraries.}, journal = {Chemical communications (Cambridge, England)}, volume = {61}, number = {59}, pages = {10952-10968}, doi = {10.1039/d5cc02904j}, pmid = {40590343}, issn = {1364-548X}, mesh = {*DNA/chemistry/genetics ; *Gene Library ; Drug Discovery ; *Small Molecule Libraries/chemistry ; Humans ; High-Throughput Screening Assays ; Combinatorial Chemistry Techniques ; }, abstract = {The DNA-encoded library (DEL), a novel high-throughput screening platform that synergistically combines the strengths of combinatorial chemistry and genetic barcoding, has transitioned from a theoretical framework to a valuable technology within the pharmaceutical research landscape. As an emerging platform for drug discovery, DEL technology has undergone rapid evolution over the past thirty years. This review aims to highlight remarkable advancements in DELs over the past five years across multiple dimensions, including encoding methods, DEL-compatible chemistry, selection methods, library design, and hit picking. It also delves into the issues that have been successfully addressed and the breakthroughs achieved. Finally, this review proposes practical strategies and outlines future research directions that have the potential to further propel the development of DELs in the upcoming five years, aiming to provide valuable insights for drug discovery endeavors.}, }
@article {pmid40590201, year = {2025}, author = {Liu, Y and Shen, F and Wang, L and Dou, J and Dong, T and Li, M and Wang, Q and Dong, S and Zhang, G and Zhao, J and Li, L and Shi, S}, title = {Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e70004}, doi = {10.1111/1755-0998.70004}, pmid = {40590201}, issn = {1755-0998}, support = {C2019205175//Natural Science Foundation of Hebei Province/ ; C2022402017//Natural Science Foundation of Hebei Province/ ; S23B053//Humanities and Social Science Research Fund of Hebei Normal University/ ; 221490222A//Shijiazhuang Science and Technology Bureau/ ; }, abstract = {Mosses represent the most species-diverse clade of bryophytes and are among the earliest land plants. These diminutive organisms hold substantial ecological importance and have significant applications in horticulture and medicine. However, their study, development and utilisation are impeded by the complex identification process and scarcity of researchers specialising in moss taxonomy. The advancement of DNA barcoding technology presents an opportunity for precise moss identification. Present molecular markers primarily originate from angiosperm research and may not be optimal for moss species. This study aims to identify suitable DNA barcodes for mosses at the chloroplast genome level. Utilising 61 complete chloroplast genome datasets of mosses, including 14 orders, 23 families and 60 species, this research presented the first construction of a reliable phylogenetic tree at the family level of mosses using whole chloroplast genomes, enabling accurate identification of most samples. Based on nucleotide polymorphism in the complete chloroplast genome, 12 highly variable regions were selected as candidate DNA barcodes for mosses. Experimental validation of the newly designed primers demonstrated high universality (> 90%). The resolution verification experiment, employing DNA barcodes from 103 samples representing 21 families and 48 genera, confirmed the efficacy of atpB-rbcL, psaI-accD, ycf2, ycf1, matK, rpoB-trnC and clpP as reliable DNA barcodes for mosses. The study also revealed inconsistencies in the chloroplast genome structures of mosses submitted to public databases, which hinder subsequent research. Consequently, we recommend that researchers upload data with a designated reference genome in future submissions.}, }
@article {pmid40587582, year = {2025}, author = {Langsiri, N and Banlunara, W and Klaychontee, O and Worasilchai, N and Cognialli, R and Queiroz-Telles, F and Spruijtenburg, B and Groot, T and Meijer, EFJ and Chindamporn, A}, title = {Targeted long-read sequencing analysis and antifungal susceptibility profiles of Sporothrix schenckii isolates from Thailand.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {6}, pages = {e0013253}, pmid = {40587582}, issn = {1935-2735}, mesh = {*Sporothrix/drug effects/genetics/isolation &amp; purification/classification ; Thailand ; *Antifungal Agents/pharmacology ; Humans ; *Sporotrichosis/microbiology/veterinary ; Phylogeny ; Calmodulin/genetics ; Microbial Sensitivity Tests ; Animals ; Sequence Analysis, DNA ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Sporothrix spp. are dimorphic fungi capable of undergoing morphological changes in response to temperature variations. The genus Sporothrix includes the species S. schenckii sensu stricto, S. brasiliensis, S. globosa, and S. luriei that cause sporotrichosis, which can range from local skin infections to systemic infections in immunocompromised individuals. As these species are morphologically similar, molecular techniques that utilize barcoding genes are required for accurate identification. While the Internal Transcribed Spacer (ITS) region is the universal fungal barcode, the calmodulin gene offers higher resolution for phylogenetic classification of Sporothrix using Sanger sequencing. This study evaluated the ability of long-read nanopore sequencing of calmodulin and ITS to identify species level and allow phylogenetic analysis of Sporothrix strains isolated from humans and felines in Thailand. We found that the calmodulin sequencing with Oxford Nanopore Technology (ONT) consistently classified all isolates as S. schenckii sensu stricto, whereas the ITS region showed a lower discriminatory power, complicating species identification in some isolates. The phylogenetic analysis of the calmodulin region indicated that all isolates localized in a specific S. schenckii sensu stricto subclade together with other isolates from Southeast Asia, while the three residual S. schenckii subclades were associated with other geographical locations. Antifungal susceptibility testing on all Sporothrix strains demonstrated elevated in vitro minimum inhibitory concentrations (MICs) to itraconazole for 8 out of 26 isolates. Altogether, this study demonstrated that ONT sequencing of calmodulin allows accurate species identification and phylogenetic analysis of S. schenckii sensu stricto isolates from Thailand, of which some also demonstrated elevated MIC values for itraconazole.}, }
@article {pmid40587561, year = {2025}, author = {Hwang, K and Veith, A and Duro, L and Wood, D and Chatterjee, G and Cajigas, Y and Lee, JH and Vasaturo, A}, title = {High-Throughput Automated Multiplex Immunofluorescence Assays for Translational Research.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {220}, pages = {}, doi = {10.3791/67584}, pmid = {40587561}, issn = {1940-087X}, mesh = {Humans ; *Fluorescent Antibody Technique/methods ; *Translational Research, Biomedical/methods ; *High-Throughput Screening Assays/methods ; }, abstract = {Multiplex immunofluorescence (mIF) is an advanced technique that allows for detailed, spatially resolved analysis of tissue samples by visualizing multiple protein biomarkers within a single section. However, most mIF technologies face significant tradeoffs between sensitivity and throughput when multiplexing, posing a critical limitation for robustly detecting low-abundance biomarkers across multiple tissue sections. A new approach for mIF uses unique DNA barcodes linked to antibodies, which are amplified through a parallel single-molecule amplification mechanism. This method achieves staining quality highly comparable to clinical-grade immunohistochemistry (IHC) while providing high multiplexing capabilities and high-throughput whole-slide imaging. This assay involves amplifying a cocktail of DNA-barcoded antibodies on the tissue, followed by sequential rounds of detection steps to visualize four fluorescent-labeled oligonucleotides per cycle. This process thus enables the detection of eight or more biomarkers per tissue sample. Key steps in this method include automated tissue preparation, application of primary antibodies conjugated with DNA barcodes, signal amplification, and iterative cycles of detection, imaging, and signal removal. Image acquisition is followed by image registration and single-cell analysis using an AI-enhanced spatial image data science platform. For this study, the protocol was applied to formalin-fixed, paraffin-embedded (FFPE) multi-tissue micro-arrays (TMAs), including tonsil, melanoma, colon, and lymph node cores in triplicate. Advanced mIF technologies provide more insights into the tumor response, the tumor microenvironment, and the immune landscape. By overcoming the inherent tradeoffs between sensitivity, multiplexing capabilities, and imaging throughput, researchers can now aim to understand the heterogeneity of challenging molecular signatures and biomarkers of therapeutic responses.}, }
@article {pmid40587398, year = {2025}, author = {Loudig, O and Ben-Dov, IZ and Shapiro, B and Mitchell, MI and Lachica, M and Topilow, A and Liu, C and Ronan, M}, title = {Ultrasensitive cDNA Library Preparation for Next-generation Sequencing of MicroRNAs from Small Extracellular Vesicles.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {220}, pages = {}, pmid = {40587398}, issn = {1940-087X}, support = {R33 HL156279/HL/NHLBI NIH HHS/United States ; }, mesh = {*MicroRNAs/genetics/analysis ; *Gene Library ; *Extracellular Vesicles/genetics/chemistry ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; }, abstract = {Recent studies demonstrate that small extracellular vesicles (sEVs), which are found in all biofluids, play critical roles in intercellular communication by channeling proteins, DNA, and RNAs. MicroRNAs (miRNAs) that are packaged in sEVs have emerged as critical deliverable regulators in recipient cells. Since sEVs secreted by normal and diseased cells carry different miRNA cargos, recent sEV-miRNA profiling studies suggest that they may help identify novel circulating biomarkers. However, cell/disease-specific sEVs circulating in diverse biofluids, once isolated, provide low miRNA quantities, which are generally difficult to quantify using conventional spectrometric methodologies. Small non-coding RNA Next Generation Sequencing (NGS), which allows for the amplification of cloned miRNA sequences, offers a valuable opportunity to evaluate the miRNA cargos of sEVs. Unfortunately, commercial cDNA library preparation procedures often require RNA inputs well above the unquantifiable amounts available from isolated sEVs. Thus, considering the robustness and multiplexing capabilities of our existing cDNA library preparation procedure (i.e., initially optimized for the analysis of low-input, highly degraded, formalin-fixed paraffin-embedded (FFPE) RNA), we sought to evaluate its applicability for the analysis of sEV miRNAs. Importantly, taking into account the recent technical clustering improvements of sequencing chips, we sought to adapt our transcript barcoding approach within a paired-end, dual index-compatible cDNA library preparation workflow to enhance our sequencing and multiplexing capabilities. Using RNA extracted from 8.4 × 10[9] sEVs in 16 replicates, and from decreasing amounts of sEVs from 10[10] sEVs to as low as 2.5 × 10[7] sEVs, we evaluated the reproducibility and sensitivity of this methodology. The data demonstrate that the 16 3' adenylated DNA barcodes allow for highly reproducible and sensitive detection of sEV-miRNA profiles across repeats using as low as 3.15 pg of total small non-coding RNAs or 1.35 pg of miRNAs.}, }
@article {pmid40584258, year = {2025}, author = {Mortlock, M and Geldenhuys, M and Keith, M and Rademan, R and Swanepoel, LH and Von Maltitz, EF and Kearney, T and Markotter, W}, title = {Paramyxo- and coronavirus diversity and host associations in non-volant small mammals: evidence of viral sharing.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf041}, pmid = {40584258}, issn = {2057-1577}, abstract = {Rodents and other non-volant small mammals (like shrews) maintain major ecological and epidemiological roles as reservoirs of zoonotic pathogens. Their presence within human-modified landscapes and interfaces with people, wildlife, and livestock create frequent opportunities for viral spillover. Despite this, the pathogen diversity and true risk of viral transmission are poorly understood by these hosts in Africa. Here, we explored the diversity and host association of paramyxoviruses and coronaviruses in non-volant small mammals from South Africa through longitudinal and opportunistic sample collection and molecular detection of viral RNA and host genetic barcoding. A high diversity of viruses was identified, with prevalences of 11.9% and 1.79% for paramyxoviruses and coronaviruses, respectively. Five instances of coinfections involving multiple paramyxoviruses and a coronavirus were detected, as well as nine Bayesian-supported paramyxovirus host genus, subfamily, and family switching, signifying frequent unrestrained viral sharing. Though the zoonotic potential of these identified viruses is unknown, the frequency of host switching suggests that these viruses may be more prone to adaptation to new host species or utilize highly conserved entry mechanisms. This highlights the risks for potential cross-species transmission events to livestock, domestic animals, and people, warranting continued surveillance.}, }
@article {pmid40584119, year = {2025}, author = {Marín-Villa, J and López-Herrera, A and Gómez-Ruiz, DA and Restrepo-Rodas, DC and Sánchez-Rodríguez, G and Úsuga-Monroy, C}, title = {Mitochondrial markers (cytochrome c oxidase subunit I and 16S ribosomal RNA) as supporting biomarkers for wild bird identification.}, journal = {Veterinary world}, volume = {18}, number = {5}, pages = {1389-1399}, pmid = {40584119}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Illegal wildlife trafficking is a critical threat to biodiversity, particularly in megadiverse countries such as Colombia. Birds, notably psittacines, are among the most targeted taxa. Morphological identification is often insufficient, especially when dealing with cryptic species or degraded samples. This study aimed to assess the utility of mitochondrial markers cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) as molecular tools for species-level identification of psittacines housed at the Conservation Park of Medellín.<br><br>MATERIALS AND METHODS: Six adult psittacines from the genera Ara and Pionus were selected based on availability. Blood samples were collected and genomic DNA was extracted using a commercial kit. Polymerase chain reaction amplification of partial COI and 16S rRNA gene fragments was performed, followed by Sanger sequencing. Sequence identity was confirmed using BLASTn and the Barcode of Life Data System (BOLD). Phylogenetic relationships were analyzed using Neighbor-Joining, Maximum Likelihood, and Bayesian Inference approaches.<br><br>RESULTS: Molecular results showed 100% concordance with prior morphological identification for all six individuals. COI and 16S rRNA sequences allowed clear species-level identification with similarity values >98%. Phylogenetic analyses for both markers yielded congruent tree topologies, with high branch support (>90%), further validating species identification. Maximum interspecific divergence for COI was observed between Ara macao and Pionus fuscus (0.15980), while 16S rRNA showed lower divergence values. All generated sequences were submitted to GenBank and BOLD in accordance with findable, accessible, interoperable, reusable principles.<br><br>CONCLUSION: This study confirms the robustness of COI and 16S rRNA mitochondrial markers in accurately identifying psittacine species. The integration of molecular and morphological approaches enhances forensic investigations, facilitates biodiversity conservation, and contributes to efforts against wildlife trafficking. Expanding genetic databases for Neotropical avifauna, especially for commonly trafficked species, is imperative. Future research should adopt integrative genomic approaches involving nuclear markers to overcome the maternal inheritance limitation of mitochondrial DNA.}, }
@article {pmid40583309, year = {2025}, author = {Li, J and Zhai, R and Xiao, H and Chen, Y and Cheng, W and Yang, X and Wang, K and Yang, Y and Huang, J}, title = {Ultrahigh-Capacity Vertical Encoded Micro-Spherical Nucleic Acids for Multiplexed Detection.}, journal = {Analytical chemistry}, volume = {97}, number = {27}, pages = {14792-14799}, doi = {10.1021/acs.analchem.5c02444}, pmid = {40583309}, issn = {1520-6882}, mesh = {*DNA/chemistry/analysis ; *Microspheres ; *Fluorescent Dyes/chemistry ; Nanotechnology ; }, abstract = {Here, we report a DNA-programmable microsphere encoding platform using spatially organized fluorophores on magnetic cores with elongated DNA scaffolds. By engineering vertically stratified DNA scaffolds on paramagnetic microspheres, we achieved orthogonal spectral separation of 2-3 fluorophores through spatial confinement, generating 96 distinct two-color and 536 three-color barcodes via tunable stoichiometric control. We validated the platform's utility for nucleic acid multiplexing by demonstrating simultaneous detection of multiple targets, establishing a foundation for scalable high-order multiplexing. The system circumvents material compatibility restrictions inherent to conventional approaches, resolves spatial encoding conflicts through programmable DNA nanostructures, and achieves exponential encoding scalability. By synergizing the operational advantages of liquid-phase microsphere assays with the precision of DNA nanotechnology, this work establishes a new paradigm for high-throughput multiplexed diagnostics, offering unprecedented potential for precision medicine and large-scale biomedical analysis.}, }
@article {pmid40582202, year = {2025}, author = {Huo, X and Xie, Y and Hu, Y and Wang, Z and Sheng, Y and Qi, H and Shao, H and Ma, Q and Yu, W and Dong, X}, title = {Electrospun perovskite quantum dots-based Janus microribbons film with white light and multicolor luminescence for optical data storage and anti-counterfeiting.}, journal = {Journal of colloid and interface science}, volume = {699}, number = {Pt 2}, pages = {138276}, doi = {10.1016/j.jcis.2025.138276}, pmid = {40582202}, issn = {1095-7103}, abstract = {In order to attain white light or multicolor luminescence of perovskite quantum dots (PQDs) materials, the prevalent method involves directly blending PQDs with different type and composition of halogen anions. However, this method allows uncontrolled halogen anion exchange between the different PQDs, thereby leading to alterations in the final fluorescence color of the material. To address this problem, we creatively design and fabricate a PQDs-based Janus microribbons film (Janus-MRF) with white light emission and multicolor fluorescence under multi-wavelength stimulation by a parallel electrospinning. [CsPbCl1.5Br1.5/Eu(BA)3phen/PS]//[CsPbBr3/Eu(BA)3phen/PS] (BA = benzoate radical, phen = 1,10-phenanthroline, PS = polystyrene) Janus microribbon (Janus-MR) serves as fundamental structural unit of Janus-MRF, CsPbCl1.5Br1.5 and CsPbBr3 PQDs respectively provide blue and green fluorescence, and Eu(BA)3phen offers red fluorescence. The introduction of Janus structure in Janus-MR allows the interior of the Janus-MR to form two independent microscopic domains, confining CsPbCl1.5Br1.5 PQDs and CsPbBr3 PQDs to their respective domains and avoiding halogen anion exchange caused by direct contact between the two PQDs and obtaining superior and designed macroscopic fluorescence. Owing to the disparity in optimal excitation wavelengths between PQDs and Eu(BA)3phen, white light and multicolor emissions of Janus-MRF can be achieved under multi-wavelength stimulation. Furthermore, the fluorescent color of Janus-MRF is sensitive to temperature changes. As an applicative demonstration of Janus-MRF, different sub-barcodes are obtained by using the identifiable fluorescence spectra emitted by Janus-MRF under multi-wavelength stimulation and the sensitivity of fluorescent color of Janus-MRF to temperature changes, and further these sub-barcodes are integrated into the large photonic barcodes encoding library for high-volume data storage and advanced anti-counterfeiting applications. This work provides a novel idea and strategy for advancing fabrication and application of materials based on PQDs.}, }
@article {pmid40580296, year = {2025}, author = {Magbanua, ZV and Hsu, CY and Pechanova, O and Arick, M and Peterson, DG}, title = {Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq).}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2943}, number = {}, pages = {189-204}, pmid = {40580296}, issn = {1940-6029}, mesh = {*Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Polymorphism, Single Nucleotide ; DNA Restriction Enzymes/metabolism ; Animals ; Gene Library ; Polymerase Chain Reaction/methods ; Gossypium/genetics ; }, abstract = {ddRAD-Seq is a reduced representation sequencing technique that results in sequence datasets that can be compared and used to identify SNPs. We present an improved ddRAD-Seq protocol that increases efficiency and decreases the time to complete a ddRAD-Seq experiment. It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Enzyme deactivation steps are eliminated, library amplification and barcoding are completed in one PCR step, highly-efficient and precise size selection with BluePippin system and cleanup steps using magnetic beads are consolidated at the end of the library generation step. The SNPs that we identified using this streamlined protocol were validated in population and evolutionary studies of cotton (plant) (Magbanua et al., Anal Biochem 662:115001, https://doi.org/10.1016/j.ab.2022.115001 , 2023) and rohu carp (animal) (Arick et al., G3 (Bethesda) 13, https://doi.org/10.1093/g3journal/jkad009 , 2023).}, }
@article {pmid40580295, year = {2025}, author = {Torres, A and Gaudino, R}, title = {Long-Range Targeted Nanopore Ligation Sequencing Workflow for Targeted Amplicon Sequencing of Secondary Metabolite Gene.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2943}, number = {}, pages = {177-188}, pmid = {40580295}, issn = {1940-6029}, mesh = {*Nanopore Sequencing/methods ; Workflow ; *Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; DNA, Plant/genetics ; *Plants/genetics/metabolism ; Nanopores ; }, abstract = {This chapter presents protocols for advanced genotyping and genetic analysis in plant science, utilizing DNA extracted from FTA samples and leaf tissue. Targeted long range PCR is employed to uncover allelic and structural variations within genes of interest, while targeted long-read nanopore sequencing offers a comprehensive view of gene targets in their native and enriched forms. The protocol for nanopore sequencing encompasses DNA preparation, barcoding of up to 96 samples, adapter ligation, purification, and sequencing, culminating in the generation of raw data files (pod5 or fastq) suitable for further analysis. Together, these methods provide a powerful toolkit for plant diagnostics and breeding.}, }
@article {pmid40577524, year = {2025}, author = {Rajasegaran, P and Tan, KK and Khoo, JJ and Mansor, MS and Ahmad Khusaini, MKS and AbuBakar, S and Ya'cob, Z and Makepeace, BL}, title = {Molecular species delimitation analysis of Leptotrombidium spp. and other chigger species parasitizing birds in Malaysia.}, journal = {Journal of medical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jme/tjaf078}, pmid = {40577524}, issn = {1938-2928}, support = {ICA\R1\191058//Royal Society International Collaboration Award/ ; }, abstract = {Trombiculid mites (Acariformes) are unique among arthropods of medical importance in that only the larval instar (chigger) is parasitic, which can result in the transmission of zoonotic scrub typhus. The use of molecular approaches for chigger species discrimination has been very limited until recently, especially for those parasitizing bird hosts, where data remain scarce. Here, we aimed to generate DNA barcodes of chiggers parasitizing birds in Malaysia based on the mitochondrial cytochrome c oxidase subunit I (COI) gene following DNA extraction, PCR and sequencing. Fifty-four COI sequences from 8 bird-associated chigger species in Malaysia were combined with 50 GenBank sequences comprising 7 genera from various countries for DNA barcode and phylogenetic analysis. The correct identification rates for the 95 COI barcodes were 96.84% (Best Match) and 86.31% (Best-Close Match). DNA barcode analyses effectively clustered the 8 nominal species from this study into their respective genera. Genetic divergence of less than 3% was observed within Ascoschoengastia lorius, Neoschoengastia gallinarum, Parascoschoengastia heynemani, Leptotrombidium imphalum, and Blankaartia acuscutellaris, all of which formed a monophyletic clade, confirming their conspecific nature. Conversely, intraspecific divergences of 17.64%, 15.49%, and 11.63% were obtained for Toritrombicula densipiliata, Odontacarus audyi, and Leptotrombidium deliense. These divergences, supported by evidence of distinct entities through delimitation analyses, indicate potential cryptic diversity within these populations. In conclusion, this study represents the first molecular genetic analysis of bird chiggers in Malaysia, revealing varying levels of genetic divergence. Our findings highlight the utility of DNA barcoding for understanding chigger diversity and aiding in accurate identification.}, }
@article {pmid40577080, year = {2025}, author = {Butti, P and Bellusci, F and Brambilla, E and Branduardi, P}, title = {Genomically integrated cassettes swapping: bringing modularity to the strain level in Saccharomyces cerevisiae.}, journal = {FEMS yeast research}, volume = {25}, number = {}, pages = {}, pmid = {40577080}, issn = {1567-1364}, support = {//University of Milano-Bicocca/ ; CN_00000033//Italian Ministry of University and Research/ ; H43C22000530001//Italian Ministry of University and Research/ ; }, mesh = {*Saccharomyces cerevisiae/genetics ; CRISPR-Cas Systems ; *Synthetic Biology/methods ; *Gene Editing/methods ; *Genome, Fungal ; }, abstract = {A large variety of synthetic biology toolkits for the introduction of multiple expression cassettes is available for Saccharomyces cerevisiae. Unfortunately, none of these tools is designed to allow the modification - exchange or removal - of the cassettes already integrated into the genome in a standardized way. The application of the modularity principle therefore ends to the steps preceding the final host engineering, making microbial cell factories construction stiff and strictly sequential. In this work, we describe a system that easily allows CRISPR-mediated swapping or removal of previously integrated cassettes, thus bringing the modularity to the strain level, enhancing the possibility of modifying existing strains with a reduced number of steps. In the system, each cassette is tagged with specific barcodes, which can be used as targets for CRISPR nucleases (Cas9 and Cas12a), allowing the excision of the construct from the genome and its substitution with another expression cassette or the restoration of the wild type locus in one single standardized step. The system has been applied to the previously developed Easy-MISE toolkit and tested by swapping fluorescent protein expression cassettes with an efficiency of ∼90% quantified by PCR and flow cytometry.}, }
@article {pmid40575388, year = {2025}, author = {Li, X and Li, X and Tong, L and Hu, L and Hong, Y and Zhou, R and Li, Z and Dong, M and Hou, J and Xu, T and Zhong, W}, title = {Systematic Evaluation of Isolation Techniques and Freeze-Thaw Effects on Plasma Extracellular Vesicle Heterogeneity and Subpopulation Profiling.}, journal = {Journal of extracellular biology}, volume = {4}, number = {6}, pages = {e70058}, pmid = {40575388}, issn = {2768-2811}, abstract = {Extracellular vesicles (EVs) are increasingly recognized as promising disease biomarkers and therapeutic carriers. However, standardizing blood-derived EV isolation remains challenging due to the heterogeneity of EV populations and variability among isolation techniques. In this study, we systematically evaluated three distinct EV isolation methods, including asymmetrical flow field-flow fractionation (AF4), size-exclusion chromatography (SEC) and automated centrifugal microfluidic disc system combined with functionalized membranes (Exo-CMDS), to compare their efficiency in isolating EVs from both freshly frozen and freeze-thawed plasma samples. We utilized an integrative approach combining Proximity-dependent Barcoding Assay (PBA) for single-EV surface protein profiling, Liquid Chromatography-Mass Spectrometry (LC-MS/MS) for bulk proteomic analysis, along with transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) to assess EV yield, morphology, surface protein expression and subpopulation diversity. Our results revealed significant differences in three EV isolation methods. AF4 is particularly enriched for EV subpopulations expressing high levels of classical tetraspanins (e.g., CD81, CD9 and CD151), and single-pass membrane proteins (e.g., ITGA4 and ITAGB1). Exo-CMDS demonstrated the highest reproducibility across samples, isolating specific EV subpopulations enriched in markers like CD5. SEC provided the highest yield but co-isolated significant amounts of non-vesicular particles, including lipoproteins. The findings contribute valuable insights toward standardized and reliable EV isolation practices for research and clinical applications.}, }
@article {pmid40574733, year = {2025}, author = {Fumo, JT and Nichols, PK and Ely, T and Marko, PB and Moran, AL and Powell, BS and Williams, TM and Kosaki, RK and Smith, CM and Lopes, KH and Smith, JE and Spalding, HL and Krueger-Hadfield, SA and McDermid, KJ and Hauk, BB and Morioka, J and O'Brien, K and Kennedy, B and Leliaert, F and Fujii, MT and Nelson, WA and Draisma, SGA and Sherwood, AR}, title = {A predictive framework for identifying source populations of non-native marine macroalgae: Chondria tumulosa in the Pacific Ocean.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19610}, pmid = {40574733}, issn = {2167-8359}, mesh = {Pacific Ocean ; *Seaweed/classification/genetics ; *Rhodophyta/classification/genetics ; Hawaii ; Ecosystem ; *Introduced Species ; }, abstract = {The cryptogenic marine red alga Chondria tumulosa was first observed in 2016 in subtidal habitats at Manawai (Pearl and Hermes Atoll) in the Papahānaumokuākea Marine National Monument (PMNM), Hawai'i. Without molecular or morphological matches to any known species, it was described in 2020 and declared cryptogenic. This alga has substantially increased in benthic cover and has been discovered on two additional atolls in PMNM: Kuaihelani (Midway) and Hōlanikū (Kure). It exhibits several characteristics indicative of non-native origins including putative prior absence in the region, persistence in high densities over nearly a decade, apparent lack of native herbivore pressure, and strong tetrasporophytic bias. Importantly, it is negatively impacting the culturally and ecologically valuable reefs of PMNM. The geographical origin of this putative invasion is unknown, and there are no published reports of the species occurring anywhere other than PMNM. The central Pacific location of Hawai'i allows a broad range of potential sources for the origin of C. tumulosa. Taxonomic ambiguities within the genus Chondria and challenges associated with sampling necessitate the development of a narrowed set of search locations and efficient search strategies to detect the species outside of PMNM. Attachment to floating debris is a potential introduction vector for C. tumulosa into PMNM, and an oceanographic model was used to identify the most likely source locations for this pathway between 2000 and 2015, including Japan in the western Pacific, Johnston Atoll, the Line Islands including Palmyra Atoll in the central Pacific, and Clipperton Atoll and the Galápagos Islands in the eastern Pacific. We used a recently developed and validated eDNA assay for detecting C. tumulosa from three of the regions of interest to screen for C. tumulosa with no samples yielding positive detections. We provide a framework for investigating positive eDNA field detections using in-water surveys, microscopy, and DNA barcoding. A parallel sampling effort targeting preserved specimens stored in global herbaria is also presented, which did not yield any detections. Several Chondria species remain targets for sequencing from global herbaria. Identification of the native range of C. tumulosa is a critical step that will allow for an evaluation of its evolutionary ecology and any shifts that may have occurred that facilitated its putative invasion and subsequent spread, offering insights crucial for the development of mitigation strategies to safeguard PMNM against further risk.}, }
@article {pmid40573282, year = {2025}, author = {Wang, W and Liu, Y and Lou, W and Chen, L and Xie, T and Wang, Z and Ma, Y and Gao, H}, title = {A Comprehensive Quality Evaluation System for Medicinal Leeches by Integrating Macromolecular Protein Analysis and Small-Molecule Marker Detection as Well as Quantitative Bioassays.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {6}, pages = {}, pmid = {40573282}, issn = {1424-8247}, support = {No. CI2021A05053//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; No. CI2021A04401//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; No. 2023YFC3504000//National Key R&amp;D Program of China/ ; No. ZYJGKX202414//Fundamental Research Funds for the Central public welfare research institutes/ ; }, abstract = {Background/Objectives: Medical leech (Hirudo in the Chinese Pharmacopoeia) is renowned in traditional medicine for its significant antithrombin activity. As an animal-derived medicine with complex and incompletely understood composition, its insufficient quality control measures are met with widespread counterfeiting caused by limited animal resources and rising demand. Methods: In this study, an integrated quality evaluation strategy guided by "Totality of the Evidence" (TOE) method is proposed. This strategy combines chemical characterization of small and macromolecular components with bioassays relevant to its clinical functions. A total of 28 batches of samples were analyzed, comprising 23 genuine and 5 counterfeit batches. Species origins were identified by morphology and DNA barcoding. Chemical characterization included TLC, HPLC and UPLC-QTOF-MS/MS for small molecules, and SDS-PAGE with HPLC-Orbitrap Fusion Lumos Tribrid-MS for macromolecules. Antithrombotic activity was assessed by thrombin titration and platelet aggregation assays. Results: Several characteristic components were discovered and identified as key quality control markers, including eight small molecules such as an unreported compound SZ-1, plus seven major differential proteins across species. Based on these markers, accurate and rapid authentication methods were established using SDS-PAGE for macromolecules, and both HPLC and TLC for small molecules. Furthermore, using bioassay methods we established for quality evaluation, Hirudo nipponica exhibits potent anti-thrombin activity and inhibits platelet aggregation, while Whitmania pigra shows weak anti-thrombin activity and promotes platelet aggregation. Conclusions: This quality evaluation strategy is not only applicable for the quality assessment of genuine Hirudo products of different origins, but also for distinguishing medical leeches from their counterfeits.}, }
@article {pmid40569485, year = {2025}, author = {Hazarika, TK and Momin, MD and Ibrahim, KS and Lalrinzuala, P and Dutta, H and Singh, TS and Debbarma, P and Das, J and Bora, A}, title = {Morphological and molecular insights into the wild Ficus species of Mizoram, Northeast India.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {643}, pmid = {40569485}, issn = {1573-4978}, mesh = {*Ficus/genetics/anatomy &amp; histology/classification ; India ; Phylogeny ; Genetic Variation/genetics ; DNA Barcoding, Taxonomic/methods ; Fruit/genetics ; }, abstract = {BACKGROUND: The genus Ficus L., commonly known as fig and belonging to the family Moraceae, is widely distributed across tropical and subtropical regions of Asia, Africa, America, and Australia. Ficus species hold significant importance in horticulture and traditional medicine due to their aesthetic, edible, and therapeutic properties. Nevertheless, the pronounced morphological diversity and intricate genetic makeup of these species require the application of molecular techniques for precise identification and comprehensive assessment of genetic diversity.<br><br>METHODS AND RESULTS: This study focuses on the morphological, molecular characterization, and phylogeny of wild Ficus species in Mizoram, Northeast India. Morphological traits of the plants and fruits were observed, and molecular analysis was conducted using DNA barcoding of the rbcL gene, with the resulting sequences submitted to NCBI GenBank. Significant variation in morphological traits was observed among the studied Ficus species. Phylogenetic analysis based on rbcL gene sequences confirmed genetic diversity, with notable genetic similarity identified in Ficus velutina (MTMZU12 and MTMZU13) despite their morphological similarity.<br><br>CONCLUSIONS: The study underscores how genetic and environmental factors shape morphology and shows that integrating molecular and morphological data improves phylogenetic resolution in Northeast India, a critical biodiversity hotspot.}, }
@article {pmid40567577, year = {2025}, author = {Sire, L and Martin, C and Parmain, G and Bézier, A and Herniou, EA and Bouget, C and Lopez-Vaamonde, C}, title = {Incorporating Neglected Insect Larvae in Species Inventories: DNA Barcoding as an Effective Tool for All-Stage Invertebrate Identification in Tree Holes.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71586}, pmid = {40567577}, issn = {2045-7758}, abstract = {Invertebrates, especially insects, are an integral part of biodiversity. Many species live in forest ecosystems where they play a key role in decomposing wood and maintaining ecosystem functions. Nevertheless, global changes, like fires, storms, and pest outbreaks, are impacting insect diversity, reinforcing the need for long-term biomonitoring to understand and tackle these issues. Forests are heterogeneous ecosystems with tree-related microhabitats (TReMs) such as tree holes, which are important for ecosystem diversity. Conventional identification approaches for species inventories are frequently hampered by the extensive and hidden diversity of insect larval stages. Thus, there is a crucial need to develop tools that facilitate inventories of these ecological niches and allow the incorporation of such hidden diversity into long-term monitoring studies. To that end, we explored the biodiversity found in tree holes within French state forests using DNA barcoding and addressed challenges associated with traditional morphological identification methods. Results demonstrate the successful application of DNA barcoding in identifying nearly 62% of all invertebrates sampled from tree holes to the species level. Sampled invertebrates comprised 44% of larvae (566 individuals), of which nearly 50% could be assigned a species name. In total, 108 species and 173 barcode index numbers (BINs, used as species proxy) were molecularly inventoried, and 39% of these identified species were solely represented by larvae in our sampling. Our study highlights the usefulness of DNA-based identification methods and the significance of including larvae in biodiversity assessments to gain insights into species abundance and functional diversity. It also underscores the necessity of ongoing and parallel developments of DNA reference libraries to improve species molecular identification rates and accuracy, and the need to investigate potential non-destructive alternatives for biomonitoring. These efforts aim to ensure thorough and precise monitoring of invertebrate communities in tree holes and similar microhabitats.}, }
@article {pmid40567417, year = {2025}, author = {Pasquariello, M and Martinelli, T and Paris, R and Moschella, A and Colombo, R and Di Bello, A and Frigerio, J and Kheloufi, A and Mirzaabolghasemi, MA and Puglisi, D and Esposito, S and Scalercio, S and Virzì, N and De Vita, P and Pecchioni, N and Bassolino, L}, title = {Exploring the chemotypic variability of Silybum marianum and Silybum eburneum by biochemical and genetic characterization.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1584104}, pmid = {40567417}, issn = {1664-462X}, abstract = {The Silybum genus belonging to the Asteraceae family, is composed of two species, marianum and eburneum, although, in the past, their classification was not always appropriate. While Silybum marianum is very well known since ancient times for the medicinal properties of a blend of different flavonolignans contained in the achenes and named silymarin, very little information is available about Silybum eburneum chemodiversity. Here, we describe the biochemical characterization of a wide ex situ germplasm collection including 83 wild Silybum accessions collected during ad hoc sampling campaigns in Italy, Spain, Iran and Algeria as well as accessions acquired by seed GenBanks and studied at both population and single plant level. Interestingly, our results confirm the presence of only three chemotypes in S. marianum, namely A, B and C. Conversely, S. eburneum accessions, exhibit a distinct and stable chemotype (D) where isosilychristin is the predominant silymarin component. Additionally, DNA barcoding based on the ribosomal DNA region ITS2 combined with morphological phenotyping and chemotyping, successfully resolves frequently found mistakes in the identification of the two species. These findings significantly expand our knowledge of the global biodiversity of the Silybum genus and provide valuable insights for future breeding programs and potential applications in nutrition and human health sciences.}, }
@article {pmid40567021, year = {2025}, author = {Xu, L and Chen, R and Wang, X and Liu, D and Liu, Y and Zhao, CX}, title = {DNA Barcoding-Enabled Tracking of Lipid Nanoparticles: Drug-Loading-Dependent Biodistribution and Tumor Microenvironment Targeting.}, journal = {Advanced healthcare materials}, volume = {}, number = {}, pages = {e2501914}, doi = {10.1002/adhm.202501914}, pmid = {40567021}, issn = {2192-2659}, support = {APP2008698//National Health and Medical Research Council/ ; }, abstract = {Lipid nanoparticles (LNPs) are versatile drug delivery systems, yet the impact of drug loading (DL) on their biodistribution and cellular uptake remains poorly understood. Optimizing drug loading is crucial for enhancing therapeutic efficacy and safety, as higher loading allows for lower LNP doses, reducing overall nanomaterial burden. Addressing this knowledge gap is essential for advancing LNP-based cancer therapies. This study integrates DNA barcoding technology with LNPs to evaluate their in vivo delivery behaviors under varying drug loadings. Using a sequential nanoprecipitation method, DNA-barcoded LNPs with low (1%), medium (16%), and high (26%) drug loadings are fabricated, each tagged with a unique DNA barcode for precise tracking. Pooled LNPs are intravenously administered to tumor-bearing mice, and their biodistribution across organs is quantified via qPCR. High drug-loading LNPs demonstrate preferential accumulation in the spleen, while low drug-loading LNPs exhibit higher liver accumulation, suggesting faster clearance. Cellular uptake analysis reveals enhanced uptake of high drug-loading LNPs by tumor-associated macrophages within the tumor microenvironment (TME). This study establishes a robust platform for simultaneous and high-sensitivity monitoring of LNP behaviors, significantly reducing animal use and interanimal variability. The findings guide the rational design for developing optimal LNPs for cancer therapies targeting specific TME components.}, }
@article {pmid40565578, year = {2025}, author = {Peña, F and Univaso, L and Román-Figueroa, C and Paneque, M}, title = {In Silico Genomic Analysis of Chloroplast DNA in Vitis Vinifera L.: Identification of Key Regions for DNA Coding.}, journal = {Genes}, volume = {16}, number = {6}, pages = {}, pmid = {40565578}, issn = {2073-4425}, support = {40035912-0/2022//FIC-&#xd1;uble/ ; }, mesh = {*Vitis/genetics/classification ; *Genome, Chloroplast/genetics ; *DNA, Chloroplast/genetics ; Phylogeny ; Microsatellite Repeats/genetics ; DNA Barcoding, Taxonomic/methods ; Genomics/methods ; Chloroplasts/genetics ; Computer Simulation ; }, abstract = {BACKGROUND/OBJECTIVES: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding.<br><br>METHODS: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties.<br><br>RESULTS: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine-cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers.<br><br>CONCLUSIONS: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera.}, }
@article {pmid40565551, year = {2025}, author = {Guo, X and Huang, W and Zhao, Z and Xue, D and Wu, Y}, title = {Comparative Analysis of Plastomes of Artemisia and Insights into the Infra-Generic Phylogenetic Relationships Within the Genus.}, journal = {Genes}, volume = {16}, number = {6}, pages = {}, pmid = {40565551}, issn = {2073-4425}, support = {LQ24C020002//Zhejiang Provincial Natural Science Foundation/ ; 32270215//National Natural Science Foundation of China/ ; }, mesh = {*Artemisia/genetics/classification ; *Phylogeny ; *Genome, Chloroplast/genetics ; Evolution, Molecular ; Base Composition ; }, abstract = {Background: Artemisia is a large and complex genus comprising about 500 species. Currently, only a limited number of plastomes (the chloroplast genome) of Artemisia are available. Their structures have not been comparatively analyzed, and a phylogenetic backbone based on plastome-scale data is still lacking. This situation has greatly hindered our understanding of the plastome variation patterns and infra-generic relationships of the genus. Methods: We newly sequenced 34 Artemisia plastomes representing 30 species and three varieties. Combining this with previously published plastomes, we comparatively analyzed their structure and constructed phylogenetic relationships using the protein-coding sequences (CDS) of plastomes. Results: Our analyses indicated that the Artemisia plastomes are conserved in terms of their structure, GC content, gene number, and order. The sequence divergence is higher in the LSC and SSC regions than in the IR regions. Three protein-coding genes and four non-coding regions, i.e., accD, petG, ycf1, rpoC1-rpoC2, rpoC2-rps2, trnG(UCC)-trnfM(CAU), and ndhG-ndhI, were highly diverse and could be chosen as candidates of DNA barcodes. Phylogenetic trees were divided into several clades, and all four main subgenera were not monophyletic. Additionally, the phylogenetic position of A. stracheyi is still controversial. Conclusions: Plastomes can provide important information for phylogenetic constructions. This study provides insights into the infra-generic relationships within Artemisia and also lays a foundation for future evolutionary studies of this genus.}, }
@article {pmid40565087, year = {2025}, author = {Li, J and Zhang, Y and Liu, Y and Wei, S and Huang, Z and Chen, L and Huang, H}, title = {Comprehensive Analysis of Genetic and Morphological Diversity in Echinochloa spp. Populations Infesting Paddy Fields in Ningxia, China.}, journal = {International journal of molecular sciences}, volume = {26}, number = {12}, pages = {}, pmid = {40565087}, issn = {1422-0067}, mesh = {*Echinochloa/genetics/classification/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; *Genetic Variation ; China ; Phylogeny ; *Plant Weeds/genetics ; Herbicide Resistance/genetics ; }, abstract = {Barnyard grass is the most problematic weed in paddy fields in Ningxia. Its substantial morphological variation complicates both identification and control, yet the genetic diversity of barnyard grass infesting paddy fields in Ningxia has not been thoroughly studied. In this research, we analyzed the genetic diversity of 46 barnyard grass populations from Ningxia's paddy fields based on the assessment of morphological traits, DNA barcoding, and SCoT-targeted gene markers. Nine morphological traits were quantitatively analyzed, among which three phenological traits, i.e., leaf length, stem diameter, and plant height, exhibited notable variations. Correlational analysis revealed a positive relationship between morphological traits and multi-herbicide resistance profiles. To assess genetic diversity, four DNA barcodes (ITS, psbA, matK, and trnL-F) were used, among which ITS demonstrated the strongest potential in single-gene barcoding for barnyard grass species identification. Cluster analysis based on ITS barcode sequences was performed to group the populations into five main categories. Additionally, SCoT marker analysis using six primers was performed to classify the 46 barnyard grass samples into five groups. The results showed that the predominant barnyard grass species in Ningxia were E. colona, E. crus-galli var. Formosensis, E. crusgalli, E. oryzoides, and E. crusgalli var. Zelayensis, with E. colona being the most prevalent. The differences observed between the morphological and molecular marker-based classifications were method-dependent. However, both SCoT molecular marker technology and DNA barcoding contributed to identifying the genetic diversity of barnyard grass. Taken together, our study revealed significant morphological and genetic variations among barnyard grass populations, which correlated with herbicide sensitivity in Ningxia's paddy fields, underscoring the necessity for an integrated weed management approach to combat this troublesome weed species.}, }
@article {pmid40564765, year = {2025}, author = {Yalçın, E and Aslan, S and Toğaçar, M and Demir, SC}, title = {A Hybrid Artificial Intelligence Approach for Down Syndrome Risk Prediction in First Trimester Screening.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {12}, pages = {}, pmid = {40564765}, issn = {2075-4418}, abstract = {Background/Objectives: The aim of this study is to develop a hybrid artificial intelligence (AI) approach to improve the accuracy, efficiency, and reliability of Down Syndrome (DS) risk prediction during first trimester prenatal screening. The proposed method transforms one-dimensional (1D) patient data-including features such as nuchal translucency (NT), human chorionic gonadotropin (hCG), and pregnancy-associated plasma protein A (PAPP-A)-into two-dimensional (2D) Aztec barcode images, enabling advanced feature extraction using transformer-based deep learning models. Methods: The dataset consists of 958 anonymous patient records. Each record includes four first trimester screening markers, hCG, PAPP-A, and NT, expressed as multiples of the median. The DS risk outcome was categorized into three classes: high, medium, and low. Three transformer architectures-DeiT3, MaxViT, and Swin-are employed to extract high-level features from the generated barcodes. The extracted features are combined into a unified set, and dimensionality reduction is performed using two feature selection techniques: minimum Redundancy Maximum Relevance (mRMR) and RelieF. Intersecting features from both selectors are retained to form a compact and informative feature subset. The final features are classified using machine learning algorithms, including Bagged Trees and Naive Bayes. Results: The proposed approach achieved up to 100% classification accuracy using the Naive Bayes classifier with 1250 features selected by RelieF and 527 intersecting features from mRMR. By selecting a smaller but more informative subset of features, the system significantly reduced hardware and processing demands while maintaining strong predictive performance. Conclusions: The results suggest that the proposed hybrid AI method offers a promising and resource-efficient solution for DS risk assessment in first trimester screening. However, further comparative studies are recommended to validate its performance in broader clinical contexts.}, }
@article {pmid40562837, year = {2025}, author = {de Medeiros, BAS and Cai, L and Flynn, PJ and Yan, Y and Duan, X and Marinho, LC and Anderson, C and Davis, CC}, title = {A composite universal DNA signature for the tree of life.}, journal = {Nature ecology &amp; evolution}, volume = {9}, number = {8}, pages = {1426-1440}, pmid = {40562837}, issn = {2397-334X}, support = {DEB-0544039//National Science Foundation (NSF)/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Neural Networks, Computer ; Biodiversity ; }, abstract = {Species identification using DNA barcodes has revolutionized biodiversity sciences. However, conventional barcoding methods may lack power and universal applicability across the tree of life. Alternative methods based on whole genome sequencing are hard to scale due to large data requirements. Here we develop a novel DNA-based identification method, varKoding, using exceptionally low-coverage genome skim data to create two-dimensional images representing the genomic signature of a species. Using these representations, we train neural networks for taxonomic identification. Applying a taxonomically verified novel genomic dataset of Malpighiales plant accessions, we optimize training hyperparameters and find the highest performance by combining a transformer architecture with a new modified chaos game representation. Greater than 91% precision is achieved despite minimal input data, exceeding alternative methods tested. We illustrate the broad utility of varKoding across several focal clades of eukaryotes and prokaryotes. We also train a model capable of identifying all species in the Sequence Read Archive of the National Center for Biotechnology Information using less than 10 Mbp sequencing data with 96% precision and 95% recall and robust to sequencing platforms. The varKoding approach offers enhanced computational efficiency and scalability, minimal data inputs robust to sequencing details and modularity for further development in biodiversity science.}, }
@article {pmid40559832, year = {2025}, author = {González-Velo, M and Espinosa-Sánchez, A and Ripa, A and Hurtado-Preciado, MA and Martínez-Estéllez, MAH and Fernández-García, JL and Bazo-Pérez, C}, title = {Contributions to Knowledge of the Dictyocaulus Infection of the Red Deer.}, journal = {Veterinary sciences}, volume = {12}, number = {6}, pages = {}, pmid = {40559832}, issn = {2306-7381}, abstract = {Dictyocaulosis is a parasitic disease that affects ungulate species, including red deer (Cervus elaphus). The genus Dictyocaulus comprises eighteen species, but only four have been reported to infect red deer. The disease is characterized by respiratory tract infection, particularly in the lungs, bronchi, and bronchioles, leading to inflammatory and hemorrhagic microscopic lesions, as well as emphysema and edema. The biological cycle involves a female ovipositing larvated eggs in the bronchi and trachea, which are expelled to the exterior through coughing or feces, releasing L1 into the environment. In this study, 106 adult red deer were collected from seven locations in Extremadura (Spain). Eight positive lungs were initially assessed by morphological identification, revealing a mean intensity of 13.3 adult worms per infected lung, with a global decrease to an average of 1.8 adult worms per sampled lung. The presence of adult worms in the upper and middle respiratory tract was confirmed through anatomopathological analysis. Molecular identification was performed by sequencing the COI gene. The results indicated the presence of three genetic groups, supported by significant subdivision using the ɸST measure. D. cervi and D. viviparus exhibited their respective matrilineal ancestry, while D. eckerti and D. cervi demonstrated matrilineal sharing. Consequently, the possibility of introgression between these two species was suggested. Although D. viviparus had previously been identified in the same Spanish region based on morphological characteristics, D. cervi and D. eckerti were reported for the first time in the explored geographic area.}, }
@article {pmid40559028, year = {2025}, author = {Shah, HK and Fathima, PA and Rahi, M and Saini, P}, title = {Report of a New Sand Fly (Diptera: Psychodidae) Species, Sergentomyia (Neophlebotomus) pradeepii n. sp. from Madhya Pradesh, India.}, journal = {Insects}, volume = {16}, number = {6}, pages = {}, pmid = {40559028}, issn = {2075-4450}, support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; }, abstract = {Madhya Pradesh, a biodiversity-rich state in central India, reports sporadic non-indigenous leishmaniasis cases. Systematic entomological surveillance as part of molecular xenomonitoring in sand flies led to the discovery of a new species, Sergentomyia (Neophlebotomus) pradeepii n. sp. (Diptera: Psychodidae), from Johariya village in Sagar district, Madhya Pradesh, India. A systematic cross-sectional survey of sand flies was conducted in Bhopal, Sagar, and Hoshangabad districts of Madhya Pradesh. Standard collection methods were employed for two months, i.e., from July to August 2023. DNA barcoding targeting the mitochondrial Cytochrome c oxidase subunit I (COI) gene was performed, and the generated sequences were phylogenetically analyzed. Se. (Neo.) pradeepii, a newly recorded sand fly species, is reported in this study. Its taxonomic relationship to other congeners of subgenus Neophlebotomus is discussed. COI barcoding and phylogenetic analysis established that the specimens fit into the same taxonomic group, exhibiting negligible gene flow within the population, while a 13.4% genetic distance from congeners establishes it as a separate species. Madhya Pradesh, with its rich biodiversity and favorable conditions for sand fly proliferation, lacks systematic entomological surveillance. This study enhances the knowledge of the state's sand fly fauna by reporting and providing a detailed morphological and molecular description of the new species.}, }
@article {pmid40559020, year = {2025}, author = {Wang, B and Ha, S and Cai, J and Ma, Y and Li, D and Chen, J and Deng, J}, title = {Exploratory Study on DNA Barcode Combined with PCR-HRM Technology for Rapid and Accurate Identification of Necrophilous Fly Species.}, journal = {Insects}, volume = {16}, number = {6}, pages = {}, pmid = {40559020}, issn = {2075-4450}, support = {Grant No. 82060341, Grant No. 82471916, Grant No. 81560304//National Natural Science Foundation of China/ ; Grant No.2024D14016//Research Innovation Team Project of Xinjiang/ ; Grant No.XYD2024C05//Research Innovation Team Project of Xinjiang Medical University,/ ; Grant No. YSPTZX202134//Hainan academician innovation platform scientific research project/ ; Grant No. HYYS2021A06//Innovative Scientific Research Project for Postgraduates of Hainan Medical College/ ; }, abstract = {Molecular species identification plays an increasingly important role in forensic entomology and is centered on selecting appropriate DNA barcodes, which there are not yet enough of. Such identification is decisive in discovering a better DNA barcode for the identification of necrophilous fly species. Here, we analyzed 10 common necrophilous fly species found on Hainan Island; designed 12 pairs of fly-specific primers from different mitochondrial regions; screened two fly DNA barcodes with better results than those of published studies, which were used as controls; and employed a high-resolution melting (HRM) curve to construct PCR-HRM technology systems for rapid and efficient necrophilous fly species identification. The results showed that, among the 14 DNA barcoding PCR-HRM systems, the newly designed COXII-519/COXII-615 primer was the best, which identified 10 necrophilous fly species in one test. The second-best system was the C1-J-2495/C1-N-2800 primer published in the literature, which identified six fly species in one test. Moreover, since the COXII-519/COXII-615 primer system performed successfully in both stale (stored over two years) and larval samples due to its short amplificated fragment (shorter than 97 bp), it may serve as a new efficient DNA barcode for necrophilic fly species identification. The new DNA barcoding PCR-HRM system established in this study enables the rapid and accurate identification of necrophilic fly species.}, }
@article {pmid40558994, year = {2025}, author = {Wu, J and Li, D and Balan, RK and George, S and Peacock, L and Pal, C}, title = {Comparative Assessment of Environmental DNA and Bulk-Sample Metabarcoding in Biosecurity Surveillance for Detecting Biting Midges (Ceratopogonidae).}, journal = {Insects}, volume = {16}, number = {6}, pages = {}, pmid = {40558994}, issn = {2075-4450}, support = {405732//Ministry for Primary Industries/ ; }, abstract = {Biting midges, Culicoides spp. (Diptera: Ceratopogonidae), are significant vectors capable of transmitting arboviruses, such as bluetongue virus, to livestock. New Zealand is free of Culicoides, and a national surveillance programme is in place for the early detection of an incursion. Traditionally, insect trap samples from the surveillance programme are analyzed using morphology-based diagnostics under microscopes, which is time-consuming and relies on specialized taxonomic expertise. Here, we assessed the effectiveness of DNA metabarcoding using insect bulk samples and environmental DNA (eDNA) from liquid samples collected in surveillance traps. Two Cytochrome oxidase I (COI) barcoding primer sets were employed to study biodiversity and detect exotic species. The results indicated that DNA metabarcoding with homogenized insect bulk samples had a higher overall detection accuracy rate (over 81% for both primer pairs) compared to ethanol fluid-derived eDNA samples from traps (68.42% and 55.26% for the primer sets LCO1490/HCO2198 and mlCOIintF/jgHCO2198, respectively) based on congruence with morphological identification. Detection failures were likely due to eDNA extraction issues or low target species abundance. Both approaches showed similar insect community composition and diversity in the surveillance trap samples, suggesting the potential of DNA metabarcoding for biosecurity surveillance and biodiversity assessments. Overall, DNA metabarcoding using bulk insect samples could enhance the efficiency of Culicoides surveillance, reducing workload and screening time.}, }
@article {pmid40558971, year = {2025}, author = {Motato-Vásquez, V and Vinasco-Diaz, LK and Londoño-Caicedo, JM and Bolaños-Rojas, AC}, title = {Hidden Treasures of Colombia's Pacific Mangrove: New Fungal Species and Records of Macrofungi (Basidiomycota).}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {40558971}, issn = {2309-608X}, abstract = {Mangrove-associated fungi represent a diverse but understudied group of eukaryotic organisms, especially in the Neotropics. The Colombian Pacific region, with approximately 1300 km of coastline covered with 194,880 ha of mangrove forests that remain largely unexplored for macrofungal diversity, is recognized as a global biodiversity hotspot. This study aimed to catalog the macrofungi associated with mangrove ecosystems in Colombia, integrating morphological characterization and molecular phylogenetics, focusing on three Valle del Cauca Pacific coast localities. A total of 81 specimens were collected from both living trees and decaying wood. Detailed macroscopic and microscopic analyses were conducted, and DNA sequences from two ribosomal DNA barcode regions (ITS and LSU) were generated for 43 specimens. Three new species-Neohypochnicium manglarense, Phlebiopsis colombiana, and Porogramme bononiae-were documented. In addition, eight species were reported as new records for both Colombia and mangrove ecosystems, including Microporus affinis, Paramarasmius palmivorus, Phlebiopsis flavidoalba, Porogramme brasiliensis, Resinicium grandisporum, Trametes ellipsospora, T. menziesii, and T. polyzona. Although previously recorded in Colombian terrestrial ecosystems, Lentinus scleropus and Oudemansiella platensis are globally reported here for the first time from mangrove habitats. Furthermore, Fomitopsis nivosella and Punctularia strigosozonata were documented for the first time in Colombia. This study addresses the first exploration of mangrove-associated macrofungi in the country and provides new insights into the hidden fungal diversity and potential of mangrove ecosystems as a latent niche for basidiomycete dispersal along Colombia's Pacific coast.}, }
@article {pmid40556097, year = {2025}, author = {Aristya, GR and Budiman, MS and Kasiamdari, RS and Widiastuti, A and Arif, MF}, title = {Genetic Variation and Phylogenetic Analysis of Strawberry (Fragaria spp.) on Yogyakarta and Central Java, Indonesia, Based on rbcL DNA Barcoding.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {28}, number = {3}, pages = {121-130}, doi = {10.3923/pjbs.2025.121.130}, pmid = {40556097}, issn = {1812-5735}, mesh = {Indonesia ; *Phylogeny ; *Genetic Variation/genetics ; *Fragaria/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Haplotypes ; *DNA, Plant/genetics ; Fruit/genetics ; }, abstract = {Background and Objective: Strawberry (Fragaria spp.) is known for producing fruit with high economic value and significant nutritional content. Recently, the growing diversity of cultivated strawberries in Indonesia has made it challenging to distinguish the original characteristics of early ancestors and identify superior traits. The DNA barcoding, mainly through the chloroplast gene rbcL, offers a precise and detailed method for this identification. This research aims to reconstruct a phylogenetic tree, analyze genetic variation and determine the haplotype distribution of six strawberry cultivars from Java, particularly Yogyakarta and Central Java, based on the rbcL gene. Materials and Methods: The rbcL gene was amplified using DNA amplification techniques with rbcL-F and rbcL-R primers. The resulting data were analyzed to construct a phylogenetic tree using ML via IQtree software and BI using MrBayes software. The alignment results were used to determine genetic distances and identify polymorphic sites. This study assessed intraspecific genetic variation by examining h, identifying polymorphic sites, generating a haplotype network using PopART v1.7 and conducting PCoA with GenAIEx 6.503. Results: The results showed that the rbcL gene was successfully amplified with a length of 1,221 bp after alignment with the GenBank database. Phylogenetic analysis using ML revealed that the six cultivars formed a single clade with a bootstrap value of 97. BI similarly indicated the formation of one clade with a posterior probability value of 1. Haplotype analysis showed that the cultivars 'Californica', 'Knia', 'Mencir', 'Moha' and 'Geolhyang' belonged to the same haplotype group, while the 'Bali×Jumbo' cultivar was placed in a different group. Conclusion: Haplotype network analysis and PCoA further indicated that the genetic variation of Indonesian strawberries, as assessed through the rbcL gene, is similar to strawberries from the United States and China.}, }
@article {pmid40555940, year = {2025}, author = {Zhai, J and Li, X and Dong, F and Ema, H}, title = {How Faithful Flt3-Cre Mouse is to Hematopoietic Lineage Tracing?.}, journal = {Stem cell reviews and reports}, volume = {}, number = {}, pages = {}, pmid = {40555940}, issn = {2629-3277}, abstract = {Flt3 gene expression is known to occur at a specific development stage of hematopoiesis in mice. Flt3-Cre reporter mice have been utilized in lineage tracing studies. This review systematically evaluates different Flt3-Cre reporter constructs, focusing on labeling efficiency and consistency with endogenous Flt3 expression patterns. We discuss the strengths and limitations associated with employing marker gene expression in lineage tracing. Furthermore, this lineage tracing strategy is compared with clonal tracing strategies such as barcoding and single-cell transplantation. Finally, we propose comparing hematopoietic stem cells identified by barcoding with those identified by transplantation to know the relationship between HSCs in non-stress and stress conditions. HIGHLIGHTS: • Flt3-Cre reporter mice are excellent models to understand hematopoiesis but may not necessarily reflect endogenous expression of Flt3. • The labeling efficiency significantly differs among the Flt3-Cre reporter mice.}, }
@article {pmid40555399, year = {2025}, author = {Lindenmaier, MP and Bernart, MW and Brinckmann, JA}, title = {Advanced Methodologies for the Quality Control of Herbal Supplements and Regulatory Considerations.}, journal = {Phytochemical analysis : PCA}, volume = {}, number = {}, pages = {}, doi = {10.1002/pca.70000}, pmid = {40555399}, issn = {1099-1565}, abstract = {INTRODUCTION: Herbal supplements and OTC herbal drugs enjoy wide popularity with consumers but their quality has been questioned by genomic methods of testing. Due to complex regulatory environments in Europe and North America, the quality assurance of herbal preparations depends on protocols, which can significantly differ between the respective national and supranational drug control agencies. Modern methods of analysis combine genetic testing (DNA barcoding) with advanced chromatographic techniques as well as traditional microscopic and macroscopic tests to detect adulterants and undesirable constituents of herbs, including alkylphenols, aristolochic acids, and pyrrolizidine alkaloids.<br><br>OBJECTIVE: This review will give an account of current trends in herbal drug analysis and explain the shortcomings of existing methodologies. The article will also discuss regulatory protocols, compendial methods and differentiate between dietary supplement testing regimens and the requirements for approved herbal drugs. The purpose of this review is to document current trends in genetic testing and reveal future developments in drug analysis to reduce the possibility of adulterations and assure the authenticity of herbal products.<br><br>RESULTS: Chemometric methods and orthogonal approaches aid in the deconvolution of chromatographic and spectral data while expanding databases for nucleotide sequences and mineable spectra support method development in herbal analysis.<br><br>CONCLUSION: Genetic testing of herbal products has further increased the capabilities to detect minute adulterations, but such assays are only meaningful in combination with chromatographic and spectroscopic analysis. Despite the advancement of genomic testing, chemometrics, UHPLC and mass spectrometry, cost-effective quality control techniques such as HPTLC in conjunction with microscopic and macroscopic examination remain important particularly in regulated environments.}, }
@article {pmid40552098, year = {2025}, author = {Ramanan, A and Quek, KH and Chung Mae Sze, N and Oo Xinyen, NI and Kim Hyun Soo, D and Sung, C and Dimitrov, V and Nix, RP and Sng, MHM and Lim, PXJ and Lim, EXY and Wainwright, BJ}, title = {In Troubled Waters: Applying DNA Barcoding to Monitor Singapore's Shark Fin Trade.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71607}, pmid = {40552098}, issn = {2045-7758}, abstract = {The global fin trade poses a significant threat to shark populations; many species of shark are at risk of extinction due to overfishing and unsustainable practices. This study examines the fin trade in Singapore, a globally significant fin trading hub, market and transit point. Using DNA barcoding techniques, we attempted to determine the species of origin for 300 processed fins that could not be identified by visual techniques. Fins were collected from a variety of outlets across Singapore. We identified 12 species, eight of which were identified as threatened on the IUCN Red List of threatened species (critically threatened n = 2, endangered n = 4 &amp; vulnerable n = 2). Of all the samples we identified to the species or genus level, 13 (12 species and 1 entire genus) are listed on CITES Appendix II. This listing means that international trade has to be controlled to prevent further population declines and utilisation incompatible with their survival. Ninety-eight percent of all the identifications made in this work belonged to species that are listed on CITES Appendix II. Demonstrating the importance of regular and repeated monitoring, we identified the blackchin guitarfish (Glaucostegus cemiculus); this is the first occurrence of fins from this species within Singapore and the wider Southeast Asian region. This is a CITES Appendix II listed species and one that has been designated as critically endangered by the IUCN. Without repeated monitoring, the presence of this species in Singpaore would likely have gone undetected.}, }
@article {pmid40549669, year = {2025}, author = {Surwase, SS and Zhou, XMM and Luly, KM and Zhu, Q and Talebian, N and Anders, RA and Green, JJ and Tzeng, SY and Sunshine, JC}, title = {DNA-barcode-based Multiplex Immunofluorescence Imaging to Analyze FFPE Specimens from Genetically Reprogrammed Murine Melanoma.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {220}, pages = {}, doi = {10.3791/68124}, pmid = {40549669}, issn = {1940-087X}, mesh = {Animals ; Mice ; Paraffin Embedding/methods ; *Fluorescent Antibody Technique/methods ; *Melanoma/genetics/pathology/chemistry ; *Melanoma, Experimental/genetics/pathology/chemistry ; Formaldehyde/chemistry ; *DNA/genetics/chemistry ; Tumor Microenvironment ; Tissue Fixation/methods ; }, abstract = {Presented here is an emerging DNA-barcode-based multiplex imaging technique based on Co-Detection-by-indEXing that analyzes the spatial proteomics of tissue microenvironments. Successful imaging requires a repertoire of well-designed and properly validated antibody panels, but very few currently exist for formalin-fixed paraffin-embedded (FFPE) samples. FFPE offers several advantages over fresh-frozen specimens, such as widespread availability, ease of handling and storage, and the ability to make tissue microarrays (TMAs). Here, we present a protocol to develop an antibody panel for visualizing and analyzing FFPE tissues from a murine melanoma model treated with nanoparticles, which deliver plasmid DNA encoding immunologic signals for tumor microenvironment reprogramming. We also describe an image analysis pipeline using open-source computational tools for annotating tissues, segmenting cells, processing proteomics data, phenotyping cell populations, and quantifying spatial metrics. The protocol offers applications for designing antibody panels in murine FFPE and generating novel insights into the spatial proteomics of complex tissue microenvironments.}, }
@article {pmid40547570, year = {2025}, author = {Mwamula, AO and Bae, CH and Lee, DG and Kim, YS and Lee, YD and Lee, DW}, title = {Description and molecular characterization of Geraldius jejuensis n. sp. (Nematoda: Chambersiellidae) from Korea.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250023}, pmid = {40547570}, issn = {0022-300X}, abstract = {A new species of the genus Geraldius isolated from the wood of a dead black pine tree is characterized using morphological data and molecular DNA barcodes. Geraldius jejuensis n. sp. is characterized by its lateral fields with two incisures; lip region conoid to rounded and continuous with body; hemizonid and excretory pore located posterior to nerve ring; excretory pore opening just at the beginning of hemizonid or within the contour of hemizonid; vulva a transverse slit in ventral view; opening in a depression, creating a circular profile in lateral view; rectum 1.4 to 1.7 times longer than anal body diameter; phasmids located 55.0 to 78.5 μm from anal opening; tail elongated, 146.0 to 177.0 μm long; gubernaculum 27.0 to 33.5 μm long, caudal papillae arrangement of seven pairs pre-cloacal, two adcloacal, and six post-cloacal; and three additional midventral papillae on anterior cloacal lip. The new species was compared with the three known species of the genus, including G. bakeri, G. galapagoensis and G. inserrai. The phylogenetic relationships among species were reconstructed using 18S-rRNA and 28S-rRNA gene sequences. Inferences from both genes corroborate the close morphological relationships between Geraldius and Diastolaimus.}, }
@article {pmid40546919, year = {2025}, author = {Levenson, HK and Tembrock, LR and Zink, FA and Mollet, KA and Tarpy, DR}, title = {Redefining the Geographic Distribution of Two Cryptic Halictus (Hymenoptera: Halictidae) Species in the Eastern United States.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71570}, pmid = {40546919}, issn = {2045-7758}, abstract = {Incomplete characterization of cryptic species complexes in pollinator communities can limit our understanding of ecosystem function, population dynamics, effects of environmental perturbations, and conservation planning. Molecular tools to distinguish morphologically indistinguishable bee species are therefore necessary but require refinement and validation to make robust inferences. Here we present newly developed primers and demonstrate their successful use for identification of two cryptic bee species, Halictus ligatus and Halictus poeyi, with overlapping ranges in the mid-Atlantic USA. We found that H. ligatus is present at higher elevations while H. poeyi is present at lower elevations, with both species present at three sample sites in central North Carolina, USA. The data generated in this study was combined with publicly available sequence data and analyzed to make inferences about the species ranges of these two bees in the Western Hemisphere. These clarified species distributions help us better understand local pollinator communities, associated habitat features, and abiotic conditions amenable to each, as well as provide insights into patterns related to their speciation.}, }
@article {pmid40546907, year = {2025}, author = {Teixeira, MAL and Aylagas, E and Pearman, JK and Carvalho, S}, title = {Gaps and Data Ambiguities in DNA Reference Libraries: A Limiting Factor for Molecular-Based Biodiversity Assessments Using Annelids as a Case Study.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71544}, pmid = {40546907}, issn = {2045-7758}, abstract = {Regional DNA reference libraries are essential to improve the accuracy of molecular-based biodiversity assessments, species identification and conservation. However, these libraries are often incomplete, limiting the full potential of molecular tools. In this study, we evaluated the completeness of DNA barcode reference data for annelids from the Red Sea, Arabian Gulf and Gulf of Oman and examined its implications for biodiversity assessments. A database of 2291 worldwide annelid species and 3131-4047 Molecular Operational Taxonomic Units (MOTUs) was compiled from the Barcode of Life Data System (BOLD). Two regional checklists -OBIS (498 species) and Wehe &amp; Fiege (892 species)-were cross-referenced against this database to identify coverage gaps and taxonomic inconsistencies. Only 24% and 23% of species in each checklist, respectively, had corresponding barcodes, and just three species were sampled from the region. Additionally, 43% of BOLD's Barcode Index Numbers (BINs) revealed taxonomic ambiguities. To further assess local annelid biodiversity, we analysed a metabarcoding dataset from 135 Autonomous Reef Monitoring Structures (ARMS) deployed on shallow reefs in the region. This yielded 5375 Amplicon Sequence Variants (ASVs), with 55% classified only to class or phylum level. Of the 1350 MOTUs identified, either none to just 14 species-level identifications were found depending on the taxonomic classification method and database, 10 of which appear to be cryptic species complexes. Based on proposed MOTU/species ratios, we estimate approximately 992 annelid species in the ARMS dataset, highlighting underexplored regional diversity. Manual inspection of clustered ASVs also revealed potential pseudogene artifacts, taxonomic misidentifications up to the class level and underestimation of species matches due to discordant MOTUs. These findings underscore the urgent need to expand regional reference libraries, apply integrative taxonomy and implement refined, user-defined MOTU clustering algorithms to improve molecular biodiversity assessments in the region.}, }
@article {pmid40546449, year = {2025}, author = {Biketova, AY and Svetasheva, TY and Taylor, AFS and Simonini, G and Gelardi, M and Morozova, OV and Polemis, E and Muñoz, JA and Albert, L and Saitta, S and Wasser, SP and Nevo, E and Zervakis, GI and Vizzini, A and Dima, B}, title = {Morphological and molecular re-assessment of European and Levantine species of the genus Hortiboletus (Boletaceae).}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e144731}, pmid = {40546449}, issn = {2210-6340}, abstract = {Hortiboletus (the former Xerocomusrubellus species complex) is one of the most taxonomically critical and difficult genera for species identification in the family Boletaceae. Here, we provide a detailed morphological and molecular re-assessment of European and Levantine species of Hortiboletus. A new species, H.hershenzoniae, is described from Israel. It is sister to H.engelii and associated with the evergreen oak Quercuscalliprinos and potentially also with Q.ithaburensis. Based on the sequence retrieved from INSDC, this species is also found in Lebanon. Accurate morphological descriptions, comprehensive sampling, type studies, biogeography, macro- and microphotographs and a historical overview on the nomenclatural issues surrounding H.rubellus, H.bubalinus, H.engelii, and H.hershenzoniae are given. An epitype collection is designated for H.rubellus. A key is provided for identification of the European and Levantine taxa. In addition, we propose a novel taxonomic combination Hortiboletusflavorubellus, which is conspecific with Boletusrubellusvar.flammeus, based on the DNA barcoding and phylogenetic analysis of type material. Boletusharrisonii is also shown to be conspecific with H.campestris. A multilocus phylogenetic analysis of four markers (ITS, LSU, tef1-α, and rpb2) reveals that Hortiboletus is a sister genus to Xerocomellus. Using the Genealogical Concordance Phylogenetic Species Recognition method, at least 19 phylogenetic species and eight putative phylogenetic species of the genus Hortiboletus can be delimited. Based on multilocus analysis, it contains from 24 to 25 species-level clades worldwide, 17 out of which represent known species, one newly described and potentially six to seven undescribed species. Tandem repeat insertions within the ITS region (both in ITS1 and ITS2) are reported for the first time, not only in the genus Hortiboletus, but in the entire subfamily Boletoideae. Their identification and characterisation were based on Tandem Repeat Finder analysis and visual assessment of the ITS alignment.}, }
@article {pmid40541962, year = {2025}, author = {Whiting, FJH and Mossner, M and Gabbutt, C and Kimberley, C and Barnes, CP and Baker, AM and Yara-Romero, E and Sottoriva, A and Nichols, RA and Graham, TA}, title = {Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {5282}, pmid = {40541962}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 202778/Z/16/Z//Wellcome Trust (Wellcome)/ ; A19771//Cancer Research UK (CRUK)/ ; DRCNPG-May21_100001//Cancer Research UK (CRUK)/ ; }, mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; Phenotype ; Cell Line, Tumor ; Fluorouracil/pharmacology ; *Colorectal Neoplasms/genetics/drug therapy ; HCT116 Cells ; *DNA Barcoding, Taxonomic/methods ; Evolution, Molecular ; }, abstract = {Cancer treatment frequently fails due to the evolution of drug-resistant cell phenotypes driven by genetic or non-genetic changes. The origin, timing, and rate of spread of these adaptations are critical for understanding drug resistance mechanisms but remain challenging to observe directly. We present a mathematical framework to infer drug resistance dynamics from genetic lineage tracing and population size data without direct measurement of resistance phenotypes. Simulation experiments demonstrate that the framework accurately recovers ground-truth evolutionary dynamics. Experimental evolution to 5-Fu chemotherapy in colorectal cancer cell lines SW620 and HCT116 validates the framework. In SW620 cells, a stable pre-existing resistant subpopulation was inferred, whereas in HCT116 cells, resistance emerged through phenotypic switching into a slow-growing resistant state with stochastic progression to full resistance. Functional assays, including scRNA-seq and scDNA-seq, validate these distinct evolutionary routes. This framework facilitates rapid characterisation of resistance mechanisms across diverse experimental settings.}, }
@article {pmid40539248, year = {2025}, author = {Stegemann, J and Augustin, MN and Ackermann, J and Fizzi, NEH and Neutsch, K and Gregor, M and Herbertz, S and Kruss, S}, title = {Levodopa Sensing with a Nanosensor Array via a Low-Cost Near Infrared Readout.}, journal = {Analytical chemistry}, volume = {97}, number = {25}, pages = {13655-13662}, doi = {10.1021/acs.analchem.5c02320}, pmid = {40539248}, issn = {1520-6882}, mesh = {Nanotubes, Carbon/chemistry ; *Levodopa/blood/analysis ; Humans ; *Biosensing Techniques/economics/instrumentation/methods ; Signal-To-Noise Ratio ; Infrared Rays ; }, abstract = {Near infrared (NIR) signals are beneficial for biomedical applications due to reduced light absorption, scattering, and autofluorescence in this range, which promises higher signal-to-noise ratios (SNR). Single-walled carbon nanotubes (SWCNTs) fluoresce in the NIR (800-1700 nm) and serve as building blocks for biosensors. To quantify the benefits of NIR fluorescence biosensing, we simulate the SNR considering wavelength-dependent scattering/absorption, autofluorescence, dark currents, and excitation background. We also compare Si and InGaAs PIN phototdiodes (pn diode with an additional intrinsic layer) as detectors for the NIR region. The simulation shows that the SNR of fluorophores in the NIR is higher, but InGaAs detectors are outperformed by Si detectors in the short NIR (<1050 nm). This was also validated in experiments with (6,5)-SWCNTs (emission 990 nm), showing a 1.2-fold higher SNR for Si PIN photodiodes. Next, SWCNTs were chemically modified to create sensor arrays/barcodes that detect levodopa. Monitoring levodopa blood levels is a crucial step for personalized Parkinson's disease treatment. We then combine nanosensors and detectors to engineer a portable low-cost fluorescence reader that scans (6,5)-SWCNT sensor barcodes. It detects levodopa at relevant concentrations (10 μM) in human blood serum. Thus, we combine NIR fluorescent sensors with high SNR and low-cost Si detectors to make use of beneficial NIR signals, which opens opportunities for point-of-care applications.}, }
@article {pmid40539017, year = {2025}, author = {Vélez, M and Rödel, MO and Carvajal, V and Donoso, DA and Guerra, MA}, title = {First report of flesh-fly (Diptera: Sarcophagidae) myiasis in little-devil poison frog (Anura: Dendrobatidae) from Ecuador.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {27}, number = {}, pages = {101093}, pmid = {40539017}, issn = {2213-2244}, abstract = {We report a case of myiasis in the poison frog Oophaga sylvatica from the Canandé Reserve located in the Chocó region of northwestern Ecuador. We identified the causal agents as larvae of flesh flies, Sarcophagidae, by means of DNA barcoding and morphological features. This represents the first record of myiasis in an anuran in Ecuador and the second record for Dendrobatidae in the Neotropics. This observation may constitute a case of facultative parasitism where larvae are deposited in the frog's wounds, but further research is needed to understand the biological mechanisms underlying this interaction.}, }
@article {pmid40533248, year = {2025}, author = {Chen, Y and Li, H and Zhao, T and Cui, J and Song, W and Li, H and Fan, G and Chen, R}, title = {Fluorescence Visual Identification of Four Main Varieties of Tibetan Medicinal Berberis cortex Based on Site-Specific PCR Technology.}, journal = {Phytochemical analysis : PCA}, volume = {36}, number = {6}, pages = {1840-1850}, doi = {10.1002/pca.70002}, pmid = {40533248}, issn = {1099-1565}, support = {82374001//National Natural Science Foundation of China/ ; 2023MS081//Special Project for Traditional Chinese Medicine Research of Sichuan Provincial Administration of Traditional Chinese Medicine/ ; KJYYB2306//Innovation and Entrepreneurship Projects for College Students in Chengdu University of Traditional Chinese Medicine Science and Technology Park/ ; 202410633067//National Undergraduate Training Program for Innovation and Entrepreneurship/ ; }, abstract = {BACKGROUND: Berberis cortex is a typical multi-origin species in Tibetan medicine, with varying medicinal effects among different species. Establishing a rapid and accurate identification method for the major species of Tibetan medicinal B. cortex, including Berberis vernae Schneid. (SY), Berberis diaphana Maxim. (XH), Berberis kansuensis Schneid. (GS), and Berberis dictyophylla Franch. (CHZ), is conducive to the quality control of B. cortex.<br><br>METHODS: Site-specific PCR visualization using SYBR Green I was developed based on rbcL SNP sites for SY, GS, and CHZ. For XH, which cannot be differentiated through rbcL and other barcoding SNP sites, RAPD-PCR methodology was employed to screen for species-specific sequences. A site-specific amplification visualization system was subsequently developed based on the identified sequence.<br><br>RESULTS: The developed site-specific PCR visualization systems demonstrated excellent sensitivity, with all systems capable of detecting genomic DNA at concentrations as low as 100&#x2009;fg. These systems were employed to analyze 16 batches of actual B.&#x2009;cortex samples. The analysis revealed that four samples were identified as SY, six samples as GS, two samples as CHZ, and three samples as XH. All results were concordant with sequencing data. One remaining negative sample was confirmed through sequencing as adulterated with Phellodendri Chinensis Cortex. Further authentication of 10 batches of Tibetan patent medicines containing B.&#x2009;cortex revealed that 2 batches contained both SY and GS, one batch contained both SY and CHZ, three batches contained exclusively GS, and three batches contained XH.<br><br>CONCLUSION: A site-specific PCR fluorescence visual identification system has been developed for the authentication of four major B.&#x2009;cortex species, enabling accurate identification of botanical origins in both B.&#x2009;cortex crude materials and Berberis-containing Tibetan patent medicines.}, }
@article {pmid40531408, year = {2025}, author = {Modeel, S and Chaurasia, M and Siwach, S and Dolkar, P and Negi, RK and Negi, RK}, title = {Mitochondrial Perspective on Species Complexes and Evolutionary Dynamics Within Genus Channa.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {40531408}, issn = {1573-4927}, support = {F. No. EEQ/2019/000214//Science and Engineering Research Board/ ; }, abstract = {The genus Channa, commonly known as Snakeheads comprises a diverse variety of species that hold great significance in the commercial sectors. Their complexity and genetic variety show how adaptable they are to different environmental settings and shed light on their evolutionary history. To delve into the genetic intricacies of the genus Channa, we analyzed mitochondrial genetic diversity using 1372 COI sequences obtained from the Barcode of Life Data System (BOLD) database. The metadata and phylogenetic analysis revealed the presence of species complex within C. gachua and C. marulius, suggesting the potential existence of intra and inter-clades within one species group. Further, we selected four ecologically and economically important taxonomic groups to study their haplotype diversity and genetic differentiation. These species/taxonomic groups include C. striata, C. punctata, gachua species complex, and marulius species complex. The analysis indicated a substantial level of genetic differentiation and haplotype diversity in species groups indicating high gene flow within populations. Mitochondrial introgression and species complexes account for a significant section of errors in DNA barcodes, which are two of the primary challenges associated with employing DNA barcoding to identify species. Highlighting these challenges and ongoing uncertainties in specific taxonomic groups of genus Channa, the study argues that the efficacy of DNA barcoding and the genetic integrity of wild variation may be weakened when speciation results in the establishment of numerous cryptic taxa in a species complex.}, }
@article {pmid40529295, year = {2025}, author = {Zhang, J and Zhang, C and Zhong, Y}, title = {On small huntsman spiders (Araneae, Philodromidae) occurring in Guizhou and Hubei provinces, China.}, journal = {ZooKeys}, volume = {1240}, number = {}, pages = {327-368}, pmid = {40529295}, issn = {1313-2989}, abstract = {Spiders of the family Philodromidae Thorell, 1869 from Guizhou and Hubei provinces, China are studied. A total of three genera and seven species are reported and illustrated, comprising Sinodromuslanyue sp. nov. (newly recorded genus for Hubei), and all known species from both provinces: Philodromusauricomus L. Koch, 1878, P.guiyang Long &amp; Yu, 2022, P.subaureolus Bösenberg &amp; Strand, 1906, P.paiki Jang, Lee, Yoo &amp; Kim, 2024 (the previously records of P.spinitarsis Simon, 1895 from Guizhou and Hubei are presumed to be misidentifications, and should belong to P.paiki), P.rufus Walckenaer, 1826 (new record for Hubei) and Tibellusjaponicus Efimik, 1999 (new record for Hubei). Detailed descriptions, diagnoses, and illustrations of S.lanyue sp. nov. and P.guiyang are given, and the male of P.guiyang is diagnosed and described in English for the first time. The other five species are also re-illustrated. Their DNA barcodes were obtained for species delimitation, matching of sexes and future use.}, }
@article {pmid40527675, year = {2025}, author = {Carrasco-Lozano, EC and Carrillo-Ordóñez, GA and Torres-Suarez, G and Noa-Carrazana, JC}, title = {Identification of Dysmicoccus brevipes and its association with PMWaV-1, -2, and -3 in Hawaiiana cultivar and MD-2 hybrid pineapple in Peru.}, journal = {Bulletin of entomological research}, volume = {}, number = {}, pages = {1-8}, doi = {10.1017/S000748532510014X}, pmid = {40527675}, issn = {1475-2670}, abstract = {Pineapple cultivation is of economic importance for farmers; however, pineapple production can be affected by pests and diseases. Recently, the presence of mealybugs and pineapple mealybug wilt-associated viruses (PMWaV)-1, -2, and -3 has been reported in the provinces of Satipo and Chanchamayo, in Peru's central jungle. This study aimed to molecularly identify mealybugs collected from the Hawaiiana cultivar and the MD-2 hybrid in those provinces to determine if they are indeed hosts of the PMWaV-1, -2, and -3. Through amplification and sequencing of the internal transcribed spacer ribosomal genes, the mealybugs were identified as Dysmicoccus brevipes. In the phylogenetic analysis of these D. brevipes, Peruvian isolates were associated with isolates from India, China, Taiwan, and Japan. In addition, our results confirmed the presence of PMWaV-1, -2, and -3 in all mealybug specimens collected from both the Hawaiiana cultivar and the MD-2 hybrid tested, with these PMWaVs showing a 99% sequence identity with others recently reported in Peru. Therefore, D. brevipes is a host and probable vector of PMWaV-1, -2, and -3 for the cultivar Hawaiiana and the hybrid pineapple MD-2 in Satipo and Chanchamayo, Peru. Based on these findings and observations of crop management strategies in these provinces, we recommend integrated management practices to control this pest.}, }
@article {pmid40526730, year = {2025}, author = {Hussain, J and Afzal, G and Haider, MZ and Qadeer, I and Perveen, S and Ahmad, HI and El-Mansi, AA and Gadallah, AA and Sakran Abass, K}, title = {Genetic diversity and phylogenetic relationships of Calotes and Uromastyx in the Cholistan Desert, Pakistan, based on COI gene analysis.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0324053}, pmid = {40526730}, issn = {1932-6203}, mesh = {Animals ; Pakistan ; *Phylogeny ; *Lizards/genetics/classification ; *Genetic Variation ; *Electron Transport Complex IV/genetics ; Desert Climate ; DNA, Mitochondrial/genetics ; Haplotypes ; Bayes Theorem ; DNA Barcoding, Taxonomic ; }, abstract = {The Cholistan Desert of Pakistan harbors unique reptile diversity, including ecologically significant agamid lizards of the genera Calotes and Uromastyx, yet their genetic structure remains poorly understood. This study presents the first mitochondrial DNA barcode assessment of these taxa in the region, analyzing 658 bp of the cytochrome c oxidase I (COI) gene from 19 specimens collected across seven desert sites. We employed a combination of distance-based (p-distance, K2P) and phylogenetic methods (Maximum Likelihood, Bayesian Inference) to evaluate genetic diversity and evolutionary relationships. Results revealed pronounced divergence between genera (24-30% K2P distance), with Uromastyx populations showing remarkably low intraspecific variation (0-1%), contrasting with higher diversity in Calotes (0-14%). Demographic analyses suggested stable populations (Tajima's D = 0.93, p > 0.10), though haplotype networks indicated limited gene flow (Nm = 0.12). Our findings: (1) provide the first genetic baseline for these ecologically important desert lizards, (2) identify Uromastyx as potentially more vulnerable to genetic erosion, and (3) demonstrate the utility of COI barcoding for rapid biodiversity assessment in understudied arid ecosystems. The study highlights the Cholistan Desert as an evolutionary significant zone for agamid lizards while underscoring the need for integrated taxonomic approaches to address potential cryptic diversity. All sequence data are publicly available (GenBank PQ896696-PQ896705) to support future conservation genomic studies.}, }
@article {pmid40526297, year = {2025}, author = {Vargas-Ortiz, M and Parra, LE}, title = {A New Species of Physocleora Warren 1897 (Lepidoptera: Geometridae) from Atacama and Puna Provinces, Northernmost Chile.}, journal = {Neotropical entomology}, volume = {54}, number = {1}, pages = {72}, pmid = {40526297}, issn = {1678-8052}, mesh = {Animals ; Chile ; Phylogeny ; Male ; Female ; *Moths/classification/anatomy &amp; histology/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {Riparian zones of the Atacama Desert and slopes of the Andes mountain range host a diversity of insect species still unknown, and some lineages of different species of Geometridae have been discovered in recent years in such areas. Here, we describe Physocleora polyphaga Vargas-Ortiz &amp; Parra sp.nov., a polyphagous species closely related to several native plants, distributed in coastal valleys and slopes of the Andes mountain range in the northernmost Chile. We present their diagnostic morphological characteristics, some ecological traits, and a representation of its evolutionary history within Physocleora Warren 1897 from DNA barcode sequence data. To validate the hypothesis of conspecificity of the specimens found, we use species delimitation methods based on genetic distances and phylogenetics.}, }
@article {pmid40525968, year = {2025}, author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA}, title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {6}, pages = {}, pmid = {40525968}, issn = {1465-2080}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; }, abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.}, }
@article {pmid40525124, year = {2025}, author = {Eygeris, Y and Jozic, A and Henderson, MI and Nelson, D and Sahay, G}, title = {Exploring the potential of saponins as adjuvants in lipid-nanoparticle-based mRNA vaccines.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {33}, number = {2}, pages = {101495}, pmid = {40525124}, issn = {2329-0501}, abstract = {Saponins are a class of phytocompounds known for their amphiphilic properties. Here, we have evaluated incorporation of 40 saponins into a model lipid nanoparticle (LNP) formulation and evaluated their performance in vitro and in vivo. We reasoned that the surfactant activity of saponins could be beneficial in the context of cell and gene therapy due to the disruption of the intracellular membranes. We established formulation methodology to incorporate saponins into LNPs and measured their endosomal disruption and transfection efficiency with DNA barcode and mRNA cargoes. We identified two saponins-quillaic acid and macranthoidin B-that increase the LNP transfection efficiency and endosomal disruption. Saponin formulations demonstrated cargo-dependent activation of the innate immune system, as measured by the cell-based assays of interferon regulatory factor (IRF) and NF-κB pathway activation. Quillaic acid LNPs resulted in higher titers of anti-OVA IgG2a in the vaccination studies compared to a "naive" LNP control, which suggests a more Th1-biased immunopathology of these vaccines. As Th2-biased vaccines can trigger an allergic response, an mRNA vaccine with a balanced Th1/Th2 response is more favorable for translation into the clinic. Overall, quillaic acid may serve as an adjuvant for mRNA vaccines and potentially decrease the risk of vaccine-associated adverse events.}, }
@article {pmid40524962, year = {2025}, author = {Parreño, MA and Werle, S and Buydens, L and Spitz, J and Härtl, F and Montoya, J and Ruedenauer, F and Arisoy, B and Seiler, R and Leroy, C and Feng-Spitz, Q and Nebauer, CA and Ferrari, A and Proessl, N and Borchardt, R and Peters, B and Siebler, S and Reese, M and Schumacher, N and Phung, T and Schildt, K and Ebensberger, J and Seiler, M and Reiter, P and Beelaert, S and Buydens, M and Koirala, S and Moreniere, J and Tänzler, R and Alaux, C and Filipiak, M and Meeus, I and Piot, N and Kuhlmann, M and Requier, F and Klein, A and Brunet, JL and Henry, M and Keller, A and Leonhardt, SD}, title = {Data on visitation records from wild bees and plants along a land use gradient in Germany and Belgium: laboratory work and protocol description for barcoding.}, journal = {Data in brief}, volume = {61}, number = {}, pages = {111672}, pmid = {40524962}, issn = {2352-3409}, abstract = {The dataset contains information on plant-bee interactions in an agricultural landscape with diverse intensities of land use management, in Germany and Belgium. It was collected during spring and early summer in 2020 and 2021 using two complementary types of sampling: standardized transects (5 transects of 50 m long in 1 h of netting) and targeted sampling in which flowers were observed for diverse periods of times, anywhere in an area of 50 to 150 m[2]. The species identity was obtained with field keys and DNA barcoding. The dataset is of use for building pollinator networks and in combination with other datasets on environmental characteristics of the area to better understand species distributions and interactions. Indeed, we include in the dataset information on environmental parameters from the plots of sampling (spatial coordinates, land use intensity index, landscape heterogeneity index, plant diversity), which can support further correlational analyses.}, }
@article {pmid40519893, year = {2025}, author = {Balaji, R and Easwaran, S and Devanathan, K and Sharma, S and Alqahtani, T and Uti, DE and Malik, T}, title = {Unfolding the Complete Chloroplast Genome of Myrica esculenta Buch.-Ham. ex D.Don (1825): Advancing Phylogenetic Insights Within Fagales and Pioneering DNA Barcodes for Precise Species Identification.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71566}, pmid = {40519893}, issn = {2045-7758}, abstract = {This study aims to delineate the chloroplast (cp) genome of Myrica esculenta Buch.-Ham. ex D.Don (1825), a traditional medicinal plant from the Myricaceae family, to elucidate its phylogenetic relationships within the Fagales order. The objective was to assemble the complete cp genome and assess its utility as a molecular marker for species identification and evolutionary analysis. The methodology involved assemby of the cp genome of M. esculenta, which was found to be 159,538 base pairs (bp) in length and exhibited a typical quadripartite structure. This included an 88,830 bp large single-copy (LSC) region, an 18,810 bp small single-copy (SSC) region, and two inverted repeats each of 25,949 bp. Phylogenetic analysis utilized the ycf1 gene sequences from 13 Fagales species. Results indicated that M. esculenta and other Myrica species form a monophyletic clade, with the ycf1 gene showing substantial divergence, suggesting its potential as a novel DNA barcode marker. This marker could significantly improve the resolution of species identification beyond traditional morphological methods. Future perspectives include expanding the genomic datasets across the Myrica genus to enhance the phylogenetic framework and further refine the utility of the ycf1 gene as a DNA barcode for broader applications in plant breeding, herbal drug authentication, and evolutionary studies.}, }
@article {pmid40509709, year = {2025}, author = {Schumacher, JD and Dusek, N and Mendoza-Suárez, M and Geddes, BA}, title = {Adaptation of Plasmid-ID Technology for Evaluation of N2-Fixing Effectiveness and Competitiveness for Root Nodulation in the Sinorhizobium-Medicago System.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70118}, doi = {10.1111/1462-2920.70118}, pmid = {40509709}, issn = {1462-2920}, support = {FF-NIA21-0000000061m//Foundation for Food and Agriculture Research/ ; //U.S. Alfalfa Farmer Research Initiative of the National Alfalfa &amp; Forage Alliance/ ; }, mesh = {*Plasmids/genetics ; *Nitrogen Fixation ; *Plant Root Nodulation ; Symbiosis ; *Sinorhizobium/genetics/physiology/metabolism ; Plant Roots/microbiology ; *Medicago sativa/microbiology ; }, abstract = {Maximising the nitrogen fixation occurring in rhizobia-legume associations represents an opportunity to sustainably reduce nitrogen fertiliser inputs in agriculture. High-throughput measurement of symbiotic traits has the potential to accelerate the identification of elite rhizobium/legume associations and enable novel research approaches. Plasmid-ID technology, recently deployed in Rhizobium leguminosarum, facilitates the concurrent assessment of rhizobium nitrogen-fixing effectiveness and competitiveness for root nodulation. This study adapts Plasmid-ID technology to function in Sinorhizobium species that are central models for studying rhizobium-legume associations and form economically important symbioses with alfalfa. New Sino-Plasmid-IDs were developed and tested for stability and their ability to measure competitiveness for root nodulation and nitrogen-fixing effectiveness. Rhizobial competitiveness is measured by identifying strain-specific nucleotide barcodes using next-generation sequencing, whereas effectiveness is measured by GFP fluorescence driven by the synthetic nifH promoter. Sino-Plasmid-IDs allow researchers to efficiently study competitiveness and effectiveness in a multitude of Sinorhizobium strains simultaneously.}, }
@article {pmid40509529, year = {2025}, author = {Zdeňková, K and Čermáková, E and Vejl, P and Čermáková, A and Vašek, J}, title = {Analytical Methods for the Identification of Edible and Feed Insects: Focus on DNA-Based Techniques.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {40509529}, issn = {2304-8158}, support = {QK23020101//Ministry of Agriculture/ ; LM2023064//Ministry of Education Youth and Sports/ ; }, abstract = {The utilization of insects as a source of essential nutrients holds considerable promise, with the potential to serve as both feed and food. Consequently, there is a necessity to develop control systems, as the undeclared addition of insects to food products and/or non-compliance with labelling regulations may pose health risks and result in financial losses for consumers. This review describes methods for identifying and detecting insect species by targeting biomolecules such as DNA, proteins, saccharides, and metabolites, with a particular focus on DNA-based approaches. This review provides a detailed overview of the application of polymerase chain reaction (PCR) and DNA sequencing methods that are suitable for the analysis of edible and forage insects. The main focus is on identifying species that are approved for use as novel foods or insect feeds within the European Union (e.g., house cricket (Acheta domesticus), common mealworm (Tenebrio molitor), migratory locust (Locusta migratoria), lesser mealworm (Alphitobius diaperinus), black soldier fly (Hermetia illucens), banded cricket (Gryllodes sigillatus), field cricket (Gryllus assimilis), silkworm (Bombyx mori)). However, insect species of global relevance are also discussed. The suitability of DNA analysis methods for accurate species identification, detection of (un)labeled contaminants, and monitoring of genetic diversity has been demonstrated.}, }
@article {pmid40506553, year = {2025}, author = {Raab, M and Schütz, L and Sommermann, L and Babin, D and Kampouris, I and Francioli, D and Grosch, R and Neumann, G and Deubel, A and Geistlinger, J and Bade, K and Rozhon, W}, title = {Two decades long-term field trial data on fertilization, tillage, and crop rotation focusing on soil microbes.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {986}, pmid = {40506553}, issn = {2052-4463}, support = {16DKWN019 - BioTrain//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {*Soil Microbiology ; *Crops, Agricultural/growth &amp; development ; *Agriculture/methods ; *Microbiota ; Rhizosphere ; Germany ; Fertilizers ; Plant Roots/microbiology ; }, abstract = {Agricultural long-term field trials provide fundamental data on crop performance and soil characteristics under diverse management practices. This information represents essential knowledge for upcoming challenges in food and nutrition security. Data provided here have been compiled since 2004 from a nitrogen(N)-fertilization intensity, tillage, and crop rotation field trial in Central Germany including standardized metrics regarding soil management, physical soil properties, crop management, crop characteristics, yield, and harvest quality parameters. In 2015, the field trial became a member of the German Agricultural Soil Research Program BonaRes. Numerous measurement results were added including plant physiology and soil and rhizosphere microbiology. DNA of bacterial/archaeal and fungal microbiomes was sequenced in the rhizosphere and root-associated soil following a meta-barcoding approach. Taxonomic and relative abundance data were included in the dataset. The dataset is the first to include information on root characteristics, soil and rhizosphere microbiomes, and crop gene expression. We encourage reuse of these biological field trial data in terms of meta-analysis, modeling and AI approaches.}, }
@article {pmid40505585, year = {2025}, author = {Holzmann, M and Siemensma, F}, title = {A new freshwater monothalamid (Rhizaria, Foraminifera) from the Pyrenees branching within a marine clade.}, journal = {European journal of protistology}, volume = {99}, number = {}, pages = {126156}, doi = {10.1016/j.ejop.2025.126156}, pmid = {40505585}, issn = {1618-0429}, mesh = {*Fresh Water/parasitology ; *Foraminifera/classification/genetics/cytology ; Phylogeny ; Species Specificity ; France ; }, abstract = {Monothalamous (single-chambered) foraminifera are widespread in marine benthic environments and are also a common part of freshwater and soil microbial communities. Based on molecular and morphological characteristics, seven non-marine families are currently recognized, branching either as sisters to marine clades or independently within the paraphyletic class Monothalamida. In this study, we describe a new monothalamous freshwater foraminifera sampled from a Pyrenean pond near the French town of Cauterets. We erect the novel genus Poseidonella, with its type species Poseidonella transaquatica sp. nov. The new species branches within the marine clade E, which includes the genera Psammophaga, Vellaria, Niveus, and Nellya. This represents the first evidence of a mixed clade comprising both marine and freshwater monothalamids, highlighting an ongoing transition from coastal marine environments to freshwater habitats.}, }
@article {pmid40504436, year = {2025}, author = {Sahin, EC and Aydin, Y and Uncuoglu, AA}, title = {Assessing the accuracy of cp-DNA barcodes in Colchicum species identification.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {584}, pmid = {40504436}, issn = {1573-4978}, support = {111T854//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; FEN-C-DRP-141112-0335//Marmara &#xdc;niversitesi/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Chloroplast/genetics ; Species Specificity ; Phylogeny ; Sequence Analysis, DNA/methods ; DNA, Plant/genetics ; Genetic Variation ; Genotype ; }, abstract = {BACKGROUND: The genus Colchicum, belonging to the family Colchicaceae, holds significant economic and medicinal value globally. However, precise identification of many species within this genus is challenging. In order to address this obstacle, we carried out a study involving 155 genotypes from various locations in Türkiye to assess the effectiveness of DNA barcoding, specifically utilizing the matK, rbcL, trnH-psbA chloroplast DNA (cp-DNA) barcode regions, by comparing their effectiveness in distinguishing Colchicum species.<br><br>METHODS AND RESULTS: Following PCR amplification and sequence analysis, multiple sequence alignment was conducted. Stop codons were detected and sequences were cleaned. Conserved region identification, and GC content analysis were carried out. Species discrimination was analysed (best match, best close-match, all species barcodes functions). The Wilcoxon Ranked Sum test was used to assess differences in genetic variation within and between species. As a result, trnH-psbA emerged as the most effective locus for species differentiation, with significantly higher intra-specific (mean: 3.915) and inter-specific distances (maximum: 1.844) compared to matK and rbcL. matK displayed moderate identification success rates, while rbcL had the lowest performance. trnH-psbA excelled in the 'best match' and 'best close match' categories; rbcL recorded the highest incorrect identification rates.<br><br>CONCLUSION: This study highlights the importance of DNA barcoding, specifically the trnH-psbA locus, in distinguishing Colchicum species. The locus shows significantly higher genetic distances than the matK and rbcL loci, underscoring its effectiveness for species identification. These insights are crucial for comprehending the genetic diversity of Colchicum species and enhancing resources for future taxonomy and conservation efforts.}, }
@article {pmid40502998, year = {2025}, author = {Li, J and Li, S and Zhang, X and Yao, Z}, title = {Diversity survey of Pholcus spiders (Araneae, Pholcidae) from eastern Sichuan and neighboring areas, with descriptions of six new species.}, journal = {ZooKeys}, volume = {1240}, number = {}, pages = {39-64}, pmid = {40502998}, issn = {1313-2989}, abstract = {Thirteen spider species of the genus Pholcus Walckenaer, 1805 are reported from a diversity survey in eastern Sichuan and neighboring areas (northeastern Yunnan and western Guizhou). They belong to three species groups and include six newly described species: Pholcusqiaojia Li, Li &amp; Yao, sp. nov. (♂♀, Yunnan) in the bidentatus group; P.aba Li, Li &amp; Yao, sp. nov. (♂♀, Sichuan) and P.wenchuan Li, Li &amp; Yao, sp. nov. (♂♀, Sichuan) in the crypticolens group; P.mengding Li, Li &amp; Yao, sp. nov. (♂♀, Sichuan), P.miyi Li, Li &amp; Yao, sp. nov. (♂♀, Sichuan) and P.yaan Li, Li &amp; Yao, sp. nov. (♂♀, Sichuan) in the yichengicus group. P.bidentatus Zhu, Zhang, Zhang &amp; Chen, 2005 is recorded from Yunnan for the first time and P.kunming Zhang &amp; Zhu, 2009 is recorded from Guizhou and Sichuan for the first time. Detailed diagnoses, descriptions, photomicroscope images, and DNA barcodes of all newly described species are provided.}, }
@article {pmid40502055, year = {2025}, author = {Morrison, J and Johnson, BK and Shen, H}, title = {Synthbar: A Lightweight Tool for Adding Synthetic Barcodes to Sequencing Reads.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40502055}, issn = {2692-8205}, support = {R37 CA230748/CA/NCI NIH HHS/United States ; }, abstract = {Preparation of single-cell sequencing libraries includes adding nucleotide barcodes to assist with pooling samples or cells together for sequencing. The popularity of droplet-based single-cell protocols has spurred the development of computational tools that expect the read structure of the assay to include a cell barcode (CB). Microwell plate-based protocols, such as the Switching Mechanism At the 5' end of the RNA Transcript (SMART) single-cell RNA sequencing (scRNA-seq) family of methods, typically do not add a CB as part of the library preparation method as there is typically one cell per well and standard unique dual indices are sufficient for multiplexing. While several tools exist to manipulate and parse varying single-cell read structures, no tool is currently available to easily add synthetic CBs to enable use of computational tooling that expects the presence of a CB, such as STARsolo, zUMIs, and Alevin. Synthbar fills this gap as a lightweight tool that is assay agnostic, can add user-defined CBs, and modify read structures.}, }
@article {pmid40501993, year = {2025}, author = {Hanna, AR and Shepherd, SJ and Datto, GA and Navarro, IB and Ricciardi, AS and Padilla, MS and Srikumar, N and Zhang, S and Yamagata, HM and Meng, NY and Buser, JR and Mitchell, MJ and Issadore, DA}, title = {Automated and parallelized microfluidic generation of large and precisely-defined lipid nanoparticle libraries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40501993}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; DP2 TR002776/TR/NCATS NIH HHS/United States ; T90 DE030854/DE/NIDCR NIH HHS/United States ; }, abstract = {Building on the success of lipid nanoparticles (LNPs) in vaccines, LNPs are being developed for a broad set of therapeutic applications by changing both the structures of the lipids used to formulate each LNP and their relative proportions. Because lipid synthesis and in vivo screening have been parallelized using combinatorial chemistry and LNP barcoding respectively, the manual and sequential microfluidic formulation of LNPs has become the rate-limiting step in the discovery process. In this work, we present a high-throughput, automated microfluidic platform capable of generating large, precisely-defined LNP libraries in parallel at a rate of one distinct formulation every three seconds. Each formulation is defined by varying the reagent flow ratios into one of eight microscale mixers using lithographically encoded fluidic resistors and dynamically controlled external pressure supplies. The microfluidic chip is integrated with custom robotic plate handling for the rapid collection of each distinct formulation. Using this platform, we produce a library of 96 formulations, which we profile physicochemically and evaluate in terms of both in vitro and in vivo transfection.}, }
@article {pmid40501638, year = {2025}, author = {Goldstein, I and Hale, JJ and Ehrenreich, IM}, title = {Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40501638}, issn = {2692-8205}, support = {R35 GM130381/GM/NIGMS NIH HHS/United States ; R56 AI171091/AI/NIAID NIH HHS/United States ; }, abstract = {Global epistasis is a phenomenon in which the effects of genetic perturbations depend on the fitness of the individuals in which they occur. In populations with natural genetic variation, global epistasis arises from interactions between perturbations and polymorphic loci that are mediated by fitness. To investigate the prevalence and characteristics of loci involved in these interactions in the budding yeast Saccharomyces cerevisiae, we used combinatorial DNA barcode sequencing to measure the fitness of 169 cross progeny (segregants) subjected to 8,126 CRISPRi perturbations across two environments. Global epistasis was evident in these data, with more fit segregants within each environment exhibiting greater sensitivity to genetic perturbations than less fit segregants. We dissected the genetic basis of this global epistasis by scanning the genome for loci whose effects covary with CRISPRi-induced reductions in population fitness. This approach identified 58 loci that interact with fitness, most of which exhibited larger effects in the absence of genetic perturbations. In aggregate, these loci explained the observed global epistasis in each environment and demonstrated that the loci contributing to global epistasis largely overlap with those influencing fitness in unperturbed conditions.}, }
@article {pmid40501448, year = {2025}, author = {Taylor, KE and Saunders, GW}, title = {First report of articuliths (free-living geniculate corallines, Corallinales, Rhodophyta) in the northern hemisphere revealed during diversity surveys of Haida Gwaii, British Columbia, Canada.}, journal = {Journal of phycology}, volume = {61}, number = {4}, pages = {1038-1042}, pmid = {40501448}, issn = {1529-8817}, support = {//Canada Foundation for Innovation/ ; //New Brunswick Innovation Foundation/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Free-living coralline beds are typically composed of rhodoliths, or unattached non-geniculate coralline algae. In 2017, the first beds comprised primarily of free-living geniculate coralline algae, termed articuliths, were documented in Arraial do Cabo Bay in southeastern Brazil. During routine barcode surveys of the Haida Gwaii, British Columbia, Canada flora, 16 rhodolith-like specimens were collected from a rhodolith bed that DNA sequences assigned to the geniculate taxa Calliarthron tuberculosum and Bossiella sp. 1heteroforma. To our knowledge, articuliths have not been documented outside of Brazil; this discovery thus documents the first instance of northern hemisphere articuliths. Despite disparate gross morphologies to attached conspecific populations, anatomical observations revealed internal anatomies consistent with those of attached forms but with a significant reduction in the number of genicula and increased uniformity in intergenicular shape.}, }
@article {pmid40500871, year = {2025}, author = {Gómez, GF and Laurito, M and Correa, MM}, title = {Molecular analysis supports at least two putative species within Anopheles pseudopunctipennis s.l. on the American mainland.}, journal = {Medical and veterinary entomology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mve.12815}, pmid = {40500871}, issn = {1365-2915}, support = {2023-66350//Escuela de Microbiolog&#xed;a, Universidad de Antioquia/ ; }, abstract = {Anopheles (Anopheles) pseudopunctipennis, involved in seasonal malaria transmission in the Andean foothills and American coastal areas, was previously proposed as a species complex based on cross-mating experiments and population genetic analyses. In this work, a fragment of the mitochondrial gene cytochrome c oxidase subunit I or COI barcode region, and the nuclear second internal transcribed spacer (ITS2) were analysed in Colombian An. pseudopunctipennis s.l. specimens; the obtained sequences were compared to publicly available data using phylogeny and distance-based species delimitation approaches. Assemble Species by Automatic Partitioning (ASAP) and coalescent-based approaches provided strong evidence of at least two putative species on the American mainland, here designated as the North-Central and Southern lineages. The North-Central lineage is primarily found in southern/southwestern United States, Central America (Mexico and Honduras) and northwestern Colombia, while the Southern lineage is mainly detected in the Colombian Pacific and Argentina; there were some co-occurrences of these lineages in the Colombian regions. The definition of these putative species is crucial for understanding their bionomy, ecology and potential role in malaria transmission. Further research, including a more comprehensive sampling and population genetic analysis, is needed to fully elucidate their evolutionary history and demographic dynamics.}, }
@article {pmid40500336, year = {2025}, author = {Moraes Zenker, M and Portella, TP and Pessoa, FAC and Bengtsson-Palme, J and Galetti, PM}, title = {Correction: Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {20045}, doi = {10.1038/s41598-025-02631-6}, pmid = {40500336}, issn = {2045-2322}, }
@article {pmid40498465, year = {2025}, author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA}, title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.}, journal = {The Analyst}, volume = {150}, number = {14}, pages = {3137-3146}, doi = {10.1039/d5an00130g}, pmid = {40498465}, issn = {1364-5528}, mesh = {*Microfluidic Analytical Techniques/instrumentation/methods ; High-Throughput Screening Assays/instrumentation ; *Microbiological Techniques/instrumentation/methods ; }, abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.}, }
@article {pmid40494311, year = {2025}, author = {van Galen, LG and Corrales, A and Truong, C and van den Hoogen, J and Kumar, S and Manley, BF and Stewart, JD and Kohout, P and Baldrian, P and Větrovský, T and Crowther, TW and Kiers, ET and Van Nuland, ME}, title = {The biogeography and conservation of Earth's 'dark' ectomycorrhizal fungi.}, journal = {Current biology : CB}, volume = {35}, number = {11}, pages = {R563-R574}, doi = {10.1016/j.cub.2025.03.079}, pmid = {40494311}, issn = {1879-0445}, mesh = {*Mycorrhizae/physiology/classification/genetics ; *Biodiversity ; *Conservation of Natural Resources ; *Soil Microbiology ; Mycobiome ; Phylogeography ; Earth, Planet ; Symbiosis ; }, abstract = {Breakthroughs in DNA sequencing have upended our understanding of fungal diversity. Only ∼155,000 of the 2-3 million fungal species on the planet have been formally described and named, and 'dark taxa' - species known only from sequences - represent the vast majority of species within the fungal kingdom. The International Code of Nomenclature requires physical type specimens to officially recognize new fungal species, making it difficult to name dark taxa. This is a significant problem for conservation because, without names, species cannot be recognized for environmental and legal protection. Symbiotic ectomycorrhizal (EcM) fungi play a particularly important role in forest carbon drawdown, but at present we have little understanding of how many EcM fungal species exist, or where to prioritize research activities to survey and describe EcM fungal lineages. In this review, we use global soil metabarcoding databases (GlobalFungi and the Global Soil Mycobiome consortium) to evaluate current estimates of the total number of EcM fungal species on Earth, outline the current state of undescribed EcM dark taxa, and identify priority regions for future dark taxa exploration. The metabarcoding databases include up to 219,730 EcM fungal operational taxonomic units (OTUs) detected from almost 39,500 samples. Using Chao richness estimates corrected for extrapolating species numbers from metabarcoding datasets, we predict that the global diversity of EcM fungi could be ∼25,500-55,500 species. Dark taxa - those that do not match species-level identities - account for 79-83% of OTUs. Oceania contains the highest percentage of dark taxa (87%), and Europe the lowest (78%). Priority 'darkspots' for future research occur predominantly in tropical regions, but also in selected temperate forests at both southern and northern latitudes. We propose concrete steps to reduce the prevalence of EcM darkspots, including performing targeted field surveys, barcoding fungaria voucher specimens, and developing new ways to describe and conserve fungal taxa from DNA alone.}, }
@article {pmid40493884, year = {2025}, author = {Loke, J and Kim, PG and Nguyen, TTP and Boileau, M and McConkey, M and Miller, AP and Shin, W and Hergott, CB and Ericsson, M and Nordstrom, A and Montero-Llopis, P and Armstrong, SA and Mancias, JD and Ebert, BL}, title = {An in vivo barcoded CRISPR-Cas9 screen identifies Ncoa4-mediated ferritinophagy as a dependence in Tet2-deficient hematopoiesis.}, journal = {Blood}, volume = {}, number = {}, pages = {}, doi = {10.1182/blood.2024028033}, pmid = {40493884}, issn = {1528-0020}, abstract = {TET2 is among the most commonly mutated genes in both clonal hematopoiesis and myeloid malignancies, thus, the ability to identify selective dependencies in TET2 deficient cells has broad translational significance. Here, we identify regulators of Tet2 knockout (KO) hematopoietic stem and progenitor cell (HSPC) expansion using an in vivo CRISPR-Cas9 KO screen, in which nucleotide barcoding enabled large-scale clonal tracing of Tet2 deficient HSPCs in a physiological setting. Our screen identified candidate genes, including Ncoa4, that are selectively required for Tet2 KO clonal outgrowth compared to wild-type (WT). Ncoa4 targets ferritin for lysosomal degradation (ferritinophagy), maintaining intracellular iron homeostasis by releasing labile iron (Fe2+) in response to cellular demands. In Tet2-deficient HSPCs, increased mitochondrial ATP production correlates with increased cellular iron requirements, and in turn, promotes Ncoa4-dependent ferritinophagy. Restricting iron availability reduces Tet2 KO stem cell numbers, revealing a dependency in TET2-mutated myeloid neoplasms.}, }
@article {pmid40492465, year = {2025}, author = {Verbruggen, H and Uthanumallian, K and Powrie, F and Jalali, T and Cremen, C and Preuss, M and Duchene, S and Diaz-Tapia, P}, title = {Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14132}, doi = {10.1111/1755-0998.14132}, pmid = {40492465}, issn = {1755-0998}, support = {4-G046WSD//Australian Biological Resources Study/ ; CEECIND:2023.06155//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {Molecular sequence data have become a ubiquitous tool for delimiting species and are particularly important in organisms where morphological traits are not informative about species boundaries. A range of statistical methods have been developed to derive species limits from molecular data, for example, by quantifying changes in branching patterns in phylogenetic trees. We aim to investigate how such methods scale up from single genes to whole organelle genomes. We gathered chloroplast genome data from 38 samples of the red algal genus Dascyclonium and analysed them with the popular species delimitation methods Assemble Species by Automatic Partitioning (ASAP), General Mixed Yule Coalescent (GMYC), and Poisson Tree Processes (PTP). We show extensive variation in inferred species boundaries depending on the method and dataset used. Genome-scale analyses differed substantially between methods, with ASAP predicting the fewest species, PTP intermediate, and GMYC inferring many species. Based on a series of simulations, we identify a tendency of GMYC to overestimate species numbers as alignments increase in length, while the other two methods are not sensitive to this scaling. Gene-by-gene analyses show strong differences in predicted species limits, which is unexpected seeing that all genes are on a single uniparentally inherited chromosome, and highlight that choosing a particular gene as a DNA barcode has significant consequences for species diversity estimates. We show extensive cryptic diversity in the genus Dasyclonium and propose a consensus solution for species limits based on our combined results, enriched with biogeographic and morphological interpretations. Finally, we make recommendations for interpreting the results and improving the inferences drawn from species delimitation methods.}, }
@article {pmid40492407, year = {2025}, author = {Shibata, D}, title = {Human brain ancestral barcodes.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40492407}, issn = {2050-084X}, support = {P01 CA196569/CA/NCI NIH HHS/United States ; R01 CA271237/CA/NCI NIH HHS/United States ; P01CA196569/NH/NIH HHS/United States ; CA271237/NH/NIH HHS/United States ; }, mesh = {Humans ; *Brain/cytology/metabolism ; Male ; *DNA Methylation ; Neurons ; CpG Islands ; Single-Cell Analysis ; Chromosomes, Human, X/genetics ; }, abstract = {Dynamic CpG methylation 'barcodes' were read from 15,000-21,000 single cells from three human male brains. To overcome sparse sequencing coverage, the barcode had ~31,000 rapidly fluctuating X-chromosome CpG sites (fCpGs), with at least 500 covered sites per cell and at least 30 common sites between cell pairs (average of ~48). Barcodes appear to start methylated and record mitotic ages because excitatory neurons and glial cells that emerge later in development were less methylated. Barcodes are different between most cells, with average pairwise differences (PWDs) of ~0.5 between cells. About 10 cell pairs per million were more closely related with PWDs <0.05. Barcodes appear to record ancestry and reconstruct trees where more related cells had similar phenotypes, albeit some pairs had phenotypic differences. Inhibitory neurons showed more evidence of tangential migration than excitatory neurons, with related cells in different cortical regions. fCpG barcodes become polymorphic during development and can distinguish between thousands of human cells.}, }
@article {pmid40492230, year = {2025}, author = {Song, WL and Jiang, ZQ and Li, M and Leontyev, D and Gao, Y and Chen, SL}, title = {Comprehensive revision of Lycogala (Myxomycetes) in subtropical China: morphological and phylogenetic insights and ten new species.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e147535}, pmid = {40492230}, issn = {2210-6340}, abstract = {In recent years, significant advancements have been made in the taxonomy and phylogenetics of Lycogala, leading to the description of numerous new species. However, Lycogala in China has never been systematically revised, and only eight species have been recorded. In this study, specimens of Lycogala from 22 sites in 11 provinces or cities of subtropical China were studied in terms of morphology, two-gene phylogenetic analysis (nuclear 18S rDNA and cytochrome oxidase subunit I), and ASAP species delimitation. We provide a checklist, which includes 21 species of Lycogala collected in subtropical China. These species include (1) seven species already known from the country, for which we report new localities, (2) four species, new to China (Lycogalaalisaulianovae, L.fossiculatum, L.skovorodaense, and L.succineum) and (3) ten species new to science, including L.annulatum sp. nov., L.chinense sp. nov., L.convexum sp. nov., L.fasciculovesiculiferum sp. nov., L.helvolum sp. nov., L.indirubinum sp. nov., L.nigrum sp. nov., L.planovesiculiferum sp. nov., L.projectum sp. nov., and L.uviforme sp. nov. A comprehensive morphological description, detailed illustrations, molecular barcoding data, and putative position in phylogenies are provided for the newly described taxa.}, }
@article {pmid40492207, year = {2025}, author = {Pimvichai, P and Enghoff, H and Breugelmans, K and Segers, B and Backeljau, T}, title = {Morphological and DNA sequence data uncover a new millipede species in the Thyropygus opinatus subgroup and assign T. peninsularis to this subgroup (Diplopoda: Spirostreptida: Harpagophoridae).}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19277}, pmid = {40492207}, issn = {2167-8359}, mesh = {Animals ; Thailand ; Phylogeny ; *Arthropods/genetics/classification/anatomy &amp; histology ; Male ; Sequence Analysis, DNA ; Female ; Species Specificity ; }, abstract = {The millipede genus Thyropygus Pocock, 1894 is one of the most diverse genera within the family Harpagophoridae in Southeast Asia. The Thyropygus opinatus subgroup, belonging to the T. allevatus group, is distinguished by the presence of an additional projection on the anterior coxal fold. Here, we describe a new species of the T. opinatus subgroup, Thyropygus payamense sp. nov., from Payam Island, Ranong Province, Thailand, based on morphological and DNA sequence data. The mean interspecific COI divergence between the new species and other Thyropygus species is 0.13 ± 0.02 (range: 0.07-0.16). The new species is distinguished by (1) a small, slender, pointed spine at base of femoral spine, (2) a short, triangular mesal process of the anterior coxal fold, and (3) a short, slender, slightly mesad-curving tibial spine. Additionally, T. peninsularis Hoffman, 1982 is confirmed as a member of the T. opinatus subgroup, because it shares key gonopodal characters with other species in this subgroup, while COI and 16S rRNA sequence data firmly support this new classification, with a mean interspecific COI sequence divergence of 0.13 ± 0.03 (range: 0.07-0.17) from other species in the T. allevatus group. An identification key for all 29 species in the T. opinatus subgroup is provided. Further research is needed to assess the taxonomic status of, and phylogenetic relationships within, this subgroup, which, except for two species, may tentatively represent an endemic species radiation in the peninsular area of Thailand, Malaysia and Myanmar.}, }
@article {pmid40491537, year = {2025}, author = {Haque, MA and Hadi, SB and Sumona, AA and Rashid, J and Khan, MGQ and Alam, MS}, title = {Morpho-Molecular Identification of Common Freshwater Loaches Collected From Different Ecosystems of Bangladesh.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71559}, pmid = {40491537}, issn = {2045-7758}, abstract = {The biodiversity of hill stream fishes, especially loaches, in Bangladesh is declining, despite limited exploration. Conservation strategies can flourish through the effective identification of species. Ambiguous loaches were collected to resolve taxonomic confusion. Morphology was analyzed through morphometric and meristic traits, with mitochondrial COI and nuclear RAG1 genes as molecular markers. Sixteen morphotypes are found in 60 specimens, and the molecular study confirmed the existence of seven species. Furthermore, the species delimitation method ASAP suggests seven species according to the best partition. A low level of intraspecific diversity is found in the RAG1 gene analysis compared with the COI gene. The lowest interspecific genetic divergence (3.7%) was observed between Botia lohachata and Botia rostrata , whereas Canthophrys gongota showed the highest interspecific genetic divergence (24.45%) with B. lohachata. A potential barcoding gap of 2.52% in the COI gene is typically the threshold for distinguishing intra-species from inter-species comparisons. In the maximum likelihood phylogenetic tree of both COI and RAG1 gene sequences, the species are divided into distinct clades with high bootstrap support, and specimens within the same species do not converge. Morphology, along with the molecular data of this study, will strengthen conservation efforts for loaches.}, }
@article {pmid40491322, year = {2025}, author = {Cao, J and Guo, Z and Xu, X and Li, P and Fang, Y and Deng, S}, title = {Advances in CRISPR-Cas9 in lineage tracing of model animals.}, journal = {Animal models and experimental medicine}, volume = {8}, number = {6}, pages = {1004-1022}, pmid = {40491322}, issn = {2576-2095}, support = {22SH19//Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Collaborative Innovation Program of the Chinese Academy of Sciences/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; }, mesh = {Animals ; *CRISPR-Cas Systems ; *Gene Editing/methods ; Humans ; *Cell Lineage/genetics ; *Models, Animal ; Mice ; Swine ; Zebrafish ; *Cell Tracking/methods ; }, abstract = {Cell lineage tracing is a key technology for describing the developmental history of individual progenitor cells and assembling them to form a lineage development tree. However, traditional methods have limitations of poor stability and insufficient resolution. As an efficient and flexible gene editing tool, CRISPR-Cas9 system has been widely used in biological research. Furthermore, CRISPR-Cas9 gene editing-based tracing methods can introduce fluorescent proteins, reporter genes, or DNA barcodes for high-throughput sequencing, enabling precise lineage analysis, significantly improving precision and resolution, and expanding its application range. In this review, we summarize applications of CRISPR-Cas9 system in cell lineage tracing, with special emphasis on its successful applications in traditional model animals (e.g., zebrafish and mice), large animal models (pigs), and human cells or organoids. We also discussed its potential prospects and challenges in xenotransplantation and regenerative medicine.}, }
@article {pmid40490500, year = {2025}, author = {Robinson, CM and Carreño, D and Weber, T and Chen, Y and Riglar, DT}, title = {A discovery platform for identification of host-induced bacterial biosensors from diverse sources.}, journal = {Molecular systems biology}, volume = {}, number = {}, pages = {}, pmid = {40490500}, issn = {1744-4292}, support = {211230/Z/18/Z//Wellcome Trust (WT)/ ; President's PhD Scholarship//Imperial College London (ICL)/ ; }, abstract = {Synthetic biology approaches such as whole-cell biosensing and 'sense-and-respond' therapeutics aim to enlist the vast sensing repertoire of gut microbes to drive cutting-edge clinical and research applications. However, well-characterised circuit components that sense health- and disease-relevant conditions within the gut remain limited. Here, we extend the flexibility and power of a biosensor screening platform using bacterial memory circuits. We construct libraries of sensory components sourced from diverse gut bacteria using a bespoke two-component system identification and cloning pipeline. Tagging unique strains using a hypervariable DNA barcode enables parallel tracking of thousands of unique clones, corresponding to ~150 putative biosensors, in a single experiment. Evaluating sensor activity and performance heterogeneity across various in vitro and in vivo conditions using mouse models, we identify several biosensors of interest. Validated hits include biosensors with relevance for autonomous control of synthetic functions within the mammalian gut and for non-invasive monitoring of inflammatory disease using faecal sampling. This approach will promote rapid biosensor engineering to advance the development of synthetic biology tools for deployment within complex environments.}, }
@article {pmid40490497, year = {2025}, author = {Löbbert, A and Lorz, N and Matthees, ESF and Rößler, P and Hoffmann, C and Gossert, AD}, title = {GPCR kinases phosphorylate GPCR C-terminal peptides in a hierarchical manner.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {899}, pmid = {40490497}, issn = {2399-3642}, support = {31-208029//Swiss National Science Foundation | National Center of Competence in Research Affective Sciences - Emotions in Individual Behaviour and Social Processes (National Centre of Competence in Research Affective Sciences)/ ; ETH-37 19-2//Eidgen&#xf6;ssische Technische Hochschule Z&#xfc;rich (Federal Institute of Technology Zurich)/ ; }, mesh = {Phosphorylation ; Humans ; *Receptors, G-Protein-Coupled/metabolism/chemistry ; *G-Protein-Coupled Receptor Kinase 2/metabolism ; *G-Protein-Coupled Receptor Kinases/metabolism ; *Peptides/metabolism/chemistry ; *G-Protein-Coupled Receptor Kinase 1/metabolism ; Rhodopsin/metabolism/chemistry ; Receptors, Adrenergic, beta-2/metabolism ; }, abstract = {Responses from G protein-coupled receptors (GPCRs) are downregulated in a precisely orchestrated process called desensitization. This process consists of two major steps: phosphorylation of the receptor by GPCR kinases (GRKs), predominantly on its C-terminus, and recruitment of arrestin, resulting in different signaling outcomes. Yet, it remains unclear how the phosphorylation pattern on the receptor is determined. We carried out an NMR-based study of the phosphorylation patterns generated by GRK1 and GRK2 on C-terminal peptides of selected receptors (rhodopsin for GRK1, and β1- and β2-adrenergic receptors (ARs) for GRK2). Our data reveal that the kinases are promiscuous with respect to the substrate peptide, but produce clearly defined phosphorylation patterns on each substrate. We found pronounced differences in the rates at which certain residues are phosphorylated, in particular in the PXPP motifs in rhodopsin and β1AR. These results show that GRKs produce well-defined phosphorylation patterns in absence of further modulators like the full receptor or Gβγ, and that the time profile of the phosphorylation barcode seems to be largely encoded in the minimal pair of C-terminal peptide and GRK. The data further suggest that arrestin might encounter different phosphorylation barcodes over time, hinting at the possibility of time-dependent arrestin responses.}, }
@article {pmid40489934, year = {2025}, author = {Arnela, M and Vidaña-Vila, E and Fantinelli, A and Moñux-Bernal, A and Vaquerizo-Serrano, J and Socoró, JC}, title = {Generation of ultrasonic and audible sound waves for the automatic classification of packaging waste in reverse vending machines.}, journal = {Waste management (New York, N.Y.)}, volume = {204}, number = {}, pages = {114934}, doi = {10.1016/j.wasman.2025.114934}, pmid = {40489934}, issn = {1879-2456}, mesh = {*Recycling/methods ; Acoustics ; Sound ; Ultrasonic Waves ; *Product Packaging ; Machine Learning ; *Waste Management/methods ; }, abstract = {Reverse vending machines (RVMs) are essential for promoting waste sorting at the source by offering incentives for recycling. However, current RVMs, which primarily rely on expensive sensors such as barcode scanners and computer vision systems, face limitations including unreadable barcodes, high computational demands, and sensitivity to environmental conditions like lighting. This paper presents an alternative approach using acoustic sensors for waste classification. The proposed method consists of emitting ultrasonic and audible sound waves towards the recyclable object and, by analyzing the variations in the acoustic field, an artificial intelligence system classifies the material. For doing so, the system uses the ultrasonic and audible impulse response of each item, measured using the exponential sine sweep (ESS) technique. To validate this approach, a proof-of-concept has been developed and tested in a controlled environment using a scaled replica of a reverberation chamber, designed to achieve ideal acoustic conditions. Acoustic impulse responses have been captured using ESS emitted by an omnidirectional parametric loudspeaker (OPL), which generates both ultrasonic and audible sound waves via the parametric acoustic array (PAA) effect. This setup allows for simultaneous collection of ultrasonic and audible impulse responses for each recyclable item. The collected acoustic data has then been used to train classical machine learning and deep learning models to classify the introduced material, specifically plastic, glass, cardboard, and metallic cans. The results demonstrate a promising classification accuracy of more than 90%, highlighting the potential of this acoustic technology for waste sorting and supporting further research into its application in RVMs.}, }
@article {pmid40489257, year = {2025}, author = {Feng, Y and Chen, D and Applegate, C and Gonzalez Medina, N and Kuo, CW and Arogundade, OH and Wright, CL and Xu, F and Drnevich, J and Smith, AM}, title = {Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.}, journal = {ACS nano}, volume = {19}, number = {24}, pages = {22079-22092}, doi = {10.1021/acsnano.5c02111}, pmid = {40489257}, issn = {1936-086X}, mesh = {*Single-Cell Analysis/methods ; *Nanoparticles/chemistry ; *Lipids/chemistry ; Animals ; Mice ; *Sequence Analysis, RNA/methods ; Humans ; Liposomes ; }, abstract = {Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling of heterogeneous cell populations. Here, we describe nanocoding, a technology that applies lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by upon cell lysis. In cultured cell lines and heterogeneous cells from tissue digests, nanocoding occurs in 40 min with stability after sample mixing and requires only commercially available reagents without complex chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples from adipose tissue of obese rodents containing lipid-rich debris and heterogeneous cells show more than 95% labeling with all known subtypes identified. Using nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. The ease of generating and tuning these constructs may afford efficient and robust sample multiplexing with minimal crosstalk.}, }
@article {pmid40488904, year = {2025}, author = {Kwasnoski, L and Brown, J and Taylor, J and Watson, JL and Oleyar, D and Ellis, VA}, title = {Avian haemosporidian parasite prevalence and diversity in two populations of the American kestrel (Falco sparverius).}, journal = {Parasitology research}, volume = {124}, number = {6}, pages = {60}, pmid = {40488904}, issn = {1432-1955}, support = {DEL00774, DEL00854, NE1943, NE2443//USDA Hatch/ ; }, mesh = {Animals ; *Falconiformes/parasitology ; *Haemosporida/genetics/isolation &amp; purification/classification ; *Bird Diseases/parasitology/epidemiology ; *Genetic Variation ; Prevalence ; Utah/epidemiology ; Cytochromes b/genetics ; *Protozoan Infections, Animal/epidemiology/parasitology ; Delaware/epidemiology ; Phylogeny ; }, abstract = {Parasite communities vary among host species and across space. However, little is known about differences in parasite communities between geographically and genetically distinct populations of the same host species. American kestrels (Falco sparverius) are small falcons with regionally distinct genetic populations across North America. We sampled kestrels from Delaware and Utah for avian haemosporidian parasites (genera: Haemoproteus, Plasmodium, and Leucocytozoon) and used molecular barcoding of the parasite cytochrome b gene (cyt b) to quantify parasite genetic lineage diversity. We identified four lineages of Haemoproteus parasites and one Leucocytozoon lineage infecting kestrels. A comparison with previous studies suggests that most of these lineages are largely restricted to kestrels. We found similar infection prevalence and lineage composition between the sites. All kestrels sampled in Utah were adults (i.e., sampled after hatch year), but in Delaware, we found adult birds had a higher infection prevalence than juveniles (i.e., hatch-year birds). Despite harboring largely the same parasite lineages, kestrels are unlikely to disperse between Utah and Delaware. The similarity in parasite lineages in the two kestrel populations could be due to a number of factors including broadly distributed vector species (of which little is known), movement of alternative and undetected host species, or transmission during migration or on overwintering grounds. Alternatively, the cyt b gene might not capture recent genetic differentiation among the parasites. Future studies should explore these various possibilities to understand the mechanisms underpinning parasite distributions across genetically structured host populations.}, }
@article {pmid40487348, year = {2025}, author = {Inumaru, M and Itokawa, K and Matsumura, R and Sawabe, K and Watanabe, M and Isawa, H and Kasai, S and Higa, Y}, title = {COI barcoding can distinguish bisexual and parthenogenetic populations of Haemaphysalis longicornis in Japan: Revisiting methods with SNP analysis as another possible method.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {27}, number = {}, pages = {101083}, pmid = {40487348}, issn = {2213-2244}, abstract = {Haemaphysalis longicornis, the Asian long-horned tick, is an important vector for various infectious diseases, such as severe fever with thrombocytopenia syndrome (SFTS) and Japanese spotted fever. In this species, a triploid parthenogenetic reproductive form occurs along with a diploid bisexual form. Several approaches have been used to distinguish these two groups, including the presence/absence of males in the population, karyotyping, flow cytometry, and most recently, mitochondrial phylogeny. Mitochondrial gene (COI) barcoding has also been casually used, although its validity has not been investigated. In the present study, the validity of COI barcoding, genotyping nuclear markers (SNPs), and morphometrics was evaluated for distinguishing the reproductive forms of H. longicornis in Japan. Ticks were collected using the flagging method at two locations in Hyogo, Japan. DNA was extracted from ticks after photography, which was used for morphometric measurements. The DNA was used for COI barcoding by direct sequencing and genotyping SNPs in the nuclear genome. The resulting COI haplotypes were clustered into two distinct haplogroups, which represented different ploidy levels, corresponding to the different reproductive groups. Genotypes of nuclear SNPs supported that the individuals from each mitochondrial haplogroup belonged to distinct reproductive populations with different ploidy levels. Meanwhile, although significant differences were observed in multiple morphometric characteristics between these reproductive groups, large overlaps were generally evident in the distribution, indicating that morphological identification is not sufficient to distinguish the reproductive groups. This study suggested for the first time that COI barcoding and SNP genotyping are both convenient and reliable methods to distinguish the two reproductive forms of H. longicornis in Japan.}, }
@article {pmid40486261, year = {2024}, author = {Barmaki, A and Rassi, Y and Absavaran, A and Akhavan, AA and Moradi-Asl, E and Zahraei-Ramazani, A and Rafizadeh, S}, title = {Discrimination of Phlebotomus perfiliewi transcaucasicus, Ph. major sensu lato and Ph. tobbi (Diptera: Psychodidae) Using Morphometric and DNA Barcoding Methods in the Endemic Foci of Visceral Leishmaniasis in Ardabil Province, North West of Iran.}, journal = {Journal of arthropod-borne diseases}, volume = {18}, number = {3}, pages = {197-217}, pmid = {40486261}, issn = {2322-1984}, abstract = {BACKGROUND: Visceral leishmaniasis, commonly known as kala-azar, and prevalent in more than 70 countries and several regions of Iran. It is one of the main diseases transmitted by sand flies. In this work, geometric morphometrics and DNA barcoding were employed as novel techniques to enhance the diagnostic tools used in this study.<br><br>METHODS: Phlebotomus perfiliewi transcaucasicus, Phlebotomus major s.l., and Phlebotomus tobbi caught from three districts in the Ardabil Province, northwest of Iran. The right wings of 286 female sand flies were analyzed using geometric morphometric (GM) tools. Additionally, the COI gene was isolated from each of the three species, amplified using universal primers, and sequenced through the DNA barcoding method for classification. This sequencing data was then formatted to generate morphometric analyses.<br><br>RESULTS: The landmarks with the most variations were found in sets 10, 12, 13, and 14, whereas the first set's landmarks at 1 and 11, along with those from the second set at positions 2, 3, and 5 exhibited the greatest variations. Analysis of the size and shape variations in the wings indicates the presence of distinct populations (P< 0.05). Furthermore, the DNA barcoding results not only confirmed the findings from the geometric morphometric analysis but also revealed both interspecific and intraspecific distances.<br><br>CONCLUSION: This study was the first attempt to assess whether wing geometry morphometrics, combined with DNA barcode techniques, can effectively distinguish the three mentioned species in the studied areas. Furthermore, the identification of Phlebotomus neglectus in this area prompted recommendations for additional research.}, }
@article {pmid40485605, year = {2025}, author = {Zhou, Z and Kang, T and Chen, J and Doctor, Y and Camposagrado, JG and Makris, Y and Pertsemlidis, A and Bleris, L}, title = {Biosecurity Primitive: Polymerase X-based Genetic Physical Unclonable Functions.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {29}, pages = {e15820}, doi = {10.1002/advs.202415820}, pmid = {40485605}, issn = {2198-3844}, support = {2300340//National Science Foundation/ ; 2029121//National Science Foundation/ ; 2114192//National Science Foundation/ ; HG012884//National Institutes of Health/NHGRI/ ; }, mesh = {*Computer Security ; *DNA-Directed DNA Polymerase/genetics/metabolism ; *DNA Nucleotidylexotransferase/genetics/metabolism ; }, abstract = {A Physical Unclonable Function (PUF) is a security primitive that exploits inherent variations in manufacturing protocols to generate unique, random-like identifiers. These identifiers are used for authentication and encryption purposes in hardware security applications in the semiconductor industry. Inspired by the success of silicon PUFs, herein it is leverage Terminal deoxynucleotidyl Transferase (TdT), a template-independent polymerase belonging to the X-family of DNA polymerases, to augment the intrinsic entropy generated during DNA lesion repair and rapidly produce genetic PUFs that satisfy the following properties: robustness (i.e., they repeatedly produce the same output), uniqueness (i.e., they do not coincide with any other identically produced PUF), and unclonability (i.e., they are virtually impossible to replicate). Furthermore, a post-sequencing feature selection methodology based on logistic regression to facilitate PUF classification is developed. This experimental and computational pipeline drastically reduces production time and cost compared to conventional genetic barcoding without compromising the stringent PUF criteria of uniqueness and unclonability. This results provide novel insights into the function of TdT and represent a major step toward utilization of PUFs as a biosecurity primitive for cell line authentication and provenance attestation.}, }
@article {pmid40483279, year = {2025}, author = {Weng, J and Wu, X and Li, C and Li, Y and Li, Q and Dou, F and Wang, T and Li, J and Wang, Y and Zhang, L}, title = {Comprehensive Dataset for Polychaetes in the IPC: Species Distribution, DNA Barcodes, and Functional Traits.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {956}, pmid = {40483279}, issn = {2052-4463}, mesh = {Animals ; *Polychaeta/genetics/classification/physiology ; *DNA Barcoding, Taxonomic ; Biodiversity ; Genome, Mitochondrial ; Ecosystem ; }, abstract = {The Indo Pacific Convergence Zone (IPC) is recognized as an area of highest taxonomic and functional diversity. The polychaetes have garnered attention as their enormous functional trait diversity and their significant role in biomonitoring ecosystems. Here, we developed a comprehensive dataset for polychaetes in the IPC, encompassing information on species distribution, DNA barcodes, and functional traits. The species distribution data were collected from 39,310 occurrence records, with over 13% newly contributed from museum collections and 350 scientific papers. This dataset also provides 29% known species coverage in the IPC, 154 mitochondrial genomes (35.1% are new contributions), and 7,052 COI/18S/16S sequences (4.6% are new contributions). Our functional traits subdatabase comprises approximately 12,000 records and 2,831 species, belonging to 696 genera and 75 families, with 90% of which are new additions. The functional trait data were categorized into 13 traits spanning morphology, life history, physiology, and behavior. The datasetbase provide an unprecedented and original contribution for conservation and for studying the biogeography, evolution processes, and ecology of tropic organisms.}, }
@article {pmid40480178, year = {2025}, author = {Kochergina, A and Schnittler, M}, title = {Epiphytic and fimicolous myxomycetes on the island Hiddensee (Germany): rare species, new genotypes and unexpected ecological preferences.}, journal = {European journal of protistology}, volume = {99}, number = {}, pages = {126153}, doi = {10.1016/j.ejop.2025.126153}, pmid = {40480178}, issn = {1618-0429}, mesh = {*Myxomycetes/genetics/classification/physiology/isolation &amp; purification ; Germany ; Islands ; Phylogeny ; *Genotype ; Species Specificity ; DNA Barcoding, Taxonomic ; Ecosystem ; }, abstract = {Hiddensee, a small island in the Baltic Sea, is characterized by a rather dry, windy, and sunny climate, resembling a periodic desert. We studied epiphytic and fimicolous myxomycetes on the island using the moist chamber method for 101 substrate samples. A total of 37 myxomycete species were identified from 124 records, including 4 species newly recorded in Germany. Molecular barcoding revealed that 67 % of the obtained DNA sequences were new, differing by more than 1 % from their closest matches in the GenBank database. We obtained the first molecular data for Didymium megalosporum (found to be related to the aethaloid species D. spongiosum and D. yulii) and C. elegans var. microspora (new data for both the species and the variety). For Trichia rapa, described in 2023 based on a single barcoded collection, we found three different ribotypes, including one already known. Presumably undescribed taxa within the morphospecies Comatricha nigra, Didymium squamulosum, Enerthenema papillatum, and Trichia contorta were identified by molecular barcoding. Substrate preferences of myxomycetes, categorized into four substrate types (bark of living trees, leaf litter, twigs, and dung), showed distinct patterns of occurrence, with each substrate type associated with a characteristic assemblage of myxomycetes. The species composition on the bark of living trees showed a well-known dependence on bark pH and hardness, with differing pH optima and tolerance ranges among the studied species. Echinostelium minutum occurred across a broad pH spectrum (6.1-8.0; 11 records), whereas Didymium leptotrichum was restricted to a narrow pH range (7.9-8.1; 7 records). Trichia munda preferred relatively acidic substrates (6.4-7.2; 9 records), while Perichaena luteola (7.4-8.0, 5 records) was more commonly found in slightly alkaline conditions.}, }
@article {pmid40476221, year = {2025}, author = {Piraonapicha, K and Kaewtongkum, N and Chomphuphuang, N and Kimsawat, P and Kumtanom, K and Samung, Y}, title = {Mukariasakaeratensis sp. nov. (Hemiptera, Cicadellidae, Deltocephalinae), a new species of bamboo leafhopper from Sakaerat Biosphere Reserve, Thailand.}, journal = {ZooKeys}, volume = {1239}, number = {}, pages = {305-320}, pmid = {40476221}, issn = {1313-2989}, abstract = {Mukariasakaeratensis Piraonapicha &amp; Chomphuphuang, sp. nov. is described based on male and female specimens recently collected in Nakhon Ratchasima, Thailand. The new species is herein described by an integrative approach combining morphological and molecular evidence. Genetic distance analyses revealed a potential barcoding gap (K2P) of 0.20-12.07% for COI in Mukaria. Species delimitation methods ABGD and ASAP demonstrated promising results for the COI gene. This species clearly differs from all its congeners in the aedeagal shaft abruptly narrowed and curved inward in the distal half, and with a pair of spines pointed anteriorly. Mukariasakaeratensis sp. nov. has been found on the bamboo Vietnamosasapusilla (A. Chev. &amp; A. Camus) T.Q. Nguyen. This finding constitutes the first recorded instance of a specialized member of the tribe Mukariini (Hemiptera: Cicadellidae: Deltocephalinae) feeding exclusively on bamboo from the genus Vietnamosasa. The holotype has been deposited in the Entomology Section, Queen Sirikit Botanic Garden, The Botanical Garden Organization, Thailand.}, }
@article {pmid40476220, year = {2025}, author = {Morinha, F and Ernest, J and Archer-Taveira, A and Rocha, AM and Iwamasa, RT}, title = {Molecular and morphological data support the synonymy of Muricanthusradix Gmelin, 1791 and Muricanthusambiguus Reeve, 1845 (Gastropoda, Muricidae).}, journal = {ZooKeys}, volume = {1239}, number = {}, pages = {281-303}, pmid = {40476220}, issn = {1313-2989}, abstract = {The Muricanthusradix/ambiguus/nigritus complex includes species with a great diversity of shell shapes and shared habitats in various regions, which has raised questions and doubts about the current taxonomic classification of these species. Muricanthusnigritus, M.radix, and M.ambiguus are three similar-looking black and white murex found commonly on the west coast of North and South America. The wide variety of morphological patterns within and between these species makes the classification of specimens difficult by visual observation. To this day, controversy persists over whether M.radix and M.ambiguus are one or two distinct species. Molecular genetic data have helped clarify the taxonomic classification of many mollusk species in recent decades, contributing to a more accurate understanding of biodiversity and ecosystems. In this study, DNA barcoding and double digest restriction-site associated DNA sequencing (ddRAD-seq) methodologies were applied to complement morphological data, establishing for the first time the phylogenetic relationships between M.nigritus, M.ambiguus and M.radix. The classic mitochondrial and nuclear barcodes obtained from 80 specimens collected from three different geographic locations differentiated only two phylogenetic clades (M.nigritus and M.radix/ambiguus from Mexico differentiated from M.radix/ambiguus from Mexico and Panama). High levels of mitochondrial DNA introgression have been observed between M.nigritus and M.radix/ambiguus. The deep-level approach performed using 3692 loci obtained from ddRAD-seq also differentiated only two genetic clusters (M.nigritus and M.radix/ambiguus). Our results clearly support the proposal that M.ambiguus should be synonymized with M.radix.}, }
@article {pmid40475874, year = {2025}, author = {Zhang, C and Hu, S and Lin, X and Huang, H and Liu, S}, title = {Crustaceans as Key Prey: Insights Into the Dietary Partitioning of Four Carnivorous Fishes in the Nansha Islands, South China Sea.}, journal = {Ecology and evolution}, volume = {15}, number = {6}, pages = {e71497}, pmid = {40475874}, issn = {2045-7758}, abstract = {Small carnivorous fishes serve as important mesopredators in coral reef ecosystems. However, the habitat and prey availability degradation within these ecosystems has intensified the trend of body size miniaturization and interspecific competition among these species. To better understand the food selection and resource partitioning strategies of mesopredators, we conducted a comprehensive study on the feeding habits of four small carnivorous fish species collected from the coral reefs of the Nansha Islands. This study employed a combination of morphological analysis and molecular identification of gut contents, along with stable isotope analysis. Similar food items, mostly semi-digested/undigested body remains/fragments from crustaceans, fish, and mollusk were detected in the guts of the analyzed fishes. High-throughput sequencing based on DNA barcoding identified approximately 24 taxa belonging to Arthropoda, Chordata, and Mollusca, with Arthropoda being the most abundant prey group, accounting for 82.2%-92% of the total sequences across the four fish species. Stable isotope analysis further revealed that the trophic levels of the four species ranged from 3.4 to 3.6. The results of food overlap analysis based on stable isotopes contrasted with those obtained from high-throughput sequencing, highlighting the distinct characteristics and complementary strengths of these methods. This study broadens the current understanding of the feeding ecology of four carnivorous fish species. The findings reveal that crustaceans are the primary food source for carnivorous fishes in the Nansha Islands, differing from previous assumptions that their diets were predominantly fish-based. Additionally, the differentiated utilization of crustacean resources among these species suggests that marine benthic invertebrates may play a crucial role in supporting mesopredators within degraded coral reef ecosystems, potentially helping to mitigate the environmental stress they face.}, }
@article {pmid40475247, year = {2025}, author = {Rammouz, S and Reichstein, A and Riehle, J and Ferner, A and Fischer, M and Schäfers, C}, title = {Authenticity in bakery products: Detection of pistachio fraud using NGS metabarcoding.}, journal = {Food chemistry. Molecular sciences}, volume = {10}, number = {}, pages = {100260}, pmid = {40475247}, issn = {2666-5662}, abstract = {Ensuring the authenticity of food ingredients is a key aspect of food safety and quality control. High-quality raw materials are often replaced by cheaper ones and not declared. In fine bakery products such as baklava, pistachios are illegally replaced by cheaper nuts. In this study we introduce a Next-generation sequencing (NGS)-based DNA metabarcoding approach as a sensitive, reliable, and semi-quantitative method that enables a successfully detection of such adulterations, even in complex and highly processed food matrices. NGS offers increased depth, efficiency and further applications compared to conventional Sanger sequencing. In the present study, the mini-rbcL region of the chloroplast genome was used and sequencing was performed on an Illumina MiSeq® instrument. The method enabled the identification of six common pistachio adulterants, including nuts, seeds, and legumes. By preparing analytical control samples, matrix effects could be observed and included in the semi-quantitative analysis. We successfully applied the method and demonstrated the high potential of NGS technologies for routine food authentication, offering a cost- and time-efficient solution for high-throughput sample analysis.}, }
@article {pmid40472750, year = {2025}, author = {Fogt-Wyrwas, R and Dabert, M and Jarosz, W}, title = {DNA barcoding shows that Toxocara cati infecting domestic and wild felids is a species complex.}, journal = {Veterinary parasitology}, volume = {338}, number = {}, pages = {110514}, doi = {10.1016/j.vetpar.2025.110514}, pmid = {40472750}, issn = {1873-2550}, mesh = {Animals ; *Toxocara/genetics/classification ; *DNA Barcoding, Taxonomic/veterinary ; Phylogeny ; Cats ; *Toxocariasis/parasitology ; Animals, Wild/parasitology ; *Felidae/parasitology ; *Cat Diseases/parasitology ; Genetic Variation ; }, abstract = {The insufficient attention paid to the importance of Toxocara cati in the epidemiology of toxocariasis has resulted in significant gaps in the understanding of the true zoonotic potential of this parasite. Therefore, further research is necessary to understand its biology and epidemiology. In this article, the hypothesis of possible speciation in the T. cati complex was tested using cox1 sequences from T. cati individuals infecting domestic and wild felids from different parts of the world. Using DNA barcoding, a phylogenetic analysis was performed that grouped T. cati representatives into five clades according to the host species. The differences in cox1 sequences between T. cati from domestic cats and T. cati from wild felids were substantial (6.68 %-10.84 %). The results of the Assemble Species by Automatic Partitioning analysis supported the species status of the clades. However, the determination of the actual species diversity of the T. cati complex would necessitate an analysis of a wider range of wild hosts. A detailed understanding of the genetic diversity and phylogenetic relationships between species in the T. cati complex will contribute to more accurate identification, diagnosis and better control of these parasites.}, }
@article {pmid40472314, year = {2025}, author = {, }, title = {Correction: DNA Barcode, chemical analysis, and antioxidant activity of Psidium guineense from Ecuador.}, journal = {PloS one}, volume = {20}, number = {6}, pages = {e0326074}, pmid = {40472314}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0319524.].}, }
@article {pmid40465191, year = {2025}, author = {Tenge, BN and Muiru, WM and Kimenju, JW and Linguya, SK and Schwake-Anduschus, C and Amata, RL and Onyango, LO}, title = {Cultural and molecular identification of fungal genera and species occurring in maize : Fungi genera and species found in maize.}, journal = {Mycotoxin research}, volume = {41}, number = {3}, pages = {437-446}, pmid = {40465191}, issn = {1867-1632}, support = {323-06.01-03-2816PROC11//German Federal Ministry of Food and Agriculture (BMEL)/ ; }, mesh = {*Zea mays/microbiology ; Kenya ; *Fungi/classification/isolation &amp; purification/genetics ; Aspergillus/isolation &amp; purification/genetics/classification ; Penicillium/isolation &amp; purification/genetics/classification ; DNA, Fungal/genetics ; Calmodulin/genetics ; Fusarium/isolation &amp; purification/genetics/classification ; Phylogeny ; Trichoderma/isolation &amp; purification/genetics/classification ; DNA Barcoding, Taxonomic ; Aflatoxins/biosynthesis ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Mycotoxins contribute to a substantial loss of global maize grain yields in terms of tonnes. However, in sub-Saharan Africa, screening of mycotoxin-producing fungi predominantly relies on culture-based methods, which are both time-consuming and labour-intensive. This study examined the major fungal species responsible for aflatoxin production in major maize-producing regions of Kenya using molecular techniques. Maize samples were collected from Kilifi, Makueni, and Kisumu counties. For fungal isolation followed by molecular identification targeting the internal transcribed spacer region (ITS) for Fusarium and calmodulin (CaM) genes for Aspergillus, Penicillium, and Trichoderma, this was followed by basic local alignment search tool (BLAST) analysis. The study revealed 14 fungal species belonging to four genera namely Aspergillus, Penicillium, Fusarium, and Trichoderma. Kisumu County had the highest diversity of fungal species, representing 47.8% of the total identified. Within Kisumu, Penicillium species were the most prevalent, with an incidence rate of 72.9%. In contrast, Aspergillus species were most common in Kilifi County (54.5% incidence). The application of DNA barcoding techniques significantly enhanced the precision of identifying aflatoxin-producing fungi compared to conventional identification methods. This study confirms the presence of multiple fungal species responsible for aflatoxin production in Kenya's maize-growing regions.}, }
@article {pmid40464340, year = {2025}, author = {Wang, Q and Wang, C and Fang, Z and Zhang, Z and Zhao, Y and Ma, T and Shang, L}, title = {Hydroxypropyl Cellulose Assembled Microspheres as Structural Color Barcodes from Revolving Microfluidics.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e06556}, doi = {10.1002/advs.202506556}, pmid = {40464340}, issn = {2198-3844}, support = {2024YFA0919100//National Key Research and Development Program of China/ ; 32271383//National Natural Science Foundation of China/ ; }, abstract = {Optical barcodes are versatile information carriers widely applied for encryption, commercial anti-counterfeiting, and biomedical fields. Hydroxypropyl cellulose (HPC), as a natural derivative, exhibits excellent biocompatibility and can self-assemble into cholesteric liquid crystals (CLCs) with structure color. However, the high viscosity of HPC CLCs is a huge hurdle for material processing and thus limits their applications. In this study, a high-speed revolving microfluidic platform is developed for emulsifying high-viscosity methacrylate functionalized HPC (HPC-MA) solution to form droplets. HPC-MA molecules in the droplets can self-assemble into CLCs by water evaporation, and the resultant CLCs droplets can be cross-linked to form structural color barcode particles. The prepared HPC-MA CLCs barcoded particles exhibit well-defined and adjustable encoding information while maintaining excellent biocompatibility. Furthermore, the prepared barcode particles also demonstrate great potential in 3D cell culture and multiplex immunoassays. This work introduces an efficient way to continuously produce HPC-MA CLCs barcode particles with finely tunable size and uniformity. Such barcode particles are promising for widespread applications in bioanalysis and biodiagnostics.}, }
@article {pmid40461651, year = {2025}, author = {Soares, RRG and García-Soriano, DA and Larsson, J and Fange, D and Schirman, D and Grillo, M and Knöppel, A and Sen, BC and Svahn, F and Zikrin, S and Ratz, M and Nilsson, M and Elf, J}, title = {Pooled optical screening in bacteria using chromosomally expressed barcodes.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {851}, pmid = {40461651}, issn = {2399-3642}, support = {2016-0621//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-03958//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-01238//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 885360//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2016.0077//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2017.0291//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2019.0439//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; }, mesh = {*Escherichia coli/genetics/metabolism ; Luminescent Proteins/genetics/metabolism ; Red Fluorescent Protein ; *Chromosomes, Bacterial/genetics ; *DNA Barcoding, Taxonomic/methods ; Gene Library ; }, abstract = {Optical pooled screening is an important tool to study dynamic phenotypes for libraries of genetically engineered cells. However, the desired engineering often requires that the barcodes used for in situ genotyping are expressed from the chromosome. This has not previously been achieved in bacteria. Here we describe a method for in situ genotyping of libraries with genomic barcodes in Escherichia coli. The method is applied to measure the intracellular maturation time of 84 red fluorescent proteins.}, }
@article {pmid40459854, year = {2025}, author = {Devitt, G and Hanrahan, N and Ramírez Moreno, M and Mudher, A and Mahajan, S}, title = {A Novel Spectral Barcoding and Classification Approach for Complex Biological Samples Using Multiexcitation Raman Spectroscopy (MX-Raman).}, journal = {Analytical chemistry}, volume = {97}, number = {23}, pages = {12189-12197}, pmid = {40459854}, issn = {1520-6882}, mesh = {*Spectrum Analysis, Raman/methods ; Humans ; *Neurodegenerative Diseases/diagnosis ; Discriminant Analysis ; Brain/pathology/metabolism ; }, abstract = {We report the development and application of a novel spectral barcoding approach that exploits our multiexcitation (MX) Raman spectroscopy-based methodology for improved label-free detection and classification of complex biological samples. To develop our improved MX-Raman methodology, we utilized post-mortem brain tissue from several neurodegenerative diseases (NDDs) that have considerable clinical overlap. For improving our methodology we used three sources of spectral information arising from distinct physical phenomena to assess which was most important for NDD classification. Spectral measurements utilized combinations of data from multiple, distinct excitation laser wavelengths and polarization states to differentially probe molecular vibrations and autofluorescence signals. We demonstrate that the more informative MX-Raman (532 nm-785 nm) spectra are classified with 96.7% accuracy on average, compared to conventional single-excitation Raman spectroscopy that resulted in 78.5% accuracy (532 nm) or 85.6% accuracy (785 nm) using linear discriminant analysis (LDA) on 5 NDD classes. By combining information from distinct laser polarizations we observed a nonsignificant increase in classification accuracy without the need of a second laser (785 nm-785 nm polarized), whereas combining Raman spectra with autofluorescence signals did not increase classification accuracy. Finally, by filtering out spectral features that were redundant for classification or not descriptive of disease class, we engineered spectral barcodes consisting of a minimal subset of highly disease-specific MX-Raman features that improved the unsupervised and cross-validated clustering of MX-Raman spectra. The results demonstrate that increasing spectral information content using our optical MX-Raman methodology enables enhanced identification and distinction of complex biological samples but only when that information is independent and descriptive of class. The future translation of such technology to biofluids could support diagnosis and stratification of patients living with dementia and potentially other clinical conditions such as cancer and infectious disease.}, }
@article {pmid40458985, year = {2025}, author = {Carné, A and Vieites, DR and van den Burg, MP}, title = {In Vouchers We (Hope to) Trust: Unveiling Hidden Errors in GenBank's Tetrapod Taxonomic Foundations.}, journal = {Molecular ecology}, volume = {34}, number = {13}, pages = {e17812}, pmid = {40458985}, issn = {1365-294X}, support = {10.13039/501100011033//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Agencia Estatal de Investigaci&#xf3;n./ ; }, mesh = {Animals ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {Genetic repositories are invaluable resources foundational to various biological disciplines. While their data and metadata reliability are essential for robust research outcomes, numerous studies have highlighted data quality and consistency issues. Here, we detect and quantify errors at the most fundamental level by analysing the congruence of sequences derived from the same genetic marker and specimen voucher across tetrapods. Our analysis reveals that 32% of re-sequenced vouchers (with identical field or museum numbers) yield unequal sequences, ranging from a few mutations to significant divergences (0.06%-33.95%). These divergences may result from sample misidentification, labelling errors, fidelity disparities between sequencing methods, or contamination at various stages of the research process. Our findings demonstrate errors within GenBank at its most basal level and suggest that, although undetectable, a similar error rate likely exists in non-re-sequenced data. These previously overlooked errors are concerning because they arise from replicated experiments, which are uncommon, and raise serious questions about the reliability of non-re-sequenced specimens. Such errors can compromise the accuracy of biodiversity assessments (e.g., taxonomic assessment, eDNA and barcoding), phylogenetic analyses and conservation planning by artificially inflating the intraspecific divergence or misidentifying (to-be-described) species. Additionally, the accuracy of large-scale biological studies that rely on such data can be compromised. Our concerning results call for protocols ensuring sample traceability to the specimens or tissues during the whole process of data generation, analysis and deposition in a database. We propose a third-party annotation system for individual GenBank records that would allow flagging common errors and alert both the original submitter and all users to potential problems without modifying the original records.}, }
@article {pmid40457637, year = {2025}, author = {Buchan, E and Rickard, JJS and Thomas, MR and Oppenheimer, PG}, title = {Advanced Multipurpose Spectroscopic Nanobio-Device for Concurrent Lab-on-a-Chip Label-Free Separation and Detection of Extracellular Vesicles as Key-Biomarkers for Point-of-Care Cardiovascular Disease Diagnostics.}, journal = {Advanced healthcare materials}, volume = {}, number = {}, pages = {e2500122}, doi = {10.1002/adhm.202500122}, pmid = {40457637}, issn = {2192-2659}, support = {//National Institute for Health Research/ ; EP/Y030206/1/ERC_/European Research Council/International ; EP/V029983/1//Engineering and Physical Sciences Research Council/ ; EP/L016346/1//Engineering and Physical Sciences Research Council/ ; 174ISSFPP/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The global aging population presents a major public health challenge, with cardiovascular diseases (CVDs) remaining the leading cause of death worldwide. Often asymptomatic in early-stages, CVDs are frequently undiagnosed until critical events like myocardial infarction or stroke occur. To address this gap, an advanced integrated multipurpose spectroscopic lab-on-a-chip bionano-device has been developed for early CVD detection through extracellular vesicle (EV). EVs, which reflect the molecular state of their originating cells, are separated and analyzed using the combined Raman spectroscopy's molecular specificity with AI-driven classification from clinical CVD biofluids. AIMSpec-LoC unprecedently achieves rapid, label-free, size-based separation of EV subtypes, including small, mid and large EVs from biofluids, whilst preserving EV integrity and eliminating extensive preprocessing. The device enables real-time, multiplexed molecular profiling of EV cargo, identifying CVD-specific biomarkers with sensitivity and specificity >96% and linking these to CVD progression, achieving >97% accuracy in identifying disease-specific molecular fingerprints. This bionanotechnological device generates quantitative barcodes to support prognostic modeling and therapeutic evaluation, providing clinicians with actionable insights for timely-diagnosis and personalized treatment. AIMSpec-LoC platform offers a transformative solution for point-of-care CVD diagnostics, addressing critical unmet needs in cardiovascular medicine, enhancing clinical decision-making, improving patient health and reducing the global burden of CVDs.}, }
@article {pmid40456603, year = {2025}, author = {Zidane, N and Rodrigues, C and Bouchez, V and Rethoret-Pasty, M and Passet, V and Brisse, S and Crestani, C}, title = {Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.}, journal = {Genome research}, volume = {35}, number = {8}, pages = {1758-1766}, pmid = {40456603}, issn = {1549-5469}, support = {INV-025280/GATES/Gates Foundation/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Klebsiella pneumoniae/genetics/classification ; Genome, Bacterial ; Humans ; *Bordetella pertussis/genetics/classification ; Genotype ; *Genotyping Techniques/methods ; Sequence Analysis, DNA/methods ; }, abstract = {High-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with the complete genome reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents an alternative that offers benefits including real-time sequencing and cost efficiency, particularly useful in resource-limited settings. However, the historically higher error rates of ONT data have so far limited its application in high-precision genomic typing. The recent release of ONT's R10.4.1 chemistry, with significantly improved raw read accuracy (Q20+), offers a potential solution to this problem. The aim of this study is to evaluate the performance of ONT's latest chemistry for bacterial genomic typing against the gold-standard Illumina technology, focusing on three respiratory pathogens of public health importance, Klebsiella pneumoniae, Bordetella pertussis, and Corynebacterium diphtheriae, and their related species. Using the Rapid Barcoding Kit V14, we generate and analyze genome assemblies with different basecalling models, at different simulated depths of coverage. ONT assemblies are compared to the Illumina reference for completeness and core genome multilocus sequence typing (cgMLST) accuracy (number of allelic mismatches). Our results show that genomes obtained from raw ONT data basecalled with Dorado SUP v0.9.0, assembled with Flye, and with a minimum coverage depth of 35×, optimized accuracy for all bacterial species tested. Error rates are consistently <0.5% for each cgMLST scheme, indicating that ONT R10.4.1 data are suitable for high-resolution genomic typing applied to outbreak investigations and public health surveillance.}, }
@article {pmid40454788, year = {2025}, author = {Bringloe, TT and Grant, WS and Zaparenkov, D and Starko, S and Fort, A and Inaba, M and Sulpice, R and Saunders, GW and Verbruggen, H}, title = {Revisiting the species problem in Northeast Pacific ribbon kelp lineages (genus Alaria): Lessons learned using whole genome data.}, journal = {Journal of phycology}, volume = {61}, number = {4}, pages = {777-791}, pmid = {40454788}, issn = {1529-8817}, support = {//University of Melbourne McKenzie Postdoctoral Fellowship/ ; //Phychological Society of America Norma J. Lang Early Career Fellowship/ ; //European Union Northern Periphery and Arctic Program/ ; 19/FFP/6841//SFI Frontiers for the Future project Pristine Coasts/ ; //Forrest Research Foundation/ ; 1618//North Pacific Research Board/ ; CEECIND:2023.06155//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, abstract = {The transition from interbreeding populations to species continues to represent difficult terrain for phylogenetic investigations. Genotyping entire genomes holds promise for enhancing insights into the process of speciation and evolutionary relationships among recently speciated taxa. Northeast Pacific ribbon kelp was once recognized as four species before they were folded into Alaria marginata based on DNA barcodes, although several lineages continue to be recognized. We used whole genome sequencing to determine whether these lineages represente species. Whole genomes of 69 individuals from five genetically distinctive lineages in the Gulf of Alaska (United States) and Salish Sea (Canada) were analyzed, along with 63 genomes from three other species of Alaria. Our analysis of >3.4 million single nucleotide polymorphisms reaffirmed that organellar and nuclear phylogenetic signals are incongruent in Alaria, producing different topologies among five organellar and six nuclear A. marginata lineages. Lineages appeared to be reproductively isolated, as evidenced by strong clustering and lack of recent admixture across nuclear genomes. Genetic divergence between A. marginata lineages also exceeded intra-lineage divergence, proxied by A. esculenta populations, but fell short of distances observed across other species of Alaria. Despite the genomic data supporting predictions of the biological and genetic species concepts, we encountered inherent limitations in declaring species status. While our work shifts taxonomic conversations toward a genome-scale framework that provides a more comprehensive picture of divergence and connectivity, our work also highlights that philosophical challenges inherent to defining species persist and that integrative approaches continue to be necessary in the genomic era.}, }
@article {pmid40454326, year = {2025}, author = {Baban, NS and Bhattacharjee, S and Song, YA and Chakrabarty, K and Karri, R}, title = {Cyber-physical security of biochips: A perspective.}, journal = {Biomicrofluidics}, volume = {19}, number = {3}, pages = {031304}, pmid = {40454326}, issn = {1932-1058}, abstract = {Microfluidic biochips (MBs) are transforming diagnostics, healthcare, and biomedical research. However, their rapid deployment has exposed them to diverse security threats, including structural tampering, material degradation, sample-level interference, and intellectual property (IP) theft, such as counterfeiting, overbuilding, and piracy. This perspective highlights emerging attack vectors and countermeasures aimed at mitigating these risks. Structural attacks, such as stealthy design code modifications, can result in faulty diagnostics. To address this, deep learning -based anomaly detection leverages microstructural changes, including optical changes such as shadows or reflections, to identify and resolve faults. Material-level countermeasures, including mechano-responsive dyes and spectrometric watermarking, safeguard against subtle chemical alterations during fabrication. Sample-level protections, such as molecular barcoding, ensure bio-sample integrity by embedding unique DNA sequences for authentication. At the IP level, techniques like watermarking, physically unclonable functions, fingerprinting, and obfuscation schemes provide robust defenses against reverse engineering and counterfeiting. Together, these approaches offer a multi-layered security framework to protect MBs, ensuring their reliability, safety, and trustworthiness in critical applications.}, }
@article {pmid40453775, year = {2025}, author = {Kubátová, A and Kunz, B and Hubka, V}, title = {Reintroducing Akanthomyces ampullifer: providing genetic barcodes, culture, and updated description for the dipteran pathogen rediscovered in Germany.}, journal = {Mycoscience}, volume = {65}, number = {6}, pages = {260-269}, pmid = {40453775}, issn = {1618-2545}, abstract = {The genus Akanthomyces (Ascomycota, Hypocreales) includes entomopathogenic species known to infect a variety of insects and spiders. In this study, we present the first isolate of A. ampullifer characterized by molecular methods, found on dead bodies of the common cave limoniid Limonia nubeculosa (Diptera) in the subterranean spaces of southwestern Germany. In total, seven specimens exhibited distinctive morphological traits that, when compared with historical records, confirm their identification as A. ampullifer-particularly noted for its affinity to dipteran hosts. Absent from culture collections and molecular repositories, this species has eluded detailed scientific documentation using modern methods. Our research bridges this knowledge gap, providing the first genetic identification barcodes of five genes, living culture, cultivation requirements, and an updated description. This overlooked fungus is phylogenetically most closely related to the species A. pyralidarum, A. laosensis, and some other species mostly associated with adult moths. It demonstrates a unique morphological signature with monoblastic phialides forming a layer on the surface of synnemata and produces long, cylindrical, chain-forming conidia. It prefers lower temperatures, exhibiting an inability to grow at 25 °C, coupled with notably slow growth in culture.}, }
@article {pmid40453413, year = {2025}, author = {Martoni, F and Tweed, JMH and Blacket, MJ and Percy, DM}, title = {An annotated checklist of the psyllids (Hemiptera, Psylloidea) of Norfolk Island with keys to species, new records, and descriptions of two new endemic species.}, journal = {ZooKeys}, volume = {1238}, number = {}, pages = {297-348}, pmid = {40453413}, issn = {1313-2989}, abstract = {Norfolk Island is a small, isolated archipelago in the Pacific Ocean, 1400 km east of the Australian mainland. The history of human colonisation and land use on the island has resulted in a substantial reduction in the extent and quality of indigenous habitat. A quarantine survey of Norfolk Island in 2012-2014 provided the first records of psyllid species, reporting six taxa from the island. Additional collection records are provided that increase the number to 14 species, of which nine are regarded as adventive, four as native of which two are endemic, and one whose additional distribution is unknown. Two species are formally described here and are the first psyllid species to be described from Norfolk Island. These new species, Pseudophacopteronaewagriini Percy &amp; Martoni, sp. nov. (Aphalaridae) and Acizziaaliceae Percy &amp; Martoni, sp. nov. (Psyllidae) are both considered endemic to Norfolk Island and are associated with native plants, the endemic Alyxiagynopogon (Apocynaceae) and the native Dodonaeaviscosa (Sapindaceae), respectively. In addition to an updated checklist, identification keys to adults and immatures of the psyllids found on Norfolk Island and DNA barcodes for all species are provided. Both new species have had complete mitochondrial genomes sequenced in a previous study and here a full annotation of the mitochondrial genome of Acizziaaliceae Percy &amp; Martoni, sp. nov. is supplied. Lastly, the barcode data was analysed in a maximum likelihood constraint framework with previous genome data to investigate the phylogenetic origins of the Norfolk Island taxa.}, }
@article {pmid40452930, year = {2025}, author = {Maslakova, S and Cherneva, I and Kahn, E and Wong, A and Paulay, G}, title = {A hundred species, mostly new-first assessment of ribbon worm diversity and distribution in Oman.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19438}, pmid = {40452930}, issn = {2167-8359}, mesh = {Animals ; Oman ; *Biodiversity ; *Invertebrates/classification/genetics ; Phylogeny ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; }, abstract = {BACKGROUND: Biodiversity is a key characteristic of any ecosystem but remains largely undescribed for most marine animals. Ribbon worms (phylum Nemertea), a diverse but poorly sampled phylum ubiquitous in the world's oceans, are a case in point. Aside from their function as predators in marine communities, nemerteans are biomedically relevant because they produce diverse toxins, and some impact bivalve, decapod, and glass eel fisheries. Identification of nemerteans is challenging because many species look alike. The task is further complicated by many descriptions being based on preserved specimens, and therefore lacking characters of external appearance of live specimens. Characters of internal anatomy form the basis of traditional systematics but are more recently shown to be of little use in distinguishing between closely related species. This makes DNA data essential in species descriptions, and assessments of diversity and distribution.<br><br>METHODS: In a first modern survey of the phylum in Arabian waters, we collected nemerteans from a variety of habitats, focusing sampling on hard-bottom substrata, especially coral reefs. Specimens were triple-documented with photos, morphological vouchers, and DNA barcodes. Species delineation was based on morphology and Cytochrome Oxidase I sequences. Sequences and associated data are deposited in public databases, and vouchers at the Florida Museum of Natural History.<br><br>RESULTS: We documented 107 nemertean species in Oman, where none were previously known. This doubles the number of genetically characterized nemertean species for the entire Indo-West Pacific-a testament to how poorly sampled the phylum is in the most biodiverse marine region of the world. As many as 98% of the species were undescribed, and 93% are not documented outside Arabia. Half of the species were rare, and most-cryptic. Undescribed species were assigned unique alphanumeric temporary names for tracking in the literature and public databases. Estimates of source diversity suggest that future surveys might uncover an additional &#x223c;200 species by including other locations and types of habitats, particularly soft bottoms, and the water column. Little overlap was observed between species found in the northern (Gulf of Oman) and southern (Sea of Arabia) regions, and many that occurred in both areas showed evidence of genetic differentiation corresponding to the major biogeographic break at R'as-al-Hadd.<br><br>CONCLUSIONS: The high diversity, novelty, and distinctiveness of this fauna underscore the importance of sampling the most biodiverse and least studied tropical marine regions of the world. The large amount of cryptic and undescribed diversity highlights the critical role of DNA barcodes and rapid approaches to species descriptions.}, }
@article {pmid40451908, year = {2025}, author = {Gusmao, ACB and van Dijk, RL and Girard, EB and Peijnenburg, KTCA and Macher, J and Kucera, M and Morard, R}, title = {Exploring the potential of the COI gene marker for DNA barcoding of planktonic foraminifera.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19205}, pmid = {40451908}, issn = {2045-2322}, mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; *Plankton/genetics/classification ; Genetic Markers ; Phylogeny ; }, abstract = {Metabarcoding is a cornerstone of modern ecology, but its accuracy is dependent on the chosen gene marker. While the small subunit ribosomal DNA (SSU) is a powerful tool to describe protist diversity, its reliability in retrieving the composition of communities is less obvious. It is particularly challenging to obtain quantitative estimates of abundance in planktonic foraminifera, where the variability of the SSU gene copy number can span three orders of magnitude. As an alternative, we explored the potential of the mitochondrial cytochrome c oxidase subunit I (COI) marker. We developed a reference barcode library of 130 sequences of a 1200 bp long COI fragment belonging to 26 morphospecies of foraminifera and performed 201 single-cell qPCR quantifications to evaluate the relationship between the number of COI copies, and the size of individual foraminifera. We found that the COI evolves between 25 and 1000 times slower than the SSU and therefore has a poor taxonomic resolution. However, we observed a significant relationship between COI copy number and foraminifera size. These results suggest that SSU and COI can play complementary roles: the SSU is well-suited for capturing taxonomic diversity, while the COI is useful to retrieve crude information on the community composition.}, }
@article {pmid40450781, year = {2025}, author = {Guidoni, L and Drais, MI and Turco, S and Mazzaglia, A and Vannini, A and Morales-Rodríguez, C}, title = {Survival of plant pathogens during composting of bio-waste: a case study for oomycetes and fungi.}, journal = {The Science of the total environment}, volume = {986}, number = {}, pages = {179767}, doi = {10.1016/j.scitotenv.2025.179767}, pmid = {40450781}, issn = {1879-1026}, mesh = {*Composting/methods ; *Fungi/physiology ; *Phytophthora/physiology ; *Oomycetes/physiology ; *Soil Microbiology ; Fagaceae/microbiology ; }, abstract = {European countries have implemented national strategies to reduce the use of peat in horticulture due to its environmental impact. Studies demonstrated the possibility of reducing peat consumption by using compost as a substitute without affecting the growth and development of potted horticulture plants. However, any substitute must be produced considering quality standards and requirements that are adopted for peat. Among others, the risk of contamination of compost with plant pathogens is particularly high. Furthermore, the assessment of the survival of specific plant pathogens during the composting process requires proper detection methods. This study evaluated the survival/presence of the oomycete Phytophthora cinnamomi, as a model plant pathogen, in woody chips of artificially inoculated Castanea sativa saplings used as a bulking agent in composting processes. Detection techniques for assessment included isolation in pure culture, quantitative PCR (qPCR) and High Throughput Sequencing (HTS). The pathogen was easily detected in woody chips at the beginning of the composting process with baiting and molecular barcoding. By the end of the maturation phase, no P. cinnamomi was detectable by any diagnostic method including baiting, confirming the efficacy of a proper composting process in eradicating the pathogen. HTS approach was also able to detect throughout the process the DNA of plant pathogenic fungal genera naturally present in the green residues and bulk agents. These findings are crucial for developing diagnostic pipelines to be included in protocols for compost biosafety certification. Finally, the present study demonstrated the possibility of processing recycled horticulture biowaste to obtain high-quality and safe compost without the need for complex and expensive composting plants.}, }
@article {pmid40448040, year = {2025}, author = {Akrami, AM and Meratian Esfahani, S and Soorni, A}, title = {Decoding the chloroplast genomes of five Iranian Salvia species: insights into genomic structure, phylogenetic relationships, and molecular marker development.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {545}, pmid = {40448040}, issn = {1471-2164}, mesh = {*Genome, Chloroplast ; *Salvia/genetics/classification ; *Phylogeny ; Iran ; *Genomics/methods ; Genetic Markers ; Base Composition ; Evolution, Molecular ; }, abstract = {BACKGROUND: The genus Salvia, a prominent member of the Lamiaceae family, is renowned for its ecological, medicinal, and economic significance. Despite its importance, molecular data, particularly chloroplast (cp.) genome information, remain scarce for many native Iranian Salvia species. In this study, we sequenced and analyzed the complete cp. genomes of five Iranian Salvia species (S. aethiopis, S. sclarea, S. glutinosa, S. verticillata, and S. officinalis) to elucidate their genomic structure, evolutionary relationships, and potential for biotechnological applications.<br><br>RESULTS: The cp. genomes of the five Salvia species exhibited a conserved quadripartite structure, with sizes ranging from 151,163 to 151,662&#xa0;bp, and a GC content of 38%. Each genome contained 132 or 131 genes, comprising 86 or 87 protein-coding, 8 rRNA, and 37 tRNA genes, with duplications in rpl2, rpl23, and rps12. Minor variations in gene content were observed, such as the absence of trnS-CGA in S. glutinosa. Comparative analysis of IR boundaries showed subtle expansions in S. officinalis and S. sclarea, while S. glutinosa remained stable. Trans-splicing of the rps12 gene was observed in all species, with complex structures in S. glutinosa and S. sclarea. Codon usage analysis revealed a preference for A/U-ending codons, with S. verticillata displaying unique patterns. Nucleotide diversity (Pi) identified highly variable regions, such as rpl14-rpl16 and psbK-psbI, as potential molecular markers. Phylogenetic analysis resolved distinct clades, with S. aethiopis and S. sclarea forming a close group, S. glutinosa clustering with S. chanryoenica, and S. officinalis showing genetic homogeneity with Mediterranean species. S. verticillata exhibited an earlier divergence, highlighting the genus's evolutionary complexity.<br><br>CONCLUSIONS: This study provides critical genomic resources for species identification, phylogenetic studies, and the development of molecular markers, facilitating the conservation of native Salvia species and their utilization in breeding programs for medicinal and aromatic traits.}, }
@article {pmid40447760, year = {2025}, author = {Hebert, JD and Xu, H and Tang, YJ and Ruiz, PA and Detrick, CR and Wang, J and Hughes, NW and Donosa, O and Siah, VP and Andrejka, L and Karmakar, S and Aboiralor, I and Tang, R and Sotillo, R and Sage, J and Cong, L and Petrov, DA and Winslow, MM}, title = {Efficient and multiplexed somatic genome editing with Cas12a mice.}, journal = {Nature biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {40447760}, issn = {2157-846X}, support = {T34FT8013//Tobacco-Related Disease Research Program (TRDRP)/ ; DGE-2146755//National Science Foundation (NSF)/ ; R01-CA234349//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R35 CA231997/CA/NCI NIH HHS/United States ; R35-CA231997//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-GM141627//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-CA231253//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; K00CA234962//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; P01-CA244114//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; PF-21-112-01-MM//American Cancer Society (American Cancer Society, Inc.)/ ; R35-HG011316//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30-CA124435//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations. However, existing models have a limited ability to create multiple targeted edits, hindering our understanding of complex genetic interactions. Here we generate transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a), which robustly generates compound genotypes, including diverse cancers driven by inactivation of trios of tumour suppressor genes or an oncogenic translocation. We integrate these modular CRISPR RNA (crRNA) arrays with clonal barcoding to quantify the size and number of tumours with each array, as well as the impact of varying the guide number and position within a four-guide array. Finally, we generate tumours with inactivation of all combinations of nine tumour suppressor genes and find that the fitness of triple-knockout genotypes is largely explainable by one- and two-gene effects. These Cas12a alleles will enable further rapid creation of disease models and high-throughput investigation of coincident genomic alterations in vivo.}, }
@article {pmid40447231, year = {2025}, author = {Rochwarger, A and Kaufmann, L and Zhao, J and Makky, A and Nguyen, NA and Lehmann, N and Samusik, N and Beschorner, C and Manmadhan, SS and Greif, K and Schürch, CM}, title = {A Validation Workflow for Novel Oligonucleotide Sequences to Expand the Multiplexing Capacity of the CO-Detection by indEXing (CODEX) Platform.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {105}, number = {10}, pages = {104200}, doi = {10.1016/j.labinv.2025.104200}, pmid = {40447231}, issn = {1530-0307}, abstract = {Antibody-based multiplexed tissue imaging has the potential to provide critical advances in biological discoveries and their translation for clinical applications. With the increasing introduction of markers and modalities for spatial analysis, there is an according demand for the expansion of multiplexing capacities of such imaging platforms. CO-Detection by indEXing (CODEX) is a widely used multiplexed tissue imaging platform that utilizes DNA-conjugated antibodies for imaging. The multiplexing capacity of CODEX is limited by the availability of unique DNA-oligonucleotide sequences for antibody barcoding. In this study, we demonstrate a workflow for the validation and the introduction of novel sets of candidate DNA-oligonucleotide sequences for CODEX. Through cross-validation multicycle experiments with the already published library of DNA barcodes, we here present a set of 27 novel oligonucleotide sequences for CODEX, increasing the potential multiplexing capacity to 85+ markers. We confirmed the utility of the new barcodes using a 74-plex antibody panel on a multitumor tissue microarray of paraffin-embedded tissues. The workflow presented here provides a reproducible method for extending the plexity of the CODEX platform, facilitating a deeper understanding of tissue microenvironments.}, }
@article {pmid40444175, year = {2025}, author = {Bhuvaneshwaran, S and Padmanaban, VS and Radja, RD and Anandan, G and Venkatesan, S and Semalaiyappan, J and Kumar, A and Kuttiatt, VS}, title = {Molecular identification of immature stages of medically important fly species, Puducherry, South India: a preliminary study.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1551807}, pmid = {40444175}, issn = {2673-8600}, abstract = {Flies and maggots are of medical importance, and it is often necessary to identify them at species level. Conventionally, this is carried out based on morphological features using taxonomic keys. However, identification of maggots based on morphology is difficult and required entomological expertise is often lacking in clinical settings. Molecular methods can be an alternative to morphology-based identification and find special application when only tiny pieces of specimens are available especially in cases of human myiasis. In this preliminary study, we explored the utility of mitochondrial COI gene based molecular method, for identifying immature stages of certain medically important flies captured from the field in Puducherry, India. Maggots were captured from different locations in Puducherry using rotten fish and kitchen waste as baits and a 700 bp segment of the COI gene was amplified and genetic relationship was assessed by performing haplotype network analysis. High quality sequences were available for 11 specimens and were subjected to BLAST analysis to identify matches from the database for identification of the species. The identified maggots belonged to Sarcophaga peregrina (Robineau-Desvoidy, 1830), Hemipyrellia ligurriens (Wiedemann, 1830) and Chrysomya megacephala (Fabricius, 1794). This study generated representative molecular sequence data for two less studied fly species of medical importance, S. peregrina and H. ligurriens from South India. In future, there is a need for further detailed molecular studies on flies in the diverse epidemiological and geographic settings in India with a view to identify cryptic species and new haplotypes.}, }
@article {pmid40444067, year = {2025}, author = {Yela, JL and Molina, D and Ortiz, AS}, title = {Agrotisvillenensis-a new species of Noctuinae (Lepidoptera, Noctuidae) from the southeastern Iberian Peninsula.}, journal = {ZooKeys}, volume = {1239}, number = {}, pages = {21-32}, pmid = {40444067}, issn = {1313-2989}, abstract = {Agrotisvillenensis sp. nov. is described from the Iberian Peninsula. Differential superficial, genital and genetic (barcode) characters from its closest Iberian and European relative species, Agrotisvestigialis (Hufnagel, 1766), are presented. Morphologically, the new species is best characterized in the male genitalia by the shape of the basal vesica and the presence of a median diverticulum and in the female genitalia by its comparatively long appendix bursae. The barcode of A.villenensis differs from those of related species and is assigned a unique BIN.}, }
@article {pmid40443187, year = {2025}, author = {Jiang, C and Wang, Q and Shi, Z and Liu, S and Chen, G and Liang, B and Li, D and Ye, X}, title = {Controlled fabrication of novel magneto-fluorescent encoded microspheres with host-guest structures for simultaneous detection of thyroxine and thyroid stimulating hormone.}, journal = {Analytical methods : advancing methods and applications}, volume = {17}, number = {23}, pages = {4734-4744}, doi = {10.1039/d5ay00554j}, pmid = {40443187}, issn = {1759-9679}, mesh = {*Thyrotropin/blood ; *Thyroxine/blood ; *Microspheres ; Humans ; Limit of Detection ; Quantum Dots/chemistry ; Fluorescent Dyes/chemistry ; }, abstract = {Simultaneous detection of serum thyroxine (T4) and thyroid stimulating hormone (TSH) is essential for diagnosis and monitoring of congenital hypothyroidism (CH). Here, we reported a novel suspension array platform based on host-guest-structured magneto-fluorescent encoded beads (HGBs) for concurrent T4 and TSH detection. The foundation of HGBs lays in low-density polystyrene microsphere templates, ingeniously transformed into micron-scale host beads through the sequential deposition of iron oxide nanoparticles, quantum dots, and silica layers, resulting in good magnetism, satisfactory suspension ability and fluorescence stability. By combining micron-scale host beads exhibiting distinct red fluorescence intensities with nano-scale guest beads displaying varying green fluorescence intensities, we could repeatedly and accurately prepare 24 discriminable HGBs easily. Then, two representative HGBs were selected to construct a suspension arrays system for concurrent T4 and TSH detection. Under the optimal detection conditions, the suspension arrays we tested on T4 and TSH could be assayed in the ranges of 4 to 400 ng mL[-1], and 0.032 to 100 mIU L[-1] with limits of detection of 1.2 ng mL[-1], and 0.014 mIU L[-1], respectively. This innovative methodology not only exhibits commendable accuracy and precision but also demonstrates strong concordance with established chemiluminescence immunoassay results. Consequently, the suspension arrays based on HGB barcodes hold immense promise for enhancing the diagnostic efficiency in the realm of CH management.}, }
@article {pmid40443169, year = {2025}, author = {Tang, CN and Lai, NW and Ho, HC}, title = {Description of a new liopropomine basslet, Liopropoma terecaudum, from northern Taiwan (Perciformes: Epinephelidae).}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70086}, pmid = {40443169}, issn = {1095-8649}, support = {//National Museum of Marine Biology and Aquarium/ ; //National Kaohsiung University of Science and Technology/ ; }, abstract = {Liopropoma terecaudum sp. nov. is described based on 12 specimens collected off northern Taiwan. The new species most closely resembles two sympatric species, L. japonicum and L. dorsoluteum, but differs from both species and all other congeneric species of Liopropoma based on the following combination of morphological and colouration characters: caudal fin round; dorsal-fin elements VIII, 13 and lacking a distinct notch; lateral side of body with a broad red stripe; base of caudal fin with a large red blotch. Phylogenetic analysis of mitochondrial DNA barcode sequences places L. terecaudum in a clade with L. dorsolutum and L. japonicum. The average genetic divergences between L. terecaudum and L. dorsoluteum, and between L. terecaudum and L. japonicum, are measured to be 11.8% and 11.9%, respectively. The description of L. terecaudum brings the total number of Liopropoma in Taiwanese waters to 11.}, }
@article {pmid40442801, year = {2025}, author = {Tepboonrueng, P and Pataradool, T and Boonserm, R and Rimmer, LW and Preativatanyou, K and Sunantaraporn, S and Siriyasatien, P}, title = {DNA barcoding of Culicoides biting midges (Diptera: Ceratopogonidae) and detection of Leishmania and other trypanosomatids in southern Thailand.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {194}, pmid = {40442801}, issn = {1756-3305}, mesh = {Animals ; *Ceratopogonidae/parasitology/genetics/classification ; Thailand ; *DNA Barcoding, Taxonomic ; *Leishmania/isolation &amp; purification/genetics/classification ; Female ; *Insect Vectors/parasitology/genetics/classification ; Phylogeny ; *Trypanosomatina/isolation &amp; purification/genetics/classification ; }, abstract = {BACKGROUND: Biting midges of the genus Culicoides play an important role in the transmission of pathogenic arboviruses and parasites. Thailand has documented more than 100 species of Culicoides; however, several cryptic species complexes remain to be clarified. Recent studies in areas with leishmaniasis indicate that several species of Culicoides might be potential vectors of Leishmania in the subgenus Mundinia, but evidence supporting the hypothesis is still lacking. Therefore, the diversity of Culicoides biting midges and their potential role as vectors of leishmaniasis in southern Thailand remains uncertain.<br><br>METHODS: Female Culicoides biting midges were collected using Centers for Disease Control and Prevention (CDC) ultraviolet (UV) light traps from four locations within leishmaniasis-affected areas in three provinces of southern Thailand, including Nakhon Si Thammarat, Krabi, and Surat Thani. Culicoides species were identified based on the morphology of wing spot patterns and subsequently confirmed by cytochrome c oxidase subunit I (COI) Sanger sequencing. A potential cryptic species was classified using an integrative taxonomic approach associated with DNA barcoding identification by Barcode of Life Database (BOLD) and Basic Local Alignment Search Tool (BLAST) searches. Furthermore, three different methods of species delimitation, namely ASAP [Assemble Species by Automatic Partitioning], TCS [Templeton, Crandall, and Sing], and PTP [Poisson Tree Processes], were employed to verify the sequences into the molecular operational taxonomic unit (MOTU). Detection of Leishmania and other trypanosomatid parasites was performed by polymerase chain reaction (PCR) based on the ITS1 region and small subunit SSU ribosomal RNA (rRNA) gene, followed by Sanger sequencing and haplotype diversity analysis. The identification of host blood sources was carried out using host-specific multiplex PCR.<br><br>RESULTS: A total of 716 unfed midges and 159 blood-fed specimens were morphologically identified into 25 species belonging to five subgenera (Avaritia, Hoffmania, Meijerehelea, Remmia, and Trithecoides) and four species groups (Clavipalpis, Ornatus, Shermani, and Shortti). Two unidentified specimens were classified into two subgenera (Trithecoides and Avaritia). The DNA barcoding identification exhibited an 82.20% success rate. Species delimitation analyses demonstrated the presence of cryptic species complexes, categorized into six species: Culicoides actoni, C. orientalis, C. huffi, C. palpifer, C. clavipalpis, and C. jacobsoni. Furthermore, 6.42% of the Culicoides biting midges tested positive for Leishmania DNA in three sampling sites in Nakhon Si Thammarat and Surat Thani provinces (with no positive results in Krabi province). Furthermore, the sympatric infection of Leishmania martiniquensis and Leishmania orientalis was identified in several Culicoides species in Ron Phibun and Phunphin districts in Nakhon Si Thammarat and Surat Thani, respectively. In contrast, L. orientalis was detected in Sichon district, Nakhon Si Thammarat province. A genetic diversity analysis revealed high haplotype diversity and relatively low nucleotide diversity in both parasite populations. Additionally, Crithidia sp. and Crithidia brevicula were detected in Culicoides peregrinus and Culicoides subgenus Trithecoides. The analysis of the host blood meal from Ron Phibun also demonstrated that Culicoides had fed on cows, dogs, and chickens, and mixed blood preferences for humans and cows or chickens and cows were detected.<br><br>CONCLUSIONS: The findings of the present study demonstrate the presence of mixed blood hosts and co-circulation of L. martiniquensis and L. orientalis in Culicoides in areas of leishmaniasis, as well as cryptic species of Culicoides biting midges, through an integrative taxonomic approach. These findings support the hypothesis that Culicoides biting midges may serve as potential vectors in southern Thailand, and vector diversity is a contributing factor to the risk of zoonotic transmission.}, }
@article {pmid40442452, year = {2025}, author = {Ohtani, H and Ichikawa, R and Mori, K and Kato, T and Nishioka, M}, title = {Single-molecule DNA analysis implicates brain mitochondria pathology in bipolar disorder.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {40442452}, issn = {1476-5578}, support = {JP24tm0424229//Japan Agency for Medical Research and Development (AMED)/ ; JP24tm0424224//Japan Agency for Medical Research and Development (AMED)/ ; }, abstract = {Bipolar disorder (BD), characterized by recurrent manic and depressive episodes, is a global medical challenge. Based on its high heritability, various genomic studies have elucidated the genetic architecture of BD. Nonetheless, the specific genomic mechanisms underpinning BD pathogenesis remain elusive. Among under-investigated genomic factors, mitochondrial variants-particularly brain heteroplasmic variants-are of particular interest, given the critical role of mitochondria in neural function and the frequent psychiatric symptoms observed in mitochondrial diseases. In this study, we analyzed 163 brain DNA samples from 54 BD patients, 54 controls, and 55 schizophrenia patients to investigate the association between BD and mitochondrial heteroplasmic variants. Duplex molecular barcoding sequencing was employed for single-molecule resolution. We found an enrichment of ultra-rare heteroplasmic variants with allele fractions exceeding 1% in BD. Among them, potentially pathogenic variants, including m.3243A>G, loss-of-function variants, and rRNA variants, were particularly enriched in BD. In contrast, single-molecule analysis did not reveal a general trend of increases in low-level heteroplasmic variants in BD, in terms of per-base mutation frequency and heteroplasmic fractions. Thus, a subset of BD patients may be stratified according to the presence of ultra-rare mitochondrial variants. Our findings provide a foundation for future research into targeted therapeutic strategies for BD, grounded in genomic stratification by mitochondrial variants.}, }
@article {pmid40439147, year = {2025}, author = {Kipen, J and Jaldén, J}, title = {Brownian motion data augmentation: a method to push neural network performance on nanopore sensors.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {6}, pages = {}, pmid = {40439147}, issn = {1367-4811}, support = {2018-06169//Swedish Research Council/ ; //Swedish Foundation for Strategic Research/ ; }, mesh = {*Nanopores ; *Neural Networks, Computer ; Sequence Analysis, DNA/methods ; Algorithms ; }, abstract = {MOTIVATION: Nanopores are highly sensitive sensors that have achieved commercial success in DNA/RNA sequencing, with potential applications in protein sequencing and biomarker identification. Solid-state nanopores, in particular, face challenges such as instability and low signal-to-noise ratios, which lead scientists to adopt data-driven methods for nanopore signal analysis, although data acquisition remains restrictive.<br><br>RESULTS: We address this data scarcity by augmenting the training samples with traces that emulate Brownian motion effects, based on dynamic models in the literature. We apply this method to a publicly available dataset of a classification task containing nanopore reads of DNA with encoded barcodes. A neural network named QuipuNet was previously published for this dataset, and we demonstrate that our augmentation method produces a noticeable increase in QuipuNet's accuracy. Furthermore, we introduce a novel neural network named YupanaNet, which achieves greater accuracy (95.8%) than QuipuNet (94.6%) on the same dataset. YupanaNet benefits from both the enhanced generalization provided by Brownian motion data augmentation and the incorporation of novel architectures, including skip connections and a soft attention mask.<br><br>The source code and data are available at: https://github.com/JavierKipen/browDataAug.}, }
@article {pmid40437799, year = {2025}, author = {Krawczyk, K and Maździarz, M and Paukszto, &#x141; and Nobis, M and Sawicki, J}, title = {Phylogenetic reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {41}, number = {4}, pages = {358-371}, pmid = {40437799}, issn = {1096-0031}, support = {2023/51/B/NZ8/01179//the National Science Centre, Poland/ ; }, mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Poaceae/genetics/classification ; }, abstract = {Compared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial genome fragments can be valuable for both molecular species identification and phylogenetic analysis in grasses of the tribe Stipeae. To explore this potential, we first assembled the complete mitochondrial genome of Nassella tenuissima-the first fully described mitogenome in Stipeae-which served as a reference for selecting 29 aligned mitochondrial genome fragments totalling 139 680 bp. These fragments were then analysed across 49 representatives of the tribe, including 43 Stipa species and six other taxa. The mitochondrial fragments achieved a species discrimination efficiency of 75%, slightly exceeding the 71% efficiency observed for plastid super-barcodes. Additionally, comparative phylogenetic analyses using plastid and mitochondrial genomes underscored the utility of mitochondrial data in resolving phylogenetic relationships within Stipeae. Our findings provide a valuable resource for future research in transcriptomics, comparative genomics, phylogenomics and phylogeography of grasses.}, }
@article {pmid40436818, year = {2025}, author = {Cao, SH and Wan, Z and Johansen, E and Ma, G and Desai, P and Zhu, H and Wang, S}, title = {Plasmonic DNA-Barcoded Virion Nano-Oscillators for Multiplexed Quantification of Small-Molecule Binding Kinetics to Membrane Proteins.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {64}, number = {30}, pages = {e202506464}, pmid = {40436818}, issn = {1521-3773}, support = {R33 CA235294/CA/NCI NIH HHS/United States ; R42 GM157918/GM/NIGMS NIH HHS/United States ; R42GM157918/NH/NIH HHS/United States ; R33CA235294/NH/NIH HHS/United States ; }, mesh = {Kinetics ; Gold/chemistry ; *DNA/chemistry ; *Membrane Proteins/chemistry/metabolism ; *Virion/chemistry ; Metal Nanoparticles/chemistry ; Biosensing Techniques ; *Small Molecule Libraries/chemistry ; }, abstract = {A high-density nano-oscillator platform using self-assembled DNA-barcoded virion sensors is developed to address the critical need for high-throughput label-free measurement of small-molecule binding to membrane proteins. By integrating virion display technology with charge-sensitive plasmonic detection, our platform enables robust, label-free quantification of small-molecule binding kinetics to membrane proteins. Gold nanoparticle-virion conjugates are self-assembled onto a plasmonic sensor chip via a flexible molecular linker to form high-density nano-oscillators. Driven by an alternating electric field, the oscillation amplitudes of the nano-oscillators are precisely measured via widefield plasmonic imaging. This charge-sensitive mechanism can sensitively detect the binding of small-molecule ligands to the membrane proteins displayed on the virions at single-nanosensor resolution, overcoming the sensitivity limit of conventional mass-sensitive techniques. More importantly, the platform employs novel affinity-discriminated DNA barcodes for multistate decoding with exponential multiplexing capacity, enabling high-throughput screening of a library of membrane proteins. For a proof-of-concept demonstration, binding kinetics of five pairs of G-protein-coupled receptors and their corresponding small molecule ligands are measured on a single sensor chip, with all individual nano-oscillators identified by just two affinity-discriminated, quadra-state DNA decoders. This technology advances membrane protein research and drug screening capabilities, offering a practical solution for biomolecular interaction studies and biosensing applications.}, }
@article {pmid40434228, year = {2025}, author = {Cho, S and Moon, W and Martino, N and Yun, SH}, title = {Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {}, number = {}, pages = {e2418710}, pmid = {40434228}, issn = {1521-4095}, support = {1541959//National Science Foundation/ ; R01 EB034687/EB/NIBIB NIH HHS/United States ; R01 EB033155/EB/NIBIB NIH HHS/United States ; R01-EB034687/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; }, abstract = {Laser particles (LPs) emitting narrowband spectra across wide spectral ranges are highly promising for high-multiplex optical barcoding of biological cells. Here, LPs based on indium phosphide (InP) nanodisks are presented, operating in the near-infrared wavelength range of 740-970 nm. Utilizing low-order whispering gallery resonance modes in size-tuned nanodisks, an ultrawide color palette with 25% spectral utilization and nanometer-scale linewidth is achieved. A simple theoretical model accurately predicts spectral ranges based on particle size. The minimum laser size is 430 nm in air and 560 nm within cells, operating at mode orders of 4 or 5. The high brightness and narrow linewidths of polymer-silica-protected InP LPs, combined with a silicon-detector spectrometer, enable spectral detection of laser peaks with high signal-to-background ratios in highly-scattering media, including 1-cm-thick chicken breast tissue and blood vessels in live mice.}, }
@article {pmid40433188, year = {2024}, author = {Mahmud, BU and Hong, GY and Sharmin, A and Asher, ZD and Hoyle, JD}, title = {Accurate Medical Vial Identification Through Mixed Reality: A HoloLens 2 Implementation.}, journal = {Electronics}, volume = {13}, number = {22}, pages = {4420}, pmid = {40433188}, issn = {2079-9292}, support = {R18 HS029283/HS/AHRQ HHS/United States ; }, abstract = {The accurate identification of medicine vials is crucial for emergency medical services, especially for vials that resemble one another but have different labels, volumes, and concentrations. This study introduces a method to detect vials in real-time using mixed reality technology through Microsoft HoloLens 2. The system is also equipped with an SQL server to manage barcode and vial information. We conducted a comparative analysis of the barcode detection capabilities of the HoloLens 2 camera and an external scanner. The HoloLens 2 effectively identified larger barcodes when they were 20-25 cm away in normal lighting conditions. However, it faced difficulties in detecting smaller barcodes that were consistently detected by the external scanner. The frame rate investigation revealed performance fluctuations: an average of 10.54 frames per second (fps) under standard lighting conditions, decreasing to 10.10 fps in low light and further reducing to 10.05 fps when faced with high barcode density. Resolution tests demonstrated that a screen resolution of 1920 × 1080 yielded the best level of accuracy, with a precision rate of 98%. On the other hand, a resolution of 1280 × 720 achieved a good balance between accuracy 93% and speed. The HoloLens 2 demonstrates satisfactory performance under ideal circumstances; however, enhancements in detecting algorithms and camera resolution are required to accommodate diverse surroundings. This approach seeks to help paramedics make quick and accurate decisions during critical situations and tackle common obstacles such as reliance on networks and human mistakes. Our new approach of a hybrid method that integrates an external Bluetooth scanner with the MR device gives optimal results compared to the scanner-only approach.}, }
@article {pmid40431228, year = {2025}, author = {Hoxha, I and Dervović, J and Ruivo, M and Wijnveld, M and Obwaller, AG and Jäger, B and Weiler, M and Walochnik, J and Kniha, E and Alić, A}, title = {Molecular Typing of Tick-Borne Pathogens in Ixodids of Bosnia and Herzegovina.}, journal = {Microorganisms}, volume = {13}, number = {5}, pages = {}, pmid = {40431228}, issn = {2076-2607}, support = {P33867//FWF Austrian Science Fund/ ; 886318//Austrian defense research program FORTE of the Federal Ministry of Finance (BMF)/ ; }, abstract = {Ticks are key vectors of zoonotic pathogens, and their expanding distribution in Europe heightens public health concerns. In Bosnia and Herzegovina, while tick distribution is well documented, molecular data on tick-borne pathogens remain limited. This study aimed to illustrate the presence and diversity of these pathogens, focusing on areas with high human activity. Ticks (n = 556) were collected in April 2022 from eight diverse locations, including urban parks, private properties, and rural sites. PCR-based screening was employed to detect Anaplasmataceae, Borrelia, Francisella, Piroplasmida, Rickettsia, and tick-borne encephalitis virus (TBEV), with subsequent sequencing to confirm results. Further characterization of Borrelia burgdorferi sensu lato was achieved via reverse line blotting (RLB) hybridization and sequencing. Ixodes ricinus was the most prevalent species, followed by Dermacentor marginatus and D. reticulatus. Our analysis revealed an overall infection rate of 22.1% in questing ticks, with Rickettsia spp. and Borrelia spp. predominating. Notably, seven Borrelia species were identified in I. ricinus, alongside Anaplasma phagocytophilum, Rickettsia helvetica, and R. monacensis, with co-infections mainly observed in peri-urban areas. This study provides the first molecular evidence of multiple tick-borne pathogens in the region, underscoring the need for further surveillance and risk assessment of tick-borne diseases in the region.}, }
@article {pmid40431057, year = {2025}, author = {Wolella, EK and Cheng, Z and Li, M and Xia, D and Zhang, J and Duan, L and Liu, L and Li, Z and Zhang, J}, title = {Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {40431057}, issn = {2223-7747}, support = {YBXM2435//Nanfan special project of CAAS/ ; }, abstract = {Rice (Oryza sativa L.) is a stable food for over half of the world population, contributing 50-80% of the daily calorie intake. The completion of rice genome sequencing marks a significant milestone in understanding functional genomics, yet the systematic identification of gene functions remains a bottleneck for rice improvement. Large-scale mutant libraries in which the functions of genes are lost or gained (e.g., through chemical/physical treatments, T-DNA, transposons, RNAi, CRISPR/Cas9) have proven to be powerful tools for the systematic linking of genotypes to phenotypes. So far, using different mutagenesis approaches, a million mutant lines have been established and about 5-10% of the predicted rice gene functions have been identified due to the high demands of labor and low-throughput utilization. DNA-barcoding-based large-scale mutagenesis offers unprecedented precision and scalability in functional genomics. This review summarizes large-scale loss-of-function and gain-of-function mutant library development approaches and emphasizes the integration of DNA barcoding for pooled analysis. Unique DNA barcodes can be tagged to transposons/retrotransposons, DNA constructs, miRNA/siRNA, gRNA, and cDNA, allowing for pooling analysis and the assignment of functions to genes that cause phenotype alterations. In addition, the integration of high-throughput phenotyping and OMICS technologies can accelerate the identification of gene functions.}, }
@article {pmid40429242, year = {2025}, author = {Ma, Y and Niu, L and Wang, B and Li, D and Gao, Y and Ha, S and Fan, B and Xiong, Y and Cong, B and Chen, J and Deng, J}, title = {Preliminary Development of Global-Local Balanced Vision Transformer Deep Learning with DNA Barcoding for Automated Identification and Validation of Forensic Sarcosaphagous Flies.}, journal = {Insects}, volume = {16}, number = {5}, pages = {}, pmid = {40429242}, issn = {2075-4450}, support = {82060341//the National Natural Science Foundation of China/ ; YSPTZX202134//Innovation Platform for Academicians of Hainan Province/ ; Grant Number: Qhys2024-464//Innovative Research Projects for Postgraduates in Hainan Province/ ; }, abstract = {Morphological classification is the gold standard for identifying necrophilous flies, but its complexity and the scarcity of experts make accurate classification challenging. The development of artificial intelligence for autonomous recognition holds promise as a new approach to improve the efficiency and accuracy of fly morphology identification. In our previous study, we developed a GLB-ViT (Global-Local Balanced Vision Transformer)-based deep learning model for fly species identification, which demonstrated improved identification capabilities. To expand the model's application scope to meet the practical needs of forensic science, we extended the model based on the forensic science practice scenarios, increased the database of identifiable sarcosaphagous fly species, and successfully developed a WeChat Mini Program based on the model. The results show that the model can achieve fast and effective identification of ten common sarcosaphagous flies in Hainan, and the overall correct rate reaches 94.00%. For the few cases of identification difficulties and suspicious results, we have also constructed a rapid molecular species identification system based on DNA Barcoding technology to achieve accurate species identification of the flies under study. As the local fly database continues to be improved, the model is expected to be applicable to local forensic practice.}, }
@article {pmid40429233, year = {2025}, author = {Huo, QB and Fan, SX and Zhu, YF and Du, YZ}, title = {Diversity and the Origin of Perlodinella Klapálek 1912 (Plecoptera: Perlodidae) in Qinghai Province, China.}, journal = {Insects}, volume = {16}, number = {5}, pages = {}, pmid = {40429233}, issn = {2075-4450}, support = {32170459; 32370480//the National Natural Science Foundation of China/ ; }, abstract = {The article presents integrative research of the perlodid genus Perlodinella in Qinghai Province, northwestern China. P. tatunga Wu, 1973 is considered a junior synonym of P. kozlovi Klapálek, 1912, with a further description of intraspecific morphological variability, while P. unimacula Klapálek, 1912 is considered to be nomen dubium. The COI barcodes of the three valid species in Qinghai, P. epiproctalis (Zwick, 1997), P. kozlovi Klapálek, 1912, and P. microlobata Wu, 1938 are firstly sequenced, enabling adult-larva matching and the analysis of genetic diversity. The larval morphology of P. kozlovi and P. microlobata is described for the first time. Additionally, the biology, ecological adaptability, and fungal infections of Perlodinella are firstly recorded with an environment-related comparison. The discussion of the origin and immigration of the genus is also provided.}, }
@article {pmid40429198, year = {2025}, author = {Jia, N and Niu, F and Wang, X and Chi, D and Yu, J}, title = {A New Threat to Conifer Cones: Cydia kamijoi (Oku, 1968) (Lepidoptera, Tortricidae), a New Record for China, Based on Morphological and DNA Barcoding Analyses.}, journal = {Insects}, volume = {16}, number = {5}, pages = {}, pmid = {40429198}, issn = {2075-4450}, support = {No. 2022YFD1401004//National Key R &amp; D Program of China/ ; No. 2572018BA06//Central University Basic Research Business Expenses Special Fund Project/ ; }, abstract = {Cydia kamijoi (Oku, 1968) (Lepidoptera, Tortricidae) is a pest of conifer cones. It was first found in Hokkaido, Japan and was considered to be an endemic species of Hokkaido, which was rarely reported. Here, we report C. kamijoi in China for the first time, whose larvae feed on Pinus koraiensis pine cones. Descriptions of the larval and adult morphology of C. kamijoi, along with the COI DNA barcoding data available and the phylogenetic analysis are provided for this species for the first time. The emergence of C. kamijoi has severely threatened the health of P. koraiensis cones. This work may have important implications for the pest control of P. koraiensis cones in Northeast China.}, }
@article {pmid40429151, year = {2025}, author = {Huemer, P and Berggren, K and Aarvik, L and Rennwald, E and Hausmann, A and Segerer, A and Staffoni, G and Aspaas, AM and Trichas, A and Hebert, PDN}, title = {Extensive DNA Barcoding of Lepidoptera of Crete (Greece) Reveals Significant Taxonomic and Faunistic Gaps and Supports the First Comprehensive Checklist of the Island's Fauna.}, journal = {Insects}, volume = {16}, number = {5}, pages = {}, pmid = {40429151}, issn = {2075-4450}, abstract = {Comprehensive genetic surveys of Lepidoptera are still largely lacking across most of the eastern Mediterranean. Consequently, there is a lack of modern, taxonomically validated checklists that meet current scientific standards. In this study, we analyze the butterfly and moth fauna of Crete (Greece) for the first time, based on 3110 DNA barcode sequences, primarily obtained from specimens based on our own sampling program. Building on these data, and incorporating previously published records from print sources and online forums, we establish the first comprehensive checklist of the island's fauna. In total, the occurrence of 1230 species from 62 families is confirmed, with 724 of them genetically verified. Among them, 75 species appear to be island endemics. The checklist includes 125 newly recorded species for Crete, validated by DNA barcoding (with 36 also being new for Greece), along with 23 species confirmed solely through morphological study, and another 16 only documented by photographs. Conversely, 212 previously reported species had to be removed as likely invalid. Furthermore, 112 unidentified sequence clusters (BINs-Barcode Index Numbers) were documented, taxonomic uncertainties that will require future integrative resolution.}, }
@article {pmid40426188, year = {2025}, author = {Bourquia, M and Zahri, A and Ahlamine, M and Balenghien, T and Meyer, P and Sauer, FG and Lühken, R}, title = {First molecular confirmation of the presence of Hippobosca longipennis (Diptera: Hippoboscidae) and infestation of sheltered dogs in Morocco.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {193}, pmid = {40426188}, issn = {1756-3305}, support = {01Kl2022//Federal Ministry of Education and Research of Germany/ ; 01Kl2022//Federal Ministry of Education and Research of Germany/ ; 01Kl2022//Federal Ministry of Education and Research of Germany/ ; }, mesh = {Animals ; Morocco/epidemiology ; Dogs ; *Diptera/genetics/classification/parasitology ; *Dog Diseases/parasitology/epidemiology ; Female ; Male ; Filarioidea/isolation &amp; purification/genetics ; *Ectoparasitic Infestations/veterinary/epidemiology/parasitology ; }, abstract = {BACKGROUND: Hippobosca longipennis (Diptera: Hippoboscidae) is an obligate hematophagous ectoparasite that infests a wide range of vertebrate hosts across Africa, Southern Europe, the Middle East, and Asia. It is a potential vector of Acanthocheilonema dracunculoides (Filarioidea: Onchocercidae) and serves as a phoretic host for Cheyletiella yasguri (Acari: Cheyletiellidae), a known causative agent of dermatitis in both dogs and humans. Due to the lack of data on hippoboscids in Morocco, this study aimed to investigate the louse fly fauna of sheltered dogs in the country as well as the filarial nematodes they may harbor.<br><br>METHODS: Between April and November 2022, 230 sheltered dogs from four cities in Central Morocco were randomly examined as part of an entomological and epidemiological study on arthropod vectors and canine vector-borne pathogens. All visible louse flies on the domestic dogs were randomly collected and then morphologically and molecularly identified. DNA was subsequently extracted for screening of filarial nematodes.<br><br>RESULTS: A total of 30 dogs (13.1%) were infested with 35 H. longipennis louse flies, consisting of 33 adults (10 males, 19 non-gravid females, and four gravid females) and two larvae. Two representative specimens were confirmed through DNA barcoding of the cytochrome oxidase subunit I gene. All fly pools (gravid females, non-gravid females, males, and larvae) tested negative for filarial nematodes in the 12S rRNA PCR.<br><br>CONCLUSIONS: This study represents the first morphological and molecular characterization of H. longipennis flies in Morocco. Further national-scale investigations are needed to address gaps in the knowledge of unrecorded hippoboscid species and the pathogens of medical and veterinary importance that they may carry.}, }
@article {pmid40424257, year = {2025}, author = {He, Q and Lu, Q and Xie, N and Liu, X and Wang, X and Pan, J and Litchev, S and Hu, Y and Li, X and Zheng, B and Lin, J and Chen, E and Chen, XG and Zhou, X and Kong, Q and Lu, S}, title = {Real-time dynamic monitoring and multiplex PCR identification of vector mosquitoes in Zhejiang, China.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {5}, pages = {e0013129}, pmid = {40424257}, issn = {1935-2735}, mesh = {Animals ; China ; *Multiplex Polymerase Chain Reaction/methods ; *Mosquito Vectors/classification/genetics ; *Culicidae/classification/genetics ; DNA Barcoding, Taxonomic ; Humans ; }, abstract = {The monitoring and identification of mosquito vectors are crucial for controlling the transmission of mosquito-borne diseases. Traditional mosquito morphological identification and surveillance methods, such as human landing catches, human-baited double net traps and BG-Sentinel mosquito traps, require a large amount of manpower but can only provide fragmented data. We utilized the MS-300, an internet-based vector mosquito monitor, to continuously capture and upload real-time data to cloud services across ten monitoring sites located in seven cities in Zhejiang Province, China from May to December 2023. A new multiplex PCR system was developed for amplifying the internal transcribed spacer 2 region, followed by employing both multiplex PCR and DNA barcoding techniques for detecting wild mosquitoes. A comprehensive monitoring of 9749 mosquitoes was conducted. The mosquito density gradually increased from May 2023, peaked around June 22nd, and then declined in a wave-like pattern. The mosquitoes have two peak activity times, the peak times may vary depending on different locations and seasons. The study showed the high specificity of a multiplex PCR system in distinguishing six mosquito species: Aedes albopictus, Aedes aegypti, Culex pipiens pallens, Armigeres subalbatus, Anopheles sinensis and Anopheles anthropophagus. Notably, the sensitivity of detecting An. anthropophagus reached an impressive 1fg/µL. With the exception of Ae. aegypti and An. anthropophagus, all four other mosquito species have been identified in Zhejiang Province, with Cx. p. pallens being the predominant population. The results were highly consistent with DNA barcoding technology. The MS-300 continuously and automatically monitors mosquito population density and activity, providing effective guidance for mosquito control based on the environment and reducing labor costs. Our newly established multiple PCR system enables precise identification of crucial vector mosquitoes, facilitating a comprehensive understanding of population structures across diverse regions for selecting effective control measures.}, }
@article {pmid40424190, year = {2025}, author = {Guery, MA and Ceesay, S and Drammeh, S and Jaiteh, FK and D'Alessandro, U and Bousema, T and Conway, DJ and Claessens, A}, title = {Household clustering and seasonal genetic variation of Plasmodium falciparum at the community-level in The Gambia.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40424190}, issn = {2050-084X}, support = {INDIE OPP1173572//Bill and Melinda Gates Foundation/ ; EQU202303016290//Fondation pour la Recherche M&#xe9;dicale/ ; ANR 18-CE15-0009-01//Agence Nationale de la Recherche/ ; MRC/LSHTM fellowship/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; Transversales//Centre National de la Recherche Scientifique/ ; MRC/LSHTM fellowship//London School of Hygiene and Tropical Medicine/ ; NWO 016.158.306//Netherlands Organisation for Scientific Research/ ; }, mesh = {Gambia/epidemiology ; *Plasmodium falciparum/genetics/isolation &amp; purification/classification ; Humans ; *Seasons ; *Genetic Variation ; *Malaria, Falciparum/epidemiology/parasitology/transmission ; Longitudinal Studies ; Male ; Female ; Adolescent ; Adult ; *Family Characteristics ; Child ; Young Adult ; Genotype ; Child, Preschool ; Middle Aged ; Cluster Analysis ; Infant ; }, abstract = {Understanding the genetic diversity and transmission dynamics of Plasmodium falciparum, the causative agent of malaria, is crucial for effective control and elimination efforts. In some endemic regions, malaria is highly seasonal with no or little transmission during up to 8 mo, yet little is known about how seasonality affects the parasite population genetics. Here, we conducted a longitudinal study over 2.5 y on 1516 participants in the Upper River Region of The Gambia. With 425 P. falciparum genetic barcodes genotyped from asymptomatic infections, we developed an identity by descent (IBD) based pipeline and validated its accuracy against 199 parasite genomes sequenced from the same isolates. Genetic relatedness between isolates revealed a very low inbreeding level, suggesting continuous recombination among parasites rather than the dominance of specific strains. However, isolates from the same household were sixfold more likely to be genetically related compared to those from other villages, suggesting close transmission links within households. Seasonal variation also influenced parasite genetics, with most differentiation occurring during the transition from the low transmission season to the subsequent high transmission season. Yet chronic infections presented exceptions, including one individual who had a continuous infection by the same parasite genotype for at least 18 mo. Our findings highlight the burden of asymptomatic chronic malaria carriers and the importance of characterizing the parasite genetic population at the community-level. Most importantly, 'reactive' approaches for malaria elimination should not be limited to acute malaria cases but be broadened to households of asymptomatic carriers.}, }
@article {pmid40423701, year = {2025}, author = {Krivina, E and Sinetova, M and Starikov, A and Anissimova, O and Temraleeva, A}, title = {Testing the Effectiveness of DNA Barcoding Markers and Species Delimitation Methods Within the Genus Coelastrella (Sphaeropleales, Chlorophyta), With a Description of Coelastrella polaris sp. nov. Isolated from Arctic Soils.}, journal = {Current microbiology}, volume = {82}, number = {7}, pages = {311}, pmid = {40423701}, issn = {1432-0991}, support = {FMRM-2022-0019//Ministry of Science and Higher Education of the Russian Federation/ ; 21-74-30003//Russian Science Foundation/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; *Soil Microbiology ; Arctic Regions ; *Chlorophyta/genetics/classification ; Russia ; DNA, Ribosomal Spacer/genetics ; Fatty Acids/analysis ; }, abstract = {The species diversity in the genus Coelastrella is not yet fully unclarified, particularly with regard to algal communities in ecosystems characterized by extreme climatic conditions, such as those found in polar regions. The study objects were strains VKM Al-421, VKM Al-488, and VKM Al-489 isolated from the soils of the Far North, Russian Federation. The analysis of the 18S-ITS1-5.8S-ITS2 fragment revealed that these strains represent a unique phylogenetic lineage outside the 'core Coelastrella' group. The species status is also confirmed by morphological differences between the studied species and its sister species (absence of edges) (lack of ribs), interspecific genetic distances, the presence of compensatory base changes in the internal transcribed spacers ITS1 and ITS2, as well as the results of delimitation using various algorithms applied to both the full-length fragment and shorter barcodes. The strain VKM Al-421 of the new species exhibits a fatty acid profile characteristic of the genus Coelastrella; however, it differs from closely related strains due to the presence of Δ7,10,13-hexadecatrienoic acid and a notably high concentration of α-linolenic acid. These features may indicate an adaptation to polar regions. In addition, the studied strain has the potential to be used as a producer of α-linolenic acid, which is essential for human health. A detailed comparative analysis of the effectiveness of different DNA barcodes showed that ITS2 is the most promising for distinguishing species within Coelastrella. Among all species delimitation algorithms, GMYC is the most accurate when working with variable barcodes. At the same time, the less laborious KoT algorithm demonstrated a similar level of accuracy for ITS1.}, }
@article {pmid40415972, year = {2025}, author = {Awad, J and Reinisch, R and Moser, M and Vasilița, C and Krogmann, L}, title = {Untangling host specialization in a "double dark taxa" system.}, journal = {Annals of the Entomological Society of America}, volume = {118}, number = {3}, pages = {206-219}, pmid = {40415972}, issn = {0013-8746}, abstract = {Platygastrine wasps (Hymenoptera: Platygastridae) are parasitoids of gall midges (Diptera: Cecidomyiidae). They and their hosts are exceptionally abundant and speciose, with great relevance to agriculture and biodiversity research. Both groups are also "dark taxa," whose species identification and ecological associations are obscured by a history of taxonomic confusion and neglect. Verified host records are few in number and limited in scope. In order to understand host specialization, more records are needed. However, rearing Cecidomyiidae is challenging, as many species require living host tissue to complete development. There is no universal rearing method for Cecidomyiidae and their parasitoids. The present work applies an exploratory approach to rearing gall midges, with the aim of obtaining accurate host associations and parasitoid identifications. We obtained 5 species of Platygastrinae from reared material, 3 of which are identified and diagnosed. Platygaster demades Walker (= Platygaster marchali Kieffer, syn. nov. = Platygaster ornata Kieffer, syn. nov.) is not host-specific, attacking Cecidomyiidae on Rosaceae worldwide, including Filipendula ulmaria. Synopeas gibberosum Buhl apparently specializes on Dasineura ulmaria (Bremi) on F. ulmaria. Synopeas rhanis (Walker) is known only from galls of D. urticae (Perris), but may attack other midge species on Urtica dioica. Amblyaspis sp. emerged from Hartigiola annulipes (Hartig) galls on Fagus sylvatica, and Synopeas sp. was associated with Mycodiplosis sp. on Rubus sp. Illustrations, DNA barcodes, and distributions are provided. We discuss challenges to understanding "double dark taxa" interactions, implications for biological control, and possible solutions for future research on these important but neglected systems.}, }
@article {pmid40413466, year = {2025}, author = {Novianto, D and Tuangpermsub, S and Ngamprasertwong, T and Kaewthamasorn, M}, title = {Host associations and genetic diversity of bat flies (Diptera: Nycteribiidae and Streblidae) in bats from Thailand.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {188}, pmid = {40413466}, issn = {1756-3305}, mesh = {Animals ; Thailand/epidemiology ; *Diptera/genetics/classification/physiology ; *Genetic Variation ; Phylogeny ; *Chiroptera/parasitology ; *Host-Parasite Interactions ; Male ; Female ; DNA Barcoding, Taxonomic ; Haplotypes ; *Ectoparasitic Infestations/veterinary/parasitology/epidemiology ; RNA, Ribosomal, 28S/genetics ; }, abstract = {BACKGROUND: Bat flies belong to the order Diptera and superfamily Hippoboscoidea. They can be divided into two families, Streblidae and Nycteribiidae, which collectively encompass 239 and 280 species worldwide, respectively. In Thailand, 43 species of Nycteribiidae and 16 species of Streblidae have been documented. Despite their diversity, the molecular characteristics and host-parasite interactions of these ectoparasites remain poorly understood.<br><br>METHODS: During a bat survey conducted between 2019 and 2022, bat flies were collected across eight sites in three provinces of Thailand. Morphological identification was performed using identification keys and a bat fly checklist endemic to Thailand. DNA barcoding targeted to the mitochondrial Cox1 and nuclear 28S rRNA genes was utilized. Infestation patterns were analyzed in relation to host sex, sampling site, and physiological status. Species identification was confirmed via BLASTN searches, and species delimitation was conducted using the ASAP algorithm under three substitution models. Phylogenetic relationships were inferred using Maximum Likelihood methods, while genetic variation was assessed through TCS haplotype network analysis. Tripartite network analysis was employed to examine site-host-parasite associations.<br><br>RESULTS: A total of 1,042 bats, representing 28 species, were captured during the study, of which 298 individuals (28.59%) were infested with bat flies. In total, 773 bat flies were collected, comprising 737 from the family Streblidae and 36 from Nycteribiidae. Morphological and molecular analyses identified three genera-Raymondia, Brachytarsina, and Nycteribia-along with seven hypothetical species. Phylogenetic reconstruction using mitochondrial (Cox1) and nuclear (28S rRNA) gene markers revealed distinct clades within each genus, underscoring substantial genetic diversity. Haplotype analyses identified 18 haplotypes in Raymondia, six in Brachytarsina, and two in Nycteribia, with evidence of site-specific host-parasite associations. Infestation rates varied by host species, sex, and location, with larger bat populations demonstrating higher infestation intensities. Raymondia sp. 1 is the most frequently encountred species an predominantly infested Hipposideros gentilis.<br><br>CONCLUSIONS: This study provides the first molecular characterization of bat fly diversity in Thailand, revealing their genetic complexity, taxonomy, host specificity, and ecological interactions. The findings establish a crucial foundation for further research concerning the biodiversity, host-parasite dynamics, and zoonotic risks associated with bat flies.}, }
@article {pmid40413247, year = {2025}, author = {Ferreira, C and Martins, T and Melo, L and Veneza, I and Santana, P and Miranda, J and Lutz, &#xcd; and Sousa, J and Cardoso, B and Miranda, A and da Costa, JL and Matos, S and Holanda, FC and Vallinoto, M and Sampaio, I and Evangelista-Gomes, G}, title = {DNA reveal new invasive species of tiger shrimp Penaeus monodon (Penaeidae) along the world's largest mangrove region in the Brazilian Blue Amazon.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {18058}, pmid = {40413247}, issn = {2045-2322}, support = {CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Penaeidae/genetics/classification ; Brazil ; DNA Barcoding, Taxonomic ; *Introduced Species ; Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Wetlands ; Biodiversity ; Haplotypes ; Ecosystem ; *DNA/genetics ; }, abstract = {Bioinvasions represent a major environmental issue, particularly when they take place in biodiversity hotspots, such as mangrove ecosystems that serve as shelter for many marine species and fisheries resources. In this work, we used an integrative approach based on DNA and morphological analyses to identify individuals and the putative presence of cryptic diversity in the invasive tiger prawn (Penaeus monodon) along a mangrove area on the northern coast of Brazil, referred to as "Blue Amazon". A fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was selected for DNA Barcode and associated with distance-based (ABGD-Automatic Barcode Gap Discovery) and probabilistic (GMYC-Generalized Mixed Yule Coalescent and bPTP-Bayesian Poisson tree processes) species delimitation methods. Furthermore, the maternal origin of collected specimens was tracked. The molecular analyses recovered two genetically divergent lineages (7.7%) within the tiger prawn, indicating the occurrence of two species of this bioinvader on the northern coast of Brazil. Even though no differences in external morphology were detected, both lineages could be differentiated by their internal structures. The molecular traceability of the origin of samples showed that lineages I and II shared haplotypes with specimens from 11 and nine countries, respectively, including a shrimp breeding center in Vietnam. This is the first record of two species of tiger prawn along the Brazilian continental shelf. These findings are useful to the development of effective management policies in a region of particular biological relevance.}, }
@article {pmid40411728, year = {2025}, author = {Laskar, BA and Adimalla, H and Banerjee, D and Song, SH and Kang, HE and Kim, HW and Kundu, S}, title = {Integrative morphometric and phylogenetic insights into Eastern Ghats channids (Teleostei: Channidae) unveil the transboundary dispersal of the Dwarf Snakehead (Channa kelaartii) across India and Sri Lanka.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {499}, pmid = {40411728}, issn = {1573-4978}, support = {This work was supported by a Research Grant of Pukyong National University (2024)//Pukyong National University, South Korea/ ; }, mesh = {Sri Lanka ; India ; Animals ; Phylogeny ; Genetic Variation/genetics ; *Fishes/genetics/classification/anatomy &amp; histology ; Haplotypes/genetics ; Bayes Theorem ; Phylogeography ; Genetics, Population ; DNA, Mitochondrial/genetics ; }, abstract = {BACKGROUND: The biogeography of Eastern Ghats channids, including the Dwarf Snakehead Channa kelaartii, poses a complex challenge, especially with recent evidence confirming its presence in both India and Sri Lanka. While the Sri Lankan population is well- documented through integrative approach, the Indian population remains unexplored, requiring further research to elucidate its genetic structure and phylogenetic relationships.<br><br>METHODS: This study examines the morphology and mtCOI-based genetic diversity of 10 channid species, including seven from the Gachua complex. An integrative approach is also applied to assess population-level variation in C. kelaartii, aiming to clarify its genetic diversity with geographically isolated Sri Lankan populations.<br><br>RESULTS: Morphological analysis distinctly identified all Channa species and indicated a close resemblance between Indian and Sri Lankan C. kelaartii populations. Genetic analysis revealed considerable divergence between C. kelaartii and other members of the Gachua group, ranging from 6.15 to 21.31%. Bayesian phylogenetic reconstruction robustly resolved all species, including C. kelaartii. Combined mitochondrial data from India and Sri Lanka revealed 13 haplotypes, with mean intra-regional genetic distances of 0.5% (Sri Lanka) and 0.7% (India), and maximum divergences of 1.24% and 2.29%, respectively. A haplotype from the Western Ghats exhibited only 0.17% divergence from Sri Lankan populations, indicating potential historical gene flow between the two regions.<br><br>CONCLUSIONS: Overall, this study provides a comprehensive assessment of Channa diversity in the Eastern Ghats and confirms the presence of C. kelaartii in both peninsular India and Sri Lanka, likely shaped by historical land connections and freshwater dispersal across the Palk Isthmus during the Plio-Pleistocene.}, }
@article {pmid40410279, year = {2025}, author = {Liao, H and Chen, H and Liu, S}, title = {The complete chloroplast genomes of four Aspidopterys species and a comparison with other Malpighiaceae species.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17893}, pmid = {40410279}, issn = {2045-2322}, mesh = {*Genome, Chloroplast ; Phylogeny ; Base Composition ; Microsatellite Repeats ; }, abstract = {The genus Aspidopterys has multiple functions in medicine, food and ecological restoration. Due to the similar morphological characteristics of some species and the limited genomic information hinder the studies on germplasm identification and molecular phylogeny analysis. In this study, we compared and explored the six complete chloroplast (cp) genomes including four Aspidopterys species (A. glabriuscula, A. concava, A. cavaleriei, A. obcordata), Banisteriopsis caapi and Bunchosia argentea. Their cp genomes in length were 158,473 to 161,091 bp, displaying the high conserved degree in the structure, gene arrangement and GC content. Moreover, 57-80 long repeats and 61-92 SSRs were identified, most of which were forward or palindromic repeats and mononucleotides, respectively. Eleven non-coding regions and 12 coding regions, especially ndhH_ndhA, rpl32_ndhF and ycf1, had the higher nucleotide diversity values that could can be regarded as DNA barcodes of Malpighiaceae species. In addition, the 9 genes (like accD, atpE, atpF, clpP) were conducted positive selection (Ka/Ks > 1). As indicated by phylogenetic analysis, those four Aspidopterys were clustered into single clade with other Malpighiaceae species and were closely related to B. caapi and B. argentea. This study sheds more lights on further phylogenetic, evolutionary and genetic diversity studies on the genus Aspidopterys and even the Malpighiaceae species.}, }
@article {pmid40409527, year = {2025}, author = {Schols, R and Henrard, A and Brecko, J and Mudavanhu, A and Goossens, E and Steffanie, N and Clegg, S and Vanhove, MPM and Huyse, T}, title = {Innovating stomach fluke identification: an integrative approach combining Micro-CT imaging and molecular tools.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2025.05.002}, pmid = {40409527}, issn = {1879-0135}, abstract = {The rapid loss of biodiversity driven by anthropogenic pressures highlights the urgent need for improved species identification methods. Parasites, vital ecosystem regulators, are being lost at disproportionate rates, with amphistomes-a broadly distributed group of trematode parasites, infecting all major vertebrate groups-facing significant challenges. Many amphistome species remain undescribed, and reference sequences for known species are scarce, partly due to the reliance on labour-intensive identification methods, such as Scanning Electron Microscopy (SEM) and median sagittal sections. While sagittal sectioning is particularly informative for diagnostic traits, it is destructive, requires toxic chemicals, and demands specialized personnel. In this study, we evaluated micro-computed tomography (micro-CT) imaging as a non-destructive alternative for identifying three amphistome species, Gigantocotyle gigantocotyle (Brandes in Otto, 1896); Carmyerius aff. chabaudi van Strydonck, 1970; and Carmyerius aff. endopapillatus Dollfus, 1962, isolated from the common hippopotamus, Hippopotamus amphibius Linnaeus, 1758. By comparing micro-CT imaging with traditional sectioning, SEM and incorporating molecular barcoding, we reveal the need for a taxonomic revision of Carmyerius, focussed on identifying new diagnostic characters, to better reflect species boundaries. Moreover, the integrated taxonomic effort represented in this work uncovered evidence that C. aff. chabaudi is a new species record from the common hippopotamus. Additionally, we provide high-resolution images of the original type specimens of Carmyerius cruciformis (Leiper, 1910) and G. gigantocotyle and designate new lectotypes and paralectotypes. Our findings demonstrate that micro-CT imaging is a powerful, non-invasive tool for amphistome identification, facilitating access to fragile natural history collections and advancing integrative taxonomy.}, }
@article {pmid40408506, year = {2025}, author = {Blois, S and Goetz, BM and Mojumder, A and Sullivan, CS}, title = {Shedding dynamics of a DNA virus population during acute and long-term persistent infection.}, journal = {PLoS pathogens}, volume = {21}, number = {5}, pages = {e1013083}, pmid = {40408506}, issn = {1553-7374}, support = {R21 AI188807/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Polyomavirus Infections/virology ; Mice ; *Polyomavirus/genetics/physiology ; *Virus Shedding/physiology ; *Persistent Infection/virology ; Mice, Inbred C57BL ; Genome, Viral ; *Tumor Virus Infections/virology ; Female ; DNA, Viral/genetics ; }, abstract = {Although much is known of the molecular mechanisms of virus infection within cells, substantially less is understood about within-host infection. Such knowledge is key to understanding how viruses take up residence and transmit infectious virus, in some cases throughout the life of the host. Here, using murine polyomavirus (muPyV) as a tractable model, we monitor parallel infections of thousands of differentially barcoded viruses within a single host. In individual mice, we show that numerous viruses (>2600) establish infection and are maintained for long periods post-infection. Strikingly, a low level of many different barcodes is shed in urine at all times post-infection, with a minimum of at least 80 different barcodes present in every sample throughout months of infection. During the early acute phase, bulk shed virus genomes derive from numerous different barcodes. This is followed by long term persistent infection detectable in diverse organs. Consistent with limited productive exchange of virus genomes between organs, each displays a unique pattern of relative barcode abundance. During the persistent phase, constant low-level shedding of typically hundreds of barcodes is maintained but is overlapped with rare, punctuated shedding of high amounts of one or a few individual barcodes. In contrast to the early acute phase, these few infrequent highly shed barcodes comprise the majority of bulk shed genomes observed during late times of persistent infection, contributing to a stark decrease in bulk barcode diversity that is shed over time. These temporally shifting patterns, which are conserved across hosts, suggest that polyomaviruses balance continuous transmission potential with reservoir-driven high-level reactivation. This offers a mechanistic basis for polyomavirus ubiquity and long-term persistence, which are typical of many DNA viruses.}, }
@article {pmid40405610, year = {2025}, author = {Liu, L and Ju, P and Yang, K and Li, X and Duan, K and Xie, J and Liu, M and Chen, J and Luo, R}, title = {Extended Linear Confined Zipper Cascaded Reaction for Highly Efficient Intracellular Imaging and Assisting Diagnosis of Thyroid Cancer.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {21}, number = {30}, pages = {e2500202}, doi = {10.1002/smll.202500202}, pmid = {40405610}, issn = {1613-6829}, support = {82302621//National Natural Science Foundation of China/ ; KJQN202300435//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0183//Future Medical Youth Innovation Team Development Support Program Project of Chongqing Medical University/ ; CSTB2023TIAD-STX0040//Technological Innovation and Application Development/ ; }, mesh = {*Thyroid Neoplasms/diagnosis/diagnostic imaging ; Humans ; MicroRNAs/metabolism/genetics ; Cell Line, Tumor ; Nucleic Acid Hybridization ; }, abstract = {Highly sensitive detection and in situ tracing analysis of small-molecule biomarkers are particularly indispensable to deciphering the pathogenesis and pathological process. Despite DNA assembly-based barcoding and amplification strategies across the breadth of molecular in situ analysis, an easy-to-design, nonenzymatic, highly efficient, background leakage-avoided, highly specific, and sensitive system is highly required yet is still in its infancy. Spatial confinement nano-assembly can increase the reaction efficiency in a localized isothermal autonomous manner. Here in this work, the DNA assembly that originally relies on random collisions between freely diffusing probes is constructed between two extended linear confined probes, by which a novel confined reaction model named as extended linear confined zipper hybridization chain reaction (ZHCR) is proposed. ZHCR can significantly improve the efficiency of probe assembly and enable stable assembly within live cells, providing precise in situ target information. ZHCR system is employed to analyze two thyroid cancer-specific miRNAs, achieving in situ tracing and serum content detection. By integrating machine learning algorithms, ZHCR demonstrates significant potential in thyroid cancer auxiliary diagnosis, establishing a versatile platform that enables both highly sensitive homogeneous detection and in situ analysis of low-abundance nucleic acid fragments.}, }
@article {pmid40404925, year = {2025}, author = {Xu, Z and Wang, Y and Cai, W and Chen, Y and Wang, Y}, title = {Single microorganism RNA sequencing of microbiomes using smRandom-Seq.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {40404925}, issn = {1750-2799}, support = {32200073//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32250710678//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82200977//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Bacteria colonize nearly every part of the human body and various environments, displaying remarkable diversity. Traditional population-level transcriptomics measurements provide only average population behaviors, often overlooking the heterogeneity within bacterial communities. To address this limitation, we have developed a droplet-based, high-throughput single-microorganism RNA sequencing method (smRandom-seq) that offers highly species specific and sensitive gene detection. Here we detail procedures for microbial sample preprocessing, in situ preindexed cDNA synthesis, in situ poly(dA) tailing, droplet barcoding, ribosomal RNA depletion and library preparation. The main smRandom-seq workflow, including sample processing, in situ reactions and library construction, takes ~2 days. This method features enhanced RNA coverage, reduced doublet rates and minimized ribosomal RNA contamination, thus enabling in-depth analysis of microbial heterogeneity. smRandom-seq is compatible with microorganisms from both laboratory cultures and complex microbial community samples, making it well suited for constructing single-microorganism transcriptomic atlases of bacterial strains and diverse microbial communities. This Protocol requires experience in molecular biology and RNA sequencing techniques, and it holds promising potential for researchers investigating bacterial resistance, microbiome heterogeneity and host-microorganism interactions.}, }
@article {pmid40401933, year = {2025}, author = {Das, J and Pal, S and Negi, A and Sundharam, SS and Yadav, A and Subramanian, S and Sinha, SK and Samanta, J and Krishnamurthi, S}, title = {Genomic insights into novel predatory myxobacteria isolated from human feces.}, journal = {Microbiology spectrum}, volume = {13}, number = {7}, pages = {e0214724}, pmid = {40401933}, issn = {2165-0497}, support = {MLP044//Council of Scientific and Industrial Research, India/ ; }, mesh = {Humans ; *Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Myxococcales/genetics/classification/isolation &amp; purification ; *Genome, Bacterial/genetics ; DNA, Bacterial/genetics ; Inflammatory Bowel Diseases/microbiology ; Genomics ; Gastrointestinal Microbiome ; }, abstract = {Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35[T] and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35[T]. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.}, }
@article {pmid40401310, year = {2025}, author = {Wang, Y and Liu, D and Wang, R and Chen, A and Fang, X}, title = {An orthogonal barcoding enabled smart nanodevice for highly efficient isolation and proteomic profiling of tumor-derived extracellular vesicles.}, journal = {The Analyst}, volume = {150}, number = {12}, pages = {2514-2523}, doi = {10.1039/d5an00348b}, pmid = {40401310}, issn = {1364-5528}, mesh = {Humans ; *Extracellular Vesicles/metabolism/chemistry ; *Proteomics/methods ; Aptamers, Nucleotide/chemistry ; Biomarkers, Tumor/metabolism ; Epithelial Cell Adhesion Molecule/metabolism ; Tetraspanin 30/metabolism ; *Prostatic Neoplasms/metabolism/pathology ; Cell Line, Tumor ; Exosomes/metabolism ; Male ; Silicon Dioxide/chemistry ; }, abstract = {Tumor-derived extracellular vesicles (T-EVs) are small, membrane-bound particles secreted by cancer cells into the extracellular environment. These vesicles carry tumor-specific molecules, making them promising candidates as biomarkers for cancer diagnosis and monitoring. Among the various molecular components of T-EVs, such as nucleic acids and lipids, proteins stand out due to their unique characteristics and functional significance in cancer progression, diagnosis, and therapy. However, the heterogeneity of T-EVs poses a significant challenge to their effective utilization. Herein, we developed an orthogonal barcoding enabled smart nanodevice for the isolation of T-EVs and proteomic profiling. The T-EVs subpopulations were recognized from complex clinical samples, specifically through an orthogonal labeling barcode, which was created using two allosteric aptamers against the exosomal marker CD63 and the tumor marker EpCAM. Simultaneously, the labeled barcode on T-EVs initiated targeted binding with the DNA complementary tag modified mesoporous silica foam (MOSF-tag), achieving in situ exosomal protein extraction and digestion within the nanopores of the MOSF-tag. This integrated strategy not only streamlines the process by eliminating complex steps and minimizing sample loss but also significantly enhances protein identification efficiency. Compared to traditional methods for T-EVs isolation and protein digestion, the smart nanodevice has demonstrated a remarkable improvement in the detection of exosomal proteins and specific proteins from the cell culture medium. As a proof of concept, we applied this strategy to serum samples from prostate cancer (PCa) patients, confirming its efficacy. A total of 832 proteins were identified, with 211 showing differential expression between patients and healthy controls. Among these, 113 proteins were significantly upregulated in the PCa group. These uniquely expressed proteins are likely associated with PCa development, invasion, and metastasis, highlighting their potential as biomarkers for the early diagnosis and prognosis of PCa in the future. This innovative approach not only advances the field of T-EVs research but also opens new avenues for the discovery of clinically relevant biomarkers in cancer.}, }
@article {pmid40400687, year = {2025}, author = {Guerrero-Flores, S and Contreras-Peruyero, H and Ibarra-Rodríguez, JM and Lovaco-Flores, JA and Nieto-de la Rosa, FS and Fontove-Herrera, F and Sélem-Mojica, N}, title = {Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1461293}, pmid = {40400687}, issn = {1664-302X}, abstract = {Antibiotic resistance, projected to cause 10 million deaths annually by 2050, remains a critical health threat. Hospitals drive multidrug resistance via horizontal gene transfer. The 2023 Critical Assessment of Massive Data Analysis challenge presents resistance markers from 146 Johns Hopkins bacterial isolates, aiming to analyze resistomes without metadata or genomic sequences. Persistent homology, a topological data analysis method, effectively captures processes beyond vertical inheritance. A 1-hole is a topological feature representing a loop or gap in the data, where relationships form a circular structure rather than a linear one. Unlike vertical inheritance, which lacks topological 1-holes, horizontal gene transfer generates distinct patterns. Since antimicrobial resistance genes often spread via horizontal gene transfer, we simulated vertical and horizontal inheritance in bacterial resistomes. The number of 1-holes from simulations and a documented horizontal gene transfer case was analyzed using persistence barcodes. In a simulated population of binary sequences, we observed that, on average, two 1-holes form for every three genomes undergoing horizontal gene transfer. Using a presence-absence gene table, we confirmed the existence of 1-holes in a documented case of horizontal gene transfer between two bacterial genera in a Pittsburgh hospital. Notably, the Critical Assessment of Massive Data Analysis resistomes of Klebsiella and Escherichia exhibit 1-holes, while Enterobacter shows none. Lastly, we provide a mathematical example of a non-tree-like space that contains no 1-holes. Persistent homology provides a framework for uncovering complex clinical patterns, offering an alternative to understanding resistance mobility using presence-absence data, which could be obtained through methods beyond genomic sequencing.}, }
@article {pmid40399693, year = {2025}, author = {Ishiguro, S and Ishida, K and Sakata, RC and Ichiraku, M and Takimoto, R and Yogo, R and Kijima, Y and Mori, H and Tanaka, M and King, S and Tarumoto, S and Tsujimura, T and Bashth, O and Masuyama, N and Adel, A and Toyoshima, H and Seki, M and Oh, JH and Archambault, AS and Nishida, K and Kondo, A and Kuhara, S and Aburatani, H and Klein Geltink, RI and Yamamoto, T and Shakiba, N and Takashima, Y and Yachie, N}, title = {A multi-kingdom genetic barcoding system for precise clone isolation.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40399693}, issn = {1546-1696}, abstract = {Cell-tagging strategies with DNA barcodes have enabled the analysis of clone size dynamics and clone-restricted transcriptomic landscapes in heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here we present a multi-kingdom genetic barcoding system, CloneSelect, which enables a target cell clone to be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first stably tagged with DNA barcodes and propagated so that their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored during the experiment using CRISPR base editing. CloneSelect is scalable and compatible with single-cell RNA sequencing. We demonstrate the versatility of CloneSelect in human embryonic kidney 293T cells, mouse embryonic stem cells, human pluripotent stem cells, yeast cells and bacterial cells.}, }
@article {pmid40399676, year = {2025}, author = {Chen, Q and Schafer, CT and Mukherjee, S and Wang, K and Gustavsson, M and Fuller, JR and Tepper, K and Lamme, TD and Aydin, Y and Agrawal, P and Terashi, G and Yao, XQ and Kihara, D and Kossiakoff, AA and Handel, TM and Tesmer, JJG}, title = {Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor.}, journal = {Nature}, volume = {643}, number = {8070}, pages = {280-287}, pmid = {40399676}, issn = {1476-4687}, support = {P30 CA023168/CA/NCI NIH HHS/United States ; R01 CA254402/CA/NCI NIH HHS/United States ; R01 HL071818/HL/NHLBI NIH HHS/United States ; R35 GM151033/GM/NIGMS NIH HHS/United States ; }, mesh = {Phosphorylation ; Humans ; *Arrestins/metabolism/chemistry ; Protein Binding ; Models, Molecular ; beta-Arrestin 2/metabolism/chemistry ; G-Protein-Coupled Receptor Kinase 5/metabolism/chemistry ; *Receptors, CXCR/metabolism/chemistry ; G-Protein-Coupled Receptor Kinase 2/metabolism/chemistry ; Immunoglobulin Fab Fragments/metabolism/chemistry/immunology ; beta-Arrestin 1/metabolism/chemistry ; }, abstract = {Unique phosphorylation 'barcodes' installed in different regions of an active seven-transmembrane receptor by different G-protein-coupled receptor (GPCR) kinases (GRKs) have been proposed to promote distinct cellular outcomes[1], but it is unclear whether or how arrestins differentially engage these barcodes. Here, to address this, we developed an antigen-binding fragment (Fab7) that recognizes both active arrestin2 (β-arrestin1) and arrestin3 (β-arrestin2) without interacting with bound receptor polypeptides. We used Fab7 to determine the structures of both arrestins in complex with atypical chemokine receptor 3 (ACKR3) phosphorylated in different regions of its C-terminal tail by either GRK2 or GRK5 (ref. [2]). The GRK2-phosphorylated ACKR3 resulted in more heterogeneous 'tail-mode' assemblies, whereas phosphorylation by GRK5 resulted in more rigid 'ACKR3-adjacent' assemblies. Unexpectedly, the finger loops of both arrestins engaged the micelle surface rather than the receptor intracellular pocket, with arrestin3 being more dynamic, partly because of its lack of a membrane-anchoring motif. Thus, both the region of the barcode and the arrestin isoform involved can alter the structure and dynamics of GPCR-arrestin complexes, providing a possible mechanistic basis for unique downstream cellular effects, such as the efficiency of chemokine scavenging and the robustness of arrestin binding in ACKR3.}, }
@article {pmid40399669, year = {2025}, author = {Scherer, M and Singh, I and Braun, MM and Szu-Tu, C and Sanchez Sanchez, P and Lindenhofer, D and Jakobsen, NA and Körber, V and Kardorff, M and Nitsch, L and Kautz, P and Rühle, J and Bianchi, A and Cozzuto, L and Frömel, R and Beneyto-Calabuig, S and Lareau, C and Satpathy, AT and Beekman, R and Steinmetz, LM and Raffel, S and Ludwig, LS and Vyas, P and Rodriguez-Fraticelli, A and Velten, L}, title = {Clonal tracing with somatic epimutations reveals dynamics of blood ageing.}, journal = {Nature}, volume = {643}, number = {8071}, pages = {478-487}, pmid = {40399669}, issn = {1476-4687}, support = {K99 HL146983/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R00 HG012579/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Clone Cells/cytology/metabolism ; *Cell Lineage/genetics ; Single-Cell Analysis ; DNA Methylation/genetics ; *Aging/genetics/blood ; *Mutation/genetics ; CpG Islands/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Male ; *Hematopoiesis/genetics ; Female ; Cell Differentiation/genetics ; *Epigenesis, Genetic ; Mice, Inbred C57BL ; Aged ; Adult ; Cellular Senescence/genetics ; Stochastic Processes ; }, abstract = {Current approaches used to track stem cell clones through differentiation require genetic engineering[1,2] or rely on sparse somatic DNA variants[3,4], which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity. We demonstrate that targeted single-cell profiling of DNA methylation[5] at single-CpG resolution can accurately extract both layers of information. To that end, we develop EPI-Clone, a method for transgene-free lineage tracing at scale. Applied to mouse and human haematopoiesis, we capture hundreds of clonal differentiation trajectories across tens of individuals and 230,358 single cells. In mouse ageing, we demonstrate that myeloid bias and low output of old haematopoietic stem cells[6] are restricted to a small number of expanded clones, whereas many functionally young-like clones persist in old age. In human ageing, clones with and without known driver mutations of clonal haematopoieis[7] are part of a spectrum of age-related clonal expansions that display similar lineage biases. EPI-Clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.}, }
@article {pmid40399518, year = {2025}, author = {}, title = {Patterns of DNA modifications provide a 'barcode' for cell-lineage tracing.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40399518}, issn = {1476-4687}, }
@article {pmid40396603, year = {2025}, author = {Verneau, O and Quinn, D and Smith, KG and Malone, JH and du Preez, L}, title = {Role of Trachemys scripta elegans in polystome (Platyhelminthes, Monogenea, Polystomatidae) spillover and spillback following the trade of freshwater turtles in southern Europe and North America.}, journal = {Parasite (Paris, France)}, volume = {32}, number = {}, pages = {30}, pmid = {40396603}, issn = {1776-1042}, mesh = {Animals ; *Turtles/parasitology ; *Introduced Species ; Fresh Water ; North America ; Europe ; Phylogeny ; Ecosystem ; Commerce ; *Trematode Infections/veterinary/parasitology/transmission/epidemiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Trematoda/genetics/classification ; }, abstract = {The red-eared slider, Trachemys scripta elegans (Wied, 1938), has been introduced worldwide, partly because of the exotic pet trade in the 1980s and 1990s. When T. s. elegans is released or escapes into natural environments, it often establishes new feral populations due to its tolerance for a variety of aquatic ecosystems. Therefore, it is now considered one of the most invasive species in the world because it can compete with native turtle species. In the present study, our objectives were to identify the potential for polystome spillover and spillback resulting from the introduction of the red-eared slider into new environments in North America. Fieldwork investigations were thus conducted mainly in aquatic habitats in Florida and North Carolina, United States, but also in Connecticut, Indiana, Kansas, Maine, Nebraska and New York. Using DNA barcoding based on cytochrome c oxidase I (COI) sequences, we surveyed the species diversity of polystome within American freshwater turtles. These included T. s. elegans but also Apalone ferox, Apalone spinifera, Chelydra serpentina, Chrysemys picta, Kinosternon baurii, Pseudemys spp., Sternotherus minor and Sternotherus odoratus. Genetic evidence confirmed that invasive populations of T. s. elegans in southern Europe have transmitted their own polystomes to native host species following spillover effects, and revealed here that T. s. elegans in non-indigenous habitats in the United States acts as a new reservoir of infection for native polystomes following spillback effects, thus increasing indigenous parasite transmission in the wild. Together, these findings raise further concern about the spread of non-native turtles and their impact on parasite transmission.}, }
@article {pmid40394107, year = {2025}, author = {Wasakul, V and Verschuuren, TD and Thuy-Nhien, N and Booth, E and Quang, HH and Thang, ND and Chindavongsa, K and Sovannaroth, S and Banouvong, V and Sengsavath, V and Mayxay, M and Tuyen, NTK and Phuong, VNL and Duc Trung, P and Gonçalves, S and Chen, S and Phalivong, S and Xayvanghang, S and Mahaphontrakoon, S and Pearson, RD and Newton, PN and Maude, RJ and Ashley, EA and Ariani, CV and Simpson, VJ and Day, NP and Dondorp, AM and Miotto, O}, title = {Genetic surveillance of Plasmodium falciparum populations following treatment policy revisions in the Greater Mekong Subregion.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {4689}, pmid = {40394107}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; INV-001927/GATES/Gates Foundation/United States ; QSE-M-UNOPS-MORU-20864-007-44//Global Fund to Fight AIDS, Tuberculosis and Malaria (Global Fund)/ ; OPP11188166, OPP1204628, INV-001927//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; }, mesh = {*Plasmodium falciparum/genetics/drug effects ; *Antimalarials/therapeutic use/pharmacology ; *Malaria, Falciparum/drug therapy/epidemiology/parasitology ; Humans ; *Drug Resistance/genetics ; Artemisinins/therapeutic use/pharmacology ; Quinolines/therapeutic use/pharmacology ; Genotype ; Protozoan Proteins/genetics ; Thailand/epidemiology ; Cambodia/epidemiology ; Vietnam/epidemiology ; Aspartic Acid Endopeptidases/genetics ; Prospective Studies ; Mefloquine/therapeutic use/pharmacology ; Piperazines ; }, abstract = {Genetic surveillance of Plasmodium falciparum (Pf) can track antimalarial-resistant strains, to inform decision-making by National Malaria Control Programmes (NMCPs). The GenRe-Mekong project prospectively collected 5982 samples in the Greater Mekong Subregion (GMS) between 2017 and 2022, genotyping drug resistance markers, and barcodes that recapitulate genetic variation. Genotypes were analyzed with the grcMalaria R package, first described in this paper, to translate genetic epidemiology data into actionable visual information. Since 2020, Pf incidences decreased rapidly, accompanied by a decline of dihydroartemisinin-piperaquine (DHA-PPQ) resistant lineages, previously dominant in the eastern GMS. The frequency of plasmepsin2/3 amplifications, conferring piperaquine resistance, dropped from 62% in 2017-2019 to 2% in 2022, coinciding with a switch in frontline therapy in Cambodia, Thailand, and Vietnam. While regional artemisinin resistance levels remained high, no evidence of emerging mefloquine resistance was found. Routine genetic surveillance proved valuable in monitoring rapid parasite population changes in response to public health interventions, providing actionable information for NMCPs.}, }
@article {pmid40392669, year = {2025}, author = {Letsch, H and Greve, C and Hundsdoerfer, AK and Irisarri, I and Moore, JM and Espeland, M and Wanke, S and Arifin, U and Blom, MPK and Corrales, C and Donath, A and Fritz, U and Köhler, G and Kück, P and Lemer, S and Mengual, X and Salas, NM and Meusemann, K and Palandačić, A and Printzen, C and Sigwart, JD and Silva-Brandão, KL and Simões, M and Stange, M and Suh, A and Szucsich, N and Tilic, E and Töpfer, T and Böhne, A and Janke, A and Pauls, S}, title = {Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syaf040}, pmid = {40392669}, issn = {1076-836X}, abstract = {Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future generations. Modern systematics increasingly depends on genetic and genomic data to differentiate and characterise species. While the results of genome sequencing are often connected to a physical voucher specimen, they are rarely derived from the ultimate taxonomic reference for a species, i.e., the name-bearing type specimens. This is a known but under-appreciated problem for ensuring the replicability of findings, especially those that affect the interpretation of biodiversity distributions and phylogenetic relationships. Destructive sampling of museum specimens, particularly of type material, often carries a high risk of sequencing failure, and thus the cost of damage to the specimen may outweigh the resulting benefit. Both taxonomic work and genome sequencing require specialist skills and there are often communication gaps between the respective experts. A new, harmonised approach, maximising information extraction while minimising risk to type specimens, is a critical step forward toward linking disciplines across biodiversity research and promoting a better taxonomic and systematic understanding of eukaryotic diversity. The genetic make-up of a type specimen is a fundamental part of its biological information, which can and should be made freely and digitally available through type genomics. Here we describe guidelines for the use of nomenclatural types in genome sequencing approaches considering different kinds of types in different stages of preservation and different data types.}, }
@article {pmid40391818, year = {2025}, author = {Sarsaiya, S and Jain, A and Chen, J and Shi, J}, title = {A comprehensive review on the quality and quantity assessment of the Narmada River of India: Current status, technological advancement, efforts and initiatives, challenges, and future outlook.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {97}, number = {5}, pages = {e70090}, doi = {10.1002/wer.70090}, pmid = {40391818}, issn = {1554-7531}, support = {[2017]5733-001//Guizhou Science and Technology Corporation Platform Talents Fund/ ; CK-1130-002//Guizhou Science and Technology Corporation Platform Talents Fund/ ; U1812403//National Natural Science Foundation of China/ ; 82373981//National Natural Science Foundation of China/ ; 82060750//National Natural Science Foundation of China/ ; [2022]026//2011 Collaborative Innovation Centre of Traditional Chinese Medicine in Guizhou Province/ ; }, mesh = {India ; *Rivers/chemistry ; *Water Quality ; *Environmental Monitoring/methods ; }, abstract = {This comprehensive review examines the current status of the Narmada River in India, focusing on the quality and quantity of its water resources. The primary objectives are to assess existing technological advancements, ongoing efforts and initiatives, and challenges, and provide a future outlook for sustainable river management. The Narmada River faces significant water quality and quantity challenges, primarily because of pollution from various sources and increasing water demand. The status of the river is a cause of concern, and monitoring is essential for informed decision-making. Various technical options are available for monitoring, analysis, and data evaluation, ranging from conventional methods to cutting-edge technologies. These include DNA barcoding and sequencing, geographic assessment tools, data mining software, geoinformatics, and statistical modeling instruments. This review underscores the alarming levels of environmental pollution in the Narmada River, highlights the feasibility of using advanced techniques to assess water quality, identify pollutants, and develop mitigation strategies. This review identifies research gaps related to the integration of advanced technologies, comprehensive water quality modeling, and the development of holistic management strategies. The review concludes with recommendations for integrating advanced monitoring technologies, policy reforms, and increasing public awareness. In conclusion, the Narmada River faces significant challenges in terms of water quality and quantity. While efforts are being made to address these challenges, a multidisciplinary and integrated approach, along with the adoption of advanced technologies, is crucial for the river's long-term health and the well-being of the communities that depend on it. PRACTITIONER POINTS: Highlight the challenges faced by the Narmada River in India concerning both water quality and quantity; Provided insights into the wide range of technological advancements available for monitoring and assessment; Emphasized the alarming levels of pollution and explores the feasibility of using advanced techniques; Discussed various efforts and initiatives aimed at improving the quality and quantity of water resources; Provided recommendations for integrating advanced technologies, policy reforms, and increasing public awareness.}, }
@article {pmid40391427, year = {2025}, author = {Oh, N and Kim, JY}, title = {Ionizable Lipids Drive Subcellular Localization and Immune Cell Targeting of Barcoded Nanoparticles in Lung Cancer.}, journal = {ACS nano}, volume = {19}, number = {21}, pages = {19841-19853}, doi = {10.1021/acsnano.5c02283}, pmid = {40391427}, issn = {1936-086X}, mesh = {Humans ; *Nanoparticles/chemistry ; *Lipids/chemistry ; Animals ; Mice ; *Lung Neoplasms/drug therapy/pathology/immunology/metabolism ; Macrophages/metabolism ; Cell Line, Tumor ; }, abstract = {To accurately predict the effect of a drug and enhance its potency, it is essential to examine not only the arrival of the carrier and its payload at the target cell but also the final destination of the subcellular organelle because a considerable number of diseases are associated with the malfunctioning of cellular organelles. Here, we present nanoparticle (NP) microscopy via signal amplification of DNA barcodes combined with the multiplexed cyclic immunofluorescence technique for quantifying multiple NP types simultaneously. This technique enhanced the fluorescence signal-to-noise by 15-fold compared to standard fluorescence in situ hybridization, thereby providing a more precise means of analyzing the intra- and interdistribution of three core-shell NPs (G0-P5, 7C1-F5, and C12-D) in vitro and in vivo. The in vitro results demonstrated that in macrophages, nucleic acids condensed with G0-C14 cationic lipids were often located in lysosomes, whereas in tumor cells, nucleic acids were mainly located in mitochondria, regardless of the type of cationic lipid. Together, the in vivo results reveal that nucleic acids condensed with G0-C14 cationic lipids demonstrated the greatest uptake by CD206+ immune cells, whereas nucleic acids condensed with 7C1 and C12-200 cationic lipids exhibited the highest level of uptake by CD206+CD11c+Arg1+ immune cells.}, }
@article {pmid40390141, year = {2025}, author = {Mittelstrass, J and Heinzelmann, R and Eschen, R and Hartmann, M and Kupper, Q and Schneider, S and Prospero, S and Franić, I}, title = {Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {53}, pmid = {40390141}, issn = {2524-6372}, support = {00.0482.PZ/B4387AFF4//Swiss Federal Office for the Environment (FOEN)/ ; 174644//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, abstract = {BACKGROUND: Culturing of fungi is labor-intensive and reveals limited diversity, while high-throughput sequencing of barcodes (i.e., metabarcoding) enables a simultaneous detection of fungi from multiple environmental samples. Metabarcoding using short-read sequencers, such as Illumina platforms, provides high sequencing depths but results in many unidentified taxa. Long-read sequencing can improve species and genus assignments but might encompass lower sequencing depth and limit diversity coverage. In this study, fungi in seeds of eleven angiosperm and gymnosperm tree species were assessed using traditional culturing, Illumina short-read metabarcoding, and Oxford Nanopore Technologies long-read metabarcoding. We focused on seed-borne fungi as understanding their diversity and potential impacts on seedlings is crucial for securing plant health. We compared (1) the number and identity of fungal genera and species between metabarcoding approaches and traditional culturing and (2) fungal alpha- and beta-diversity between metabarcoding methods, considering different hosts and fungal lifestyles.<br><br>RESULTS: In both short- and long-read metabarcoding datasets, similar numbers of fungal reads and operational taxonomic units were assigned to comparable numbers of fungal genera and species. About one-third of the identified genera were plant pathogens, followed by saprotrophs and endophytes. Culturing overall revealed fewer fungal genera, while most of the fungal reads in short-read metabarcoding datasets stemmed from cultured taxa. Long-read metabarcoding revealed lower per-sample diversity than short-read metabarcoding and distinct fungal communities compared to those from the short-read datasets. Host-dependent patterns in alpha- and beta-diversity were observed across methods, with angiosperms harboring more fungal taxa than gymnosperms, and distinct community structuring across host tree groups and species, although the differences were stronger in short-read than long-read metabarcoding datasets.<br><br>CONCLUSIONS: Illumina and Oxford Nanopore Technologies metabarcoding captured similar host-dependent diversity patterns despite observed differences in numbers and composition of fungi. Short-read metabarcoding might be optimal for fungal biodiversity studies due to higher sequencing depths and resultant breadth of diversity. As error rates are continuing to decrease, reference databases expand, and throughput improves, long-read metabarcoding is becoming a strong candidate for future diagnostic studies of fungi. Traditional culturing captures most of the fungi from short-read metabarcoding and remains valuable for obtaining isolates for further research.}, }
@article {pmid40387751, year = {2025}, author = {Xu, ZY and Huang, SD and Zou, J and Zeng, WH and Guo, YC and Jiang, JH}, title = {An Integrated Solution for Application of Next-Generation Sequencing in Newborn Screening.}, journal = {Clinical laboratory}, volume = {71}, number = {5}, pages = {}, doi = {10.7754/Clin.Lab.2024.241006}, pmid = {40387751}, issn = {1433-6510}, mesh = {Humans ; *Neonatal Screening/methods ; *High-Throughput Nucleotide Sequencing/methods ; Infant, Newborn ; Computational Biology ; *Genetic Testing/methods ; *Genetic Diseases, Inborn/diagnosis/genetics ; Multiplex Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) has greatly improved the diagnostic process for hereditary diseases, and incorporation of NGS into newborn screening (NBS) programs for more actionable diseases has been widely discussed. The aim of this study was to evaluate an integrated solution for application of NGS in newborn screening.<br><br>METHODS: An NGS panel targeting 155 genes related to inborn errors of metabolism, hearing loss, severe combined immunodeficiency, congenital hypothyroidism, and other actionable genetic diseases, was designed. An all-in-one library preparation strategy was developed to combine multiplex PCR target enrichment and sample barcoding. A clinical genetic analysis system was assembled to facilitate bioinformatics analysis and reporting. The integrated solution was validated using 160 samples with known variants.<br><br>RESULTS: The end-to-end time from DNA isolation to sequencing was approximately 34 hours, and bioinformatics analysis pipeline took 4 hours for 160 samples in parallel. This allowed reporting of results on day 3. All known variants were confirmed by the NGS workflow, and two large insertion/deletions were additionally detected in two cases with previously clinically but not genetically confirmed diseases.<br><br>CONCLUSIONS: The integrated solution for application of NGS in NBS provided reasonable turnaround time to meet the NBS timeframe and could be implemented at scale.}, }
@article {pmid40387421, year = {2025}, author = {Aggarwal, SD and Toussaint, J and Lees, JA and Weiser, JN}, title = {Colonization dynamics of Streptococcus pneumoniae are determined by polymorphisms in the BlpAB transporter.}, journal = {Infection and immunity}, volume = {93}, number = {6}, pages = {e0006125}, pmid = {40387421}, issn = {1098-5522}, support = {R01 AI038446/AI/NIAID NIH HHS/United States ; R01 AI50893//National Institute of Allergy and Infectious Diseases/ ; //European Molecular Biology Laboratory/ ; }, mesh = {*Streptococcus pneumoniae/genetics ; Animals ; Mice ; *Pneumococcal Infections/microbiology ; Humans ; *Bacterial Proteins/genetics/metabolism ; Bacteriocins/genetics/metabolism ; *Polymorphism, Genetic ; *Membrane Transport Proteins/genetics/metabolism ; Female ; }, abstract = {Colonization of the human airways, the first step in the pathogenesis of Streptococcus pneumoniae (Spn), is the determining factor in the ecological spread of the bacterium. Since co-colonization by multiple strains is common, within-host bacterial competition contributes to the success of Spn strains. Competition both between and within strains is mediated by bacteriocin gene clusters, notably the quorum sensing-regulated bacteriocin-like peptide (blp) locus. A key component of this system is the BlpAB transporter that exports pheromones and bacteriocins expressed by the blp locus. However, ~75% of Spn strains lack a functional BlpAB transporter and instead rely on the paralogous ComAB transporter for this export, raising questions about the evolutionary persistence of BlpAB(+) strains. Using molecular barcoding, we demonstrate that BlpAB(+) and BlpAB(-) strains show major differences in population dynamics during colonization modeled in mice. The BlpAB(+) strains exhibit slower loss of clonal diversity as a consequence of intrastrain competition relative to their isogenic BlpAB(-). The contribution of a functional BlpAB transporter was then examined in an association study of >2,000 human carriage isolates from a highly colonized population. The median carriage duration was ~177 days longer for BlpAB(+) relative to BlpAB(-) strains. This increased duration of natural carriage correlates with a competitive advantage for BlpAB(+) strains when tested in the murine model. Thus, our work provides insight into how differences in the population dynamics of Spn mediated by bacterial competition impact host colonization.IMPORTANCESpn is a frequent colonizer of the human upper respiratory tract. Success during colonization is dictated by the arsenal of weapons these bacteria possess, which provides them with an advantage over their competitors. A key example includes the blp bacteriocins that are exported by the cell through both BlpAB and ComAB transporters. While most Spn strains lack a functional BlpAB, a subset of the strains retains it. Given this redundancy in export systems, our study questioned the evolutionary advantage of retaining BlpAB. Herein, we show that a functional BlpAB transporter causes a slower loss of clonal diversity in vivo. This correlates with longer Spn carriage duration in the human population and a competitive advantage during experimental co-colonization. Our work highlights the reasons behind the persistence of Spn with a functional BlpAB. These findings reveal how genetic variability in the blp locus shapes Spn colonization and evolutionary success.}, }
@article {pmid40386686, year = {2025}, author = {Fernandez-Triana, JL and Boudreault, C and Whitfield, JB and Höcherl, A and Smith, MA and Hallwachs, W and Janzen, DH}, title = {A revision of the parasitoid wasp genus Dolichogenidea Viereck (Hymenoptera, Braconidae) in the Neotropical region, with the description of 102 new species.}, journal = {ZooKeys}, volume = {1237}, number = {}, pages = {1-250}, pmid = {40386686}, issn = {1313-2989}, abstract = {The parasitoid wasp genus Dolichogenidea is currently the second most speciose within the subfamily Microgastrinae (Hymenoptera: Braconidae), with 366 world species known so far, but with hundreds awaiting to be described. Here, the fauna of the Neotropical region is revised, with an emphasis in the Area de Conservación Guanacaste (ACG), Costa Rica. In addition to 23 species previously recorded from the Neotropics, 102 additional species are described as new, increasing the regional and world richness to 125 and 468 species, respectively. All species are diagnosed and described by using a combination of basic morphology (dichotomous key and brief diagnostic descriptions) and, when available DNA COI barcodes, biology (host data and wasp cocoon strategy), and distribution data. Neither morphology, biology, nor molecular data alone were sufficient to unambiguously separate all taxa, as all approaches were found to have limitations, but the combination of all three approaches provided stronger support to species delimitation. Morphology allowed the inclusion of all known species, therefore building a foundation upon which to improve as more molecular and biological data become available and new species are discovered; however, it was not sufficient (or it was very difficult to use) to separate at least 15% of all species keyed out in the dichotomous key. DNA barcoding was better able to separate species, and it is likely to become the most efficient way to identify species in the near future; however, DNA failed to identify 8.3% of the species with molecular data available, in addition to one third of the described species currently lacking molecular data. Biological data is currently the most incomplete, with only 42% of the species having associated host information, with a strong data availability bias towards ACG specimens. A total of 11 Lepidoptera families are here recorded to be parasitized by Neotropical Dolichogenidea, mainly Depressariidae (34% of all host data available), Gelechiidae (17%), Crambidae (14%), Tortricidae (10%), Thyrididae (8%) and Pyralidae (7%). Most of the wasps seem to be monophagous or at most oligophagous, as 56% are known to only parasitize a single host species, whereas 23% parasitize two host species and 10% parasitize three hosts; in almost all cases, the hosts species belong to one genus (or related genera) in the same Lepidoptera family. Most species of Dolichogenidea are found between 400-1,500 m, but a few have been found at higher elevations, including a few examples higher than 3,000 m (Costa Rica) and 4,000-4,100 m in the Andes (South America). The following nomenclatural acts are proposed: 1) the genus Exoryza is synonymized under Dolichogenidea, syn. nov.; 2) a total of 16 species are transferred to Dolichogenidea as comb. nov., one species formerly in the genus Apanteles: Dolichogenideacroceicornis (Muesebeck, 1958) and all 15 species formerly placed within Exoryza (six of them from the Neotropics): Dolichogenideaasotae (Watanabe, 1932), Dolichogenideabelippicola (Liu &amp; You, 1988), Dolichogenideahylas (Wilkinson, 1932), Dolichogenideamariabustosae (Fernandez-Triana, 2016), Dolichogenideamegagaster (de Saeger, 1944), Dolichogenideaminnesota (Mason, 1981), Dolichogenideamonocavus (Valerio &amp; Whitfield, 2004), Dolichogenideaoryzae Walker, 1994, Dolichogenideareticarina (Song &amp; Chen, 2003), Dolichogenidearichardashleyi (Fernandez-Triana, 2016), Dolichogenidearitaashleyae (Fernandez-Triana, 2016), Dolichogenidearosamatarritae (Fernandez-Triana, 2016), Dolichogenideasafranum (Rousse &amp; Gupta, 2013), Dolichogenideaschoenobii (Wilkinson, 1932) and Dolichogenideayeimycedenoae (Fernandez-Triana, 2016); 3) Dolichogenideayeimycedenoae (Fernandez-Triana, 2016) becomes a senior secondary homonym of Dolichogenideayeimycedenoae Fernandez-Triana &amp; Boudreault, 2019; therefore, Dolichogenideacedenoae Fernandez-Triana &amp; Boudreault, 2025 is a replacement name for Dolichogenideayeimycedenoae Fernandez-Triana &amp; Boudreault, 2019; 4) the following 102 species, all authored by Fernandez-Triana &amp; Boudreault, are described as sp. nov.: D.aceituno, D.alanflemingi, D.alejandromarini, D.alerce, D.alexamasisae, D.alexandrei, D.alixhamiltonae, D.amazonas, D.anacamposae, D.andreamezae, D.angelsolisi, D.anikenpalolae, D.anniapicadoae, D.annlisterudae, D.annychaverae, D.antioquia, D.antjevirkusae, D.arenal, D.bernardoespinozai, D.beryllacosteae, D.bradzlotnicki, D.caldas, D.carlosalvaradoi, D.carlosviquezi, D.chichicastenango, D.christinaagapakisae, D.claudiadoblesae, D.dole, D.encruzilhada, D.ericpalolai, D.ericsimoni, D.escobarae, D.felipechavarriai, D.frankjoycei, D.fredhicksi, D.helenedumasae, D.heredia, D.ingredolsonae, D.isabelleae, D.isidrochaconi, D.jaimelewisi, D.jasonkelleyi, D.jennyphillipsae, D.jessiehillae, D.johnrobinsoni, D.jorgecarvajali, D.jorgecortesi, D.josephfridmani, D.joshdarfleri, D.juanmatai, D.junhyongkimi, D.kasiiya, D.katiemccluskeyae, D.kenzabaddouae, D.lacochaparamo, D.leahdennisae, D.limoncocha, D.luishamiltoni, D.luzmariaromeroae, D.machupichu, D.mehdirheljari, D.moniqueae, D.moniquegilbertae, D.ninamasisae, D.nothofagus, D.oiketicus, D.palenque, D.papallacta, D.paulfryi, D.pedroleoni, D.puschendorfi, D.putumayo, D.puyo, D.rexhamiltoni, D.robertofernandezi, D.robinsherwoodae, D.robmacewani, D.robpringlei, D.rociocordobae, D.rodrigogamezi, D.ronaldzunigai, D.rubymacpearsae, D.rudyamadori, D.sallydaleyae, D.sarahoconnorae, D.scottmilleri, D.shelleymcsweeneyae, D.sigifredomarini, D.stephmae, D.stevestroudi, D.susanabramsae, D.teremariae, D.tiboshartae, D.timrichi, D.tomdaleyi, D.tristanpalolai, D.tucuman, D.verobrondexae, D.virgendelparamo, D.weaversway, D.yungas, D.yvesbraeti.}, }
@article {pmid40385613, year = {2025}, author = {Yu, CJ and Du, XC}, title = {Revision of the genus Hemopsis Kirti &amp; Rose, 1987 (Lepidoptera, Crambidae), with descriptions of three new species from China.}, journal = {ZooKeys}, volume = {1238}, number = {}, pages = {17-31}, pmid = {40385613}, issn = {1313-2989}, abstract = {The genus Hemopsis is revised based on adult morphological characteristics and DNA barcodes. Hemopsisabstracta sp. nov., H.coalita sp. nov., and H.heteroidea sp. nov. are described as new to science, and Hemopsisdissipatalis (Lederer, 1863) is DNA barcoded and redescribed based on new material from southern China. A key to Hemopsis species is given based on external morphology of adults and their genitalia characteristics. Images of adults and genitalia are provided.}, }
@article {pmid40385519, year = {2025}, author = {Haro, M and Ramos, S and Magalhães, T}, title = {Electronic Transfusion Safety System: Characterization of Patient Safety Incidents.}, journal = {Portuguese journal of public health}, volume = {}, number = {}, pages = {1-17}, pmid = {40385519}, issn = {2504-3145}, abstract = {INTRODUCTION: The healthcare system is complex and dynamic, and the implementation of information technology is seen as an important aid to patient safety. Data reveal that 1 in every 10 patients in developed countries is affected by a clinical error. The transfusion process involves several stakeholders and multiple stages with various critical points within the hospital. This study aims to understand patient safety incidents caused by failures in the Electronic Transfusion Safety System (ETSS) based on barcode technology in a hospital setting, from storage to the administration of blood components to the patient.<br><br>METHODS: A retrospective study spanning 3 years (2021-2023) with a mixed-methods approach was chosen. A Focus Group with six experts was conducted, and 136 reports from the anonymized incident reporting database with the typology "Blood and Blood Products" from a hospital in Lisbon were analyzed.<br><br>RESULTS: The ETSS diagram using barcodes allowed for the identification and description of all stages and their stakeholders. The critical points identified were patient identification, multiple relabeling, and transportation. A higher incidence rate of near-miss events was observed during sample collection and prescription.<br><br>DISCUSSION: This ETSS is hybrid, meaning that it has both human and technological components. Since 96% of the incidents did not cause harm to the patient, error detection and prevention mechanisms are being activated. This study has demonstrated the importance of IT in the transfusion process, as well as the relevance of continuous investment and the involvement of all stakeholders for a better patient safety environment.}, }
@article {pmid40385223, year = {2025}, author = {Alsanie, SI and Abd-Elgawad, ME}, title = {Influence of Soil Salinity on Genetic Diversity and Phylogenetic Relationships in Tetraena Species: Insights from Electrical Conductivity Analysis, Inter-retrotransposon Amplified Polymorphism Markers, and DNA Barcoding.}, journal = {ACS omega}, volume = {10}, number = {18}, pages = {18629-18640}, pmid = {40385223}, issn = {2470-1343}, abstract = {Soil salinity is a significant environmental stressor that impacts species distribution, plant development, and genetic diversity. Conservation and ecological management depend on an understanding of how Tetraena species respond to salinity. The genus Tetraena, which includes several species of succulent shrubs native to arid regions, is of significant interest for studying plant adaptation mechanisms. The study aims to evaluate the genetic diversity and ecological characteristics of eight groups of Tetraena species in Saudi Arabia using inter-retrotransposon amplified polymorphism (IRAP) markers, ycf5 and trnH gene sequences, as well as soil pH and electrical conductivity (EC). Soil pH indicated slightly alkaline conditions, while electrical conductivity (EC) ranged from 822 μS/cm in the T. propinqua population at Al Thumama Road (population 8) to 23,800 μS/cm in the T. hamiensis population at Al Jawhara-Dammam Road (population 2). The genetic relationships were determined by analyzing IRAP marker polymorphism, generated using 10 primers. Clustering through principal component analysis and biostatistical methods distinguished the populations of T. propinqua subsp. Migahidii (6, 7, and 8) from the populations of T. hamiensis var. qatarensis (1, 3), (4, 5), and (2). Ten primers had high polymorphism (60.5%) according to IRAP analysis between T. hamiensis and T. propinqua. The evolutionary trees of T. propinqua and T. hamiensis cluster together. Analysis of conserved motifs revealed common motifs that support the use of ycf5 and trnH as barcodes. The genetic diversity and population clustering of T. hamiensis and T. propinqua are influenced by environmental salinity and species-specific genetic adaptations. While T. hamiensis has more differentiation, maybe as a result of historical separation or localized adaptations, T. propinqua exhibits strong genetic similarities. These results demonstrate that common environmental stresses and species-specific characteristics are the main drivers of genetic diversity. Future studies should explore adaptive genetic mechanisms at the molecular level and assess the functional roles of salinity-responsive genes in support conservation efforts.}, }
@article {pmid40382734, year = {2025}, author = {Swaraj, P and Reshmi, MVN and Rijin, K and Drisya, OK and Priya, TAJ and Kappalli, S}, title = {Bomolochidae Claus, 1875 (Cyclopoida: Copepoda) Parasitizing the Marine Fishes of Kerala Coast (India): Host-Parasite Interaction and Species Diversity.}, journal = {Acta parasitologica}, volume = {70}, number = {3}, pages = {111}, doi = {10.1007/s11686-025-01052-9}, pmid = {40382734}, issn = {1896-1851}, support = {No. DST/INSPIRE Fellowship/2017/IF170696, 04.07.2018//DST INSPIRE/ ; SR/WOS-A/LS/78/2018(G, 28.06.2019)//DST-WOS-A/ ; No. INT/RUS/RFBR/P-330, 10.01.2019//DST-RFBR collaborative research project/ ; No. DST INT JSPS P-316 2020, dated 30.07.2021//DST-JSPS collaborative research project/ ; No. EMR/2016/001163/ AS, 28 August 2017//DST-SERB research project/ ; No. KSCSTE/5224/2017-SRSLS, dated: 03/04/2018//KSCSTE/ ; }, mesh = {Animals ; *Copepoda/classification/genetics/physiology ; India/epidemiology ; *Fish Diseases/parasitology/epidemiology ; Phylogeny ; *Fishes/parasitology ; *Host-Parasite Interactions ; Biodiversity ; *Ectoparasitic Infestations/veterinary/parasitology/epidemiology ; Electron Transport Complex IV/genetics ; Host Specificity ; Prevalence ; }, abstract = {PURPOSE: This study aims to assess region-wise host-parasite interaction and diversity indices of bomolochid species infecting marine fishes along the Kerala coast. Also, it aims to generate COI barcodes and analyse the phylogenetics.<br><br>METHODS: Marine fish species along the Kerala coast were sampled for the period 2016-2023 and examined for parasitization by bomolochid copepods. Host preference, prevalence, site-specificity, mean intensity, and biodiversity indices of recovered parasite species were assessed specifically in northern and southern regions of this coast. Mitochondrial COI sequences from bomolochid species were also generated, and their phylogenetic relationships were assessed with those of their counterparts found in the NCBI database.<br><br>RESULTS: Among the sampled fishes, 21 species from 20 genera and 14 families showed parasitization with 20 species of bomolochids. Four host families: Sciaenidae, Acanthuridae, Engraulidae, and Sillaginidae were recorded as new to the bomolochid infection along the Indian coast. Recovered bomolochid species, including nine Bomolochus species, six Nothobomolochus species, two Pumiliopes species, and one each of Pseudorbitacolax, Ceratocolax, and Orbitacolax species, with overall prevalence ranging from 0.28% to 57%. 65% of species prefer single-host, and 35% rely on two or three host species. The northern region encompassed all 20 bomolochid species, whereas only 10 species represented the southern region. Six species showed no region-specific host preference, but their prevalence showed marked differences (4.8-73.8%). The host preference of some bomolochid species spans multiple fish species within the same genus or family, as well as across different genera and families, with a varying degree of prevalence, either region-dependent or independent. The northern region displayed the highest species richness and diversity index compared to the southern region. However, the evenness values from both regions were found to be similar. The mitochondrial COI sequences from five bomolochid species signify the reliability of COI DNA barcoding for the identification of bomolochids at the species level. The analysis of phylogenetic relationships with those of its counterparts found in the NCBI database revealed that Bomolochidae constituted a biphyly topology that is distinct from that of the outgroup, i.e., Harpacticoida.<br><br>CONCLUSION: The generated information on bomolochid new host record, host preference, prevalence, site specificity, seasonality, diversity and genetic divergence forms the basis not only for further exploration of the species diversity and genetic variation of bomolochids but for analyzing the ecological and evolutionary aspects of species diversity and genetic variation of bomolochids and new host record along the Indian coasts and Indo-pacific region as well.}, }
@article {pmid40378848, year = {2025}, author = {Weber, TS and Biben, C and Miles, DC and Glaser, SP and Tomei, S and Lin, CY and Kueh, A and Pal, M and Zhang, S and Tam, PPL and Taoudi, S and Naik, SH}, title = {LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs.}, journal = {Cell}, volume = {188}, number = {14}, pages = {3882-3896.e19}, doi = {10.1016/j.cell.2025.04.026}, pmid = {40378848}, issn = {1097-4172}, mesh = {Animals ; *Germ Layers/cytology/metabolism ; Mice ; *Cell Lineage ; Cell Differentiation ; Integrases/metabolism ; *Fetus/cytology/metabolism ; Female ; Embryo, Mammalian/cytology/metabolism ; Clone Cells/cytology ; *DNA Barcoding, Taxonomic/methods ; Single-Cell Analysis ; Embryonic Development ; }, abstract = {Much remains to be learned about the clonal fate of mammalian epiblast cells. Here, we develop high-diversity Cre recombinase-driven LoxCode barcoding for in vivo clonal lineage tracing for bulk tissue and single-cell readout. Embryonic day (E) 5.5 pre-gastrulation embryos were barcoded in utero, and epiblast clones were assessed for their contribution to a wide range of tissues in E12.5 embryos. Some epiblast clones contributed broadly across germ layers, while many were biased toward either blood, ectoderm, mesenchyme, or limbs, across tissue compartments and body axes. Using a stochastic agent-based model of embryogenesis and LoxCode barcoding, we inferred and experimentally validated cell fate biases across tissues in line with shared and segregating differentiation trajectories. Single-cell readout revealed numerous instances of asymmetry in epiblast contribution, including left-versus-right and kidney-versus-gonad fate. LoxCode barcoding enables clonal fate analysis for the study of development and broader questions of clonality in murine biology.}, }
@article {pmid40376947, year = {2025}, author = {Sun, Y and Fan, J and Zong, Y and Jin, B and Yao, W and Wang, Z and Fu, T and Fang, L and Liu, Y and Tan, W}, title = {Aptamer-Signatured Nanoparticle Protein Corona for Size-Dependent Fluorescent Barcoding Diagnosis.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {21}, number = {26}, pages = {e2410434}, doi = {10.1002/smll.202410434}, pmid = {40376947}, issn = {1613-6829}, support = {2022YFC3401002//National Key Research and Development Program of China/ ; 2023SDYXS0001//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; YXD24B0402//Zhejiang Provincial Natural Science Foundation of China/ ; 22204144//National Natural Science Foundation of China/ ; 21CAA02059//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Aptamers, Nucleotide/chemistry ; *Protein Corona/chemistry ; *Nanoparticles/chemistry ; Flow Cytometry ; Carcinoma, Hepatocellular/diagnosis/blood ; Liver Neoplasms/diagnosis/blood ; Fluorescence ; Biomarkers, Tumor ; Particle Size ; }, abstract = {Cancer-specific nanoparticl protein corona (NPC) opens a new avenue for biomarker discovery and diagnosis. However, the simultaneous detection of multiplex protein biomarkers from NPC is very challenging owing to ultra-low abundance and limited detection probes. Here, an aptamer-signatured NPC (ASNC)-based size-dependent fluorescence barcode is developed for flow cytometry profiling (FBFC) sensing platform to diagnose hepatocellular carcinoma (HCC). First, HCC-specific NPC is obtained from incubating magnetic nanoparticles with clinical serum samples. A 12-aptamer panel is incubated with NPC for the assembly of ASNC. Six aptamers are selected from the preliminary profiling of 30 HCC and healthy controls, resulting in ASNC for subsequent multiplex detection. To achieve simultaneous and orthogonal detection in one pot, advantage of the size-dependent fluorescent microbeads are taken to profile the signature aptamers eluted from NPC via flow cytometry-distinguishable barcodes. With 84 clinical HCC and healthy serum samples, a diagnostic accuracy of 94.12%, have attained which is higher than other single biomarkers or any combinations. Overall, by transferring protein biomarkers to ASNC, a simultaneous and multiplex ASNC-based FBFC platform have developed which holds immense potential in facile and precise cancer diagnosis.}, }
@article {pmid40376620, year = {2025}, author = {Merchán Mayorga, JI and Quiroga, SY and Posada-Restrepo, I and García-Ramos, KA}, title = {Free-living clinging flatworms (Rhabditophora, Polycladida) associated with Sargassum from the Caribbean Coast of Colombia.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e150699}, pmid = {40376620}, issn = {1314-2828}, abstract = {BACKGROUND: Polyclads are a diverse group of marine free-living flatworms, with some species adapted to life in floating Sargassum mats. Recent studies suggest that, rather than being inherently pelagic, these flatworms should be classified as "clinging fauna", as they rely on floating substrates for habitat.<br><br>NEW INFORMATION: This study documents, for the first time, the occurrence of Gnesiocerossargassicola and Chatziplanagrubei in Sargassum along the Caribbean coast of Colombia. High-definition photographs of whole mounts and histological sections are provided for both species, along with detailed observations of their reproductive structures and 28S rDNA barcodes. These findings underscore the importance of exploring the fauna associated with Sargassum, contributing to a better understanding of polyclad distribution and raising the number of recorded species for Colombia to 26.}, }
@article {pmid40376046, year = {2025}, author = {Kang, X and Wang, Y and Zheng, R and Mamy Jayne Nelly, R and Liu, L and Li, S and Sun, X and Kang, L and Zhang, N and Zou, Z and Xia, Q}, title = {Variations in the Bacterial Ecosystems of Mosquito Populations - Haikou and Sanya Cities, Hainan Province, China, 2019.}, journal = {China CDC weekly}, volume = {7}, number = {16}, pages = {523-530}, pmid = {40376046}, issn = {2096-7071}, abstract = {INTRODUCTION: This study explores the midgut microbiota of mosquitoes in Haikou and Sanya cities, regions critical for understanding vector-borne disease dynamics in Hainan Province, China. It provides baseline data on microbial composition and examines their potential role in influencing mosquito biology and vector competence, while highlighting the need for further research into their association with vector-borne viral infections.<br><br>METHODS: Adult mosquitoes were collected using light traps and human bait methods. Species identification was conducted through morphological examination and DNA barcoding using the cytochrome c oxidase subunit 1 gene (cox1). The V3-V4 hypervariable regions of the microbial 16S ribosomal RNA (rRNA) gene were sequenced using high-throughput methods to investigate the midgut microbiota. Statistical analyses, including Alpha and Beta diversity assessments of the sequencing results, were performed using SPSS 21.0 and R version 3.11.<br><br>RESULTS: The predominant mosquito species identified were Aedes albopictus, Armigeres subalbatus, and Culex pipiens. Microbiota analysis of 281 midguts revealed that Proteobacteria dominated (85.28%), with significant fractions being Alphaproteobacteria (52.14%), Gammaproteobacteria (29.90%), and Betaproteobacteria (3.22%). Other notable phyla included Firmicutes (6.24%), Actinobacteria (3.81%), and lesser quantities of Thermi, Cyanobacteria, and Bacteroidetes. Significant geographic variation in bacterial communities was observed between Haikou and Sanya (P<0.05), with unique taxa like Thermi and Cyanobacteria identified only in Haikou and Chlamydiae found solely in Sanya. The analysis revealed 204 overlapping species, with 473 unique to Haikou and 64 to Sanya.<br><br>CONCLUSIONS: This study revealed significant geographic differences in the midgut microbiota of mosquitoes from Haikou and Sanya, providing foundational data for understanding their potential impact on mosquito biology and disease transmission. While the direct relationship between these microbial variations and vector-borne disease dynamics requires further investigation, these findings underscore the importance of mosquito microbiota research as part of broader strategies to mitigate vector-borne disease risks.}, }
@article {pmid40375325, year = {2025}, author = {Chong, SQY and Yeo, D and Arceo, AVV and Ong, JLY and Lee, CHE and Yeak, RJY and Wee, ASZ and Teo, PYZ and Tay, MKJ and Chan, AHJ and Fernandez, CJ and Xie, R and Wong, AMS and How, CB and Chang, SF}, title = {Cytauxzoon paradoxurus n. sp., a novel Cytauxzoon species identified in common palm civets in Singapore.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {175}, pmid = {40375325}, issn = {1756-3305}, mesh = {Animals ; Singapore/epidemiology ; *Viverridae/parasitology ; Phylogeny ; *Protozoan Infections, Animal/parasitology/epidemiology ; Male ; Female ; RNA, Ribosomal, 18S/genetics ; *Piroplasmida/isolation &amp; purification/genetics/classification ; DNA, Protozoan/genetics ; }, abstract = {BACKGROUND: The common palm civet (Paradoxurus musangus) is a species native to Southeast Asia. Highly adapted to urbanised environments, these civets can often be found in proximity to humans and companion animals, raising the concern of pathogen transmission at the human-wildlife and wildlife-domestic animal interface. Whilst there have been reports of various bacteria and viruses detected in civets, little is known about the protozoa that they may harbour. In this study, we screened the common palm civets in Singapore for tick-borne protozoan parasites known as piroplasms.<br><br>METHODS: Over a 2-year period, blood samples were opportunistically collected from 135 wild common palm civets following a physical examination. The sex and weight of each civet were recorded, and any ectoparasites detected were identified through DNA barcoding. DNA extracts of blood samples were screened using a PCR assay targeting the 18S rRNA gene of piroplasmids.<br><br>RESULTS: A novel Cytauxzoon species was detected in 29 civets (21.5%), and a statistically significant association was found between infection and the civet's weight. Two cat flea (Ctenocephalides felis) specimens were discovered on two sampled civets; however, Cytauxzoon DNA was not detected in either the flea or the sampled civet. Phylogenetic analysis of the Cytauxzoon 18S rRNA gene sequences from 29 civets revealed that this piroplasmid is most closely related to a Cytauxzoon sp. detected in meerkats in South Africa but molecularly distinct from the six currently described Cytauxzoon species.<br><br>CONCLUSIONS: This detection documents the first molecular confirmation of Cytauxzoon sp. infection in Southeast Asia and the first report of Cytauxzoon sp. in a viverrid host. Further studies are required to determine the vector involved in the transmission of this novel Cytauxzoon species, as no ticks were found on the sampled civets. The discovery of Cytauxzoon paradoxurus n. sp. highlights the importance of expanded biosurveillance to better understand the diversity of piroplasms harboured by wildlife in the region and its potential for cross-species transmission.}, }
@article {pmid40374562, year = {2025}, author = {Zhang, F and Dai, W and Zhang, M and Dong, H and Zhang, X}, title = {Programmed Fluorescence-Encoding DNA Nanoflowers for Cell-Specific-Target Multiplexed MicroRNA Imaging.}, journal = {Analytical chemistry}, volume = {97}, number = {20}, pages = {10588-10596}, doi = {10.1021/acs.analchem.4c06960}, pmid = {40374562}, issn = {1520-6882}, mesh = {*MicroRNAs/analysis/genetics ; Humans ; *DNA/chemistry ; *Fluorescent Dyes/chemistry ; Aptamers, Nucleotide/chemistry ; *Optical Imaging/methods ; Nucleic Acid Amplification Techniques ; Fluorescence ; *Nanostructures/chemistry ; MCF-7 Cells ; Cell Line, Tumor ; }, abstract = {The precise identification and differentiation of multiple microRNAs (miRNAs) with high spatial resolution in specific cells remain a significant challenge, primarily due to the limited availability of spectrally distinguishable fluorophores and the absence of cell-specific recognition capabilities. In this study, we introduce a programmed fluorescence-encoding DNA nanoflower (CNFs) system based on the self-assembly of rolling circle amplification (RCA), enabling multiplexed miRNA imaging in living cells. The CNFs system is rationally designed to consist of three key components: a CD63 aptamer region, dual fluorophore encoding regions, and an miRNA recognition region. The polyvalent tandem CD63 aptamer enhances the cellular targeting specificity and endocytic uptake efficiency. By controlling dual fluorophores and three levels of intensity within encoding regions, it generates 9 distinct barcodes for labeling multiple targets. Additionally, when conjugated with molecular beacons (MBs), CNFs facilitate the simultaneous detection of multiplexed intracellular miRNAs. Using this CNFs system, we successfully evaluated the expression profiles of nine miRNAs in breast cancer. Overall, we expect that this CNFs system will be a valuable tool for disease-related multiplex miRNAs biomarker imaging in specific cells and the exploration of miRNAs' molecular regulation mechanisms.}, }
@article {pmid40370916, year = {2025}, author = {Hammond, A and Mankad, A}, title = {Retrospective Lineage Tracing: An Optimal Approach for the Study of Intrinsic Cellular Development.}, journal = {Cureus}, volume = {17}, number = {4}, pages = {e82241}, pmid = {40370916}, issn = {2168-8184}, abstract = {Lineage tracing is an essential tool for understanding cellular development and tissue dynamics. This review examines retrospective lineage tracing as an optimal approach for studying cellular development and contrasts retrospective with prospective lineage tracing methods. Retrospective lineage tracing approaches leverage naturally occurring genetic barcodes, such as single nucleotide polymorphisms (SNPs), copy number variants (CNVs), and mitochondrial DNA mutations, which enables the detailed reconstruction of cell lineages without prior genetic manipulation. Researchers can ultimately infer developmental trajectories and clonal relationships across hematopoiesis and tumorigenesis by analyzing these endogenous markers. This paper considers how retrospective lineage tracing methods circumvent the limitations of prospective approaches, such as the need for exogenous labeling, and is valuable for studying human hematopoiesis.}, }
@article {pmid40370429, year = {2025}, author = {Firouzi, S and Solouki, M and Fazeli-Nasab, B and Salehi-Sardoei, A and Hatami, M and Ghorbanpour, M and Zhang, B}, title = {Ability to use ITS and rbcL sequencing for determination of the genetic diversity and relationships among olive (Olea europaea L.) genotypes.}, journal = {3 Biotech}, volume = {15}, number = {6}, pages = {161}, pmid = {40370429}, issn = {2190-572X}, abstract = {UNLABELLED: Olives are of considerable economic and commercial importance and are mostly used in both daily life and industries. The DNA barcode method has a lot of potential for reviving the science of arithmetics and traditional biodiversity studies, so it has been widely used on plants and for classification and arithmetic purposes. In this study, we sequenced seven different olive genotypes (Olea europaea cv. Olive yellow, O. europaea cv. Oliy, O. europaea cv. Roodbar Oily, O. europaea cv. Mari, O. europaea cv. Fishemi, O. europaea cv. Manzanila, O. europaea cv. Koroneiki) to study their diversity and evolution. The data were analyzed using Clustalw2 and BioEdit software. The homology rate of rbcL and ITS sequences was all in the range of 97-100%. It was identified, for ITS, 1,059 genetic luci (580 luci without deletion and addition and 479 luci with deletion and addition (328 luci polymorphs, 151 monomorphs), 217 singletons, and for rbcL, 565 genetic luci with (60 luci without deletion and addition and 505 luci with deletion and addition (2 luci with polymorphs, 503 monomorphs), 1 singleton. It was determined that the number of four haplotypes (haplotype diversity index = 0.80) was determined for ITS and three haplotypes (haplotype diversity index = 0.71) for RBCL. The results indicated that in the nucleotide sequence of the ITS gene among olive varieties, guanine was the most abundant base at 28.7%, while adenine had the lowest abundance at 5%. In contrast, the rbcL gene showed that thymine was the most abundant base at 29.8%, with cytosine being the least abundant at 20.6%. Estimates of nucleotide transitions in the ITS gene revealed a high frequency of pyrimidine transitions, with a thymine-to-cytosine transition rate of 16.84% and a cytosine-to-thymine transition rate of 11.63%. The ITS primer successfully identified and separated only six genotypes, whereas rbcL identified all seven genotypes. Although the success rates of 60-70% for both ITS and rbcL may not seem particularly high, they still significantly contribute to large-scale biodiversity inventories, especially for olive species.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04336-z.}, }
@article {pmid40370263, year = {2025}, author = {Cui, X and Liu, Y and Wu, T and Tay, MZ and Cheow, LF}, title = {Microfluidic-Enabled Production of DNA Barcoded APC Library (MEDAL) for High Throughput T Cell Epitope Screening.}, journal = {Small methods}, volume = {}, number = {}, pages = {e2500150}, doi = {10.1002/smtd.202500150}, pmid = {40370263}, issn = {2366-9608}, support = {MOE-T2EP30224-0047//Ministry of Education of Singapore/ ; NRF-F-CRP-2024-0003//National Research Foundation Frontier Competitive Research Programme/ ; }, abstract = {Screening for peptide fragments that can be displayed on antigen-presenting cells is an essential step in vaccine development. The current approach for this process is slow and costly as it involves separately pulsing cells with chemically synthesized peptides. This study presents Microfluidic-Enabled production of DNA-barcoded APC Library (MEDAL), a high throughput microfluidic droplet platform for parallel production of DNA-barcoded Antigen Presenting Cells (APCs) loaded with enzymatically synthesized peptides. Droplets containing peptides and their encoding DNA are produced from microfluidic PCR-IVTT reaction. APCs presenting both peptides and DNA barcodes are obtained by injecting cells into these droplets. Up to 9000 different APCs can be produced and screened within a 10-h workflow. This approach allows to identify peptide sequences that bind to APCs expressing H-2Kb MHC class I molecule with next-generation sequencing of DNA barcodes. Finally, co-culture of T cells and APC libraries prepared with MEDAL identified specific epitopes recognized by T cells.}, }
@article {pmid40367034, year = {2025}, author = {Ocaña-Cabrera, JS and Martin-Solano, S and Ron-Román, J and Rivas, J and Garigliany, MM and Saegerman, C}, title = {Pot-pollen DNA barcoding as a tool to determine the diversity of plant species visited by Ecuadorian stingless bees.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0323306}, pmid = {40367034}, issn = {1932-6203}, mesh = {Bees/physiology ; Animals ; *DNA Barcoding, Taxonomic/methods ; Ecuador ; *Pollen/genetics/classification ; Biodiversity ; *DNA, Plant/genetics ; *Plants/genetics/classification ; }, abstract = {Identifying the main species of plants from where Ecuadorian stingless bees collect pollen is one of the key objectives of management and conservation improvement for these insects. This study aims to determine the botanical origin of pot-pollen using two barcodes, comparing two methodologies (DNA barcoding versus electron microscopy and morphometric tools) and determine the genus and species of pollen source plants of the main honey-producing stingless bees in Ecuador. As main results, Prockia crucis, Coffea canephora, Miconia nervosa, Miconia notabilis, Laurus nobilis, Cecropia ficifolia, Theobroma sp., Artocarpus sp., Croton sp., Euphorbia sp., Mikania sp., and Ophryosporus sp., were the genera and species with the highest presence in the nests (n = 35) of three genera of stingless bees of two provinces located in different climatic regions inside the continental Ecuador. Plant species richness in both areas was statistically similar (p-value = 0.21). We concluded that floral sources' molecular identification with the ITS2 region had a higher number of genera and species detected, than the rbcL gene and microscopy tools, for the Ecuadorian landscapes. We confirmed that the foraging behavior of Melipona sp., Scaptotrigona sp., and Tetragonisca sp., could include non-native flora (27%, 12/44 identifications) that provide a rich source of pollen. Stingless beekeepers could use this information to create flower calendars and establish a schedule for better management of stingless bees in secondary and modified environments.}, }
@article {pmid40364976, year = {2025}, author = {Meadow, ME and Broas, S and Hoare, M and Ahmed, M and Alimohammadi, F and Welle, KA and Swovick, K and Hryhorenko, JR and Jain, A and Martinez, JC and Seluanov, A and Gorbunova, V and Buchwalter, A and Ghaemmaghami, S}, title = {Proteome Birthdating: A Single-Sample Approach for Measuring Global Turnover Dynamics and "Protein Age".}, journal = {Bio-protocol}, volume = {15}, number = {9}, pages = {e5296}, pmid = {40364976}, issn = {2331-8325}, support = {P01 AG047200/AG/NIA NIH HHS/United States ; R35 GM119502/GM/NIGMS NIH HHS/United States ; S10 OD025242/OD/NIH HHS/United States ; }, abstract = {Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To facilitate such studies, we recently developed a technique termed "proteome birthdating" that differentially labels proteins based on their time of synthesis. Proteome birthdating enables analyses of age distributions of the proteome by tandem mass spectrometry (LC-MS/MS) and provides a methodology for investigating the protein age selectivity of diverse cellular pathways. Proteome birthdating can also provide measurements of protein turnover kinetics from single, sequentially labeled samples. Here, we provide a practical guide for conducting proteome birthdating in in vitro model systems. The outlined workflow covers cell culture, isotopic labeling, protein extraction, enzymatic digestion, peptide cleanup, mass spectrometry, data processing, and theoretical considerations for interpretation of the resulting data. Key features • Proteome birthdating barcodes the proteome with isotopically labeled precursors based on time of synthesis or "age." • Global protein turnover kinetics can be analyzed from single, sequentially labeled biological samples. • Protein age distributions of subsets of the proteome can be analyzed (e.g., ubiquitinated proteins). • Age selectivity of protein properties, cellular pathways, or disease states can be investigated.}, }
@article {pmid40364432, year = {2025}, author = {Chedao, N and Pandey, AC and Suraninpong, P}, title = {Identification of Indigenous Thai Phlegmariurus Genotypic Population by Integrating Morphological and Molecular Studies.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, pmid = {40364432}, issn = {2223-7747}, support = {0000//Walailak University/ ; }, abstract = {Phlegmariurus, a diverse genus within the Lycopodiaceae family, has wide diversity in tropical regions, including Thailand. Accurate species delimitation in the tropical clubmoss genus Phlegmariurus is challenged by high morphological plasticity and genetic complexity. This study applied an integrative multilocus approach combining morphometric analysis of 27 complete specimens, 35 Phlegmariurus and one Lycopodiella accessions for AFLP genotyping (926 loci; PIC 0.32), SSR profiling (44 loci; PIC 0.57; expected heterozygosity 0.35), and chloroplast barcoding using rbcL (1308 bp; bootstrap 89-99%) and the psbA-trnH intergenic spacer (308 bp; bootstrap ≥ 94%). A total of 13 were identified as belonging to seven known species, including P. nummulariifolius (NST01, NST15, NST36), P. goebelii (JP04), P. phlegmaria (NST13), P. verticillatus (PHI16), P. squarrosus (NST21, NST22, MY31), P. tetrastichus (NST30), and P. carinatus (MY32, MY33, NST34). Morphological clustering and molecular markers consistently distinguished Phlegmariurus accessions from the Lycopodiella outgroup. Additionally, 19 previously unclassified Phlegmariurus accessions were successfully identified as belonging to the species P. nummulariifolius (NST23), P. goebelii (NST03, JP05, STN12, PNA14, SKA25, CPN26, KRB27, PNA28), P. phlegmaria (NWT07, STN08, NST09, NST10, PHI29), P. squarrosus (NST17), and P. carinatus (PNA06, STN18, CPN19, JP24). Moreover, this study identified three novel lineages (NST02, STN11, NST20) with strong support across datasets. The combination of broad genomic coverage (AFLP), fine-scale allelic resolution (SSR), deep-branch backbone (rbcL), and terminal-branch discrimination (psbA-trnH) yields a robust framework for species identification. These results define clear operational units for conservation prioritization and establish a foundation for marker-assisted development of ornamental Phlegmariurus cultivars.}, }
@article {pmid40362097, year = {2025}, author = {Zhang, J and Cui, X and Lin, L and Liu, Y and Ye, J and Zhang, W and Li, H}, title = {Unraveling Fish Community Diversity and Structure in the Yellow Sea: Evidence from Environmental DNA Metabarcoding and Bottom Trawling.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {9}, pages = {}, pmid = {40362097}, issn = {2076-2615}, support = {2024YFF0808802; FREU2020-03; 2020-A-06//National Key Research and Development Program of China; the Fund of Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, P. R. China; Doctoral Research Initiation of Foundation of Nat/ ; }, abstract = {The use of environmental DNA (eDNA) metabarcoding to analyze fish species diversity across different aquatic ecosystems is well documented. Nonetheless, there is a gap in validating eDNA metabarcoding studies on the diversity and structure of fish communities in coastal ecosystems, particularly in comparing these findings with bottom trawl catch data. In this study, we employed eDNA metabarcoding to explore species composition and relative abundance in fish communities, taxonomic-level diversity variations, and the interplay between community structures and environmental factors in the Yellow Sea and compared these results with those obtained from bottom trawl catches. In addition, we compared the various methods used to estimate the distributions of taxonomic, phylogenetic, and functional diversity factors. We found that eDNA metabarcoding detected a greater number of species (86 vs. 41), genera (73 vs. 37), and families (42 vs. 25) than bottom trawl results at each sampling station. eDNA metabarcoding provided higher Shannon, Simpson, and Chao1 alpha diversity indices than the bottom trawl results. The PCoA results showed that eDNA metabarcoding samples could be more clearly separated at the sampling sites in the Zhuanghe (ZH) and Lianyungang (LYG) areas than bottom trawling samples. The RDA analysis indicated that temperature, along with NO3- and NH4[+] concentrations, were pivotal in shaping the geographical patterns of fish communities, as identified through eDNA metabarcoding, echoing findings from bottom trawling studies. Furthermore, our findings suggest that eDNA barcoding surpasses bottom trawling in detecting taxonomic and phylogenetic diversity, as well as in uncovering greater functional diversity at the local level. Conclusively, eDNA metabarcoding emerges as a valuable complement to bottom trawling, offering a multifaceted approach to biodiversity monitoring that not only boosts efficiency but also reduces environmental impact on coastal ecosystems.}, }
@article {pmid40362082, year = {2025}, author = {Wang, D and Li, Q and Gao, J and Hou, L and Zou, Y and Lian, X}, title = {Dietary Differentiation Mitigates Interspecific Interference Competition Between Sympatric Pallas's Cats (Otocolobus manul) and Red Foxes (Vulpes vulpes).}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {9}, pages = {}, pmid = {40362082}, issn = {2076-2615}, abstract = {The comparative analysis of the feeding ecology among sympatric small carnivores reveals both differentiation and overlap in resource utilization patterns, which serves as a critical pathway for understanding interspecific interactions and maintaining ecosystem stability. In this study, we collected fecal samples from sympatric Pallas's cats (Otocolobus manul, n = 26) and red foxes (Vulpes vulpes, n = 13) within the Sanjiangyuan National Park (SNP) in China. Subsequently, DNA barcoding technology was employed to analyze the dietary composition and interspecific differences of these two small carnivores. The results demonstrated that both species primarily prey on plateau pikas (Ochotona curzoniae) and small rodents. Despite a high trophic niche overlap between Pallas's cats and red foxes (Ojk = 0.81), interspecific competition is mitigated through differentiate feeding proportions of shared prey species. Furthermore, the trophic niche breadth of red foxes (B = 267.89) exceeds that of Pallas's cats (B = 162.94), reflecting a greater diversity of prey resources utilized by red foxes. Consequently, the two small carnivores achieve sympatric coexistence via differentiated resource utilization. These findings enhance our understanding of the coexistence mechanisms within carnivore communities and provide a scientific basis for the conservation of wildlife in the SNP.}, }
@article {pmid40362051, year = {2025}, author = {Chetverikov, PE and Peralta Alba, LE}, title = {First Bisexually Dimorphic Phytoptid Taxon (Eriophyoidea, Phytoptidae) from Gondwanian Angiosperm Host.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {9}, pages = {}, pmid = {40362051}, issn = {2076-2615}, support = {125013001089-0//Zoological Institute of Russian Academy of Sciences/ ; }, abstract = {Acariform mites of the superfamily Eriophyoidea are permanent parasites of higher vascular plants. Seasonal morphological dimorphism in females has been documented across various eriophyoid taxa, while male dimorphism remains poorly understood. In this study, we analyzed morphological, molecular, and biological data from the genus Austracus Keifer 1944, with a particular focus on the type species, A. havrylenkonis Keifer 1944, associated with Nothofagus. Using new material collected from Chile and Argentina, we demonstrated that this species exhibits two distinct forms of both males and females, making it the first known bisexually dimorphic taxon within the family Phytoptidae. The summer form of A. havrylenkonis displays the unstable annulation of the dorsal opisthosoma, characterized by a significant variation in the number of thin, microtuberculated dorsal annuli interspersed among the broader, plate-like annuli typical of the winter form. This finding aligns with the previous observations of atypical deuterogyny in Eriophyoidea and leads us to hypothesize that gall mites employ diverse adaptive strategies-manifesting as either gradual or discrete morphological changes-to cope with seasonal environmental fluctuations. Investigating the genetic mechanisms underlying these adaptive strategies, along with further studies of eriophyoids associated with Nothofagus in the Southern Hemisphere, represents a promising direction for future research.}, }
@article {pmid40361631, year = {2025}, author = {Andronache, J and Cichna-Markl, M and Dobrovolny, S and Hochegger, R}, title = {Development of a DNA Metabarcoding Method for the Identification of Crustaceans (Malacostraca) and Cephalopods (Coleoidea) in Processed Foods.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {9}, pages = {}, pmid = {40361631}, issn = {2304-8158}, abstract = {Seafood is a valuable commodity with increasing demand, traded for billions of USD each year. The volatility in supply chains and fluctuating prices contribute to the susceptibility of the seafood market to food fraud. Analytical methods are required to identify seafood in processed foods to ensure food authenticity and compliance with European laws. To address this need, we developed and validated a DNA metabarcoding method for the authentication of crustaceans and cephalopods in processed food samples, as both are prone to food fraud, especially in mixed products. A ~200 bp barcode of the mitochondrial 16S rDNA was selected as the marker for identification and sequenced on Illumina platforms. The DNA metabarcoding method utilizes two primer systems, one for the amplification of crustacean DNA and another for cephalopods. The crustacean primer system comprises two forward and two reverse primers, while the cephalopod primer system includes three forward and one reverse primer. DNA extracts from reference materials, model foods, processed foodstuffs, and DNA extract mixtures were investigated. Even species with a close phylogenetic relationship were successfully identified and differentiated in commercial samples, while single species were detected at amounts as low as 0.003% in model foods. However, false-negative results were obtained for certain species in DNA extract mixtures, which are most likely due to degraded or low-quality DNA and can best be prevented by optimized DNA extraction procedures. Our DNA metabarcoding method demonstrates strong potential as a qualitative screening tool in combination with other in-house DNA metabarcoding methods for food authentication in routine analysis.}, }
@article {pmid40359979, year = {2025}, author = {Iwaszkiewicz-Eggebrecht, E and Goodsell, RM and Bengsson, B&#xc5; and Mutanen, M and Klinth, M and van Dijk, LJA and Łukasik, P and Miraldo, A and Andersson, A and Tack, AJM and Roslin, T and Ronquist, F}, title = {High-throughput biodiversity surveying sheds new light on the brightest of insect taxa.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2046}, pages = {20242974}, pmid = {40359979}, issn = {1471-2954}, support = {Career Support grant to TR//Swedish University of Agricultural Sciences/ ; 2017.088//Knut and Alice Wallenberg Foundation/ ; //Uppsala Multidisciplinary Center for Advanced Computational Science/ ; 2018/31/B/NZ8/01158//Polish National Science Centre/ ; Synergy Grant 856506/ERC_/European Research Council/International ; PPN/PPO/2018/1/00015//Polish National Agency for Academic Exchange/ ; 2018-04620, 2021-03784, 2021-05563//Swedish Research Council/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Sweden ; *Lepidoptera/genetics/classification ; }, abstract = {DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known taxa in underexplored regions. This study evaluates what an extensive sampling effort combined with metabarcoding can tell us about the lepidopteran fauna of Sweden-one of the best-understood insect taxa in one of the most-surveyed countries of the world. We deployed 197 Malaise traps across Sweden for a year, generating 4749 bulk samples for metabarcoding, and compared the results to existing data sources. We detected more than half (1535) of the 2990 known Swedish lepidopteran species and 323 species not reported during the sampling period by other data providers. Full-length barcoding confirmed three new species for the country, substantial range extensions for two species and eight genetically distinct barcode variants potentially representing new species, one of which has since been described. Most new records represented small, inconspicuous species from poorly surveyed regions, highlighting components of the fauna overlooked by traditional surveying. These findings demonstrate that DNA metabarcoding is a highly efficient and accurate biodiversity sampling method, capable of yielding significant new discoveries even for the most well known of insect faunas.}, }
@article {pmid40359875, year = {2025}, author = {Morán Torres, JP and Lyu, J and Chen, X and Klaas, AM and Vonk, PJ and Lugones, LG and de Cock, H and Wösten, HAB}, title = {Single and combinatorial gene inactivation in Aspergillus niger using selected as well as genome-wide gRNA library pools.}, journal = {Microbiological research}, volume = {298}, number = {}, pages = {128204}, doi = {10.1016/j.micres.2025.128204}, pmid = {40359875}, issn = {1618-0623}, mesh = {*Aspergillus niger/genetics ; CRISPR-Cas Systems ; Gene Editing/methods ; *RNA, Guide, CRISPR-Cas Systems/genetics ; Plasmids/genetics ; *Gene Silencing ; Gene Library ; Genome, Fungal ; Genetic Vectors ; Phenotype ; Genes, Fungal ; Transformation, Genetic ; }, abstract = {Aspergillus niger is a saprotroph, a pathogen, an endophyte, a food spoiler and an important cell factory. Only a minor fraction of its genes has been experimentally characterized. We here set up a CRISPR/Cas9 mutagenesis screen for functional gene analysis using co-transformation of a pool of gene editing plasmids that are maintained under selection pressure and that each contain a gRNA. First, a pool of gRNA vectors was introduced in A. niger targeting five genes with easy selectable phenotypes. Transformants were obtained with all possible single, double, triple, quadruple and quintuple gene inactivation phenotypes. Their genotypes were confirmed using the gRNA sequences in the transforming vector as barcodes. Next, a gRNA library was introduced in A. niger targeting > 9600 genes. Gene nsdC was identified as a sporulation gene using co-transformation conditions that favored uptake of one or two gRNA construct(s) from the genome-wide vector pool. Together, CRISPR/Cas9 vectors with a (genome-wide) pool of gRNAs can be used for functional analysis of genes in A. niger with phenotypes that are the result of the inactivation of a single or multiple genes.}, }
@article {pmid40359386, year = {2025}, author = {Rodriguez, LG and Lombard-Banek, C and Quach, VM and Choi, SB and Manzini, MC and Nemes, P}, title = {A Multipoint Validation of Quantification in Capillary Electrophoresis Mass Spectrometry Proteomics: Isobaric Multiplexing with Tandem Mass Tags.}, journal = {Analytical chemistry}, volume = {97}, number = {20}, pages = {10901-10909}, doi = {10.1021/acs.analchem.5c01832}, pmid = {40359386}, issn = {1520-6882}, mesh = {Electrophoresis, Capillary/methods ; Animals ; *Tandem Mass Spectrometry/methods ; *Proteomics/methods ; Mice ; *Proteome/analysis ; Peptides/analysis ; Reproducibility of Results ; Saccharomyces cerevisiae/chemistry/metabolism ; }, abstract = {Multiplexing quantification using isobaric barcoding has gained traction in trace-sensitive and single-cell mass spectrometry (MS), both in nanoflow liquid chromatography (nanoLC) and capillary electrophoresis (CE). In nanoLC-MS, ratio compression from isobaric interferences is known to challenge quantification accuracy during tandem MS (MS[2]), which is effectively remedied using simultaneous precursor selection (SPS) MS[3]. Despite mounting interest in CE-MS for trace-sensitive bottom-up proteomics, the fidelity of multiplexed quantification is unknown using this technology. Here, we address this fundamental knowledge gap by holistically investigating quantification depth, reproducibility, and accuracy using a validated mouse-yeast two-proteome model. CE-based quantification via the MS[2] and SPS-MS[3] strategies were benchmarked against the nanoLC SPS-MS[3] gold standard. We found electrophoresis-correlative (Eco) ion sorting to order peptides into high-flux transients of nominally isobaric m/z values (Δm/z < 1-2 Th). While the MS[2] approach struggled with ratio distortion, the SPS-MS[3] robustly eliminated them for both separations. The reproducibility and accuracy proved indistinguishable between CE and nanoLC using MS[2] or SPS-MS[3] quantification. CE enhanced the depth of quantification by ∼12-fold. These analytical insights can be used to design trace CE-MS studies with high scientific rigor.}, }
@article {pmid40359107, year = {2025}, author = {Nguyen, LV and Eyal-Lubling, Y and Guerrero-Romero, D and Kronheim, S and Chin, SF and Manzano Garcia, R and Sammut, SJ and Lerda, G and Lui, AJW and Bardwell, HA and Greenwood, W and Shin, HJ and Masina, R and Kania, K and Bruna, A and Esmaeilishirazifard, E and Kolyvas, EA and Aparicio, S and Rueda, OM and Caldas, C}, title = {Fitness and transcriptional plasticity of human breast cancer single-cell-derived clones.}, journal = {Cell reports}, volume = {44}, number = {5}, pages = {115699}, pmid = {40359107}, issn = {2211-1247}, mesh = {Humans ; *Single-Cell Analysis/methods ; *Breast Neoplasms/genetics/pathology ; Female ; Animals ; Clone Cells/metabolism ; Mice ; Transcriptome/genetics ; *Transcription, Genetic ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; }, abstract = {Clonal fitness and plasticity drive cancer heterogeneity. We used expressed lentiviral-based cellular barcodes combined with single-cell RNA sequencing to associate single-cell profiles with in vivo clonal growth. This generated a significant resource of growth measurements from over 20,000 single-cell-derived clones in 110 xenografts from 26 patient-derived breast cancer xenograft models. 167,375 single-cell RNA profiles were obtained from 5 models and revealed that rare propagating clones display a highly conserved model-specific differentiation program with reproducible regeneration of the entire transcriptomic landscape of the original xenograft. In 2 models of basal breast cancer, propagating clones demonstrated remarkable transcriptional plasticity at single-cell resolution. Dichotomous cell populations with different clonal growth properties, signaling pathways, and metabolic programs were characterized. By directly linking clonal growth with single-cell transcriptomes, these findings provide a profound understanding of clonal fitness and plasticity with implications for cancer biology and therapy.}, }
@article {pmid40352821, year = {2025}, author = {Jin, D and Kim, SS and Shin, B and Choi, SW}, title = {An updated list of the genus Hypena Schrank (Lepidoptera, Erebidae) from Korea with five additional records to the fauna.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e155581}, pmid = {40352821}, issn = {1314-2828}, abstract = {BACKGROUND: The paper provides the updated checklist of the genus Hypena Schrank from Korea. This genus is one of the largest genera within the Noctuoidea comprising more than 680 species worldwide and the genus is the monophyletic group based on the morphological characters. The external examination along with the genitalia examination and DNA barcoding could reveal the diversity of the genus in Korea.<br><br>NEW INFORMATION: In this study, we examined a total of 192 specimens and barcoded 16 species and listed a total of 29 species of Hypena including five new additions, Hypenatamsi Filipjev (1927), Hypenaobacerralis Walker (1859), Hypenapulverulenta Wileman (1911), Hypenaperspicua Leech (1900) and Hypenamandarina Leech (1900) to the Korean fauna. We provided the detailed distribution of each species of the genus across South Korea and the photographs of adults and genitalia. In addition, the monophyly of the genus was also confirmed using two outgroup species of Herminiinae. This study significantly contributes to the knowledge of erebid fauna in Korea and the phylogenetic relationship amongst the species of the genus.}, }
@article {pmid40352767, year = {2025}, author = {Vasu, AC and Ravidas, VA and Tharakan, ST and Kadunganattil, S}, title = {Toxicity profiling and HR-LCMS analysis of Indigofera longiracemosa leaf methanolic extract exhibiting anti-inflammatory activity.}, journal = {3 Biotech}, volume = {15}, number = {6}, pages = {160}, pmid = {40352767}, issn = {2190-572X}, abstract = {Indigofera longiracemosa, a member of the Fabaceae family documented in traditional medicine for its therapeutic potential, holds promise as a viable natural indigo source. The dearth of reliable and coherent research on the safety and medicinal advantages of phytochemicals obtained from this specific plant species prompted us to examine therapeutic potential of extracts prepared from the leaf and stem of this dye yielding plant. The aerial parts (leaf and stem) of I. longiracemosa were extracted separately using solvents of increasing polarity. In vitro anti-inflammatory studies such as lipoxygenase inhibition, albumin denaturation, and protease inhibitory activity revealed leaf methanolic extract (LME) to show the best anti-inflammatory property. Furthermore, short term toxicity studies (acute and sub-acute) were done in Balb/c mice to evaluate LME's toxicity. In acute toxicity study, LME administered at 2000 mg/kg body weight was found to be non-toxic. Consequently, sub-acute toxicity study was done in both male and female Balb/c mice at three doses (100, 200 and 400 mg/kg body weight, respectively). Following sub-acute toxicity study for 28 days, serum analysis and histological evaluation of tissues did not reveal any signs of toxicity at the administered doses, thereby indicating non-toxic nature of LME. Furthermore, to identify phytochemicals associated with LME, HRLCMS-QTOF untargeted metabolomics was done, and the predominant phytochemicals identified were phenols. The enhanced anti-inflammatory property observed in LME may be attributed to the predominance of phenols. Our studies have, therefore, illustrated the non-toxic nature and therapeutic potential of LME, an extract prepared from I. longiracemosa.}, }
@article {pmid40350868, year = {2025}, author = {Li, H and Zeng, YJ and Li, XY and Abdullah,  and Huang, YH and Yan, RS and Shao, R and Wang, Y and Tian, XX}, title = {[Mini-barcode development based on chloroplast genome of Descurainiae Semen Lepidii Semen and its adulterants and its application in Chinese patent medicine].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {50}, number = {7}, pages = {1758-1769}, doi = {10.19540/j.cnki.cjcmm.20250113.101}, pmid = {40350868}, issn = {1001-5302}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Drugs, Chinese Herbal/chemistry ; *Drug Contamination ; *Genome, Chloroplast ; Medicine, Chinese Traditional ; }, abstract = {Descurainiae Semen Lepidii Semen, also known as Tinglizi, originates from Brassicaceae plants Descurainia sophia or Lepidium apetalum. The former is commonly referred to as "Southern Tinglizi(Descurainiae Semen)", while the latter is known as "Northern Tinglizi(Lepidii Semen)". To scientifically and accurately identify the origin of Tinglizi medicinal materials and traditional Chinese medicine products, this study developed a specific DNA mini-barcode based on chloroplast genome sequences. By combining the DNA mini-barcode with DNA metabarcoding technology, a method for the qualitative and quantitative identification of Tinglizi medicinal materials and Chinese patent medicines was established. In this study, chloroplast genomes of Southern Tinglizi and Northern Tinglizi and seven commonly encountered counterfeit products were downloaded from the GenBank database. Suitable polymorphic regions were identified to differentiate these species, enabling the development of the DNA mini-barcode. Using DNA metabarcoding technology, medicinal material mixtures of Southern and Northern Tinglizi, as well as the most common counterfeit product, Capsella bursa-pastoris seeds, were analyzed to validate the qualitative and quantitative capabilities of the mini-barcode and determine its minimum detection limit. Additionally, the mini-barcode was applied to Chinese patent medicines containing Tinglizi to authenticate their botanical origin. The results showed that the developed mini-barcode(psbB) exhibited high accuracy and specificity, effectively distinguishing between the two authentic origins of Tinglizi and commonly encountered counterfeit products. The analysis of mixtures demonstrated that the mini-barcode had excellent qualitative and quantitative capabilities, accurately identifying the composition of Chinese medicinal materials in mixed samples with varying proportions. Furthermore, the analysis of Chinese patent medicines revealed the presence of the adulterant species(Capsella bursa-pastoris) in addition to the authentic species(Southern and Northern Tinglizi), indicating the occurrence of adulteration in commercially available Tinglizi-containing products. This study developed a method for the qualitative and quantitative identification of multi-origin Chinese medicinal materials and related products, providing a model for research on other multi-origin Chinese medicinal materials.}, }
@article {pmid40349990, year = {2025}, author = {Yuda, A and Nakamura, T and Momose, S and Ishii, S and Tanaka, H and Yamamoto-Hanada, K and Fukuie, T and Ohya, Y and Nomura, T and Noguchi, E}, title = {A comprehensive approach for identifying filaggrin mutations and copy number variants by long-read sequencing.}, journal = {Genomics}, volume = {117}, number = {4}, pages = {111055}, doi = {10.1016/j.ygeno.2025.111055}, pmid = {40349990}, issn = {1089-8646}, mesh = {Filaggrin Proteins ; *DNA Copy Number Variations ; Humans ; *Intermediate Filament Proteins/genetics ; *Mutation ; High-Throughput Nucleotide Sequencing/methods ; Polymorphism, Single Nucleotide ; INDEL Mutation ; }, abstract = {Filaggrin (FLG) is essential for skin barrier function, but has highly diverse and complex mutations linked to various allergic and dermatological diseases. Current genotyping methods often fail to capture the full range of FLG variants, especially in regions with high sequence homology. To overcome this limitation, we developed a singleplex PCR method that amplifies FLG exon 3 using FLG-specific primers tailed with barcodes for sample identification, followed by long-read sequencing on the PacBio Sequel IIe system. After demultiplexing with the barcode sequences, pbmm2 and GATK HaplotypeCaller were used for alignment and variant calling, respectively. This method successfully identified single nucleotide variants, insertion-deletion variants, and copy number variations (CNVs), including several loss-of-function mutations. We also determined the FLG copy number in each allele, which ranged from 7 to 20 repeats. This comprehensive, convenient genotyping approach could significantly enhance diagnostic accuracy and personalized treatment strategies for allergy- and skin-related conditions.}, }
@article {pmid40348924, year = {2025}, author = {Brunet, S and Grankvist, A and Jaen-Luchoro, D and Bergdahl, M and Tison, JL and Wester, A and Elfving, K and Brandenburg, J and Gullsby, K and Lindsten, C and Arvidsson, LO and Larsson, H and Eilers, H and Strand, AS and Lannefors, M and Keskitalo, J and Rylander, F and Welander, J and Jungestrom, MB and Geörg, M and Kaden, R and Karlsson, I and Linde, AM and Mernelius, S and Berglind, L and Feuk, L and Kerje, S and Karlsson, L and Sjödin, A and Guerra-Blomqvist, L and Wallin, F and Fagerström, A and Vondracek, M and Mölling, P and Hallbäck, ET}, title = {Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {8}, pages = {1907-1916}, pmid = {40348924}, issn = {1435-4373}, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Nanopore Sequencing/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Sweden ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Nanopores ; *Bacterial Infections/diagnosis/microbiology ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {PURPOSE: Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.<br><br>METHODS: Thirteen mock samples comprised of various bacterial strains and an External Quality Assessment (EQA) panel from QCMD (Quality Control for Molecular Diagnostics) were analysed by 20 microbiological laboratories across Sweden, using the recent v14 chemistry. Most laboratories generated full-length 16S rRNA sequencing libraries using an optimized protocol for the 16S Barcoding Kit 24, while two laboratories employed in-house PCR coupled with the Ligation Sequencing Kit. The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).<br><br>RESULTS: Seventeen out of 20 laboratories successfully sequenced and analysed the samples. Laboratories that used sodium acetate-containing elution buffers faced compatibility issues during library construction, resulting in reduced read count. High bacterial load samples were generally well-characterized, whereas hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance. The GMS-16S tool provided improved species-level identification compared to the 1928-16S pipeline, particularly for closely related taxa within the Streptococcus and Staphylococcus genera.<br><br>CONCLUSION: Nanopore sequencing demonstrated promising potential for bacterial identification in a clinical setting. The results prompt further optimization of the protocol to improve detection of a broader range of species. This multicentre study highlights the feasibility of implementing Nanopore sequencing into clinical microbiological laboratories, for improved national precision diagnostics.}, }
@article {pmid40343328, year = {2025}, author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G}, title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.}, journal = {Plant direct}, volume = {9}, number = {5}, pages = {e70078}, pmid = {40343328}, issn = {2475-4455}, abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.}, }
@article {pmid40342730, year = {2025}, author = {Cometti, V and Cecchetto, M and Guzzi, A and Grillo, M and Noli, NF and Corsolini, S and Schiaparelli, S}, title = {Checklist of pioneer benthic taxa found on Autonomous Reef Monitoring Structures (ARMS) in Terra Nova Bay (Ross Sea, Antarctica).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e148863}, pmid = {40342730}, issn = {1314-2828}, abstract = {BACKGROUND: Benthic communities studies in the Southern Ocean highlight their potential for assessing climate and anthropogenic impacts. However, the lack of standardised methods limits result reliability and interpretation. This dataset presents the first checklist focus on the Antarctic pioneer benthic communities collected using a standardised approach such as Autonomous Reef Monitoring Structures (ARMS) located at 25 m depth in the surroundings of the Italian research station "Mario Zucchelli" (MZS) in the Terra Nova Bay (TNB) area of the Ross Sea, Antarctica. The data encompass ARMS time series corresponding to deployments of 1, 2, 3 and 5 years, from which 277 occurrence data corresponding to 12 phyla, 43 families, 49 genera and 39 species were obtained. All retrieved specimens are curated by the Italian National Antarctic Museum (MNA, section of Genoa). This dataset is a contribution to the Antarctic Biodiversity Portal, the thematic Antarctic node for both the Ocean Biogeographic Information System (AntOBIS) and the Global Biodiversity Information Facility Antarctic Biodiversity Information Facility (ANTABIF). The dataset was uploaded and integrated with the SCAR-AntOBIS database under the licence CC-BY 4.0. Please follow the guidelines from the SCAR Data Policy (ISSN 1998-0337) when using the data. If you have any questions regarding this dataset, please contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at the biodiversity-aq GitHub project.<br><br>NEW INFORMATION: We describe the biodiversity of the Antarctic pioneer benthic communities of TNB sampled using the ARMS installed at the Italian research station "Mario Zucchelli". ARMS is a standardised, reproducible and comparable method for quantifying biodiversity. This dataset provides essential baseline data on the occurrence and abundance of pioneer benthic communities in this study area, representing an important contribution for understanding the dynamics of benthic pioneer communities in an area where these structures have never been deployed and, in general, for an exposure time that largely exceed the standard one, which is usually of one year only.The 277 occurrences reported here have been classified at the lowest possible taxonomic level and comprise 39 recognised species, 49 genera and 43 families. Approximately 98% of the samples are stored in 96% ethanol, while the others at -20&#xb0;C, representing a potential resource for future genetic studies. To date, the entire ARMS collection has not been DNA barcoded, although preliminary metabarcoding analyses have already been published in Cecchetto et al. (2024). Outcomes of the barcoding activity will be the target of another future publication (Cometti et al., in prep). The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n&#xb0;FR/36/AN1/AntaBIS) in the framework of EU-Lifewatch as a contribution to the SCAR Antarctic Biodiversity Portal (bio diversity.aq).}, }
@article {pmid40342375, year = {2025}, author = {Klaiklueng, N and Kumlert, R and Moonmake, S and Ruang-Areerate, T and Siriyasatien, P and Sunantaraporn, S and Wanachiwanawin, D and Ruenchit, P and Wongkamchai, S}, title = {Species distribution and screening of Trypanosoma DNA in phlebotomine sand flies from four southern provinces of Thailand.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {7}, number = {}, pages = {100263}, pmid = {40342375}, issn = {2667-114X}, abstract = {Sand flies are principal vectors of Leishmania spp. and Trypanosoma spp. Identifying precise vector species is crucial for effective control. We conducted a study on the species distribution of phlebotomine sand flies in cave-dwelling and non-cave-dwelling in four southern provinces of Thailand. In this study, we collected 621 sand flies (346 females and 275 males) and identified all specimens based on morphology and DNA barcoding, employing cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes. In female specimens, we also screened the small subunit 18S ribosomal RNA (18S rRNA) gene for Leishmania spp. and Trypanosoma spp. Morphologically, 467 (75.2%) sand flies were identified to species level, 47 (7.57%) to subgenus level, and 107 (17.23%) to genus level. These included Idiophlebotomus asperulus (43.48%), Sergentomyia khawi (26.73%), S. anodontis (2.25%), S. brevicaulis (2.25%), Grassomyia indica (0.48%), Phlebotomus (Euphlebotomus) spp. (4.83%), Phlebotomus (Lewisius) spp. (2.74%), Sergentomyia spp. (9.18%), and Phlebotomus spp. (8.05%). Among the 107 specimens identified to genus level, DNA barcoding further identified 49 (45.79%) as Sergentomyia barraudi (1.61%), S. bailyi (0.16%), Phlebotomus kiangsuensis (2.9%), and Ph. stantoni (1.61%). No Leishmania DNA was detected, but Trypanosoma DNA was found in females of S. khawi from Narathiwat Province. Expanding genetic reference databases of sand flies located in four provinces of southern Thailand will improve barcoding accuracy. Understanding sand fly species composition and distribution is imperative for vector control and disease prevention in Thailand.}, }
@article {pmid40339340, year = {2025}, author = {Wang, Q and Wu, Y and Wang, Y and Mei, R and Zhao, R and Wang, X and Chen, L}, title = {Surface enhanced Raman scattering tag enabled ultrasensitive molecular identification of Hippocampus trimaculatus based on DNA barcoding.}, journal = {Talanta}, volume = {294}, number = {}, pages = {128289}, doi = {10.1016/j.talanta.2025.128289}, pmid = {40339340}, issn = {1873-3573}, mesh = {*Spectrum Analysis, Raman/methods ; *DNA Barcoding, Taxonomic/methods ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Limit of Detection ; *DNA/genetics/analysis ; Polymerase Chain Reaction ; Surface Properties ; Polystyrenes/chemistry ; }, abstract = {Rapid and precise DNA barcode-based identification of biological species holds significant potential for pharmaceutical authentication and biomedical diagnostics. Herein, we present a polymerase chain reaction (PCR)-surface-enhanced Raman scattering (SERS) platform that integrates SERS tags for ultrasensitive and fast authentication of Hippocampus trimaculatus, a high-value traditional Chinese medicine (TCM). The SERS tags are composed of gold nanostars, near-infrared cyanine7 Raman reporters and carboxylated polystyrene shells, which achieve single-particle detection sensitivity under 780 nm irradiation. The tags also show excellent colloidal and SERS stability under physiologically relevant conditions (e.g., phosphate buffer saline, serum, 1 mM NaCl, and pH 1-12), with signal variations less than 5 %. The carboxylated polystyrene shells enable efficient DNA functionalization. Leveraging these advancements, the PCR-SERS assay detects genomic DNA (gDNA) at concentrations as low as 10 copies/μL within 20 thermal cycles, with remarkable specificity for Hippocampus trimaculatus over four common adulterant species. Notably, the method reduces amplification requirements to 5 thermal cycles (detection limit of 10[6] copies/μL) while completing the entire workflow in less than 30 min (conventional qPCR, 20-30 cycles, 1-2 h). Beyond TCM verification, this PCR-SERS platform holds broad applicability for rapid nucleic acid detection in fields ranging from environmental eDNA monitoring to point-of-care diagnostics.}, }
@article {pmid40338382, year = {2025}, author = {Gil-Fernández, M and Carthey, AJR and Mendoza, E and Godínez-Gómez, O and G, MCM and Blanco-García, A and Delfín-Alfonso, CA and Le Roux, JJ}, title = {The impact of land use change on mycorrhizal fungi and their associations with rodents: insights from a temperate forest in Mexico.}, journal = {Mycorrhiza}, volume = {35}, number = {3}, pages = {36}, pmid = {40338382}, issn = {1432-1890}, support = {20224755//Macquarie University/ ; OSP Fellowship//Macquarie University/ ; }, mesh = {*Mycorrhizae/classification/physiology/genetics/isolation &amp; purification ; Mexico ; *Forests ; *Soil Microbiology ; Animals ; *Rodentia/microbiology ; Biodiversity ; DNA, Fungal/genetics ; Ecosystem ; }, abstract = {Ecosystem functioning is influenced by biological diversity, ecological interactions, and abiotic conditions. Human interactions with ecosystems can cause major changes in how they function when involving changes in the vegetation cover and structure (i.e., land use change). This study examines how land use change affects the diversity of arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) in soil and rodent scats in temperate forest sites. We collected soil and rodent scat samples at five paired sites (i.e., disturbed vs. undisturbed) in Michoacan, Mexico. We identified 112 putative mycorrhizal fungi species using DNA barcoding based on partial internal transcribed region 1 (ITS) sequences. We found a higher richness of EMF in undisturbed soil samples compared to disturbed soil samples and a higher AMF diversity in rodent scat samples from disturbed than undisturbed sites. Scat samples had a high incidence of both AMF (75%) and EMF (100%). We found significant differences in the diversity of both AMF and EMF depending on the rodent species associated with them. We also found a higher diversity of EMF in scats in the wet season than in the dry season. We also report, for the first time, associations between Sigmodon hispidus and numerous AMF and EMF species. Overall, our study highlights the role of rodents as important dispersal vectors of mycorrhizal fungi, particularly for EMF that could be essential to build up mycorrhizal fungi spore banks in disturbed forests.}, }
@article {pmid40337478, year = {2025}, author = {Abele, S and Alanis-Lobato, G and Oti, M and Rust, W and Blazevic, D and Danner-Liskus, J and Mayer, C and Zimmermann, G and Zuckschwerdt, K and Schönberger, T and Gross, P and Lempp, C and Michelfelder, S and Strobel, B}, title = {Mapping administration route-dependent transduction profiles of commonly used AAV variants in mice by barcode amplicon sequencing.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {33}, number = {2}, pages = {101468}, pmid = {40337478}, issn = {2329-0501}, abstract = {The tissue transduction profiles and transgene expression efficiencies of adeno-associated viruses (AAVs) depend not only on the utilized capsid and dose but also on the administration route. Yet, despite the plethora of available natural and capsid-engineered variants, a comprehensive evaluation of the administration route dependency of AAV tropism has been lacking so far. Therefore, we here compared transduction and transgene expression profiles for 34 well-known AAV capsids following intravenous (i.v.) and intraperitoneal (i.p.) injection in male C57BL/6 mice by multiplexed biodistribution analyses based on AAV genome-barcoding. Readout on viral genome and transcript level confirmed pronounced liver targeting by most AAV variants after i.v. administration, as well as known tissue tropism for benchmark capsids (e.g., AAV-PHP.eB: brain and AAV2-ESGHGYF: lung). In contrast, i.p. administration generally decreased liver targeting, while concurrently increasing expression in other abdominal organs in a capsid-specific fashion. For example, AAV6.2 and AAV-DJ, which showed almost exclusive liver transduction after i.v. administration, displayed differential biodistribution profiles with enhanced expression in the diaphragm, adipose tissue, and pancreas when administered intraperitoneally. In summary, our data guide study design by enabling the selection of optimal vector and administration route combinations for refined tissue targeting approaches in preclinical in vivo experiments.}, }
@article {pmid40336863, year = {2025}, author = {Zhang, H and Hoang, QD and Lei, S}, title = {Description of two new huntsman spiders from Vietnam (Araneae, Sparassidae).}, journal = {ZooKeys}, volume = {1236}, number = {}, pages = {129-140}, pmid = {40336863}, issn = {1313-2989}, abstract = {Two new species of the sparassid genera Heteropoda Latreille, 1804 and Pseudopoda Jäger, 2000 are described from Vietnam: Heteropodataygiangensis sp. nov. (♂) from Quang Nam Province and Pseudopodatadungensis sp. nov. (♀) from Dak Nong Province. The new Pseudopoda species is described and diagnosed based on both morphological characteristics and DNA barcoding. DNA barcode data (COI) are provided for both new species.}, }
@article {pmid40334225, year = {2025}, author = {Ngai, HL and Cheng, SW and Tse, TS and Lee, HK and Shaw, PC}, title = {Quality assessment of medicinal material Daqingye and Banlangen from Isatis tinctoria Fort. reveals widespread substitution with Strobilanthes species.}, journal = {PloS one}, volume = {20}, number = {5}, pages = {e0323084}, pmid = {40334225}, issn = {1932-6203}, mesh = {*Isatis/chemistry/genetics ; Chromatography, High Pressure Liquid ; *Drugs, Chinese Herbal/chemistry/standards ; *Plants, Medicinal/chemistry/genetics ; Drug Contamination ; DNA Barcoding, Taxonomic ; Plant Leaves/chemistry ; Plant Roots/chemistry ; Hong Kong ; Quality Control ; }, abstract = {BACKGROUND: Isatidis Folium (Daqingye, DQY) and Isatidis Radix (Banlangen, BLG) are the leaf and root of the plant Isatis tinctoria Fort. (syn. Isatis indigotica Fort.), commonly prescribed for detoxification, and the inhibition of viral and oxidative activities. Given their widespread use, we set forth to investigate the authenticity and chemical composition of DQY and BLG samples obtained from eighteen administrative districts in the Hong Kong market.<br><br>METHODS: The present study screened the identities and chemical composition of DQY and BLG through molecular authentication and HPLC methods, respectively. Molecular authentication utilized DNA barcoding, focusing on nuclear ribosomal and chloroplast regions. The HPLC methods were conducted in accordance with the Hong Kong Chinese Materia Medica Standards (HKCMMS).<br><br>RESULTS: We found that only one sample was genuine according to the species definition in the Chinese Pharmacopoeia and HKCMMS for both herbs. The chemical composition of the adulterated and the genuine samples were completely different, that the adulterant samples did not have the standard chemical markers epigoitrin and indirubin of Banlangen and Daqingye as listed in the Chinese Pharmacopoeia.<br><br>CONCLUSION: Our investigation underscores the widespread substitution by Strobilanthes (Nanbanlangen and Nandaqingye) species, mainly due to the preference of use of this herb in southern China. The adulteration of Daqingye by Blumea balsamifera (Ainaxiang) was probably due to mislabeling in the herb shop, though the error might have originated from the supplying sources. We recommend providing education on the necessity of using authentic Daqingye and Banlangen, especially in combined regimens, to standardize treatment effects. More education is also needed on the morphological differentiation of Banlangen from Nanbanlangen and Daqingye from Nandaqingye. The implementation of a track-and-trace system is strongly recommended to prevent and deter incorrect supply chain practices that lead to substitution or adulteration.}, }
@article {pmid40332883, year = {2025}, author = {Yao, Y and Chen, JY and Gong, XL and Li, CH and Liu, Z and Lin, XL}, title = {Species Delimitation and Cryptic Diversity in Rheotanytarsus Thienemann &amp; Bause, 1913 (Diptera: Chironomidae) Based on DNA Barcoding.}, journal = {Insects}, volume = {16}, number = {4}, pages = {}, pmid = {40332883}, issn = {2075-4450}, support = {A2-2006-23-200303//Shanghai Ocean University/ ; 31900344//National Natural Science Foundation of China/ ; }, abstract = {The genus Rheotanytarsus Thienemann &amp; Bause, 1913 (Diptera: Chironomidae) currently includes more than 120 recognized species worldwide, but precise species-level identification based solely on morphology remains challenging. Pronounced morphological differences among life stages and the time-consuming inefficiency of rearing larvae further complicate life-stage matching in this genus. In this study, we assessed species diversity by integrating morphological examination and DNA barcoding, analyzing 911 DNA barcodes from newly collected samples and a public database. Based on these results, we further constructed a relatively complete life-history framework. Our results show that 911 Rheotanytarsus DNA barcodes belong to 69 putative species. The maximum intraspecific divergence reached 7.35% in R. pentapoda, and the average minimal interspecific distance was 11.44%. Substantial intraspecific divergence in certain species complexes suggests the presence of cryptic species. Therefore, to resolve these potential cryptic species issues, more extensive sampling and morphological examination of specimens from geographically distant regions-supplemented by nuclear and ecological data-are required.}, }
@article {pmid40332868, year = {2025}, author = {Adnan, A and Mona, S and Rakha, A and Nazir, S and Wang, H and Ren, F}, title = {Molecular Diversity of Three Forensically Relevant Dipterans from Cadavers in Lahore, Pakistan.}, journal = {Insects}, volume = {16}, number = {4}, pages = {}, pmid = {40332868}, issn = {2075-4450}, support = {(2024021179-JH2/1019)//Department of Science and Technology of Liaoning province PR China/ ; }, abstract = {Molecular diversity, which reflects variation in species abundance and genetic structure, plays a pivotal role in forensic entomology by enabling the accurate identification of insect evidence through tools such as DNA barcoding. In Pakistan, the absence of trained forensic entomologists and limited research on insect biodiversity hinder the effective use of entomological evidence in criminal investigations. Traditional morphological identification methods are insufficient for resolving complex forensic cases, particularly when dealing with immature insect stages. This highlights the urgent need for molecular approaches, such as DNA barcoding, to enhance species identification and genetic analysis of forensically relevant insects. This study uniquely focuses on evaluating the utility of a 658 bp fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene for identifying dipteran species collected from cadavers in Lahore, Pakistan. The primary goal was to identify forensically relevant insect species, assess their genetic diversity and population structure, and compare these findings with global data to contextualize the results within forensic entomology. Three blow fly species were identified: Chrysomya megacephala (Fabricius, 1794), Chrysomya saffranea (Bigot, 1877), and Chrysomya rufifacies (Macquart, 1843). Low genetic diversity was observed within populations, while significant genetic differentiation among populations was indicated by a high fixation index (FST = 0.83992). These findings suggest unique genetic signatures for blow fly populations in Lahore. This study underscores the importance of molecular tools like DNA barcoding for species identification and highlights the need for further research to establish a comprehensive database of forensically relevant insects in Pakistan, given the limited species diversity and unique genetic profiles observed. By laying the groundwork for future research, this study contributes to advancing forensic entomology in Pakistan by improving species identification, which, when combined with future thermobiological data, can enhance postmortem interval (PMI) estimation and forensic investigations.}, }
@article {pmid40332859, year = {2025}, author = {Lesieur, V and Thomann, T and Jourdan, M and Kashefi, J and Bon, MC}, title = {Fly in the Ointment: Host-Specificity Challenges for Botanophila turcica, a Candidate Agent for the Biological Control of Saffron Thistle in Australia.}, journal = {Insects}, volume = {16}, number = {4}, pages = {}, pmid = {40332859}, issn = {2075-4450}, support = {PRJ--010527//AgriFutures Australia/ ; }, abstract = {In classical biological control of weeds, the risk posed by a candidate agent to close relatives of the target weed in the intended area of release is a key criterion (i.e., candidate agents that demonstrate a high degree of host specificity). In this study, we investigated if the rosette crown-feeding fly Botanophila turcica Hennig (Diptera: Anthomyiidae) could meet this criterion and thus be considered a good candidate to control saffron thistle Carthamus lanatus L. (Asteraceae: Cardueae) in Australia. Previous studies indicated that B. turcica is specific to Ca. lanatus and did not infest the closely related crop, safflower (Carthamus tinctorius L.). However, more recent field observations made in Greece reported that B. turcica infested safflower in cultivated fields. To determine if B. turcica is safe for release as a biocontrol agent, we re-examined the host range of B. turcica by performing new host-specificity testing combined with field surveys carried out in the south of France during two consecutive years. We also investigated the species identity of the flies by comparing DNA sequences (COI barcode region) of specimens collected in France from Ca. lanatus and Centaurea solstitialis L. with those from Greece collected from Ce. solstitialis and Centaurea diffusa Lam. Our COI analyses confirmed that French and Greek samples identified as B. turcica belonged to the same species, while a second group of Greek samples matched B. brunneilinea, indicating two distinct species. Our results also demonstrated that B. turcica has a wider host range than previously suggested. Laboratory testing indicated that Ca. lanatus, Ca. tinctorius, and Ce. solstitialis are suitable for the development of B. turcica. Field surveys also revealed that Ce. diffusa is part of the host range of the fly. Based on the results reported here, B. turcica may have the potential to control both the target weed, Ca. lanatus, and Ce. Solstitialis, but it may also be a threat to safflower, Ca. tinctorius. Further investigations to assess under what conditions B. turcica attacks Ca. tinctorius may help clarify the level of risk to Australian growers.}, }
@article {pmid40332619, year = {2025}, author = {Rai, M and Dhanker, R and Sharma, N and Kamakshi,  and Kamble, SS and Tiwari, A and Du, ZY and Mohamed, HI}, title = {Responses of natural plastisphere community and zooplankton to microplastic pollution: a review on novel remediation strategies.}, journal = {Archives of microbiology}, volume = {207}, number = {6}, pages = {136}, pmid = {40332619}, issn = {1432-072X}, mesh = {*Microplastics/metabolism/toxicity/analysis ; Animals ; *Zooplankton/drug effects/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; Ecosystem ; *Environmental Restoration and Remediation/methods ; Microbiota ; Biodegradation, Environmental ; }, abstract = {The ubiquitous presence of microplastics (MP) in different environments has been well documented. Microplastic contamination has rapidly become a serious environmental issue, threatening marine ecosystems and human health. MP has been reported to accumulate organic pollutants associated with various microbial communities. The MP hazard is specifically serious in urban lakes, near-shore beaches, and benthic sediments. To prevent the further spread of MP and mitigate the increasing level of MP contamination, along with its associated environmental and economic concerns, it is essential to address mitigation strategies and their negative impacts. Contributed by low degradability, hydrophobicity, and sorption potential, the plastic surface acts as an important substrate colonized by several microorganisms known as the plastisphere community. Adaptive responses of the plastisphere community, MP ingestion, and surface modifications by the zooplankton provide insight into novel remediation strategies based on integrated natural community-level approaches. Zooplankton studies are extensive and encompass assessments of their abundance, biomass, distribution, and DNA meta-barcoding. Additionally, zooplankton has been utilized as an indicator in various freshwater environmental policies. Overall, employing zooplankton as an indicator in environmental policies is a vital tool for assessing the health of aquatic ecosystems and can assist in guiding management and conservation efforts. This review summarizes (i) the current literature on the estimation of MP distribution in aquatic environments, (ii) the effects of MP accumulation on the environment and its inhabitants, i.e., the interactions with marine microbiota,, (iii) addresses the bioremediation strategies with an emphasis on microbial degradation, ecological functioning and adaptive responses of marine microbes and finally, (iv) the directions of further research aiming to in situ mitigation of MP pollution. Recent advancements have focused on innovative methods such as membrane bioreactors, synthetic biology, organosilane-based techniques, biofilm-mediated remediation, and nanomaterial-enabled strategies. Nano-enabled technologies show substantial potential to enhance microplastic removal efficiency. Further investigation is necessary to develop advanced treatment technologies that can enhance the removal efficiency of microplastics (MPs) in drinking water. Additionally, more research is needed to understand the toxic impacts of MPs on marine ecosystems, including coral reefs, seagrass beds, mangroves, and other important habitats.}, }
@article {pmid40331605, year = {2025}, author = {Bu, AX and Wu, GY and Hu, LH}, title = {[Progress and prospect of separation and analysis of single-cell and single-particle exosomes].}, journal = {Se pu = Chinese journal of chromatography}, volume = {43}, number = {5}, pages = {399-412}, pmid = {40331605}, issn = {1872-2059}, mesh = {*Exosomes/chemistry ; *Single-Cell Analysis/methods ; Humans ; Animals ; }, abstract = {Exosomes are nanoscale vesicles secreted by cells and are encapsulated in lipid bilayers. They play crucial roles in cell communication and are involved in a variety of physiological and pathological processes, including immune regulation, angiogenesis, and tumor initiation and metastasis. Exosomes carry a variety of biomolecules from maternal cells and are therefore important vehicles for discovering disease markers. Traditional detection methods only provide average cell-population information for a given sample and cannot establish clear relationships between the biological functions of exosomes and subtype owing to the significant heterogeneity associated with exosomes from different cell subsets. Therefore, characterizing exosomes at the single-cell and single-particle levels requires exosome specificities to be further explored and the characteristics of various exosome subtypes to be distinguished. Commonly used single-particle exosome characterization technologies include flow cytometry, super-resolution microscopy, atomic force microscopy, surface-enhanced Raman spectroscopy, proximity barcoding assay and MS. In this paper, we summarize recent advances in the separation and characterization of single-cell exosomes based on microfluidics and provide future applications prospects for emerging technologies (such as Olink proteomics, click chemistry, and molecular imprinting) for studying single-cell and single-particle exosomes.}, }
@article {pmid40330878, year = {2025}, author = {Baglamis, S and Sheraton, VM and van Neerven, SM and Logiantara, A and Nijman, LE and Hageman, LA and Léveillé, N and Elbers, CC and Bijlsma, MF and Vermeulen, L and Krawczyk, PM and Lenos, KJ}, title = {Clonal dispersal is associated with tumor heterogeneity and poor prognosis in colorectal cancer.}, journal = {iScience}, volume = {28}, number = {5}, pages = {112403}, pmid = {40330878}, issn = {2589-0042}, abstract = {Clonal dispersal, resulting from the intermingling of tumor cell subpopulations, is thought to be a key driver of tumor heterogeneity. Despite advances in spatial modeling of cancer biology, quantification of clonal dispersal has been challenging. This study introduces a straightforward method, relying on fluorescent cell barcoding, to quantify clonal dispersal in various in vitro and in vivo models of colorectal cancer (CRC). Our approach allows for precise localization of clones and uncovering the degree of clonal mixing across different CRC models. Our findings suggest that clonal dispersal is correlated with the expression of genes involved in epithelial-mesenchymal transition and CMS4-related signaling pathways. We further identify a dispersal gene signature, associated with intratumor heterogeneity, which is a robust clinical predictor of poor prognosis and recurrence in CRC, highlighting its potential as a prognostic marker and a putative direction for therapeutic targeting.}, }
@article {pmid40330101, year = {2025}, author = {Nolan, JM and Skujina, I and Hurpy, G and Tighe, AJ and Whelan, C and Teeling, EC}, title = {Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation.}, journal = {Ecology and evolution}, volume = {15}, number = {5}, pages = {e71333}, pmid = {40330101}, issn = {2045-7758}, abstract = {Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial COI mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (Plecotus auritus) roosts. We showed that MinION data provided a similar taxonomic assignment to NovaSeq but only if the reference species barcode database was accurate and comprehensive. The P. auritus diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. This pipeline can be used to guide future metabarcoding studies using nanopore sequencing to minimise the cost and effort while optimising results.}, }
@article {pmid40329956, year = {2024}, author = {Frank, LE and Lindsey, LL and Kipp, EJ and Faulk, C and Stone, S and Roerick, TM and Moore, SA and Wolf, TM and Larsen, PA}, title = {Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling.}, journal = {Journal of mammalogy}, volume = {105}, number = {5}, pages = {965-975}, pmid = {40329956}, issn = {0022-2372}, abstract = {Accurate taxonomic species identification is essential to the study of mammals. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for noninvasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a polymerase chain reaction (PCR)-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from 9 mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS barcoding of noninvasive samples. By mapping to the entire National Center for Biotechnology Information mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all fecal samples. Eight of 9 species identifications matched previous PCR or animal/fecal appearance-based identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications-particularly in field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts cause changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies.}, }
@article {pmid40328385, year = {2025}, author = {Ahmad, H and Rahman, S and Ali, M}, title = {Molecular identification and genetic diversity of Pteropus giganteus and Pipistrellus javanicus from Pakistan: A non-invasive approach.}, journal = {Gene}, volume = {960}, number = {}, pages = {149540}, doi = {10.1016/j.gene.2025.149540}, pmid = {40328385}, issn = {1879-0038}, mesh = {Animals ; *Chiroptera/genetics/classification ; Pakistan ; *Genetic Variation ; Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Haplotypes ; Cytochromes b/genetics ; }, abstract = {The scarcity of genetic data hinders bat species identification in Pakistan. Despite more than 1480 bat species worldwide, morphology-based identification remains challenging due to the similarity in physical characteristics and the lack of distinct morphological features among many species. This study addresses this gap by employing DNA barcoding (cytochrome b) to identify bat species non-invasively from fecal samples, collected samples without harming the bats, across various regions of Pakistan and identified two bat species, Pteropus giganteus and Pipistrellus javanicus. Phylogenetic analysis of Pipistrellus javanicus sequences clustered with a sequence previously reported sequences from India and China while Pteropus giganteus was made and clustered with previously reported sequences from Bangladesh indicating possible gene flow. We investigated haplotype diversity and nucleotide diversity that revealed P. giganteus displayed moderate genetic diversity (h = 0.714, π = 0.003 respectively) and P. javanicus showed high genetic diversity (h = 1.000, π = 0.020). Pairwise genetic distances (K2P and matrix analysis) revealed varying levels of differentiation among populations within each species, while the negative value in neutrality tests suggested potential/sudden population expansion for both species. The current study offers important insights into the genetic landscape and population dynamics of bat species in Pakistan. Future studies should incorporate additional genetic markers, morphological examinations, and ecological data to definitively characterize these potential new species and contribute to a more comprehensive understanding of Pakistan's bat fauna.}, }
@article {pmid40326708, year = {2025}, author = {Lu, X and Pritko, DJ and Abravanel, ME and Huggins, JR and Ogunleye, O and Biswas, T and Ashy, KC and Woods, SK and Livingston, MWT and Blenner, MA and Birtwistle, MR}, title = {Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.}, journal = {ACS synthetic biology}, volume = {14}, number = {5}, pages = {1533-1548}, pmid = {40326708}, issn = {2161-5063}, support = {R35 GM133803/GM/NIGMS NIH HHS/United States ; R35 GM141891/GM/NIGMS NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; *Flow Cytometry/methods ; Humans ; *Luminescent Proteins/genetics/metabolism ; Gene Library ; Fluorescence ; Animals ; HEK293 Cells ; DNA Barcoding, Taxonomic/methods ; Green Fluorescent Proteins/genetics/metabolism ; }, abstract = {Genetically encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), nondestructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are nondestructive, fast, and inexpensive to readout but lack high diversity. We recently proposed a theory for how fluorescent protein combinations may generate a high-diversity barcode library with nondestructive, fast, and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ∼150 barcodes from two-way combinations of 18 fluorescent proteins, 61 of which are tested experimentally. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ∼10[5] and more) generated from hundreds of spectrally resolvable tandem fluorescent protein probes.}, }
@article {pmid40322669, year = {2025}, author = {Prasetiya, FS and Jauffrais, T and Mohamed-Benkada, M and Callac, N and Ansquer, D and Yılmaz, E and Lemieux, C and Turmel, M and Mouget, JL and Prabowo, DA and Purbani, DC and Noerdjito, DR and Fahmi, V and Arsad, S and Gastineau, R}, title = {Diving into Diversity: Hasleaberepwari (Bacillariophyceae, Naviculaceae), a new species of marine diatom from New Caledonia.}, journal = {PhytoKeys}, volume = {255}, number = {}, pages = {215-234}, pmid = {40322669}, issn = {1314-2011}, abstract = {The current article introduces and describes Hasleaberepwari sp. nov., a new species of diatom discovered in the vicinity of Boulouparis, New Caledonia. Under light microscopy, H.berepwari sp. nov. strongly resembles Hasleapseudostrearia, but preliminary molecular barcoding conducted using partial 18S and rbcL genes suggested that it was a distinct species. This was confirmed first by scanning electron microscopy which showed the differences in stria densities between both species. A short-reads genome-skimming protocol applied on H.berepwari sp. nov. led us to obtain its complete mitochondrial and plastid genomes. The mitogenome is 36,572 bp in length and as already observed among other species of Haslea spp., the nad6 and nad2 genes are fused within a single open-reading frame. The plastome is 131,897 bp length, and unlike the mitogenome, it is not colinear with those of H.pseudostrearia. The results derived from the sequencing of the plastome allowed to perform a 123-gene multigene maximum likelihood phylogeny that associates H.berepwari sp. nov. to H.pseudostrearia with maximum support at the nodes but also strictly distinguishes them, suggesting a greater genetic distance between these species than what has been previously observed between other marennine-producing species.}, }
@article {pmid40322611, year = {2025}, author = {Javaheri Tehrani, S and Rezazadeh, E and Alaei Kakhki, N and Nourani, L and Ebadi, V and Karimi, S and Karami, M and Ashouri, F and Sarshar, A and Gossmann, TI and Aliabadian, M}, title = {DNA barcoding of passerine birds in Iran.}, journal = {ZooKeys}, volume = {1236}, number = {}, pages = {19-39}, pmid = {40322611}, issn = {1313-2989}, abstract = {Exploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful complementary method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 546 COI sequences from 94 species across 23 families and 53 genera. There is a pronounced barcode gap, with average intraspecific divergence at 0.41% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sittatephronota) and the Lesser whitethroat (Currucacurruca), while the European goldfinch (Cardueliscarduelis) and the grey-crowned goldfinch (Cardueliscaniceps) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits in C.curruca and S.tephronota, reflecting Iran's geographic and zoogeographic boundaries. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing Iran's key role as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in the COI gene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.}, }
@article {pmid40321907, year = {2025}, author = {Liang, RN and Lin, XH and An, MM and Zhao, GZ}, title = {Two new species of Penicillium (Eurotiales, Aspergillaceae) from China based on morphological and molecular analyses.}, journal = {MycoKeys}, volume = {116}, number = {}, pages = {255-274}, pmid = {40321907}, issn = {1314-4049}, abstract = {Penicillium is a large and significant genus of fungi, exhibiting widespread distribution across diverse substrates. Ongoing taxonomic and nomenclatural revisions have led to an annual increase in the number of newly described species. This study described two new Penicillium species, i.e., P.lentum and P.tibetense, discovered in China. They have been identified and characterized through morphological examination and both single gene and multigene phylogenetic analyses. Based on these analyses, P.lentum was classified within the section Brevicompacta, while P.tibetense was placed in the section Lanata-Divaricata. Both species exhibited the morphological features typical of their respective sections. Penicilliumlentum is characterized by restricted growth with dense colonies on agar media and predominantly generates terverticillate conidiophores. Penicilliumtibetense demonstrates rapid growth on media and has vigorous growth on CYA at 30 °C, producing biverticillate conidiophores. Comprehensive descriptions and detailed illustrations of these new species were presented. A morphological comparison between the new species and their closely related taxa was provided.}, }
@article {pmid40319451, year = {2025}, author = {Baeza, JA and Umaña-Castro, R and Behringer, DC and Castillo, A}, title = {A cryptic species of the nemertean egg predator Carcinonemertes conanobrieni (Simpson et al., 2017) detected using a barcoding approach infects the Caribbean spiny lobster Panulirus argus (Latreille, 1804) in the southwestern Caribbean Sea.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {}, number = {}, pages = {1-6}, doi = {10.1080/24701394.2025.2499461}, pmid = {40319451}, issn = {2470-1408}, abstract = {A recently discovered nemertean egg predator, Carcinonemertes conanobrieni, inhabiting Panulirus argus egg masses poses a potential threat to this ecologically and commercially relevant lobster. This study assessed the prevalence of C. conanobrieni in the southwestern Caribbean Sea; Costa Rica and Panama. Brooding females of P. argus were collected by fishermen near Punta Uva beach, Costa Rica (n = 17), and Guna Yala, Panama (n = 19) and examined for the presence of C. conanobrieni. Prevalence of C. conanobrieni in brooding lobsters, determined as the presence/absence of adults, juveniles, encysted juvenile worms, or carcinonemertid egg masses was 47.06% and 31.58% in Costa Rica and Panama, respectively. Moreover, when indirect evidence (empty capsules and/or dead embryos presumably attacked/consumed by worms) of the presence of C. conanobrieni in brooding lobsters is considered in addition to direct evidence, prevalence of C. conanobrieni in brooding lobsters was 64.71% and 47.37% in Costa Rica and Panama, respectively. The observations suggest that this parasitic worm completes its life cycle locally in the southwestern Caribbean. Notably, a Maximum Likelihood phylogenetic analysis based on a fragment of the mitochondrial cox1 gene clustered two specimens collected in Costa Rica together with four other specimens previously collected in Saint Kitts into a single fully supported monophyletic clade that segregated from a second clade containing six specimens of C. conanobrieni collected in Colombia, Florida, and Saint Kitts. The barcoding analysis suggests that there is an undescribed species of Carcinonemertes, anatomically like C. conanobrieni, infecting P. argus in Costa Rica.}, }
@article {pmid40318160, year = {2025}, author = {Williams, DM}, title = {What is Fragilaria koensabbei and does it matter what it is called? (Meta)barcoding and the science of taxonomy.}, journal = {Journal of phycology}, volume = {61}, number = {3}, pages = {433-439}, pmid = {40318160}, issn = {1529-8817}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Diatoms/classification/genetics ; *Classification/methods ; }, abstract = {Commentary is provided on the use of barcoding and metabarcoding in diatom studies and its broader relevance to the principles of taxonomy. The claims that taxonomy, however it is performed, is time-consuming and that it requires extensive expertise, due to a constantly evolving taxonomy, are questioned as good, even useful, criteria by which to judge a science.}, }
@article {pmid40317890, year = {2025}, author = {Ang, YS and Low, DKX and Yung, LL}, title = {DNA-Programmed Reaction to Evaluate Specific IgE for Allergy Point-of-Care Testing.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {21}, number = {30}, pages = {e2500575}, doi = {10.1002/smll.202500575}, pmid = {40317890}, issn = {1613-6829}, support = {A-0009534-01-00//Singapore Ministry of Education Academic Research Fund/ ; A-0000065-97-00//NUS Resilience and Growth Postdoctoral Fellowship/ ; }, mesh = {*Immunoglobulin E/immunology ; *Point-of-Care Testing ; *Hypersensitivity/diagnosis/immunology ; Humans ; *DNA/chemistry ; }, abstract = {A DNA-programmed reaction to evaluate non-nucleic acids inputs with computation speed (≈30 min) and sensitivity (sub-picomolar) suitable for analyzing physiologically relevant biomarkers in a one-pot format and point-of-care testing setting is reported. Specifically, a DNA programme based on the proximity-activation exponential amplification reaction (PEAR) is designed to evaluate specific IgE (sIgE) against Der p 2 implicated in dust mite allergy which affects millions worldwide. In this work, we tailored the molecular components of the input-to-oligo barcode conversion module as an AND gate to detect inputs with binding specificity to Der p 2 antigen and is of an IgE isotype. In addition, an in situ biotinylation method is developed to generate amplified oligo barcodes amendable for direct visualization on a lateral flow format. As a proof-of-concept demonstration of its potential clinical utility, 21 clinical samples are evaluated by the as-developed sIgE PEAR programme using the dual readout modality of real-time fluorescence measurement for precise input quantification and simple lateral flow yes/no answer.}, }
@article {pmid40316679, year = {2025}, author = {McFadden, CS and Erickson, KL and Lane, A and Nassongole, B and Aguilar, S and Dunakey, SK and Durkin, KM and Lalas, JAA and Kushida, Y and Macrina, L and Minor, NP and Morales-Paredes, M and Nelson, J and Peddada, A and Poole, S and Porto, R and Purow-Ruderman, R and Snyder, KE and Wismar, T and Samimi-Namin, K and Baria-Rodriguez, MV and Benzoni, F and Huang, D and Reimer, JD and Paulay, G and Quattrini, AM and Ekins, M and Benayahu, Y}, title = {Biodiversity and biogeography of zooxanthellate soft corals across the Indo-Pacific.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {15461}, pmid = {40316679}, issn = {2045-2322}, support = {DEB-1929319//National Science Foundation/ ; DEB-1856245//National Science Foundation/ ; Rasmussen Summer Research Fund//Harvey Mudd College/ ; Munzer Summer Research Fund//Harvey Mudd College/ ; Emily Mudd Summer Research Fund//Harvey Mudd College/ ; baseline funds//King Abdullah University of Science and Technology/ ; BSF-2019624//United States - Israel Binational Science Foundation/ ; }, mesh = {*Anthozoa/genetics/classification ; Animals ; *Biodiversity ; Coral Reefs ; Pacific Ocean ; Indian Ocean ; Phylogeography ; Phylogeny ; DNA Barcoding, Taxonomic ; Australia ; }, abstract = {Documentation of biodiversity and its geographical distribution is necessary to understand the processes and drivers of evolutionary diversification as well as to guide conservation and management initiatives. Among the most emblematic patterns of biodiversity in the world's oceans is the Coral Triangle (Indo-Australian Archipelago), widely recognized to be the center of species richness for a variety of marine life forms. The distribution of biodiversity remains incompletely documented, however, for a majority of reef-associated invertebrate taxa, including the zooxanthellate soft corals (Octocorallia) that dominate hard substrate on many Indo-Pacific reefs. We used a genetic approach to document the diversity of Indo-Pacific soft corals, sequencing two single-locus barcoding markers for > 4400 soft coral specimens and assigning individuals to molecular operational taxonomic units as proxies of species. We document two centers of species richness for zooxanthellate soft corals, one in the Indo-Australian Archipelago and a second, equally diverse center in the Western Indian Ocean. Centers of endemicity for soft corals are coincident with these centers of species richness, although the peripheral Red Sea and Hawaii also support high proportions of endemic taxa. The patterns documented here suggest that biogeographic distributions of soft coral families may be driven in part by larval dispersal potential: taxa with benthic larvae are absent from most oceanic islands of the central Pacific and are represented by higher proportions of endemic taxa in other geographic regions. Our findings demonstrate the distinct biogeographic patterns among reef taxa and underscore the need to document and analyze species distributions of more reef-associated invertebrate groups to derive a complete picture of reef biogeography.}, }
@article {pmid40314098, year = {2025}, author = {Wei, YH and Lin, F}, title = {Barcodes based on nucleic acid sequences: Applications and challenges (Review).}, journal = {Molecular medicine reports}, volume = {32}, number = {1}, pages = {}, pmid = {40314098}, issn = {1791-3004}, mesh = {Humans ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Nucleic Acids/genetics ; Neoplasms/genetics/pathology ; Cell Differentiation ; Stem Cells/metabolism/cytology ; }, abstract = {Cells are the fundamental structural and functional units of living organisms and the study of these entities has remained a central focus throughout the history of biological sciences. Traditional cell research techniques, including fluorescent protein tagging and microscopy, have provided preliminary insights into the lineage history and clonal relationships between progenitor and descendant cells. However, these techniques exhibit inherent limitations in tracking the full developmental trajectory of cells and elucidating their heterogeneity, including sensitivity, stability and barcode drift. In developmental biology, nucleic acid barcode technology has introduced an innovative approach to cell lineage tracing. By assigning unique barcodes to individual cells, researchers can accurately identify and trace the origin and differentiation pathways of cells at various developmental stages, thereby illuminating the dynamic processes underlying tissue development and organogenesis. In cancer research, nucleic acid barcoding has played a pivotal role in analyzing the clonal architecture of tumor cells, exploring their heterogeneity and resistance mechanisms and enhancing our understanding of cancer evolution and inter‑clonal interactions. Furthermore, nucleic acid barcodes play a crucial role in stem cell research, enabling the tracking of stem cells from diverse origins and their derived progeny. This has offered novel perspectives on the mechanisms of stem cell self‑renewal and differentiation. The present review presented a comprehensive examination of the principles, applications and challenges associated with nucleic acid barcode technology.}, }
@article {pmid40313148, year = {2025}, author = {Seo, CW and Yoo, S and Cho, Y and Kim, JS and Steinegger, M and Lim, YW}, title = {FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {4}, pages = {e2411017}, doi = {10.71150/jm.2411017}, pmid = {40313148}, issn = {1976-3794}, support = {//National Research Foundation of Korea/ ; 2023R1A2C1005130//Ministry of Science and ICT/ ; NIBR202304107//National Institute of Biological Resources/ ; NIBR202402106//National Institute of Biological Resources/ ; }, mesh = {*Phylogeny ; *Fungi/classification/genetics/isolation &amp; purification ; *Software ; Sequence Analysis, DNA ; DNA, Fungal/genetics ; Databases, Nucleic Acid ; }, abstract = {The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.}, }
@article {pmid40307692, year = {2025}, author = {Shen, Z and Feng, Y and Möller, M and Burgess, KS and Qin, H and Yang, J and Mo, Z and Li, H and Li, D and Gao, L}, title = {Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae).}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {570}, pmid = {40307692}, issn = {1471-2229}, support = {2024PVA0087//Chinese Academy of Sciences (CAS) President's International Fellowship Initiative/ ; 202101BC070003//Key Basic Research Program of Yunnan Province, China/ ; 31970363//National Natural Science Foundation of China/ ; }, mesh = {*DNA Barcoding, Taxonomic ; *Camellia/genetics/classification ; Phylogeny ; Genome, Chloroplast ; *Genome, Plant ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Species delimitation within Camellia sect. Thea is taxonomically challenging due to its complex evolutionary history. This study aims to utilize nuclear and chloroplast data as genomic DNA barcodes to delimit species within this economically important group of plants.<br><br>RESULTS: Whole genome sequencing (WGS) data were obtained for 98 accessions representing all but one species in C. sect. Thea. Based on 759 high-quality SCNs, 98 whole chloroplast genomes, and by using 2&#xd7; coverage clean reads from WGS for Skmer analyses, we found that combining the findings from these three data sets resulted in nearly complete species delimitation and resolution of all interspecific relationships within C. sect. Thea. We also found support for the taxonomic elevation of two varieties (C. sinensis var. assamica and C. tachangensis var. remotiserrata) to species status (C. assamica and C. remotiserrata, respectively). Furthermore, we confirmed that C. formosensis represents a distinct species. Gene tree discordances, chloroplast-nuclear conflicts and complex network-like phylogenetic relationships were observed in C. sect. Thea.<br><br>CONCLUSION: Compared with the use of single parentally inherited chloroplast data sources, utilizing both uniparentally inherited chloroplast data and biparentally inherited nuclear data improved the species delimitation of taxa within C. sect. Thea. The intricate phylogenetic relationships observed are likely a result of widespread past hybridization and chloroplast capture events among species within this group, which may have blurred the species boundaries. Our novel approach to species delimitation within C. sect. Thea may serve as a blueprint for employing genomic DNA barcodes in other taxa with complex histories, and will significantly contribute to the conservation of cultivated tea plant species and their wild relatives.}, }
@article {pmid40306561, year = {2025}, author = {Cai, FM and Jiang, S and Daly, P and Bakhshi, M and Cartwright, K and Druzhinina, IS}, title = {Guidelines toward ecologically-informed bioprospecting for microbial plastic degradation.}, journal = {Biotechnology advances}, volume = {82}, number = {}, pages = {108590}, doi = {10.1016/j.biotechadv.2025.108590}, pmid = {40306561}, issn = {1873-1899}, mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bioprospecting/methods ; *Bacteria/metabolism ; Ecosystem ; Humans ; Fungi ; }, abstract = {Biological degradation of plastics by microbial enzymes offers a sustainable alternative to traditional waste management methods that often pollute the environment. This review explores ecologically-informed bioprospecting for microorganisms possessing enzymes suitable for biological plastic waste treatment. Natural habitats enriched in plastic-like polymers, such as insect-derived polyesters, epicuticular microbial biofilms in the phyllosphere of plants in extreme environments, or aquatic ecosystems, are highlighted as promising reservoirs for bioprospecting. Anthropogenic habitats, including plastic-polluted soils and the plastisphere, have yielded potent enzymes such as PETases and cutinases, which are being exploited in biotechnology. However, bioprospecting in plastispheres and artificial environments frequently leads to the isolation of environmental opportunistic microorganisms, such as Pseudomonas aeruginosa, Aspergillus fumigatus, Parengyodontium album, or species of Fusarium, which are capable of becoming human and/or plant pathogens. These cases necessitate stringent biosecurity measures, including accurate molecular identification, ecological assessment, and containment protocols. Beyond advancing bioprospecting approaches toward a broader scope of relevant habitats, this review underscores the educational value of such screenings, specifically, in understudied natural habitats, emphasizing its potential to uncover novel enzymes and microorganisms and engage the next generation of researchers in interdisciplinary study integrating environmental microbiology, molecular biology, enzymology, polymer chemistry, and bioinformatics. Finally, we offer guidelines for microbial bioprospecting in various laboratory settings, ranging from standard environmental microbiology facilities to high-biosecurity facilities, thereby maximizing the diversity of scientists who may contribute to addressing urgent environmental challenges associated with plastic waste.}, }
@article {pmid40303148, year = {2024}, author = {Yap, PSX and Yeo, LF and Teh, CSJ and Dhanoa, A and Phipps, ME}, title = {Plasmid-Mediated Co-Occurrence of mcr-1.1 in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Isolated From the Indigenous Seminomadic Community in Malaysia.}, journal = {Transboundary and emerging diseases}, volume = {2024}, number = {}, pages = {9223696}, pmid = {40303148}, issn = {1865-1682}, mesh = {Malaysia/epidemiology ; *beta-Lactamases/genetics/metabolism ; *Escherichia coli/genetics/drug effects/enzymology/isolation &amp; purification ; *Plasmids/genetics ; Humans ; *Escherichia coli Infections/microbiology/epidemiology ; *Escherichia coli Proteins/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; }, abstract = {The growing prevalence of commensal antibiotic resistant Escherichia coli poses a significant concern for the global spread of antibiotic resistance. Stool samples (n = 35) from a seminomadic indigenous community in Malaysia, the Jehai, were screened for multidrug-resistant bacteria, specifically the extended-spectrum β-lactamase (ESBL) producers. Subsequently, whole-genome sequencing was used to provide genomic insights into eight ESBL-producing E. coli that colonised eight individuals. The ESBL E. coli isolates carry resistance genes from various antibiotic classes such as the β-lactams (bla TEM, bla CTX-M-15 and bla CTX-M-55), quinolones (gyrA, qnrS and qnrS1) and aminoglycosides (aph(3')-Ia, aph(6)-Id and aac(3)-IId). Three concerning convergence of ESBL, colistin and metal resistance determinants, with three plasmids from H-type lineage harbouring bla CTX-M and mcr-1.1 genes were identified. Using the Oxford Nanopore Technology (ONT) Native Barcoding Kit (SQK-NBD114.24) in conjunction with the R10.4.1 flow cell, which achieved an average read accuracy (Q > 10) of 99.84%, we further characterised the mcr-1.1-bearing plasmids, ranging in size from 25 to 28 kb, from three strains of E. coli. This report represents the first whole genome analysis of multidrug-resistant bacteria, specifically those resistant to colistin, found within the indigenous population in Malaysia. It strongly indicates that the pertinent issue of colistin resistance in the country is far more significant than previously estimated.}, }
@article {pmid40302921, year = {2025}, author = {Goraichuk, IV and Suarez, DL}, title = {Custom barcoded primers for influenza A nanopore sequencing: enhanced performance with reduced preparation time.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1545032}, pmid = {40302921}, issn = {2235-2988}, mesh = {*Nanopore Sequencing/methods ; *Influenza A virus/genetics/isolation &amp; purification ; Animals ; *DNA Primers/genetics ; Humans ; Influenza in Birds/virology ; Whole Genome Sequencing/methods ; Influenza, Human/virology ; *DNA Barcoding, Taxonomic/methods ; Genome, Viral ; Time Factors ; Polymorphism, Single Nucleotide ; }, abstract = {Highly pathogenic avian influenza is endemic and widespread in wild birds and is causing major outbreaks in poultry worldwide and in U.S. dairy cows, with several recent human cases, highlighting the need for reliable and rapid sequencing to track mutations that may facilitate viral replication in different hosts. SNP analysis is a useful molecular epidemiology tool to track outbreaks, but it requires accurate whole-genome sequencing (WGS) with sufficient read depth across all eight segments. In outbreak situations, where timely data is critical for controlling the spread of the virus, reducing sequencing preparation time while maintaining high-quality standards is particularly important. In this study, we optimized a custom barcoded primer strategy for influenza A whole-genome sequencing on the nanopore sequencing platform, combining the high performance of the Native Barcoding Kit with the prompt preparation time of the Rapid Barcoding Kit. Custom barcoded primers were designed to perform barcode attachment during RT-PCR amplification, eliminating the need for separate barcoding and clean-up steps, thus reducing library preparation time. We compared the performance of the custom barcoded primer method with the Native and Rapid barcoding kits in terms of read quality, read depth, and sequencing output. The results show that the custom barcoded primers provided performance comparable to the Native Barcoding Kit while reducing library preparation time by 2.3X compared to the Native kit and being only 15 minutes longer than the Rapid kit with better depth of sequencing. Additionally, the custom barcoded primer method was evaluated on a variety of clinical sample types. This approach offers a promising solution for influenza A sequencing, providing both high throughput and time efficiency, which significantly improves the time-to-result turnaround, making sequencing more accessible for real-time surveillance.}, }
@article {pmid40297676, year = {2025}, author = {Usmani, S and Gebhardt, ME and Simubali, L and Saili, K and Hamwata, W and Chilusu, H and Muleba, M and McMeniman, CJ and Martin, AC and Moss, WJ and Norris, DE and Ali, RLMN}, title = {Phylogenetic taxonomy of the Zambian Anopheles coustani group using a mitogenomics approach.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {40297676}, issn = {2693-5015}, support = {T32 AI138953/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Mosquito species belonging to the Anopheles coustani group have been implicated in driving residual malaria transmission in sub-Saharan Africa and are regarded as an established primary vector in Madagascar. The morphological identification of mosquitoes in this group is challenging due to cryptic features and their molecular confirmation is difficult due to a paucity of reference sequence data representing all members of the group. Conventional molecular barcoding with the cytochrome oxidase I (COI) gene and the internal transcribed spacer 2 (ITS2) region targets is limited in their discrimination and conclusive identification of members of species complexes. In contrast, complete mitochondrial genomes (mitogenomes) have demonstrated much improved power over barcodes to be useful in rectifying taxonomic discrepancies in Culicidae.<br><br>METHODS: We utilized a genome skimming approach via shallow shotgun sequencing on individual mosquito specimens to generate sequence reads for mitogenome assembly. Bayesian inferred phylogenies and molecular dating estimations were perfomed on the concatenated protein coding genes using the Bayesian Evolutionary Analysis by Sampling Trees 2 (BEAST 2) platform. Divergence estimates were calibrated on published calucations for Anopheles-Aedes.<br><br>RESULTS: This study generated 17 new complete mitogenomes which were comprable to reference An. coustani mitogenomes in the GenBank repository by having 13 protein coding, 22 transfer RNA and 2 ribosomal RNA genes, with an average length of 15,400 bp and AT content of 78.3%. Bayesian inference using the concatenated protein coding genes from the generated and publicly available mitogenomes yielded six clades: one for each of the four taxa targeted in this study, the GenBank references, and a currently unknown species. Divergence times estimated that the An. coustani group separated from the An. gambiae complex approximately 110 million years ago (MYA), and members within the complex diverged at times points ranging from~34 MYA to as recent as ~7 MYA.<br><br>CONCLUSIONS: These findings demonstrate the value of mitochondrial genomes in differentiating cryptic taxa and help to confirm morphological identities of An. coustani s.s., An. paludis, An. zeimanni and An. tenebrosus. Divergence estimates with the An. coustani group are similar to those for well-studied anopheline vector groups. These analyses also highlight the likely prescence of other cryptic An. coustani group members circulating in Zambia.}, }
@article {pmid40296507, year = {2025}, author = {Dong, X and Edwards, S and Deng, YM and Dapat, C and Hirankitti, A and Wordsworth, R and Whitney, P and Baird, R and Freeman, K and Daley, AJ and Barr, IG}, title = {An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing.}, journal = {Influenza and other respiratory viruses}, volume = {19}, number = {5}, pages = {e70106}, pmid = {40296507}, issn = {1750-2659}, support = {//Department of Health and Aged Care, Australian Government/ ; }, mesh = {Humans ; *Respiratory Syncytial Virus Infections/virology/diagnosis ; *Whole Genome Sequencing/methods ; *Respiratory Syncytial Virus, Human/genetics/isolation &amp; purification ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Nanopores ; Australia ; *Nanopore Sequencing/methods ; Multiplex Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Whole-genome sequencing (WGS) provides critical insights into the respiratory syncytial virus (RSV) transmission and any emerging mutations that could impair the efficacy of monoclonal antibodies or vaccines that have been recently licenced for clinical use worldwide. However, the ability to sequence RSV genomes at large scale is limited by expensive and time-consuming sequencing methods. Oxford Nanopore Technology (ONT) offers significant improvements in next generation sequencing (NGS) both in turnaround time and cost, compared with other platforms for viral WGS.<br><br>METHODS: We have developed and modified an RSV long amplicon-based WGS protocol for the ONT platform using a one-step multiplex RT-PCR assay and the rapid barcoding kit. One hundred thirty-five RSV positive Australian clinical specimens (91 RSV-A and 44 RSV-B) sampled in 2023 with cycle threshold (Ct) values between 14 to 35 were tested in this study. This ONT workflow was compared with other recent RSV WGS amplification assays based on short amplicons.<br><br>RESULTS: A PCR amplicon clean-up step prior to library preparation significantly improved WGS result for samples with poor amplicon generation, but it is not necessary or beneficial for ones that generated high concentrations of amplicons. Overall, a success rate of 85.9% was achieved for WGS. This method performed as well as the more complex short amplicon methods in terms of genome coverage and sequencing depth.<br><br>CONCLUSIONS: The workflow described here was highly successful in generating RSV WGS on ONT platform and had improved turnaround times and excellent results with RSV clinical samples with Ct values up to 30.}, }
@article {pmid40295995, year = {2025}, author = {Jiang, S and Ding, Y and Zhao, G and Ye, S and Liu, S and Yin, Y and Li, Z and Zou, X and Xie, D and You, C and Guo, X}, title = {Species-specific RNA barcoding technology for rapid and accurate identification of four types of influenza virus.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {409}, pmid = {40295995}, issn = {1471-2164}, support = {H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; H202191490139//Key Research &amp; Development Project of Nanhua Biomedical/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; }, mesh = {*RNA, Viral/genetics ; Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Orthomyxoviridae/genetics/classification ; Species Specificity ; Polymorphism, Single Nucleotide ; Humans ; }, abstract = {BACKGROUND: The influenza virus (IV) is responsible for seasonal flu epidemics. Constant mutation of the virus results in new strains and widespread reinfections across the globe, bringing great challenges to disease prevention and control. Research has demonstrated that barcoding technology efficiently and cost-effectively differentiates closely related species on a large scale. We screened and validated species-specific RNA barcode segments based on the genetic relationships of four types of IVs, facilitating their precise identification in high-throughput sequencing viral samples.<br><br>RESULTS: Through the analysis of single nucleotide polymorphism, population genetic characteristics, and phylogenetic relationships in the training set, 7 IVA type, 29 IVB type, 40 IVC type, and 5 IVD type barcode segments were selected. In the testing set, the nucleotide-level recall rate for all barcode segments reached 96.86%, the average nucleotide-level specificity was approximately 55.27%, the precision rate was 100%, and the false omission rate was 0%, demonstrating high accuracy, specificity, and generalization capabilities for species identification. Ultimately, all four types of IVs were visualized in a combination of one-dimensional and two-dimensional codes and stored in an online database named Influenza Virus Barcode Database (FluBarDB, http://virusbarcodedatabase.top/database/index.html).<br><br>CONCLUSION: This study validates the effective application of RNA barcoding technology in the detection of IVs and establishes criteria and procedures for selecting species-specific molecular markers. These advancements enhance the understanding of the genetic and epidemiological characteristics of IVs and enable rapid responses to viral genetic mutations.}, }
@article {pmid40293989, year = {2025}, author = {Hasan, M and Kambayashi, C and Anik, ZH and Islam, MS}, title = {Cryptic biodiversity of freshwater fish species in Bangladesh.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0318982}, pmid = {40293989}, issn = {1932-6203}, mesh = {Bangladesh ; *Biodiversity ; Animals ; Fresh Water ; Phylogeny ; *Fishes/genetics/classification ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; }, abstract = {Unrecognized cryptic species impede conservation planning and biodiversity assessments. DNA barcoding has tremendously expanded the number of novel and cryptic species in biological science. Despite few sporadic studies, the exact number of freshwater species found in Bangladesh is not known. To assess this biodiversity, we sequenced the COI gene of 124 freshwater specimens, which were gathered from various localities around Bangladesh. Seven cryptic species hidden among the currently studied specimens were identified based on the findings of phylogenetic and species delimitation analyses. The preliminary assessment also encompassed a restricted morphological examination of these cryptic taxa. The appearance of cryptic species, some of them possibly endemic, has been hypothesized. This raises concerns regarding the true diversity and evolutionary history of freshwater species in Bangladesh, which are significantly underrepresented in the current systematic frameworks that do not account for DNA data. Our current study provides baseline data that might aid local ichthyologists in their quest to identify additional new species by combining several variables (morphology and ecology). Further research is warranted to protect the priceless freshwater species in Bangladesh.}, }
@article {pmid40285927, year = {2025}, author = {Lee, YI and Zahn, FE and Xie, QY and Wu, SH and Gebauer, G}, title = {Diverse mycorrhizal associations and nutrition in Didymoplexis orchids.}, journal = {Mycorrhiza}, volume = {35}, number = {3}, pages = {34}, pmid = {40285927}, issn = {1432-1890}, support = {107-2923-B-178-001-MY3//Ministry of Science and Technology, Taiwan/ ; Deutsche Forschungsgemeinschaft GE 565/9-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Mycorrhizae/physiology/classification ; *Orchidaceae/microbiology ; Symbiosis ; Taiwan ; }, abstract = {Fully mycoheterotrophic (FMH) orchids rely entirely on mycorrhizal fungi for carbon and nutrients, with tropical Asian FMH orchids typically associating with saprotrophic fungi, though some known relationships also with ectomycorrhizal fungi, leaving much to learn about their fungal partners. Didymoplexis belongs to tribe Gastrodieae, which represents one of the largest fully mycoheterotrophic orchid lineages. Although mycorrhizal associations of its sister genus Gastrodia have been relatively well-studied, those of Didymoplexis remain largely unexplored. Here, we used molecular barcoding to analyze fungal associations and stable isotope analysis to elucidate the nutritional strategies of Didymoplexis micradenia, Didymoplexis pallens, and Didymoplexis siamensis in subtropical and tropical forests across Taiwan. In Didymoplexis pallens and Didymoplexis micradenia, most fungal partners were litter-decaying fungi (Mycena, Clitocybula, Marasmius, Gymnopus) with smaller contributions from ectomycorrhizal and rhizoctonia fungi. In Didymoplexis siamensis, ectomycorrhizal fungi dominated, particularly Sebacinales, however, with additional associations with wood-decaying Delicatula. The pattern of carbon and nitrogen isotope enrichments found for the three Didymoplexis species was in the typical range known for fully mycoheterotrophic orchids associated with litter- or wood-decaying fungi. [15]N enrichments of all investigated Didymoplexis species distinguished from fully mycoheterotrophic orchids associated with ectomycorrhizal fungi. Despite its ectomycorrhizal association, Didymoplexis siamensis was weakly enriched in [15]N and more enriched in [13]C than found for exclusively ectomycorrhizal fully mycoheterotrophic orchids. Thus, Didymoplexis siamensis covered its carbon and nitrogen demand obviously through the additional association with wood-decaying Delicatula. These findings enhance our understanding of the diverse fungal associations and physiological ecology of Didymoplexis species in subtropical and tropical ecosystems.}, }
@article {pmid40284697, year = {2025}, author = {Montalvo-Sabino, E and Villegas-Pingo, M and Zumaeta, J and Gonzales, L and Tapia-Limonchi, R and Moreno, M and González, CR and Chenet, SM}, title = {Molecular Identification of Anopheles (Diptera: Culicidae) Species in Native Communities of a Northeastern Region of Peru.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284697}, issn = {2076-2607}, support = {N&#xb0;: 050-2021-FONDECYT//PROCIENCIA/ ; }, abstract = {BACKGROUND: Malaria is a severe health problem in native communities of Condorcanqui in the Amazonas region of Peru. Recently, the number of malaria cases has increased considerably following a Plasmodium falciparum outbreak in 2019. However, there is no information on the anophelines acting as Plasmodium vectors in this area. This study aimed to identify Anopheles species circulating in previously unexplored native communities of Condorcanqui. Additionally, we sought to detect the presence of DNA from P. vivax and P. falciparum parasites in mosquitoes.<br><br>METHODS: During three exploratory visits between March and September 2022, 453 mosquitoes were collected using Shannon traps and CDC light traps. Only specimens morphologically identified as Anopheles sp. were subjected to molecular confirmation through PCR amplification and sequencing of the Cox1 barcode region. Plasmodium parasites were detected using nested PCR targeting of the 18S rRNA subunit, while human blood meal feeding was evaluated using a human &#x3b2;-globin marker.<br><br>RESULTS: A total of 66 specimens were molecularly confirmed as anopheline species: An. benarrochi B, An. triannulatus, An. Costai, and An. nimbus. Six specimens of An. benarrochi B were exclusively positive for Plasmodium parasites by PCR. Moreover, four specimens tested positive for Plasmodium and the presence of human blood, suggesting the anthropophilic behavior of An. benarrochi B and its possible role as a potential malaria vector in this area.<br><br>CONCLUSIONS: In conclusion, while this study provides valuable insights into the potential role of Anopheles benarrochi as a malaria vector in Amazonas, further research is essential to fully understand its behavior and transmission dynamics in the region.}, }
@article {pmid40283945, year = {2025}, author = {Yang, M and Yuan, Y and Wei, J and Pei, Y and Niu, Y and Zhao, Y and Kong, X and Zhang, Z}, title = {Comparison of the Blood-Brain Barrier Penetration Ability and Anti-Neuroinflammatory Activity of Chromones in Two Types of Agarwood.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {4}, pages = {}, pmid = {40283945}, issn = {1424-8247}, support = {CI2021A04009//the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; }, abstract = {Background/Objectives: Agarwood has a good neuroprotective effect and is often used to relieve anxiety and treat insomnia. This study compared the similarities and differences in the chromone components of two types of agarwood. It further investigated the absorption and brain distribution characteristics of these components in rats and their neuroprotective effects mediated through anti-neuroinflammatory pathways. Methods: This study confirmed, through ITS2 barcoding and chloroplast genome analysis, that both the ordinary and Qi-Nan agarwood are derived from Aquilaria sinensis. A comparative analysis of chromones in ethanol extracts derived from ordinary and Qi-Nan agarwood, as well as those capable of penetrating the blood-brain barrier in vivo, was conducted using UPLC-Q-TOF-MS. Subsequently, an in vitro neuroinflammatory model was established via lipopolysaccharide (LPS)-stimulated BV-2 cells to evaluate the anti-neuroinflammatory activity of differential chromones. Results: UPLC-Q-TOF-MS characterization revealed the chromone components in the two types of agarwood: A total of 81 chromone compounds were identified in the ethanol extracts of ordinary agarwood (OAE) (20 THPECs, 42 FTPECs, and 19 BI), while 41 were identified in the ethanol extracts of Qi-Nan agarwood (QNE) (11 THPECs and 30 FTPECs). Pharmacokinetic analysis in rats showed that 14 components from OAE (eight THPECs and six FTPECs) penetrated the rat serum, and 10 of these 14 components penetrated the blood-brain barrier (BBB). Twelve FTPECs from QNE penetrated the rat serum, all of which penetrated the BBB. The total peak area of the total ion current (TIC) was calculated for the samples, and the TIC of the serum was compared to that of the brain tissue from the same rat to roughly estimate the ratio. The results demonstrated that the capability of FTPECs to traverse the blood-brain barrier is substantially superior to that of THPECs. Correspondingly, only FTPECs were detected using DESI-MS imaging; no THPECs were detected in rat brain tissue, and DESI-MS imaging localized FTPECs to neuroanatomic regions (cerebral cortex, thalamus, and hippocampus). In vitro neuroinflammatory assays revealed the superior anti-inflammatory efficacy of QNE over OAE (IL-6/TNF-α suppression, p < 0.05), correlating with its FTPEC-rich composition. Conclusions: Structure-activity relationships identified FTPECs as potent inhibitors of pro-inflammatory cytokines, exhibiting enhanced BBB penetration (blood-brain relative abundance > 1). These findings establish FTPECs as prioritized candidates for CNS-targeted therapeutics, with QNE's pharmacological superiority attributed to its FTPEC dominance and optimized BBB transit capacity.}, }
@article {pmid40282357, year = {2025}, author = {Jung, J and Kim, HJ and Kim, JH}, title = {Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex.}, journal = {Genes}, volume = {16}, number = {4}, pages = {}, pmid = {40282357}, issn = {2073-4425}, support = {KNA1-1-13, 14-1//Korea National Arboretum/ ; }, mesh = {Phylogeny ; *Polygonatum/genetics/classification ; *Genome, Plastid/genetics ; Republic of Korea ; *Plastids/genetics ; }, abstract = {Background/Objectives:Polygonatum grandicaule Y.S.Kim, B.U.Oh &amp; C.G.Jang (Asparagaceae Juss.), a Korean endemic species, has been described based on its erect stem, tubular perianth shape, and pedicel length. However, its taxonomic status remains unclear due to limited molecular data. Methods: This study presents the complete plastid genomes (plastomes) of two P. grandicaule individuals and its close relative, P. odoratum (Mill.) Druce var. thunbergii (C.Morren &amp; Decne.) H.Hara. Results: The plastomes, ranging from 154,578 to 154,579 base pairs (bp), are identical to those of P. falcatum A.Gray, P. odoratum var. odoratum, and another Korean endemic species, P. infundiflorum Y.S.Kim, B.U.Oh &amp; C.G.Jang. All contain 78 plastid protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes, except for the pseudogene infA. Phylogenetic analyses using 78 plastid PCGs and whole intergenic spacer (IGS) regions strongly support the three sections within Polygonatum Mill. and show that P. odoratum and its variety are nested within P. falcatum, P. grandicaule, and P. infundiflorum. Conclusions: Given the limited genomic variation and phylogenetic relationships, we propose treating P. falcatum, P. grandicaule, and P. infundiflorum as part of the P. odoratum complex, despite their morphological differences. This study offers valuable putative molecular markers for species identification and supports the application of plastome-based super-barcoding in the morphologically diverse genus Polygonatum.}, }
@article {pmid40281442, year = {2025}, author = {Tseng, YH and Chien, HC and Zhu, GX}, title = {Comparative plastome analyses and phylogenetic insights of Elatostema.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {537}, pmid = {40281442}, issn = {1471-2229}, support = {MOST 111-2621-B-005-001-MY3//National Science and Technology Council, Taiwan/ ; }, mesh = {*Phylogeny ; *Genome, Plastid/genetics ; Evolution, Molecular ; *Plastids/genetics ; }, abstract = {BACKGROUND: Elatostema, one of the largest genera in Urticaceae, comprises approximately 570 species. The taxonomic delimitation of Elatostema and its closely related genera, Elatostematoides and Procris and the infrageneric classification of Elatostema, have historically been challenging. Previous studies have been limited by insufficient molecular data, hindering our understanding of species-level relationships and the evolution of plastid genomes in this group. To address these limitations, we assembled and analyzed a comprehensive plastome analysis of 42 species across Elatostema and its allied genera. Our study focused on plastome structure, sequence diversity, and phylogenetic relationships to elucidate the evolutionary history of these taxa.<br><br>RESULTS: Our findings reveal that Elatostema plastomes exhibit a typical quadripartite structure, with genome sizes ranging from 149,152&#xa0;bp to 164,019&#xa0;bp. Comparative analysis of plastome structures across Elatostema and its related genera indicates high conservation in genome size, structure, gene content, and inverted repeat boundary configuration. Our findings indicate a strong association between the length of small single-copy (SSC) regions and phylogenetic grouping within Elatostema and between Elatostema, Elatostematoides and Procris. The length variations in the ndhF-rpl32, rpl32-trnL, and rps15-SSC/IRa regions may account for this observed correlation, highlighting the utility of SSC sequences in resolving phylogenetic relationships within this genus. Furthermore, we identified seven highly variable regions with potential as DNA barcodes for species identification and phylogenetic analysis. Our phylogenomic analysis provides robust support for the taxonomic delimitation of Elatostema s.l. into three distinct genera: Elatostema, Procris, and Elatostematoides. We also reconfirm the infrageneric classification of Elatostema into four major clades.<br><br>CONCLUSIONS: The utilization of plastome sequences has enabled a highly resolved phylogenetic framework, shedding light on the evolutionary history and speciation mechanism within Elatostema, particularly its species-rich core Elatostema clade. These findings provide a valuable foundation for future taxonomic revisions and evolutionary studies within this challenging plant group.}, }
@article {pmid40281336, year = {2025}, author = {Xu, Z and Lyu, Y and Chen, H and Chen, Y and Wang, Y}, title = {Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {40281336}, issn = {1750-2799}, support = {32200073//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32250710678//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82200977//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Formalin-fixed paraffin-embedded (FFPE) samples represent a vast and valuable resource of patient material, often linked to extensive clinical history and follow-up data. However, achieving single-cell or single-nucleus RNA (sc/snRNA) profiling in these archived tissues remains challenging. To address this, we have developed snRandom-seq, a droplet- and random primer-based single-nucleus total RNA sequencing technology specifically designed for FFPE tissues. This method captures total RNAs by using random primers and demonstrates a low doublet rate (0.3%), increased RNA coverage and enhanced detection of non-coding and nascent RNAs compared to state-of-the-art high-throughput sc/snRNA-seq technologies. This protocol provides a comprehensive guide to isolating single nuclei from FFPE samples; performing in situ DNA blocking, reverse transcription and dA tailing reactions; barcoding single-nucleus droplets; and preparing sequencing libraries. The entire snRandom-seq process can be completed in 4 d. This platform serves as a powerful tool for snRNA-seq of clinical specimens, with broad applications in studying complex biological systems.}, }
@article {pmid40280882, year = {2025}, author = {Sudermann, MA and Foster, ZSL and Dawson, SCL and Phan, H and Fieland, VJ and Martin, FN and Chang, JH and Grünwald, NJ}, title = {Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {PHYTO02250043FI}, doi = {10.1094/PHYTO-02-25-0043-FI}, pmid = {40280882}, issn = {0031-949X}, abstract = {Metabarcoding is a widely used approach relying on short DNA sequences to identify organisms present in a community. Although established workflows exist for analysis of single metabarcodes, these are cumbersome when multiple metabarcodes are required to study diverse taxa, such as those in plant- and soil-associated microbial communities, or when analyzing newly developed metabarcodes. To address this, we developed demulticoder, an R package automating the use of DADA2 to analyze data derived from multiple metabarcodes. It has novel capabilities that streamline data analysis by reducing the number of manual input steps and enabling automated processing of multiplexed metabarcodes. Additionally, demulticoder modularizes data processing to allow for iterative quality control and reformats data for downstream analyses. We also updated the oomycete-specific rps10 barcode database by revising the taxonomic information of select entries based on updates to the classifications within the NCBI Taxonomy database. A multiplex sequenced dataset consisting of ITS1 and rps10 metabarcodes from 162 samples and 12 controls was analyzed to compare demulticoder against a standard analysis workflow. Demulticoder required manual input at only four steps in comparison with 28 steps required for the standard workflow. Data quality and results from downstream exploratory, diversity, and differential abundance analyses were comparable to those from the standard workflow. Demulticoder is versatile and can be used to analyze datasets consisting of single metabarcodes, multiplexed and pooled metabarcode types, and different metabarcode types generated in separate experiments. The demulticoder R package, example datasets, and instructions are publicly accessible and open source.}, }
@article {pmid40280670, year = {2025}, author = {Zamri, NAS and Baharudin, S and Harun, AAC and Ariffin, NA and Khong, HY and Wahab, W and Kamaludeen, J and Zakariah, MI and Tosin, OV and Manaf, SR}, title = {Parasite infestation in red hybrid Tilapia across Sarawak: Morphological, DNA barcoding and water quality assessment under different culture systems.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {60}, number = {}, pages = {101238}, doi = {10.1016/j.vprsr.2025.101238}, pmid = {40280670}, issn = {2405-9390}, mesh = {Animals ; *Fish Diseases/parasitology/epidemiology ; Aquaculture/methods ; DNA Barcoding, Taxonomic/veterinary ; *Tilapia/parasitology ; *Water Quality ; Prevalence ; *Ectoparasitic Infestations/veterinary/epidemiology/parasitology ; Phylogeny ; Trematoda/genetics ; *Parasitic Diseases, Animal/epidemiology/parasitology ; Cichlids ; }, abstract = {Red Hybrid Tilapia (RHT) is a vital species in aquaculture but remains highly vulnerable to parasitic infestations, which can compromise productivity and overall fish health. This study assessed the prevalence, intensity, and species identification of ecto- and endoparasites in RHT across different aquaculture systems in Sarawak from May to December 2022. A total of 120 RHT samples were analyzed using both morphological and molecular approaches. Results indicated a high prevalence of ectoparasites in ST1, ST2, and ST3 (100 %) compared to ST4 (96.67 %). Trichodina spp. was the most common ectoparasite (70.83 %), while molecular analysis identified Cichlidogyrus thurstonae. Endoparasites were detected only in ST1, with greater occurrence in the intestine (53 %) than in the stomach (40 %). Despite being morphologically identified as a Digenean Trematode, BLAST and phylogenetic analysis failed to provide a definitive match, suggesting a potentially novel species. Interestingly, water quality parameters did not vary significantly across sites, implying that parasite prevalence is more influenced by aquaculture system design, stocking density, and management practices rather than environmental factors alone. Poor biosecurity, high fish densities, and insufficient parasite control measures may contribute to high infestation rates. This study highlights the need for enhanced biosecurity protocols, regular parasite monitoring, and improved management strategies to mitigate parasitic infections. The findings provide valuable baseline data for sustainable RHT farming, emphasizing the importance of proactive health management to ensure long-term productivity and food security.}, }
@article {pmid40278563, year = {2025}, author = {Ingegneri, M and Smeriglio, E and Zebbiche, Y and Cornara, L and Visalli, L and Smeriglio, A and Trombetta, D}, title = {The Dark Side of "Smart Drugs": Cognitive Enhancement vs. Clinical Concerns.}, journal = {Toxics}, volume = {13}, number = {4}, pages = {}, pmid = {40278563}, issn = {2305-6304}, abstract = {The European Union Drugs Agency has emphasized the increasing difficulty in monitoring the drug market due to the emergence of new psychoactive substances, often marketed as legal highs. The proliferation of fake pharmacies, drugstores, and e-commerce platforms has made access to illicit substances alarmingly rapid and inexpensive. These substances are readily available without medical prescriptions, lacking proper risk assessments or monitoring of potential adverse effects, raising significant public health concerns. Today, the relentless pursuit of validation and success-often, at any cost-has led to an exponential rise in the use of cognitive and mood enhancers. Such substances are frequently consumed to manage demands related to work, diet, sexuality, sleep, achievement, and interpersonal relationships. Consequently, investigating these phenomena is critically important for institutions, as they represent a serious threat to individual development and health. Developing effective preventive and protective systems is essential. This review provides an overview of currently available smart drugs, discussing their desired and adverse neuropharmacological effects, psychological implications, and cognitive decline resulting from their excessive and unregulated use. This review concludes that a multidisciplinary approach combining molecular identification, micro-morphological analysis, and chemical characterization is crucial for the accurate detection, monitoring, and risk mitigation of new psychoactive substances.}, }
@article {pmid40278070, year = {2025}, author = {Baramidze, V and Sella, L and Japaridze, T and Dzotsenidze, N and Lamazoshvili, D and Abashidze, N and Basilidze, M and Tomashvili, G}, title = {A Barcoded ITS Primer-Based Nanopore Sequencing Protocol for Detection of Alternaria Species and Other Fungal Pathogens in Diverse Plant Hosts.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {40278070}, issn = {2309-608X}, support = {YS 18-1446//Shota Rustaveli National Science Foundation/ ; }, abstract = {Alternaria is a genus that contains several important plant pathogens affecting nearly 400 plant species worldwide, including economically important crops such as grapes, citrus, and ornamental plants. Rapid, scalable, and efficient methods of pathogen detection are crucial for managing plant diseases and ensuring agricultural productivity. Current amplicon sequencing protocols for Alternaria detection often require the enzymatic barcoding of amplicons, increasing hands-on time, cost, and contamination risk. We present a proof-of-concept study using custom barcoded primers, combining universal primers targeting ITS1 and ITS2 regions (600 bp) coupled with Oxford Nanopore Technologies (ONT) barcode sequences. Sequencing was performed on infected grapevine, mandarin orange, thuja, and maple tree samples. In total, we analyzed 38 samples using qPCR; 8 tested positive for Alternaria, which were sequenced using a newly developed protocol. As a result, we could identify Alternaria in every positive sample, and besides the pathogen of interest, we could identify the associated mycobiome. This protocol reduces hands-on time and cost, making a significant advancement over current sequencing methods. Future work will focus on optimizing our approach for high-throughput sequencing of up to 96 samples and determining the method's applicability for large-scale mycobiome analysis.}, }
@article {pmid40276957, year = {2025}, author = {Mavridis, K and Evangelou, V and Grigoriadou, AM and Papachristos, DP and Vontas, J}, title = {Molecular surveillance of resistance mutations in invasive populations of Spodoptera frugiperda in Europe, for evidence-based pest control.}, journal = {Pest management science}, volume = {81}, number = {8}, pages = {4821-4830}, pmid = {40276957}, issn = {1526-4998}, support = {InnoPP-TAEDR-0535675//European Union - National Recovery and Resilience Plan Greece 2.0- NextGenerationEU/ ; 101212676//European Union's Horizon Europe research and innovation program EUFAWREADY/ ; //Hellenic Ministry of Rural Development and Food/ ; }, mesh = {Animals ; *Insecticide Resistance/genetics ; *Spodoptera/genetics/drug effects/growth &amp; development ; Introduced Species ; *Mutation ; Greece ; *Insecticides/pharmacology ; Insect Control ; Insect Proteins/genetics/metabolism ; Bacillus thuringiensis ; Larva/growth &amp; development/genetics/drug effects ; }, abstract = {BACKGROUND: The invasive fall armyworm (Spodoptera frugiperda, FAW), a highly destructive pest affecting more than 350 plant species, has recently invaded Europe raising urgent management concerns. Insecticide resistance profiling is essential to support evidence-based pest control strategies. In this study, we analyzed target-site insecticide resistance mutations in FAW populations from Greece to inform pest control strategies. In addition, DNA barcoding through cytochrome oxidase subunit 1 (COI) gene sequencing was used to trace the pest's geographic origin and potential invasion pathways.<br><br>RESULTS: All Spodoptera frugiperda specimens in Greece were identified as the rice strain, exhibiting two almost balanced haplotypes (Haplotype 1: 58.6%; Haplotype 2: 41.4%), suggesting a likely origin from a single, genetically diverse source population. Resistance-associated mutations were identified in the ABCC2 gene (A&#x2009;>&#x2009;G single-nucleotide polymorphism (SNP); up to 80.9%) and the Ace-1 gene (F290V: up to 37.5%; A201S: up to 3.85%), conferring resistance to Bacillus thuringiensis (Bt) and organophosphates/carbamates, respectively. By contrast, no resistance-associated mutations were detected for other key insecticides (diamides, pyrethroids, oxadiazines, spinosyns, and avermectins), suggesting their current efficacy in Greece.<br><br>CONCLUSION: This study provides a critical baseline for monitoring insecticide resistance in invasive FAW populations in Europe, supporting the development of sustainable integrated pest management strategies in line with the European Union Green Deal. Continuous monitoring with molecular diagnostics, alongside complementary bioassays, is recommended to mitigate the impact of FAW on European agriculture. &#xa9; 2025 The Author(s). Pest Management Science published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid40276244, year = {2025}, author = {He, ZS and Yang, JX and Huang, JL and Li, DZ and Yang, JB}, title = {Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study in Cymbidium Subgenus Jensoa.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71323}, pmid = {40276244}, issn = {2045-7758}, abstract = {Standard barcodes and ultra-barcode encounter significant challenges when delimiting and discriminating closely related species characterized by deep coalescence, hybrid speciation, gene flow, or low sequence variation. Single-copy orthologs (SCOs) have been widely recognized as standardized nuclear markers in metazoan DNA taxonomy, yet their application in plant taxonomy remains unexplored. This study evaluates the efficacy of SCOs for identifying recently diverged species within the Cymbidium subgenus Jensoa, where ultra-barcodes have previously shown limited resolution. Remarkably, over 90% of the 9094 targeted reference SCOs, inferred from three Cymbidium genomes, were successfully retrieved for all 11 representative species in subg. Jensoa using ALiBaSeq at a minimal 5× depth from whole genome shotgun sequences. The species tree, reconstructed from multiple refined SCO matrices under the coalescent model, effectively distinguished all species and identified mislabeled or misidentified specimens. The comprehensive and refined SCO matrices produced by our pipeline not only enhance phylogenetic analysis but also improve the precision of species diagnosis. Additionally, biparentally inherited SCOs, serving as multi-locus markers, not only augment the effectiveness of DNA barcoding but also support a transition to multi-locus, species-tree-based specimen assignment strategies.}, }
@article {pmid40271218, year = {2025}, author = {Tomsia, M and Grzywacz, A and Szpila, K and Walczak, K and Mahlerová, K and Vaněk, D and Matuszewski, S}, title = {Human costal cartilage, tooth cavities, and femur nutrient canals-new niches for insects used in forensic entomology.}, journal = {Forensic sciences research}, volume = {10}, number = {2}, pages = {owae028}, pmid = {40271218}, issn = {2471-1411}, abstract = {UNLABELLED: The study aimed to analyze the entomological material collected during 13 autopsies performed on the unidentified cadavers revealed at different stages of decay in the Upper Silesia Region (Poland) over 2016-2022. During the preparation of human tissues for genetic identification, we revealed larvae, puparia, and adult insects in previously undescribed locations: costal cartilage, femur nutrient canals (foramen nutrients), and tooth cavities. The taxonomical assessment was done using morphological examination or DNA barcoding, where necessary. Based on our observations, we conclude that the apical constriction, foramen, and cavities may serve as migration paths inside teeth, and the femur nutrient canals to the bone marrow. The study also revealed that the beetle Necrobia ruficollis (Fabricius, 1775) and the moth family Pyralidae Latreille, 1802 (Phycitinae) moths can form pupal chambers inside the costal cartilage, indicating that these insects can complete their life cycle inside this cache. We believe that the newly reported locations of carrion insects in human remains may be relevant to forensic entomology, as they provide new opportunities to collect insect evidence.<br><br>KEY POINTS: Costal cartilage may serve as an occasional cache for adults and immatures of carrion insects.Tooth cavities and apical foramen may serve as entryways for necrophilous insect larvae.Insect larvae use nutrient canals as migratory pathways to the bone marrow.}, }
@article {pmid40270798, year = {2025}, author = {Kireta, D and van Dijk, KJ and Crotty, S and Malik, A and Bell, K and Hogendoorn, K and Lowe, AJ}, title = {A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture-Based DNA Metabarcoding.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71311}, pmid = {40270798}, issn = {2045-7758}, abstract = {Pollen identification (ID) and quantification is important in many fields, including pollination ecology and agricultural sciences, and efforts to explore optimal molecular methods for identifying low concentrations of DNA from plant mixtures are increasing, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy is time-consuming, requires expertise and has limited accuracy and throughput. Molecular barcoding approaches being explored offer improved accuracy and throughput. The common approach, amplicon sequencing, employs PCR amplification to isolate DNA barcodes, but introduces significant bias, impairing downstream quantification. We apply a novel molecular hybrid capture approach to artificial pollen mixtures to improve upon current taxon ID and quantification methods. The method randomly fragments DNA and uses RNA baits to capture DNA barcodes, which allows for PCR duplicate removal, reducing downstream quantification bias. Four reference databases were used to explore identification and quantification. A restricted matK database containing only mixture species yielded sequence proportions highly correlated with input pollen proportions, demonstrating the potential usefulness of hybrid capture for metabarcoding and quantifying pollen mixtures. Identification power was further tested using two reference libraries constructed from publicly available sequences: the matK plastid barcode and RefSeq complete chloroplast references. Single barcode-based taxon ID did not consistently resolve to species or genus level. The RefSeq chloroplast database performed better qualitatively but had limited taxon coverage (relative to species used here) and introduced ID issues. At the family level, both databases yielded comparable qualitative results, but the RefSeq database performed better quantitatively. Whilst the method developed here has tremendous potential, the choice and expansion of reference databases remains one of the most important factors allowing qualitative and quantitative accuracy using the full set of genomic regions screened by this hybrid capture method.}, }
@article {pmid40270465, year = {2025}, author = {Borer, G and Monteiro, C and Lima, FP and Martins, FMS}, title = {Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14115}, doi = {10.1111/1755-0998.14115}, pmid = {40270465}, issn = {1755-0998}, support = {BIOINTERACT/https://doi.org/10.54499/2022.02887//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECInd/10.54499/CEECIND/03185/2018/CP1546/CP164//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; OceanLog/10.54499/PTDC/BIA-BMA/4848/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; ANERIS/101094924//Horizon 2020 Framework Programme/ ; FutureMares/869300//Horizon 2020 Framework Programme/ ; NORTE-01-0246-FEDER-000063//European Commission/ ; }, abstract = {Large biogeographical shifts in marine communities are taking place in response to climate change and biological invasions yet we still lack a full understanding of their diversity and distribution. An important example of this is turf and foliose algae that are key coastal primary producers in several regions and are expanding into new environments. Traditionally, monitoring turf and foliose algae communities involves species identification based on morphological traits, which is challenging due to their reduced dimensions and highly variable morphology. Molecular methods promise to revolutionise this field, but their effectiveness in detecting turf and foliose algae has yet to be tested. Here, we evaluate the performance of DNA metabarcoding (COI and rbcL markers) and morphological identification (in situ and photoquadrat) to describe intertidal turf and foliose algae communities along the Portuguese coast. Both molecular markers detected more taxa than the morphological methods and showed greater discrimination of turf and foliose algae communities between regions, matching our knowledge of the geographical and climatic patterns for the region. In sum, our multi-marker metabarcoding approach was more efficient than morphology-based methods in characterising turf and foliose algae communities along the Portuguese coast, differentiating morphologically similar species, and detecting unicellular organisms. However, certain taxa that were identified by in situ and photoquadrat approaches were not detected through metabarcoding, partly due to lack of reference barcodes or taxonomic resolution. Metabarcoding emerges as a valuable tool for monitoring these communities, particularly in long-term programmes requiring accuracy, speed, and reproducibility.}, }
@article {pmid40270210, year = {2025}, author = {Pedersen, FB and Hauge, AW and Hansen, JF and Andersen, LS and Blomsterberg, S and Bruunsgaard, H}, title = {Cost-Effective and Highly Scalable Typing of HLA Classes I and II Genes of up to 96 Individuals Using Nanopore Sequencing.}, journal = {HLA}, volume = {105}, number = {4}, pages = {e70164}, pmid = {40270210}, issn = {2059-2310}, support = {FF 2022/01//Bloddonorernes Forskningsfond/ ; }, mesh = {Humans ; *Histocompatibility Testing/methods/economics ; *Nanopore Sequencing/economics/methods ; Cost-Benefit Analysis ; Alleles ; *Histocompatibility Antigens Class II/genetics ; Multiplex Polymerase Chain Reaction/economics ; }, abstract = {HLA typing of large donor registries and biobanks as well as acute single patient/donor samples remains expensive, slow and logistically challenging, despite recent developments in the field. We have tested and validated a cost-effective, accurate and highly scalable method for typing specific genes in the HLA region. This enables HLA typing from 1 to 96 individuals simultaneously, using a targeted PCR and Native Barcoding kit from Oxford Nanopore Technologies. A primer set for seven HLA genes (HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1) was developed to work in a multiplex PCR reaction. The resulting amplicons provide a possible four-field resolution of the HLA Class I genes and G-group resolution of the HLA Class II genes. The entire process, from DNA to HLA typing result, takes a total of 5.5-10.5 h depending on the number of samples processed simultaneously. Data analysis was conducted using NGSEngine-Turbo from GenDx (Utrecht, The Netherlands), with analysis time ranging from 1 to 5 min per sample. Samples from 96 Danish registered stem cell donors were typed using this method. One allele out of 1128 analysed alleles was inaccurately called homozygous, leading to an accuracy of 99.91%. The rapid turnaround, low cost and high accuracy make this new method highly relevant for HLA typing of large biobanks and donor registries, as well as for acute single samples. HLA typing can be obtained within 1 day, with a cost per sample of approximately €7 when 96 samples are sequenced simultaneously.}, }
@article {pmid40269967, year = {2025}, author = {Isiye, E and Valcarcel Olmeda, A and Curran, T and O'Neill, D and de Waal, T and Barry, G and O'Hanlon, A and O'Shaughnessy, J and Keohane McCarthy, N and Vellinga, A and Jenkinson, A and Johnson, A and Barrett, D and Costello, S and Zintl, A and O'Meara, D}, title = {Molecular characterisation of common Culicoides biting midges (Diptera: Ceratopogonidae) in Ireland.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {149}, pmid = {40269967}, issn = {1756-3305}, mesh = {Animals ; *Ceratopogonidae/genetics/classification/virology ; Ireland ; *Insect Vectors/genetics/classification/virology ; DNA Barcoding, Taxonomic ; Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Bluetongue virus ; Bluetongue/transmission ; Female ; }, abstract = {BACKGROUND: Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques.<br><br>METHODS: Adult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. In addition, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland.<br><br>RESULTS: DNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides spp. that could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector.<br><br>CONCLUSIONS: DNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.}, }
@article {pmid40266812, year = {2025}, author = {Wu, Y and Liu, Y and Huang, Z and Yin, H and Xu, X}, title = {New Species of the Purse-Web Spider Genus Atypus Latreille, 1804 from Southern China (Araneae, Atypidae), with the General Natural History of Atypus Spiders.}, journal = {Insects}, volume = {16}, number = {3}, pages = {}, pmid = {40266812}, issn = {2075-4450}, support = {32070429/31772423/31471963/31372160//National Natural Sciences Foundation of China/ ; 2023JJ30399//Hunan Provincial Natural Science Foundation of China/ ; CX20230525//Hunan Provincial Innovation Foundation for Postgraduate/ ; }, abstract = {Three species of the purse-web spider genus Atypus Latreille, 1804, collected from Hunan and Sichuan Provinces of China, are diagnosed and described as new to science: A. yaozu sp. nov. (♂♀), A. siyiensis sp. nov. (♂♀) and A. yanjingensis sp. nov. (♂♀). Detailed descriptions, photographs and DNA barcodes of the three new species and a distribution map of Atypus species in China are provided. Additionally, we enrich the general natural history of the genus Atypus through a decade of observation.}, }
@article {pmid40265169, year = {2025}, author = {Renou, L and Sun, W and Friedrich, C and Galant, K and Conrad, C and Consalus, A and Plantier, E and Schallmoser, K and Krisch, L and Barroca, V and Devanand, S and Dechamps, N and Reinisch, A and Martinovic, J and Magnani, A and Faivre, L and Lewandowski, D and Calvo, J and Perie, L and Kosmider, O and Pflumio, F}, title = {Orchestration of human multi-lineage hematopoietic cell development by humanized in vivo bone marrow models.}, journal = {HemaSphere}, volume = {9}, number = {4}, pages = {e70120}, pmid = {40265169}, issn = {2572-9241}, abstract = {Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate the differentiation and preservation of hematopoietic stem and progenitor cells (HSPCs). Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, but the physiology of these models is questioned as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h) in vivo BM model, developed from fetal (F/) and post-natal (P-N/) mesenchymal stromal cell (MSC) differentiation (called hOssicles [hOss]), in which human hematopoietic cells are generated following the transplantation of CD34[+] cells. Serial isolation and transplant experiments of hMSCs and HSPCs from hOss revealed the dynamic nature of these hBM niches. hOss modified human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels, with no major transcriptional changes in HSPCs at the single-cell level. Clonal tracking using genetic barcodes highlighted hematopoietic cell cross-talks between the endogenous murine BM and hOss and differences in clonal myeloid/multipotent cell production between F/hOss and P-N/hOss, uncovering ontogeny-related impact of the BM on human hematopoietic cell production.}, }
@article {pmid40263935, year = {2025}, author = {Becker, J and Domenger, C and Choksi, P and Krämer, C and Baumgartl, C and Maiakovska, O and Kim, JJ and Weinmann, J and Huber, G and Schmidt, F and Thirion, C and Müller, OJ and Willenbring, H and Grimm, D}, title = {Identification of a robust promoter in mouse and human hepatocytes by in vivo biopanning of a barcoded AAV library.}, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {33}, number = {8}, pages = {3881-3901}, doi = {10.1016/j.ymthe.2025.04.027}, pmid = {40263935}, issn = {1525-0024}, support = {P30 DK026743/DK/NIDDK NIH HHS/United States ; }, mesh = {*Dependovirus/genetics ; Humans ; Animals ; *Promoter Regions, Genetic ; Mice ; *Hepatocytes/metabolism ; *Genetic Vectors/genetics ; Transgenes ; Glial Fibrillary Acidic Protein/genetics ; Gene Library ; Genetic Therapy ; Gene Expression ; }, abstract = {Recombinant adeno-associated viruses (AAVs) are leading vectors for in vivo human gene therapy. An integral vector element is promoters, which control transgene expression in either a ubiquitous or cell-type-selective manner. Identifying optimal capsid-promoter combinations is challenging, especially when considering on- versus off-target expression. Here, we report a pipeline for in vivo promoter biopanning in AAV building on our AAV capsid barcoding technology and illustrate its potential by screening 53 promoters in 16 murine tissues using an AAV9 vector. Surprisingly, the 2.2-kb human glial fibrillary acidic protein (GFAP) promoter was the top hit in the liver, where it outperformed robust benchmarks such as the human α-1-antitrypsin promoter or the clinically used liver-specific promoter 1 (LP1). Analysis of hepatic cell populations revealed preferred GFAP promoter activity in hepatocytes. Notably, the GFAP promoter also surpassed the LP1 and cytomegalovirus promoters in human hepatocytes engrafted in an immune-deficient mouse. These findings establish the GFAP promoter as an exciting alternative for research and clinical applications requiring efficient and specific transgene expression in hepatocytes. Our pipeline expands the arsenal of technologies for high-throughput in vivo screening of viral vector components and is compatible with capsid barcoding, facilitating the combinatorial interrogation of complex AAV libraries.}, }
@article {pmid40263541, year = {2025}, author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and McCrea, EM and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD}, title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.}, journal = {Cell death and differentiation}, volume = {}, number = {}, pages = {}, pmid = {40263541}, issn = {1476-5403}, support = {T32 CA009302/CA/NCI NIH HHS/United States ; T31DT1713//Tobacco-Related Disease Research Program (TRDRP)/ ; R35CA197591//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R35 CA197591/CA/NCI NIH HHS/United States ; T32CA009302//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 28IP-0037//Tobacco-Related Disease Research Program (TRDRP)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq[Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.}, }
@article {pmid40263346, year = {2025}, author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N}, title = {Non-invasive molecular species identification using spider silk proteomics.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13844}, pmid = {40263346}, issn = {2045-2322}, support = {23K21203//Japan Society for the Promotion of Science/ ; }, mesh = {*Spiders/chemistry/classification ; Animals ; *Silk/chemistry/genetics ; Proteome/analysis ; Reference Standards ; }, abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.}, }
@article {pmid40262372, year = {2025}, author = {Finney, J and Kuraoka, M and Song, S and Watanabe, A and Liang, X and Liao, D and Moody, MA and Walter, EB and Harrison, SC and Kelsoe, G}, title = {Fluorescence-barcoded cell lines stably expressing membrane-anchored influenza neuraminidases.}, journal = {Vaccine}, volume = {56}, number = {}, pages = {127157}, pmid = {40262372}, issn = {1873-2518}, support = {/HHMI/Howard Hughes Medical Institute/United States ; P01 AI089618/AI/NIAID NIH HHS/United States ; }, mesh = {*Neuraminidase/immunology/genetics/metabolism ; Animals ; Humans ; Antibodies, Viral/blood/immunology ; Macaca mulatta ; Cell Line ; Influenza Vaccines/immunology ; Orthomyxoviridae Infections/immunology/prevention &amp; control ; *Viral Proteins/immunology/genetics ; Immunoglobulin G/immunology/blood ; Flow Cytometry ; }, abstract = {The discovery of broadly protective antibodies to the influenza virus neuraminidase (NA) has raised interest in NA as a vaccine target. However, recombinant, solubilized tetrameric NA ectodomains are often challenging to express and isolate, hindering the study of anti-NA humoral responses. To address this obstacle, we established a panel of 22 non-adherent cell lines stably expressing native, historical N1, N2, N3, N9, and NB NAs anchored on the cell surface. The cell lines are barcoded with fluorescent proteins, enabling high-throughput, 16-plex analyses of antibody binding with commonly available flow cytometers. The cell lines were at least as efficient as a Luminex multiplex binding assay at identifying NA antibodies from a library of unselected clonal IgGs derived from human memory B cells. The cell lines were also useful for measuring the magnitude and breadth of the serum antibody response elicited by experimental infection of rhesus macaques with influenza virus. The membrane-anchored NAs are catalytically active and are compatible with established sialidase activity assays. NA-expressing K530 cell lines therefore represent a useful tool for studying NA immunity and evaluating influenza vaccine efficacy.}, }
@article {pmid40262024, year = {2025}, author = {Tong, Y and Wang, H and Li, H and Jia, Y and Zhou, Z}, title = {Molecular Diet Analysis of Leaf-Grazing Katydids Based on DNA Barcoding.}, journal = {Archives of insect biochemistry and physiology}, volume = {118}, number = {4}, pages = {e70062}, doi = {10.1002/arch.70062}, pmid = {40262024}, issn = {1520-6327}, support = {//This study was supported by Engineering Research Center of Ecological Safety and Conservation in Beijing-Tianjin-Hebei (Xiong'an New Area) of MOE, China (2024-11)./ ; }, mesh = {*DNA Barcoding, Taxonomic ; Animals ; China ; *Herbivory ; Diet ; Plant Leaves ; *Heteroptera/physiology/genetics ; DNA, Plant ; *Coleoptera/physiology/genetics ; }, abstract = {The diversity of herbivorous insects is associated with host plant diversity. The determination of dietary profile is a central topic in insect ecology. DNA barcoding, that is, taxon identification using a standardized DNA region, have been important to the recent advances in food web understandings. In this study, three commonly plant barcoding loci (i.e., rbcL, matK, and trnH-psbA) were chosen for screening of ingested plant DNA in 207 specimens of 18 leaf-grazing katydid species representing 4 subfamilies in China. The obtained sequences were queried against the Barcode of Life Database (BOLD) and GenBank for taxa identification. The results of identification were as follow: 3 Conocephalinae species consumed 10 plant families, with preference for Poaceae; 1 Mecopodinae species consumed 18 plant families, with preference for Fabaceae and Vitaceae; 11 Phaneropterinae species consumed 43 plant families, with preference for Juglandaceae; 3 species Pseudophyllinae species consumed 9 plant families, with preference for Balsaminaceae. Among these, only 81 out of 207 samples were identified at the species level when compares with NCBI and BOLD database. Our study added a significant amount of dietary information for leaf-grazing katydids in China. It is crucial to fully understand coevolution of katydids and plant, katydids diet resource requirements, and best practices for habitat conservation.}, }
@article {pmid40261157, year = {2025}, author = {Kumar, A and Mishra, DK and Kanojiya, S}, title = {Identification of Botanicals Based on Their Mass Spectrum Fingerprints Using Ultra-Performance Liquid Chromatography-Mass Spectrometry.}, journal = {Journal of mass spectrometry : JMS}, volume = {60}, number = {5}, pages = {e5131}, doi = {10.1002/jms.5131}, pmid = {40261157}, issn = {1096-9888}, support = {YSS/2015/001048//Science &amp; Engineering Research Board (SERB) DST Government of India/ ; }, mesh = {Chromatography, High Pressure Liquid/methods ; *Mass Spectrometry/methods ; *Plants, Medicinal/chemistry/classification ; *Plant Extracts/chemistry/analysis ; Liquid Chromatography-Mass Spectrometry ; }, abstract = {In the current scenario, herbal raw materials are identified via morphotaxonomy, microscopic pharmacognosy, or DNA barcoding. However, these methods do not reveal their chemical integrity, while plant raw materials play a crucial role in the quality of plant-based medicine. To overcome this limitation, we used a mass spectrometry-based method to identify 30 botanicals. This assay followed a standard operating procedure (SOP) from sample preparation to the reference library's mass spectrum fingerprint (MSFP) search. The MS1 score showed a similarity index between the input data and the reference mass spectrum. A more than 50% MS1 score was the critical threshold for accurately identifying botanicals based on their chemical integrity. Interestingly, the analysis of 30 different plant species yielded no false results. The results were 100% accurate and selective for tested botanical samples. However, we found that the standard deviation of analytical assays and biological replicates was ± 3.5 and ± 6.3 (MS1 score) for all analyzed samples, respectively. Intraspecies variability showed MS1 scores > 50% ± 10, whereas interspecies variability was observed with MS1 scores < 50% ± 10. The MS1 score was observed, dependent on the plant species, ranging from 53.00% (± 2.65) to 89.76% (± 4.08). In addition, the method was tested to see how seasonal and geographical changes affected search results. The MS1 score changed by less than 15%. We simultaneously created a chemical barcode (unique molecular weight sequence) for each plant species to validate search results and ensure the reliable identification of botanicals.}, }
@article {pmid40260151, year = {2025}, author = {Shapkin, V and Caboň, M and Kolařík, M and Adamčíková, K and Baldrian, P and Michalková, T and Větrovský, T and Adamčík, S}, title = {Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71352}, pmid = {40260151}, issn = {2045-7758}, abstract = {The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.}, }
@article {pmid40260148, year = {2025}, author = {Wong, A and Eizirik, E and Koepfli, KP and de Ferran, V and Shihepo, T and Lay, AR and Zumbroich, J and Rooney, N and Marker, L and Schmidt-Küntzel, A}, title = {Identifying Cryptic Mammals With Non-Invasive Methods: An Effective Molecular Species Identification Tool to Survey Southern African Terrestrial Carnivores.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71223}, pmid = {40260148}, issn = {2045-7758}, abstract = {Carnivores play a vital role in ecosystem health and are thus an important focus for conservation management. Non-invasive methods have gained traction for carnivore monitoring as carnivores are often elusive and wide-ranging, making visual counts particularly difficult. Faecal mini-barcoding combines field collection of scats with genetic analysis for species identification. Here, we assessed the applicability of a mini-barcode based on the mitochondrial ATP6 gene in southern Africa. We predicted amplification success based on in silico evaluation of reference sequences from 34 of the 42 terrestrial carnivore species existing in southern Africa, including the Congo clawless otter (Aonyx congicus) for which we contributed a mitochondrial assembly. We further tested amplification success on available reference samples of 23 species. We expanded the existing ATP6 mini-barcode reference database by contributing additional sequences for 22 species, including the Cape genet (Genetta tigrina) and the side-striped jackal (Lupulella adusta) for which no complete mini-barcode sequences were available on GenBank, and compiled a representative reference dataset of 61 unique sequences as a tool for species identification. As a proof of principle, we applied the ATP6 mini-barcode to a small scat-based carnivore survey conducted in Namibia 13 years prior, which showed a 95% identification success and detected six species among 157 samples collected. With southern Africa's mammalian carnivores facing escalating threats, this robust mini-barcode offers a vital tool for accurate species identification from non-invasive samples, enabling crucial monitoring and conservation efforts.}, }
@article {pmid40259706, year = {2025}, author = {Woodford, DJ and Magoro, M and Kadye, WT and Scheepers, M and Sithole, Y and Mutizwa, TI and Ntokoane, T and Chakona, A}, title = {Freshwater fishes of the Waterberg aquatic ecoregion, South Africa: Diversity, taxonomic conflicts and conservation concerns.}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70007}, pmid = {40259706}, issn = {1095-8649}, support = {FBIP-211006643719//National Research Foundation/ ; IBIP-BS13100251309//National Research Foundation/ ; FBIC200227507229//National Research Foundation/ ; }, abstract = {Southern Africa is a region denoted by both high levels of fish diversity, some of it cryptic and unrecognised by current taxonomy, and severely threatened freshwater ecosystems. The Waterberg, a key aquatic ecoregion of the greater Limpopo River basin in South Africa, represents an area with high terrestrial conservation value but is lacking in aquatic biodiversity information. This study characterised this unique aquatic ecoregion's fish diversity, their biogeographic patterns and threats to this biodiversity. A total of 29 fish species (11 families, 19 genera) were identified, with many distinct upland fish communities occurring within the high-altitude headwaters of the ecoregion, whereas lowland fish communities tended to be more homogeneous. Mitochondrial CO1 barcoding revealed genetically distinct lineages in four presumed-widespread southern African species: the shortfin barb, Enteromius brevipinnis (Jubb, 1966); hyphen barb, Enteromius bifrenatus (Fowler, 1935); straightfin barb, Enteromius paludinosus (Peters, 1852) and snake catfish, Clarias theodorae Weber, 1897, that were restricted to the Waterberg aquatic ecoregion. The level of genetic divergence suggests that these four Waterberg-restricted lineages are likely new candidate species. These findings indicate the Waterberg to be a biogeographic island within the greater Zambezian ichthyofaunal region of southern Africa, which should be prioritised for aquatic ecosystem conservation. Current terrestrial conservation structures in the region, encapsulated within the Waterberg Biosphere Reserve, appear to protect this distinct ichthyofauna from human land-use-derived impacts. Nonetheless, the presence of the invasive predatory largemouth bass (Micropterus nigricans) inside the biosphere represents a credible conservation threat. Engagement with biosphere stakeholders will be critical for managing this threat to the Waterberg's unique ichthyofauna going forward.}, }
@article {pmid40258808, year = {2025}, author = {van der Toorn, W and Bohn, P and Liu-Wei, W and Olguin-Nava, M and Gribling-Burrer, AS and Smyth, RP and von Kleist, M}, title = {Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3742}, pmid = {40258808}, issn = {2041-1723}, support = {955974//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; ANR 20-SFRI-0012//Universit&#xe9; de Strasbourg (University of Strasbourg)/ ; 01KI2016//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; VH-NG-1347//Helmholtz Association/ ; U54 AI170660/AI/NIAID NIH HHS/United States ; 390685689//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*SARS-CoV-2/genetics ; RNA, Viral/genetics ; Humans ; *Sequence Analysis, RNA/methods ; *Nanopore Sequencing/methods ; COVID-19/virology ; *Nanopores ; Software ; Algorithms ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing rapid phenotypic profiling of different SARS-CoV-2 viruses through multiplexed sequencing of longitudinal samples on a single flowcell, identifying systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX represents a broadly applicable, high-performance, economical multiplexing solution for dRNA-seq, facilitating advanced (epi-) transcriptomic research.}, }
@article {pmid40258437, year = {2025}, author = {Kioulos, I and Grigoriadou, AM and Papadakis, A and Vontas, J and Mavridis, K}, title = {Molecular genotyping of pyrethroid resistant mutations and their haplotypes in bed bug populations from Greece.}, journal = {Acta tropica}, volume = {265}, number = {}, pages = {107624}, doi = {10.1016/j.actatropica.2025.107624}, pmid = {40258437}, issn = {1873-6254}, mesh = {Animals ; *Pyrethrins/pharmacology ; *Bedbugs/genetics/drug effects/classification ; Greece ; *Insecticide Resistance/genetics ; Haplotypes ; Mutation ; *Insecticides/pharmacology ; Genotype ; Electron Transport Complex IV/genetics ; Voltage-Gated Sodium Channels/genetics ; Insect Proteins/genetics ; }, abstract = {The resurgence of bed bugs poses significant risks to public health and tourism-driven economies in Southern Europe, including Greece. Control efforts largely rely on pyrethroids; however, the widespread selection of knockdown resistance (kdr) mutations has compromised their effectiveness. Molecular monitoring is therefore essential for accurate species identification and resistance surveillance to support evidence-based pest management strategies. In this study, we analyzed bed bug populations collected from Athens, Thessaloniki, and Heraklion between 2021 and 2024. Species identification was performed via DNA barcoding of the cytochrome oxidase I (COI) gene, while kdr mutations in the voltage-gated sodium channel (VGSC) gene-specifically V419L, L925I, and I936F-were assessed to determine their frequencies and haplotype distributions. All specimens were identified as Cimex lectularius. The L925I mutation reached fixation (100 %) in Thessaloniki and Heraklion, while V419L was detected at frequencies of 30.00 % and 50.00 %, respectively; I936F was not detected in these populations. In Athens, L925I was highly prevalent (98.40 %), while V419L (5.27 %) and I936F (0.60 %) were detected at lower frequencies. Haplotype analysis revealed Haplotype B (L925I only) as the most common in Athens (91.20 %) and Thessaloniki (60.0 %), while Haplotype C (L925I + V419L) predominated in Heraklion (76.92 %). Additional haplotypes were identified in Athens, including Haplotype B[b] (L925I + I936F), marking its first detection in Europe. These findings highlight the widespread presence of kdr mutations and underscore the urgent need for integrated pest management (IPM) strategies, incorporating resistance monitoring, alternative insecticides, and non-chemical control methods to mitigate the growing challenge of pyrethroid resistance in bed bugs.}, }
@article {pmid40257565, year = {2025}, author = {Marsolier, J and Moutaux, E and Grosselin, K and Griffiths, A and Vallot, C}, title = {Single-cell Epigenomic Profiling with High-throughput Droplet scChIP-seq.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2919}, number = {}, pages = {213-239}, pmid = {40257565}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; *Epigenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Histones/genetics ; Microfluidics/methods ; *Epigenesis, Genetic ; }, abstract = {Our high-throughput scChIP-seq approach combines droplet microfluidics with single-cell DNA barcoding to study the heterogeneity of epigenomes (H3K27me3, H3K4me3, H3K27Ac, H3K4me1) in a cellular population of several thousand cells with a coverage of up to 10,000 unique loci per cell.}, }
@article {pmid40253081, year = {2025}, author = {Llera-Oyola, J and Pérez-Moraga, R and Parras, M and Rosón, B}, title = {How to view the female reproductive tract through single-cell looking glasses.}, journal = {American journal of obstetrics and gynecology}, volume = {232}, number = {4S}, pages = {S21-S43}, doi = {10.1016/j.ajog.2024.08.040}, pmid = {40253081}, issn = {1097-6868}, mesh = {Female ; Humans ; *Single-Cell Analysis/methods ; *Genitalia, Female/cytology ; Sequence Analysis, RNA ; Pregnancy ; }, abstract = {Single-cell technologies have emerged as an unprecedented tool for biologists and clinicians, allowing them to assess organs and tissues at the level of individual cells. In the field of women's reproductive biology, single-cell studies have provided insights into the cellular and molecular processes that regulate reproductive and obstetrical functions in health and disease. The knowledge that these studies generate is helping clinicians to improve the understanding and diagnosis of infertility related issues or pregnancy complications and to find new avenues for their treatment. However, navigating the expansive landscape of this type of transcriptomic data analysis represents a pivotal challenge in current research. Single cell RNA sequencing involves isolating cells into droplets, reverse transcribing RNA to generate complementary DNA, with each droplet content uniquely labeled by a barcode. Upon sequencing the complementary DNAs, the barcodes enable the reassignment of sequencing reads to individual droplets, facilitating the reconstruction of the cellular landscape of the sample obtained from a tissue or organ and beyond. Researchers, equipped with the metaphorical 'single-cell glasses,' must adequately choose from a plethora of strategies to dissect and interpret cellular information. Sophisticated algorithms and the decision-making process are often underestimated, resulting in artefactual or cumbersome interpreted results. Computational biologists apply and innovate computational tools designed to process, model, and interpret expansive datasets. The ramifications of their work extend far beyond the realm of data processing; they give shape to the outcome of analyses, playing a pivotal role in drawing meaningful conclusions from the wealth of information garnered. In this review, we describe the wide variety of approaches and analytical steps available with enough detail to gain a concise picture of what a complete examination of a single-cell dataset would be. We commence with a discussion on key points in experimental design, highlighting crucial questions one should consider. Following this, we delve into the various preprocessing and quality control steps essential for any single-cell dataset. The subsequent section offers a detailed guide on constructing a single-cell atlas, exploring nuances such as differential characteristics in visualization and clustering techniques, as well as strategies for assigning identity to cell populations through gene marker annotations. Moving beyond the creation of an atlas, we explore methods for investigating pathological conditions. This involves conducting cell population comparison tests between conditions and analyzing specific cell-to-cell communications and cellular differentiation trajectories in both health and disease scenarios. This work aims to furnish a newcomer researcher and/or clinician with essential guidelines to embark on a single-cell adventure without succumbing to common pitfalls. By bridging the gap between theory and practice, it facilitates the translation of single-cell technologies into clinically relevant applications. Throughout the manuscript, practical examples of its usage in women's reproductive health studies are provided. Various sections delve into specific clinical scenarios, demonstrating how these guidelines can be instrumental in unraveling the molecular landscapes of diseases and physiological processes related to women's reproduction.}, }
@article {pmid40248651, year = {2025}, author = {Liu, WW and Yin, CZ and Zhang, ZX and Wang, XS and Meng, Z and Zhang, XG and Wang, S}, title = {Four new species of Beltraniella (Amphisphaeriales, Beltraniaceae) revealed by morphology and phylogenetic analyses from China.}, journal = {MycoKeys}, volume = {116}, number = {}, pages = {125-144}, pmid = {40248651}, issn = {1314-4049}, abstract = {Beltraniella is a widely-distributed genus on Earth, although its abundance is relatively limited in relation to other dematiaceous hyphomycetes. In the present study, diseased leaves of Myristicafragrans and decaying leaves were collected from Hainan and Sichuan Province. Fungal DNA was amplified and sequenced using two barcodes, the internal transcribed spacer (ITS) and large subunit of ribosomal RNA (LSU), and phylogenetic analyses were conducted through maximum likelihood (ML) and Bayesian inference (BI) algorithms. Four new species of Beltraniella, B.dujiangyanensis, B.jianfengensis, B.myristicae, and B.xinglongensis are identified through phylogenetic analyses and morphological comparison during a survey of fungal diversity in Hainan and Sichuan Provinces, China. Detailed descriptions of the morphological characteristics of these four new species are provided and illustrated with figures.}, }
@article {pmid40248647, year = {2024}, author = {Wibisana, JN and Plessy, C and Dierckxsens, N and Masunaga, A and Miao, J and Luscombe, NM}, title = {The complete mitogenome of an unidentified Oikopleura species.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {1357}, pmid = {40248647}, issn = {2046-1402}, mesh = {*Genome, Mitochondrial ; Animals ; *Urochordata/genetics/classification ; Japan ; Sequence Analysis, DNA ; }, abstract = {Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of Oikopleura dioica. This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.}, }
@article {pmid40248491, year = {2025}, author = {Fulci, V}, title = {Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {2}, pages = {lqaf044}, pmid = {40248491}, issn = {2631-9268}, mesh = {*Software ; *Gene Expression Profiling/methods ; *Transcriptome ; Humans ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Recently, several protocols repurposing the Illumina flow cells or DNA nanoballs as an RNA capture device for spatial transcriptomics have been reported. These protocols yield high volumes of sequencing data which are usually analyzed through the use of high-performance computing clusters. I report Fast analysis of Spatial Transcriptomic (FaST), a novel pipeline for the analysis of subcellular resolution spatial transcriptomics datasets based on barcoding. FaST is compatible with OpenST, seq-scope, Stereo-seq, and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of >500 M million reads in as little as 1 h on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented Spatial Transcriptomics datasets suitable for subsequent analysis through commonly used packages (e.g scanpy or seurat). Notably, the pipeline I present relies on the spateo-release package for RNA segmentation and does not require hematoxylin/eosin or any other imaging procedure to guide cell segmentation. Nevertheless, integration with other software for imaging-guided cell segmentation is still possible. FaST is publicly available on github (https://github.com/flcvlr/FaST).}, }
@article {pmid40248452, year = {2025}, author = {Hrivniak, &#x13d; and Sroka, P and Godunko, RJ and Martynov, AV and Palatov, DM and Bojková, J}, title = {Discovering diversity of Central Asian and Himalayan Epeorus (Caucasiron) mayflies (Ephemeroptera, Heptageniidae) using DNA barcoding and morphology.}, journal = {ZooKeys}, volume = {1234}, number = {}, pages = {89-125}, pmid = {40248452}, issn = {1313-2989}, abstract = {The mayflies of the genus Epeorus Eaton, 1881 subgenus Caucasiron Kluge, 1997 are distributed from the eastern Mediterranean to the mountains of south-west China. In contrast to the Caucasus, the Mediterranean and Irano-Anatolian regions, where E. (Caucasiron) represents one of the most extensively studied mayfly taxa, the species diversity in the more eastern mountains of Asia has been studied only sporadically. In this study, the species diversity of E. (Caucasiron) from the mountains of Central Asia (Pamir, Tian Shan) and the western part of the Himalayas was analysed using DNA barcoding and the morphology of larvae and adults. The distance- and phylogenetic tree-based molecular species delimitation analyses revealed five E. (Caucasiron) species occurring in the study area. Three of them did not correspond morphologically to any known species of the genus Epeorus. These species were described herein as E. (C.) himalayensis Hrivniak &amp; Sroka, sp. nov., E. (C.) lanceolatus Hrivniak &amp; Sroka, sp. nov. and E. (C.) lineatus Hrivniak &amp; Sroka, sp. nov. All new species were compared with other representatives of the subgenus and other related species of the genus Epeorus, and appropriate morphological diagnostic characters were provided. Morphological revision, main diagnostic characters, and information on the distribution of E. (C.) guttatus Braasch &amp; Soldán, 1979 and two other potentially related Epeorus species from the area, E.psi Eaton, 1885 and E.suspicatus (Braasch, 2006), are also given.}, }
@article {pmid40247933, year = {2025}, author = {Moulin, N}, title = {MANGF: a reference library of DNA barcodes for Mantodea from French Guiana (Insecta, Dictyoptera).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e149486}, pmid = {40247933}, issn = {1314-2828}, abstract = {BACKGROUND: Mantodea plays a special role in the food chain as a group charismatic generalist predators. They regulate invertebrate populations while themselves being prey for many larger animals such as reptiles and birds. The present study focuses on Fench Guiana where about 78 species are known within eight families. This diversity represents a challenge for specimen identification.<br><br>NEW INFORMATION: The MANGF project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of mantises as indicators in ecological studies. As a first step towards that goal, we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 425 records representing 68 species in eight different families. Species were identified by expert taxonomists and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.}, }
@article {pmid40246065, year = {2025}, author = {Oskolas, H and Nogueira, FCN and Domont, GB and Yu, KH and Semenov, YR and Sorger, P and Steinfelder, E and Corps, L and Schulz, L and Wieslander, E and Fenyö, D and Kárpáti, S and Holló, P and Kemény, LV and Döme, B and Megyesfalvi, Z and Pawłowski, K and Nishimura, T and Kwon, H and Encarnación-Guevara, S and Szasz, AM and Veréb, Z and Gyulai, R and Németh, IB and Appelqvist, R and Rezeli, M and Baldetorp, B and Horvatovich, P and Malmström, J and Pla, I and Sanchez, A and Knudsen, B and Kiss, A and Malm, J and Marko-Varga, G and Gil, J}, title = {Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center.}, journal = {Journal of proteomics}, volume = {316}, number = {}, pages = {105442}, doi = {10.1016/j.jprot.2025.105442}, pmid = {40246065}, issn = {1876-7737}, support = {R01 HL174679/HL/NHLBI NIH HHS/United States ; R35 GM142879/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Biological Specimen Banks ; *Neoplasms/metabolism/pathology ; Precision Medicine ; Europe ; Proteomics/methods ; }, abstract = {This white paper presents a comprehensive biobanking framework developed at the European Cancer Moonshot Lund Center that merges rigorous sample handling, advanced automation, and multi-omic analyses to accelerate precision oncology. Tumor and blood-based workflows, supported by automated fractionation systems and standardized protocols, ensure the collection of high-quality biospecimens suitable for proteomic, genomic, and metabolic studies. A robust informatics infrastructure, integrating LIMS, barcoding, and REDCap, supports end-to-end traceability and realtime data synchronization, thereby enriching each sample with critical clinical metadata. Proteogenomic integration lies at the core of this initiative, uncovering tumor- and blood-based molecular profiles that inform cancer heterogeneity, metastasis, and therapeutic resistance. Machine learning and AI-driven models further enhance these datasets by stratifying patient populations, predicting therapeutic responses, and expediting the discovery of actionable targets and companion biomarkers. This synergy between technology, automation, and high-dimensional data analytics enables individualized treatment strategies in melanoma, lung, and other cancer types. Aligned with international programs such as the Cancer Moonshot and the ICPC, the Lund Center's approach fosters open collaboration and data sharing on a global scale. This scalable, patient-centric biobanking paradigm provides an adaptable model for institutions aiming to unify clinical, molecular, and computational resources for transformative cancer research.}, }
@article {pmid40245615, year = {2025}, author = {Wu, Q and Nakano, T and Ishida, S and Komai, T and Fujiwara, Y and Yoshida, T and Kawato, M and Oka, SI and Fujikura, K and Miya, M and Minamoto, T}, title = {Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity.}, journal = {Marine environmental research}, volume = {208}, number = {}, pages = {107094}, doi = {10.1016/j.marenvres.2025.107094}, pmid = {40245615}, issn = {1879-0291}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Cephalopoda/genetics ; DNA Primers ; Polymerase Chain Reaction ; *DNA, Environmental/analysis ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Environmental Monitoring/methods ; }, abstract = {Cephalopods play crucial roles in marine ecosystems, acting as both predators and prey for apex predators, thereby contributing to the distribution of energy and nutrients across the food web. Traditional net capture methods are often ineffective for studying cephalopods owing to their wide distribution in marine environments, necessitating the development of simple and efficient surveying techniques to assess cephalopod diversity. Therefore, in this study, we aimed to establish universal polymerase chain reaction primers specifically targeting mitochondrial 16S rRNA genes for environmental DNA metabarcoding in cephalopods. Two primer sets, Cep16S_D and Cep16S_O, were designed for squids and octopuses, respectively. Taxonomic specificity, resolution, and coverage of these primers were evaluated via in silico and in vitro analyses. Additionally, efficiency of these primer sets was assessed using tissue samples and mock communities. Finally, their applicability and performance were tested at various depths. The developed primers exhibited a relatively large amplification size with mixed bases that enhanced their amplification efficiency and sensitivity for cephalopod detection. We successfully identified cephalopod species with different body sizes, from small species, such as Heteroteuthis dagamensis, to large species, such as Architeuthis dux, at varying water depths. Overall, the primer sets established in this study serve as powerful tools to study cephalopod diversity and exhibit great potential for barcoding and genetic diversity investigations.}, }
@article {pmid40242636, year = {2025}, author = {Munkhtulga, D and Baasanmunkh, S and Nyamgerel, N and Park, JH and Tsegmed, Z and Tojibaev, KS and Choi, HJ}, title = {Morphological and phylogenetic analysis approach to three new species and a new section of Astragalus (Fabaceae) from Mongolia.}, journal = {PhytoKeys}, volume = {255}, number = {}, pages = {51-73}, pmid = {40242636}, issn = {1314-2011}, abstract = {Astragalus L. is the largest genus worldwide, comprising more than 3,100 species belonging to 250 sections. In Mongolia, approximately 130 species, including 15 endemic and 25 subendemic species have been previously recognized from 42 sections and 6 subgenera. In this study, we investigated several species within section Laguropsis in Mongolia based on extensive morphological analyses and molecular evidence. Based on these results, we describe three new species and a new section. Two of the newly described species, A.oyunicus and A.teshigicus, belong to the section Laguropsis, whereas the remaining species, A.uvsicus, is the type species of the new section Uvsicus. Furthermore, our findings revealed that (i) A.tamiricus, previously considered endemic to Mongolia, is an additional synonym of A.laguroides, and (ii) A.gobi-altaicus, previously a synonym of A.laguroides, is an independent species. Finally, we provide taxonomic nomenclature, morphological observations, distribution maps and wild photo illustrations of each species.}, }
@article {pmid40238250, year = {2025}, author = {Zhao, J and Yang, W and Cai, H and Cao, G and Li, Z}, title = {Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {40238250}, issn = {2304-8158}, support = {Grant No. ZDYF2024GXJS316//Key Research and Development Projects in Hainan Province/ ; }, abstract = {Addressing the pervasive issue of food adulteration and fraud driven by economic interests has long presented a complex challenge. Such adulteration not only compromises the safety of the food supply chain and destabilizes the market economy but also poses significant risks to public health. Food adulteration encompasses practices such as substitution, process manipulation, mislabeling, the introduction of undeclared ingredients, and the adulteration of genetically modified foods. Given the diverse range of deceptive methods employed, genomics-based identification techniques have increasingly been utilized for detecting food adulteration. Compared to traditional detection methods, technologies such as polymerase chain reaction (PCR), next-generation sequencing (NGS), high-resolution melt (HRM) analysis, DNA barcoding, and the CRISPR-Cas system have demonstrated efficacy in accurately and sensitively detecting even trace amounts of adulterants. This paper provides an overview of genomics-based approaches for identifying food adulteration, summarizes the latest applications in certification procedures, discusses current limitations, and explores potential future trends, thereby offering new insights to enhance the control of food quality and contributing to the development of more robust regulatory frameworks and food safety policies.}, }
@article {pmid40237570, year = {2025}, author = {Bignotto, TS and de Souza, HB and da Silva Bronzim, RC and Maniglia, TC and Baumgartner, D}, title = {Integrative morphometric and molecular analyses reveal possible genetic contamination of silver catfish populations of the genus Rhamdia in Neotropical River basins.}, journal = {Journal of fish biology}, volume = {107}, number = {2}, pages = {535-546}, pmid = {40237570}, issn = {1095-8649}, abstract = {Rhamdia quelen, Rhamdia branneri and Rhamdia voulezi are morphologically similar species that, until recently, were considered synonymous. Although R. quelen has wide distribution in the Neotropical region, R. branneri and R. voulezi are sympatric and endemic species of the Iguaçu River basin. We used an integrative approach, including morphometric and molecular data (barcodes DNA, COI gene), to assist in the identification and delimitation of these species. We also intended to investigate genetic contamination of the Paraná III and lower Iguaçu River basins, as silver catfish production has increased in southern Brazil, and accidental or occasional escapes to nature may pose risks to the genetic integrity of native populations. COI sequences and morphometric data were efficient in the characterization and differentiation of Rhamdia species and may be helpful tools in correctly identifying R. quelen, R. branneri and R. voulezi. Both morphometric and molecular analyses indicated the segregation of specimens into three groups. Although this separation coincided with the taxonomy and the collection site in the morphometric analyses, the taxonomic identification of most samples did not coincide with the molecular identification. This fact may be due to (i) incorrect morphological identification and/or (ii) escapes of pure species and/or interspecific hybrids from fish farms. The detection of COI haplotypes of R. quelen in the lower Iguaçu River, as well as COI haplotypes of R. branneri and R. voulezi in the Paraná III basin, combined with the morphometric and morphological characteristics of the specimens, reinforces the occurrence of hybrid specimens in these river basins. These results reveal the importance of characterizing species and interspecific hybrids of Rhamdia and the urgency to regulate aquaculture activities.}, }
@article {pmid40236044, year = {2025}, author = {Blois, S and Goetz, BM and Mojumder, A and Sullivan, CS}, title = {Shedding dynamics of a DNA virus population during acute and long-term persistent infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.31.646279}, pmid = {40236044}, issn = {2692-8205}, abstract = {UNLABELLED: Although much is known of the molecular mechanisms of virus infection within cells, substantially less is understood about within-host infection. Such knowledge is key to understanding how viruses take up residence and transmit infectious virus, in some cases throughout the life of the host. Here, using murine polyomavirus (muPyV) as a tractable model, we monitor parallel infections of thousands of differentially barcoded viruses within a single host. In individual mice, we show that numerous viruses (>2600) establish infection and are maintained for long periods post-infection. Strikingly, a low level of many different barcodes is shed in urine at all times post-infection, with a minimum of at least 80 different barcodes present in every sample throughout months of infection. During the early acute phase, bulk shed virus genomes derive from numerous different barcodes. This is followed by long term persistent infection detectable in diverse organs. Consistent with limited productive exchange of virus genomes between organs, each displays a unique pattern of relative barcode abundance. During the persistent phase, constant low-level shedding of typically hundreds of barcodes is maintained but is overlapped with rare, punctuated shedding of high amounts of one or a few individual barcodes. In contrast to the early acute phase, these few infrequent highly shed barcodes comprise the majority of bulk shed genomes observed during late times of persistent infection, contributing to a stark decrease in bulk barcode diversity that is shed over time. These temporally shifting patterns, which are conserved across hosts, suggest that polyomaviruses balance continuous transmission potential with reservoir-driven high-level reactivation. This offers a mechanistic basis for polyomavirus ubiquity and long-term persistence, which are typical of many DNA viruses.<br><br>AUTHOR SUMMARY / IMPORTANCE: Polyomavirus infections, mostly benign but potentially fatal for immunocompromised individuals, undergo acute and long-term persistent infections. Typically, polyomavirus-associated diseases arise due to virus infection occurring in the context of a persistently infected individual. However, little is understood regarding the mechanisms of how polyomaviruses establish, maintain, and reactivate from persistent infection. We developed a non-invasive virus shedding assay combining barcoded murine polyomavirus, massively parallel sequencing technology, and novel computational approaches to track long-term infections in mice. We expect these methods to be of use not only to the study of DNA viruses but also for understanding persitent infection of diverse microbes. The study revealed organ-specific virus reservoirs and two distinct shedding patterns: constant low-level shedding of numerous barcodes and episodic high-level shedding of few barcodes. Over time, the diversity of shed barcodes decreased substantially. These findings suggest a persistent low-level infection in multiple reservoirs, with occasional bursts of replication in a small subset of infected cells. This combination of broad reservoirs and varied shedding mechanisms may contribute to polyomavirus success in transmission and maintaining long-term infections.}, }
@article {pmid40236020, year = {2025}, author = {Tasca, JA and Doherty, JF and Shields, EJ and Mudiyanselage, SD and Reich, LN and Sarma, K and Garcia, BA and Bonasio, R}, title = {Pooled scanning of protein variants identifies novel RNA-binding mutants.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.04.02.646914}, pmid = {40236020}, issn = {2692-8205}, abstract = {Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying separation-of-function mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein for its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein-RNA interactions.}, }
@article {pmid40235722, year = {2025}, author = {Chai, Y and Tian, T and Wang, L and Wei, J and Xu, Y and Liu, P and Xiang, C and Yue, M}, title = {Using Plant DNA Barcodes and Functional Traits to Assess Community Assembly of Quercus Forests at Different Scales in the Semiarid Loess Plateau of China.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71103}, pmid = {40235722}, issn = {2045-7758}, abstract = {Trait and evolutionary differences among coexisting species are increasingly used to comprehend the processes shaping communities. However, they do not consistently yield congruent insights due to methodological limitations and scale dependence. Utilizing two plastid DNA genes (rbcL and matK) and one nuclear DNA gene (internal transcribed spacer, ITS), we first constructed the phylogenies of 147 woody species from 98 line transects in the forest areas of the Loess Plateau and subsequently measured three functional traits. Five plots (2500 m[2]) were constructed within Quercus forests to analyze the functional and phylogenetic structures at three spatial scales (100, 400, 2500 m[2]) and two vertical structural layers (tree colonization and shrub layer). In contrast to the phylogenetic convergence observed at the genus level, using plant DNA barcodes, we found that the entire forest communities and the tree layer exhibited phylogenetic randomness across all three spatial scales; even the shrub layer showed phylogenetic overdispersion with increasing scale. Specific leaf area (SLA) exhibited functional convergence in both the shrub and tree layers. In contrast, seed mass (SM) and plant height (PH) displayed distinct functional structures. In the tree layer, these traits showed phylogenetic overdispersion, while in the shrub layer, they demonstrated functional convergence. This contrast highlights the different ecological roles and processes at play in the two layers. Specifically, the scale dependency of assembly patterns in the shrub layer was more pronounced than in the tree layer for both functional and phylogenetic structures. Our findings underscore the significance of employing DNA barcodes to assess the phylogenetic structure of communities with closely related coexisting species and emphasize niche-based functional assembly and multi-process phylogenetic assembly among vertical structural layers in the Quercus community. Decoupling functional and phylogenetic disparities between species could facilitate the understanding of complex species differences influencing community assembly.}, }
@article {pmid40234750, year = {2025}, author = {Shen, X and Li, Y and Liu, Y and Jiang, D}, title = {Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus).}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {475}, pmid = {40234750}, issn = {1471-2229}, support = {2021C02071-4-2//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; }, mesh = {*Prunus/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Genome, Chloroplast/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; }, abstract = {BACKGROUND: Cherries, a subgenus of Cerasus within Rosaceae, as fruit trees with high economic value and elegant garden plants, have broad prospects for development and utilization. However, traditional morphology and molecular data have struggled to accurately identify cherry species due to their extensive overlap in the distribution, frequent hybridization, both open and closed flowers, hysteranthy and limited species coverage, hindering the advancement of the cherry industry. In this study, 61 well-documented cherry species were collected and whole chloroplast genome data was used to develop an effective DNA identification system for precise species identification.<br><br>RESULTS: 36 new cherry chloroplast genomes were added to the public database, resulting in the most comprehensive phylogenetic relationship of cherry species to date. While whole chloroplast genome data achieved an 85.26% species identification success rate, it did not fully resolve all species identification. Relying solely on whole chloroplast genome data is resource-intensive. Therefore, we explored using highly variable regions, species-specific SNPs, and structural variations for accurate species identification. This study revealed that 14 newly developed DNA barcodes could identify 71.88% of cherry samples, while 106 SNPs and Indels allowed for precise identification of 59 out of 61 cherry species.<br><br>CONCLUSIONS: This study not only clarified the phylogenetic relationships of major cherry species but also developed a precise identification system, providing a robust tool for accurate species identification and laying a solid foundation for breeding and the broader promotion of cherry species.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40231940, year = {2025}, author = {Grbin, D and Zrnčić, S and Oraić, D and Alfier, M and Cindrić, M and Jović, L and Sučec, I and Zupičić, IG}, title = {Seafood Labeling in Croatia: Molecular Evidence and Regulatory Insights.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {6}, pages = {}, pmid = {40231940}, issn = {2304-8158}, support = {Project MetaPatvor NPOO.C3.2.R3-I1.04.0122//European Union NextGenerationEU/ ; }, abstract = {Fisheries and aquaculture play a crucial role in global food security, yet species mislabeling remains a persistent challenge, undermining consumer trust and market transparency. Proper food labeling is essential for protecting public health due to the presence of unknown toxic or allergenic substances and preventing illegally sourced products from entering the market. Despite extensive research across Europe, seafood mislabeling in Croatia has remained unexplored. This study aims to provide the first comprehensive assessment of seafood labeling accuracy in Croatia, where fisheries are integral to the coastal economies and tourism. Using DNA barcoding of the COI gene, 109 seafood samples were collected over two years from various sources, including restaurants, markets, and fishing vessels, and analyzed for potential mislabeling. Results revealed a mislabeling rate of 3% among fish samples and 20% among cephalopods, with notable substitutions, such as the yellowfin tuna mislabeled as bigeye tuna and Bluefin tuna and the European squid mislabeled as Patagonian squid. Additionally, 38.5% of samples were partially labeled, while 32% lacked clear country-of-origin information, complicating traceability. While the findings align with the mislabeling rates in other European countries, this study underscores the ongoing challenges in seafood labeling compliance. Establishing standardized monitoring protocols will be essential for improving comparability and effectively addressing seafood fraud.}, }
@article {pmid40228207, year = {2025}, author = {Leibovich, N and Goyal, S}, title = {Limitations and optimizations of cellular lineages tracking.}, journal = {PLoS computational biology}, volume = {21}, number = {4}, pages = {e1012880}, pmid = {40228207}, issn = {1553-7358}, mesh = {*Cell Lineage/genetics ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Cell Tracking/methods ; Humans ; Animals ; }, abstract = {Tracking cellular lineages using genetic barcodes provides insights across biology and has become an important tool. However, barcoding strategies remain ad hoc. We show that elevating barcode insertion probability and thus increasing the average number of barcodes within the cells, adds to the number of traceable lineages but may decrease the accuracy of lineages inference due to reading errors. We establish the trade-off between accuracy in tracing lineages and the total number of traceable lineages, and find optimal experimental parameters under limited resources concerning the populations size of tracked cells and barcode pool complexity.}, }
@article {pmid40226864, year = {2025}, author = {Huang, Y and Zhang, Z and Yang, T and Zhang, Y and Cheng, X and Kang, Y and Guang, Y and Zou, Y and Zhang, X and Luo, Z and Chen, J and Cheng, W}, title = {Gemini Molecular Assembly Colocalization (GOAL): Accurate and Efficient Fusion Genotyping for Chronic Myeloid Leukemia Intelligent Diagnosis.}, journal = {Small methods}, volume = {}, number = {}, pages = {e2500194}, doi = {10.1002/smtd.202500194}, pmid = {40226864}, issn = {2366-9608}, support = {82372334//National Natural Science Foundation of China/ ; 82302621//National Natural Science Foundation of China/ ; U24A20751//National Natural Science Foundation of China/ ; KJZD-K202200404//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; KJQN202300435//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; CSTB2023NSCQ-LZX0022//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0183//Future Medical Youth Innovation Team Development Support Program Project of Chongqing Medical University/ ; CYYY-DSTDXM-202305//The First Affiliated Hospital of Chongqing Medical University Graduate Tutor Team Building Project Grants/ ; CYYY-YJSJXCX-202303//The First Affiliated Hospital of Chongqing Medical University Graduate Teaching Innovation Team Project Grants/ ; }, abstract = {RNA small fragment aberrances are associated with diseases by mediating a range of pathogenesis and pathological processes. DNA assembly-based barcoding and amplification technologies are currently being actively explored for RNA in situ analysis. However, these modular integrated DNA assembly processes are inevitably accompanied with false positive signals caused by unexpected misassembly. Completely avoiding this phenomenon through simple and universal methods is challenging. Here, a novel dual-input to dual-output in situ analysis paradigm is proposed, aiming to improve target specificity through co-recognition (dual-input) and to eliminate false positive misassembly through fluorescent signal co-localization (dual-output). Based on this paradigm, Gemini molecular assembly co-localization (GOAL) in situ imaging system is launched to accurately distinguish the fusion gene subtypes associated with chronic myeloid leukemia (CML), and to precisely report the proportion of minimum residual cancer cells in clinical samples by intelligent co-localization counting and sorting. GOAL achieves highly sensitive and accurate genotyping recognition of 0.01% CML tumor cells and realizes fully automatic rapid diagnosis with a customized Intelligent Cell Image Sorter (iCis). iCis-assisted GOAL represents an innovative and versatile molecular toolkit for accurate, rapid, user-friendly, and professional-independent profiling of cancer cells with RNA small fragment aberrances, providing efficient clinical decision support for disease diagnosis.}, }
@article {pmid40221509, year = {2025}, author = {Siriwan, W and Charoenlappanit, S and Phaonakrop, N and Thaisakun, S and Roytrakul, S}, title = {Identification of peptidome-based biomarkers of cassava mosaic disease resistance in different cassava varieties.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {12653}, pmid = {40221509}, issn = {2045-2322}, support = {FF(KU)18.65//Kasetsart University Research and Development (KURDI)/ ; }, mesh = {*Manihot/virology/metabolism/genetics ; *Disease Resistance ; Biomarkers/metabolism/analysis ; *Plant Diseases/virology/genetics ; *Peptides/metabolism/analysis ; Tandem Mass Spectrometry ; Chromatography, Liquid ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Plant Proteins/metabolism ; Proteomics/methods ; }, abstract = {Cassava, a major economic crop in Thailand, yielded over 3 million USD in exports in 2023. However, its production has been declining since 2021 due to cassava mosaic disease (CMD) outbreaks, which affect cassava plantations. CMD infections have recently increased due to the scarcity of healthy stems and CMD-resistant varieties, the latter being key to controlling its spread. Developing novel methods is critical for accelerating the cultivation of high-yield, CMD-resistant varieties. In this study, signature peptide patterns were determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem MS (LC-MS/MS) to screen for CMD-resistant varieties. Peptide mass fingerprint (PMF) analyses revealed distinct peptide barcodes across 11 varieties, clearly delineating CMD-resistant and CMD-tolerant phenotypes. LC-MS/MS and orthogonal partial least squares-discriminant analysis (OPLS-DA) further demonstrated clear distinctions between the peptide profiles of different phenotypes. Heatmap and PMF analyses consistently revealed unique peptide patterns across the varieties. Volcano plot analysis identified seven upregulated peptides-TATTVAGS, PAAGGGGG, PNELLSYSE, SSIEEGGS, GGGVGGPL, NNGGGFSV, and GPGPAPAA-in CMD-resistant plants. These peptides were associated with proteins containing CONSTANS-like zinc finger, C2H2-type, GST N-terminal, Tubby-like F-box, nuclear-localized AT-hook motif, auxin response factor, and C2 domains. Altogether, this study identified peptidome-based biomarkers for screening CMD-resistant varieties; however, further validation using larger samples is necessary.}, }
@article {pmid40221395, year = {2025}, author = {Huayamares, SG and Lian, L and Rab, R and Hou, Y and Radmand, A and Kim, H and Zenhausern, R and Achyut, BR and Gilbert Ross, M and Lokugamage, MP and Loughrey, D and Peck, HE and Echeverri, ES and Da Silva Sanchez, AJ and Shajii, A and Li, A and Tiegreen, KE and Santangelo, PJ and Sorscher, EJ and Dahlman, JE}, title = {Nanoparticle delivery of a prodrug-activating bacterial enzyme leads to anti-tumor responses.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3490}, pmid = {40221395}, issn = {2041-1723}, support = {R01 DE026941/DE/NIDCR NIH HHS/United States ; R01DE026941//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Animals ; *Prodrugs/administration &amp; dosage/metabolism/pharmacology ; *Purine-Nucleoside Phosphorylase/genetics/metabolism ; *Nanoparticles/chemistry/administration &amp; dosage ; Mice ; Humans ; Cell Line, Tumor ; Escherichia coli/enzymology/genetics ; *Antineoplastic Agents/pharmacology/administration &amp; dosage ; Vidarabine/analogs &amp; derivatives/metabolism/pharmacology/administration &amp; dosage ; Female ; Vidarabine Phosphate/analogs &amp; derivatives/pharmacology/metabolism ; Xenograft Model Antitumor Assays ; RNA, Messenger/metabolism/genetics ; *Head and Neck Neoplasms/drug therapy ; Drug Delivery Systems ; *Escherichia coli Proteins/genetics/metabolism ; }, abstract = {Most cancer patients diagnosed with late-stage head and neck squamous cell carcinoma are treated with chemoradiotherapy, which can lead to toxicity. One potential alternative is tumor-limited conversion of a prodrug into its cytotoxic form. We reason this could be achieved by transient and tumor-specific expression of purine nucleoside phosphorylase (PNP), an Escherichia coli enzyme that converts fludarabine into 2-fluoroadenine, a potent cytotoxic drug. To efficiently express bacterial PNP in tumors, we evaluate 44 chemically distinct lipid nanoparticles (LNPs) using species-agnostic DNA barcoding in tumor-bearing mice. Our lead LNP, designated LNP intratumoral (LNP[IT]), delivers mRNA that leads to PNP expression in vivo. Additionally, in tumor cells transfected with LNP[IT], we observe upregulated pathways related to RNA and protein metabolism, providing insight into the tumor cell response to LNPs in vivo. When mice are treated with LNP[IT]-PNP, then subsequently given fludarabine phosphate, we observe anti-tumor responses. These data are consistent with an approach in which LNP-mRNA expression of a bacterial enzyme activates a prodrug in solid tumors.}, }
@article {pmid40220447, year = {2025}, author = {Duft, RG and Griffin, JL and Stead, DA}, title = {MEATiCode: A comprehensive proteomic LC-MS/MS method for simultaneous species identification in meat authentication.}, journal = {Food chemistry}, volume = {483}, number = {}, pages = {144231}, doi = {10.1016/j.foodchem.2025.144231}, pmid = {40220447}, issn = {1873-7072}, mesh = {*Tandem Mass Spectrometry/methods ; *Food Contamination/analysis ; *Proteomics/methods ; Animals ; Chickens ; Cattle ; *Meat/analysis/classification ; Swine ; Sheep ; *Meat Products/analysis ; Chromatography, Liquid/methods ; Liquid Chromatography-Mass Spectrometry ; }, abstract = {Food fraud in the meat industry threatens consumer trust, market stability, and public health. Traditional methods like DNA barcoding are limited, especially for processed foods where DNA is often degraded. This paper introduces the workflow MEATiCode, a comprehensive proteomic liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the simultaneous identification of species in meat authentication. Application of a novel database search approach - MEATiCode - enabled the differentiation of meat species (as demonstrated for beef, pork, chicken and lamb) in raw and cooked food products following a simple sample preparation procedure and LC-MS/MS analysis of extracted meat peptides. The efficacy of the MEATiCode method was demonstrated through its application to a range of meat products, achieving high sensitivity (0.5 % Limit of Detection (LoD)) and reliability in the detection of adulteration, even in highly processed or cooked meats.}, }
@article {pmid40218301, year = {2025}, author = {Yang, S and Zhao, Z and Xu, Z and Liu, Y and Jiang, M and Fu, L and Zhang, J and Jing, Z and Pang, X and Shao, W and Zhang, C and Li, Y and Du, X and Wu, J}, title = {Identification of Hybrid Sturgeon (Acipenser baerii × Acipenser schrenckii) from Their Parents Using Germplasm.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {7}, pages = {}, pmid = {40218301}, issn = {2076-2615}, support = {2021YFYZ0015//the Sichuan Science and Technology Program/ ; SCCXTD-2024-15//Project of Sichuan Innovation Team of National Modern Agricultural Industry Technology System/ ; kczx2023-2025-19//2023 Aquaculture Breeding Research Project, Integration and application demonstration of key technologies for sturgeon breeding/ ; }, abstract = {The hybrid sturgeon Acipenser baerii × A. schrenckii is the most widely cultured commercial sturgeon in China. However, its morphological similarity to the parental species frequently leads to misuse of germplasm in the breeding process, resulting in a decline in the quality of the sturgeon production. In this study, we have developed a protocol by using mitochondrial DNA barcoding and microsatellite locus analysis for the accurate identification of sturgeon species. Genetic distance and phylogenetic analysis based on the mitochondrial COI segment showed that A. baerii exhibited the closest genetic relationship with orthogonal individuals A. baerii (♀) × A. schrenckii (♂). Conversely, A. schrenckii displayed the highest genetic similarity with reciprocal individuals A. schrenckii (♀) × A. baerii (♂). Additionally, genetic structure analysis and factor correlation analysis (FCA) were conducted using six microsatellite loci among 100 samples, including eight species and two hybrid sturgeon. The results showed that all samples, encompassing both hybrid sturgeon (A. baerii × A. schrenckii) and their parental species, were accurately grouped into ten clusters, thereby validating the precision of this species assignment method.}, }
@article {pmid40212379, year = {2025}, author = {Qiu, Y and Fan, D and Wang, J and Zhou, X and Teng, X and Rao, C}, title = {High throughput construction of species characterized bacterial biobank for functional bacteria screening: demonstration with GABA-producing bacteria.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1545877}, pmid = {40212379}, issn = {1664-302X}, abstract = {Bacteria and their metabolites exhibit remarkable diversity, offering substantial potential for industrial biotechnology. However, the low throughput for constructing and screening bacterial biobanks limits the exploration and utilization of this diversity. In this study, we developed a cost-effective, high-throughput platform for bacterial biobank construction and functional screening. We employed a double-ended barcoding strategy, enabling thousands of bacterial isolates to be pooled for simultaneous Nanopore sequencing of full-length 16S rDNA for species identification. This approach demonstrated 99% accuracy compared to Sanger sequencing while reducing per-sample costs to under 10%. Using this platform, we established a bacterial biobank comprising 15,337 bacterial isolates derived from fermented foods and infant feces collected across China. To identify functional bacteria within the biobank, we designed a versatile fluorescence-based biosensor system employing dual plasmids to decouple metabolite sensing from signal reporting. This modular biosensor framework can be readily adapted for detecting diverse metabolites. As a proof-of-concept, we screened 1,740 isolates and identified 46 with high γ-aminobutyric acid (GABA)-producing capacity, demonstrating potential for probiotic development. Together, our integrated bacterial identification and functional screening platform provides an efficient pipeline for the discovery of functional bacteria, advancing industrial biotechnology through synthetic biology.}, }
@article {pmid40208941, year = {2025}, author = {Zhao, X and Zhao, Y and Li, Z and Liu, H and Fu, W and Chen, F and Sun, Y and Song, D and Fan, C and Zhao, Y}, title = {Proximity-activated DNA scanning encoded sequencing for massive access to membrane proteins nanoscale organization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {15}, pages = {e2425000122}, pmid = {40208941}, issn = {1091-6490}, support = {22125404//MOST | National Natural Science Foundation of China (NSFC)/ ; 22004096//MOST | National Natural Science Foundation of China (NSFC)/ ; 22474107//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023YFB3210103//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023JC-JQ-23//Natural Science Foundation of Shaanxi Province (Shaanxi Natural Science Foundation)/ ; 2023-CX-TD-62//Innovation Capability Support Program of Shaanxi/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Membrane Proteins/genetics/metabolism ; *Sequence Analysis, DNA/methods ; Breast Neoplasms/genetics/metabolism ; Epithelial Cell Adhesion Molecule/metabolism/genetics ; Receptor, ErbB-2/metabolism/genetics ; DNA Probes/genetics ; Cell Line, Tumor ; Female ; DNA, Single-Stranded/genetics ; }, abstract = {Cellular structure maintenance and function regulation critically depend on the composition and spatial distribution of numerous membrane proteins. However, current methods face limitations in spatial coverage and data scalability, hindering the comprehensive analysis of protein interactions in complex cellular nanoenvironment. Herein, we introduce proximity-activated DNA scanning encoded sequencing (PADSE-seq), an innovative technique that utilizes flexible DNA probes with adjustable lengths. These dynamic probes are anchored at a single end, enabling free swings within a nanoscale range to perform global scanning, recording, and accumulating of information on diverse proximal proteins in random directions along unrestricted paths. PADSE-seq leverages the autonomous cyclic cleavage of single-stranded DNA to sequentially activate encoded probes distributed throughout the local area. This process triggers strand displacement amplification and bidirectional extension reactions, linking proteins barcodes with molecular barcodes in tandem and further generating millions to billions of amplicons embedded with the combinatorial identifiers for next-generation sequencing analysis. As a proof of concept, we validated PADSE-seq for mapping the distribution of over a dozen kinds of proteins, including HER1, EpCAM, and PDL1, in proximity to HER2 in breast cancer cell lines, demonstrating its ability to decode multiplexed protein proximities at the nanoscale. Notably, we observed that the spatial distribution of proximal proteins around low-abundance target proteins exhibited greater diversity across regions with variable proximity ranges. This method offers a massive access for high-resolution and comprehensive mapping of cellular molecular interactions, paving the way for deeper insights into complex biological processes and advancing the field of precision medicine.}, }
@article {pmid40208109, year = {2025}, author = {Stevenson, ZC and Laufer, E and Estevez, AO and Robinson, K and Phillips, PC}, title = {Precise lineage tracking using molecular barcodes demonstrates fitness trade-offs for ivermectin resistance in nematodes.}, journal = {G3 (Bethesda, Md.)}, volume = {15}, number = {6}, pages = {}, pmid = {40208109}, issn = {2160-1836}, support = {P40 OD010440/OD/NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; R35GM131838/NH/NIH HHS/United States ; U24 AG056052/AG/NIA NIH HHS/United States ; T32 GM007413-42//PCP/ ; U24AG056052/NH/NIH HHS/United States ; R35 GM131838/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Ivermectin/pharmacology ; *Caenorhabditis elegans/genetics/drug effects ; *Drug Resistance/genetics ; *DNA Barcoding, Taxonomic/methods ; *Genetic Fitness ; Caenorhabditis elegans Proteins/genetics ; Anthelmintics/pharmacology ; }, abstract = {A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci vary with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans to implement the first randomly inserted genomic-barcode fitness experiment within an animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, with the frequency of each barcode then being measured at multiple time points via sequencing at deep coverage and used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wild-type genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2 nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high-precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.}, }
@article {pmid40204808, year = {2025}, author = {Xu, S and Ouyang, Y and Qin, Y and Chen, D and Duan, Z and Song, D and Harries, D and Xia, F and Willner, I and Huang, F}, title = {Spatiotemporal dynamic and catalytically mediated reconfiguration of compartmentalized cyanuric acid/polyadenine DNA microdroplet condensates.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {3352}, pmid = {40204808}, issn = {2041-1723}, support = {21874121//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*DNA/chemistry ; Catalysis ; *Triazines/chemistry ; *Poly A/chemistry ; *Artificial Cells/chemistry/metabolism ; }, abstract = {Native cells possess membrane-bound subcompartments, organelles, such as mitochondria and lysosomes, that intercommunicate and regulate cellular functions. Extensive efforts are directed to develop synthetic cells, or protocells, that replicate these structures and functions. Among these approaches, phase-separated coacervate microdroplets composed of polymers, polysaccharides, proteins, or nucleic acids are gaining interest as cell-mimicking systems. Particularly, compartmentalization of the synthetic protocell assemblies and the integration of functional constituents in the containments allowing signaling, programmed transfer of chemical agents, and spatiotemporal controlled catalytic transformations across the protocell subdomains, are challenging goals in developing artificial cells. Here, we report the assembly of compartmentalized, phase-separated cyanuric acid/polyadenine coacervate microdroplets. Hierarchical, co-centric compartmentalization is achieved through the dynamic and competitive spatiotemporal occupation of pre-engineered barcode domains within the polyadenine microdroplet framework by invading DNA strands. By encoding structural and functional information within these DNA-invaded compartments, the light-triggered, switchable reconfiguration of compartments, switchable catalytic reconfiguration of containments, and reversible aggregation/deaggregation of the compartmentalized microdroplets are demonstrated.}, }
@article {pmid40204203, year = {2025}, author = {Zhou, X and Faust, K}, title = {A high-throughput and time-efficient Nanopore full-length 16S rRNA gene sequencing protocol for synthetic microbial communities.}, journal = {Methods (San Diego, Calif.)}, volume = {240}, number = {}, pages = {14-20}, doi = {10.1016/j.ymeth.2025.04.003}, pmid = {40204203}, issn = {1095-9130}, mesh = {*RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; *Nanopore Sequencing/methods ; *Sequence Analysis, DNA/methods ; Nanopores ; Reproducibility of Results ; Gene Library ; Bacteria/genetics ; }, abstract = {Next-generation sequencing (NGS) has transitioned from primarily research-focused applications to a mature technology. However, resolving microbial community composition on the species level based on the 16S rRNA gene is impeded by several critical bottlenecks that limit the efficiency and scalability of analyses. Specifically, standard MiSeq sequencing suffers from read-length limitation; library preparation requires multiple labour-intensive steps from DNA isolation to amplification and barcoding; and prolonged turnaround times delay results. These challenges underscore the need for improved methods, which our study aims to address. Recent advances in Oxford Nanopore long-read sequencing technology (ONT), including a smaller and cheaper benchtop instrument and support for diverse sample types, have enabled faster sequencing in-house with reduced costs. To address the need for standardized, reproducible workflows, we present an optimized and state-of-the-art protocol for full-length 16S rRNA gene sequencing using the ONT MinION sequencing device. Furthermore, we quantified the reproducibility and accuracy of our protocol and compared it with previous MiSeq results. The results showed that the accuracy of our sequencing pipeline for synthetic communities is significantly higher than for MiSeq pipeline. In summary, our protocol elucidates the composition of synthetic microbial communities in an easy, fast and accurate manner while ensuring reproducible results.}, }
@article {pmid40202150, year = {2025}, author = {Tnah, LH and Ahmad-Farhan, NR and Nur-Nabilah, A and Soo, P and Hazwani-Humaira', Z and Ng, K and Lee, C and Ng, C and Lee, S}, title = {Genetic insights: integrating DNA barcoding with taxonomy in the study of Baccaurea (Phyllanthaceae).}, journal = {Genome}, volume = {68}, number = {}, pages = {1-7}, doi = {10.1139/gen-2024-0105}, pmid = {40202150}, issn = {1480-3321}, mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA, Plant/genetics ; }, abstract = {Traditional taxonomic revisions based on macromorphological and leaf anatomical traits may have limitations in accurately distinguishing certain species within the genus. To improve taxonomic clarity, this study applied DNA barcoding to enhance the understanding of the taxonomy and phylogeny of Baccaurea Lour., a plant genus widely utilized for food, medicine, and building materials. DNA barcode regions, including rbcL, ITS2, and trnH-psbA, were used to analyze 64 samples representing 19 Baccaurea species. Using similarity Basic Local Alignment Search Tool and phylogenetic tree inference, we determined the discriminatory efficiencies of rbcL, ITS2, trnH-psbA, and their combinations rbcL + ITS2 and rbcL + ITS2 + trnH-psbA as 21.1%, 89.5%, 87.5%, 89.5%, and 89.5%, respectively. The Neighbor-Joining tree revealed well-defined, monophyletic species clusters that largely align with phylogenetic positions based on macromorphological features. Notably, our results indicate that Baccaurea parviflora and the synonymized Baccaurea scortechinii are distinct species, recommending the re-establishment of B. scortechinii as a separate species. DNA barcoding is useful in delineating species boundaries, facilitating routine specimen identification, and flagging atypical samples for detailed examination.}, }
@article {pmid40202117, year = {2025}, author = {Shapiro, JR and Simard, N and Bolotin, S and Watts, TH}, title = {Fluorescent Cell Barcoding of Peripheral Blood Mononuclear Cells for High-Throughput Assessment of Vaccine-Induced T Cell Responses in Low-Volume Research Samples.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {107}, number = {5}, pages = {321-332}, doi = {10.1002/cyto.a.24933}, pmid = {40202117}, issn = {1552-4930}, support = {//Donation from Juan and Stefania Speck/ ; //Canadian Immunization Research Network/ ; /CAPMC/CIHR/Canada ; /CAPMC/CIHR/Canada ; }, mesh = {Humans ; *Leukocytes, Mononuclear/immunology/cytology ; *T-Lymphocytes/immunology/cytology ; *Flow Cytometry/methods ; *High-Throughput Screening Assays/methods ; *Vaccines/immunology ; Fluorescent Dyes/chemistry ; Cytokines/metabolism/immunology ; Staining and Labeling/methods ; }, abstract = {T cell responses are rarely measured in large-scale human vaccine studies due to the sample volumes required, as well as the logistical, technical, and financial challenges associated with available assays. Fluorescent cell barcoding has been proposed in other contexts to allow for more high-throughput flow cytometry-based assays. Here, we aimed to expand on existing barcoding approaches to develop a reagent and sample-sparing assay for in-depth assessment of T cell responses to vaccine antigens. By using various concentrations of two fixable viability dyes in a matrix format, up to 25 samples that were pooled and acquired together could be successfully deconvoluted based on their unique fluorescent signature. This fluorescent cell barcoding approach was then combined with extracellular and intracellular staining to identify functional (i.e., producing at least one cytokine) and polyfunctional (i.e., producing multiple cytokines) T cells in response to vaccine antigen stimulation. As a proof-of-concept, we plated just 200,000 peripheral blood mononuclear cells (PBMC) per condition, and by staining and acquiring only two pooled samples, we were able to detect rare antigen-specific T cell responses in eight donors to four stimulants each. The frequencies of antigen-induced cytokine-positive cells detected in barcoded samples with 200,000 input PBMC were strongly correlated with those detected in non-barcoded samples from the same donors with 1 million input PBMC, demonstrating the validity of this approach. In conclusion, by reducing the number of PBMC needed by five-fold, and the volume of staining reagents needed by 25-fold, this assay has widespread potential applications to human vaccine studies.}, }
@article {pmid40201216, year = {2025}, author = {Huang, MC and Kawai, T}, title = {A new species of supergiant Bathynomus A. Milne-Edwards, 1879 (Isopoda: Cirolanidae) from the Paracel Islands, South China Sea.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e144238}, pmid = {40201216}, issn = {1314-2828}, abstract = {BACKGROUND: Bathynomusparacelensis sp. nov., a medium-sized supergiant Bathynomus, is described from specimens obtained at Zhengbin fishing port in Keelung, Taiwan and had been caught in the water near Paracel Islands, South China Sea. Due to its similar shape to B.jamesi, this species has often been mistaken for juveniles or immatures of B.jamesi by fishermen working in this area. Species of Bathynomus can be distinguished morphologically and genetically. The differences from B.jamesi are in the shorter body, clypeus shape, uropod endopod and gene sequence. The difference from B.vaderi is in the body shape, clypeus shape, hook number of maxilliped endite and spines number of maxilulla. Based on the morphological and genetic data results, the specimen is a hitherto undescribed species. The samples were collected as a bycatch species in the deep-sea bottom trawl fishery. The distribution area and depth of this new species and population size are still unclear.<br><br>NEW INFORMATION: B.paracelensis sp. nov. is the third supergiant Bathynomus discovered in the South China Sea after B.jamesi and B.vaderi. Its remarkable feature is its short body length and sub-parallel shape. In addition, it is different from B.jamesi and B.vaderi in features such as clypeus shape, number of maxillula keratinised spine and pleotelson spine almost straight. Phylogenetic and barcoding gap analyses confirm that B.paracelensis sp. nov. is not the same species as B.jamsei. Many morphological differences also indicate that it should be a different species from B.vaderi. B.paracelensis sp. nov. may be an intermediate species between giant and supergiant, possessing characteristics of both categories, which can increase researchers' understanding of Bathynomus biodiversity.}, }
@article {pmid40201215, year = {2025}, author = {Fetnassi, N and Er-Rguibi, O and Aglagane, A and Ghamizi, M and Õunap, E}, title = {Updates to the checklist of nocturnal Macroheterocera (Lepidoptera) of the Central High Atlas of Morocco: One new species added for Morocco.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e137839}, pmid = {40201215}, issn = {1314-2828}, abstract = {BACKGROUND: This paper provides updates to the checklist of Macroheteroceran moths (Lepidoptera) of the central High Atlas of Morocco, following the initial inventory conducted by Charles Rungs nearly five decades ago. Sampling was carried out using sugar bait traps deployed across various habitat types in the region (natural, semi-natural and agricultural lands). Identification of the collected specimens involved a comprehensive approach, including examination of external morphology, dissections of genitalia and DNA barcoding.<br><br>NEW INFORMATION: In this study, we recorded a total of 123 species belonging to the families Noctuidae, Erebidae, Geometridae, Eutelidae and Drepanidae. Euxoacos (Noctuidae) was recorded as a new species for Morocco. The presence of Apameamaroccana (Noctuidae) and Chersotisrungsi (Noctuidae), both endemic to Morocco, was verified in the study area. Four of the 123 species were only identified at the genus level. Our inventory also sheds light on species that were previously not known to occur within our study area, reporting twelve species from the High Atlas Mountains for the first time. We also suggest omitting Eupitheciafarinosa (Geometridae) from the Moroccan Lepidoptera list. This study significantly contributes to uncovering an overlooked aspect of Lepidopteran biodiversity in Morocco, which is crucial for future conservation efforts.}, }
@article {pmid40201154, year = {2025}, author = {Li, Y and Lu, JJ and An, YB and Jiang, L and Wu, HJ and Wang, K and Phurbu, D and Luobu, J and Ma, C and Yang, RH and Dong, CH and Yao, YJ}, title = {An attempt of DNA barcodes based geographical origin authentication of the Chinese caterpillar fungus, Ophiocordycepssinensis.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e144783}, pmid = {40201154}, issn = {2210-6340}, abstract = {Ophiocordycepssinensis is one of the best-known traditional Chinese medicines with distribution confined to the Tibetan Plateau and its surrounding regions. Harvesting the fungus contributes greatly to the livelihood of local communities. The quality and price varies amongst different production regions, usually resulting in an intentional mix-up of its production locality during trading processes, which leads to a demand of developing a reliable way that can trace the geographical origin of this fungus. In the present study, a DNA barcoding-based method applying two universal DNA barcodes for identifying fungal and insect, respectively i.e. the nuclear ribosomal internal transcribed spacer (ITS) and the mitochondrial cytochrome oxidase I (COI), was evaluated and used for geographical origin authentication of O.sinensis. A total of 24 ITS and 78 COI haplotypes were recognised from 215 individuals collected from 75 different geographic localities (county level). Ninety-nine haplotypes were defined using the combination of ITS and COI, discriminating the 75 investigated production counties into 99 distinct regions. A "core" production region was recognised which covers areas of Nagqu and Qamdo in Xizang, Yushu and Guoluo in Qinghai, Gannan (Maqu and Xiahe) in Gansu and certain regions in Nyingch (Bomi and Zayü) and Lhasa (Damxung) in Xizang and Garzê (Sêrxü) in Sichuan Province. Haplotype analyses using the combined barcodes of ITS and COI showed an excellent performance in the geographical origin authentication of O.sinensis and the definition of "core" and "non-core" production region.}, }
@article {pmid40200683, year = {2025}, author = {Wang, Y and Ma, J and Cai, W and Song, M and Wang, Z and Xu, Z and Shen, Y and Zheng, S and Zhang, S and Tang, Z and Wang, Y}, title = {Fast Encapsulation of Microbes into Dissolvable Hydrogel Beads Enables High-Throughput Microbial Single-Cell RNA Sequencing of Clinical Microbiome Samples.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {37}, number = {24}, pages = {e2500481}, doi = {10.1002/adma.202500481}, pmid = {40200683}, issn = {1521-4095}, support = {32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; 52203282//National Natural Science Foundation of China/ ; LY23B040002//Natural Science Foundation of Zhejiang Province/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//"Pioneer" R&amp;D programs of Zhejiang Province/ ; 2024SSYS0022//Key R&amp;D Program of Zhejiang/ ; }, mesh = {*Hydrogels/chemistry ; Humans ; *Single-Cell Analysis/methods ; *Microbiota/genetics ; *Sequence Analysis, RNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Microspheres ; Lab-On-A-Chip Devices ; }, abstract = {Microbial single-cell RNA-seq (mscRNA-seq) can achieve resolution at the cellular level, enhancing the understanding of microbial communities. However, current high-throughput mscRNA-seq methods are limited by multiple centrifugation steps, which can lead to microbial loss and bias. smGel-seq is reported, a high-throughput single-microbe RNA sequencing method for clinical microbiome samples that employs hydrogel beads to encapsulate individual microbes to reduce microbial loss and input requirements. In this method, a novel microchannel array device is implemented for encapsulating single microbe in dissolvable hydrogel beads (smDHBs), along with an optimized automated microfluidic platform to co-encapsulate barcoded beads and smDHBs, enabling high-throughput barcoding of individual microbes. smGel-seq significantly increases the microbial recovery rate in a gut microbiome sample from 8.8% to 91.8%. Furthermore, this method successfully processes clinical microbiome samples with microbial inputs 20 times lower than those required by previous methods. Notably, smGel-seq enables the first mscRNA-seq in a clinical sputum microbiome sample, revealing a specific microbial subpopulation that may play a key role in environmental adaptability, antibiotic resistance, and pathogenicity. These results highlight the compatibility of smGel-seq with clinical microbiome samples and demonstrate its potential for widespread application in diverse clinical and research settings.}, }
@article {pmid40200529, year = {2025}, author = {Barro, SG and Ouattara, TA and Staccini, P}, title = {Assignment of Unique Specimen IDs and Barcodes to Pathology Image Samples in Medical Laboratories in Burkina Faso.}, journal = {Studies in health technology and informatics}, volume = {323}, number = {}, pages = {458-462}, doi = {10.3233/SHTI250132}, pmid = {40200529}, issn = {1879-8365}, mesh = {Burkina Faso ; Humans ; *Specimen Handling/methods ; *Laboratories, Clinical/organization &amp; administration ; *Patient Identification Systems/methods ; *Clinical Laboratory Information Systems/organization &amp; administration ; }, abstract = {The accurate and efficient assignment of unique identifiers to biomedical specimens, along with the generation of barcodes for pathology samples, are crucial elements in ensuring the quality and reliability of medical diagnostics. In Burkina Faso, the adoption of an automated system for these tasks marks a significant advancement in laboratory management. This article explores the impact of this automation on reducing human errors, improving sample traceability, and optimizing operational processes. Indeed, the integration of AJAX queries for the dynamic management of specimen numbers allows for real-time updates and reduces the risks of duplication or incorrect assignment. Furthermore, the use of specialized libraries for the automatic generation of barcodes ensures a unique and secure identification of each sample, thereby facilitating its tracking throughout the analysis process. This modernization of sample management practices not only improves the efficiency of laboratories but also optimizes processing times, thus enhancing the quality of care and diagnostics provided to patients.}, }
@article {pmid40198433, year = {2025}, author = {Watanabe, K and Imanishi, S and Kayukawa, T and Tateishi, K}, title = {Establishment of 27 cell lines derived from various insects.}, journal = {In vitro cellular &amp; developmental biology. Animal}, volume = {}, number = {}, pages = {}, pmid = {40198433}, issn = {1543-706X}, support = {20K06083//Japan Society for the Promotion of Science/ ; 23K05264//Japan Society for the Promotion of Science/ ; }, abstract = {Insect cell lines are valuable for basic and applied biological research. In this study, we established 27 cell lines from various insect species, including Hemiptera: Nilaparvata lugens, Coleoptera: Sitophilus oryzae, Hymenoptera: Allantus luctifer and Trichogramma ssp., Diptera: Culicoides oxystoma, Lepidoptera: Spodoptera litura, Mythimna separata, Bombyx mori, Agrius convolvuli, Plodia interpunctella, and Cryptophlebia horii. This is the first report of cell lines derived from A. luctifer, C. oxystoma, A. convolvuli, and C. horii. Additionally, cell lines from S. litura and M. separata were established from different tissues including the hemocytes, fat bodies, embryos, and Malpighian tubules. Eighteen cell lines were successfully adapted to commercial culture media, with the population doubling time ranging from 1 to 8 d. The identities of the cell lines were confirmed using DNA barcoding. These established cell lines could be valuable for various research applications.}, }
@article {pmid40197720, year = {2025}, author = {Snoeck, HW}, title = {Direct megakaryopoiesis.}, journal = {Current opinion in hematology}, volume = {32}, number = {4}, pages = {213-220}, pmid = {40197720}, issn = {1531-7048}, mesh = {Humans ; *Megakaryocytes/cytology/metabolism ; *Thrombopoiesis ; *Hematopoietic Stem Cells/cytology/metabolism ; Animals ; Cell Differentiation ; }, abstract = {PURPOSE OF REVIEW: Megakaryocytes are large, polyploid cells that produce platelets and originate from hematopoietic stem cells (HSCs) in the bone marrow. While in the classical paradigm, megakaryocytes are generated in a stepwise fashion through increasingly committed progenitor stages, studies using in-vivo barcoding, transplantation, and in-vitro culture have suggested that, in addition, a more direct pathway existed. The relevance of this direct pathway and its functional and phenotypic characteristics were unclear, however.<br><br>RECENT FINDINGS: Recent publications using fate-mapping and single-cell transplantation now unequivocally demonstrate the existence of a direct megakaryocyte differentiation pathway, provide molecular characterization, and indicate distinct roles and regulation of both pathways. The direct pathway originates from a separate subset of 'top' HSCs, is enhanced by hematopoietic stress, inflammation and aging, bypasses multipotential progenitors, may be more active in myeloproliferative neoplasms, and generates phenotypically distinct megakaryocyte progenitors and more reactive platelets.<br><br>SUMMARY: Novel insights into the direct megakaryocyte differentiation pathway provide a deeper understanding of HSC biology, hematological recovery after myeloablation, and aging of the hematopoietic system, and suggest that this pathway may contribute to the increase in thrombotic incidents with age and in myeloproliferative neoplasms.}, }
@article {pmid40197053, year = {2025}, author = {Langsiri, N and Meyer, W and Irinyi, L and Worasilchai, N and Pombubpa, N and Wongsurawat, T and Jenjaroenpun, P and Luangsa-Ard, JJ and Chindamporn, A}, title = {Optimizing fungal DNA extraction and purification for Oxford Nanopore untargeted shotgun metagenomic sequencing from simulated hemoculture specimens.}, journal = {mSystems}, volume = {10}, number = {6}, pages = {e0116624}, pmid = {40197053}, issn = {2379-5077}, support = {N11A650143//National Research Council of Thailand/ ; RA-MF 47/64//Faculty of Medicine, Chulalongkorn University/ ; HEA663000027//Chulalongkorn University/ ; }, mesh = {*DNA, Fungal/isolation &amp; purification/genetics ; Humans ; *Metagenomics/methods ; *Fungi/genetics ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopores ; }, abstract = {UNLABELLED: Long-read metagenomics provides a promising alternative approach to fungal identification, circumventing methodological biases, associated with DNA amplification, which is a prerequisite for DNA barcoding/metabarcoding based on the primary fungal DNA barcode (Internal Transcribed Spacer (ITS) region). However, DNA extraction for long-read sequencing-based fungal identification poses a significant challenge, as obtaining long and intact fungal DNA is imperative. Comparing different lysis methods showed that chemical lysis with CTAB/SDS generated DNA from pure fungal cultures with high yields (ranging from 11.20 ± 0.17 µg to 22.99 ± 2.22 µg depending on the species) while preserving integrity. Evaluating the efficacy of human DNA depletion protocols demonstrated an 88.73% reduction in human reads and a 99.53% increase in fungal reads compared to the untreated yeast-spiked human blood control. Evaluation of the developed DNA extraction protocol on simulated clinical hemocultures revealed that the obtained DNA sequences exceed 10 kb in length, enabling a highly efficient sequencing run with over 80% active pores. The quality of the DNA, as indicated by the 260/280 and 260/230 ratios obtained from NanoDrop spectrophotometer readings, exceeded 1.8 and 2.0, respectively. This demonstrated the great potential of the herein optimized protocol to extract high-quality fungal DNA from clinical specimens enabling long-read metagenomics sequencing.<br><br>IMPORTANCE: A novel streamlined DNA extraction protocol was developed to efficiently isolate high molecular weight fungal DNA from hemoculture samples, which is crucial for long-read sequencing applications. By eliminating the need for labor-intensive and shear-force-inducing steps, such as liquid nitrogen grinding or bead beating, the protocol is more user-friendly and better suited for clinical laboratory settings. The automation of cleanup and extraction steps further shortens the overall turnaround time to under 6 hours. Although not specifically designed for ultra-long DNA extraction, this protocol effectively supports fungal identification through Oxford Nanopore Technology (ONT) sequencing. It yields high molecular weight DNA, resulting in longer sequence fragments that improve the number of fungal reads over human reads. Future improvements, including adaptive sampling technology, could further simplify the process by reducing the need for human DNA depletion, paving the way for more automated, bioinformatics-driven workflows.}, }
@article {pmid40196009, year = {2025}, author = {Smolka, M and Comstock, W and Navarro, M and Maybee, D and Rho, Y and Wagner, M and Wang, Y}, title = {Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {40196009}, issn = {2693-5015}, support = {F31 CA281247/CA/NCI NIH HHS/United States ; R01 HD095296/HD/NICHD NIH HHS/United States ; R35 GM141159/GM/NIGMS NIH HHS/United States ; }, abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo. In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.}, }
@article {pmid40191542, year = {2025}, author = {Liu, B}, title = {Contribution to the knowledge of the genus Calcyopa Stüning, 2000 (Lepidoptera, Geometridae, Ennominae, Boarmiini), with description of a new species.}, journal = {ZooKeys}, volume = {1233}, number = {}, pages = {125-138}, pmid = {40191542}, issn = {1313-2989}, abstract = {The genus Calcyopa Stüning, 2000, is briefly reviewed. A new species, Calcyopahainana Liu, sp. nov., is described from Hainan Province, China. Within the genus Calcyopa, two species groups are identified, characterized by shared traits yet distinguished by a set of consistent features. The difoveata-group, comprises C.difoveata, C.fansipana and C.hainana sp. nov., and the rosearia-group, includes C.rosearia, C.prasina and C.subprasina. The relationship of both species groups is discussed, and an identification key of all known Calcyopa species is presented. Illustrations are provided for adult males and females of the difoveata-group, along with their genitalia, except for C.fansipana, which is known only from males. DNA barcodes are provided for the type species and the newly described species.}, }
@article {pmid40190802, year = {2025}, author = {McCulloch, GA and Pohe, SR and Wilkinson, SP and Drinan, TJ and Waters, JM}, title = {Targeted eDNA Metabarcoding Reveals New Populations of a Range-Limited Stonefly.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71244}, pmid = {40190802}, issn = {2045-7758}, abstract = {Understanding the geographic distributions of rare species can be crucial for conservation management. New environmental DNA (eDNA) technologies offer the potential to efficiently document the distributions of endangered species, but to date, such screening has focused largely on vertebrate taxa. Here we use freshwater eDNA to assess the geographic distribution of the Maungatua stonefly, Zelandoperla maungatuaensis, a flightless insect previously known from only a handful of streams draining a 4-km section of the Maungatua mountain range in southern New Zealand. We analyzed freshwater eDNA from 12 stream localities across the Maungatua range. Screening with commercial eDNA COI primers failed to detect the focal species Z. maungatuaensis. However, newly designed species-specific primers detected this taxon from four adjacent east-flowing streams known to contain Z. maungatuaensis, and two streams from which it had not previously been detected. Subsequent manual surveys confirmed the presence of two newly discovered Z. maungatuaensis populations, with COI barcoding revealing that they together represent a previously unknown, genetically divergent subclade. Our results illustrate the potential of eDNA metabarcoding to help delineate the geographic ranges of rare taxa, and highlight the importance of primer specificity when screening for rare taxa. These findings also have considerable implications for commercial companies offering biodiversity and stream health eDNA services targeting invertebrates.}, }
@article {pmid40188161, year = {2025}, author = {Ramesh, KB and Mahendra, C and Gouda, MNR and Salim, R and Subramanian, S}, title = {Genetic structure and haplotype analysis of predominant genetic group of Bemisia tabaci Asia II 1 from Asia and India.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {11672}, pmid = {40188161}, issn = {2045-2322}, mesh = {Animals ; *Hemiptera/genetics/classification ; *Haplotypes ; India ; Genetic Variation ; Phylogeny ; Asia ; }, abstract = {Whitefly, Bemisia tabaci is a globally recognized invasive cryptic pest species complex and a primary vector for 90% of begomoviruses. Understanding the species composition and diversity within the B. tabaci cryptic species complex is essential for developing effective pest management strategies. The Asia II 1 genetic group of B. tabaci is notably widespread in India and across Asia, demonstrating significant genetic diversity. Our study investigates the haplotype diversity of Asia II 1 using the mtCOI barcoding gene, analyzing 676 sequences from various Asian countries and 190 sequences from India. We identified 241 distinct haplotypes in Asia II 1 across Asia, with the highest haplotype diversity in China (Hd: 1.000) and the lowest in Vietnam (Hd: 0.667). Nucleotide diversity peaked in Pakistan (pi: 0.0145) and was lowest in Vietnam (pi: 0.0010). In India, we identified 77 haplotypes with a diversity of 0.926 and nucleotide diversity of 0.0076. When grouped by hostplant families, 79 haplotypes were recorded, with the highest diversity in Cucurbitaceae and the lowest in Solanaceae. Our findings suggest that hostplants and geographical location significantly influence genetic group development, offering novel insights into Asia II 1's genetic structure and evolution. This marks the first comprehensive study of Asia II 1 genetic diversity in Asia and India.}, }
@article {pmid40187791, year = {2025}, author = {He, Z and Wang, H and Chen, Y and Chen, N}, title = {Comparative genomic and phylogenetic analysis of mitochondrial genomes of the Pseudo-nitzschia HAB species.}, journal = {Harmful algae}, volume = {144}, number = {}, pages = {102829}, doi = {10.1016/j.hal.2025.102829}, pmid = {40187791}, issn = {1878-1470}, mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Diatoms/genetics/classification ; DNA, Mitochondrial/genetics ; Harmful Algal Bloom ; Genomics ; }, abstract = {The genus Pseudo-nitzschia within Bacillariophyta (diatoms) is best known for its rich collection of toxigenic harmful algal bloom (HAB) species capable of producing the neurotoxin domoic acid (DA), which causes amnesic shellfish poisoning (ASP) in humans. Molecular markers such as 18S rDNA, ITS1, and ITS2 have been applied to facilitate Pseudo-nitzschia species identification because morphology-based methods often could not adequately distinguish different species due to their morphological similarities and plasticity. In this study, we constructed mitochondrial genomes (mtDNAs) for 11 Pseudo-nitzschia species and assessed their utility as "super-barcodes" for species identification and evolutionary analysis. These mtDNAs exhibited conserved genome structures despite variability in repeat regions. A potential tatA-tatC gene fusion event was observed in a single Pseudo-nitzschia species P. brasiliana. We also observed intron variability in cox1 genes. Phylogenetic analyses of mtDNAs, chloroplast genomes (cpDNAs), and nuclear ribosomal DNA (nrDNA) arrays revealed consistent results, supporting the closely related but distinct clustering of the genera Fragilariopsis and Pseudo-nitzschia. We further designed a high-resolution molecular marker tatA for species identification based on the comparative analysis of these mtDNAs, which could be used to track Pseudo-nitzschia diversity. These findings offer new genome resources and new insights into the genetic evolution and classification of Pseudo-nitzschia, underscoring the need for continued research in this field.}, }
@article {pmid40187273, year = {2025}, author = {Prasetyo, DB and Yean, S and Boyer, S}, title = {Reevaluating the presence of Rhipicephalus australis (Acari: Ixodidae) in Southeast Asia: A phylogenetic approach based on Cambodian tick samples.}, journal = {Ticks and tick-borne diseases}, volume = {16}, number = {3}, pages = {102478}, doi = {10.1016/j.ttbdis.2025.102478}, pmid = {40187273}, issn = {1877-9603}, mesh = {Cambodia/epidemiology ; *Rhipicephalus/anatomy &amp; histology/classification/genetics ; Phylogeny ; Cattle ; DNA Barcoding, Taxonomic/veterinary ; *Animal Distribution ; Animals ; *Cattle Diseases/diagnosis/epidemiology/parasitology ; *Tick Infestations/diagnosis/epidemiology/parasitology/veterinary ; Male ; Female ; }, abstract = {Morphological variability between Rhipicephalus australis and R. microplus has led to taxonomic ambiguity, leading to species misidentification. Rhipicephalus australis is reported to have a distribution range in Pacific Ocean region extending to several Southeast Asian countries, including Cambodia, although its presence in continental Southeast Asia has not been supported by molecular data. With growing evidence of conflicting morphological characters, this study aimed to evaluate the presence of R. australis in Cambodia using both morphological and molecular identification. Tick specimens were collected from cattle across 21 provinces of Cambodia, and a subset of 95 R. microplus complex (37 morphologically identified as R. australis, 39 R. microplus, and 19 nymphs) was selected for molecular analysis. DNA barcoding of the cox1 gene was performed, and a maximum likelihood phylogenetic tree revealed that all specimens clustered within R. microplus clade A. These findings, along with previous observations from other regions, suggest that, in the absence of molecular data, there is no definitive evidence to support the presence of R. australis in continental Southeast Asia, particularly in Cambodia.}, }
@article {pmid40186944, year = {2025}, author = {Solbach, MD and Siemensma, F and Holzmann, M}, title = {A remarkable new monothalamid (Rhizaria, Foraminifera) from the shoreline of Livingston Island, Antarctica.}, journal = {European journal of protistology}, volume = {99}, number = {}, pages = {126148}, doi = {10.1016/j.ejop.2025.126148}, pmid = {40186944}, issn = {1618-0429}, mesh = {Antarctic Regions ; Phylogeny ; *Foraminifera/classification/genetics/cytology/isolation &amp; purification ; *Geologic Sediments/parasitology ; RNA, Ribosomal, 18S/genetics ; Islands ; *Rhizaria/classification/genetics/cytology ; Species Specificity ; }, abstract = {In this study, we describe a novel monothalamous Foraminifera, discovered in shoreline sediment samples from the Southern Ocean. The individuals, approximately 75 μm in diameter, are relatively small for Foraminifera, mostly spherical, with an organic-walled test. Notably, these Foraminifera exhibit a unique behavior in culture: they surround themselves in planktonic diatoms, enabling them to float in the water column. This floating behavior is unusual for Foraminifera, which are often larger and possess a thick test made of calcite or agglutinated particles. We hypothesize that the small size of the organism, its lightweight organic test, and the habit of surrounding itself with centric diatoms may enable the floating behavior observed in culture and potentially aid dispersal in nature. Phylogenetic analysis of the 18S rDNA barcoding fragment places this undescribed organism as an independent lineage among monothalamid Foraminifera. We erect the novel genus Pensilisphaera with its type species Pensilisphaera antarcticaensis.}, }
@article {pmid40185067, year = {2025}, author = {Papapetrou, EP}, title = {The clones have STRACK: Tracing responses to leukemic mutations.}, journal = {Cell stem cell}, volume = {32}, number = {4}, pages = {499-501}, doi = {10.1016/j.stem.2025.03.001}, pmid = {40185067}, issn = {1875-9777}, mesh = {Animals ; *Mutation/genetics ; *Leukemia/genetics/pathology ; Clone Cells/pathology ; Mice ; *Hematopoietic Stem Cells/metabolism/pathology ; Humans ; }, abstract = {Rodriguez-Fraticelli and colleagues combine genetic barcoding with ex vivo expansion and sister-cell analysis of murine hematopoietic stem cells (HSCs) carrying inducible leukemia driver mutations. This approach allows them to capture the intrinsic heterogeneity of clonal cell behaviors and study how these impact cell fates upon acquisition of leukemia driver mutations.}, }
@article {pmid40183470, year = {2025}, author = {Haley, RM and Padilla, MS and El-Mayta, RD and Joseph, RA and Weber, JA and Figueroa-Espada, CG and Mukalel, AJ and Ricciardi, AS and Palanki, R and Geisler, HC and Jester, MT and Davidson, BL and Mitchell, MJ}, title = {Lipid Nanoparticles for In Vivo Lung Delivery of CRISPR-Cas9 Ribonucleoproteins Allow Gene Editing of Clinical Targets.}, journal = {ACS nano}, volume = {19}, number = {14}, pages = {13790-13804}, doi = {10.1021/acsnano.4c16617}, pmid = {40183470}, issn = {1936-086X}, support = {T90 DE030854/DE/NIDCR NIH HHS/United States ; F99 CA284294/CA/NCI NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; F30 HL162465/HL/NHLBI NIH HHS/United States ; DP2 TR002776/TR/NCATS NIH HHS/United States ; P30 CA016520/CA/NCI NIH HHS/United States ; }, mesh = {*Gene Editing/methods ; *CRISPR-Cas Systems/genetics ; *Ribonucleoproteins/genetics/chemistry/administration &amp; dosage/metabolism ; *Lung/metabolism ; Animals ; *Nanoparticles/chemistry ; Humans ; *Lipids/chemistry ; Mice ; *CRISPR-Associated Protein 9 ; Liposomes ; }, abstract = {In the past 10 years, CRISPR-Cas9 has revolutionized the gene-editing field due to its modularity, simplicity, and efficacy. It has been applied for the creation of in vivo models, to further understand human biology, and toward the curing of genetic diseases. However, there remain significant delivery barriers for CRISPR-Cas9 application in the clinic, especially for in vivo and extrahepatic applications. In this work, high-throughput molecular barcoding techniques were used alongside traditional screening methodologies to simultaneously evaluate LNP formulations encapsulating ribonucleoproteins (RNPs) for in vitro gene-editing efficiency and in vivo biodistribution. This resulted in the identification of a lung-tropic LNP formulation, which shows efficient gene editing in endothelial and epithelial cells within the lung, targeting both model reporter and clinically relevant genomic targets. Further, this LNP shows no off-target indel formation in the liver, making it a highly specific extrahepatic delivery system for lung-editing applications.}, }
@article {pmid40182483, year = {2025}, author = {Kipkoech, A and Li, K and Milne, RI and Oyebanji, OO and Wambulwa, MC and Fu, XG and Wakhungu, DA and Wu, ZY and Liu, J}, title = {An integrative approach clarifies species delimitation and biogeographic history of Debregeasia (Urticaceae).}, journal = {Plant diversity}, volume = {47}, number = {2}, pages = {229-243}, pmid = {40182483}, issn = {2468-2659}, abstract = {Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.}, }
@article {pmid40181733, year = {2025}, author = {Congrains, C and Bremer, F and Dupuis, JR and Barr, NB and Garzón-Orduña, IJ and Rubinoff, D and Doorenweerd, C and Jose, MS and Morris, K and Kauwe, A and Geib, S}, title = {CCS-Consensuser: A Haplotype-Aware Consensus Generator for PacBio Amplicon Sequences.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14113}, doi = {10.1111/1755-0998.14113}, pmid = {40181733}, issn = {1755-0998}, support = {8130-0565-CA//U.S. Department of Agriculture-Animal and Plant Health Inspection Service/ ; 8130-0984-IA//U.S. Department of Agriculture-Animal and Plant Health Inspection Service/ ; }, abstract = {DNA sequencing technology has undergone substantial improvements in recent years, to the extent that Third Generation Sequencing platforms are capable of massively generating long-reads. Amplicon sequencing has been among the most popular techniques due to its wide application in diverse fields of biological sciences. However, there is a lack of software specifically designed to analyse intra-individual genetic variation using amplicon long-read data. Here, we present CCS-consensuser, an end-to-end pipeline that generates consensus sequences from amplicon sequencing using high-fidelity reads produced by PacBio circular consensus sequencing (CCS). We evaluated the concordance of the results produced using CCS + CCS-consensuser and other sequencing platforms (Illumina and Sanger), as well as accuracy using a simulated dataset. This assessment showed that CCS amplicon data coupled with CCS-consensuser can produce high-quality sequences (PHRED > 30). The pipeline resulted in high proportions of identical sequence bins for real data, achieving up to 94.94% concordance with COI Sanger sequences and 92.61% with nuclear loci Illumina sequences (considering heterozygous loci), and 95.55% with a fully phased nuclear simulated dataset. Furthermore, our pipeline can be used to detect heteroplasmy in mtDNA, cross-contamination, resolve the phase of nuclear genes in diploid organisms, and conceivably for multi-copy gene systems such as rDNA. These results not only support its potential for application in studies using haploid data such as DNA barcoding, but also demonstrate its unique capacity to explore within individual haplotype variation. Therefore, our strategy shows promise for a broad range of applications in biology and medicine that have been challenging to assess using traditional techniques.}, }
@article {pmid40180452, year = {2025}, author = {Schares, HAM and Hayes, MJ and Balsamo, JA and Thirman, HL and Bachmann, BO and Irish, JM}, title = {Multiplexed cytometry for single cell chemical biology.}, journal = {Methods in cell biology}, volume = {195}, number = {}, pages = {143-172}, pmid = {40180452}, issn = {0091-679X}, support = {R01 CA226833/CA/NCI NIH HHS/United States ; U01 TR002625/TR/NCATS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 GM092218/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Flow Cytometry/methods ; *Single-Cell Analysis/methods ; Animals ; Mice ; Small Molecule Libraries ; Histones/metabolism ; DNA Damage ; }, abstract = {Flow cytometry has great potential for screening in translational research areas due to its deep quantification of cellular features, ability to collect millions of cells in minutes, and consistently expanding suite of validated antibodies that detect cell identity and functions. However, cytometry remains under-utilized in discovery chemical biology due to the differences in expertise between chemistry groups developing chemical libraries and cell biologists developing single cell assays. This chapter is designed to bridge this gap by providing a detailed protocol aimed at both chemistry and biology audiences with the goal of helping train novice researchers. Assay users select from three elements: a small molecule input, a target cell type, and a module of cytometry readouts. For each, we explore basic and advanced examples of inputs, including screening fractionated microbial extracts and pure compounds, and target cells, including primary human blood cells, mouse cells, and cancer cell lines. One such module of cytometry readouts focuses on cell function and measures DNA damage response (γH2AX), growth (phosphorylated S6), DNA content, apoptosis (cleaved Caspase3), cell cycle M phase (phosphorylated Histone H3), and viability (membrane permeabilization). The protocol can also be adapted to measure different functional readouts, such as cell identity or differentiation and contrasting cell injury mechanisms. The protocol is designed to be used in 96-well plate format with fluorescent cell barcoding and the debarcodeR algorithm. Ultimately, the goal is to encourage the next generation of chemical biologists to use functional cell-based cytometry assays in discovery and translational research.}, }
@article {pmid40179197, year = {2025}, author = {de Haan, S and He, J and Corbat, AA and Belicova, L and Ratz, M and Vinsland, E and Frisén, J and Kelley, MW and Andersson, ER}, title = {Ectoderm barcoding reveals neural and cochlear compartmentalization.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6742}, pages = {60-68}, doi = {10.1126/science.adq9248}, pmid = {40179197}, issn = {1095-9203}, mesh = {Animals ; Mice ; Cell Lineage ; *Cochlea/embryology/cytology ; *DNA Barcoding, Taxonomic/methods ; *Ectoderm/embryology/cytology ; *Nervous System/embryology ; *Neural Crest/embryology/cytology ; Neurogenesis ; Single-Cell Analysis ; }, abstract = {Placodes and the neural crest are defining features of vertebrates. In this study, we investigate their lineages in mice using in utero approaches. We demonstrated that nanoinjection at embryonic day 7.5 targeted the ectoderm, including the future nervous system, placodes, and neural crest, allowing highly efficient manipulation of the future nervous system and inner ear. By using heritable DNA barcodes and high-throughput next-generation single-cell lineage tracing, we elucidated convergent differentiation pathways and identified distinct nervous system-, neural crest-, and otic placode-derived lineages. Clonal analyses identified early neural and cochlear compartmentalization, linking differentiated cell types to their progenitors or cellular siblings. This provides foundational insights for neuroscience and developmental biology.}, }
@article {pmid40179100, year = {2025}, author = {Long, Z and Yu, J and Bing, T}, title = {Theoretical Basis for the Highly Efficient Aptamer Selection Using Unique Molecular Identifiers.}, journal = {Analytical chemistry}, volume = {97}, number = {14}, pages = {7606-7609}, doi = {10.1021/acs.analchem.5c00118}, pmid = {40179100}, issn = {1520-6882}, mesh = {*Aptamers, Nucleotide/chemistry/isolation &amp; purification ; *SELEX Aptamer Technique/methods ; Gene Library ; Humans ; High-Throughput Nucleotide Sequencing ; }, abstract = {Rapid selection methods are crucial for promoting the discovery and application of aptamers across various fields. We previously reported a highly efficient aptamer selection strategy by using unique molecular identifiers (UMIs), enabling the efficient isolation of aptamers from a single cell by only one round. The strategy integrates an ultrasensitive DNA barcoding technology with high-throughput sequencing to accurately quantify aptamer candidates, thereby mitigating issues such as PCR bias and sequence overenrichment that are inherent in traditional multiround selection. Here, we conduct a systematically theoretical analysis of this strategy in the elucidation of the theoretical basis, advantages, and applicability. The feasibility and advantages of isolating aptamers from low-enriched DNA libraries was investigated at a theoretical level, showing that this strategy is effective in reducing nonspecific binding and thus increasing the success of selecting high-affinity aptamers. Our theoretical analysis supports the broad applicability of the strategy for the single-round aptamer selection, paving the way for its widespread adoption in high-efficiency aptamer discovery and aptamer-based cell atlas.}, }
@article {pmid40177347, year = {2025}, author = {Gong, L and Zhong, Y}, title = {Re-description of Sinopodacurva Zhong, Jäger, Chen &amp; Liu, 2019 (Araneae, Sparassidae), with a first description of the female.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e152100}, pmid = {40177347}, issn = {1314-2828}, abstract = {BACKGROUND: Sinopoda Jäger, 1999 is a relatively large spider genus that currently comprises 141 species distributed worldwide. However, the genus remains inadequately studied because nearly half of the species are known from a single sex or juvenile specimens. Sinopodacurva Zhong, Jäger, Chen &amp; Liu, 2019 was described, based on two male specimens from Damingshan National Nature Reserve, Guangxi Zhuang Autonomous Region, China and no additional specimens have been recorded since.<br><br>NEW INFORMATION: Recently, new materials of huntsman spiders have been collected from Mt. Wuyishan, including specimens of both sexes. Several males were identified as S.curva, based on morphological comparison with the holotype. Based on morphological characters and DNA barcodes, we confidently matched the females and males as S.curva. Herein, S.curva is re-described, based on these new materials and the female is described and illustrated for the first time.}, }
@article {pmid40174196, year = {2025}, author = {Kohlmann, B and Solís, &#xc1;}, title = {A review of the species groups of the Western Hemisphere Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae) using COI barcoding and gene trees.}, journal = {Zootaxa}, volume = {5604}, number = {4}, pages = {401-447}, doi = {10.11646/zootaxa.5604.4.1}, pmid = {40174196}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera/genetics/classification/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; Phylogeny ; Animal Distribution ; Male ; Female ; Electron Transport Complex IV/genetics ; Ecosystem ; Organ Size ; }, abstract = {Species groups of Western Hemispheric Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) are suggested using COI barcoding and gene trees and supported by congruence with external morphology, behavior, ecology, and biogeographic evidence. New species groups, complexes, and taxonomic statuses are offered, and other preexisting proposals are confirmed. No barcoding gap w as found between the intragroup and intergroup genetic distance blocks, but the average intragroup (8.38%) and intergroup (13.88%) Kimura-two-parameter distances are statistically different. The following seven preexisting species groups were supported by the congruence between the mtDNA barcode analysis and other independent evidence: O. chevrolati, O. clypeatus, O. dicranius, O. gazellinus, O. hircus, O. landolti, and O. mexicanus. Eight new species groups are suggested: O. crinitus, O. curvicornis, O. eulophus, O. hecate, O. hoepfneri, O. marginatus, O. nasutus, and O. velutinus. Possible behavioral/ecological adaptations of morphological characters are also discussed. New biogeographic and evolutionary hypotheses are also advanced. An identification key for species groups is presented.}, }
@article {pmid40174133, year = {2025}, author = {Mori, E and Viviano, A and Baratti, M and Serafini, E and Gabbrielli, B and Picchi, MS and Giannetti, D and Mascalchi, C and Ancillotto, L}, title = {A light in the dark: DNA barcoding provides new data about the taxonomy of the Italian Luciola (Coleoptera, Lampyridae) fireflies.}, journal = {Zootaxa}, volume = {5609}, number = {4}, pages = {525-536}, doi = {10.11646/zootaxa.5609.4.4}, pmid = {40174133}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Italy ; *Fireflies/classification/genetics/anatomy &amp; histology/growth &amp; development ; Male ; Phylogeny ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {Environmental pollution and agricultural intensification are threatening insects worldwide, and reliable taxonomy is pivotal to protect these taxa, particularly endemic species. Despite their wide distribution, lampyrid beetles (Lampyridae)-well-known as fireflies-are poorly studied in terms of taxonomy, particularly in Europe. Accordingly, as for almost all insects, the description of most species is only based on a few morphological featuresSince genetic analyses can provide valuable support in taxonomic studies, in this work, we investigated the species identity of an Italian endemic firefly, Luciola pedemontana (Curtis, 1843), with respect to other congeneric species, namely Luciola italica (Linnaeus, 1767) and Luciola lusitanica (Charpentier, 1825) by applying Barcoding technique. Particularly, L. pedemontana has been for long considered as a synonym of L. lusitanica or as a subspecies of L. italica. Italy hosts the highest diversity of firefly species in Europe, but the Luciola inter-specific phylogenetic relationships and species delimitations are still poorly known. With the aim to assist morphological analyses in the taxonomic characterization of species of the genus Luciola in Italy, we sequenced the cytochrome oxidase subunit I gene (COI) fragment of 40 individuals from 18 sites in Central Italy. Our analysis confirmed L. pedemontana as a well-supported monophyletic clade and as the sister taxon of L. italica. Furthermore, a low intraspecific genetic variation was found between L. lusitanica and L. pedemontana and between Luciola unmunsana + Luciola papariensis. Genetic data obtained for the Luciola species can help to improve conservation measures for L. pedemontana, strongly required to protect this Italian endemic taxon, which is currently threatened by light pollution and environmental alterations.}, }
@article {pmid40174117, year = {2025}, author = {Girdley, J and Garre, M and Rubio, RM and Ortiz, AS}, title = {Eucosma callei sp. nov.-a new species of Olethreutinae from South-eastern Iberian Peninsula (Lepidoptera, Tortricidae).}, journal = {Zootaxa}, volume = {5583}, number = {1}, pages = {186-194}, doi = {10.11646/zootaxa.5583.1.11}, pmid = {40174117}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; Animal Distribution ; Spain ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; DNA Barcoding, Taxonomic ; }, abstract = {Eucosma callei sp. nov. is described and illustrated from the Iberian Peninsula. It differs from its Iberian congener, Eucosma gonzalezalvarezi Agenjo, 1970, in external appearance and genitalia. The 5' barcode fragments of the mitochondrial gene COI (the DNA barcode) are presented and confirms the description of this new species.}, }
@article {pmid40174108, year = {2025}, author = {Cava, S and Rijllo, G and Zucco, G and Scalercio, S}, title = {Revisiting the genus Diplodoma Zeller, 1852 in Europe: DNA barcoding reveals the presence of an undescribed species from forested habitats of southern Italy (Lepidoptera: Psychidae).}, journal = {Zootaxa}, volume = {5583}, number = {2}, pages = {371-382}, doi = {10.11646/zootaxa.5583.2.8}, pmid = {40174108}, issn = {1175-5334}, mesh = {Animals ; Male ; DNA Barcoding, Taxonomic ; Female ; Italy ; Animal Distribution ; Ecosystem ; Phylogeny ; Forests ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; *Moths/classification/genetics/anatomy &amp; histology/growth &amp; development ; }, abstract = {Diplodoma Zeller, 1852 is a Eurasian genus belonging to the family Psychidae Boisduval, 1829 of which three species are known in Europe: Diplodoma adspersella Heinmann, 1870, D. laichartingella (Goeze, 1783), and D. taurica Zagulajev, 1986. Some authors have argued that Diplodoma adspersella may be a subspecies or even a form of D. laichartingella. The revision of literature and the study of DNA barcoding fragments confirmed the inconsistency of D. adspersella as a valid species, and therefore we propose the new synonymy of Diplodoma adspersella with D. laichartingella (syn. nov.). During recent surveys in southern Italy, three specimens of Diplodoma were collected. DNA barcoding and morphological analyses showed that COI sequences and male genitalia significantly differ from any previously studied specimen. As a result, we described Diplodoma giulioregenii sp. nov., leaving unaltered the number of species belonging to this genus known from Europe.}, }
@article {pmid40174101, year = {2025}, author = {Thiel, R and Knebelsberger, T and Chernova, N and Eidus, I}, title = {Two new species of eelpout genus Lycenchelys (Perciformes: Zoarcidae) from the Kuril-Kamchatka Trench, based on morphological and molecular evidence.}, journal = {Zootaxa}, volume = {5583}, number = {3}, pages = {491-508}, doi = {10.11646/zootaxa.5583.3.4}, pmid = {40174101}, issn = {1175-5334}, mesh = {Animals ; *Perciformes/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; Male ; Animal Distribution ; Phylogeny ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; Body Size ; Ecosystem ; }, abstract = {Two new species of eelpout genus Lycenchelys Gill, 1884 are described based on eight specimens caught at a depth between 3517 and 3580 m at the western slope of the upper margin of the Kuril-Kamchatka Trench, relatively close to the Bussol Strait and Simushir Island in the center of the Kuril Islands chain. Lycenchelys delanglei sp. nov. differs from its congeners by the following combination of characters: vertebrae 28-29 + 91-93 = 120-121; interorbital and occipital pores absent; postorbital pores 4; suborbital pores 10-12; preoperculomandibular pores 4 + 5; gill rakers 11-16; dorsal-fin rays 114-117, 2-3 free pterygiophores at the beginning of dorsal fin; anal-fin rays 96-98; pelvic-fin rays 2; pectoral-fin rays 16-17, ray tips of the pectoral fin exserted, especially the middle and lower ones; lateral line absent; pyloric caeca not developed. Lycenchelys renatae sp. nov. differs from its congeners by the following combination of characters: vertebrae 26-27 + 99-103 = 125-130; interorbital pores 0-1; occipital pores absent; postorbital pores 1-4; suborbital pores 6-9; preoperculomandibular pores 3-4 + 5; gill rakers 13-15; dorsal-fin rays 115-122, 1-3 free pterygiophores at the beginning of dorsal fin; anal-fin rays 102-106; pelvic-fin rays two; pectoral-fin rays 16-17, ray tips of the pectoral fin exserted, the middle and lower ones more so than the upper ones; lateral line mediolateral, poorly developed; pyloric caeca not developed. For each of the two described new species four mitochondrial COI sequences were analysed and share the same haplotype within species. The obtained DNA barcodes allowed discrimination of L. delanglei sp. nov. and L. renatae sp. nov. from each other and exhibit a genetic distance of 2,61%. The closest match of L. delanglei sp. nov. with already published sequences was Lycenchelys lenzeni with a sequence similarity of 98.47%, whereas the closest match of L. renatae sp. nov. with already published sequences was Lycenchelys jordani with a similarity of 98.62%. A new analysis of radiographs of the type specimens confirmed that L. birsteini should be considered as synonym of L. plicifera, especially due to similar numbers of free pterygiophores at the beginning of dorsal fin.}, }
@article {pmid40174087, year = {2025}, author = {Luengo, E and Genis-Armero, R and Clark, PF and Palero, F}, title = {Final stage phyllosoma of Galearctus sp. (Decapoda: Scyllaridae) from the Coral Sea.}, journal = {Zootaxa}, volume = {5584}, number = {1}, pages = {101-112}, doi = {10.11646/zootaxa.5584.1.6}, pmid = {40174087}, issn = {1175-5334}, mesh = {Animals ; Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Female ; Male ; Animal Distribution ; *Decapoda/classification/anatomy &amp; histology/growth &amp; development/genetics ; Body Size ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; DNA Barcoding, Taxonomic ; Ecosystem ; }, abstract = {Larval stages are known for only four out of eight Galearctus Holthuis, 2002 (Crustacea: Scyllaridae) species, a slipper lobster genus widely distributed throughout the Indo-Pacific region. DNA barcoding analyses of phyllosomae collected from the Coral Sea by the Australian Institute of Marine Science suggest the presence of two new genetic clades in the area, for which larvae cannot be discriminated morphologically. The last instar larva of an unknown species of Galearctus is described and illustrated in detail here. It is possible that this larval material may be assigned to G. umbilicatus, the only species of the genus lacking a DNA barcode. Morphological analyses and a literature review allowed the re-evaluation of previous Galearctus larval studies, identifying several misidentifications and inconsistencies. Further morphological and molecular revision of adult Galearctus species is required to confirm larval identities, but the results presented here indicate that the diversity of Galearctus may be underestimated.}, }
@article {pmid40174058, year = {2025}, author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Hendrix, SV and Helmick, EE and Bahder, BW}, title = {A new species of Cyclopoliarus (Hemiptera: Auchenorrhyncha: Fulgoromorpha: Cixiidae) from American oil palms (Elaeis oleifera) in Caño Negro, Costa Rica.}, journal = {Zootaxa}, volume = {5584}, number = {4}, pages = {523-538}, doi = {10.11646/zootaxa.5584.4.4}, pmid = {40174058}, issn = {1175-5334}, mesh = {Animals ; Costa Rica ; Male ; *Hemiptera/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; Phylogeny ; Animal Distribution ; *Arecaceae/parasitology ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Recent palm survey work in Costa Rica focusing on planthoppers has resulted in the discovery of several new taxa, primarily in Cixiidae and Derbidae. Here a new species of Cyclopoliarus Fennah, C. nigelwatsoni sp. nov., is described from Caño Negro, Limón Province, Costa Rica. The new species is compared with C. omani, the only other described Central American Cyclopoliarus. Supplemental molecular data is presented for the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and D9 to D10 expansion region of the 28S rRNA gene. A phylogeny is presented to place the new species relative to other available taxa.}, }
@article {pmid40174054, year = {2025}, author = {Lukhtanov, VA and Makhov, IA and Gagarina, AV and Romanovich, AE}, title = {Taxonomy of the West Palaearctic butterfly genus Palaeophilotes Forster, 1938 (Lepidoptera: Lycaenidae) based on combined analysis of COI barcodes and multilocus nuclear markers.}, journal = {Zootaxa}, volume = {5584}, number = {4}, pages = {570-580}, doi = {10.11646/zootaxa.5584.4.8}, pmid = {40174054}, issn = {1175-5334}, mesh = {Animals ; Phylogeny ; Male ; Female ; Animal Distribution ; DNA Barcoding, Taxonomic ; *Butterflies/classification/genetics/anatomy &amp; histology/growth &amp; development ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; Body Size ; Electron Transport Complex IV/genetics ; }, abstract = {Based on molecular phylogenetic analysis of all relevant taxa, we propose to consider the species previously classified as members of Pseudophilotes, Palaeophilotes, Rubrapterus, and Inderskia as belonging to a single genus, the valid name of which is Palaeophilotes. This genus can be divided into two subgenera: Rubrapterus with species P. bavius and P. fatma, and Palaeophilotes sensu stricto. The latter subgenus includes four lineages and nine species: (1) the P. abencerragus lineage (single species P. abencerragus), (2) P. barbagiae lineage (single species P. barbagiae), (3) P. panope lineage (P. panope and P. triphysina), and (4) P. baton lineage (P. panoptes, P. baton, P. vicrama, P. jacuticus and P. sinaicus). The name Borisinia Korb, 2013, syn. nov. is shown to be an objective synonym of Palaeophilotes Forster, 1938. The previously proposed synonymy of P. svetlana and P. marina with P. panope is supported by the identity of their DNA-barcodes. Palaeophilotes panope is reported for the Kazakhstan part of the Altai mountains for the first time. Palaeophilotes jacuticus is confirmed for the Lake Baikal region in Siberia.}, }
@article {pmid40174049, year = {2025}, author = {Serbina, L&#x160; and Malenovský, I and Queiroz, DL and Burckhardt, D}, title = {Jumping plant-lice of the tribe Paurocephalini (Hemiptera: Psylloidea: Liviidae) in Brazil.}, journal = {Zootaxa}, volume = {5585}, number = {1}, pages = {1-164}, doi = {10.11646/zootaxa.5585.1.1}, pmid = {40174049}, issn = {1175-5334}, mesh = {Animals ; Brazil ; Female ; Male ; *Hemiptera/anatomy &amp; histology/classification/genetics/growth &amp; development ; Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {The predominantly tropical tribe Paurocephalini of jumping plant-lice currently consists of seven genera and 94 described species worldwide, of which the genera Klyveria Burckhardt et al. and Melanastera Serbina et al. have been recorded from Brazil with two and one species, respectively. Here we review the taxonomy of the Brazilian species based on material collected from extensive fieldwork carried out in 15 states over the last decade. One species of Klyveria and 59 species of Melanastera are newly described, bringing the number of extant Klyveria spp. to three (both in Brazil and worldwide) and that of extant Melanastera spp. to 69 (60 in Brazil, 67 in the Neotropical region and one each in the Afrotropical and Oriental regions). The new species are described and illustrated, and identification keys for the Brazilian species are provided for adults and last instar immatures. The most diagnostically important structures are the distal segment of the aedeagus and the paramere, the forewing (shape, venation, surface spinules and colour pattern) and the female terminalia in the adults, and the chaetotaxy, tarsal arolium and shape of the additional pore fields on the caudal plate in the last instar immatures. The species descriptions are complemented by mitochondrial DNA barcodes (COI and cytB) and information on host plants. Klyveria spp. are restricted to Luehea (Malvaceae), while in Brazil 28 Melanastera spp. develop or are likely to develop on Melastomataceae, 18 spp. on Annonaceae, four spp. each on Asteraceae and Myristicaceae, and one species on Cannabaceae. Only three of the 63 species of Paurocephalini reported here from Brazil, are also known from other countries: two from Paraguay and one from Trinidad. Probably many more species of Melanastera are yet to be discovered and described. Priority in fieldwork should be given to areas that are at high risk of destruction or degradation by human activities, such as the Amazon rainforest, the Atlantic Forest and the Cerrado.}, }
@article {pmid40174044, year = {2024}, author = {Borkent, A and Spinelli, GR and Díaz, F and Steinke, D and Perez, KHJ and Stur, E and Hallwachs, W and Janzen, DH}, title = {Looking Into the Abyss-How Many Species of Biting Midges (Diptera: Ceratopogonidae) Are There? Their Remarkable Diversity in Costa Rica and Elsewhere.}, journal = {Zootaxa}, volume = {5555}, number = {3}, pages = {331-384}, doi = {10.11646/zootaxa.5555.3.3}, pmid = {40174044}, issn = {1175-5334}, mesh = {Animals ; Costa Rica ; *Ceratopogonidae/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; Male ; Animal Distribution ; *Biodiversity ; Body Size ; Ecosystem ; }, abstract = {The biting midges (Ceratopogonidae) are one of the most species-rich families of insects on the planet with over 6,200 named species. However, their true diversity is unknown and this paper is the first to address the question. Our systematic study of the family in Costa Rica indicates that 192 species were present in a four hectare area of cloudforest at Zurquí de Moravia, at 1,600 m after a year of intensive sampling. Combined with a collection from a single Malaise trap at Tapantí for one year, about 40 kms away and also at 1,600 m, the total was 245 species with significant differences between the two areas and with the strong majority unnamed. This compares to 430 named species for all of Costa Rica and 1,314 for the entire Neotropical Region. Barcoding of 221,407 specimens from Costa Rica similarly indicates large numbers of unnamed species with 4,023 BINs present. On this basis, we project at least 5,000 species in Costa Rica and using ratios of named species here and elsewhere, we suggest that nearly 73,000 are present worldwide. Details from Malaise traps in the Área de Conservación Guanacaste also indicate various levels of endemism. Samples from Bolivia support an interpretation of high diversity. The diversification of the family was examined by comparing phyletic lineages, rather than merely comparing numbers of species in various genera, providing insight as to why some lineages are more diverse than others. Zoogeographic patterns of named species suggest stronger southern connections for Costa Rican Ceratopogonidae in both cloudforest habitats as well as the country as a whole, although many are also more broadly distributed north and south of the country. Comparisons between various collecting methods at Zurquí de Moravia indicate the efficacy of Malaise traps but also the importance of light traps and other methods in sampling adults of Ceratopogonidae. Phenological data from the Malaise traps in the Área de Conservación Guanacaste suggest some patterns of emergence of adults in Costa Rica, the first for any tropical country anywhere.}, }
@article {pmid40173973, year = {2025}, author = {Huber, BA and Meng, G}, title = {Like grains of sand: Ninetis spiders on the Arabian Peninsula (Araneae, Pholcidae).}, journal = {Zootaxa}, volume = {5563}, number = {1}, pages = {290-335}, doi = {10.11646/zootaxa.5563.1.19}, pmid = {40173973}, issn = {1175-5334}, mesh = {Animals ; *Spiders/classification/anatomy &amp; histology/growth &amp; development/genetics ; Male ; Female ; Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Saudi Arabia ; Oman ; Phylogeny ; Ecosystem ; }, abstract = {Ninetinae is a group of small to tiny, short-legged daddy-longlegs spiders (Pholcidae) that has its highest diversity in the New World. Only two genera are known to occur in the Old World: the nominotypical genus Ninetis Simon, 1890 on the Arabian Peninsula and in Africa, and the monotypic genus Magana Huber, 2019 in Oman. Here we redescribe the type species of Ninetis, N. subtilissima Simon, 1890, and describe three new species from the Arabian Peninsula: N. amoud sp. nov. from Saudi Arabia, N. marnif sp. nov. and N. samail sp. nov. from Oman. All species descriptions are based on males and females, supported by CO1 barcodes, and accompanied by SEM photographs. While N. amoud sp. nov. is morphologically and genetically similar to N. subtilissima (and to the known African species, of which no CO1 barcodes are available), the two new Omani species are morphologically very distinct. Intraspecific genetic (K2P) distances are partly very high, in particular in N. amoud sp. nov. (up to 17%) and N. marnif sp. nov. (up to 13%). An exploratory species delimitation analysis suggests that these two nominal species might in fact represent several cryptic species each. No corresponding morphological variation was detected.}, }
@article {pmid40173932, year = {2025}, author = {Zuñiga, R and Valerio, AA and Hanson, P and Hallwachs, W and Janzen, DH}, title = {Endoparasitoid wasps of the genus Cubus (Hymenoptera, Ichneumonidae, Metopiinae) reared from caterpillars of Área de Conservación Guanacaste, Costa Rica.}, journal = {Zootaxa}, volume = {5590}, number = {3}, pages = {365-385}, doi = {10.11646/zootaxa.5590.3.4}, pmid = {40173932}, issn = {1175-5334}, mesh = {Animals ; Costa Rica ; *Wasps/anatomy &amp; histology/classification/growth &amp; development/genetics ; Female ; Male ; Animal Distribution ; *Moths/parasitology/growth &amp; development ; Body Size ; Larva/parasitology/growth &amp; development ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {As a result of COI barcoding over 200 reared specimens of what appeared to be Cubus validus from northwestern Costa Rica, and matching them with their host caterpillars and morphological traits, we describe eleven new sympatric species. All are endoparasitoids of leaf-rolling Crambidae (Lepidoptera). The new species, authored by Zúñiga, Valerio &amp; Hanson, are: Cubus alanflemingi, C. christhompsoni, C. curtsabrowskyi, C. duvalierbricenoi, C. gracewoodae, C. jeffcummingi, C. jimoharai, C. johnstiremani, C. manuelzumbadoi, C. montywoodi, and C. normwoodleyi. We also provide an illustrated key, a table of key morphological characters of each species, and a table of host records.}, }
@article {pmid40173915, year = {2025}, author = {Brodin, Y}, title = {Procladius (Diptera, Chironomidae) of Europe and a global view.}, journal = {Zootaxa}, volume = {5591}, number = {1}, pages = {1-127}, doi = {10.11646/zootaxa.5591.1.1}, pmid = {40173915}, issn = {1175-5334}, mesh = {Animals ; Male ; Europe ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development ; Female ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; }, abstract = {A project initiated in 1991 to untangle species-taxonomy of European Procladius (Chironomidae) has been accomplished. Increasing amount of material, loans and especially the development of barcodes and the BIN-system of BOLD, made finalization possible after about 33 years. An iterative process based on detailed studies of male morphology and barcode clusters, BINs, resulted in identification of 27 species present in Europe, most of them also in Asia (China, Japan, Mongolia and Russia) and North America (Canada and the United States). One hundred morphological characters were adopted for species identification of which the 30 most important ones were used to construct a species key and an additional helpdesk. The key contains three characters for each species separation as this is frequently needed for reliable identification. The ratio GspR, the outer length of the gonostylus process versus length of outer margin in gonostylus, proved to be the most important character for species identification. All but two of the 27 species have barcodes and BINs. All but one BIN contained only one species. The exception is a BIN that previously was divided into two BINs each containing one morphologically distinct species. Intraspecific divergence within the species ranged from 0‒3.3% and interspecific divergence from 2.0‒8.8%. Four new species are presented. These are P. exilis Brodin, new species, P. gemma Brodin, new species, P. saeticubitus Brodin, new species and P. tenebricosus Brodin &amp; Hellberg, new species. The other 23 species presented are as follows with new synonyms within brackets: P. appropinquatus (Lundström, 1916) [P. ruris Roback, 1971], P. bellus (Loew, 1866) [Tanypus rufovittatus van der Wulp, 1874, P. latifrons Kieffer, 1922, P. leucocoma Kieffer, 1922, P. profundorum Kieffer, 1923], P. breviatus Remmert, 1953, P. choreus (Meigen, 1804) [Chironomus incomptus Walker, 1856], P. clavus Roback, 1971, P. crassinervis (Zetterstedt, 1838) [Tanypus pectinatus Kieffer, 1909, P. bifasciatus Goetghebuer, 1936, P. cinereus Goetghebuer, 1936, P. abetus Roback, 1971], P. culiciformis (Linnaeus, 1767) [Tanypus sagittalis Kieffer, 1909, Trichotanypus scapularis Kieffer, 1924, P. freemani Sublette, 1964 in part], P. dentus Roback, 1971, P. ferrugineus (Kieffer, 1918) [Trichotanypus parvulus Kieffer, 1918, Trichotanypus fulvus Kieffer, 1924, Trichotanypus profundorum Kieffer, 1924, P. rugulosus Saether 2010], P. fimbriatus Wülker, 1959, P. flavifrons Edwards, 1929, P. floralis Kieffer, 1915, P. frigidus (Holmgren, 1869) [P. gretis Roback, 1971], P. imicola Kieffer, 1922 [P. bathyphilus Kieffer, 1922, P. nietus Roback, 1971], P. islandicus (Goetghebuer, 1931) [P. fuscus Brundin, 1949, P. vesus Roback, 1971], P. longistilus (Kieffer, 1916) [P. suecicus Brundin, 1949], P. lugens Kieffer, 1915 [P. macrotrichus Roback, 1971], P. lugubris (Zetterstedt, 1850) [P. barbatus Brundin, 1949, P. johnsoni Roback, 1980], P. nudipennis Brundin, 1947, P. pruinosus (Kieffer, 1924), P. signatus (Zetterstedt, 1850) [Trichotanypus nigriventris Kieffer, 1924, P. denticulatus Sublette, 1964 in part], P. simplicistilus Freeman, 1948, P. tatrensis Gowin, 1944. In addition, 12 species of Procladius not found in Europe are briefly described and it is indicated where they appear in the species-key. Species of Procladius have been reported from 133 countries or autonomies worldwide. As many as 12 species have been found in extreme cold places of the northern hemisphere, with mean annual temperature ‒10 C or more. Altitude records are at 4 730 m above sea level in the Himalayas. Larvae of most European species are known to be omnivorous, although predation might be more beneficial for growth. Synonyms and dubious names reduce the number of valid (accepted) species of Procladius according to Catalogue of Life and Systema Dipterorum with 34% worldwide. After the inclusion of four new species of the present study and two others from Asia the number or valid species of Procladius worldwide land on 69.}, }
@article {pmid40173762, year = {2025}, author = {Wang, M and Lai, Y and Liu, X}, title = {The green lacewing genus Kuwayamachrysa Tsukaguchi &amp; Tago, 2018 from China, with description of two new species based on morphological and molecular evidence.}, journal = {Zootaxa}, volume = {5570}, number = {1}, pages = {138-150}, doi = {10.11646/zootaxa.5570.1.6}, pmid = {40173762}, issn = {1175-5334}, mesh = {Animals ; China ; Male ; Female ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; *Neoptera/anatomy &amp; histology/classification/genetics/growth &amp; development ; Phylogeny ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; }, abstract = {Previously, Kuwayamachrysa Tsukaguchi &amp; Tago, 2018 (Neuroptera: Chrysopidae: Chrysopinae) was known as a monotypic green lacewing genus from the Palearctic region. Here we described two new species of Kuwayamachrysa from China: Kuwayamachrysa wujiaoensis sp. nov. and Kuwayamachrysa neptuna sp. nov. Also, Mallada qinlingensis Yang, 1989, currently named as Apertochrysa qinlingensis (Yang, 1989), is recognized as a junior synonym of Kuwayamachrysa kichijoi (Kuwayama, 1936). A key to the Kuwayamachrysa species is provided. The standard DNA barcoding region of cytochrome c oxidase subunit I (COI) of these species was sequenced for the verification of the new species.}, }
@article {pmid40173760, year = {2025}, author = {Słomczyński, K and Matera, T and Brodecki, J and Gadawski, P and Płóciennik, M}, title = {The first report from Poland and larvae description of Eukiefferiella dittmari Lehmann, 1972 (Diptera: Chironomidae) based on morphological and molecular characteristics.}, journal = {Zootaxa}, volume = {5570}, number = {1}, pages = {169-178}, doi = {10.11646/zootaxa.5570.1.8}, pmid = {40173760}, issn = {1175-5334}, mesh = {Animals ; *Chironomidae/anatomy &amp; histology/classification/genetics/growth &amp; development ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Poland ; Male ; Animal Distribution ; Female ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; Organ Size ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; }, abstract = {Eukiefferiella is a large genus in the family Chironomidae with over 50 species worldwide. Their immature stages have so far been described in many species in the western Palearctic. Nevertheless, some species are still known only from adult males. Presented below is a description of Eukiefferiella dittmari Lehmann, 1972 larvae first recorded in Poland in the pristine river Rawka. The larvae were collected from water moss and identified to the species level using a DNA barcode from BOLD database. E. dittmari larvae belong to E. ilkleyensis group having bifid SIII seta, and mentum with wide central tooth and four pairs of lateral teeth. At the genetic and morphological level, E. dittmari is a sister species to Nearctic E. endobryonia, also an aquatic moss dweller. The phylogenetic relation of these two species should be further investigated.}, }
@article {pmid40173718, year = {2025}, author = {Verdone, CJ and Williams, BW and Beaty, SR and Holland, VB and Grubbs, SA and Dewalt, RE}, title = {The adults, larvae, and systematics of the Nearctic Oemopteryx Klapálek, 1902 (Plecoptera: Taeniopterygidae).}, journal = {Zootaxa}, volume = {5595}, number = {1}, pages = {1-94}, doi = {10.11646/zootaxa.5595.1.1}, pmid = {40173718}, issn = {1175-5334}, mesh = {Animals ; Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Male ; Female ; Animal Distribution ; *Insecta/classification/anatomy &amp; histology/growth &amp; development/genetics ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; Body Size ; }, abstract = {The adult and larval life stages of the Nearctic species of Oemopteryx Klapálek, 1902 (Plecoptera: Taeniopterygidae) are reviewed using color images, scanning electron microscopy photomicrographs, variation in the barcode region of the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene, and distributional information. Two new species are described from the southeast Nearctic region. Adult and larval keys to Oemopteryx species are presented in addition to revised keys to genera for Nearctic Taeniopterygidae.}, }
@article {pmid40173671, year = {2024}, author = {Eiseman, CS and Feldman, TS and Palmer, MW}, title = {New larval host records, parasitoid records, and DNA barcoding data for North American leaf-mining leaf beetles (Coleoptera: Chrysomeloidea).}, journal = {Zootaxa}, volume = {5549}, number = {1}, pages = {1-60}, doi = {10.11646/zootaxa.5549.1.1}, pmid = {40173671}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera/parasitology/classification/genetics/growth &amp; development/anatomy &amp; histology ; DNA Barcoding, Taxonomic ; Larva/classification/parasitology/growth &amp; development/genetics/anatomy &amp; histology/physiology ; Female ; Male ; Animal Distribution ; Body Size ; Plant Leaves ; Animal Structures/growth &amp; development/anatomy &amp; histology ; *Hymenoptera/physiology/classification/genetics ; Organ Size ; }, abstract = {We discuss 46 species of North American leaf-mining leaf beetles (Coleoptera: Chrysomelidae, Megalopodidae), plus one external feeder observed to spin its cocoon within the leaf mine of another insect. For each species, we review previous records of larval and adult hosts and associated hymenopteran parasitoids, augmenting these with our own observations, including the first accounts of oviposition and larval habits for many species. We present the first rearing records for 12 of these species: Anisostena californica Van Dyke, A. funesta (Baly), A. lecontii (Baly), A. perspicua (Horn), Microrhopala excavata (Olivier), Odontota floridana Butte, Stenopodius lateralis (Schaeffer), Altica lazulina LeConte, Dibolia obscura Parry, Monoxia inornata Blake, Zeugophora puberula Crotch, and Z. varians Crotch; as well as 18 new state and provincial records for chrysomeloids, although some of these are based on tentative identifications. We also present original DNA barcoding data showing intra- and interspecific variation among 18 species of hispines (Chrysomelidae: Chalepini). Our data do not provide evidence for cryptic species within Baliosus nervosus (Panzer), Sumitrosis inaequalis (Weber), and S. rosea (Weber) hypothesized based on differences in larval hosts and leaf mines. However, they do suggest the possibility of cryptic species within Tilia-feeding B. nervosus, as well as within S. ancoroides (Schaeffer) and perhaps Microrhopala excavata and Odontota horni Smith. Our barcoding data also support the recognition of the Silphium-feeding M. laetula LeConte as distinct from the Solidago-feeding M. vittata (Fabricius).}, }
@article {pmid40173657, year = {2024}, author = {Loh, KH and Poong, SW and DU, J and Ong, JJL and Zheng, X and Li, Y and Hu, W}, title = {First record of the blue-and-yellow grouper Epinephelus flavocaeruleus (Lacepède 1802) (Perciformes: Epinephelidae) from the Borneo waters, Malaysia.}, journal = {Zootaxa}, volume = {5550}, number = {1}, pages = {133-144}, doi = {10.11646/zootaxa.5550.1.14}, pmid = {40173657}, issn = {1175-5334}, mesh = {Animals ; Malaysia ; Phylogeny ; Animal Distribution ; Male ; Female ; Borneo ; *Perciformes/classification/genetics/anatomy &amp; histology/growth &amp; development ; *Bass/classification/genetics/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; DNA Barcoding, Taxonomic ; }, abstract = {Groupers of the family Epinephelidae constitute a diverse and commercially valuable group of reef fishes globally. They comprise an assemblage of carnivorous marine fishes, comprising more than 177 species across 16 genera. The epinephelid genus Epinephelus, which consists of over 90 species, is found worldwide in the tropics and subtropics. To date, the ichthyofauna of Malaysia has documented a total of 43 epinephelid species. Apart from these, Epinephelus flavocaeruleus (Lacepède, 1802), commonly known as the blue-and-yellow grouper, is rarely reported in the Indo-Pacific Ocean. The present study extends the documented distribution range of E. flavocaeruleus eastwards from the Andaman Sea to the Borneo waters of Sabah, Malaysia. Five specimens of the blue-and-yellow grouper were collected from a local fish market. Species identification was confirmed by the color patterns and DNA barcoding of 630 base pairs of the cytochrome C oxidase I gene for all E. flavocaeruleus specimens, Epinephelus cyanopodus (Richardson, 1846), and 10 closely related Epinephelus species. The interspecies genetic distance ranged from 0.002-0.168. Results from the Templeton, Crandall, and Sing (TCS) haplotype network analysis and maximum likelihood phylogeny based on the COI marker indicate a close genetic relationship between E. flavocaeruleus and E. cyanopodus. However, we refrain from proposing any taxonomic revisions given that more in-depth studies using multiple molecular markers or phylogenomic analysis on a larger sample size are necessary to confirm the taxonomic status of both species. This study significantly contributes to a better understanding of the taxonomy, phylogenetic relationship, and genetic diversity of E. flavocaeruleus.}, }
@article {pmid40173619, year = {2024}, author = {Leong, WI and Yu, JK and Tsai, IJ and Kaczmarek, &#x141; and Lee, YC and Lin, CP}, title = {Echiniscus gemmatussp. nov. (Heterotardigrada: Echiniscidae; the spinulosus morphogroup) from Macau, China.}, journal = {Zootaxa}, volume = {5551}, number = {2}, pages = {333-352}, doi = {10.11646/zootaxa.5551.2.5}, pmid = {40173619}, issn = {1175-5334}, mesh = {Animals ; *Tardigrada/classification/anatomy &amp; histology/genetics/growth &amp; development ; China ; Animal Distribution ; Phylogeny ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Body Size ; Organ Size ; Female ; DNA Barcoding, Taxonomic ; Male ; Ecosystem ; }, abstract = {The study of tardigrades in urban environments, particularly in natural areas within cities, has been significantly overlooked. A recent discovery of a new species of tardigrade in lichens collected from Mong Há Hill Municipal Park in Macau provides new insights into the population of tardigrades within the city. Echiniscus gemmatus sp. nov. was identified based on distinct morphological characters, morphometric measurements, and DNA sequences of nuclear (18S rRNA, 28S rRNA, ITS-1, and ITS-2), as well as a mitochondrial (COI) markers. Our research indicates that Ech. gemmatus sp. nov. belongs to the Echiniscus spinulosus morphogroup and is most similar to Ech. tropicalis, as confirmed by both qualitative characters and DNA barcoding. Notably, Echiniscus gemmatus sp. nov. exhibits distinct characteristics that differentiate it from other members of the Ech. spinulosus morphogroup, including (1) often asymmetrical short spines B, C, Cd, Dd, and E, and (2) larger and more visible pores tend to be concentrated in the median and posterior portions of the first and second paired plates, with their visibility gradually decreasing towards the anterior and lateral suture regions.}, }
@article {pmid40173612, year = {2024}, author = {Jiang, ZH and Li, T and Yan, M and Wang, JX and Zheng, XY and Hu, SJ}, title = {The life history of Smerinthus minor Mell, 1937, with a review of the East Asian species of the genus Smerinthus Latreille, 1802 (Lepidoptera: Sphingidae).}, journal = {Zootaxa}, volume = {5551}, number = {3}, pages = {453-478}, doi = {10.11646/zootaxa.5551.3.2}, pmid = {40173612}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; Animal Distribution ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Asia, Eastern ; Body Size ; China ; DNA Barcoding, Taxonomic ; *Moths/anatomy &amp; histology/classification/growth &amp; development/genetics ; Organ Size ; Phylogeny ; }, abstract = {The six species of the genus Smerinthus Latreille, 1802 known from China, namely S. caecus Ménétriés, 1857, S. kindermannii Lederer, 1853, S. minor Mell, 1937, S. ocellata (Linnaeus, 1758), S. planus Walker, 1856, and S. szechuanus (Clark, 1938) (Lepidoptera, Sphingidae, Smerinthinae, Smerinthini), are examined and illustrated, including the first description of the life history and female genitalia of S. minor. Diagnostic features and distribution maps of all Smerinthus species in East Asia are provided, together with a phylogenetic analysis based on DNA barcode sequences and a global checklist of all Smerinthus species.}, }
@article {pmid40173608, year = {2024}, author = {Kodama, M and Kodama, N and Mukaida, Y and Hosoki, TK and Nakamoto, K and Tanita, I and Yamada, H}, title = {First record of the genus Cymadusa Savigny, 1816 (Crustacea: Amphipoda: Ampithoidae) from Japan, with redescription and DNA barcoding for C. imbroglio Rabindranath, 1972.}, journal = {Zootaxa}, volume = {5551}, number = {3}, pages = {556-568}, doi = {10.11646/zootaxa.5551.3.6}, pmid = {40173608}, issn = {1175-5334}, mesh = {Animals ; *Amphipoda/classification/genetics/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; Japan ; Female ; Male ; Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Ecosystem ; }, abstract = {The ampithoid amphipod Cymadusa imbroglio Rabindranath, 1972 was collected from Ishigaki Island, southwest Japan, as the first Japanese record of the genus. The specimens collected from Ishigaki Island also represent the northernmost record of the species. We herein provide a detailed description and illustration of the specimens from Ishigaki Island. Sequences of COI were determined from two specimens for DNA barcoding and future taxonomic studies.}, }
@article {pmid40173599, year = {2024}, author = {Eiseman, CS and Lonsdale, O and Montgomery, GA and Jacobsen, JM and Kahn, EX and Rosati, MC and Hauser, M and Parikh, GR and Yu, D}, title = {Invasive Cape ivy (Asteraceae: Delairea odorata Lem.) confirmed as a host for the North American leafminer Liriomyza temperata Spencer (Diptera: Agromyzidae).}, journal = {Zootaxa}, volume = {5555}, number = {1}, pages = {24-34}, doi = {10.11646/zootaxa.5555.1.2}, pmid = {40173599}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; Introduced Species ; *Asteraceae/parasitology ; *Diptera/classification/anatomy &amp; histology/growth &amp; development/genetics/physiology ; Animal Distribution ; California ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; *Tephritidae/classification/anatomy &amp; histology ; }, abstract = {A leafminer reared in California from Cape ivy (Asteraceae: Delairea odorata Lem.), an invasive plant introduced from South Africa, is identified as Liriomyza temperata Spencer (Diptera: Agromyzidae). This is believed to be a novel host association for a native Nearctic fly, which appears to have been introduced in Hawaii along with Cape ivy. Liriomyza tricornis Lonsdale syn. nov. is treated as a junior synonym of L. temperata. There are no previous host records for either taxon. We review previously published rearing records of North American Liriomyza spp. from other plants in the tribe Senecioneae, as well as observations of unidentified Liriomyza mines on these plants. We also discuss the leaf mine and DNA barcode of an undetermined Trypeta sp. (Diptera: Tephritidae) found mining leaves of Cape ivy in California.}, }
@article {pmid40173572, year = {2025}, author = {Ps, FP and Arjunan, JK and Venu, S and Eranhottu, S and Ummath, A and Kalita, S and Pv, MR and Sadaka, S}, title = {Taxonomic redescription and molecular confirmation of Lutjanus rufolineatus (Acanthuriformes: Lutjanidae) from the Andaman Islands, India.}, journal = {Zootaxa}, volume = {5566}, number = {2}, pages = {370-380}, doi = {10.11646/zootaxa.5566.2.7}, pmid = {40173572}, issn = {1175-5334}, mesh = {Animals ; Animal Distribution ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Body Size ; DNA Barcoding, Taxonomic ; Ecosystem ; India ; Organ Size ; Phylogeny ; *Fishes/anatomy &amp; histology/classification ; }, abstract = {We provide a detailed taxonomic redescription of Lutjanus rufolineatus, based on six specimens collected from the Andaman Islands, India. The species' taxonomic status and distribution have historically been misinterpreted within Indian waters due to close similarities with congeners, leading to frequent misidentification. To address this, we performed comprehensive morphological and molecular analyses, including DNA barcoding and phylogenetic reconstruction, to confirm the identity of L. rufolineatus and clarify its relationships with related species. Our findings emphasize the value of thorough taxonomic assessment in delineating species boundaries, particularly for understudied marine fauna. Additionally, this research fills critical gaps in the taxonomy of Indian marine fishes, addressing past ambiguities and enhancing regional biodiversity records. By integrating morphological and molecular data, this study underscores the importance of precise species identification for improved biodiversity conservation and management efforts in the Indo-Pacific.}, }
@article {pmid40173511, year = {2025}, author = {Zaldívar-Riverón, A and Castañeda-Osorio, R and Shaw, SR}, title = {Three new species and phylogenetic affinity of the neotropical genus Sericobracon Shaw (Braconidae: Doryctinae).}, journal = {Zootaxa}, volume = {5613}, number = {1}, pages = {171-185}, doi = {10.11646/zootaxa.5613.1.9}, pmid = {40173511}, issn = {1175-5334}, mesh = {Animals ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Costa Rica ; Organ Size ; Phylogeny ; *Hymenoptera/anatomy &amp; histology/classification ; }, abstract = {Sericobracon Shaw is a small doryctine genus which was erected based on two species from Trinidad and the U.S. Virgin Islands (St. Croix) in the Caribbean Sea (S. arimaensis Shaw and S. evansi Shaw). Its type species, S. arimaensis, was reported as endoparasitoid of an Embioptera species, which is a unique biology for known Braconidae. Here we describe three new species of Sericobracon from Costa Rica: S. paulmarshi Zaldívar-Riverón &amp; Shaw, S. puravida Zaldívar-Riverón &amp; Shaw, and S. zunigai Zaldívar-Riverón &amp; Shaw. The former species is characterized with DNA barcoding, providing the first such molecular data for any species in this genus. We also investigated the phylogenetic affinity of the genus within the subfamily Doryctinae based on nuclear UCE data. Sericobracon was recovered within the main Neotropical doryctine clade closely related to Bolivar Zaldívar-Riverón &amp; Rodríguez-Jiménez and Parallorhogas Marsh. We discuss the higher taxonomic classification of Sericobracon and the latter two genera within the Doryctinae based on these relationships recovered and their shared morphological features. A key to species and digital photographs of the five described species of Sericobracon are provided.}, }
@article {pmid40173502, year = {2025}, author = {Jaroenchaiwattanachote, C and Pramual, P and Wangwasit, K and Bunchalee, P and Thanee, I}, title = {Integrative taxonomy and DNA barcoding of Thai Caddisflies (Trichoptera), with the description of a new Species.}, journal = {Zootaxa}, volume = {5613}, number = {2}, pages = {307-322}, doi = {10.11646/zootaxa.5613.2.6}, pmid = {40173502}, issn = {1175-5334}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Thailand ; *Insecta/classification/genetics/anatomy &amp; histology/growth &amp; development ; Male ; Female ; Phylogeny ; Electron Transport Complex IV/genetics ; Animal Distribution ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; Body Size ; }, abstract = {Caddisflies (Trichoptera) are abundant and diverse aquatic insects. Their immature stages inhabit a wide range of aquatic environments, making them ideal candidates for water quality biomonitoring. However, the limited morphological characteristics available for species identification in the immature stages pose a significant challenge to their application in biomonitoring. In this study, we evaluated the effectiveness of DNA barcoding, based on mitochondrial cytochrome c oxidase I (COI) sequences, for species identification of caddisflies in Thailand. A total of 1,487 adult specimens were collected and morphologically identified into 13 species across 8 genera and 4 families. From these taxa, 88 COI sequences were generated from representative specimens. Maximum intraspecific genetic divergence ranged from 0% to 3.08%. Only three species were successfully matched to COI sequences in the BOLD database, while nine species are reported here for the first time, and one species remained ambiguous. Integrating COI barcoding sequences with morphological data revealed that one species, morphologically similar to Triplectides indicus (Walker 1852), represents a novel species, Triplectides buengkanensis sp. nov. We provide a detailed description, illustrations, diagnostic features, and DNA barcoding sequences for this new species.}, }
@article {pmid40173501, year = {2025}, author = {Kerkig, P and Quicke, DLJ and Latibari, MH and Butcher, BA}, title = {World checklist of the genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with description of a new species from Thailand.}, journal = {Zootaxa}, volume = {5613}, number = {2}, pages = {323-336}, doi = {10.11646/zootaxa.5613.2.7}, pmid = {40173501}, issn = {1175-5334}, mesh = {Animals ; Thailand ; Male ; Female ; Phylogeny ; *Wasps/classification/anatomy &amp; histology/genetics/growth &amp; development ; Animal Distribution ; Organ Size ; Checklist ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {We describe and illustrate a new species of the aphidiine braconid genus Lipolexis Förster, Lipolexis khaoyaiensis sp. nov., from Thailand, using an integrative approach. Morphologically, the new species is similar to L. peregrinus Tomanović and Kocić, 2020, but molecular analysis showed clear separation of at least 27 independent Lipolexis lineages, only eight of which correspond to previously known species, plus the one which represents the new species described here. A molecular phylogeny based on all available barcodes support that the genus comprises two well supported clades, with L. khaoyaiensis sp. nov. being recovered in the gracilis species-group with strong support (100% ultrafast bootstrap). A modified section of the identification key to species of Lipolexis is added to include the new species. Reported host associations for each of the described species as well as a distribution map of all records of species plus provenances of all barcoded specimens is provided.}, }
@article {pmid40173486, year = {2025}, author = {Lee, DJ and Roh, SJ}, title = {A new species of the genus Unilepidotricha (Lepidoptera, Meessiidae) from Ulleungdo island, Korea.}, journal = {Zootaxa}, volume = {5613}, number = {3}, pages = {585-592}, doi = {10.11646/zootaxa.5613.3.10}, pmid = {40173486}, issn = {1175-5334}, mesh = {Animals ; Male ; Republic of Korea ; Female ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; Animal Distribution ; Animal Structures/growth &amp; development/anatomy &amp; histology ; Organ Size ; Body Size ; Islands ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {In this study, we describe a new species, Unilepidotricha ulleungensis sp. nov., from Korea. All available information on U. ulleungensis is presented, including collecting locations and illustrations of adult and male genitalia. Additionally, DNA barcodes for the species are provided.}, }
@article {pmid40170826, year = {2025}, author = {Liu, Y and Liu, K and Dong, W and Dong, S and Wang, Y and Xu, C and Li, E and Sun, J}, title = {Chloroplast Genome Evolution of Hamamelidaceae at Subfamily Level.}, journal = {Ecology and evolution}, volume = {15}, number = {4}, pages = {e71141}, pmid = {40170826}, issn = {2045-7758}, abstract = {The Hamamelidaceae is significant for its contributions to construction, furniture making, and ornamental use, including 26 genera and 119 species. However, complete chloroplast genome sequences of Hamamelidaceae species have been reported less frequently. In this study, five species were newly sequenced, and seven others available complete chloroplast genomes were added to compare the chloroplast genome evolution in Hamamelidaceae at the subfamily level. The results indicated that the chloroplast genome size ranged from 158,116 to 159,941 bp, encoding 79 to 81 protein-coding genes, four ribosomal RNA genes, and 30 to 31 transfer RNA genes. A robust phylogenetic tree of Hamamelidaceae was obtained using complete chloroplast genomes, supporting that all Hamamelidaceae species formed a monophyletic group and divided into four subfamilies. Exbucklandioideae was the first diverged group within Hamamelidaceae, followed by Mytilarioideae, Disanthoideae, and Hamamelidoideae, which formed a clade. Furthermore, three new potential DNA barcodes were provided: trnH-psbA, psbJ-petA, and ycf1. This study confirms that the complete chloroplast genome data provide a more accurate and confident resolution of the phylogenetic relationships within the Hamamelidaceae. These new genomic data not only enhance the understanding of genome evolution but also provide a better understanding of the phylogenetic relationships of Hamamelidaceae.}, }
@article {pmid40170416, year = {2025}, author = {Surmacz, B and Vecchi, M and Fontaneto, D and Budzik, K and Godziek, J and Matsko, Y and Stec, D}, title = {COI Metabarcoding With a Curated Reference Database and Optimized Protocol Provides a Reliable Species-Level Diversity Assessment of Tardigrades.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12972}, pmid = {40170416}, issn = {1749-4877}, support = {2022/45/N/NZ8/01992//the National Science Centre, Poland/ ; 2022/44/C/NZ8/00050//the National Science Centre, Poland/ ; //the National Biodiversity Future Centre (NBFC)/ ; CN00000033//the Italian Ministry of University and Research, PNRR, Missione 4 Componente 2, "Dalla ricerca all'impresa," Investimento 1.4/ ; }, abstract = {DNA metabarcoding is revolutionizing biodiversity research by providing rapid and efficient ways of collecting species occurrence data. However, it has not yet been effectively applied to many taxonomic groups, mainly due to a significant lack of reference sequences and dedicated protocols. One such group is the tardigrades-a charismatic phylum of microinvertebrates known for their extremophilic and cryptobiotic capabilities. In this study, we provide the first curated database of 3194 tardigrade COI sequences sourced from public databases and supplemented with newly produced barcodes. We demonstrate tardigrade metabarcoding in action with optimized PCR primers and a sample processing protocol using 78 samples collected in Poland and Italy. The metabarcoding revealed the presence of more than a hundred operational taxonomic units classified as Tardigrada, representing 23 genera. We compared the metabarcoding results with a morphological survey, which revealed the presence of the same genera, but a lower number of species-level taxa identified morphologically. We observed congruent patterns of tardigrade species richness and taxonomic composition between metabarcoding and morphological surveys in both within-sample and regional fauna composition levels. The metabarcoding had a higher discriminatory power, revealing cryptic diversity, and distinguishing species belonging to taxonomically challenging species complexes. By combining metabarcoding with morphological study, we were able to find rare taxa, including novel biogeographic records and putative species new to science, showing also that this approach can be extremely powerful and effective in meiofauna research.}, }
@article {pmid40169572, year = {2025}, author = {Martino, N and Yan, H and Abbott, G and Fahlberg, M and Forward, S and Kim, KH and Wu, Y and Zhu, H and Kwok, SJJ and Yun, SH}, title = {Large-scale combinatorial optical barcoding of cells with laser particles.}, journal = {Light, science &amp; applications}, volume = {14}, number = {1}, pages = {148}, pmid = {40169572}, issn = {2047-7538}, support = {K99 HG013129/HG/NHGRI NIH HHS/United States ; R01 EB034687/EB/NIBIB NIH HHS/United States ; R01-EB033155//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R44 CA281529/CA/NCI NIH HHS/United States ; R44CA281529//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-EB034687//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 EB033155/EB/NIBIB NIH HHS/United States ; }, abstract = {The identification of individual cells is crucial for advancements in single-cell analysis. Optically readable barcodes provide a means to distinguish and track cells through repeated, non-destructive measurements. Traditional fluorophore-based methods are limited by the finite number of unique barcodes they can produce. Laser particles (LPs), which emit narrowband peaks over a wide spectral range, have emerged as a promising technology for single-cell barcoding. Here, we demonstrate the use of multiple LPs to generate combinatorial barcodes, enabling the identification of a vast number of live cells. We introduce a theoretical framework for estimating the number of LPs required for unique barcodes and the expected identification error rate. Additionally, we present an improved LP-tagging method that is highly effective across a variety of cell types and evaluate its biocompatibility. Our experimental results show successful barcoding of several million cells, closely matching our theoretical predictions. This research marks a significant step forward in the scalability of LP technology for single-cell tracking and analysis.}, }
@article {pmid40168522, year = {2025}, author = {Men, J and Lv, S and Wang, Y and Wang, X and Bi, Y and Bi, S}, title = {Stimuli-Responsive Barcode Probe-Mediated Self-Powered Biosensor Enables Dual-Signal Amplification for Ultrasensitive Detection of Circulating Tumor Cells.}, journal = {Analytical chemistry}, volume = {97}, number = {14}, pages = {8056-8064}, doi = {10.1021/acs.analchem.5c00601}, pmid = {40168522}, issn = {1520-6882}, mesh = {Humans ; *Neoplastic Cells, Circulating/pathology ; *Biosensing Techniques/methods ; Hep G2 Cells ; Aptamers, Nucleotide/chemistry ; Limit of Detection ; Hyaluronic Acid/chemistry ; }, abstract = {Circulating tumor cells (CTCs) serve as valuable biomarkers for early cancer diagnosis in low abundance in the bloodstream. Therefore, the development of a biosensor for the ultrasensitive detection of CTCs is imperative. Herein, an enzymatic biofuel cell (EBFC)-based self-powered biosensor has been developed in which the recognition of CTCs with a stimuli-responsive barcode probe (SRBP) triggers the opening of a circuit "lock" and further activates the DNA dual-signal amplification, achieving ultrasensitive detection of CTCs. The SRBP is fabricated based on the hyaluronic acid (HA)-modified ZIF-8 framework, which is functionalized with Trigger and H2 at a certain ratio and further connected on magnetic beads via the hybridization between Trigger and the aptamer (Apt) of HepG2 cells. The specific recognition of target CTCs, hepatocellular carcinoma cell line G2 (HepG2) cells, by Apt results in the release of SRBP. Upon the stimuli of glutathione (GSH) under weakly acidic conditions (pH 5-6), ZIF-8 is disintegrated, leading to the releasing of Zn[2+], accompanied by the liberation of H2 and Trigger. As a result, the dual-signal amplification, that is, DNAzyme-mediated cyclic cleavage of substrate-linked SiO2 (Sub-SiO2) on the bioanode and catalytic hairpin assembly (CHA) on the biocathode, is activated. This self-powered biosensor achieves ultrasensitive detection of HepG2 cells with a detection limit as low as 3 cells/mL and excellent specificity, which exhibits substantial potential for early diagnosis of cancers.}, }
@article {pmid40166335, year = {2025}, author = {Schaefer, NK and Pavlovic, BJ and Pollen, AA}, title = {CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40166335}, issn = {2692-8205}, support = {P51 OD011132/OD/NIH HHS/United States ; S10 OD028511/OD/NIH HHS/United States ; DP2 MH122400/MH/NIMH NIH HHS/United States ; R01 MH134981/MH/NIMH NIH HHS/United States ; R01 AG087959/AG/NIA NIH HHS/United States ; }, abstract = {Pooled processing, in which cells from multiple sources are cultured or captured together, is an increasingly popular strategy for droplet-based single cell sequencing studies. This design allows efficient scaling of experiments, isolation of cell-intrinsic differences, and mitigation of batch effects. We present CellBouncer, a computational toolkit for demultiplexing and analyzing single-cell sequencing data from pooled experiments. We demonstrate that CellBouncer can separate and quantify multi-species and multi-individual cell mixtures, identify unknown mitochondrial haplotypes in cells, assign treatments from lipid-conjugated barcodes or CRISPR sgRNAs, and infer pool composition, outperforming existing methods. We also introduce methods to quantify ambient RNA contamination per cell, infer individual donors' contributions to the ambient RNA pool, and determine a consensus doublet rate harmonized across data types. Applying these tools to tetraploid composite cells, we identify a competitive advantage of human over chimpanzee mitochondria across 10 cell fusion lines and provide evidence for inter-mitochondrial incompatibility and mito-nuclear incompatibility between species.}, }
@article {pmid40166332, year = {2025}, 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 Ras -Driven Lung Adenocarcinoma.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.15.642187}, pmid = {40166332}, issn = {2692-8205}, abstract = {The TBX2 subfamily of T-box transcription factors (including Tbx2 , Tbx3 , Tbx4 , Tbx5) plays an essential role in lung development. Downregulation of these genes in human Lung adenocarcinoma (LUAD) suggests that these genes may be tumor suppressive, however because downregulation 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 TuBa-seq, a high-throughput tumor-barcoding system, we quantified the growth effects of these knockouts during early and late tumorigenesis. Chd2 loss consistently suppressed tumor progression, while Tbx2 loss exhibited stage-dependent effects. Notably, Egr1 emerged as a potent tumor suppressor, with its knockout increasing tumor size (∼5x) at 20 weeks, surpassing 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 LUAD.}, }
@article {pmid40166312, year = {2025}, author = {Monge, M and Giovanetti, SM and Ravishankar, A and Sadhu, MJ}, title = {Highly replicated experiments studying complex genotypes using nested DNA barcodes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40166312}, issn = {2692-8205}, support = {ZIA HG200401/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Many biological experiments involve studying the differences caused by genetic modifications, including genotypes composed of modifications at more than one locus. However, as the number and complexity of the genotypes increases, independently generating and tracking the necessary number of biological replicate samples becomes a major challenge. We developed a barcode-based method to track large numbers of independent replicates of combinatorial genotypes in a pooled format, enabling robust detection of subtle phenotypic differences. To construct a plasmid library of combinatorial genotypes, we utilized a nested serial cloning process to combine gene variants of interest that have associated DNA barcodes. The final plasmids each contain variants of multiple genes of interest, and a combined barcode that specifies the genotype of all the genes while also encoding a random sequence for tracking individual replicates. Sequencing of the pool of barcodes by next-generation sequencing allows the whole population to be studied in a single flask, enabling a high degree of replication even for complex genotypes. Using this approach, we tested the functionality of combinations of yeast, human, and null orthologs of the nucleotide excision repair factor I (NEF-1) complex and found that cells expressing all three yeast NEF-1 subunits had superior growth in DNA-damaging conditions. We also assessed the sensitivity of our method by simulating downsampling of barcodes across different degrees of phenotypic differentiation. Our results demonstrate the utility of NICR barcodes for high-throughput combinatorial genetic screens and provide a scalable framework for exploring complex genotype-phenotype relationships.}, }
@article {pmid40166192, year = {2025}, author = {Mazelis, I and Sun, H and Kulkarni, A and Torre, T and Klein, AM}, title = {Multi-step genomics on single cells and live cultures in sub-nanoliter capsules.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40166192}, issn = {2692-8205}, support = {R21 HG012771/HG/NHGRI NIH HHS/United States ; R33 CA278392/CA/NCI NIH HHS/United States ; }, abstract = {Single-cell genomics encompasses a set of methods whereby hundreds to millions of cells are individually subjected to multiplexed assays including sequencing DNA, chromatin accessibility or modification, RNA, or combinations thereof[1,2]. These methods enable unbiased, systematic discovery of cellular phenotypes and their dynamics[1-3]. Many functional genomic methods, however, require multiple steps that cannot be easily scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells, mRNA, and gDNA, while allowing free diffusion of media, enzymes and reagents. CAGEs enable carrying out high-throughput assays that require multiple steps, including combining genomics with live-cell assays. We establish methods for barcoding CAGE DNA and RNA libraries, and apply them to measure persistence of gene expression programs by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extend them to live-cell assays.}, }
@article {pmid40163932, year = {2025}, author = {Richard Beaulieu, S and Ribéreau-Gayon, A and Devèze, T and Forbes, SL and Germain, H}, title = {Molecular identification of fungi associated with advanced decomposition at a human taphonomy facility in Canada.}, journal = {Forensic science international}, volume = {370}, number = {}, pages = {112451}, doi = {10.1016/j.forsciint.2025.112451}, pmid = {40163932}, issn = {1872-6283}, mesh = {Humans ; *Postmortem Changes ; *Fungi/genetics/isolation &amp; purification ; DNA, Fungal/isolation &amp; purification/genetics ; Polymerase Chain Reaction ; Quebec ; Male ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Forensic Pathology ; Female ; }, abstract = {Forensic taphonomy investigates the postmortem processes of human remains, focusing on the environmental factors that influence decomposition. Recent studies have highlighted the potential forensic relevance of fungi in this context, but the knowledge base remains limited. This study explored fungal communities associated with outdoor human decomposition at the REST[ES] facility in Quebec. Nested PCR amplification and Illumina MiSeq sequencing were used to identify fungal species on discolored patches of twelve samples of desiccated soft tissues from three donors. Twelve fungal species were putatively identified, some of which were previously unknown on human remains, including Leucosporidium yakuticum, Tausania pullulans, and Fusicolla species. These fungi may contribute to tissue discoloration and following longitudinal investigation, could serve as biomarkers for forensic reconstructions, including place and time of death. This study emphasizes the need for further research into the role of fungi in human decomposition processes and their applications in forensic science.}, }
@article {pmid40163300, year = {2025}, author = {Umkehrer, C and Obenauf, A}, title = {Functional Lineage Tracing Using CaTCH.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2905}, number = {}, pages = {95-120}, pmid = {40163300}, issn = {1940-6029}, mesh = {*Flow Cytometry/methods ; *Cell Lineage/genetics ; Humans ; Animals ; *DNA Barcoding, Taxonomic/methods ; }, abstract = {CaTCH is a functional lineage tracing tool using genetic barcodes to label and follow million of cell clones in a selection experiment. Furthermore, CaTCH allows to isolate specific cell clones from heterogeneous populations by their barcode. Thus, founding clones of a phenotype of interest can be retrospectively isolated alive using FACS (fluorescence-activated cell sorting), allowing to perform functional experiments. Example applications of this method are investigating the evolutionary selection of resistance to therapies or other evolutionary pressures.}, }
@article {pmid40162456, year = {2024}, author = {Jose, AT and Kaur, T and Sarangi, S and Khan, S and Tripathi, S and Chandrasekaran, S and Kashwani, R}, title = {Innovations in denture marking: Forensic applications and clinical implications: A review.}, journal = {Bioinformation}, volume = {20}, number = {11}, pages = {1542-1548}, pmid = {40162456}, issn = {0973-2063}, abstract = {Denture marking is a vital tool in forensic odontology and clinical practice, aiding in the identification of dental prostheses, especially in disaster victim identification and cases where traditional methods fail. Techniques are categorized into surface methods like engraving and laser etching and inclusion methods such as embedding RFID tags or barcodes. These markers provide reliable identification, assist in recovering lost prostheses and can be implemented at low cost in routine dental practice. Advancements like RFID technology have made denture marking more efficient and reliable. Overall, denture marking enhances patient safety, reduces redundancy and holds significant medico-legal value.}, }
@article {pmid40161029, year = {2025}, author = {Mwamula, AO and Bae, CH and Kim, YS and Lee, DW}, title = {Description of Deladenus uljinensis n. sp., and additional DNA barcode data for Deladenus posteroporus (Nematoda: Neotylenchidae) from Korea.}, journal = {Journal of nematology}, volume = {57}, number = {1}, pages = {20250013}, pmid = {40161029}, issn = {0022-300X}, abstract = {A new species of the genus Deladenus isolated from a dead red pine tree was characterized using morphometric and molecular DNA data. Deladenus uljinensis n. sp. is characterized by its lateral fields with six to seven lines, pharyngeal corpus without a distinct median bulb and lacking a chamber, esophageal-intestinal junction located immediately behind the nerve ring, hemizonid located posterior to nerve ring, excretory pore opening within the contour of hemizonid or just at the base of hemizonid, vulva with no lateral vulval flaps, post-uterine sac rudimentary or absent, vulva-anus distance ca. equal to tail length, tail conoid, gradually tapering to a broadly rounded terminus, and slender spicules, 18.5-21.5 μm long. The new species was compared with morphologically close species including D. gilanica, D. brevis, D. pakistanensis, D. oryzae, D. uteropinusus, D. aridus, and D. durus. Additionally, D. posteroporus was also characterized and the population represents the first record of the species outside its type locality. The phylogenetic relationships among species were reconstructed using 18S-rRNA, 28S-rRNA and COI gene sequences. Inferences from the more informative 28S-rRNA gene suggest that D. uljinensis n. sp. is a sister species to the morphologically close D. gilanica.}, }
@article {pmid40151624, year = {2025}, author = {Sheng, W}, title = {The complete chloroplast genome of Gerbera piloselloides (L.) Cass., 1820 (Carduoideae, Asteraceae) and its phylogenetic analysis.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20251070}, pmid = {40151624}, issn = {2391-5412}, abstract = {Gerbera piloselloides (L.) Cass., 1820 of the genus Gerbera is of importance in Chinese ethnic medicine. In this research, the whole genome DNA of G. piloselloides was extracted and sequenced using the Illumina NovaSeq platform, its chloroplast genome was assembled and annotated, and its sequence characteristics were analyzed using bioinformatic methods. The results showed that its chloroplast genome has a length of 151,871 bp and contains 133 annotated genes, consisting of 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. In total, 202 simple sequence repeat sites and 43 long repeats were detected in G. piloselloides, mainly consisting of mono-nucleotide and tri-nucleotide repeats, with A/T as the major base composition. The chloroplast genome of G. piloselloides contains 22,772 codons, with leucine-coding codons being the most abundant. Comparative genomics showed that the genome structure, composition and variation were basically the same in the Asteraceae family. The phylogenetic tree analysis indicated a close relationship between the genus Atractylodes and Gerbera, consistent with the morphological classification. The research of the G. piloselloides chloroplast genome will lay a foundation for species discrimination, genetic evolution analysis, and DNA barcode construction in Gerbera plants.}, }
@article {pmid40151605, year = {2025}, author = {Li, J and He, Q and Li, S and Yao, Z}, title = {Filling a zoogeographical gap in China: Taxonomic descriptions of six new spider species of the Pholcusphungiformes species group (Araneae, Pholcidae).}, journal = {ZooKeys}, volume = {1232}, number = {}, pages = {285-310}, pmid = {40151605}, issn = {1313-2989}, abstract = {The spiders of the Pholcusphungiformes species group in China are distributed across the Lüliang Mountains and the Yanshan-Taihang Mountains in northern China, and the Changbai Mountains, which border northeastern China and North Korea. This study presents the first collection of the P.phungiformes species group from mountainous regions situated between the Yanshan-Taihang and Changbai Mountains, revealing six new species: Pholcuschaoyang S. Li &amp; Yao, sp. nov., P.hebei S. Li &amp; Yao, sp. nov., P.huludao S. Li &amp; Yao, sp. nov., P.jinzhou S. Li &amp; Yao, sp. nov., P.liaoning S. Li &amp; Yao, sp. nov., and P.qin S. Li &amp; Yao, sp. nov. Detailed diagnoses, descriptions, photomicroscopy images, and DNA barcodes of new species are provided.}, }
@article {pmid40150400, year = {2025}, author = {Tuncharoen, S and Panase, P and Panprommin, N and Wangkahart, E and Ruenkoed, S and Mongkolwit, K and Panprommin, D}, title = {New Data on Rhinogobius chiengmaiensis and Rhinogobius mekongianus in Thailand by DNA Barcoding and Morphological Methods.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {6}, pages = {}, pmid = {40150400}, issn = {2076-2615}, support = {Fundamental Fund 2025, Grant No. 5051/2567//University of Phayao and Thailand Science Research and Innovation Fund/ ; }, abstract = {A combination of morphological analysis and DNA barcoding (partial sequences of the cytochrome c oxidase I (COI) gene) was used to differentiate four gobiid fish species in the family Oxudercidae. Rhinogobius chiengmaiensis and Rhinogobius mekongianus were found in Thailand, while Eugnathogobius siamensis and Pseudogobiopsis oligactis were used for comparative purposes. Morphological identification relied on appearances, counts, and measurements. The 707-base pair COI sequences from eleven samples of four gobiid species were compared with reference sequences in public databases to confirm their scientific names. The average AT content was 51.8 ± 0.5% and the GC content was 48.2 ± 0.5%. Intraspecific genetic distances ranged from 0.00-0.28%, while interspecific genetic distances ranged from 0.86-16.63%. A neighbor-joining (NJ) phylogenetic tree depicted the relationships among the COI sequences of these species. Morphological analysis and COI sequences successfully distinguished the four gobiid species. Notably, the COI sequences of R. chiengmaiensis, R. mekongianus, and E. siamensis were previously unreported, hence, this study is the first report to add their sequences to public databases. These results can serve as valuable information for the management of aquatic resources, conservation, and aquaculture efforts.}, }
@article {pmid40149407, year = {2025}, author = {Chatzoglou, E and Tsaousi, N and Spetsieri, A and Malandrakis, EE and Miliou, H}, title = {Rapid Detection of Epinephelus Species Substitution in the Greek Market Using High-Resolution Melting Analysis.}, journal = {Genes}, volume = {16}, number = {3}, pages = {}, pmid = {40149407}, issn = {2073-4425}, mesh = {Animals ; Greece ; Polymorphism, Single Nucleotide ; *Seafood/analysis ; *DNA Barcoding, Taxonomic/methods ; *Bass/genetics/classification ; Endangered Species ; }, abstract = {Background/Objectives: Fish are vital in the Mediterranean diet, offering protein, nutrients, and ω-3 fatty acids. Greek consumers favor wild-caught, high-value fish like the dusky grouper (Epinephelus marginatus) classified as "vulnerable" and the white grouper (Epinephelus aeneus) classified as "near threatened" species, according to the IUCN Red List. Due to their premium prices and complex supply chains, these species are susceptible to fraud, especially through mislabeling. This practice not only deceives consumers but also poses health risks and encourages illegal fishing. DNA-based methods have shown effectiveness in accurately identifying species, even in processed samples. The aim of this study is to apply high-resolution melting analysis (HRM) as a rapid, effective method for monitoring the appropriate labeling of the two Epinephelus species in the Greek market. Methods: In this study, fresh fish from Greek catches as well as cooked, frozen, and filleted samples collected from the Greek market were identified using DNA barcoding. HRM analysis based on single nucleotide polymorphisms (SNPs) was used to differentiate between locally sourced E. marginatus and E. aeneus from their imported counterparts or from other species available in the Greek market that could be used in substitution incidents. Results: Using HRM analysis, cases of species mislabeling were identified and were also confirmed using sequencing. Conclusions: HRM analysis proved to be an accurate and cost-effective method for rapidly processing a large number of samples; therefore, it could serve as a valuable tool in extensive market controls as well as for bio-diversity conservation monitoring.}, }
@article {pmid40149301, year = {2025}, author = {Arakelyan, A and Sirunyan, T and Khachatryan, G and Hakobyan, S and Minasyan, A and Nikoghosyan, M and Hakobyan, M and Chavushyan, A and Martirosyan, G and Hakobyan, Y and Binder, H}, title = {Assigning Transcriptomic Subtypes to Chronic Lymphocytic Leukemia Samples Using Nanopore RNA-Sequencing and Self-Organizing Maps.}, journal = {Cancers}, volume = {17}, number = {6}, pages = {}, pmid = {40149301}, issn = {2072-6694}, support = {21AG-1F021//State Committee of Science/ ; }, abstract = {Background/Objectives: Massively parallel sequencing technologies have advanced chronic lymphocytic leukemia (CLL) diagnostics and precision oncology. Illumina platforms, while offering robust performance, require substantial infrastructure investment and a large number of samples for cost-efficiency. Conversely, third-generation long-read nanopore sequencing from Oxford Nanopore Technologies (ONT) can significantly reduce sequencing costs, making it a valuable tool in resource-limited settings. However, nanopore sequencing faces challenges with lower accuracy and throughput than Illumina platforms, necessitating additional computational strategies. In this paper, we demonstrate that integrating publicly available short-read data with in-house generated ONT data, along with the application of machine learning approaches, enables the characterization of the CLL transcriptome landscape, the identification of clinically relevant molecular subtypes, and the assignment of these subtypes to nanopore-sequenced samples. Methods: Public Illumina RNA sequencing data for 608 CLL samples were obtained from the CLL-Map Portal. CLL transcriptome analysis, gene module identification, and transcriptomic subtype classification were performed using the oposSOM R package for high-dimensional data visualization with self-organizing maps. Eight CLL patients were recruited from the Hematology Center After Prof. R. Yeolyan (Yerevan, Armenia). Sequencing libraries were prepared from blood total RNA using the PCR-cDNA sequencing-barcoding kit (SQK-PCB109) following the manufacturer's protocol and sequenced on an R9.4.1 flow cell for 24-48 h. Raw reads were converted to TPM values. These data were projected into the SOMs space using the supervised SOMs portrayal (supSOM) approach to predict the SOMs portrait of new samples using support vector machine regression. Results: The CLL transcriptomic landscape reveals disruptions in gene modules (spots) associated with T cell cytotoxicity, B and T cell activation, inflammation, cell cycle, DNA repair, proliferation, and splicing. A specific gene module contained genes associated with poor prognosis in CLL. Accordingly, CLL samples were classified into T-cell cytotoxic, immune, proliferative, splicing, and three mixed types: proliferative-immune, proliferative-splicing, and proliferative-immune-splicing. These transcriptomic subtypes were associated with survival orthogonal to gender and mutation status. Using supervised machine learning approaches, transcriptomic subtypes were assigned to patient samples sequenced with nanopore sequencing. Conclusions: This study demonstrates that the CLL transcriptome landscape can be parsed into functional modules, revealing distinct molecular subtypes based on proliferative and immune activity, with important implications for prognosis and treatment that are orthogonal to other molecular classifications. Additionally, the integration of nanopore sequencing with public datasets and machine learning offers a cost-effective approach to molecular subtyping and prognostic prediction, facilitating more accessible and personalized CLL care.}, }
@article {pmid40148595, year = {2025}, author = {Qian, N and Weinstein, JA}, title = {Spatial transcriptomic imaging of an intact organism using volumetric DNA microscopy.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40148595}, issn = {1546-1696}, support = {NSF-2121044//National Science Foundation (NSF)/ ; Runyon-Rachleff Innovation Award//Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation)/ ; R01 HG009276/HG/NHGRI NIH HHS/United States ; NIH-1R35GM143017-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35 GM143017/GM/NIGMS NIH HHS/United States ; Moore Inventor Fellowship//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Lymphatic, nervous and tumor tissues exhibit complex physiology arising from three-dimensional interactions within genetically unique microenvironments. Here we develop a technology capable of volumetrically imaging transcriptomes, genotypes and morphologies in a single measurement, without relying on prior knowledge of spatial organization or genetic sequences. Our method extends DNA microscopy into three dimensions at scales involving 10[7] molecules by forming a distributed intermolecular network of proximal unique DNA barcodes tagging complementary DNA molecules inside the specimen. After sequencing the DNA-encoded network, an image of molecular positions is inferred using geodesic spectral embeddings, a dimensionality reduction approach that we show to be especially suitable for this data-inverse problem. Applying whole-transcriptome volumetric DNA microscopy to intact zebrafish embryos, we demonstrate that three-dimensional image inference recapitulates zebrafish morphology and known gene expression patterns, capturing the spatial organization of gene sequences. Our extension of spatial genetic measurements to three dimensions, independent of prior templates, opens the door to detailed joint resolution of genomics and morphology in biological tissues.}, }
@article {pmid40144949, year = {2025}, author = {Pešić, V and Zawal, A and Gülle, P and Gülle, &#x130; and Jovanović, M and Bańkowska, A and Musielak, S and Smit, H}, title = {Water mite diversity from southwestern Türkiye through the lens of the DNA barcodes, with the description of one new species (Acari, Hydrachnidia).}, journal = {ZooKeys}, volume = {1232}, number = {}, pages = {205-236}, pmid = {40144949}, issn = {1313-2989}, abstract = {This study presents the molecular and morphological results from an analysis of water mites collected in southwestern Türkiye. 83 COI barcodes are provided, clustered into 40 BINs, with 23 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). The first DNA barcodes for eight water mite species are uploaded into the BOLD database. In total, 34 water mite species were identified and one of them, Iranothyasmarismortui (Gerecke, 1999) is newly reported from Türkiye. Iranothyasalhajarica Pešić, Gerecke &amp; Smit, 2009 is excluded from the fauna of Türkiye. Sperchonfundamentalis Bader &amp; Sepasgozarian, 1980, a species previously synonymized with S.glandulosus Koenike, 1886 is resurrected as a valid species. One species, Atractidesturani Pešić, Zawal, Gülle &amp; Smit, sp. nov. (Hygrobatidae), is described as new to science.}, }
@article {pmid40144381, year = {2025}, author = {Kryukov, AA and Yurkov, AP and Gorbunova, AO and Kudriashova, TR and Gorenkova, AI and Kosulnikov, YV and Laktionov, YV}, title = {Evaluation of the biodiversity of arbuscular mycorrhizal fungi during regenerative succession in quarries.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {29}, number = {1}, pages = {72-78}, doi = {10.18699/vjgb-25-09}, pmid = {40144381}, issn = {2500-0462}, abstract = {Arbuscular mycorrhizal fungi (AMF) play a key role in the regenerative successions of plant communities after anthropogenic disturbances, particularly in quarries. AMF help plants with water and mineral nutrition, contributing to the restoration rate of vegetation cover. The research is aimed to study the biodiversity of AMF using molecular genetic methods at different stages of overgrowth of two quarries in the Leningrad region. Molecular genetic identification of fungi was carried out using Illumina MiSeq analysis of the ITS1 and ITS2 regions as barcodes for the identification of operational taxonomic units (OTUs) with species-level identification. An adapted and error-checked AMF genetic sequence database from NCBI was used as a reference. The study applied an optimized nucleic acid isolation technique for sandy soils. The results showed maximum AMF biodiversity at the initial stages of overgrowth - pioneer and grass stages - with minimum diversity observed at the shrub stage, where it decreased by five times. At the forest stage, the biodiversity of AMF was almost restored to the level seen at the grass stage. It has been shown that the biodiversity and species composition of AMF can vary greatly between the stages of regenerative succession and probably depends primarily on the biodiversity of grasses, with which AMF most effectively enter into symbiotic relationships. The analysis showed a reliable negative correlation between the number of AMF species and the number of woody plant species. Such studies can aid in understanding how plant-fungal symbiosis develops in regenerative successions and which AMF most effectively contribute to vegetation cover restoration.}, }
@article {pmid40144380, year = {2025}, author = {Gokhman, VE and Ryabinin, AS and Bykov, RA and Ilinsky, YY}, title = {The lowest chromosome number in the family Pteromalidae (Hymenoptera: Chalcidoidea): the karyotype and other genetic features of Pachycrepoideus vindemmiae (Rondani, 1875).}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {29}, number = {1}, pages = {108-112}, doi = {10.18699/vjgb-25-12}, pmid = {40144380}, issn = {2500-0462}, abstract = {Various genetic features of the hitman strain of the widespread parasitoid of Drosophilidae (Diptera), Pachycrepoideus vindemmiae (Rondani, 1875) (Pteromalidae, Pachyneurinae) were studied. This strain was established and is maintained at the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (Novosibirsk, Russia). An analysis of air-dried chromosome preparations from prepupae of this parasitoid showed that it has n = 4 and 2n = 8 in males and females, respectively, which is the lowest known chromosome number in the family Pteromalidae. All chromosomes in the karyotype of this species are metacentric. The first and second chromosomes are of similar size, the remaining ones are substantially shorter. The same results were obtained for an additional strain of this species kept at the Moscow State University (Moscow, Russia). A comparison of the DNA sequence of the barcoding region of the mitochondrial cytochrome c oxidase (COI) gene of the hitman strain of P. vindemmiae with those available from the GenBank and BoLD databases demonstrated that this strain clustered together with conspecifics originating from China, Turkey and Italy. Despite certain endosymbionts being previously reported for the genus Pachycrepoideus Ashmead, 1904 as well as for P. vindemmiae itself, the hitman strain turned out to be free of endosymbiotic bacteria in the genera Arsenophonus Gherna et al., 1991, Cardinium Zchori-Fein et al., 2004, Rickettsia da Rocha-Lima, 1916, Spiroplasma Saglio et al., 1973 and Wolbachia Hertig, 1936. The above-mentioned results improve our knowledge of various genetic features of parasitoids of the family Pteromalidae and those of P. vindemmiae in particular.}, }
@article {pmid40144376, year = {2025}, author = {Smirnov, AV and Korablev, AN and Serova, IA and Yunusova, AM and Muravyova, AA and Valeev, ES and Battulin, NR}, title = {Studying concatenation of the Cas9-cleaved transgenes using barcodes.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {29}, number = {1}, pages = {26-34}, doi = {10.18699/vjgb-25-04}, pmid = {40144376}, issn = {2500-0462}, abstract = {In pronuclear microinjection, the Cas9 endonuclease is employed to introduce in vivo DNA double-strand breaks at the genomic target locus or within the donor vector, thereby enhancing transgene integration. The manner by which Cas9 interacts with DNA repair factors during transgene end processing and integration is a topic of considerable interest and debate. In a previous study, we developed a barcode-based genetic system for the analysis of transgene recombination following pronuclear microinjection in mice. In this approach, the plasmid library is linearized with a restriction enzyme or a Cas9 RNP complex at the site between a pair of barcodes. A pool of barcoded molecules is injected into the pronucleus, resulting in the generation of multicopy concatemers. In the present report, we compared the effects of in vivo Cas9 cleavage (RNP+ experiment) and in vitro production of Cas9- linearized transgenes (RNP- experiment) on concatenation. In the RNP+ experiment, two transgenic single-copy embryos were identified. In the RNP- experiment, six positive embryos were identified, four of which exhibited lowcopy concatemers. Next-generation sequencing (NGS) analysis of the barcodes revealed that 53 % of the barcoded ends had switched their initial library pairs, indicating the involvement of the homologous recombination pathway. Out of the 20 transgene-transgene junctions examined, 11 exhibited no mutations and were presumably generated through re-ligation of Cas9-induced blunt ends. The majority of mutated junctions harbored asymmetrical deletions of 2-4 nucleotides, which were attributed to Cas9 end trimming. These findings suggest that Cas9-bound DNA may present obstacles to concatenation. Conversely, clean DNA ends were observed to be joined in a manner similar to restriction-digested ends, albeit with distinctive asymmetry. Future experiments utilizing in vivo CRISPR/ Cas cleavage will facilitate a deeper understanding of how CRISPR-endonucleases influence DNA repair processes.}, }
@article {pmid40141343, year = {2025}, author = {Cai, S and Liao, X and Xi, Y and Chu, Y and Liu, S and Su, H and Dou, D and Xu, J and Xiao, S}, title = {Screening and Application of DNA Markers for Novel Quality Consistency Evaluation in Panax ginseng.}, journal = {International journal of molecular sciences}, volume = {26}, number = {6}, pages = {}, pmid = {40141343}, issn = {1422-0067}, support = {CI2023E002//Scientific and technological innovation project of China Academy of Chinese Medical Sciences/ ; 2023YFC3504000//National Key Research and Development Program of China/ ; ZZ13-YQ-047//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, mesh = {*Panax/genetics ; Genetic Markers ; Quality Control ; *DNA, Plant/genetics ; Microsatellite Repeats ; Polymorphism, Genetic ; Medicine, Chinese Traditional ; Genetic Variation ; Genome, Chloroplast ; }, abstract = {Quality control remains a challenge in traditional Chinese medicine (TCM). This study introduced a novel genetic-based quality control method for TCM. Genetic variations in ginseng were evaluated across whole-genome, chloroplast genome, and ITS2 DNA barcode dimensions. Significant genetic variations were found in whole-genome comparison, leading to the use of inter-simple sequence repeat markers to assess the genetic diversity of ginseng decoction pieces (PG), garden ginseng (GG), and ginseng under forest (FG). Fingerprints of ginseng samples revealed instability within some batches. These evaluations were transformed into information entropy to calculate the size of Hardy-Weinberg equilibrium population (HWEP). FG had significantly higher genetic and chemical minimum HWEP than GG (p < 0.05). Notably, a significant positive correlation was observed between the minimum HWEP for genetics and for chemistry (r = 0.857, p = 0.014). Genetic polymorphism analysis of ginseng has the potential to evaluate chemical quality consistency, offering a new method to ensure quality consistency in TCM.}, }
@article {pmid40139723, year = {2025}, author = {Singh, M and Zhang, M and Espinal-Ruiz, M and Rathnayake, S and Xue, J and Shi, J and Liu, X and Hanner, R and Corradini, MG}, title = {Maple Syrup Adulteration: Fluorescence Fingerprints as a Source of Information for Enhanced Detection.}, journal = {Journal of AOAC International}, volume = {}, number = {}, pages = {}, doi = {10.1093/jaoacint/qsaf029}, pmid = {40139723}, issn = {1944-7922}, abstract = {BACKGROUND: Maple syrup is often adulterated by dilution or substitution with other syrups due to its high demand and price. Fingerprinting techniques, e.g., DNA barcoding, detect adulteration in other foods. However, extensive processing during the transformation of sap into syrup degrades the genetic material, lowering the efficacy of this approach. In contrast, fluorescence fingerprints (EEMs) rely on a sample's intrinsic fluorophores to provide valuable information for detecting adulteration.<br><br>OBJECTIVE: This study evaluates the capabilities and limitations of EEMs to scout for adulteration markers and discriminate between pure and adulterated maple syrup samples.<br><br>METHODS: EEMs of pure amber and dark maple syrups and admixtures with common adulterants (beet, corn, and rice syrups at 1-50%) were obtained using a spectrophotometer (&#x3bb;ex=250-500&#x2009;nm, and &#x3bb;em=280-650&#x2009;nm).&#x202f;The major components of the EEMs were identified using PARAFAC and confirmed by LC-MS/MS. The ratio of intensities of the two most prevalent EEM features was calculated. An artificial neural network (ANN) and a convolutional neural network (CNN) were developed to analyze the EEMs based on emissions at two selected excitation wavelengths and the full EEM image, respectively, to discriminate presence and level of adulteration.<br><br>RESULTS: EEMs of the samples allowed identifying valuable discriminatory information. The efficacy of the ratio of the emission intensities at &#x3bb;em=350 and 425 (I425/I350) when &#x3bb;ex= 290&#x2009;nm to identify potential fraud (70-86% correct identifications) depended on the adulterant. This ratio was particularly effective for beet syrup adulteration, even at concentrations <2%. Applying machine learning algorithms improved detection for all adulterants. ANN correctly identified adulteration type and level (90 &amp; 82%). The CNN approach accurately classified 75-99% of adulterated syrups but required additional computational power and denser data sets.<br><br>CONCLUSION: This study aids in providing a quick, non-destructive and green monitoring tool for maple syrup adulteration based on its intrinsic fluorophores.<br><br>HIGHLIGHTS: Maple syrup is often adulterated with other syrups due to high demand and price. DNA barcoding is ineffective in detecting maple syrup adulteration due to DNA degradation. Fluorescence fingerprints or EEMs allow scouting for discriminatory markers in maple syrup. Machine learning algorithms (ANN and CNN) applied to EEM data can aid detection.}, }
@article {pmid40134468, year = {2025}, author = {Ge, X and Wang, J and Chai, L and Yan, C}, title = {Descriptions of hitherto unknown larvae of the genus Hydropsyche Pictet, 1834 from China (Trichoptera, Hydropsychidae).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e151321}, pmid = {40134468}, issn = {1314-2828}, abstract = {BACKGROUND: Hydropsyche Pictet, 1834 is the largest genus of Hydropsychinae. In China, larval descriptions exist for only about 20 species. Although the number of Hydropsyche larvae described in China has increased rapidly in recent years, larvae of more than 75% of Chinese Hydropsyche species remain unknown.<br><br>NEW INFORMATION: In this paper, we describe and illustrate the larvae of Hydropsychebriareus Malicky &amp; Chantaramongkol, 2000 and Hydropsychekozhantschikovi Martynov, 1924 for the first time. Neighbour-joining trees were reconstructed, based on known partial Hydropsyche species mtCOI barcodes.}, }
@article {pmid40134031, year = {2025}, author = {Wang, X and Wang, K and Zhang, W and Tang, Z and Zhang, H and Cheng, Y and Zhou, D and Zhang, C and Zhong, WZ and Ma, Q and Xu, J and Hu, Z}, title = {Clonal expansion dictates the efficacy of mitochondrial lineage tracing in single cells.}, journal = {Genome biology}, volume = {26}, number = {1}, pages = {70}, pmid = {40134031}, issn = {1474-760X}, support = {32300493//National Natural Sciences Foundation of China/ ; 32070870//National Natural Sciences Foundation of China/ ; 32070644//National Natural Sciences Foundation of China/ ; 82241236//National Natural Sciences Foundation of China/ ; 2022M723301//China Postdoctoral Science Foundation/ ; 2021B1515020042//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Humans ; *Single-Cell Analysis/methods ; *Cell Lineage/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Mutation ; }, abstract = {BACKGROUND: Mitochondrial DNA (mtDNA) variants hold promise as endogenous barcodes for tracking human cell lineages, but their efficacy as reliable lineage markers are hindered by the complex dynamics of mtDNA in somatic tissues.<br><br>RESULTS: Here, we use computational modeling and single-cell genomics to thoroughly interrogate the origin and clonal dynamics of mtDNA variants across various biological settings. Our findings reveal that the majority of mtDNA variants which are specifically present in a cell subpopulation, termed subpopulation-specific variants, are pre-existing heteroplasmies in the first cell instead of de novo somatic mutations during divisions. Moreover, subpopulation-specific variants demonstrate limited discriminatory power among different genuine lineages under weak clonal expansion; however, certain subpopulation-specific variants with consistently high frequencies among a subpopulation are capable of faithfully labeling cell lineages in scenarios of stringent clonal expansion, such as strongly expanded T cell populations in diseased conditions and clonal hematopoiesis in aged individuals. Inspired by our simulations, we introduce a lineage informative score, facilitating the identification of reliable mitochondrial lineage tracing markers across different modalities of single-cell genomic data.<br><br>CONCLUSIONS: Combining computational modeling and single-cell sequencing, our study reveals that the performance of mitochondrial lineage tracing is highly dependent on the extent of clonal expansion, which thus should be considered when applying mitochondrial lineage tracing.}, }
@article {pmid40133646, year = {2025}, author = {Neurauter, M and Vinzelj, JM and Strobl, SFA and Kappacher, C and Schlappack, T and Badzoka, J and Podmirseg, SM and Huck, CW and Rainer, M}, title = {Application of MALDI TOF and DART mass spectrometry as novel tools for classification of anaerobic gut fungi strains.}, journal = {Analytical and bioanalytical chemistry}, volume = {417}, number = {15}, pages = {3245-3256}, pmid = {40133646}, issn = {1618-2650}, support = {10.55776/I3808//Austrian Science Fund/ ; }, mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Fungi/classification/isolation &amp; purification/genetics ; Anaerobiosis ; *Gastrointestinal Microbiome ; *Mass Spectrometry/methods ; }, abstract = {Anaerobic gut fungi (AGF) have emerged as promising candidates for optimized biogas and biofuel production due to their unique repertoire of potent lignocellulose-degrading enzymes. However, identifying AGF strains through standard fungal DNA barcodes still poses challenges due to their distinct genomic features. This study explored the applicability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI) and direct analysis in real-time (DART) mass spectrometry (MS) as alternative methods for AGF identification. Further, the capability of the methods to differentiate strains from different growth phases was investigated. The study found that both MALDI and DART were viable methods for AGF strain identification. MALDI proved to be a precise and robust technique for strain discrimination with prediction accuracies of 94% for unknown standard samples. Even at longer growth times (>3 weeks) MALDI achieved good prediction accuracies with 84%; however, younger cultures (72 h) were only predicted with 63% accuracy. The fast on-target lysis with minimal chemical demand yielded suitable spectra for strain differentiation. DART MS, while effective with prediction accuracies of samples with the same age of up to 93%, exhibited lower prediction accuracies for cultures of different ages, with 14% for young (72 h) and 71% for old (>3 weeks) samples. Further research could enhance the capabilities of these mass spectrometry methods for AGF identification and broaden their application to species-level discrimination and a wider range of AGF genera.}, }
@article {pmid40126103, year = {2025}, author = {Warner, TC and Marando, VM and Santiago-Reyes, OA and Hart, EM and Smelyansky, SR and Carter, AW and Bernhardt, TG and Bryson, BD and Kim, DE and Kiessling, LL}, title = {Intercepting a Mycobacterial Biosynthetic Pathway with Covalent Labeling.}, journal = {Journal of the American Chemical Society}, volume = {147}, number = {13}, pages = {11189-11198}, doi = {10.1021/jacs.4c17913}, pmid = {40126103}, issn = {1520-5126}, mesh = {*Mycobacterium tuberculosis/metabolism/chemistry ; Azides/chemistry ; Biosynthetic Pathways ; *Polysaccharides/biosynthesis/chemistry ; Lactones/chemistry/metabolism ; }, abstract = {The mycobacterial cell envelope plays both infectious and protective roles. Understanding its structure is crucial for unlocking the molecular basis underlying these functions. Studying glycans, the primary components of the cell envelope, is challenging due to their limited native functional handles for chemoselective modification. New labeling methods exploit biorthogonal chemistry, using small molecule mimics that intercept cellular metabolism or late-stage glycan biosynthesis. However, these strategies can have practical limitations, including probe delivery and effectiveness. An ideal small molecule probe should be easily deployed and exploit the critical enzyme-substrate relationships of natural substrates. To this end, we developed a "probegenic" strategy to label mycobacteria. Our approach eliminates the need for explicit substrate mimicry, as the relevant functionality is revealed by a target enzyme. Specifically, we synthesized an azide-substituted trans-β-lactone probe (AzLac), which adopts a substrate-like structure upon covalent enzyme labeling. This probe is incorporated by mycolyltransferases into a core mycobacterial cell envelope glycan, including in the pathogen Mycobacterium tuberculosis. Unlike other probes of the cell envelope, AzLac facilitates selective covalent labeling of the inner leaflet of the mycomembrane. Using Corynebacterium glutamicum mycolyltransferase deletion strains, we implicated Cmt2 as the primary mycolyltransferase target. We leveraged the ability to modify the cell envelope by demonstrating that AzLac could be used to attach a DNA barcode to mycobacteria, which would help track infection dynamics. Thus, we expect AzLac will be a valuable means of monitoring and tracking the mycobacterial cell envelope. Moreover, we anticipate masking and revealing recognition motifs in probes can be applied to diverse cellular targets.}, }
@article {pmid40125407, year = {2025}, author = {Koffi, ADK and Babin, R and Delvare, G and Chérasse, S and Ouvrard, D and Shimbori, EM and Koigny, KJH and Kpangui, SK and Benoit, L and Galan, M and Yodé, CDV and Ouali N'goran, MS and Haran, JM}, title = {A barcode database for insects associated with the spread of the Cocoa Swollen Shoot Virus Disease in Côte d'Ivoire.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e144017}, pmid = {40125407}, issn = {1314-2828}, abstract = {Swollen Shoot is a viral disease affecting cocoa trees, transmitted by several species of mealybugs (Insecta, Hemiptera, Sternorrhyncha, Pseudococcidae). These insects maintain trophobiotic relationships with a complex and species-rich assemblage of ants protecting them and natural enemies controlling their populations. Here, we provide a curated DNA barcode database to characterise this insect community. Systematic observation of 7,500 cocoa trees was conducted, coupled with the collection of mealybug colonies and associated insect communities (parasitoids, predators and ants). Natural enemies were reared from mealybug colonies collected from 1,430 cocoa trees. Specimens were identified morphologically and sequenced for fragments of the standard DNA barcode region of the COI. We recovered 17 species of mealybugs from the family Pseudococcidae. Amongst these species, eight are new to the Ivorian cocoa orchard: Dysmicoccusneobrevipes Beardsley, Ferrisiadasylirii (Cockerell), Maconellicoccusugandae (Laing), Paracoccusmarginatus Williams &amp; Granara de Willink, Phenacoccussolenopsis Tinsley, Planococcusminor (Maskell), Pseudococcusconcavocerarii James and Pseudococcusocciduus De Lotto. Three of these species were identified for the first time in cocoa orchards in Africa: D.neobrevipes, Fe.dasylirii and Ph.solenopsis. A total of 54 ant species were identified and represented the first record of these species associated with mealybug colonies in cocoa in Côte d'Ivoire. Amongst the species associated with the mealybugs, 22 primary parasitoids, eight hyperparasitoids, 11 ladybirds beetles (Coccinellidae), seven gall midges (Cecidomyidae), one predatory lepidopteran species and four spider species were identified. Nine species of mealybugs parasitoids are newly recorded in the African cocoa orchards: Acerophagusaff.dysmicocci, Aloencyrtus sp., Anagyruskamali, Anagyrusaff.pseudococci, Aenasiusadvena, Clauseniaaff.corrugata, Gyranusoideaaff.tebygi, Zaplatycerusaff.natalensis (Encyrtidae) and Coccophaguspulvinariae (Aphelinidae) and one hyperparasitoid, Pachyneuronmuscarum (Pteromalidae). For Côte d'Ivoire in particular, besides the previously mentioned nine parasitoids and one hyperparasitoid, five additional species are recorded for the first time, including four primary parasitoids, Blepyrusinsularis (Encyrtidae), Clauseniacorrugata (Encyrtidae), Clausenia sp. (Encyrtidae), and Coccidoctonuspseudococci (Encyrtidae) and one hyperparasitoid, Cheiloneuruscyanonotus (Encyrtidae). These results significantly enhance the knowledge of the diversity of the entomofauna associated with Swollen Shoot disease and pave the way for developing control methods based on the natural regulation of its mealybug (Pseudococcidae) vectors.}, }
@article {pmid40124603, year = {2025}, author = {de Sousa, VE and da Silva Cortinhas, MCF and Creed, JC and Batista, MGS and Proietti, MC and Copertino, M}, title = {Assessing morphological variations in the seagrass genus Halodule (Cymodoceaceae) along the Brazilian coast through genetic analyses.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19038}, pmid = {40124603}, issn = {2167-8359}, mesh = {Brazil ; Phylogeny ; *Plant Leaves/anatomy &amp; histology/genetics ; *Alismatales/genetics/anatomy &amp; histology/classification ; Genetic Variation ; Ecosystem ; }, abstract = {BACKGROUND: Seagrass meadows are distributed globally and provide critical ecological functions and ecosystem services, but seagrasses are still poorly studied compared with other coastal and marine foundation species. Species taxonomy is uncertain in various seagrass genera, such as the genus Halodule. Until recently, the morphological characteristics of leaves were the major criteria for species identification. In Brazil, three species of Halodule are recognized and separated solely using leaf morphology criteria by some authors; however, the leaves present high variability and plasticity, resulting in great uncertainty about species diversity. A review of seagrass species validation using both morphological and phylogenetic methods is needed. This includes examining the genus Halodule with the aim of better understanding its diversity and spatial distribution and consequently supporting management and conservation goals.<br><br>METHODS: Plant samples with the morphological forms of H. beaudettei and H. wrightii were collected at five sites across three Brazilian marine ecoregions. Leaf tip format and leaf width and length were compared among all the sites and between the two populations with different leaf tip forms. Molecular diversity and divergence indices and analyses were used to estimate the genetic distance between H. wrightii and H. beaudettei populations. To determine the phylogenetic relationship between the two morphologies, we sequenced two molecular markers, the internal transcribed spacer (ITS) fragment and the rbcL gene, to construct phylogenetic trees using Bayesian inference.<br><br>RESULTS: We identified H. beaudettei morphology at two sites in Northeast Brazil, while H. wrightii was found in all the ecoregions in the remaining areas, distinguished by the leaf tip shape that occurred at each site. Leaf width and length varied across the five sites, and leaf length differed between H. wrightii and H. beaudettei, with higher values observed in H. beaudettei. Variations in morphological measurements may be related to habitat conditions at each site studied. No divergence was observed for the DNA sequences of two molecular markers, except for a single base in the ITS region, resulting in the Brazilian specimens merging at a single node in the phylogenetic trees. AMOVA and genetic distance analysis revealed low genetic variation but high structuring within populations. The ITS marker showed insufficient genetic variance to delineate the two morphologies as different species which indicating H. wrightii and H. beaudettei are closely related. A genomic approach is needed to fully resolve this issue. This study represents the first step toward the complete determination of the Halodule genus on the Brazilian coast.}, }
@article {pmid40123593, year = {2025}, author = {Silva, SE and Silva, LS and Eufrasio, LG and Cruz, GS and Lucini, F and Vechi, HT and Alves, MDM and Ribeiro, LRF and de Souza, KL and Moreira, JA and de Souza, JG and Morio, F and da Costa, GL and Baptista, BO and Tomé, LMR and Pedroso, SHSP and Iani, FCM and Adelino, T&#xc9;R and Castelo-Branco, D and Rossato, L and Peres, NTA and Santos, DA and Oliveira, MME and da Silva, KJG and Bastos, RW}, title = {Kodamaea ohmeri: An emergent yeast from a One Health perspective.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100359}, pmid = {40123593}, issn = {2666-5174}, abstract = {Kodamaea ohmeri is an emerging and opportunistic yeast associated with a high mortality rate in humans. As it is commonly found in the environment, it is possible that environmental conditions and agricultural practices contribute to the adaptation of this yeast and the selection of antifungal resistance. During a multicentric study in Brazil, conducted under a One Health perspective, 14 isolates of K. ohmeri were identified from different sources: three from blood cultures, three from animals (swine and poultry), and eight from animal environments (swine and poultry). Yeasts were isolated using CHROmagar® Candida medium and identified by MALDI-TOF MS and ITS rDNA barcoding. Minimum inhibitory concentration (MIC) was determined using the broth microdilution method for clinical (azoles, echinocandins, pyrimidine analogs, and polyenes), and environmental antifungals (tebuconazole, pyraclostrobin, carbendazim, and mancozeb), and hospital disinfectants (quaternary ammonium compounds). Of note, color variations of K. ohmeri were noted on CHROmagar® depending on the incubation time, which is likely to complicate its identification. Following polyphasic identification and taxonomic confirmation, all isolates demonstrated low MIC values for clinical antifungals, disinfectants, and tebuconazole. However, all isolates were able to grow in the presence of carbendazim, mancozeb, and pyraclostrobin. Together, these findings highlight the risks associated with the use of environmental azoles, such as tebuconazole, as they may impact non-target fungi of medical importance, but other fungicides do not present the same risk. This is the first study to demonstrate that K. ohmeri, an important emerging yeast in human medicine, can be isolated from various sources, including patients. Although the isolates exhibited low MIC values for clinical antifungals, it is crucial to monitor changes in sensitivity patterns over time in emerging microorganisms to prevent the development of multidrug resistance, which may originate in the environment.}, }
@article {pmid40121084, year = {2025}, author = {Zhao, A and Chan, MM}, title = {Cloning and validating systems for high throughput molecular recording.}, journal = {Methods in enzymology}, volume = {712}, number = {}, pages = {453-473}, doi = {10.1016/bs.mie.2025.01.015}, pmid = {40121084}, issn = {1557-7988}, mesh = {*Cloning, Molecular/methods ; CRISPR-Cas Systems ; Humans ; Animals ; Gene Editing/methods ; Cell Lineage/genetics ; Single-Cell Analysis/methods ; }, abstract = {Molecular recording technologies record and store information about cellular history. Lineage tracing is one form of molecular recording and produces information describing cellular trajectories during mammalian development, differentiation and maintenance of adult stem cell niches, and tumor evolution. Our molecular recorder technology utilizes CRISPR-Cas9 barcode editing to generate mutations in genomically integrated, engineered DNA cassettes, which are read out by single-cell RNA sequencing and used to produce high-resolution lineage trees. Here, we describe optimized cloning and validation procedures to construct the molecular recorder lineage tracing system. We include information on considerations of technology design, cloning procedures, the generation of lineage tracing cell lines, and time course experiments to assess their performance.}, }
@article {pmid40119005, year = {2025}, author = {Li, H and Bao, S and Farzad, N and Qin, X and Fung, AA and Zhang, D and Bai, Z and Tao, B and Fan, R}, title = {Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&amp;Tag-RNA-seq.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {40119005}, issn = {1750-2799}, support = {U54AG076043//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54AG079759//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UG3CA257393//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UH3CA257393//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01CA245313//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1MH128876//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54CA274509//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U01CA294514//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54CA268083//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {The epigenome of a cell is tightly correlated with gene transcription, which controls cell identity and diverse biological activities. Recent advances in spatial technologies have improved our understanding of tissue heterogeneity by analyzing transcriptomics or epigenomics with spatial information preserved, but have been mainly restricted to one molecular layer at a time. Here we present procedures for two spatially resolved sequencing methods, spatial-ATAC-RNA-seq and spatial-CUT&amp;Tag-RNA-seq, that co-profile transcriptome and epigenome genome wide. In both methods, transcriptomic readouts are generated through tissue fixation, permeabilization and in situ reverse transcription. In spatial-ATAC-RNA-seq, Tn5 transposase is used to probe accessible chromatin, and in spatial-CUT&amp;Tag-RNA-seq, the tissue is incubated with primary antibodies that target histone modifications, followed by Protein A-fused Tn5-induced tagmentation. Both methods leverage a microfluidic device that delivers two sets of oligonucleotide barcodes to generate a two-dimensional mosaic of tissue pixels at near single-cell resolution. A spatial-ATAC-RNA-seq or spatial-CUT&amp;Tag-RNA-seq library can be generated in 3-5 d, allowing researchers to simultaneously investigate the transcriptomic landscape and epigenomic landscape of an intact tissue section. This protocol is an extension of our previous spatially resolved epigenome sequencing protocol and provides opportunities in multimodal profiling.}, }
@article {pmid40119004, year = {2025}, author = {Li, L and Bowling, S and Lin, H and Chen, D and Wang, SW and Camargo, FD}, title = {DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity.}, journal = {Nature protocols}, volume = {20}, number = {8}, pages = {2319-2344}, pmid = {40119004}, issn = {1750-2799}, support = {32470700//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; K99 HL164969/HL/NHLBI NIH HHS/United States ; R01 HL128850/HL/NHLBI NIH HHS/United States ; RC2 DK131963/DK/NIDDK NIH HHS/United States ; R01 HL158192/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Cell Lineage/genetics ; Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; CRISPR-Cas Systems ; Gene Editing/methods ; }, abstract = {Lineage tracing is a powerful tool to study cell history and cell dynamics during tissue development and homeostasis. An increasingly popular approach for lineage tracing is to generate high-frequent mutations at given genomic loci, which can serve as genetic barcodes to label different cell lineages. However, current lineage tracing mouse models suffer from low barcode diversity and limited single-cell lineage coverage. We recently developed the DARLIN mouse model by incorporating three barcoding arrays within defined genomic loci and combining Cas9 and terminal deoxynucleotidyl transferase (TdT) to improve editing diversity in each barcode array. We estimated that DARLIN generates 10[18] distinct lineage barcodes in theory, and enables the recovery of lineage barcodes in over 70% of cells in single-cell assays. In addition, DARLIN can be induced with doxycycline to generate stable lineage barcodes across different tissues at a defined stage. Here we provide a step-by-step protocol on applying the DARLIN system for in vivo lineage tracing, including barcode induction, estimation of induction efficiency, barcode analysis with bulk and single-cell sequencing, and computational analysis. The execution time of this protocol is ~1 week for experimental data collection and ~1 d for running the computational analysis pipeline. To execute this protocol, one should be familiar with sequencing library generation and Linux operation. DARLIN opens the door to study the lineage relationships and the underlying molecular regulations across various tissues at physiological context.}, }
@article {pmid40117582, year = {2025}, author = {Catalano, R and Zhao, Y and Pecak, M and Korten, T and Diez, S}, title = {Barcoding Microtubules: Encoding Information onto Macromolecules by Photobleaching.}, journal = {Nano letters}, volume = {25}, number = {13}, pages = {5283-5290}, pmid = {40117582}, issn = {1530-6992}, mesh = {*Microtubules/chemistry/ultrastructure ; *Kinesins/chemistry ; *Photobleaching ; *Nanotechnology/methods ; Macromolecular Substances/chemistry ; Fourier Analysis ; }, abstract = {Kinesin-1-powered microtubules have emerged as versatile components in biocomputing and biosensing technologies. However, the inability to identify and track individual microtubules has constrained their applications to ensemble behaviors, limiting their potential for single-entity-based nanotechnologies. To address this challenge, we present a novel method for encoding digital information directly onto individual microtubules using photobleaching patterns. Binary numbers (1 to 15) were encoded within ∼12 μm segments of moving microtubules by photobleaching with a stationary pulsed laser, creating spatial frequency patterns corresponding to distinct bits of information. Fourier analysis enabled the accurate retrieval of the encoded data, demonstrating the feasibility of direct information storage and retrieval on macromolecular structures. This approach offers a transformative solution for recording microtubule trajectories within nanotechnological devices by encoding path information directly onto microtubules at branch points, obviating the need for video-based tracking. We anticipate that this innovation will advance the development of individualized microtubule-based technologies.}, }
@article {pmid40117330, year = {2025}, author = {Abdel-Glil, MY and Brandt, C and Pletz, MW and Neubauer, H and Sprague, LD}, title = {High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, pmid = {40117330}, issn = {2057-5858}, mesh = {*Nanopore Sequencing/methods/standards ; Reproducibility of Results ; *Bacteria/genetics/classification ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Nanopores ; }, abstract = {Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.}, }
@article {pmid40115270, year = {2025}, author = {Wu, Q and Xiang, P and Wang, C and Jing, C and Lin, X and Wang, Y and Chen, G and Lin, M and Xing, B}, title = {Diversity of lanternfish (Myctophidae) larvae along the Ninety East Ridge, Indian Ocean.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19144}, pmid = {40115270}, issn = {2167-8359}, mesh = {Animals ; Indian Ocean ; Larva/genetics/classification ; Phylogeny ; *Fishes/genetics/classification ; Zooplankton ; *Biodiversity ; Haplotypes ; }, abstract = {Since the 19th century, the impact of seamounts on the distribution of plankton has been a topic of considerable interest. The influence of seamounts on the biogeographic patterns of marine organisms is complex, with some aspects still under debate. It is generally accepted that seamounts can drive the upwelling of nutrient-rich deep waters. Tidal amplification, flow acceleration, and internal waves can further enhance vertical mixing, leading to increased primary productivity near seamounts. Seamounts may also act as barriers to the migration of marine organisms, affecting gene flow. Research on Pacific seamounts suggests these features might serve as "stepping stones" for the dispersal of marine species across the ocean. However, investigations of seamounts in the eastern Indian Ocean remain limited. Focusing on the Ninety East Ridge region in the eastern Indian Ocean, this study collected zooplankton samples using horizontal (surface) and vertical (0-200 m) plankton nets and measured temperature and salinity profiles with a conductivity, temperature, and depth (CTD) sensor. A total of 544 fish larvae were identified, including 260 lanternfish larvae, representing 38 species across 12 genera, determined through COI DNA barcoding. Phylogenetic trees and haplotype networks were constructed to analyze genetic distances and population structures of lanternfish species. Among the samples, intra-specific genetic distances ranged from 0% to 2.99%, while inter-specific distances ranged from 1.88% to 25.71%. Except for Notolychnus valdiviae (Brauer, 1904), the maximum intra-specific distances were lower than the minimum inter-specific distances for all species. Haplotype analysis of nine species revealed significant variations in haplotype number, structure, and spatial distribution. Specifically, Ceratoscopelus warmingii (Lütken, 1892) and N. valdiviae exhibited a notable north-south divergence pattern, consistent with the temperature and salinity distribution of the region's water masses. This conclusion was supported by analysis of molecular variance analysis, suggesting that larval stages of certain lanternfish species may struggle to cross boundaries between water masses. However, the remaining species showed no significant north-south distribution differences, possibly due to their adaptive capabilities, vertical migration patterns, or the duration of their planktonic larval stages. These findings suggest that seamounts and water mass distribution have varying implications for lanternfish species, potentially influencing gene flow and horizontal distribution patterns, which could contribute to speciation. Global climate change-induced alterations in ocean currents may profoundly impact the genetic diversity of fish species. This study provides new insights into the diversity of lanternfish in the Ninety East Ridge region and offers valuable data for understanding the biogeography of seamounts.}, }
@article {pmid40114041, year = {2025}, author = {Guo, X and Xie, P and Zhang, G and Wang, T and Li, J and Zhang, X and Su, W and Ji, Y}, title = {Complete plastomes serve as desirable molecular makers for precise identification of Asparagus cochinchinensis (Asparagaceae) and nine other congeneric species frequently utilized as its adulterants.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {366}, pmid = {40114041}, issn = {1471-2229}, support = {202305AT350001//Yunnan Revitalization Talent Support Program "Top Team" Project/ ; }, mesh = {*Asparagus Plant/genetics/classification ; Phylogeny ; Drug Contamination ; Genetic Markers ; DNA, Plant/genetics ; *Genome, Plastid/genetics ; Quality Control ; }, abstract = {BACKGROUD: The processed tuberous roots of Asparagus cochinchinensis (Asparagaceae), known as Asparagi Radix, have long been used in East Asia (particularly in China) as traditional medicines and play an indispensable role in the pharmaceutical industry. However, the frequent adulteration of Asparagi Radix with processed tuberous roots obtained from nine other congeneric species could potentially compromise the quality control measures for related pharmaceutical products, while also posing challenges to the conservation and rational exploitation of the nine adulterant congeneric species that are also used as traditional ethnomedicines. Given this issue, this study aims to develop a molecular authentication method for the accurate identification of A. cochinchinensis and the nine congeneric adulterants, employing the genome skimming approach to generate complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) arrays as the candidate molecular markers.<br><br>RESULTS: Through comprehensive phylogenetic and genetic distance analyses based on extensive sampling at both inter- and intra-specific levels, the efficacy of the two candidate molecular markers was assessed by investigating whether their inter-specific genetic divergences align with the taxonomically delineated species boundaries.<br><br>CONCLUSION: The results indicated that complete plastomes exhibit superior performance for accurately identifying A. cochinchinensis (the botanical source of Asparagi Radix) and the nine congeneric adulterants, thus can serve as the optimal molecular markers for effective authentication of Asparagi Radix. The desirable discriminative power demonstrated by complete plastomes suggests that the PCR-free molecular authentication method developed in this study will not only contribute to the quality control of pharmaceutical products derived from Asparagi Radix but also facilitate the conservation efforts and rational exploitation of the nine Asparagus species commonly used as adulterants.}, }
@article {pmid40109892, year = {2025}, author = {Gastineau, R and Mianowicz, K and Dąbek, P and Otis, C and Stoyanova, V and Krawcewicz, A and Abramowski, T}, title = {Genomic investigation of benthic invertebrates from the Clarion-Clipperton fields of polymetallic nodules.}, journal = {ZooKeys}, volume = {1231}, number = {}, pages = {11-44}, pmid = {40109892}, issn = {1313-2989}, abstract = {The abyssal plains of the Clarion-Clipperton Zone (CCZ) are famous for their fields of polymetallic nodules, which are inhabited by benthic invertebrates. Ten specimens from the Interoceanmetal Joint Organisation (IOM) licence area in the CCZ were collected in 2014 and submitted to a short-read genome skimming sequencing. In total, mitochondrial genomes and nuclear ribosomal genes were retrieved for nine different organisms belonging to Ophiuroidea, Holothuroidea, Polychaeta, Bryozoa, Porifera, and Brachiopoda (assigned to these phyla immediately upon retrieval from the seafloor). As many of these samples were partial and physically deteriorated following their seven-year storage in IOM's collections, their morphology-based taxonomic identification could rarely be performed at the lowest possible level (species or genus) prior to preparing the samples for molecular or genomic investigations. Therefore, it was not possible to apply the reverse identification scheme recommended for such investigations. However, several of these specimens represent poorly studied groups for which few molecular references are available as of now. In two cases, the presence of introns in the mitochondrial genome questions the practicability of using the cox1 gene for further routine molecular barcoding of these organisms. These results might be useful in future DNA primers design, molecular barcoding, and phylogeny or population genetic studies when more samples are obtained.}, }
@article {pmid40106513, year = {2025}, author = {Vielma-Puente, JE and Santos-Ordóñez, E and Cornejo, X and Chóez-Guaranda, I and Pacheco-Coello, R and Villao-Uzho, L and Moreno-Alvarado, C and Mendoza-Samaniego, N and Fonseca, Y}, title = {DNA Barcode, chemical analysis, and antioxidant activity of Psidium guineense from Ecuador.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319524}, pmid = {40106513}, issn = {1932-6203}, mesh = {*Antioxidants/chemistry/pharmacology ; Ecuador ; *DNA Barcoding, Taxonomic ; *Psidium/genetics/chemistry/classification ; Plant Leaves/chemistry/genetics ; Plant Extracts/chemistry/pharmacology ; Flavonoids/analysis ; Phenols/analysis/chemistry ; }, abstract = {This study investigates the phytochemical, genetic, and antioxidant properties of Psidium guineense, a species native to the tropical dry forests of Ecuador. Leaves were collected, preserved in recognized herbaria, and subjected to Soxhlet extraction using polar and non-polar solvents. Phytochemical screening revealed the presence of secondary metabolites, while GC-MS analysis detected chemical compounds in the extracts. Antioxidant assays demonstrated high phenolic (54.34 ± 0.49 mg GAE/g) and flavonoid (6.43 ± 0.38 mg QE/g) content, with significant antioxidant activity in DPPH (0.57 ± 0.04 mg TE/g), FRAP (105.52 ± 6.85), and ABTS (1.25 ± 0.01 mg TE/g) assays. DNA barcoding of nine loci, (seven from the chloroplast genome and two nuclear genome) using a CTAB extraction protocol and PCR, provides the first genetic characterization of this species, contributing to genetic diversity assessments and phylogenetic studies. These findings underscore the importance of P. guineense as a source of potent bioactive compounds with significant antioxidant potential, highlighting its applicability in nutritional and pharmaceutical industries. Additionally, the genetic insights gained support efforts to expand DNA barcoding databases for tropical biodiversity conservation.}, }
@article {pmid40106335, year = {2025}, author = {Chen, A and Nchinda, N and Cira, NJ}, title = {Scalable genotyping of microbial colonies.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, pmid = {40106335}, issn = {2057-5858}, support = {T32 GM144273/GM/NIGMS NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Polymerase Chain Reaction/methods ; *Genotyping Techniques/methods ; DNA, Bacterial/genetics ; Genotype ; Sequence Analysis, DNA/methods ; }, abstract = {The sequence of the 16S region is taxonomically informative and widely used for genotyping microbes. While it is easy and inexpensive to genotype several isolates by Sanger sequencing the 16S region, this method becomes quite costly if scaled to many isolates. High-throughput sequencing provides one potential avenue for obtaining 16S sequences at scale but presents additional challenges. First, DNA purification workflows for high-throughput sample preparation are labour-intensive and expensive. Second, cost-effective multiplexing and library preparation schemes are difficult to implement for many libraries on a single sequencing run. Therefore, we implemented a scalable protocol for isolate genotyping involving colony polymerase chain reaction (PCR) with simple cell lysis as well as a four-barcode indexing scheme that enables scalable multiplexing and streamlined library preparation by amplifying with four primers simultaneously in a single reaction. We tested this protocol on 93 colonies cultured from environmental samples, and we were able to ascertain the identity of ~90% of microbial isolates.}, }
@article {pmid40104553, year = {2025}, author = {Cazal-Martínez, CC and Reyes-Caballero, YM and Chávez, AR and Pérez-Estigarribia, PE and Kohli, MM and Rojas, A and Arrua, AA and Moura-Mendes, J and Souza-Perera, R and Zúñiga Agilar, JJ and Gluck-Thaler, E and Lopez-Nicora, H and Iehisa, JCM}, title = {Pyricularia pennisetigena and Pyricularia oryzae isolates from Paraguay's wheat-growing regions and the impact on wheat.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100361}, pmid = {40104553}, issn = {2666-5174}, abstract = {The Pyricularia genus includes species causing blast disease in monocots, posing significant challenges for disease management due to their ability to infect multiple hosts. This study aimed to identify the pathogenicity and species identity of Pyricularia isolates from 11 plant species in wheat-growing regions of Paraguay and assess their capacity to infect wheat. Twenty-four monosporic isolates were analyzed based on macroscopic and microscopic and phylogenetic characteristics. Three phylogenetic clades corresponding to P. oryzae, P. grisea, and P. pennisetigena were identified through five barcoding genes. For the first time, wheat blast was reported in San Pedro Department, and blast disease was observed in weeds in Cordillera and Central Departments. In greenhouse trials, P. oryzae isolates from wheat successfully infected both susceptible and resistant wheat cultivars, whereas isolates from non-wheat hosts did not elicit symptoms. Notably, P. pennisetigena isolates derived from Cenchrus echinatus were capable of infecting wheat spikes, producing typical blast symptoms, highlighting the potential for cross-species pathogen transmission. This finding suggests P. pennisetigena may pose an emerging threat to wheat in Paraguay, as its primary host is prevalent near wheat fields. These results highlight the critical importance of integrated disease management strategies, particularly the identification of inoculum sources, to mitigate cross-species pathogen transmission. This approach aligns with the One Health paradigm by addressing interconnected risks to plant health, food security, and environmental sustainability.}, }
@article {pmid40103772, year = {2025}, author = {Al-Dhafer, HM and Balaji, R and Abdel-Dayem, MS and Rasool, I and Mohamed, A and Palanisamy, S}, title = {Simple DNA extraction for museum beetle specimens to unlock genetic data from historical collections.}, journal = {MethodsX}, volume = {14}, number = {}, pages = {103236}, pmid = {40103772}, issn = {2215-0161}, abstract = {Museum beetle specimens are valuable resources for genetic analyses; however, obtaining DNA from aged specimens remains challenging due to degradation, desiccation, and contamination. In this study, we present a simple, low-cost protocol for extracting DNA from museum beetles, optimized using cetyltrimethylammonium bromide (CTAB). This method effectively addresses common issues such as DNA fragmentation and contamination, enabling the recovery of DNA suitable for downstream applications such as PCR and next-generation sequencing. It provides a reproducible, non-destructive approach to extracting genetic material from fragile beetle specimens, thereby facilitating molecular investigations in fields such as taxonomy and conservation biology. The protocol is summarized as follows:•A method for DNA extraction is optimized for museum beetle specimens preserved for over 45 years.•The protocol is non-destructive and compatible with PCR and next-generation sequencing.•Multiple extractions can be pooled to increase yields, particularly when DNA concentrations are low. This method broadens the possibilities for genetic analysis of historical specimens, offering new insights into long-term ecological and evolutionary processes.}, }
@article {pmid40102722, year = {2025}, author = {Luo, C and Peters, BA and Zhou, XM}, title = {Large indel detection in region-based phased diploid assemblies from linked-reads.}, journal = {BMC genomics}, volume = {26}, number = {Suppl 2}, pages = {263}, pmid = {40102722}, issn = {1471-2164}, support = {R35 GM146960/GM/NIGMS NIH HHS/United States ; GET 300538//Complete Genomics/ ; R35 GM146960/NH/NIH HHS/United States ; }, mesh = {*Diploidy ; *INDEL Mutation ; Haplotypes ; Humans ; Algorithms ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing ; Computational Biology/methods ; Software ; *Genomics/methods ; }, abstract = {BACKGROUND: Linked-reads improve de novo assembly, haplotype phasing, structural variant (SV) detection, and other applications through highly-multiplexed genome partitioning and barcoding. Whole genome assembly and assembly-based variant detection based on linked-reads often require intensive computation costs and are not suitable for large population studies. Here we propose an efficient pipeline, RegionIndel, a region-based diploid assembly approach to characterize large indel SVs. This pipeline only focuses on target regions (50kb by default) to extract barcoded reads as input and then integrates a haplotyping algorithm and local assembly to generate phased diploid contiguous sequences (contigs). Finally, it detects variants in the contigs through a pairwise contig-to-reference comparison.<br><br>RESULTS: We applied RegionIndel on two linked-reads libraries of sample HG002, one using 10x and the other stLFR. HG002 is a well-studied sample and the Genome in a Bottle (GiaB) community provides a gold standard SV set for it. RegionIndel outperformed several assembly and alignment-based SV callers in our benchmark experiments.&#xa0;After assembling all indel SVs, RegionIndel achieved an overall F1 score of 74.8% in deletions and 61.8% in insertions for 10x linked-reads, and 64.3% in deletions and 36.7% in insertions for stLFR linked-reads, respectively. Furthermore, it achieved an overall genotyping accuracy of 83.6% and 80.8% for 10x and stLFR linked-reads, respectively.<br><br>CONCLUSIONS: RegionIndel can achieve diploid assembly and detect indel SVs in each target region. The phased diploid contigs can further allow us to investigate indel SVs with nearby linked single nucleotide polymorphism (SNPs) and small indels in the same haplotype.}, }
@article {pmid40102719, year = {2025}, author = {Zhang, S and Ma, A and Xie, X and Lian, Z and Wang, Y}, title = {CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.}, journal = {BMC genomics}, volume = {26}, number = {Suppl 2}, pages = {264}, pmid = {40102719}, issn = {1471-2164}, mesh = {Algorithms ; Binding Sites ; Chromatin Immunoprecipitation Sequencing ; Computational Biology/methods ; *Convolutional Neural Networks ; DNA/metabolism ; *Neural Networks, Computer ; Protein Binding ; *Software ; *Transcription Factors/metabolism ; }, abstract = {BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent years, convolutional neural networks (CNNs) have succeeded in TF-DNA binding prediction, but existing DL methods' accuracy needs to be improved and convolution function in TF-DNA binding prediction should be further explored.<br><br>RESULTS: We develop a cascaded convolutional neural network model named CacPred to predict TF-DNA binding on 790 Chromatin immunoprecipitation-sequencing (ChIP-seq) datasets and seven ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode, and single ligation) datasets. We compare CacPred to six existing DL models across nine standard evaluation metrics. Our results indicate that CacPred outperforms all comparison models for TF-DNA binding prediction, and the average accuracy (ACC), matthews correlation coefficient (MCC), and the area of eight metrics radar (AEMR) are improved by 3.3%, 9.2%, and 6.4% on 790 ChIP-seq datasets. Meanwhile, CacPred improves the average ACC, MCC, and AEMR of 5.5%, 16.8%, and 12.9% on seven ChIP-nexus datasets. To explain the proposed method, motifs are used to show features CacPred learned. In light of the results, CacPred can find some significant motifs from input sequences.<br><br>CONCLUSIONS: This paper indicates that CacPred performs better than existing models on ChIP-seq data. Seven ChIP-nexus datasets are also analyzed, and they coincide with results that our proposed method performs the best on ChIP-seq data. CacPred only is equipped with the convolutional algorithm, demonstrating that pooling processing of the existing models leads to losing some sequence information. Some significant motifs are found, showing that CacPred can learn features from input sequences. In this study, we demonstrate that CacPred is an effective and feasible model for predicting TF-DNA binding. CacPred is freely available at https://github.com/zhangsq06/CacPred .}, }
@article {pmid40102641, year = {2025}, author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J}, title = {Information storage across a microbial community using universal RNA barcoding.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40102641}, issn = {1546-1696}, support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; }, abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.}, }
@article {pmid40102404, year = {2025}, author = {Nadal-Ribelles, M and Solé, C and Díez-Villanueva, A and Stephan-Otto Attolini, C and Matas, Y and Steinmetz, L and de Nadal, E and Posas, F}, title = {A single-cell resolved genotype-phenotype map using genome-wide genetic and environmental perturbations.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2645}, pmid = {40102404}, issn = {2041-1723}, mesh = {*Saccharomyces cerevisiae/genetics ; *Single-Cell Analysis/methods ; *Genome, Fungal ; Transcriptome/genetics ; Genotype ; Phenotype ; Gene Expression Regulation, Fungal ; Mutation ; Gene Expression Profiling ; }, abstract = {Heterogeneity is inherent to living organisms and it determines cell fate and phenotypic variability. Despite its ubiquity, the underlying molecular mechanisms and the genetic basis linking genotype to-phenotype heterogeneity remain a central challenge. Here we construct a yeast knockout library with a clone and genotype RNA barcoding structure suitable for genome-scale analyses to generate a high-resolution single-cell yeast transcriptome atlas of 3500 mutants under control and stress conditions. We find that transcriptional heterogeneity reflects the coordinated expression of specific gene programs, generating a continuous of cell states that can be responsive to external insults. Cell state plasticity can be genetically modulated with mutants that act as state attractors and disruption of state homeostasis results in decreased adaptive fitness. Leveraging on intra-genetic variability, we establish that regulators of transcriptional heterogeneity are functionally diverse and influenced by the environment. Our multimodal perturbation-based single-cell Genotype-to-Transcriptome Atlas in yeast provides insights into organism-level responses.}, }
@article {pmid40100602, year = {2025}, author = {Ayala, LA and Nguyen, PU and Zhou, C and Hisoire, GL and Ahmedani, AH and Chen, X and Daud, A and Valdovinos, A and Varady, ES and Inlay, MA and Scarfone, VM}, title = {Mass Cytometry Immunophenotyping of Graft-Conditioned Cells Following Major Histocompatibility Complex Mismatched Murine Allograft.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2907}, number = {}, pages = {259-286}, pmid = {40100602}, issn = {1940-6029}, mesh = {Animals ; Mice ; *Immunophenotyping/methods ; *Graft vs Host Disease/immunology/prevention &amp; control ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; *Flow Cytometry/methods ; *Major Histocompatibility Complex/immunology ; Transplantation, Homologous ; *Transplantation Conditioning/methods ; Allografts/immunology ; T-Lymphocytes/immunology ; }, abstract = {Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative therapy for a variety of blood disorders but primarily reserved for blood cancer patients due to the life-threatening risk of acute graft-versus-host disease (aGVHD). Development of aGVHD is driven by alloreactive T cells that recognize the recipient's tissues as foreign and initiate a robust immune response causing severe tissue damage of the skin, liver, and gut. While methods to reduce aGVHD incidence and severity exist including posttransplant cyclophosphamide, relapse rates and transplantation-related mortality remain. We previously published a study using graft conditioning with glucocorticoids as a strategy to modify the immune repertoire in the donor grafts prior to transplantation to reduce aGVHD. Here, we describe a protocol to characterize the T-cell response in recipient mice given transplantation of graft-conditioned allogeneic donor cells via mass cytometry. Mass cytometry is a technology that uses heavy metal tags in place of fluorochromes to allow high-dimensional flow cytometric analysis. In this protocol, we include an antibody panel of 39 different antibodies conjugated to 41 different heavy metal tags that have been validated and titrated for barcoding and immunophenotyping by lineage markers, activation markers, cytokine secretion, and transcription factors. This chapter details the graft conditioning, transplantation, processing, barcoding, staining, and mass cytometric analysis of immune cells following murine allo-HCT.}, }
@article {pmid40097444, year = {2025}, author = {Jin, W and Ma, J and Rong, L and Huang, S and Li, T and Jin, G and Zhou, Z}, title = {Semi-automated IT-scATAC-seq profiles cell-specific chromatin accessibility in differentiation and peripheral blood populations.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2635}, pmid = {40097444}, issn = {2041-1723}, mesh = {Animals ; Humans ; *Chromatin/metabolism/genetics ; Mice ; *Cell Differentiation/genetics ; *Single-Cell Analysis/methods ; Leukocytes, Mononuclear/metabolism/cytology ; Mouse Embryonic Stem Cells/metabolism/cytology ; Chromatin Assembly and Disassembly ; High-Throughput Nucleotide Sequencing/methods ; *Chromatin Immunoprecipitation Sequencing/methods ; Gene Library ; Epigenomics/methods ; }, abstract = {Single-cell ATAC-seq (scATAC-seq) enables high-resolution mapping of chromatin accessibility but is often limited by throughput, cost, and equipment requirements. Here, we present indexed Tn5 tagmentation-based scATAC-seq (IT-scATAC-seq), a semi-automated, cost-effective, and scalable approach that leverages indexed Tn5 transposomes and a three-round barcoding strategy. This workflow prepares libraries for up to 10,000 cells in a single day, reduces the per-cell cost to approximately $0.01, and maintains high data quality. Comprehensive benchmarking demonstrates that IT-scATAC-seq achieves robust library complexity, high signal specificity, and improved cost-efficiency compared to existing methods. We apply IT-scATAC-seq to mouse embryonic stem cells, capturing chromatin remodelling during early differentiation, and to human peripheral blood mononuclear cells, resolving cell-type-specific regulatory programs. Here, we show that IT-scATAC-seq provides a robust and efficient approach for high-resolution single-cell epigenomic investigations, balancing scalability, data quality, and accessibility.}, }
@article {pmid40095752, year = {2025}, author = {Suetsugu, K and Okada, H}, title = {Green, variegated, and albino Cremastra variabilis provide insight into mycoheterotrophic evolution associated with wood-decaying fungi.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {27}, number = {4}, pages = {602-613}, doi = {10.1111/plb.70014}, pmid = {40095752}, issn = {1438-8677}, support = {JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; }, mesh = {*Mycorrhizae/physiology ; *Orchidaceae/microbiology/physiology/metabolism ; Chlorophyll/metabolism ; *Wood/microbiology ; *Biological Evolution ; Symbiosis ; Heterotrophic Processes ; Plant Leaves/microbiology ; }, abstract = {With approximately 31,000 species, orchids begin life as mycoheterotrophs, relying on fungi to meet their carbon demands. Notably, some green orchids retain the ability to acquire carbon through fungal associations (partial mycoheterotrophy) and occasionally produce albino or, more rarely, variegated phenotypes. A linear relationship has been observed between leaf chlorophyll content and dependence on fungal-derived carbon, particularly in orchids associated with ectomycorrhizal (ECM) fungi, but whether such plasticity is similarly robust among orchids associated with non-ECM fungi remains underexplored. Here, we focused on the green, variegated, and albino forms of Cremastra variabilis, which likely lack ECM associations, to investigate (i) whether the degree of mycoheterotrophy, indicated by [13]C enrichment, correlates with chlorophyll content, and (ii) whether nutritional shifts align with changes in plant structure and mycorrhizal communities. Our results show that rhizoctonia fungi were dominant in green individuals with high chlorophyll levels and lacking coralloid rhizomes, whereas albino and most variegated individuals possessing coralloid rhizomes primarily associate with Psathyrellaceae fungi. Chlorophyll content and carbon stable isotope abundances were negatively correlated, indicating a gradient of increasing mycoheterotrophy from green to albino forms in individuals with coralloid rhizomes. In conclusion, C. variabilis maintains a flexible balance between photosynthesis and mycoheterotrophy, likely shaped by its subterranean morphology and fungal associations, with wood-decaying Psathyrellaceae fungi providing greater support for mycoheterotrophic nutrition than rhizoctonia fungi.}, }
@article {pmid40094434, year = {2025}, author = {Mukherjee, A and Kar, O and Mukherjee, K and Mukherjee, B and Naskar, A and Banerjee, D}, title = {Molecular Identification of Onchocerciasis Vectors (Diptera: Simuliidae) from the Central Himalayan Landscape of India: A DNA Barcode Approach.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {25}, number = {4}, pages = {258-268}, doi = {10.1089/vbz.2024.0123}, pmid = {40094434}, issn = {1557-7759}, mesh = {Animals ; *Simuliidae/genetics/classification ; *DNA Barcoding, Taxonomic ; India ; *Insect Vectors/genetics/classification ; Onchocerciasis/transmission ; Phylogeny ; Electron Transport Complex IV/genetics ; }, abstract = {Background: Black flies (Diptera: Simuliidae) are a notorious group of blood-sucking insects acting as vectors of various diseases in humans and other animals, most notable being Onchocerciasis. Due to its medical and veterinary significance, accurate and quick species identification is of utmost importance in the field of black fly research. DNA barcoding is one such taxonomic tool, aiding in quick and efficient species identification using molecular methods. Despite sporadic reports of ocular and cutaneous Onchocerciasis, especially from North-East India, Indian Simuliidae has been understudied due to lack of expertise on morphological taxonomy and lack of genetic library. Materials and Methods: Blackflies were collected from eight distinct locations in the Central Himalayan region that are part of the West Bengal, India, districts of Kalimpong and Darjeeling. Various traps were used to collect the specimens, and they were kept it in 70% ethyl alcohol. Following the morphological identification of each fly specimen, genomic DNA was extracted from its dissected legs using the QIAmp DNA extraction kit (QIAGEN, Germany). The voucher specimen slide was deposited in the National Zoological collection, ZSI, Kolkata, India. Results: This is the first comprehensive DNA barcoding study of black flies (Feuerborni and Multistriatum species group) using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences along with morphological identification from the Central Himalayan region of West Bengal involving four species: Simulium dentatum, Simulium digitatum, Simulium praelargum, and Simulium senile. DNA barcode approach through ML tree clearly distinguished all the species with supporting PTP, ASAP, and GMYC analysis. Interspecific genetic distances were also calculated where S. dentatum and S. digitatum showed minimum distances in the study area. Conclusion: Coupled with a robust morpho-taxonomic framework, the DNA barcodes generated here will help with accurate species identification, which will lead to better management and control strategies for these harmful vector species at the study site.}, }
@article {pmid40093169, year = {2025}, author = {Manian, KV and Ludwig, CH and Zhao, Y and Abell, N and Yang, X and Root, DE and Albert, ML and Comander, J}, title = {A comprehensive map of missense trafficking variants in rhodopsin and their response to pharmacologic correction.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40093169}, issn = {2692-8205}, support = {P30 EY014104/EY/NEI NIH HHS/United States ; R01 EY031036/EY/NEI NIH HHS/United States ; }, abstract = {Rhodopsin (RHO) missense variants are a leading cause of autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration with no currently approved therapies. Interpreting the pathogenicity of the growing number of identified RHO variants is a major clinical challenge, and understanding their disease mechanisms is essential for developing effective therapies. Here, we present a high-resolution map of RHO missense variant trafficking using two complementary deep mutational scanning (DMS) approaches based on a surface abundance immunoassay and a membrane proximity assay. We generated a comprehensive dataset encompassing all 6,612 possible single-residue missense variants, revealing a strong correlation between the two methods. Over 700 variants were identified with pathogenic trafficking scores, significantly expanding the number of RHO variants with functional evidence supporting pathogenicity. We demonstrate a high concordance between the trafficking scores and ClinVar pathogenicity classifications, highlighting this approach's utility in resolving variants of uncertain significance (VUS). The data also identified structurally clustered trafficking-deficient variants, predominantly within the N-terminal region and second extracellular loop, in and above the extracellular/intradiscal beta-plug region. Furthermore, we evaluated the efficacy of the non-retinoid pharmacological chaperone YC-001, observing significant rescue of trafficking defects in a majority of mistrafficking variants. This comprehensive functional map of RHO missense variants provides a valuable resource for pathogenicity assessment, genotype-phenotype correlations, and the development of targeted therapeutic strategies for RHO-adRP, paving the way for improved diagnosis and treatment for patients.}, }
@article {pmid40087979, year = {2025}, author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A}, title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14099}, pmid = {40087979}, issn = {1755-0998}, support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnolo&#x161;kog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; }, mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; }, abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.}, }
@article {pmid40081365, year = {2025}, author = {Vicario, R and Fragkogianni, S and Pokrovskii, M and Meyer, C and Lopez-Rodrigo, E and Hu, Y and Ogishi, M and Alberdi, A and Baako, A and Ay, O and Plu, I and Sazdovitch, V and Heritier, S and Cohen-Aubart, F and Shor, N and Miyara, M and Nguyen-Khac, F and Viale, A and Idbaih, A and Amoura, Z and Rosenblum, MK and Zhang, H and Karnoub, ER and Sashittal, P and Jakatdar, A and Iacobuzio-Donahue, CA and Abdel-Wahab, O and Tabar, V and Socci, ND and Elemento, O and Diamond, EL and Boisson, B and Casanova, JL and Seilhean, D and Haroche, J and Donadieu, J and Geissmann, F}, title = {Role of clonal inflammatory microglia in histiocytosis-associated neurodegeneration.}, journal = {Neuron}, volume = {113}, number = {7}, pages = {1065-1081.e13}, doi = {10.1016/j.neuron.2025.02.007}, pmid = {40081365}, issn = {1097-4199}, support = {R01 AI130345/AI/NIAID NIH HHS/United States ; R01 HL138090/HL/NHLBI NIH HHS/United States ; R01 NS115715/NS/NINDS NIH HHS/United States ; }, mesh = {*Microglia/pathology/metabolism ; Animals ; Mice ; Humans ; *Neurodegenerative Diseases/pathology/genetics ; Female ; Male ; *Histiocytosis, Langerhans-Cell/pathology/genetics/complications ; Disease Models, Animal ; Middle Aged ; Adult ; Receptors, Granulocyte-Macrophage Colony-Stimulating Factor/antagonists &amp; inhibitors ; }, abstract = {Langerhans cell histiocytosis (LCH) and Erdheim-Chester disease (ECD) are clonal myeloid disorders associated with mitogen-activated protein (MAP)-kinase-activating mutations and an increased risk of neurodegeneration. We found microglial mutant clones in LCH and ECD patients, whether or not they presented with clinical symptoms of neurodegeneration, associated with microgliosis, astrocytosis, and neuronal loss, predominantly in the rhombencephalon gray nuclei. Neurological symptoms were associated with PU.1[+] clone size (p = 0.0003) in patients with the longest evolution of the disease, indicating a phase of subclinical incipient neurodegeneration. Genetic barcoding analysis suggests that clones may originate from definitive or yolk sac hematopoiesis, depending on the patients. In a mouse model, disease topography was attributable to a local clonal proliferative advantage, and microglia depletion by a CSF1R-inhibitor limited neuronal loss and improved survival. These studies characterize a neurodegenerative disease associated with clonal proliferation of inflammatory microglia. The long preclinical stage represents a therapeutic window before irreversible neuronal depletion.}, }
@article {pmid40079026, year = {2025}, author = {Ossowska, EA and Moncada, B and Lücking, R and Sérusiaux, E and Magain, N}, title = {Stictaflakusiorum and S.kukwae-two additional new species from the Neotropics (Peltigerales, Peltigeraceae).}, journal = {MycoKeys}, volume = {114}, number = {}, pages = {259-276}, pmid = {40079026}, issn = {1314-4049}, abstract = {Two additional species of Sticta are described as new to science based on material from Bolivia and Peru and supported by phylogenetic analysis of the fungal ITS barcoding marker. The two new species represent lineages within clade I on the global Sticta phylogeny. Stictaflakusiorum Ossowska, B. Moncada &amp; Lücking is a species in the S.humboldtii morphodeme and is characterized by lobes partly to entirely covered with white hairs, also covering the margins of submarginal and laminal apothecia, and the scabrid basal membrane of cyphellae, which is white to yellow, or partly brown, and when yellow K+ purple. The taxon was discovered at a single locality in Bolivia, but it is closely related to a potentially new Sticta species from Peru, which is here left undescribed. The other new species, S.kukwae Ossowska, Magain &amp; Sérus., belongs to the S.weigelii morphodeme. It has lobes with sinuous margins and dark, palmate to corymbose phyllidia. It was collected at several locations in Peru and a single locality in Bolivia.}, }
@article {pmid40078476, year = {2025}, author = {Zhang, M and Zhai, X and He, L and Wang, Z and Cao, H and Wang, P and Ren, W and Ma, W}, title = {Morphological description and DNA barcoding research of nine Syringa species.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1544062}, pmid = {40078476}, issn = {1664-8021}, abstract = {INTRODUCTION: Syringa plants are highly valued for their ornamental qualities. However, traditional morphological identification methods are inefficient for discriminating Syringa species. DNA barcoding has emerged as a powerful alternative for species identification, but research on Syringa DNA barcodes is still limited.<br><br>METHODS: This study employed a multi-locus strategy, combining the nuclear ITS2 region with chloroplast genome regions psbA-trnH, trnL-trnF, and trnL to evaluate the effectiveness of Syringa DNA barcodes. The assessment involved genetic distance analysis, BLAST searches in NCBI, sequence character analysis, and phylogenetic tree construction, examining both individual and combined sequences.<br><br>RESULTS: The genetic distance analysis showed that the sequence combination of ITS2 + psbA-trnH + trnL-trnF exhibited a variation pattern where most interspecific genetic distances were greater than intraspecific genetic distances. The Wilcoxon signed-rank test results indicated that, except for psbA-trnH, the interspecific differences of the ITS2 + psbA-trnH + trnL-trnF sequence were greater than those of all single and combined sequences. BLAST analysis revealed that the identification rate for nine Syringa species using ITS2 + psbA-trnH + trnL-trnF could reach 98.97%. The trait-based method also demonstrated that ITS2 + psbA-trnH + trnL-trnF could effectively identify the nine Syringa species. Furthermore, the neighbor-joining (NJ) tree based on ITS2 + psbA-trnH + trnL-trnF clustered each of the nine Syringa species into distinct clades.<br><br>DISCUSSION: The study ultimately selected the barcode ITS2 + psbA-trnH + trnL-trnF, with an identification rate of 93.6%, as the optimal barcode for identifying nine species of Syringa trees. This combination proved to be highly effective in discriminating Syringa species, highlighting the potential of DNA barcoding as a reliable tool for species identification in Syringa. Future research could focus on expanding the sample size and exploring additional genetic markers to further enhance the accuracy and applicability of DNA barcoding in Syringa species identification.}, }
@article {pmid40078454, year = {2025}, author = {Sterling, MJ and Price, BW and Lees, DC}, title = {A revision of the hitherto neglected genus Topiris Walker, 1863 (Lepidoptera, Xyloryctidae) with taxonomic notes on the genus Athrypsiastis Meyrick, 1910.}, journal = {ZooKeys}, volume = {1229}, number = {}, pages = {297-368}, pmid = {40078454}, issn = {1313-2989}, abstract = {The genus Topiris Walker, 1863 is revised. This genus, previously neglected or deemed unrecognisable, comprised only Walker's damaged and misrepaired type specimen of Topiriscandidella Walker, 1863. Evidence is provided that this specimen was collected by Alfred Russel Wallace in 1855-56 in Sarawak, Malaysian Borneo. The mitogenome of this specimen was assembled using low coverage whole genome sequencing (genome skimming). The COI-5P portion of this mitogenome (658 bp) differs by 1-3 bp from two haplotypes sequenced from early 1990's Brunei specimens. Another specimen recently discovered at NHMUK with an identical label to that of the type perfectly matches the Brunei specimens in its genitalia. Based on these four specimens, we present a fuller description of the morphology of T.candidella. Topiris includes the following additional species authored by Sterling and Lees: Topirisalbidella sp. nov., T.albogrisella sp. nov., T.cinderella sp. nov., T.digiticosta sp. nov., T.lacteella sp. nov., T.madonna sp. nov., T.meyricki sp. nov., T.ochrotincta sp. nov., T.schneeweissella sp. nov., T.sericella sp. nov., and T.thunbergella sp. nov. The following new combinations are also established: T.salva (Meyrick, 1932), comb. nov. and T.sampitella (Lvovsky, 2014), comb. nov. The type of Athrypsiastissalva Meyrick is confirmed as lost and so a neotype and paraneotype of this species are designated. A published mitogenome of "Linoclostisgonatias" is shown to be correctly identified as T.salva, and references to L.gonatias, identified in some literature as a pest of Theaceae, are likely misidentified. The genus Topiris is divided into three groups, the candidella group, the salva group, and the albidella group, based on characters in the male genitalia. The candidella group and albidella group are supported sub-clades of Topiris. The phylogenetic placement of Topiris and Athrypsiastis within 'core' Xyloryctidae (as subtended by its type species, X.luteotactella) is confirmed by analysis of COI and seven nuclear genes, whereas the genera Eumenodora Meyrick, 1906 and Izatha Walker, 1864 do not fall within this clade. The morphology of Athrypsiastisphaeoleuca Meyrick, 1910 (the type species of Athrypsiastis; Xyloryctidae) is more fully described. The following new species authored by Sterling and Lees are described: Athrypsiastischeesmanae sp. nov., A.edelweissella sp. nov., and A.penumbrella sp. nov. Two taxa are newly combined: Athrypsiastishalmaherella (Lvovsky, 2014), comb. nov. and Paralectarosiflora (Meyrick, 1930), comb. nov.}, }
@article {pmid40077453, year = {2025}, author = {Wildbacher, M and Andronache, J and Pühringer, K and Dobrovolny, S and Hochegger, R and Cichna-Markl, M}, title = {Authentication of EU-Authorized Edible Insect Species in Food Products by DNA Barcoding and High-Resolution Melting (HRM) Analysis.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, pmid = {40077453}, issn = {2304-8158}, abstract = {The consumption of edible insects is a promising approach to meet the increasing global demand for food. Commercialization of edible insects in the EU is regulated by the Novel Food regulation. To date, the yellow mealworm (Tenebrio molitor larva), the migratory locust (Locusta migratoria), the house cricket (Acheta domesticus), and the buffalo worm (Alphitobius diaperinus larva) have been authorized in the EU for human consumption. We aimed to develop a method based on DNA barcoding and high-resolution melting (HRM) analysis for the identification and differentiation of these four EU-authorized edible insect species in food. A primer pair previously designed for DNA metabarcoding, targeting a ~200 bp sequence of mitochondrial 16S rDNA, allowed discrimination between the four insect species in highly processed food. However, house cricket and migratory locust could not unambiguously be differentiated from tropical house cricket, desert locust, superworm, cowpea weevil, and sago worm, respectively. This problem could be solved by designing primers specific for house cricket and migratory locust. By combining these primers with the insect primers, additional polymerase chain reaction (PCR) products for house cricket and migratory locust were obtained, resulting in more complex melt curves compared to the unauthorized insect species. The optimized PCR-HRM assay is a very cost-efficient screening tool for authentication of EU-authorized edible insect species in food.}, }
@article {pmid40076024, year = {2025}, author = {Miller, C and Linzey, D and Hallerman, E}, title = {Morphological and Genetic Assessments of Coyote Diet in Qualla Boundary, North Carolina, Show Interaction with Humans.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, pmid = {40076024}, issn = {2076-2615}, abstract = {Throughout the 20th century, coyotes (Canis latrans) expanded from their historical geographic range west of the Mississippi River to a current range of almost all of North America. Over the course of this expansion, coyotes have demonstrated diverse and variable omnivorous diets that change with the food resources available. This study examined the stomach contents of 25 coyotes in an area where they are relatively new, the Qualla Boundary in North Carolina, to better understand the diets of coyotes in this area. A combination of morphological identification and DNA barcoding was used to characterize the stomach contents of coyotes. Both plant and animal material were identified from anthropogenic and natural sources, the latter including native mammals. This study provides one example of the breadth and flexibility of coyote diets and helps build an understanding of how coyotes can adapt to new conditions.}, }
@article {pmid40075470, year = {2025}, author = {Miao, K and Zhang, A and Yang, X and Zhang, Y and Lin, A and Wang, L and Zhang, X and Sun, H and Xu, J and Zhang, J and Feng, Y and Shao, F and Guo, S and Weng, Z and Luo, P and Wang, D and Gao, S and Zhao, XY and Xu, X and Deng, CX}, title = {Lymphatic system is the mainstream for breast cancer dissemination and metastasis revealed by single-cell lineage tracing.}, journal = {Molecular cancer}, volume = {24}, number = {1}, pages = {75}, pmid = {40075470}, issn = {1476-4598}, mesh = {Animals ; Female ; Humans ; Mice ; *Breast Neoplasms/pathology/metabolism/genetics ; Cell Line, Tumor ; *Cell Lineage ; Cell Tracking/methods ; Lymphatic Metastasis ; *Lymphatic System/pathology/metabolism ; Neoplasm Metastasis ; *Single-Cell Analysis/methods ; Tumor Microenvironment ; }, abstract = {Cancer metastasis is the primary cause of cancer-related death, yet the forces that drive cancer cells through various steps and different routes to distinct target organs/tissues remain elusive. In this study, we applied a barcoding system based single-cell lineage tracing approach to study the metastasis rate and route of breast cancer cells and their interactions with the tumor microenvironment (TME) during metastasis. The results indicate that only a small fraction of cells, accounting for fewer than 3% of total barcodes, can intravasate from the primary site into the blood circulation, whereas more cells disseminate through the lymphatic system to different organs. Tumor cells derived from the same progenitor cell exhibit different gene expression patterns in different soils, and the cancer cell-TME communication paradigm varies significantly between primary and metastatic tumors. Furthermore, metastable cells require a prewired particular cytokine expression ability which may be specific for lymph metastasis route although the underlying mechanism requires further investigation. In summary, leveraging a single-cell lineage tracing system, we demonstrate that the crosstalk between tumor cells and the TME is the driving force controlling the preferential metastatic fate of cancer cells through the lymphatic system.}, }
@article {pmid40067649, year = {2025}, author = {Cho, JM and Kang, M and Park, S and Oh, J and Ku, H and Shin, HY and Koh, JH and Cho, S and Kim, Y and Lee, S and Kim, YC and Han, SS and Joo, KW and Kim, YS and Yang, SH and Moon, KC and Lee, H and Kim, HJ and Kim, DK and , }, title = {Identification of conserved gene expression changes across common glomerular diseases by spatial transcriptomics.}, journal = {Journal of nephrology}, volume = {}, number = {}, pages = {}, pmid = {40067649}, issn = {1724-6059}, support = {RS-2024-00403375//Ministry of Health &amp; Welfare, Republic of Korea/ ; RS-2024-00345867//National Research Foundation of Korea (NRF)/ ; }, abstract = {BACKGROUND: Glomerular diseases encompass a group of kidney diseases that may share common gene expression pathways. Here, we analyzed glomerular-specific gene expression profiles across various glomerular diseases.<br><br>METHODS: We performed spatial transcriptomic profiling using formalin-fixed paraffin-embedded kidney biopsy specimens of controls and patients with five types of glomerular diseases using the GeoMx Digital Spatial Profiler. Disease-representative glomerular regions of interest (ROIs) were configured, probed with oligonucleotide barcodes linked with target complimentary sequence. The UV-cleaved barcodes were amplified to generate libraries and subsequently sequenced. Common differentially expressed genes across glomerular diseases were identified and Gene Ontology annotation was performed using the ToppGene suite.<br><br>RESULTS: The mean age of patients with glomerular diseases and kidney donors was 49.5&#x2009;&#xb1;&#x2009;12.2 and 49.5&#x2009;&#xb1;&#x2009;9.8&#xa0;years, respectively. A total of 35 differentially expressed genes were consistently downregulated in glomeruli across the disease compared to the control, while none of the differentially expressed genes were consistently upregulated. Twelve of 35 downregulated differentially expressed genes, including the two hub genes JUN and FOS, were annotated with molecular function Gene Ontology terms related to DNA-binding transcription factor activity. The annotated biological process Gene Ontology terms included response to lipid-related (17/35 differentially expressed genes), response to steroid hormone (12/35 differentially expressed genes), or cell cycle regulation (10/35 differentially expressed genes). Xenium and immunofluorescence staining confirmed the reduced expression of JUN, ZFP36, and KLF9 in intraglomerular cells of glomerular diseases.<br><br>CONCLUSIONS: Identifying common differentially expressed genes by spatial transcriptomic analysis provides insights into the underlying molecular mechanisms of glomerular diseases and may lead to novel assessment or therapeutic strategies.}, }
@article {pmid40066677, year = {2025}, author = {Ascenzi, A and Wührl, L and Feng, V and Klug, N and Pylatiuk, C and Cerretti, P and Meier, R}, title = {EntoSieve: Automated Size-Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14097}, pmid = {40066677}, issn = {1755-0998}, support = {B85F21005360001//Ministero dell'Universit&#xe0; e della Ricerca, Programma Operativo Nazionale/ ; }, mesh = {Animals ; *Insecta/genetics/classification/anatomy &amp; histology ; *DNA Barcoding, Taxonomic/methods ; *Specimen Handling/methods ; *Entomology/methods ; Body Size ; Automation/methods ; }, abstract = {Widespread insect decline necessitates the development and use of standardized protocols for regular monitoring. These methods have to be rapid, efficient and cost-effective to allow for large-scale implementation. Many insect sampling and molecular methods have been developed. These include Malaise trapping, high-throughput DNA barcoding ('megabarcoding') and metabarcoding. The latter allows for assessing the species diversity in whole samples using few steps, but sample heterogeneity in terms of body size remains a challenge since large insects contribute disproportionately more mtDNA than small ones. This can potentially overwhelm the template DNA from small species that then go undetected. Size-sorting can mitigate this problem, but no satisfying automated, rapid and non-destructive solutions are available. We introduce the EntoSieve, a low-cost and DIY motorized instrument that disentangles and sorts abundant insect bulk samples into several body size fractions while minimizing damage to specimens, thus reducing the risk of DNA contamination across size fractions (e.g. legs of large specimens in small body size fraction). EntoSieve utilizes readily available components, 3D-printed parts and customizable meshes, thus enabling parallelization at low cost. We here show the efficiency of the EntoSieve for three samples with more than 10,000 specimens using three sieving protocols and assess the impact on specimen integrity. Efficiency ranged from 92% to 99%, achieved within 18-60 min, and specimen damage was not significant for subsamples. By facilitating rapid pre-processing, the device contributes to producing morphologically valuable vouchers for megabarcoding and is likely to improve compositional diversity accuracy across size classes when using metabarcoding.}, }
@article {pmid40066512, year = {2025}, author = {Lv, Y and Liu, X and Liang, J and Dong, L and Zhang, Y and Lin, C and Xiang, S and Chen, B and Zhang, Z}, title = {Monochromatic Responsive HOF Heterostructures via VIA-Group-Based Framework Hybridization for Fully-Covert Photonic Barcode.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {37}, number = {16}, pages = {e2420486}, doi = {10.1002/adma.202420486}, pmid = {40066512}, issn = {1521-4095}, support = {22475047//National Natural Science Foundation of China/ ; 22373015//National Natural Science Foundation of China/ ; W2431013//National Natural Science Foundation of China/ ; 22271046//National Natural Science Foundation of China/ ; 22105039//National Natural Science Foundation of China/ ; 22425102//National Science Fund for Distinguished Young Scholars/ ; HFNKL2023WW04//Foundation of National Key Laboratory of Human Factors Engineering/ ; }, abstract = {Luminescent responsive heterostructures with region-domained emission and integrated responsiveness exhibit great potential in information security, but always suffer from the direct exposure of fingerprint information at the initial state, making it easy to decode the hidden confidential information. Herein, the first monochromatic responsive hydrogen-bonded organic framework (HOF) heterostructures are reported based on VIA-group-based framework hybridization toward fully-covert photonic barcodes. Designed HOF blocks with different VIA-group elements are integrated via a configuration-assimilation-based assembly method to generate the intrinsic monochromatic HOF heterostructures. Differentiated electronegativity of VIA-group elements endows each HOF block with distinct bonding stability, which triggers different responsive actions to the same stimuli, finally forming the multicolor emission mode at a responsive state. These monochromatic responsive HOF heterostructures can effectively hide the intrinsic fingerprint information, which further demonstrates the fully-covert photonic coding capability as high-security anti-counterfeiting labels. These findings offer novel insight on the exploitation of smart-responsive hetero-HOF systems for advanced information encryption and anticounterfeiting applications.}, }
@article {pmid40065744, year = {2025}, author = {Marline, L and Ranaivoson, NAS and Smith, R and Ah-Peng, C and Hedderson, TAJ and Wilding, N and Antonelli, A}, title = {Advancing bryophyte research and conservation, a case study on Madagascar.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcaf035}, pmid = {40065744}, issn = {1095-8290}, abstract = {BACKGROUND: Bryophytes are a group of plant that are ecologically important, diverse and include many undescribed species. Setting like Madagascar is well known for its charismatic species, less conspicuous groups, such as bryophytes, are virtually unknown to the public and the scientific community. Bryophyte diversity is a highly overlooked component of Madagascar's rich biodiversity, underlined by geographical sampling biases, sparse representation, and an evident research and conservation deficit as compared to more charismatic groups. With a significant bryophytes research gap and conservation, Madagascar can serve as model for addressing knowledge gaps and talking the global issue of bryophytes blindness. Here we first summarise historical research and current knowledge on the diversity and distribution of Malagasy bryophytes; address the issue of 'bryophyte blindness'; and propose future directions.<br><br>SCOPE: We give reason to think that to advance research and ensure the effective conservation of the bryophytes, it is crucial to build robust foundations for their study and appreciation. Investments on herbarium collections paired with leveraging technology and resources for identification, including an image bank and DNA barcodes, will facilitate taxonomic revisions, evolutionary biology and ecological research. Addressing geographical imbalances and fostering comprehensive research to elevate the scientific and public appreciation of bryophytes are key to advancing the integration of bryophytes into national, regional and global conservation initiatives. Key prospects also include research on ecosystems with high and/or endemic bryophyte diversity, facilitating the integration of bryophytes into conservation programs. Training the new generation of students and professionals on bryophytes is an imperative underlying all these initiatives. This is highly important to foster more equitable research and conservation in countries like Madagascar and help tackle bryophyte blindness in science and society, alongside with an urgently needed financial support for professional training to advance bryophytes research.<br><br>CONCLUSIONS: Overall, bryophytes need urgent research and conservation investments. Researchers, organisations, governments, and universities should collaborate to raise scientific and public awareness of their importance. Addressing key questions about bryophyte diversity, threats, and conservation requires a holistic, collaborative, and inclusive approach to bryophyte research.}, }
@article {pmid40063875, year = {2025}, author = {Suzuki, M and Terada, R}, title = {DNA-based floristic survey of red algae (Rhodophyta) growing in the mesophotic coral ecosystems (MCEs) offshore of Tanegashima Island, northern Ryukyu Archipelago, Japan.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0316067}, pmid = {40063875}, issn = {1932-6203}, mesh = {*Rhodophyta/genetics/classification/growth &amp; development ; Japan ; *Ecosystem ; *Anthozoa ; Islands ; Animals ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; Ribulose-Bisphosphate Carboxylase/genetics ; Coral Reefs ; }, abstract = {A molecular-based floristic survey of marine red algal biodiversity was conducted offshore Tanegashima Island, which is located at the northern end of mesophotic coral ecosystems (MCEs), in the Ryukyu Archipelago, Japan. This study provides the first comprehensive catalog of red algae comprising the sublittoral marine flora of offshore Tanegashima Island, Japan, and represents the first exhaustive molecular-assisted survey of red algal marine flora in Japan. Morphological and molecular analyses using plastid-encoded rbcL and mitochondrion-encoded cox1 genes revealed a total of 129 species, which included nine newly recognized species in Japan. Morphologically, 82 species were assigned to known species. Among the 82 species, 17 included cryptic species, and 25 appeared to have misapplied names. The remaining 47 species could not be identified to the species level, which indicates the necessity of a detailed reference library containing validated DNA barcodes and further taxonomic studies based on morpho-molecular analyses.}, }
@article {pmid40061916, year = {2025}, author = {Arabeyyat, Z and Sweiss, M and Alajlouni, A and Al-Ajlouni, N and Mahmoud, M and Shartooh, S and Alsoqi, F and Kteifan, M}, title = {Identification and phylogenetic analysis of marine sponges in the Jordanian Gulf of Aqaba using DNA barcoding.}, journal = {Heliyon}, volume = {11}, number = {4}, pages = {e42771}, pmid = {40061916}, issn = {2405-8440}, abstract = {Sponges (Porifera) are the largest biomass component of coral reefs benthic fauna among marine organisms and are very morphologically diverse. In the present work, we aimed to identify marine sponges in the Jordanian Gulf of Aqaba using the partial 18S rRNA and the 28S rRNA genes as DNA barcoding markers. A total of nine morphologically different marine sponge samples from 6.6m to approximately 22m depth were collected. Sponge fragments were frozen at -80 °C prior to DNA extraction. The sponge's DNA was extracted using a commercial kit and subjected directly to PCR amplification for the 18S rRNA and 28S rRNA genes. The DNA sequences were analyzed using the Basic Local Alignment Search Tool (BLAST) to determine the sponge's identity, and phylogenetic trees were constructed to clarify the relationship among the samples. The results obtained revealed the presence of the following genera: Axinella, Negombata, Siphonochalina, Diacarnus, and an unidentified genus within the order Haplosclerida. Identification of sponge species was difficult due to the scarcity of diagnostic morphological characters. To our knowledge, this is the first study in the Jordanian Gulf of Aqaba that focuses on the morphological and molecular taxonomy of marine sponges using DNA barcoding markers.}, }
@article {pmid40060715, year = {2025}, author = {Moura, CJ and Wirtz, P and Nhanquê, FT and Barbosa, C and Serrão, E}, title = {Hotspot of Exotic Benthic Marine Invertebrates Discovered in the Tropical East Atlantic: DNA Barcoding Insights From the Bijagós Archipelago, Guinea-Bissau.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70964}, pmid = {40060715}, issn = {2045-7758}, abstract = {This study aimed to explore and document putative exotic marine benthic invertebrate species in the Bijagós Archipelago, Guinea-Bissau, to enhance understanding of marine biodiversity and address the extent of marine species introductions. The research was conducted in the Bijagós Archipelago, a UNESCO Biosphere Reserve located in Guinea-Bissau. The study involved the region's first scuba-diving survey of marine biodiversity. DNA barcoding was employed to assist in the identification of benthic invertebrate species. Molecular phylogenetic analyses were conducted with the available DNA barcodes to ensure accurate taxonomic assignments, detect cryptic species, and investigate the phylogeography of the taxa. The survey resulted in the discovery of 28 new species records for the Bijagós Archipelago, including octocorals, scleractinians, hydroids, bryozoans, barnacles, and ascidians. Among these, six species were documented for the first time in the East Atlantic: Stragulum bicolor, Nemalecium lighti, Diphasia sp., Amathia alternata, A. distans, and Symplegma rubra. Molecular analyses revealed pervasive cryptic diversity within species previously listed as exotic, suggesting that some, such as the hydroids Plumularia setacea, Obelia geniculata, and Dynamena disticha, are not exotic due to their restricted biogeographic distributions. Many other species reported as introduced present only a few genetic lineages capable of long-distance dispersal due to human activities. The study highlights considerable gaps in the knowledge of West African marine biodiversity and suggests a substantial underestimation of the anthropogenic trade in exotic marine species between the Tropical East Atlantic and the Americas, and between the Indo-Pacific, Mediterranean, and West Africa. Detailed taxonomic and genomic analyses are necessary for understanding marine exotic species' biogeography and adaptive traits. Our findings challenge current classifications of exotic species and underscore the need for improved monitoring and management to prevent the spread of non-native marine species.}, }
@article {pmid40060547, year = {2025}, author = {Feldman, D and Sims, JN and Li, X and Johnson, R and Gerben, S and Kim, DE and Richardson, C and Koepnick, B and Eisenach, H and Hicks, DR and Yang, EC and Wicky, BIM and Milles, LF and Bera, AK and Kang, A and Brackenbrough, E and Joyce, E and Sankaran, B and Lubner, JM and Goreshnik, I and Vafeados, D and Allen, A and Stewart, L and MacCoss, MJ and Baker, D}, title = {Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40060547}, issn = {2692-8205}, support = {P30 GM133893/GM/NIGMS NIH HHS/United States ; U19 AG065156/AG/NIA NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 AG063845/AG/NIA NIH HHS/United States ; R01 AI160052/AI/NIAID NIH HHS/United States ; R01 CA240339/CA/NCI NIH HHS/United States ; }, abstract = {Library screening and selection methods can determine the binding activities of individual members of large protein libraries given a physical link between protein and nucleotide sequence, which enables identification of functional molecules by DNA sequencing. However, the solution properties of individual protein molecules cannot be probed using such approaches because they are completely altered by DNA attachment. Mass spectrometry enables parallel evaluation of protein properties amenable to physical fractionation such as solubility and oligomeric state, but current approaches are limited to libraries of 1,000 or fewer proteins. Here, we improved mass spectrometry barcoding by co-synthesizing proteins with barcodes optimized to be highly multiplexable and minimally perturbative, scaling to libraries of >5,000 proteins. We use these barcodes together with mass spectrometry to assay the solution behavior of libraries of de novo-designed monomeric scaffolds, oligomers, binding proteins and nanocages, rapidly identifying design failure modes and successes.}, }
@article {pmid40060545, year = {2025}, author = {Jang, J and Ko, KP and Zhang, J and Jun, S and Park, JI}, title = {Deciphering Precursor Cell Dynamics in Esophageal Preneoplasia via Genetic Barcoding and Single-Cell Transcriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40060545}, issn = {2692-8205}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R03 CA256207/CA/NCI NIH HHS/United States ; R01 CA278967/CA/NCI NIH HHS/United States ; K99 CA286761/CA/NCI NIH HHS/United States ; R03 CA279867/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 CA278971/CA/NCI NIH HHS/United States ; R01 CA193297/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, abstract = {Cancer cells exhibit high heterogeneity and lineage plasticity, complicating studies of tumorigenesis and development of therapies. Recently, preneoplastic cells, although histologically normal, have been shown to possess high plasticity and early genetic alterations, yet their origins and lineage trajectories remain unclear. Herein, we introduce a lineage-tracing tool integrating genetic barcoding with single-cell RNA sequencing to map preneoplastic esophageal cell lineages. We identified preneoplastic precursor cells (PNPCs) as a distinct progenitor-like population with unique transcriptional profiles and high plasticity, contributing to proliferative and basal cell populations. To enhance lineage mapping, we developed the eXamined Ridge (XR) score, accurately identifying high-plasticity cells. Nfib and Qk emerged as conserved PNPC markers, peaking in early preneoplasia and declining after malignant transformation. These findings reveal PNPCs as key players in early tumorigenesis and highlight their potential as biomarkers for early cancer detection and therapeutic intervention, offering new strategies for preventing esophageal cancer progression.}, }
@article {pmid40058416, year = {2025}, author = {Munir Ahamed, J and Dahms, HU and Schizas, NV and Rathinam, AJ and Ouddane, B and Huang, YL}, title = {Isolation of Pseudonocardia strains associated with the shallow water hydrothermal vent crab Xenograpsus testudinatus from a metal-rich environment: Biochemical characterization and enzymatic characterization, molecular identification, antibacterial, antibiofilm and antioxidant activity.}, journal = {Microbial pathogenesis}, volume = {203}, number = {}, pages = {107457}, doi = {10.1016/j.micpath.2025.107457}, pmid = {40058416}, issn = {1096-1208}, mesh = {*Biofilms/drug effects/growth &amp; development ; Animals ; *Antioxidants/pharmacology/metabolism ; *Anti-Bacterial Agents/pharmacology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Brachyura/microbiology ; Phylogeny ; *Hydrothermal Vents/microbiology ; Taiwan ; DNA, Bacterial/genetics/chemistry ; *Actinomycetales/isolation &amp; purification/classification/genetics ; Metals/analysis ; Sequence Analysis, DNA ; Microbial Sensitivity Tests ; DNA Barcoding, Taxonomic ; }, abstract = {A shallow hydrothermal vent at Kueishantao Island, Taiwan provides a challenging environment and has been less explored for its microbial communities, especially the actinomycetes and their antibacterial and antioxidant activity. Nine actinomycete strains were isolated from the endemic hydrothermal vent crab Xenograpsus testudinatus and were identified as belonging to the rare actinomycete genus Pseudonocardia sp. Physiochemical results showed that the optimum growth conditions of these nine isolates were at pH 7, 35 °C, and 0.5-2% NaCl. Biochemical characterization showed differences between the strains. These isolates were further characterized at genetic barcoding (16s rRNA sequencing) and phenotypic levels and identified at the species/strain level as Pseudonocardia alni SCSW01, Pseudonocardia yuanmonensis SCSW02, Pseudonocardia sp. strains SCSW03, SCSW04, SCSW05, SCSW06, BCSW29, ECSW09, and ECSW018. The morphology of the strains was analyzed using an environmental scanning electron microscope (ESEM). The nine isolates showed potential antibacterial activity against gram-positive and gram-negative pathogenic strains. The confocal laser scanning microscopy (CLSM) images show live and dead cells and biofilm/antibiofilm activity of the actinomycete supernatant and crude extracts against pathogenic bacterial strains. The crude extracts of SCSW02, SCSW06, BCSW29, ECSW09, and ECSW018 showed antibiofilm activity against P. aeruginosa, E. coli, and S. aureus. The antioxidant activity such as DPPH and H2O2 scavenging assay results showed that the nine actinomycetes crude extracts hold more substantial radical scavenging properties than supernatants. Our results marked the first report of Pseudonocardia genera from the vent crab Xenograpsus testudinatus of the HV region at Kueishantao island, Taiwan.}, }
@article {pmid40057837, year = {2025}, author = {Zajta, E and Peskó, G and Knapp, GD and Vad, E and Bödör, C and Sinkó, J}, title = {[Opportunities offered by molecular diagnostics in the management of invasive fungal infections of oncohematological patients].}, journal = {Orvosi hetilap}, volume = {166}, number = {10}, pages = {363-376}, doi = {10.1556/650.2025.33241}, pmid = {40057837}, issn = {1788-6120}, mesh = {Humans ; *Invasive Fungal Infections/diagnosis/drug therapy/microbiology ; *Hematologic Neoplasms/complications ; Mucormycosis/diagnosis ; Antifungal Agents/therapeutic use ; *Molecular Diagnostic Techniques ; }, abstract = {Invasive fungal infections pose a particular threat to oncohematological patients. Candidiasis, aspergillosis, mucormycosis, cryptococcosis and Pneumocystis pneumonia are the most common manifestations. Despite various available approaches (culture, histology, serology, imaging), diagnosis of invasive mycoses is challenging. Owing to rapid technological advancements, molecular biological methods are routinely used in diagnostics of bacterial and viral infections. At the same time, molecular tests can be of substantial assistance in the detection and characterization of mycoses, therefore several international guidelines contain recommendations on them. Although some molecular fungal tests have been introduced in Hungarian healthcare, their widespread application is lagging. Here, we provide a review of molecular tools for clinical fungal diagnostics focusing on taxon-specific polymerase chain reaction (PCR), sequencing techniques (Sanger sequencing, next-generation sequencing) and their roles in identification of fungal pathogens and detection of resistance to antifungal medication. Tests available in South-Pest Central Hospital – National Institute of Hematology and Infectious Diseases and at the Department of Pathology and Experimental Cancer Research of Semmelweis University are briefly discussed. Finally, the utility of molecular fungal diagnostics is demonstrated through two case reports. This article aims to contribute to larger implementation of molecular tools in fungal diagnostics in the Hungarian healthcare system. Orv Hetil. 2025; 166(10): 363–376.}, }
@article {pmid40056601, year = {2025}, author = {Wu, SR and Sharpe, J and Tolliver, J and Groth, AJ and Chen, R and Guerra García, ME and Valentine, V and Williams, NT and Jacob, S and Reitman, ZJ}, title = {Combining the RCAS/tv-a retrovirus and CRISPR/Cas9 gene editing systems to generate primary mouse models of diffuse midline glioma.}, journal = {Neoplasia (New York, N.Y.)}, volume = {62}, number = {}, pages = {101139}, pmid = {40056601}, issn = {1476-5586}, support = {K08 CA256045/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *CRISPR-Cas Systems ; Mice ; Disease Models, Animal ; *Glioma/genetics/pathology ; *Gene Editing/methods ; *Brain Neoplasms/genetics/pathology ; Tumor Suppressor Protein p53/genetics ; Retroviridae/genetics ; Humans ; }, abstract = {Diffuse midline gliomas (DMGs) are lethal brain tumors that arise in children and young adults, resulting in a median survival of less than two years. Genetically engineered mouse models (GEMMs) are critical to studying tumorigenesis and tumor-immune interactions, which may inform new treatment approaches. However, current midline glioma GEMM approaches are limited in their ability to multiplex perturbations and/or target specific cell lineages in the brain for genetic manipulation. Here, we combined the RCAS/tv-a avian retrovirus system and CRISPR/Cas9 genetic engineering to drive midline glioma formation in mice. CRISPR/Cas9-based disruption of Trp53, a tumor suppressor that is frequently disrupted in midline gliomas, along with the oncogene PDGF-B resulted in high grade tumor formation with moderate latency (median time to tumor formation of 12 weeks). We confirmed CRISPR-mediated Trp53 disruption using next-generation sequencing (NGS) and immunohistochemistry (IHC). Next, we disrupted multiple midline glioma tumor suppressor genes (Trp53, Pten, Atm, Cdkn2a) in individual mouse brains. These mini-pooled in vivo experiments generated primary midline gliomas with decreased tumor latency (median time to tumor formation of 3.6 weeks, P < 0.0001, log-rank test compared to single-plex gRNA). Quantification of gRNA barcodes and CRISPR editing events revealed that all tumors contained cells with various disruptions of all target genes and suggested a multiclonal origin for the tumors as well as stronger selection for Trp53 disruption compared to disruption of the other genes. This mouse modeling approach will streamline midline glioma research and enable complex experiments to understand tumor evolution and therapeutics.}, }
@article {pmid40052334, year = {2025}, author = {Lu, Y and Dong, Y and Zhang, M and Mao, L}, title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14095}, doi = {10.1111/1755-0998.14095}, pmid = {40052334}, issn = {1755-0998}, support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; }, mesh = {*DNA, Environmental/genetics/isolation &amp; purification ; *Metagenome ; *Sequence Analysis, DNA/methods ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.}, }
@article {pmid40052073, year = {2025}, author = {Schnittler, M and Leontyev, D and Yatsiuk, I and Ronikier, A}, title = {Species descriptions in myxomycetes - can we settle on rules for good taxonomic practice?.}, journal = {IMA fungus}, volume = {16}, number = {}, pages = {e141199}, pmid = {40052073}, issn = {2210-6340}, abstract = {Myxomycetes are a unique branch of life, recognisable by sporophores showing a fungus-like dispersal biology. These structures bear nearly all diagnostic characters for species identification and develop by rapid transformation of plasmodia. During this short period of time, external factors can significantly influence the formation of morphological characters. Therefore, the description of a new species must be carried out with utmost care. Over the last 50 years, approximately 10-15 new species of myxomycetes have been described per year and only some of the latest publications underpin this with molecular data. In this paper, we discuss a set of recommendations for the description of myxomycete species new to science, striving for the following goals: (i) to minimise the number of erroneous descriptions of the species, whose names later have to be put into synonymy; (ii) to make all respective data easily accessible for the scientific community; and (iii) to comply with existing rules of nomenclature. We recommend (1) whenever possible not to describe a new taxon from a single specimen; however, an exception could be made only if supported by molecular data and by unique morphological characters which are unlikely to fall in the range of infraspecific variation of related species; (2) preparing detailed descriptions, including data on developmental stages, microhabitats, ecology, phenology and associated species; (3) providing at least two independent diagnostic characters that tell the new species apart from all others; (4) obtaining a molecular barcode and, whenever possible, providing proof for reproductive isolation of the new species from related taxa; and (5) depositing type specimens in public herbaria. To comply with nomenclatural rules, (6) the new name must be registered in a recognised repository, (7) all published names should be checked for usability before proposing a new name and (8) a unique name should be chosen, preferably highlighting a distinct character of the new species.}, }
@article {pmid40051454, year = {2025}, author = {Zavala, E and Britzke, R and Siccha-Ramírez, Z and Ramirez, JL}, title = {DNA barcoding of marine rocky reef fishes from northern Peru suggests a parapatric speciation in the Tropical Eastern Pacific.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70125}, pmid = {40051454}, issn = {2045-7758}, abstract = {Northern Peru marks the end of an extensive coastal marine region: The Panama province, which is characterized by predominantly tropical and equatorial features and is home to the only rocky reefs known in Peruvian territory. This unique ecosystem could explain the presence of a diverse range of fish species. However, due to the difficulty of sampling and accessing reef areas, our knowledge of this biodiversity is incomplete. To address this issue, we used DNA barcoding for the study of the fish biodiversity and revealed patterns that may have influenced their evolution throughout the Tropical Eastern Pacific (TEP). A fragment of Cytochrome oxidase subunit I (COI) of 177 samples of rocky reef fishes was sequenced. Intra and interspecific K2P distances were calculated and three species delimitation methods (GMYC, PTP, and bPTP) were used to obtain MOTUs. Both analyses support the conformation of additional MOTUs in samples of Mugil cephalus, Ophichthus zophochir, Malacoctenus tetranemus, Ariopsis seemanni and Halichoeres dispilus, species with a divergence above 2%. By comparing these sequences with public data, our analysis revealed the existence of COI lineages and suggested potential ecological parapatric speciation in the TEP. More studies using other markers and different approaches are required to confirm the existence of species complexes that could be related to the presence of cryptic species.}, }
@article {pmid40048560, year = {2025}, author = {Bi, W and Cao, X and Li, J and Gao, Y and Song, Y and He, B}, title = {Ultrasensitive Detection of Extracellular Vesicles Based on Metal-Organic Framework DNA Biobarcodes Triggered G-Quadruplex Coupled with Rolling Circle Amplification Assay.}, journal = {ACS sensors}, volume = {10}, number = {3}, pages = {2136-2146}, doi = {10.1021/acssensors.4c03384}, pmid = {40048560}, issn = {2379-3694}, mesh = {*G-Quadruplexes ; *Extracellular Vesicles/chemistry ; *Metal-Organic Frameworks/chemistry ; *Nucleic Acid Amplification Techniques/methods ; *DNA/chemistry/genetics ; Humans ; Limit of Detection ; *Biosensing Techniques/methods ; }, abstract = {Extracellular vesicles (EVs), as liquid biopsy markers for accurate tumor diagnosis, are considered to hold great promise. However, effectively isolating and sensitively detecting EVs with convenience still face challenges. Herein, we propose a highly sensitive and specific platform for EV detection by integrating a metal-organic framework (MOF)-based DNA biobarcodes strategy with a rolling circle amplification (RCA)/G-quadruplex system. In this study, first, Zr-MOFs act as signal converters by comodification with DNA barcodes and antibodies, converting and amplifying the abundance of EVs into DNA barcodes. Second, the released DNA can trigger RCA, followed by G-quadruplex formation to further amplify the signal. Consequently, this approach significantly enhances the sensitivity for EV biomarker detection, achieving a low limit of detection of 100 EVs mL[-1]. Furthermore, the strategy offers high sensitivity, specificity, accuracy, and simplicity, highlighting its potential for clinical applications in noninvasive EV detection.}, }
@article {pmid40047956, year = {2025}, author = {Meghana, BN and Reshma, SV}, title = {DNA barcoding of geographical indication tagged Byadagi chilli and its cultivars using ITS2, matK and rbcL coding sequences.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {286}, pmid = {40047956}, issn = {1573-4978}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Capsicum/genetics/classification ; Phylogeny ; DNA, Plant/genetics ; *Ribulose-Bisphosphate Carboxylase/genetics ; Geography ; }, abstract = {BACKGROUND: Byadagi chilli, a Geographical Indication (GI)-tagged chilli variety known for its special aroma and bright red colour, was accorded the GI tag in February 2011 with the GI number 129. The two traditional varieties of Byadagi chilli, namely: Dabbi and Kaddi, are the GI-tagged varieties. In this study, GI-tagged Byadagi Dabbi, Byadagi Kaddi and other cultivars of Byadagi chilli, such as Byadagi Lali (BL), Byadagi HPH 2043 (B2), Byadagi BSS 355 (B3) and another popular GI-tagged chilli variety, Guntur Sannam, were analysed to assess their inter-relationships. Due to the high market value and demand, it is important to identify and differentiate the original variety of Byadagi chilli and its associated cultivars from the other chilli cultivars, which are sold under the name of Byadagi chilli. In this study, molecular assessment by DNA barcoding was performed to establish the identity of authentic Byadagi chilli varieties.<br><br>METHODS AND RESULTS: Five samples of Byadagi chilli and another GI-tagged chilli variety, Guntur Sannam, were analysed using three DNA barcodes: ITS2, matK and rbcL. The PCR products were sequenced, nucleotide BLAST was performed and ITS2 showed 97.7% identity, matK 99.1%, and rbcL 99.19% with Capsicum annuum at the genus and species levels. Phylogenetic analysis of the DNA sequences of all the six chilli samples was performed using ClustalW multiple sequence alignment in MEGA11. The genetic distance between the six samples was calculated using the maximum likelihood approach.<br><br>CONCLUSIONS: This study distinctly demonstrates that the chloroplast DNA barcodes matK and rbcL, along with the nuclear DNA barcode, ITS2, can be used for accurate identification of Byadagi chilli cultivars. This study offers significant molecular identification and establishes a robust barcoding foundation for Byadagi chilli. The phylogenetic trees generated from the barcode sequences clearly indicated the relationships among the selected cultivars.}, }
@article {pmid40046838, year = {2025}, author = {Yang, G and Wang, W and Tong, Y and Zhou, Z}, title = {Species delimitation and DNA barcoding for Chinese Mantodea (Insecta, Dictyoptera).}, journal = {ZooKeys}, volume = {1229}, number = {}, pages = {25-42}, pmid = {40046838}, issn = {1313-2989}, abstract = {DNA barcoding has been proposed as a rapid and reliable tool for animal identification and species delineation. The 5' end of the mitochondrial cytochrome c oxidase I gene (COI-5P) was sequenced for 318 specimens of 55 mantis species. Of these, 44 species had not been sequenced before, thus being new COI-5P barcode sequences to science. Another 61 COI-5P barcode sequences comprising five species were retrieved from the Barcode of Life Database (BOLD; www.boldsystems.org). Five species delimitation algorithms were employed to sort barcode sequences into Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, Generalized Mixed Yule Coalescent (GMYC), a Java program that uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Assemble Species by Automatic Partitioning (ASAP), and Bayesian implementation of the Poisson Tree Processes model (bPTP). All species, except Hierodulachinensis Werner, 1929, were recovered as monophyletic on the neighbor-joining (NJ) tree. For the final dataset, 379 COI-5P barcode sequences were assigned to 68 BINs. Fifty-five out of 68 BINs obtained were new to BOLD. The low level of BIN overlap with other nations highlights the importance of constructing a regional DNA barcode reference library. The algorithms ASAP, jMOTU, bPTP, and GMYC clustered barcode sequences into 32, 58, 68, and 60 MOTUs, respectively. All species delimitation algorithms (except ASAP analysis) split Anaxarchasinensis Beier, 1933, Anaxarchazhengi Ren &amp; Wang, 1994, H.chinensis, Spilomantisoccipitalis (Westwood, 1889), Titanodulaformosana Giglio-Tos, 1912 into more than one MOTUs. All algorithms merged Hierodula sp. BCM-2019 and H.chinensis into the same MOTU, as for Tenoderaaridifolia Stoll, 1813 and Tenoderasinensis Saussure, 1871. More accurate identification results need to be supplemented by detailed morphological classification.}, }
@article {pmid40045661, year = {2025}, author = {Chiyo, PI and King'ori, E}, title = {Genetic identification of Stephanofilaria sp. isolated from ulcerative dermal lesions in black rhinoceros.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e42}, doi = {10.1017/S0022149X25000112}, pmid = {40045661}, issn = {1475-2697}, mesh = {Animals ; *Perissodactyla/parasitology ; Phylogeny ; Genetic Variation ; DNA, Ribosomal Spacer/genetics/chemistry ; Electron Transport Complex IV/genetics ; *Filarioidea/genetics/isolation &amp; purification/classification ; DNA, Helminth/genetics/chemistry ; Sequence Analysis, DNA ; DNA Barcoding, Taxonomic ; *Skin Ulcer/parasitology/veterinary ; }, abstract = {Stephanofilaria is a genus of nematodes that cause ulcerative dermal lesions in large mammals. However, there is a dearth of knowledge on the molecular genetics of Stephanofilaria species infecting critically endangered rhinoceros. This study employed genetic barcoding genes to identify Stephanofilaria species and to determine its genetic diversity and evolution. Phylogenetic analyses on partial genes of the second internal transcribed spacer Ribosomal DNA (ITS-2) and cytochrome c oxidase subunit 1 (Cox-1), revealed a 77% and 93% bootstrap support at the Cox-1 and ITS-2 loci respectively to a clade containing previously identified Stephanofilaria species. Morphological examination also confirmed features diagnostic of Stephanofilaria dinniki previously known to infect rhinoceros. Gene diversity of Cox-1 was 0.931 ± 0.030 and 0.579 ± 0.104 for the ITS-2, whereas nucleotide diversity was 0.008 ± 0.002 and 0.00197 ± 0.0016 for the Cox-1 and ITS-2 genes respectively. Neutrality tests (Fu and Li's D* and Fu and Li's F*) were significantly negative (p<0.05) at all loci, whereas Tajima D and Fu's FS were each statistically significant (p<0.05) at the Cox-1 and ITS-2 loci respectively. The high gene diversity, low nucleotide diversity and negative neutrality tests are consistent with positive selection at the Cox-1 gene. Stephanofilaria infection among rhinoceros is currently restricted to highland sanctuaries compared to a widespread distribution in both lowlands and highlands in the 1960s suggesting an adaptation to vectors thriving in cooler highland temperatures. This is the first genetic identification of S. dinniki, in rhinoceros and will aid in diagnosis, treatment, studies, and rhinoceros conservation.}, }
@article {pmid40045410, year = {2025}, author = {Franco Martins, J and Dina Troco, A and Marques, C and Chipepa, V and Seixas, G and Pinto, J and Garcia, L and Pedro Jorge, C and Manuel, E and Alves, G}, title = {Asian tiger mosquito in the oil-producing city of Soyo: the first report of Aedes (Stegomyia) albopictus (Skuse, 1894) in Angola.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {90}, pmid = {40045410}, issn = {1756-3305}, mesh = {Animals ; Angola ; *Aedes/classification/genetics ; Phylogeny ; *Mosquito Vectors/classification/genetics ; Larva/classification/genetics ; Humans ; Electron Transport Complex IV/genetics ; Introduced Species ; Cities ; }, abstract = {BACKGROUND: The Asian tiger mosquito, Aedes albopictus (Skuse, 1894), is a highly invasive species that has successfully colonized many tropical and temperate regions worldwide. Its rapid global spread is strongly associated with human activities and has created favorable conditions for the emergence of human arboviruses in new geographic areas.<br><br>METHODS: Mosquito larvae were collected by community health workers from different breeding sites and reared to adults in a field insectary. Adult mosquitoes were morphologically identified to species level. Species identification was confirmed by cytochrome oxidase subunit I DNA barcoding.<br><br>RESULTS: We report the first detection of Aedes albopictus in Angola during an Anopheles stephensi survey conducted in Soyo, Zaire Province. Phylogenetic analysis indicated that the Angolan Ae. albopictus population clusters with sequences from Central African countries, suggesting an introduction from within the continent.<br><br>CONCLUSIONS: The presence of Ae. albopictus in Angola highlights the need for enhanced vector surveillance and control measures to prevent the emergence of arboviral diseases. This finding emphasizes the relevance of collaboration between local health authorities, communities, and international organizations in monitoring the spread of invasive mosquito species.}, }
@article {pmid40043011, year = {2025}, author = {Tineo, D and Bustamante, DE and Calderon, MS and Oliva, M}, title = {Comparative analyses of chloroplast genomes of Theobroma cacao from northern Peru.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0316148}, pmid = {40043011}, issn = {1932-6203}, mesh = {*Cacao/genetics/classification ; *Genome, Chloroplast/genetics ; Peru ; Phylogeny ; DNA Barcoding, Taxonomic ; Evolution, Molecular ; Genotype ; }, abstract = {Theobroma cacao is the most economically important species within the genus Theobroma. Despite its importance, the intraspecific relationships of this species has not been fully elucidated due to insufficient molecular information. To facilitate a better understanding of the intraspecific evolutionary relationships of T. cacao, Sequencing technology has been to decode the plastid genomes, with the objective of identify potential DNA barcode genetic markers, explore intraspecific relationships, and infer divergence times. The plastid genome of the seven cocoa genotypes analyzed in this study, exhibited a typical angiosperm genomic structure. However, the structure of each plastid genome reflects notable changes in each genotype; for example, the infA gene was present in all the analyzed samples, unlike in previously published cocoa plastid genomes, while the complete ycf1 gene sequence has potential for use as DNA Barcoding in T. cacao. The estimated age of the node connecting T. cacao and T. grandiflorum, which was 10.11 Ma, supports this indication. It can be inferred that T. cacao diverged at approximately 7.55 Ma, and it is highly likely that T. cacao populations diversified during the Pliocene or Miocene. Therefore, it is crucial to perform mitochondrial and nuclear-based analyses on a broader spectrum of cocoa samples to validate these evolutionary mechanisms, including genetic estimates and divergence. This approach enables a deeper understanding of the evolutionary relationships among cocoa.}, }
@article {pmid40041862, year = {2025}, author = {Amavet, P and Fernández, GP and Solís Neffa, V}, title = {Editorial: Challenges and prospects for conservation genetics at XXI century.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1554590}, pmid = {40041862}, issn = {1664-8021}, }
@article {pmid40041568, year = {2025}, author = {Liu, Y and Chen, K and Wang, L and Yu, X and Xu, C and Suo, Z and Zhou, S and Shi, S and Dong, W}, title = {Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae).}, journal = {Plant diversity}, volume = {47}, number = {1}, pages = {115-126}, pmid = {40041568}, issn = {2468-2659}, abstract = {DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.}, }
@article {pmid40038725, year = {2025}, author = {Deng, LH and Li, MZ and Huang, XJ and Zhao, XY}, title = {Single-cell lineage tracing techniques in hematology: unraveling the cellular narrative.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {270}, pmid = {40038725}, issn = {1479-5876}, support = {No.82070184, 82350105, 82270228//National Natural Science Foundation of China/ ; No. 2023ZD0501200//National Major Science and Technology Projects of China/ ; No. 2023XACX0004//5511 Science and Technology Innovation Talent Project of Jiangxi Province/ ; JWZQ20240101001//Beijing Outstanding Young Scientists Project/ ; Z240019//Natural Science Foundation of Beijing Municipality/ ; }, mesh = {*Single-Cell Analysis/methods ; *Cell Lineage ; Humans ; *Hematology/methods ; Animals ; Hematopoietic Stem Cells/cytology ; }, abstract = {Lineage tracing is a valuable technique that has greatly facilitated the exploration of cell origins and behavior. With the continuous development of single-cell sequencing technology, lineage tracing technology based on the single-cell level has become an important method to study biological development. Single-cell Lineage tracing technology plays an important role in the hematological system. It can help to answer many important questions, such as the heterogeneity of hematopoietic stem cell function and structure, and the heterogeneity of malignant tumor cells in the hematological system. Many studies have been conducted to explore the field of hematology by applying this technology. This review focuses on the superiority of the emerging single-cell lineage tracing technologies of Integration barcodes, CRISPR barcoding, and base editors, and summarizes their applications in the hematology system. These studies have suggested the vast potential in unraveling complex cellular behaviors and lineage dynamics in both normal and pathological contexts.}, }
@article {pmid40037839, year = {2025}, author = {Chakravarty, S and Logsdon, G and Lonardi, S}, title = {RAmbler resolves complex repeats in human Chromosomes 8, 19, and X.}, journal = {Genome research}, volume = {35}, number = {4}, pages = {863-876}, pmid = {40037839}, issn = {1549-5469}, support = {R01 AI169543/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Repetitive Sequences, Nucleic Acid ; *Software ; Genome, Human ; *Chromosomes, Human, X/genetics ; Algorithms ; Sequence Analysis, DNA/methods ; *Chromosomes, Human, Pair 19/genetics ; *Chromosomes, Human/genetics ; Contig Mapping ; }, abstract = {Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (3) uses the relative location of single-copy k-mers to barcode each HiFi read, (4) clusters HiFi reads based on their shared barcodes, (5) generates contigs by assembling the reads in each cluster, and (6) generates a consensus assembly from the overlap graph of the assembled contigs. Here, we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually curated Telomere-to-Telomere human genome assembly. Across more than 250 synthetic data sets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates, and depth of sequencing.}, }
@article {pmid40037039, year = {2025}, author = {Osman, E and Saxena, S and Qian, S and L'Heureux-Hache, J and Li, P and Manek, J and Gu, J and Hoare, T and Li, Y and Soleymani, L}, title = {Electrochemical detection of Legionella pneumophila using DNAzymes and under continuous flow in cooling tower water.}, journal = {Biosensors &amp; bioelectronics}, volume = {278}, number = {}, pages = {117283}, doi = {10.1016/j.bios.2025.117283}, pmid = {40037039}, issn = {1873-4235}, mesh = {*Legionella pneumophila/isolation &amp; purification/genetics ; *Biosensing Techniques/methods ; *Water Microbiology ; *DNA, Catalytic/chemistry ; *Electrochemical Techniques/methods ; Limit of Detection ; Humans ; Legionnaires' Disease/microbiology ; }, abstract = {Rapid detection of Legionella pneumophila in cooling tower water is crucial to mitigate the fatal consequences of Legionnaires disease. This study presents a microfluidic system that employs RNA-cleaving DNAzymes (RCDs) for continuous real time monitoring of this pathogen directly in a single sample of cooling tower water without the need for lengthy bacterial culture. The RCDs, coupled to microgel magnetic beads, are programmed to release an electroactive DNA barcode in the presence of L. pneumophila, which is detected by a downstream electrochemical sensor in real time. Our system identifies key parameters such as peak current, slope of signal increase, and lag time that correlate with L. pneumophila concentration, achieving a limit of detection of 1.4 × 10[3] CFU/mL in buffer and 1.9 × 10[3] CFU/mL in cooling tower water, meeting regulatory requirements. This system was further used to identify different serotypes of L. pneumophila amongst other waterborne bacterial species including non pneumophila species of Legionella, creating a highly specific tool for identifying this high-risk pathogen.}, }
@article {pmid40036401, year = {2025}, author = {Srisuka, W and Aupalee, K and Takaoka, H and Otsuka, Y and Saeung, A}, title = {Taxonomy and molecular phylogeny of a new species of black fly (Diptera: Simuliidae) in the Simulium striatum species-group from central Thailand.}, journal = {Journal of medical entomology}, volume = {62}, number = {3}, pages = {506-524}, doi = {10.1093/jme/tjaf016}, pmid = {40036401}, issn = {1938-2928}, support = {//National Research Council of Thailand/ ; N42A660464//Chiang Mai University/ ; }, mesh = {Animals ; *Simuliidae/classification/genetics/anatomy &amp; histology/growth &amp; development ; Thailand ; Phylogeny ; Male ; Female ; Electron Transport Complex IV/genetics/analysis ; DNA Barcoding, Taxonomic ; Larva/growth &amp; development/anatomy &amp; histology/genetics/classification ; Pupa/anatomy &amp; histology/growth &amp; development/genetics/classification ; Insect Proteins/genetics ; }, abstract = {Generally, the DNA barcode relying on a short fragment of the cytochrome c oxidase I (COI) gene is a powerful tool for facilitating species discovery and taxonomic resolution in Diptera, including black flies. However, the COI barcode lacks sufficient resolution to identify several species or infer phylogenetic relationships of black flies in the Simulium striatum species-group, whereas the fast-evolving nuclear big zinc finger (BZF) gene has been suggested as a key marker for identifying the species. In this study, a new species of black fly in the S. striatum species-group from Kamphaeng Phet province, central Thailand, was discovered and characterized through an integrated method combining morphological analysis and molecular data based on the BZF gene. The new species, Simulium (Simulium) concitatum sp. nov., was morphologically described for all life stages, excluding the egg. It shares many morphological similarities with other species of the S. striatum species-group, particularly S. thilorsuense Takaoka, Srisuka &amp; Saeung, 2022 described from Tak province, western Thailand. Sequence analysis and phylogeny inferred from the BZF gene further confirmed that S. concitatum sp. nov. is a distinct species of the S. striatum species-group and revealed its close genetic relationship to S. wangkwaiense Takaoka, Srisuka &amp; Saeung, 2020. The morphological differences between the new species and all known species of the S. striatum species-group documented in Thailand and other countries are provided to assist in species identification. Furthermore, this study underscores the BZF gene as an effective genetic marker to differentiate the species.}, }
@article {pmid40035969, year = {2025}, author = {Feng, Y and Liu, G and Li, H and Cheng, L}, title = {The landscape of cell lineage tracing.}, journal = {Science China. Life sciences}, volume = {68}, number = {7}, pages = {1941-1963}, pmid = {40035969}, issn = {1869-1889}, mesh = {*Cell Lineage/genetics ; Humans ; Animals ; *Cell Tracking/methods ; CRISPR-Cas Systems ; Cell Differentiation ; }, abstract = {Cell fate changes play a crucial role in the processes of natural development, disease progression, and the efficacy of therapeutic interventions. The definition of the various types of cell fate changes, including cell expansion, differentiation, transdifferentiation, dedifferentiation, reprogramming, and state transitions, represents a complex and evolving field of research known as cell lineage tracing. This review will systematically introduce the research history and progress in this field, which can be broadly divided into two parts: prospective tracing and retrospective tracing. The initial section encompasses an array of methodologies pertaining to isotope labeling, transient fluorescent tracers, non-fluorescent transient tracers, non-fluorescent genetic markers, fluorescent protein, genetic marker delivery, genetic recombination, exogenous DNA barcodes, CRISPR-Cas9 mediated DNA barcodes, and base editor-mediated DNA barcodes. The second part of the review covers genetic mosaicism, genomic DNA alteration, TCR/BCR, DNA methylation, and mitochondrial DNA mutation. In the final section, we will address the principal challenges and prospective avenues of enquiry in the field of cell lineage tracing, with a particular focus on the sequencing techniques and mathematical models pertinent to single-cell genetic lineage tracing, and the value of pursuing a more comprehensive investigation at both the spatial and temporal levels in the study of cell lineage tracing.}, }
@article {pmid40034080, year = {2025}, author = {Fan, S and Li, X and Liu, H and Ye, M and He, Y and Fu, W and Chen, F and Zhao, Y}, title = {Molecule Differentiation Encoding Microscopy to Dissect Dense Biomolecules in Cellular Nanoenvironments below Spatial Resolution.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {64}, number = {21}, pages = {e202425136}, doi = {10.1002/anie.202425136}, pmid = {40034080}, issn = {1521-3773}, support = {22125404//National Natural Science Foundation of China/ ; 22474107//National Natural Science Foundation of China/ ; 92068118//National Natural Science Foundation of China/ ; 2023-JC-JQ-13//Natural Science Basic Research Program of Shaanxi/ ; 2023-CX-TD-62//Innovation Capability Support Program of Shaanxi/ ; }, mesh = {Humans ; *DNA/chemistry/analysis ; Polysaccharides/analysis ; *Microscopy/methods ; *RNA/analysis ; Algorithms ; }, abstract = {Cellular biomolecules may exhibit dense distribution and organization at the nanoscale to govern vital biological processes. However, it remains a common challenge to digitize the spatially dense biomolecules under the spatial resolution of microscopies. Here, a proof-of-principle method, molecule differentiation encoding microscopy by orthogonal tandem repeat DNA identifiers is reported, to resolve the copy numbers of dense biomolecules in cellular nanoenvironments. The method encodes each copy of the same biomolecules into different types of DNA barcodes based on stochastic multiplexed reactions. It can transform the overlap of the same spectrum into the overlap of different spectra. Furthermore, an algorithm is developed to automatically quantitate overlapping spots and individual spots. Using this method, RNAs in the cytoplasm, DNA epigenetic modifications in the cell nucleus, and glycans and glycoRNAs on the cell surface are dissected, respectively. It is found that all these biomolecules present dense distribution with diverse degrees in crowded cellular nanoenvironments. Especially, an average 17% copies of U1 glycoRNA of single cells are gathered in various nano environments on the cell surface. The strategy provides a powerful tool for digitally quantitative visualization of dense biomolecules below the spatial resolution of microscopies and can provide insights into underlying functions and mechanisms of the dense distribution information.}, }
@article {pmid40031227, year = {2025}, author = {Tinarrage, R and Ponciano, JR and Linhares, CDG and Traina, AJM and Poco, J}, title = {ZigzagNetVis: Suggesting temporal resolutions for graph visualization using zigzag persistence.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/TVCG.2025.3528197}, pmid = {40031227}, issn = {1941-0506}, abstract = {Temporal graphs are commonly used to represent complex systems and track the evolution of their constituents over time. Visualizing these graphs is crucial as it allows one to quickly identify anomalies, trends, patterns, and other properties that facilitate better decision-making. In this context, selecting an appropriate temporal resolution is essential for constructing and visually analyzing the layout. The choice of resolution is particularly important, especially when dealing with temporally sparse graphs. In such cases, changing the temporal resolution by grouping events (i.e., edges) from consecutive timestamps - a technique known as timeslicing - can aid in the analysis and reveal patterns that might not be discernible otherwise. However, selecting an appropriate temporal resolution is a challenging task. In this paper, we propose ZigzagNetVis, a methodology that suggests temporal resolutions potentially relevant for analyzing a given graph, i.e., resolutions that lead to substantial topological changes in the graph structure. ZigzagNetVis achieves this by leveraging zigzag persistent homology, a well-established technique from Topological Data Analysis (TDA). To improve visual graph analysis, ZigzagNetVis incorporates the colored barcode, a novel timeline-based visualization inspired by persistence barcodes commonly used in TDA. We also contribute with a web-based system prototype that implements suggestion methodology and visualization tools. Finally, we demonstrate the usefulness and effectiveness of ZigzagNetVis through a usage scenario, a user study with 27 participants, and a detailed quantitative evaluation.}, }
@article {pmid40030848, year = {2025}, author = {Pham, P and Bui, QT and Thanh Nguyen, N and Kozma, R and Yu, PS and Vo, B}, title = {Topological Data Analysis in Graph Neural Networks: Surveys and Perspectives.}, journal = {IEEE transactions on neural networks and learning systems}, volume = {36}, number = {6}, pages = {9758-9776}, doi = {10.1109/TNNLS.2024.3520147}, pmid = {40030848}, issn = {2162-2388}, abstract = {For many years, topological data analysis (TDA) and deep learning (DL) have been considered separate data analysis and representation learning approaches, which have nothing in common. The root cause of this challenge comes from the difficulties in building, extracting, and integrating TDA constructs, such as barcodes or persistent diagrams, within deep neural network architectures. Therefore, the powers of these two approaches are still on their islands and have not yet combined to form more powerful tools for dealing with multiple complex data analysis tasks. Fortunately, we have witnessed several remarkable attempts to integrate DL-based architectures with topological learning paradigms in recent years. These topology-driven DL techniques have notably improved data-driven analysis and mining problems, especially within graph datasets. Recently, graph neural networks (GNNs) have emerged as a popular deep neural architecture, demonstrating significant performance in various graph-based analysis and learning problems. Explicitly, within the manifold paradigm, the graph is naturally considered as a topological object (e.g., the topological properties of the given graph can be represented by the edge weights). Therefore, integrating TDA and GNN is considered an excellent combination. Many well-known studies have recently presented the effectiveness of TDA-assisted GNN-based architectures in dealing with complex graph-based data representation analysis and learning problems. Motivated by the successes of recent research, we present systematic literature about this nascent and promising research direction in this article, which includes general taxonomy, preliminaries, and recently proposed state-of-the-art topology-driven GNN models and perspectives.}, }
@article {pmid40028202, year = {2025}, author = {Silva-Morales, I and Carrera-Parra, LF}, title = {Redescription of Aspidosiphon (Paraspidosiphon) steenstrupii Diesing, 1859 (Sipuncula: Aspidosiphonidae) and the reinstatement of three species.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19003}, pmid = {40028202}, issn = {2167-8359}, mesh = {Animals ; Atlantic Ocean ; Phylogeny ; Species Specificity ; *Annelida/anatomy &amp; histology/classification ; }, abstract = {Sipuncula, specifically the family Aspidosiphonidae, faces taxonomic challenges due to brief original descriptions and the poor condition or loss of the type material. Detailed standardized redescriptions are essential to understanding the diversification in this group. Herein, a comprehensive redescription of Aspidosiphon (Paraspidosiphon) steenstrupii based on an extensive material collection from the tropical Western Atlantic is provided. Based on morphological data and the analysis of COI sequences, we delimited A. (P.) steenstrupii morphologically, restricting its distribution to the tropical Western Atlantic. Also, the redescriptions and proposals for reinstatement of A. (P.) exostomum, A. (P.) ochrus, and A. (P.) speculator, previously considered junior synonyms of A. (P.) steenstrupii, are included. Furthermore, a comprehensive discussion on diagnostic morphological features to recognize aspidosiphonid species and a detailed revision of synonyms of A. (P.) steenstrupii are included. Notable differences in morphology and genetic data suggest the need for revising the taxonomic status of several synonyms within the family, highlighting underestimated diversity in sipunculans.}, }
@article {pmid40027782, year = {2025}, author = {Fukushima, T and Kristiansen, TA and Wong, LP and Keyes, S and Tanaka, Y and Mazzola, M and Zhao, T and He, L and Yagi, M and Hochedlinger, K and Yamazaki, S and Sadreyev, RI and Scadden, DT}, title = {Hematopoietic stem cells undergo bidirectional fate transitions in vivo.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40027782}, issn = {2692-8205}, support = {P01 HL131477/HL/NHLBI NIH HHS/United States ; P01 HL142494/HL/NHLBI NIH HHS/United States ; }, abstract = {Transitions between subsets of differentiating hematopoietic cells are widely regarded as unidirectional in vivo. Here, we introduce clonal phylogenetic tracer (CP-tracer) that sequentially introduces genetic barcodes, enabling high-resolution analysis of ~100,000 subclones derived from ~500 individual hematopoietic stem cells (HSC). This revealed previously uncharacterized HSC functional subsets and identified bidirectional fate transitions between myeloid-biased and lineage-balanced HSC. Contrary to the prevailing view that the more self-renewing My-HSCs unidirectionally transition to balanced-HSCs, phylogenetic tracing revealed durable lineage bidirectionality with the transition favoring My-HSC accumulation over time[1,2]. Further, balanced-HSCs mature through distinct intermediates-My-HSCs and lymphoid-biased-HSCs-with lymphoid competence here shown by CRISPR/Cas9 screening to be dependent on the homeobox gene, Hhex. Hhex enables Ly-HSC differentiation, but its expression declines with age. These findings establish HSC plasticity and Hhex as a determinant of myeloid-lymphoid balance with each changing over time to favor the age-related myeloid bias of the elderly.}, }
@article {pmid40027328, year = {2025}, author = {Guo, P and Li, C and Liu, J and Wu, T and Chai, B}, title = {Contribution of environmental and biological factors to bacterial community structure and stability in a subalpine lake.}, journal = {Marine life science &amp; technology}, volume = {7}, number = {1}, pages = {176-186}, pmid = {40027328}, issn = {2662-1746}, abstract = {UNLABELLED: Bacterial community play an essential role in regulating water quality and the global biogeochemical cycle in aquatic ecosystems. However, how trophic interactions (i.e., biotic factors) regulate the diversity and composition of bacterial community in lake ecosystems remains unknown. Here, we employed DNA meta-barcoding of water samples to explore the impact of bacterivorous protozoans on the bacterial community. The results showed significant seasonal variations in the diversity and composition of both bacterial and protist communities. The composition of bacterivorous protozoans was identified as the primary predictor for the bacterial community alpha diversity in spring and summer, and for beta diversity in spring and autumn, indicating that biotic interactions play a greater role in driving the diversity of bacterial community across different seasons. Biological factors were more important than environmental factors for explaining the variations in the relative abundance of several bacterial genera (i.e., Pseudoxanthomonas, hgcI_clade, and Pseudorhodobacter). Network analyses showed that bacterial networks differed among seasons, and the autumn network exhibited the highest stability. Our findings indicated that the bacterial community stability was significantly affected by environmental factors, specifically SO4 [2-]and PO4 [3-], rather than bacterivorous protozoans. Overall, our findings provide new perspectives on the role of trophic interactions in maintaining the structure of bacterial community in different seasons, and enhance our understanding of the bacterial community assembly in lake ecosystems.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00256-8.}, }
@article {pmid40027105, year = {2025}, author = {Flores-Zambrano, K and Tapia, W and Castillejo, P}, title = {Microalgae strains isolated from piggery wastewater in Ecuador: Effective nitrogen compound removal and growth potential in extremophile conditions.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {45}, number = {}, pages = {e00883}, pmid = {40027105}, issn = {2215-017X}, abstract = {Effluents generated by anthropogenic activities are a significant source of pollution and eutrophication in natural water bodies. In Ecuador, the increase in pig production has exacerbated this issue due to the untreated discharge of pig effluents. This study focused on the characterization of native microalgae present in pig effluents and the evaluation of their capacity to remove nitrogenous compounds under various conditions, with the aim of identifying efficient strains for phycoremediation. Four microalgal strains were isolated and molecularly identified as Radiococcus polycoccus, Chlorolobion braunii, Micractinium sp., and Desmodesmus multivariabilis. The cultures were exposed to initial concentrations of 100 mg L[-1] N-NH4 and 49.97 mg L[-1] N-NO3 for 12 days to assess their cellular growth and nutrient removal rates. Growth kinetics were analyzed under conditions of 2000 mg L[-1] N-NH4 and extreme pH levels of 3 and 10. Chlorolobion braunii demonstrated the highest productivity, achieving a removal of 67.73 % of N-NH4 and 30.59 % of N-NO3, and reached the highest cellular density under extreme ammonium conditions, being the only strain capable of growing at acidic pH. Conversely, Micractinium sp. exhibited the highest growth under alkaline conditions. These results highlight the promising potential of native microalgae from pig effluents for wastewater remediation and their adaptation to environmental conditions.}, }
@article {pmid40026382, year = {2025}, author = {Crabo, LG and Keegan, K}, title = {Revision of the North American genus Supralathosea Barnes &amp; Benjamin (Lepidoptera, Noctuidae, Oncocnemidinae) with description of two genera and three species.}, journal = {ZooKeys}, volume = {1228}, number = {}, pages = {197-223}, pmid = {40026382}, issn = {1313-2989}, abstract = {The noctuid genus Supralathosea Barnes &amp; Benjamin (Noctuidae, Oncocnemidinae) is revised to include three species for the United States of America, Supralathoseababoquivariensis Barnes &amp; Benjamin from southeast Arizona, Supralathoseayavapai sp. nov. from central Arizona, and Supralathoseasolastella sp. nov. from Texas. Two genera are described for species formerly included in Supralathosea. Infralathosea gen. nov. includes Infralathoseapronuba comb. nov. from Arizona and New Mexico and Infralathoseaunicornis sp. nov. from west Texas. Eulathosea gen. nov. contains only Eulathoseaobtusa Smith, comb. nov. from Arizona. A key to genera and species is presented and adults and genitalia of all taxa are illustrated. Infralathosea and Eulathosea are assigned to Oncocnemidinae based on molecular evidence.}, }
@article {pmid40023120, year = {2025}, author = {Liu, D and Wang, X and Xu, L and Al-Delfi, ZNS and Mekonnen, ZA and Gao, S and Grubor-Bauk, B and Zhao, CX}, title = {Screening lipid nanoparticles using DNA barcoding and qPCR.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {251}, number = {}, pages = {114598}, doi = {10.1016/j.colsurfb.2025.114598}, pmid = {40023120}, issn = {1873-4367}, mesh = {Animals ; *Nanoparticles/chemistry ; *Lipids/chemistry ; Mice ; RNA, Messenger/genetics/metabolism ; Tissue Distribution ; *DNA/chemistry/genetics ; *DNA Barcoding, Taxonomic ; Luciferases/genetics/metabolism ; Polymerase Chain Reaction/methods ; Particle Size ; Liposomes ; }, abstract = {Quantifying the biodistribution of lipid nanoparticles (LNPs) is critical for optimizing mRNA delivery systems, yet current approaches have inherent limitations. This study introduces a cost-effective method utilizing double-stranded DNA (dsDNA) barcodes and quantitative polymerase chain reaction (qPCR) for rapid analysis of a small library of mRNA-LNPs biodistribution and functional delivery in vivo. Three unique 100-bp dsDNA barcodes were designed to represent for three FDA-approved LNP formulations. Concurrently, these three formulations carrying luciferase mRNA were mixed with DNA-barcoding LNPs as a pool. Following intravenous administration of the pooled LNPs in mice, qPCR analysis revealed the highest abundance of DNA barcodes and accumulation of luciferase mRNA in spleen, with positive correlation between barcodes presence and mRNA localization across organs, validating DNA barcodes as reliable indicators of mRNA-LNPs biodistribution in vivo. Bioluminescence imaging further confirmed successful delivery and protein translation of luciferase mRNA facilitated by the LNPs in vivo. Integrating DNA barcodes for biodistribution analysis and luciferase mRNA for assessing functional delivery enabled comprehensive evaluation of LNP performance. This robust methodology provides valuable insights into the localization patterns and mRNA delivery capabilities of different LNP formulations, paving the way for the development of more effective and targeted mRNA-based therapeutics.}, }
@article {pmid40019731, year = {2025}, author = {Sinha, T and Shashank, PR}, title = {A Molecular Phylogeny of the Subfamily Plusiinae (Lepidoptera: Noctuidae) in India Inferred from Mitochondrial and Nuclear Ribosomal DNA Sequences.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40019731}, issn = {1559-0305}, support = {DST-SERB (SB/YS/LS-126/2014)//DST-SERB (SB/YS/LS-126/2014)/ ; }, abstract = {The subfamily Plusiinae, an economically important moth pest group, belongs to the species-rich family Noctuidae (Lepidoptera). Despite their enormous economic importance, the evolutionary history of this subfamily has not been completely resolved. In India, they are represented by a species complex, but the taxonomic delineation among these organisms is unclear. This study represents an insight into the comprehensive phylogenetic relationship among species supported by molecular approach based on mitochondrial (Cytochrome Oxidase I) and nuclear gene markers (Ribosomal Protein S5), emphasizing tribal-level classification. A total of 125 plusiinae taxa were analysed from eight biogeographical zones of India. The results revealed that Plusiinae tribes were monophyletic and considered sister groups that shared many derived characteristics. The ML/MP cladogram based on the barcoding gene successfully separates all species but not all tribes. The nuclear gene marker RPS5, separated all the species according to their tribes. The combined analysis of both genes showed tribe resolution into distinct clades. This is the first comprehensive study on phylogenetic studies of 25 species of plusiinae from India that clarifies deep divergence and gives information about species position and arrangement within taxa.}, }
@article {pmid40018971, year = {2025}, author = {Kartzinel, TR and Hoff, HK and Divoll, TJ and Littleford-Colquhoun, BL and Anderson, H and Burak, MK and Kuzmina, ML and Musili, PM and Rogers, H and Troncoso, AJ and Kartzinel, RY}, title = {Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research.}, journal = {Molecular ecology}, volume = {34}, number = {7}, pages = {e17712}, doi = {10.1111/mec.17712}, pmid = {40018971}, issn = {1365-294X}, support = {1930820//Division of Environmental Biology/ ; 2026294//Division of Environmental Biology/ ; 2046797//Division of Environmental Biology/ ; 2033823//Office of Integrative Activities/ ; P22AC00332//National Park Service/ ; P23AC00378//National Park Service/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Plants/genetics/classification ; *DNA, Plant/genetics ; *Genomics/methods ; *Embryophyta/genetics/classification ; Conservation of Natural Resources ; }, abstract = {Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the >373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science - most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives - such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.}, }
@article {pmid40017781, year = {2025}, author = {Aknine, N and Pelletier, R and Klymchenko, AS}, title = {Lipid-Directed Covalent Labeling of Plasma Membranes for Long-Term Imaging, Barcoding and Manipulation of Cells.}, journal = {JACS Au}, volume = {5}, number = {2}, pages = {922-936}, pmid = {40017781}, issn = {2691-3704}, abstract = {Fluorescent probes for cell plasma membranes (PM) generally exploit a noncovalent labeling mechanism, which constitutes a fundamental limitation in multiple bioimaging applications. Here, we report a concept of lipid-directed covalent labeling of PM, which exploits transient binding to the lipid membrane surface generating a high local dye concentration, thus favoring covalent ligation to random proximal membrane proteins. This concept yielded fluorescent probes for PM called MemGraft, which are built of a dye (cyanine Cy3 or Cy5) bearing a low-affinity membrane anchor and a reactive group: an activated ester or a maleimide. In contrast to specially designed control dyes and commercial Cy3-based labels of amino or thiol groups, MemGraft probes stain efficiently PM, revealing the crucial role of the membrane anchor combined with optimal reactivity of the activated ester or the maleimide. MemGraft probes overcome existing limitations of noncovalent probes, which makes them compatible with cell fixation, permeabilization, trypsinization, and the presence of serum. The latter allows long-term cell tracking and video imaging of cell PM dynamics without the signs of phototoxicity. The covalent strategy also enables staining and long-term tracking of cocultured cells labeled in different colors without exchange of probes. Moreover, the combination of MemGraft-Cy3 and MemGraft-Cy5 probes at different ratios enabled long-term cell barcoding in at least 5 color codes, important for tracking and visualizing multiple populations of cells. Ultimately, we found that the MemGraft strategy enables efficient biotinylation of the cell surface, opening the path to cell surface engineering and cell manipulation.}, }
@article {pmid40015720, year = {2025}, author = {Gallina, M and Testagrossa, M and Provenzani, A}, title = {Unit dose drug dispensing systems in hospitals: a systematic review of medication error reduction and cost-effectiveness.}, journal = {European journal of hospital pharmacy : science and practice}, volume = {}, number = {}, pages = {}, doi = {10.1136/ejhpharm-2024-004444}, pmid = {40015720}, issn = {2047-9956}, abstract = {BACKGROUND: Medical errors pose significant risks to patient safety and public health. Automated unit dose drug dispensing systems (UDDSs) have emerged as valuable tools to reduce medication errors while optimising economic and logistical resources.<br><br>OBJECTIVES: This systematic review aims to evaluate studies specifically focused on the impact of automated UDDSs in reducing medication errors and streamlining processes.<br><br>METHODS: A literature search was performed on PubMed, Scopus, and Web of Science, focusing on peer-reviewed articles published between 2019 and 2024. The search, concluded on 24 September 2024, included studies conducted in inpatient hospital settings that assessed automated UDDS effects on medication errors, therapy management and inventory control. Outcomes examined included effects on patient safety, cost-effectiveness and inventory management. Results were synthesised qualitatively.<br><br>RESULTS: From 3346 references, four studies met the inclusion criteria: a cost-effectiveness analysis, an uncontrolled before-and-after study, and two observational studies. UDDS improved medication processes, reducing drug-related problems, medication handling and dispensing time by 50% per patient per day. Integrated with barcode scanning, UDDS lowered medication administration errors (MAEs) from 19.5% to 15.8% and harmful MAEs from 3.0% to 0.3%. Overall, medication errors dropped by 45-70%, enhancing safety and reducing manual handling risks. UDDS demonstrated cost-effectiveness by significantly reducing MAEs. The study estimated a reduction in MAEs, with a cost-effectiveness ratio of &#x20ac;17.69 per avoided MAE. For potentially harmful MAEs, the cost-effectiveness ratio was estimated at &#x20ac;30.23 per avoided error. These findings suggest substantial long-term savings potential, though the exact magnitude may vary depending on hospital size and implementation specifics CONCLUSIONS: Automated UDDSs improve patient safety by significantly reducing medication errors and delivering cost savings through better inventory management. Challenges such as high initial costs and workflow adjustments can be mitigated through gradual implementation and staff training. Further integration with other healthcare technologies, such as barcoding, real-time tracking, artificial intelligence (AI)-driven error prevention tools and fully automated restocking systems could enhance UDDS benefits and further support hospital processes.}, }
@article {pmid40015300, year = {2025}, author = {Prakash, PS and Joshi, FM and Vogelsberg, E and Cremers, GAO and Gür, FN and Sato, Y and de Greef, TFA and Ader, M and Kurth, T and Nunes Gonçalves, DP and Schmidt, TL}, title = {DNA Origami Barcodes for Immunostaining.}, journal = {ACS applied materials &amp; interfaces}, volume = {17}, number = {10}, pages = {15813-15823}, pmid = {40015300}, issn = {1944-8252}, support = {R35 GM142706/GM/NIGMS NIH HHS/United States ; }, mesh = {*DNA/chemistry ; Gold/chemistry ; Metal Nanoparticles/chemistry ; *Immunohistochemistry/methods ; Animals ; Antibodies/chemistry ; Humans ; Nanotechnology/methods ; Mice ; }, abstract = {In histology, immunostaining of biological samples is a gold standard for studying cellular processes, such as the expression of cell surface markers or the cellular uptake of proteins and drug molecules. Immuno-gold labeling is a commonly used technique to achieve nanometer spatial resolution, but simultaneous visualization of multiple antigens in parallel is an unresolved challenge. Herein, we demonstrate a DNA nanotechnology-based approach to label antigens in transmission electron microscopy images of tissue sections with high contrast patterns. For this, we attached gold nanoparticles to designated binding positions on DNA origami structures that act as visual "barcodes." These barcodes are then hybridized to complementary strands of DNA-modified antibodies that are bound to their respective antigens on ultrathin tissue resin sections. As a proof of concept, we demonstrate several types of barcodes and two different antibody labeling techniques that will expand the multiplexing abilities of immunostaining in a highly modular way.}, }
@article {pmid40013788, year = {2025}, author = {Pfordt, A and Douanla-Meli, C and Schäfer, BC and Schrader, G and Tannen, E and Chandarana, MJ and von Tiedemann, A}, title = {Phylogenetic analysis of plant-pathogenic and non-pathogenic Trichoderma isolates on maize from plants, soil, and commercial bio-products.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {3}, pages = {e0193124}, pmid = {40013788}, issn = {1098-5336}, support = {FKZ2221NR014A//Bundesministerium f&#xfc;r Ern&#xe4;hrung und Landwirtschaft (BMEL)/ ; }, mesh = {*Zea mays/microbiology ; *Trichoderma/genetics/pathogenicity/classification/isolation &amp; purification ; *Phylogeny ; *Plant Diseases/microbiology ; *Soil Microbiology ; }, abstract = {Fungi of the genus Trichoderma are primarily associated with the mycobiome of dead wood but can also be occasionally found in soil and plant rhizospheres. Several Trichoderma spp. are used in crop health management to promote growth and control plant diseases. Although widely considered beneficial to plants, some members have been reported to be pathogenic to maize, causing a disease called Trichoderma ear rot. Since 2018, Trichoderma afroharzianum has caused significant infections of maize cobs in Germany, France, and Italy. This study aimed to investigate the pathogenicity and phylogenetic relationships among different Trichoderma strains from diverse sources and geographical origins. While previous studies primarily identified T. afroharzianum as the main species causing Trichoderma ear rot, this study found that isolates of T. asperellum, T. atroviride, and T. guizhouense may also exhibit pathogenicity on maize cobs. Additionally, Trichoderma strains from commercial biocontrol products displayed unexpected pathogenicity inducing up to 92% disease severity on maize cobs. Most T. afroharzianum strains induced high levels of disease severity, although some isolates of the same species did not cause any disease, indicating a large heterogeneity in pathogenicity within the species. Notably, phylogeny reconstruction based on the tef1-α and rpb2 genes did not result in any discernible clustering between pathogenic and non-pathogenic isolates. A further novel finding is the isolation of pathogenic Trichoderma isolates from agricultural soil, demonstrating that soil can serve as a reservoir for pathogenic species. This study highlights the need for biosecurity assessment and monitoring of Trichoderma strains for agricultural use, considering their beneficial and pathogenic potential.IMPORTANCEIn this study, we explored the ability of different Trichoderma species to infect maize plants. Trichoderma is a group of fungi known for its beneficial role in agriculture, often used as a biological pesticide to control fungal plant diseases. However, some species within this genus can also act as pathogens, causing infections in crops like maize. We found that one species, T. afroharzianum, is particularly aggressive, capable of infecting maize without the plant being wounded first. This makes it a potentially serious threat to crop health. In contrast, other species, such as T. atroviride and T. asperellum, only caused infections when maize plants were injured before. Our research suggests that pathogenic Trichoderma species not only effectively infect plants but can also survive well in soil, making their control difficult. These findings highlight the need for better understanding of how these fungi operate in order to manage the risks they pose to important crops like maize, while still taking advantage of their beneficial uses in agriculture.}, }
@article {pmid40012563, year = {2025}, author = {Kim, Y and Park, J and Hwang, UW and Park, JK}, title = {Taxonomic review of Korean Siphonaria species (Mollusca, Gastropoda, Siphonariidae).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e139388}, pmid = {40012563}, issn = {1314-2828}, abstract = {BACKGROUND: Many molluscan species exhibit a high degree of shell morphological plasticity in their shape (including sculptures), size and colour patterns, which can vary significantly depending on environmental conditions. These shell morphological variations make it challenging to differentiate species, based on morphology alone, often resulting in various taxonomic errors, such as misidentifications, overlooking cryptic species diversity or a plethora of nominal species. The genus Siphonaria constitutes a significant component of the macrobenthic invertebrate fauna in intertidal habitats across temperate to tropical regions. Given the limited attention to shell variation in previous taxonomic studies on the Korean Siphonaria species, the extensive range of ecophenotypic shell variations documented in this group raises questions about the taxonomic validity of previously reported Siphonaria species in Korea.<br><br>NEW INFORMATION: The present study provides a comprehensive taxonomic review of Korean Siphonaria species using a combination of shell morphology, radula structure and phylogenetic analysis of the mtDNA cox1 sequences. This integrative analysis confirmed the validity of S.acmaeoides, S.japonica and S.sirius in Korea, highlighting differences in shell and siphonal groove morphology amongst these species. Detailed descriptions of shell and radula characteristics, along with mtDNA cox1 sequences as DNA barcodes, are also provided, which are very useful for the accurate identification of Siphonaria species. Unlike these three Siphonaria species, the taxonomic validity of the four other species (S.coreensis, S.javanica, S.laciniosa and S.rucuana) previously reported from Korean waters is questionable, given their documented geographic distribution ranges and the potential misidentification of shell variants in Korean malacofaunal studies.}, }
@article {pmid40012562, year = {2025}, author = {Bergman, LA and Montenegro, J and Seid, CA and Bachtel, TS and Mann, F and Thuesen, EV and Lindsay, DJ and Drazen, JC}, title = {Checklist of ichthyoplankton of NORI-D polymetallic nodule exploration claim (eastern Clarion-Clipperton Zone) during winter 2021.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e137744}, pmid = {40012562}, issn = {1314-2828}, abstract = {BACKGROUND: There been increasing interest in polymetallic nodule mining within the Clarion-Clipperton Zone (CCZ). Polymetallic nodule mining within NORI-D will release a sediment plume within the water column and a previous mining collector test within the Nauru Ocean Resources Inc. (NORI-D) contract area released surface pollution from mining tailings. The mid-water plume, as well as accidental surface pollution, indicate that polymetallic nodule mining could impact surface plankton. Although the ichthyoplankton within the eastern tropical Pacific have been well-studied, recent data from within polymetallic nodule mining licence areas is lacking. Environmental Expedition C5e conducted an environmental baseline assessment of both pelagic and benthic fauna within the NORI-D region of the CCZ, which included the opportunistic collection of ichthyoplankton.<br><br>NEW INFORMATION: Ichthyoplankton were collected within NORI-D from November-December 2021 using two plankton nets and a Remotely Operated Vehicle (ROV). Here, we present a checklist of ichthyoplankton within the NORI-D licence area during this winter campaign. Eighteen samples were collected and identified through morphology, with a limited number identified through genetic sequencing. Specimens were from five orders, including Argentiniformes, Stomiiformes, Myctophiformes, Beloniformes and Scombriformes. This checklist will aid contractors and scientists conducting work within the CCZ to examine how wastewater discharge from polymetallic nodule mining could impact fish reproduction and ichthyoplankton survival.}, }
@article {pmid40011951, year = {2025}, author = {Liu, LQ and Fu, WQ and Ma, YY and Liu, ZY and Ge, CF and Yang, YR and Qing, X and Zeng, QL}, title = {Draft genome of pin nematode Paratylenchus projectus recovered from rhizosphere of blueberry.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {77}, pmid = {40011951}, issn = {1756-3305}, support = {2023BCF01022//Key Research &amp; Development Project of Ningxia Autonomous Region, China/ ; }, mesh = {Animals ; Phylogeny ; *Blueberry Plants/parasitology ; *Tylenchoidea/genetics/classification/isolation &amp; purification ; *Rhizosphere ; *Genome, Helminth ; Plant Roots/parasitology ; Plant Diseases/parasitology ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; }, abstract = {BACKGROUND: The pin nematode, belonging to the genus Paratylenchus, parasitizes higher plants, often causing reduced or inhibited root tip development.<br><br>METHODS: Pin nematodes were isolated from the roots and rhizosphere of blueberry plants and subsequently identified as representatives of Paratylenchus projectus based on morphological characteristics and molecular barcoding. The P. projectus draft genome was sequenced using the Illumina platform.<br><br>RESULTS: Phylogenetic analysis based on 18S, 28S and ITS rRNA placed this species in highly supported clades alongside other P. projectus specimens. The draft genome of P. projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae. The assembled genome, though fragmented, had a total length of 191.36 Mb and an estimated genome size of 64.9 Mb. Protein-coding genes were predicted using four different databases, with particular focus on carbohydrate-active enzymes from the GH5 and GH18 families. The recovered GH5 genes were distributed among three distinct clades: one forming a basal group relative to other nematodes, one as a sister clade to the fungivorous nematode Aphelenchus avenae and one nested within a fungal clade. The GH18 chitinase genes were grouped into two clades: one closely related to sedentary plant-parasitic nematodes of the genera Heterodera and Globodera and the other closely related to the fungivorous nematode Ditylenchus.<br><br>CONCLUSIONS: The draft genome of Paratylenchus projectus was sequenced and assembled, representing the first genomic data for both the genus Paratylenchus and the family Tylenchulidae to our knowledge.}, }
@article {pmid40011622, year = {2025}, author = {Eroğlu, M and Çelik, I and Düşükcan, M and Ünal, EM and Çoban, MZ and Gündüz, F and Keskin, E}, title = {Author Correction: DNA barcoding of invasive Gambusia holbrooki Girard, 1859 and Atherina boyeri Risso, 1810 inhabiting Upper Euphrates River Basin, Türkiye.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6886}, doi = {10.1038/s41598-025-91131-8}, pmid = {40011622}, issn = {2045-2322}, }
@article {pmid40010350, year = {2025}, author = {Singh, I and Fernandez-Perez, D and Sanchez, PS and Rodriguez-Fraticelli, AE}, title = {Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations.}, journal = {Cell stem cell}, volume = {32}, number = {4}, pages = {564-580.e6}, doi = {10.1016/j.stem.2025.01.012}, pmid = {40010350}, issn = {1875-9777}, mesh = {Animals ; *Mutation/genetics ; Nucleophosmin ; Mice ; Humans ; DNA Methyltransferase 3A ; Clone Cells/pathology ; *Neoplastic Stem Cells/pathology/metabolism ; DNA (Cytosine-5-)-Methyltransferases/genetics ; Cell Differentiation ; *Leukemia/genetics/pathology ; Cell Lineage ; Nuclear Proteins/genetics ; *Genetic Heterogeneity ; *Stem Cells ; }, abstract = {Cancer cells display wide phenotypic variation even across patients with the same mutations. Differences in the cell of origin provide a potential explanation, but traditional assays lack the resolution to distinguish clonally heterogeneous subsets of stem and progenitor cells. To address this challenge, we developed simultaneous tracking of recombinase activation and clonal kinetics (STRACK), a method to trace clonal dynamics and gene expression before and after the acquisition of cancer mutations. Using mouse models, we studied two leukemic mutations, Dnmt3a-R878H and Npm1c, and found that their effect was highly variable across different stem cell states. Specifically, a subset of differentiation-primed stem cells, which normally becomes outcompeted with time, expands with both mutations. Intriguingly, Npm1c mutations reversed the intrinsic bias of the clone of origin, with differentiation-primed stem cells giving rise to more primitive malignant states. Thus, we highlight the relevance of single-cell lineage tracing to unravel early events in cancer evolution and posit that different cellular histories carry distinct cancer phenotypic potential.}, }
@article {pmid40009639, year = {2025}, author = {Huang, R and Ting, AY}, title = {Directed evolution of a sequence-specific covalent protein tag for RNA labeling.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {9}, pages = {e2422085122}, pmid = {40009639}, issn = {1091-6490}, support = {2330686//National Science Foundation (NSF)/ ; N/A//Chan Zuckerberg Biohub - San Francisco/ ; N/A//Stanford University (SU)/ ; }, mesh = {*Directed Molecular Evolution/methods ; *RNA/chemistry/metabolism/genetics ; Humans ; Animals ; Staining and Labeling/methods ; *RNA-Binding Proteins/genetics/metabolism/chemistry ; }, abstract = {Efficient methods for conjugating proteins to RNA are needed for RNA delivery, imaging, editing, interactome mapping, and barcoding applications. Noncovalent coupling strategies using viral RNA binding proteins such as MS2/MCP have been widely applied but are limited by tag size, sensitivity, and dissociation over time. We took inspiration from a sequence-specific, covalent protein-DNA conjugation method based on the Rep nickase of a porcine circovirus called "HUH tag". Though wild-type HUH protein has no detectable activity toward an RNA probe, we engineered an RNA-reactive variant, called "rHUH", through 7 generations of yeast display-based directed evolution. Our 13.4 kD rHUH has 12 mutations relative to HUH and forms a covalent tyrosine-phosphate ester linkage with a 10-nucleotide RNA recognition sequence ("rRS") within minutes. We engineered the sensitivity down to 1 nM of target RNA, shifted the metal ion requirement from Mn[2+] toward Mg[2+], and demonstrated efficient labeling in mammalian cell lysate. This work paves the way toward a potentially powerful methodology for sequence-specific covalent protein-RNA conjugation in biological systems.}, }
@article {pmid40009600, year = {2025}, author = {Tursky, ML and Artuz, CM and Rapadas, M and Wittert, GA and Molloy, TJ and Ma, DD}, title = {Error-corrected ultradeep next-generation sequencing for detection of clonal haematopoiesis and haematological neoplasms - sensitivity, specificity and accuracy.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0318300}, pmid = {40009600}, issn = {1932-6203}, mesh = {Humans ; *Hematologic Neoplasms/genetics/diagnosis ; *High-Throughput Nucleotide Sequencing/methods ; *Clonal Hematopoiesis/genetics ; Sensitivity and Specificity ; Reproducibility of Results ; Gene Frequency ; Neoplasm, Residual/genetics/diagnosis ; }, abstract = {Clonal haematopoiesis of indeterminate potential (CHIP) is an aging-associated phenomenon that has recently been correlated with a broad spectrum of human diseases, including haematological malignancy, cytopenia, coronary heart disease, stroke, and overall mortality. CHIP is defined as a somatic variant in blood cells with an allele frequency (VAF) ≥ 0.02, however recent reports show smaller clones are associated with poorer clinical outcome. Error-corrected ultradeep next-generation sequencing (NGS) assays detecting variants < 0.02 VAF also have clinical value for monitoring measurable residual disease (MRD) for myeloid neoplasms. However, limited data are available on optimal parameters, limits of detection, and accuracy of ultra-sensitive detection. We investigated parameters to improve accuracy of Illumina sequencing-by-synthesis method, including read depth, input DNA quantity, and molecular barcoding-based data filtering, while adhering to clinical accreditation criteria. Validation data were generated from reference standards and reference samples from a clinically accredited pathology laboratory. Analytical range measurements included linearity and bias, and precision included repeatability, reproducibility and detection rate. The lower limit of detection was ≥ 0.004 (0.4%) at depth > 3,000 × . Trueness measured using reference standards demonstrated a sensitivity, specificity, positive and negative predictive values, and accuracy of 100%, including FLT3-ITD, and 100% concordance was achieved with reference samples for reported variants and absence of variants. Sequencing blood samples from 383 community-dwelling adults (mean depth 3758×) revealed 2,190 somatic variants/sample, > 99.9% were < 0.02 VAF. Our data including cost-benefit analysis enables pathology and research laboratories to make informed decisions for detection of CHIP (VAF ≥ 0.02), sub-CHIP (VAF 0.01-0.02) and MRD (VAF ≥ 0.004).}, }
@article {pmid40006878, year = {2025}, author = {Peng, Y and Chen, Y and Ding, H and Liu, X and Cao, F and Xu, L}, title = {From Phenotypes to Genotypes: Enhancing the Identification of Cymbidium Species with DNA Barcoding.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40006878}, issn = {2223-7747}, support = {No. 2019JJ50232//Hunan Provincial Science and Technology Department/ ; }, abstract = {The genus Cymbidium, with its intricate floral elements, pronounced endemicity, and patchy distribution, evolves a rich diversity of morphological forms and a wide variety of species while causing an indistinctness in the classification of its species. To elucidate the phylogenetic relationships among Cymbidium species and enhance their taxonomic classification by DNA barcoding, this study conducted amplification and sequence results of nuclear (ITS) and chloroplast genes (matK, rbcL, trnL-F, psbA-trnH) with phenotypic genetic diversity analysis, genetic distance analysis, and phylogenetic analysis from 48 samples of Cymbidium species. The comparison of genetic distance variations showed that psbA-trnH, ITS + psbA-trnH, and ITS + matK + psbA-trnH exhibit minimal overlap and significant genetic variation within Cymbidium species. The phylogenetic analysis indicated that the combination, ITS + matK + psbA-trnH, has the highest identification rate. Notably, both the phylogenetic analysis and the genetic diversity analysis of phenotypic traits consistently indicated a clear divergence between epiphytic and terrestrial orchids, with epiphytic orchids forming a distinct clade. This provides reference evidence for studying the ecological adaptations and evolutionary differences between epiphytic and terrestrial orchids, as well as a scientific basis for the classification and identification, germplasm conservation, resource utilization, and phylogenetic evolution of orchids.}, }
@article {pmid40005642, year = {2025}, author = {Chittavichai, T and Sathitnaitham, S and Utthiya, S and Prompichai, W and Prommarit, K and Vuttipongchaikij, S and Wonnapinij, P}, title = {Limitations of 18S rDNA Sequence in Species-Level Classification of Dictyostelids.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005642}, issn = {2076-2607}, support = {//Kasetsart University through the Graduate School Fellowship Program/ ; FF(KU)13.64//Kasetsart University Research and Development Institute (KURDI)/ ; N42A650286//The National Research Council of Thailand (NRCT) and Kasetsart University Research and Development Institute (KURDI)/ ; }, abstract = {Dictyostelid species classification has traditionally relied on morphology, a time-intensive method requiring expert knowledge. This study evaluated the potential and limitations of using the 18S rDNA sequence for species-level classification. 18S rDNA sequences of 16 samples from the Dicty stock center, including 14 samples found in Thailand, were analyzed. Signature sequence analyses confirmed genus-level identification with high accuracy. These sequences were analyzed alongside 309 database entries retrieved from the GenBank database. The analyses confirmed genus-level identification accuracy but highlighted challenges in distinguishing species due to overlapping intraspecific and interspecific variations, negative barcoding gaps, and incorrectly grouped samples to putative taxa by species delimitation analyses. Species delimitation methods, including maximum likelihood (ML) phylogenetic analysis, achieved limited success, with ML showing the highest accuracy but not exceeding 50%. However, species with high barcoding gaps, such as Raperostelium and Rostrostelium, demonstrated potential for accurate classification. These findings support using 18S rDNA for genus-level identification and suggest its possible application for certain species. Expanded sampling is needed to improve species-level classification and to identify more robust DNA markers for dictyostelid diversity studies.}, }
@article {pmid40003852, year = {2025}, author = {Jiang, ZH and Kitching, IJ and Xu, XD and Xu, ZB and Yan, M and Yu, WB and Liu, CQ and Hu, SJ}, title = {A Review of the Genus Ambulyx Westwood, 1847 (Lepidoptera: Sphingidae) from China Based on Morphological and Phylogenetic Analyses, with the Description of a New Species.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003852}, issn = {2075-4450}, support = {202305AF150037//Academician (Expert) Working Station (202305AF150037), Yunnan Provincial De-partment of Science, Technology/ ; Grant No. 2019FY101800//National Science &amp; Technology Fundamental Resources Investigation Program of Chi-na/ ; Grant Nos. 32100352&#xff0c;32100355//National Natural Science Foundation of China/ ; }, abstract = {The taxonomy of genus Ambulyx Westwood, 1847 from China is reviewed based on analysis of wing morphology, male and female genitalia and phylogenetic relationships derived from DNA barcodes. A new species, Ambulyx wukong sp. nov. is described from NW Yunnan, China. A male of the rare species, A. zhejiangensis from Yintiaoling Nature Reserve, Chongqing, China is examined and its male genitalia illustrated for the first time. Two taxa are newly recorded from China, A. tattina tattina from Xishuangbanna, Yunnan, and A. semiplacida montana from Pingbian, Yunnan. Distribution maps, biological notes, and ecological records are also given.}, }
@article {pmid40003849, year = {2025}, author = {Gwiazdowska, A and Rutkowski, R and Sielezniew, M}, title = {Conservation Genetics of the Endangered Danube Clouded Yellow Butterfly Colias myrmidone (Esper, 1780) in the Last Central European Stronghold: Diversity, Wolbachia Infection and Balkan Connections.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003849}, issn = {2075-4450}, support = {EZ.271.3.7.2021//General Directorate of the Polish State Forests/ ; }, abstract = {The Danube Clouded Yellow (Colias myrmidone) has experienced one of the most dramatic declines among European butterflies. To estimate genetic diversity in the last population in Poland that has survived in the Knyszyn Forest (KF), we analyzed mitochondrial (COI) and nuclear (EF-1α) polymorphisms in individuals sampled in 2014 and 2022. The results were compared with genetic data obtained in 2014 from a recently extirpated nearby population (Czerwony Bór, CB). Because mtDNA polymorphisms in insects can be modulated by endosymbionts, the samples were screened for Wolbachia. The polymorphism of EF-1α indicated that diversity was gradually decreasing. The KF experienced rapid demographic processes, manifested by a significant change in allele frequency. The small differentiation in nuclear markers between the KF and CB in 2014 suggests that the regional population used to be genetically uniform. Four COI haplotypes that were identified in this study probably belong to two different haplogroups. Wolbachia was detected only in individuals with one specific haplotype, and the prevalence was female-biased, suggesting the induction of two reproductive manipulations. The most common COI haplotype found in Poland was the same as that reported from other parts of Europe, not only for C. myrmidone but also C. caucasica. These results allow us to question the distinctiveness of each taxa.}, }
@article {pmid40003799, year = {2025}, author = {Ricupero, M and Porcu, E and Russo, A and Zappalà, L and Siscaro, G}, title = {New Records of Phenacoccus solenopsis Natural Enemies in Europe and Taxonomic Additions on Anagyrus matritensis.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003799}, issn = {2075-4450}, support = {CN00000022//the European Union Next-Generation EU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022/ ; E73C22000240006//Agroecology-inspired Strategies and Tools to Enhance Resilience and ecosystem services in to-mato crop" (ASTER), PRIMA SECTION 2 2021 - MULTI-TOPIC/ ; 101136611//the European Union's Horizon Europe research and innovation programme (NextGenBioPest project)/ ; }, abstract = {The cotton mealybug Phenacoccus solenopsis (Hemiptera: Pseudococcidae) is a polyphagous invasive species native to America and considered one of the major cotton pests in Asia. It is currently threatening horticultural and ornamental protected crops in Mediterranean countries. Due to ecological and environmental concerns, the conventional chemical control of P. solenopsis in new areas of introduction is being replaced by exploring the potential of indigenous natural enemies as a sustainable biological control tool. After P. solenopsis introduction in Sicily (Italy), field surveys were conducted on native natural enemies attacking the mealybug to select promising biocontrol agents for field applications. For the first time, Aenasius arizonensis (Hymenoptera: Encyrtidae) was reported in Europe, and the native Anagyrus matritensis (Hymenoptera: Encyrtidae) was recorded in association with P. solenopsis. The two parasitoid species were identified by morphological features and molecularly using a portion of the mitochondrial cytochrome oxidase subunit I (mtCOI) gene. Because of missing information, additional morphological features were provided for the morphological identification of A. matritensis. In addition, the generalist predators Cryptolaemus montrouzieri, Hippodamia variegata and Parexochomus nigripennis (Coleoptera: Coccinellidae) were also recorded attacking the invasive mealybug.}, }
@article {pmid40003760, year = {2025}, author = {Qian, P and Fan, J and Zhang, X and Zeng, M and Han, X and Li, Y and Luo, X}, title = {Morphogenetic Identification of a New Record Condica capensis (Lepidoptera: Noctuidae) in Yunnan, China.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003760}, issn = {2075-4450}, support = {202301BD070001-185//Joint Agricultural Project of Yunnan Province/ ; }, abstract = {Condica capensis (Lepidoptera: Noctuidae), a newly identified pest in Yunnan Province, China, poses a threat to safflower crops. Discovered in Nanhua County in November 2023, the pest damages safflower at multiple life stages, especially during its larval stage, when it feeds on leaves, tender stems, and flower filaments, sometimes causing the entire plant to die. Morphological and molecular analyses, including mitochondrial cytochrome C oxidase I (COI) gene sequencing, confirmed its identity as C. capensis, a new species record for Yunnan. The study also documented the pest's life cycle, reproductive behavior, and natural enemies, highlighting the potential for biological control using parasitic wasps such as Cotesia sp. This research emphasizes the need for accurate pest identification and monitoring to develop effective, sustainable pest management strategies. As safflower cultivation grows in Yunnan, managing C. capensis is critical to safeguarding local agriculture and preventing broader agricultural threats.}, }
@article {pmid40002052, year = {2025}, author = {Jiang, Y and Wei, S and Ge, H and Zhang, Y and Wang, H and Wen, X and Guo, C and Wang, S and Chen, Z and Li, P}, title = {Advances in the Identification Methods of Food-Medicine Homologous Herbal Materials.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {40002052}, issn = {2304-8158}, support = {(No. 61975053, No. 62271191)//National Natural Science Foundation of China/ ; No. 222300420040//Natural Science Foundation of Henan Province/ ; (No. 22HASTIT017, No. 23HASTIT024)//Program for Science and Technology Innovation Talents in Universities of Henan Province/ ; No. CSKFJJ-2024-26//Open Project of Institute for Complexity Science, Henan University of Technology/ ; No. 201300210100//Major public welfare projects of Henan Province/ ; No. 2021ZKCJ04//Innovative Funds Plan of Henan University of Technology/ ; }, abstract = {As a key component of both traditional medicine and modern healthcare, Food-Medicine Homologous Herbal Materials have attracted considerable attention in recent years. However, issues related to the quality and authenticity of medicinal materials on the market often arise, not only compromising their efficacy but also presenting potential risks to consumer health. Therefore, the establishment of accurate and efficient identification methods is crucial for ensuring the safety and quality of Food-Medicine Homologous Herbal Materials. This paper provides a systematic review of the research progress on the identification methods for Food-Medicine Homologous Herbal Materials, starting with traditional methods such as morphological and microscopic identification, and focusing on the applications of modern techniques, including biomimetic recognition, chromatography, mass spectrometry, chromatography-mass spectrometry coupling, hyperspectral imaging, near-infrared spectroscopy, terahertz spectroscopy, and DNA barcoding. Moreover, it provides a comprehensive analysis of the fundamental principles, advantages, and limitations of these methods. Finally, the paper outlines the current challenges faced by identification methods and suggests future directions for improvement, aiming to offer a comprehensive technical perspective on identifying Food-Medicine Homologous Herbal Materials and foster further development in this field.}, }
@article {pmid39997428, year = {2025}, author = {Motta, BDS and Almeida-Silva, F and Teixeira, MM and Bernardes-Engemann, AR and Almeida-Paes, R and de Macedo, PM and Zancopé-Oliveira, RM}, title = {Paracoccidioides Species Circulating in the Endemic Area of Rio de Janeiro, Brazil: Updates into Their Genetic Diversity.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {39997428}, issn = {2309-608X}, support = {001//CAPES/ ; E-26/211.430/2021//FAPERJ/ ; 308315/2021-9//CNPq/ ; E-26/200.381/2023//FAPERJ/ ; }, abstract = {Paracoccidiodomycosis (PCM) is the most important systemic mycosis in Brazil, and is usually associated with rural work. PCM is caused by inhalation of infective propagules of thermodimorphic fungi from the genus Paracoccidioides. In the past, it was believed that Paracoccidioides brasiliensis was the single species responsible for PCM cases. However, recent advances in molecular methods allowed the description of several new species, using phylogenetic concordance as the gold standard. Aside from P. brasiliensis sensu stricto, Paracoccidioides americana is also endemic in Rio de Janeiro state, Brazil. This study aimed to evaluate intraspecific genetic variability of Paracoccidioides isolates from patients diagnosed with PCM at a reference center for endemic mycoses in Rio de Janeiro state, from 2015 to 2021. Among the sixteen retrieved isolates, three (18.75%) were identified as P. americana and thirteen (81.25%) as P. brasiliensis sensu stricto. No intraspecific genetic variation was observed by the M-13 primer in P. americana isolates from this geographic region. However, P. brasiliensis sensu stricto isolates were clustered into two distinct molecular profiles, despite being grouped in a single clade in the phylogenetic tree after partial sequencing of arf and gp43 genes. The results suggest a single P. americana lineage and two P. brasiliensis populations causing PCM in Rio de Janeiro, Brazil.}, }
@article {pmid39997392, year = {2025}, author = {Zuleta, MC and Gómez, OM and Misas, E and Torres, S and Rúa-Giraldo, &#xc1;L and McEwen, JG and Garcia, AM and Borges, CL and Hernández, O and López, AM}, title = {Species Identification and Orthologous Allergen Prediction and Expression in the Genus Aspergillus.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {39997392}, issn = {2309-608X}, support = {221384467683//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; }, abstract = {The genus Aspergillus comprises a diverse group of fungi that can cause a range of health issues, including systemic infections and allergic reactions. In this regard, A. fumigatus has been recognized as the most prevalent allergen-producing species. This genus taxonomic classification has been subject to frequent updates, which has generated considerable difficulties for its classification when traditional identification methodologies are employed. To demonstrate the feasibility of this approach, we sequenced the whole genomes of 81 Aspergillus isolates and evaluated a WGS-based pipeline for precise species identification. This pipeline employed two methodologies: (i) BLASTn web using four barcode genes and (ii) species tree inference by OrthoFinder. Furthermore, we conducted a prediction of allergenic capacity based on a homology analysis across all the isolated species and confirmed by RT-qPCR the expression of three orthologous allergens (Asp f 1, Asp f 3 and Asp f 22) in fifteen different Aspergillus species. The species-level identification rate with the barcoding and the species tree were calculated at 64.2% and 100%, respectively. The results demonstrated that A. fumigatus, A. flavus and A. niger were the most prevalent species. The species A. hortae, A. uvarum, A. spinulosporus, A. sydowii, A. westerdijkiae, A. amoenus and A. rhizopodus identified in this study represent the inaugural report of their presence in our region. The results of the homology analysis indicated the presence of orthologous allergens in a wide range of non-fumigatus species. This study presents a novel approach based on WGS that enables the classification of new species within the genus Aspergillus and reports the genomic sequences of a great diversity of species isolated in our geographic area that had never been reported before. Additionally, this approach enables the prediction of allergens in species other than A. fumigatus and demonstrates their genetic expression, thereby contributing to the understanding of the allergenic potential of different species within this fungal genus.}, }
@article {pmid39997216, year = {2025}, author = {Chovanec, P and Yin, Y}, title = {Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility.}, journal = {Nucleic acids research}, volume = {53}, number = {4}, pages = {}, pmid = {39997216}, issn = {1362-4962}, support = {R35 GM142511/GM/NIGMS NIH HHS/United States ; R35GM142511/GF/NIH HHS/United States ; 5R35GM142511/GM/NIGMS NIH HHS/United States ; DFS-43-20/DRCRF/Damon Runyon Cancer Research Foundation/United States ; }, mesh = {*Chromatin/genetics/chemistry/metabolism ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Single-Cell Analysis/methods ; *RNA/genetics ; DNA Replication ; }, abstract = {Single-cell combinatorial indexing (sci) methods have addressed major limitations of throughput and cost for many single-cell modalities. With the incorporation of linear amplification and three-level barcoding in our suite of methods called sci-L3, we further addressed the limitations of uniformity in single-cell genome amplification. Here, we build on the generalizability of sci-L3 by extending it to template strand sequencing (sci-L3-Strand-seq), genome conformation capture (sci-L3-Hi-C), and the joint profiling of RNA and chromatin accessibility (sci-L3-RNA/ATAC). We demonstrate the ease of adapting sci-L3 to these new modalities by only requiring a single-step modification of the original protocol. As a proof of principle, we show our ability to detect sister chromatid exchanges, genome compartmentalization, and cell state-specific features in thousands of single cells. We anticipate sci-L3 to be compatible with additional modalities, including DNA methylation (sci-MET) and chromatin-associated factors (CUT&amp;Tag), and ultimately enable a multi-omics readout of them.}, }
@article {pmid39997191, year = {2025}, author = {Turner, AD and Maskrey, BH and Stone, D and Mudge, EM and Robertson, A}, title = {First Confirmed Occurrence of Ciguatera Poisoning in the UK from Imported Pinjalo Snapper (Pinjalo pinjalo).}, journal = {Marine drugs}, volume = {23}, number = {2}, pages = {}, pmid = {39997191}, issn = {1660-3397}, support = {P01 ES028949/ES/NIEHS NIH HHS/United States ; Atlantic Area Program project Alertox-Net (EAPA-317-2016//Interreg Atlantic Area/ ; }, mesh = {*Ciguatera Poisoning/diagnosis/etiology/epidemiology ; Animals ; *Ciguatoxins/toxicity/analysis ; Humans ; United Kingdom ; *Seafood/analysis ; Mice ; *Perciformes ; Male ; Chromatography, Liquid ; }, abstract = {Three people in England consumed fish steaks labeled as Red Snapper (Lutjanus bohar) originating from the Indian Ocean. Within 12 h, all three experienced sickness including nausea, vomiting, diarrhea, as well as myalgia and paresthesia. Three steaks from a single package of fish obtained from a grocery store were consumed, leaving one uneaten, which was submitted for analysis. Cytotoxicity testing via the mouse neuroblastoma assay confirmed the presence of sodium channel specific activity consistent with a ciguatoxin standard, and the levels detected were above established guidance limits for safe consumption. Chemical detection using liquid chromatography coupled with high-resolution mass spectrometry of both intact toxins and periodate oxidation products was used to confirm the presence of chromatographic peaks consistent with tri- and di-hydroxylated Pacific ciguatoxin 3C congeners. Taking the shared medical symptoms of patients, the recent dietary history, and the known potential for ciguatera poisoning to occur in snapper species, the subsequent evidence for CTX-like activity and CTXs in the same fish sample provides very strong evidence that the fish steaks consumed were similarly contaminated with CTXs. Furthermore, given the levels reported, such toxicity would be expected to cause intoxication in humans. Fish species identification based on DNA barcoding confirmed that the fish products were mislabeled, with the tissues instead being the Pinjalo snapper, Pinjalo pinjalo. This is the first confirmed ciguatera poisoning incident in both the UK and from the Pinjalo snapper and highlights the need for monitoring of these emerging toxins in reef fish imports to prevent future human intoxication.}, }
@article {pmid39996828, year = {2025}, author = {Zhu, H and Yue, C and Li, H}, title = {Mitochondrial Genome Characteristics and Comparative Genomic Analysis of Spartina alterniflora.}, journal = {Current issues in molecular biology}, volume = {47}, number = {2}, pages = {}, pmid = {39996828}, issn = {1467-3045}, support = {2024C02002//"Leading Goose"R&amp;D Program of Zhejiang/ ; 2022SY06//Zhejiang Forestry Science and Technology Project/ ; }, abstract = {The mitochondrial genome of Spartina alterniflora, an invasive species with significant ecological and economic impacts, was analyzed to provide a theoretical basis for understanding its phylogenetic relationships and molecular biology. Mitochondrial genome sequences of S. alterniflora and 23 related species from NCBI were utilized for bioinformatics and comparative genomic analyses. A sliding window analysis identified three genes (rps2, atp9, and nad6) as potential DNA barcodes for species identification. Intracellular gene transfer (IGT) events between mitochondrial and chloroplast genome were detected, highlighting the dynamic nature of genomic evolution. A selective pressure analysis revealed that most protein-coding genes (PCGs) underwent purifying selection (Ka/Ks < 1), while the nad2 and ccmB genes showed signs of positive selection pressure (Ka/Ks > 1), indicating their role in adaptation. A phylogenetic analysis demonstrated a close relationship between S. alterniflora and Eleusine indica, supported by a collinearity analysis, which suggests environmental convergence. This study provides novel insights into the structural and evolutionary characteristics of the S. alterniflora mitochondrial genome, offering valuable genomic resources for future research on invasive species management and evolutionary biology.}, }
@article {pmid39995615, year = {2025}, author = {Changbunjong, T and Weluwanarak, T and Laojun, S and Chaiphongpachara, T}, title = {Species classification of Tabanus (Diptera: Tabanidae) in Western Thailand: Integrating DNA barcoding and modern morphometrics.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {7}, number = {}, pages = {100243}, pmid = {39995615}, issn = {2667-114X}, abstract = {The species of Tabanus, commonly known as horse flies, are remarkable ectoparasites capable of transmitting various pathogens to animals and humans. Given their role in disease transmission, accurate identification of horse fly species is critical but traditionally relies on morphological characteristics, requiring significant expertise and posing a high potential for error, especially with damaged specimens. To address the limitations of traditional morphological identification, this study highlights the importance of alternative techniques, including DNA barcoding and geometric morphometrics (GM). To enhance the reliability of species identification, DNA barcoding was employed to analyze 30 cytochrome c oxidase subunit 1 (cox1) gene sequences from 15 horse fly species, which were then compared with sequences in the GenBank and BOLD databases. Most cox1 sequences aligned with existing data, with similarity percentages ranging from 96% to 100%. However, discrepancies were noted, including Tabanus helvinus, misidentified as Tabanus aurilineatus, and Tabanus minimus, whose sequences matched those of both Tabanus minimus and Tabanus mesogaeus. Besides DNA barcoding, GM analyses were conducted to enhance species classification accuracy. Our GM analyses employed the landmark-based method for the entire wing and the outline-based method for the first submarginal cell. While shape-based GM analyses demonstrated high reliability, with adjusted total accuracy scores of 97% and 96%, size-based GM analyses yielded significantly lower accuracy, with scores of only 27% and 23%, respectively. These findings provide a foundation for refining horse fly species classification by integrating DNA barcoding and GM approaches, offering valuable advances in species identification and developing targeted control measures.}, }
@article {pmid39994544, year = {2025}, author = {Wu, Y and Sun, Z and Liu, Z and Qiu, T and Li, X and Leng, L and Chen, S}, title = {Assembly and analysis of stephania japonica mitochondrial genome provides new insights into its identification and energy metabolism.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {185}, pmid = {39994544}, issn = {1471-2164}, support = {030040016/030//This work is supported by the talented person scientific research start funds subsidization project of Chengdu University of Traditional Chinese Medicine/ ; }, mesh = {*Genome, Mitochondrial ; *Energy Metabolism/genetics ; Phylogeny ; Electron Transport Complex IV/genetics ; Molecular Sequence Annotation ; Genome, Plant ; Plant Proteins/genetics ; Stephania ; }, abstract = {Stephania japonica, a popular indoor ornamental and medicinal plant widely found in southern China, contains many natural compounds with potential medicinal value. S. japonica is also favored by researchers for its ability to produce catharanthine. Energy metabolism functions in plant development, and the composition of mitochondrial genome is regarded as the foundation for understanding energy metabolism and getting insights into plant environmental adaptation. In present investigation, the whole mitochondrial genome of S. japonica was assembled from both second- and third-generation sequencing data. The mitochondrial genome size of S. japonica is 555,117 bp. It is depicted as a complex polycyclic structure. In addition, we conducted an in-depth study of the cytochrome c oxidase (cox) gene, of which expression levels in different tissues of S. japonica were measured by real-time quantification PCR. Two phylogenetic trees were established in the light of sequences concerning 19 conserved mitochondrial protein-coding genes and cox gene, respectively. Both phylogenetic trees show that S. japonica is more closely related to Aconitum kusnezoffii. The result showed that the cox genes were the most highly expressed in the roots. A high-quality mitochondrial genome exhibits potential application value for the progress of molecular markers, identification of species as super DNA barcoding, and resolve mitochondrial energy metabolism mechanisms in response to the environment using genomic information. With the recognition of the medicinal value of Stephania plants, the genomic information of S. japonica has been thoroughly studied and the comprehensive analysis of its mitochondrial genome in this investigation can offer valuable insights for the breeding of new plant varieties.}, }
@article {pmid39991452, year = {2025}, author = {Ziganira, M and Downs, CT}, title = {Significant Progress in the Study of African Freshwater Snails Over the Past 260 Years.}, journal = {Ecology and evolution}, volume = {15}, number = {2}, pages = {e71031}, pmid = {39991452}, issn = {2045-7758}, abstract = {Globally, freshwater ecosystems are threatened. Research progress concerning African freshwater snails was reviewed using a systematic review process. Since 1757, the number of publications produced has increased, particularly in the last decade. In the first 50 years (1757-1800), 0.1% of publications on freshwater snails in Africa were conducted, followed by 0% (1801-1850), 3.3% (1851-1900), 3.5% (1901-1950) and 48.7% (1951-2000). The last 23 years (2001-2024) exhibited a large increase (44.3%) in publications of the total conducted. Studies on freshwater snails varied in number across the 10 major African water basins, with the majority of studies in the Nile (21.7%), followed by the Congo Basin (17.6%) and Niger (12.4%). The Orange Basin and Lake Tanganyika also received a high number of studies (10.9%) and (7.2%), respectively. Most freshwater snail study objectives related to conservation and taxonomy (70%), followed by disease vector (20.5%), with genetics/genomic/DNA barcoding/eDNA receiving significant focus as well (5.2%). Studies focusing on geology and palaeontology (2.5%), followed by climate change (1.5%) and machine learning (0.4%). The modern phase in the study of African freshwater snails came around the early 20th century with the discovery of Bulinus truncatus and Biomphalaria alexandrina as intermediate hosts for the parasites causing human schistosomiasis. African freshwater malacology has since then benefited from African and overseas malacologists based at universities and medical laboratories across Africa and overseas. In addition to taxonomic studies, there was a steady rise in contributions relating to ecology, disease vectors, palaeontology and genetics. These contributed knowledge on local endemism and speciation, invasive species, species origins and distribution across African water basins, as well as the spread of infectious diseases and impacts of climate change. In the last decade, there have been shifts in methods with the application of DNA barcoding, genomics, environmental DNA and, most recently, machine learning approaches.}, }
@article {pmid39990951, year = {2025}, author = {Wang, KC and Young, TL and Chen, J and Tsai, SN and Xu, Y and Varley, AJ and Solek, NC and Gong, F and Lu, RXZ and Hubbard, BP and Li, B}, title = {A Reverse Transcription Nucleic-Acid-Based Barcoding System for In Vivo Measurement of Lipid Nanoparticle mRNA Delivery.}, journal = {ACS bio &amp; med chem Au}, volume = {5}, number = {1}, pages = {35-41}, pmid = {39990951}, issn = {2694-2437}, abstract = {Lipid nanoparticles (LNPs) are the most extensively validated clinical delivery vehicles for mRNA therapeutics, exemplified by their widespread use in the mRNA COVID-19 vaccines. The pace of lipid nanoparticle (LNP) development for mRNA therapeutics is restricted by the limitations of existing methods for large-scale LNP screening. To address this challenge, we developed Quantitative Analysis of Reverse Transcribed Barcodes (QuART), a novel nucleic-acid-based system for measuring LNP functional delivery in vivo. QuART uses a bacterial retron reverse transcription system to couple functional mRNA delivery into the cytoplasm with a cDNA barcode readout. Our results demonstrate that QuART can be used to identify functional mRNA delivery both in vitro in cell culture and in vivo in mice. Multiplexing of QuART could enable high-throughput screening of LNP formulations, facilitating the rapid discovery of promising LNP candidates for mRNA therapeutics.}, }
@article {pmid39990434, year = {2025}, author = {Kinsler, G and Fagan, C and Li, H and Kaster, J and Dunne, M and Vander Velde, RJ and Boe, RH and Shaffer, S and Herlyn, M and Raj, A and Heyman, Y}, title = {SpaceBar enables clone tracing in spatial transcriptomic data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39990434}, issn = {2692-8205}, support = {T32 CA009140/CA/NCI NIH HHS/United States ; T32 GM007170/GM/NIGMS NIH HHS/United States ; T32 HG000046/HG/NHGRI NIH HHS/United States ; }, abstract = {We report a cellular barcoding strategy, SpaceBar, that enables simultaneous clone tracing and spatial transcriptomics profiling. Our approach uses a library of 96 synthetic barcode sequences that can be robustly detected by imaging based spatial transcriptomics (seqFISH), delivered such that each cell is labeled with a combination of barcodes. We used these barcodes to label melanoma cells in a tumor xenograft model and profiled both clone identity and spatial gene expression in situ. We developed a gene scoring metric that quantifies how strongly gene expression is driven by intrinsic cellular cues or extrinsic environmental signals. Our framework distinguishes between clonal dynamics and environmentally-driven transcriptional regulation in complex tissue contexts.}, }
@article {pmid39990189, year = {2025}, author = {Faltlhauser, AC and Cabrera, N and Hernández, MC and Sánchez Restrepo, AF and Hill, M and Sosa, AJ}, title = {Lysathiaflavipes and Lysathiacilliersae Cabrera sp. nov. (Coleoptera, Chrysomelidae): genetic and morphological unravelling of biocontrol agents for two invasive aquatic plants.}, journal = {ZooKeys}, volume = {1228}, number = {}, pages = {11-52}, pmid = {39990189}, issn = {1313-2989}, abstract = {In the search for specific natural enemies to control two invasive aquatic plants (IAP) from South America, Ludwigiagrandiflorasubsp.hexapetala (Onagraceae) and Myriophyllumaquaticum (Haloragaceae), taxonomic challenges associated with two Lysathia Bechyné, 1959 (Chrysomelidae; Alticini) species had to be resolved. Lysathiaflavipes (Boheman, 1859) exhibits significant morphological variation, causes heavy damage to both IAPs, and may represent more than one species due to the phylogenetic gap between hosts. Additionally, an undescribed Lysathia species (previously published as Lysathia sp.), sourced from Brazil, has been successfully used as a control agent for M.aquaticum in South Africa since 1994. An integrative taxonomic approach combining genetic and morphological analyses was employed. A lectotype and paralectotypes for Graptoderaflavipes Boheman, 1859 are here designated. Phylogenetic studies revealed that L.flavipes had greater genetic and morphological variation than originally described, and no evidence suggested that L.flavipes represented a species complex associated with its host plants. As a result, the species description was expanded. On the other hand, genetic and morphological differences such as body size, colouration, and genital structures further supported the description of Lysathiacilliersae Cabrera, sp. nov. and its differentiation from other closely related species, including L.flavipes and L.ludoviciana (Fall, 1910). Specimens of L.cilliersae sp. nov. collected in Misiones, Argentina, matched those from South Africa. Genetic sequences correlated with morphological vouchers, images, and illustrations of morphology and genitalia, as well as new distribution records, are provided. This research contributes to the taxonomic knowledge of the Lysathia genus and supports accurate species identification in applied entomological contexts, such as biological control programmes.}, }
@article {pmid39985775, year = {2025}, author = {Xiong, EH and Zhang, X and Robbins, N and Myers, CL and Cowen, LE}, title = {Protocol to identify genes important for Candida albicans fitness in diverse environmental conditions using pooled bar-seq screening approach.}, journal = {STAR protocols}, volume = {6}, number = {1}, pages = {103645}, pmid = {39985775}, issn = {2666-1667}, support = {R01 AI127375/AI/NIAID NIH HHS/United States ; }, mesh = {*Candida albicans/genetics ; *Genes, Fungal/genetics ; Genomics/methods ; *Sequence Analysis, DNA/methods ; DNA, Fungal/genetics ; DNA Barcoding, Taxonomic/methods ; *Genetic Fitness ; Gene Library ; }, abstract = {Identifying genes important for fitness in Candida albicans advances our understanding of this important pathogen of humans. Here, we present a functional genomics approach for assessing fitness through the quantification of strain-specific barcodes. We describe steps for library preparation, propagation of strains, genomic DNA extraction, amplification of barcodes, and sequencing. We then detail the computational analysis of data to determine effect size and statistical significance. For complete details on the use and execution of this protocol, please refer to Xiong et al.[1].}, }
@article {pmid39984340, year = {2025}, author = {Nishimura, M and Takahashi, K and Hosokawa, M}, title = {Recent advances in single-cell RNA sequencing of bacteria: Techniques, challenges, and applications.}, journal = {Journal of bioscience and bioengineering}, volume = {139}, number = {5}, pages = {341-346}, doi = {10.1016/j.jbiosc.2025.01.008}, pmid = {39984340}, issn = {1347-4421}, mesh = {*Single-Cell Analysis/methods ; *Bacteria/genetics ; *Sequence Analysis, RNA/methods ; *RNA, Bacterial/genetics ; }, abstract = {Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity in complex biological systems. While this technology has been widely applied to eukaryotic cells, its adaptation to bacterial systems has been challenging due to the unique characteristics of bacterial transcripts. This review surveys the recent developments in bacterial scRNA-seq techniques, highlighting the technical challenges, methodological innovations, and emerging applications in microbiology. We discuss the key differences between eukaryotic and bacterial RNA-seq approaches, focusing on the strategies to overcome limitations such as the lack of poly-A tails in bacterial mRNAs and the low RNA content in individual bacterial cells. The review covers various bacterial scRNA-seq methods, including plate-based, split-pool barcoding, and droplet-based techniques, comparing their strengths and limitations in terms of sensitivity, throughput, and applicability to different bacterial species. Furthermore, we explore the biological insights gained from these techniques, such as identifying rare cell states, characterization of antibiotic responses, and analysis of bacterial communities. Finally, we discuss future perspectives and potential applications of bacterial scRNA-seq in understanding microbial physiology, host-pathogen interactions, and complex microbial ecosystems. This comprehensive overview aims to provide researchers with a clear understanding of the current state and future directions of single-cell transcriptomics in bacteria.}, }
@article {pmid39984010, year = {2025}, author = {Ya'cob, Z and Mintara, R and Belabut, DM and Halim, MRA and Pramual, P}, title = {DNA barcoding and host blood meal identification of Culicoides Latreille (Diptera, Ceratopogonidae) from Malaysia.}, journal = {Acta tropica}, volume = {263}, number = {}, pages = {107564}, doi = {10.1016/j.actatropica.2025.107564}, pmid = {39984010}, issn = {1873-6254}, mesh = {Animals ; Malaysia ; *Ceratopogonidae/classification/genetics/physiology ; *DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; Phylogeny ; Genetic Variation ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial cytochrome oxidase I (COI) sequences were used to determine the genetic diversity and species identification efficacy of Culicoides from Malaysia. In total, 100 COI sequences were obtained from 13 morphologically identified species. Intraspecific genetic divergence varied from 0.48 % in C. parahumeralis to 14.88 % in C. palpifer. However, most (8 of 13) had low (<3 %) intraspecific genetic divergence. Identification of these species based on best match (BM) and best close match (BCM) methods revealed a high efficiency of the COI sequences with 100 % and 99 % success for BM and BCM, respectively. Identification in the BOLD database revealed that 10 species were successfully determined and agreed with morphological identifications. There remained three taxa which were ambiguous (C. jacobsoni) or had no species level identity match (C. palpifer and C. flavescens). Phylogenetic analyses found that all Malaysian specimens were clustered with conspecifics except C. palpifer. Specimens of this taxon separated into two divergent clades, one with members of a BIN (BOLD:ADT9601) of C. palpifer whereas the other formed a novel genetic lineage. Molecular species delimitation identified the morphologically identified species of the Malaysian Culicoides in the respective species. The exceptions were two divergent lineages found in C. palpifer because they were treated as two different taxa. Molecular identification of the host blood meal source revealed that all were from water buffalo (Bubalus bubalis).}, }
@article {pmid39982940, year = {2025}, author = {Talaga, S and Guidez, A and de Thoisy, B and Lavergne, A and Carinci, R and Gaborit, P and Issaly, J and Dusfour, I and Duchemin, JB}, title = {A DNA barcode library for Culex mosquitoes (Diptera: Culicidae) of South America with the description of two cryptic species of subgenus Melanoconion.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0310571}, pmid = {39982940}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Culex/genetics/classification ; Phylogeny ; Electron Transport Complex IV/genetics ; South America ; Female ; French Guiana ; Male ; *Gene Library ; Species Specificity ; }, abstract = {Among mosquitoes (Diptera: Culicidae), the genus Culex Linnaeus is one of the most diverse in the world and includes numerous known vector species of parasites and viruses to humans. Morphological identification of Culex species is notoriously difficult and relies mostly on the examination of properly dissected male genitalia which largely prevents female and immature identification during entomological, ecological or arboviral surveys. The aims of this study were (i) to establish a DNA barcode library for Culex mosquitoes of French Guiana based on the mitochondrial gene cytochrome c oxidase I (COI) marker, (ii) to compare three approaches of molecular delimitation of species to morphological identification, (iii) to test the effectiveness of the COI marker at a broader geographical scale across South America, and (iv) to discuss the internal classification of the genus Culex as regard to our phylogenetic analysis. Mosquitoes used in this study were sampled in French Guiana between 2013 and 2023. We provide 246 COI sequences for 90 morphologically identified species of Culex, including five new country records and two newly described species. Overall, congruence between morphological identification and molecular delimitations using the COI barcode was high. The Barcode of Life Data clustering approach into Barcode Index Numbers gives the best result in terms of species delimitation. Inconsistencies between morphological identification and molecular delimitation can be explained by introgression, incomplete lineage sorting, imperfect taxonomy or the effect of geographical gap in sampling. This increases by almost two-fold the number of mosquito species for which a DNA barcode is available in French Guiana, including 75% of the Culex species currently known in the territory. Finally, this study confirms the usefulness of the COI barcode in identifying Culex of South America, but also points the limits of this marker for some groups of species within the subgenera Culex and Melanoconion.}, }
@article {pmid39982486, year = {2025}, author = {Yadav, A and Nimi, C and Kapoor, M and Singh, R}, title = {A quick and non-destructive approach to combat timber adulteration using attenuated total reflectance Fourier transform infrared spectroscopy and chemometrics.}, journal = {Die Naturwissenschaften}, volume = {112}, number = {2}, pages = {21}, pmid = {39982486}, issn = {1432-1904}, support = {200510156051//University Grants Commission/ ; }, mesh = {Spectroscopy, Fourier Transform Infrared/methods ; *Chemometrics/methods ; Discriminant Analysis ; Principal Component Analysis ; Least-Squares Analysis ; }, abstract = {Timber adulteration, illegal harvesting, and logging of legally protected timber species are a major threat to biodiversity. Identifying and differentiating low-value timber species from high-grade ones is a prerequisite to combat timber-related crimes. Timber adulteration can be detected by techniques such as DNA barcoding. However, these techniques have some drawbacks as they are time-consuming and destructive. To address all these issues, in this study, a quick and non-destructive approach has been used to detect timber adulteration by identifying and discriminating selective timber species using vibrational spectroscopy along chemometric methods such as principal component analysis (PCA), linear discriminant analysis (LDA), and partial least square discriminant analysis (PLS-DA) that successfully differentiated Tectona grandis (teak) from Magnolia champaca (champ) with 96.25% accuracy, Swietenia macrophylla (mahogany) from Magnolia champaca with 97.5% accuracy, and Artocarpus heterophyllus (Jack) from Mangifera indica (mango) with 100% PCA LDA training accuracies. Partial least square discriminant analysis successfully differentiated the timber species with 100% accuracy. ATR-FTIR spectroscopy and chemometric tools proved to be effective in detecting timber adulteration, which will help the investigating agencies combat timber-related crimes.}, }
@article {pmid39982230, year = {2025}, author = {Ding, S and Lu, N and Abolhassani, H}, title = {Assessing the Influence of Selected Permeabilization Methods on Lymphocyte Single-Cell Multi-Omics.}, journal = {Antibodies (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39982230}, issn = {2073-4468}, support = {HA//Jonas S&#xf6;derquist scholarship/ ; }, abstract = {(1) Background: Single-cell multi-omics is a powerful method for the dissection and detection of complicated immunologic functions and synapses. However, most currently available technologies merge datasets of different omics from separate portions of the same sample to generate combined multi-omics. This process is a source of bias, mainly in the field of immunology on cells originating from pluripotent hematopoietic stem cells with high flexibility during maturation. (2) Methods: Although new multi-omics approaches have been developed to use the advantages of cellular and molecular barcoding and next-generation sequencing to solve this issue, one of the main current challenges is intracellular proteomics, which should be combined with other omics data with high importance for immune system studies. We designed this study to evaluate previously recommended minimal permeabilization and fixation methods on the quality and quantity of transcriptomics and proteomics data generated by the BD Rhapsody™ Single-Cell Analysis System. (3) Results: Our findings showed that high-throughput sequencing with advanced quality and read-out is required for the combination of multi-omics outcomes from a permeabilized single cell. Therefore, the HiseqX platform was selected for further analysis. The effect of immune stimulation was observed clearly as the separated clusters of helper and cytotoxic T cells using unsupervised clustering. Importantly, fixation and permeabilization did not affect the general expression profile of unstimulated cells. However, fixation and permeabilization were proved to negatively impact the detection of the whole transcriptome for single-cell assay. Nevertheless, about 60% of the transcriptomic signature of the stimulation was detected. If the measurement of combined surface and intracellular markers is required to be achieved, the modified fixation and permeabilization method is recommended because of a lower transcriptomic loss and more precise proteomic fingerprint detected. (4) Conclusions: The findings of this study support the potential possibility for integrating intracellular proteomics, which needs to be optimized and tested with newly designed oligonucleotide-tagged antibodies targeting intracellular proteins.}, }
@article {pmid39981117, year = {2025}, author = {González, MA and López-de-Felipe, M and Magallanes, S and Alarcón-Elbal, PM and Barceló, C and Martínez-Barciela, Y and Polina, A and García-López, AM and Blanco-Sierra, L and Peláez Guerra, MA and Delacour, S and Figuerola, J and Ruiz-Arrondo, I and Bravo-Barriga, D}, title = {Distribution, identification and ecology of Phortica genus (Diptera: Drosophilidae) in Spain.}, journal = {International journal of veterinary science and medicine}, volume = {13}, number = {1}, pages = {1-11}, pmid = {39981117}, issn = {2314-4599}, abstract = {The genus Phortica (Diptera: Drosophilidae) includes five species of small flies in Europe. Phortica variegata, the zoophilic fruit fly, is the main vector of Thelazia callipaeda, a zoonotic parasite that is rapidly spreading througout Europe. Despite extensive studies on thelaziosis in animals and humans, there is limited knowledge about the geographical distribution and hovering activity of these vector flies. In 2023, 1,462 Phortica flies were sampled across 12 Spanish provinces, providing new records of Phortica variegata and Phortica oldenbergi. Surprisingly, P. oldenbergi, previously considered a rare Afrotropical species, was prevalent in most regions sampled in Spain. However, Phortica semivirgo was not collected. The abundance of Phortica spp. correlated positively with altitude and certain tree species. Rural oak-wooded areas in central and northern Spain showed the highest densities of P. variegata. Both drosophilid species were analysed morphologically and molecularly, providing new morphological descriptors and sequence barcodes for species identification. Phylogenetic analysis based on COI sequences, showed P. oldenbergi grouped with Asian origin Phortica species, while P. variegata in America was closer to Spanish sequences than those from other European countries. The hovering activity of P. variegata causes significant discomfort to humans during outdoor activities. This paper also reviews the historic records of P. variegata, P. semivirgo and P. oldenbergi in Spain over the last 90 years. This study enhances the understanding of the distribution, identification, ecology, and behaviour of these zoophilic flies in Europe.}, }
@article {pmid39981057, year = {2025}, author = {Slater-Baker, MR and Fagan-Jeffries, EP and Oestmann, KJ and Portmann, OG and Bament, TM and Howe, AG and Guzik, MT and Bradford, TM and McClelland, AR and Woodward, A and Clarke, S and Ducker, N and Fernández-Triana, J}, title = {DNA barcoding, integrative taxonomy, citizen science, and Bush Blitz surveys combine to reveal 34 new species of Apanteles (Hymenoptera, Braconidae, Microgastrinae) in Australia.}, journal = {ZooKeys}, volume = {1227}, number = {}, pages = {1-128}, pmid = {39981057}, issn = {1313-2989}, abstract = {Microgastrinae is a megadiverse subfamily of wasps in the family Braconidae. As parasitoids of caterpillars, members of the subfamily play important roles in regulating native caterpillar populations, and several species are used commercially as biological control agents. The genus Apanteles comprises a large portion of total microgastrine diversity, however it has not been studied in Australia for more than 30 years, with only nine described species previously known from the continent. We explore the diversity and systematics of Apanteles in Australia, using cytochrome c oxidase subunit I (COI) and Wingless (wg) DNA barcodes from more than 400 Australian Apanteles specimens. Using molecular species delimitation in combination with reduced morphological diagnoses, at least 48 distinct molecular lineages of Apanteles are confirmed in Australia, and 34 new species are formally described, all authored by Slater-Baker, Fagan-Jeffries, Fernández-Triana, Portmann &amp; Oestmann: A.adustus, A.aeternus, A.alatomicans, A.allapsus, A.amicalis, A.apollo, A.apricus, A.artemis, A.aurantius, A.auroralis, A.banrock, A.breviflagellarius, A.brockhedgesi, A.cuprum, A.darthvaderi, A.doreenwatlerae, A.ethanbeaveri, A.fenestrinus, A.ferripulvis, A.focusalis, A.hades, A.insulanus, A.kelpiellus, A.lamingtonensis, A.ligdus, A.magicus, A.margaritarius, A.pellucidus, A.phantasmatus, A.pharusalis, A.ramsaris, A.rufiterra, A.sinusulus, and A.translucentis.}, }
@article {pmid39981046, year = {2025}, author = {Borsato, ND and Lunn, K and Garrett, NR and Biganzoli-Rangel, AJ and Marquina, D and Steinke, D and Floyd, R and Clare, EL}, title = {Identification of potential insect ecological interactions using a metabarcoding approach.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18906}, pmid = {39981046}, issn = {2167-8359}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Bees/genetics ; *Moths/genetics ; *Insecta/genetics ; Wasps/genetics ; }, abstract = {Species interactions are challenging to quantify, particularly when they happen cryptically. Molecular methods have become a key tool to uncover these interactions when they leave behind a DNA trace from the interacting organism (e.g., pollen on a bee) or when the taxa are still present but morphologically challenging to identify (e.g., microbial or fungal interactions). The decreasing costs of sequencing makes the mass analysis of thousands of target species possible. However, the challenge has shifted to selecting molecular markers which maximize information recovery while analyzing these data at broad biological scales. In this manuscript we use model arthropod groups to compare molecular markers and their analysis across life stages. We develop protocols for two ecologically and economically devastating pests, the spongy moth (Lymantria dispar dispar) and the emerald ash borer (Agrilus planipennis), and a group of pollinators including bees and wasps which regularly deposit eggs in "bee hotels" where the larvae develop. Using Illumina MiSeq and Oxford Nanopore MinION platforms we evaluate seven primer pairs for five molecular markers which target plants, fungi, microbes, insects, and parasitic phyla (e.g., nematodes). Our data reveals hundreds of potential ecological interactions and establishes generalized methods which can be applied across arthropod host taxa with recommendations on the appropriate markers in different systems. However, we also discuss the challenge of differentiating co-occurring DNA signals and true ecological interactions, a problem only starting to be recognized as eDNA from the environment accumulates on living organisms.}, }
@article {pmid39980701, year = {2025}, author = {Park, SY and Sohee, K and Eunjin, K and Eo, JK and Lee, H}, title = {Taxonomic Revision of Korean Saddle Fungi (Helvella, Helvellaceae).}, journal = {Mycobiology}, volume = {53}, number = {1}, pages = {79-112}, pmid = {39980701}, issn = {1229-8093}, abstract = {Helvella, commonly known as saddle fungi, is a genus in the Helvellaceae family and is distributed globally. Recent comprehensive studies on Helvella have revealed that some Helvella species exhibit endemic traits and that many morphologically similar, cryptic species are phylogenetically distant. In this study, 202 Korean Helvella specimens collected between 1986 and 2023 were reevaluated through morphological analysis and phylogenetic characterization using barcode sequences, including nrLSU (nuclear Large Subunit Ribosomal DNA), hsp90 (Heat Shock Protein 90), and ITS (Internal Transcribed Spacer). The investigation confirmed the presence of at least 35 phylogenetic species in Korea. Among these, eight species (H. atroides, H. fistulosa, H. liquii, H. lobata, H. rugosa, H. subglabroides, H. sublactea, H. varia) were identified as previously unrecorded species in Korea, and seven new species (H. densipila, H. flavopus, H. macrospora, H. griseobrunnea, H. pseudolobata, H. parviflava, H. suborentitomentosa) were discovered. Of the 13 previously recorded Korean Helvella species, only three (H. ephippioides, H. macropus, H. orienticripsa) were confirmed, while the remaining ten species (H. acetabulum, H. atra, H. compressa, H. costifera, H. crispa, H. elastica, H. sublicia, H. fibrosa, H. lacunosa, H. pezizoides) were not detected in the samples studied. This study enhances our understanding of the distribution of Helvella species of Korea, revealing significant discrepancies between historical records and current findings. The discovery of new species and previously un-recorded species underscores the importance of continuous monitoring and reevaluation of fungal biodiversity.}, }
@article {pmid39980019, year = {2025}, author = {Miyamoto, AT and Shimagami, H and Kumanogoh, A and Nishide, M}, title = {Spatial transcriptomics in autoimmune rheumatic disease: potential clinical applications and perspectives.}, journal = {Inflammation and regeneration}, volume = {45}, number = {1}, pages = {6}, pmid = {39980019}, issn = {1880-9693}, support = {JP24K11596//Japan Society for the Promotion of Science/ ; JP18H05282//Japan Society for the Promotion of Science/ ; JPMJFR235B//Fusion Oriented REsearch for disruptive Science and Technology/ ; 223fa627002h0001//Japan Agency for Medical Research and Development/ ; }, abstract = {Spatial transcriptomics is a cutting-edge technology that analyzes gene expression at the cellular level within tissues while integrating spatial location information. This concept, which combines high-plex RNA sequencing with spatial data, emerged in the early 2010s. Spatial transcriptomics has rapidly expanded with the development of technologies such as in situ hybridization, in situ sequencing, in situ spatial barcoding, and microdissection-based methods. Each technique offers advanced mapping resolution and precise spatial assessments at the single-cell level. Over the past decade, the use of spatial transcriptomics on clinical samples has enabled researchers to identify gene expressions in specific diseased foci, significantly enhancing our understanding of cellular interactions and disease processes. In the field of rheumatology, the complex and elusive pathophysiology of diseases such as rheumatoid arthritis, systemic lupus erythematosus, and Sjögren's syndrome remains a challenge for personalized treatment. Spatial transcriptomics provides insights into how different cell populations interact within disease foci, such as the synovial tissue, kidneys, and salivary glands. This review summarizes the development of spatial transcriptomics and current insights into the pathophysiology of autoimmune rheumatic diseases, focusing on immune cell distribution and cellular interactions within tissues. We also explore the potential of spatial transcriptomics from a clinical perspective and discuss the possibilities for translating this technology to the bedside.}, }
@article {pmid39979460, year = {2025}, author = {Langerman, J and Baghdasarian, S and Cheng, RY and James, RG and Plath, K and Di Carlo, D}, title = {Linking single-cell transcriptomes with secretion using SEC-seq.}, journal = {Nature protocols}, volume = {20}, number = {7}, pages = {2034-2055}, pmid = {39979460}, issn = {1750-2799}, support = {2023-332386//Silicon Valley Community Foundation (SVCF)/ ; }, mesh = {*Single-Cell Analysis/methods ; *Transcriptome/genetics ; Humans ; *Sequence Analysis, RNA/methods ; Flow Cytometry/methods ; *Gene Expression Profiling/methods ; }, abstract = {Cells secrete numerous proteins and other biomolecules into their surroundings to achieve critical functions-from communicating with other cells to blocking the activity of pathogens. Secretion of cytokines, growth factors, extracellular vesicles and even recombinant biologic drugs defines the therapeutic potency of many cell therapies. However, gene expression states that drive specific secretory phenotypes are largely unknown. We provide a protocol that enables the secretion amount of a target protein encoded (SEC) by oligonucleotide barcodes to be linked with transcriptional sequencing (seq) for thousands of single cells. SEC-seq leverages microscale hydrogel particles called Nanovials to isolate cells and capture their secretions in close proximity, oligonucleotide-labeled antibodies to tag secretions on Nanovials and flow cytometry and single-cell RNA-sequencing (scRNA-seq) platforms for readout. Cells on Nanovials can be sorted on the basis of viability, secretion amount or other surface markers without fixation or permeabilization, and cell- and secretion-containing Nanovials are directly introduced into microfluidic droplets-in-oil emulsions for single-cell barcoding of cell transcriptomes and secretions. We have used SEC-seq to link T cell receptor sequences to the relative amount of associated cytokine secretions, surface marker gene expression with a highly secreting and potential regenerative population of mesenchymal stromal cells and the transcriptome with high immunoglobulin secretion from plasma cells. Nanovial modification and cell loading takes <4 h, and once the desired incubation time is over, staining, cell sorting and emulsion generation for scRNA-seq can also be completed in <4 h. Compared to related techniques that link secretions to a cell's surface, SEC-seq provides a general solution across any secretion target because of the ease with which biotinylated Nanovials can be modified. By linking gene expression and secretory strength, SEC-seq can expand our understanding of cell secretion, how it is regulated and how it can be engineered to make better therapies.}, }
@article {pmid39979452, year = {2025}, author = {Wu, HC and Chiu, YT and Wu, IC and Liou, CH and Cheng, HW and Kuo, SC and Lauderdale, TL and Sytwu, HK and Liao, YC and Chen, FJ}, title = {Streamlining whole genome sequencing for clinical diagnostics with ONT technology.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6270}, pmid = {39979452}, issn = {2045-2322}, support = {IV-111-PP-11//National Health Research Institutes/ ; PH-112-PP-05//National Health Research Institutes/ ; IV-111-PP-23//National Health Research Institutes/ ; 111-2314-B-400-033//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Whole Genome Sequencing/methods ; Humans ; Computational Biology/methods ; Workflow ; Software ; *Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Recent advances in whole-genome sequencing (WGS) have increased the accessibility of this tool, offering substantial potential for pathogen surveillance, outbreak response, and diagnostics. However, the routine clinical adoption of WGS is hindered by factors such as high costs, technical complexity, and the requirement for bioinformatics expertise for data analysis. To address these challenges, we propose RapidONT, a workflow designed for cost-effective and accessible WGS-based pathogen analysis. RapidONT employs a mechanical shearing-based DNA extraction protocol, followed by library construction by using a multiplexing Oxford nanopore technologies (ONT) rapid barcoding kit. Flye software is used for de novo assembly without manual intervention, followed by basic assembly polishing using Medaka and Homopolish. The polished assemblies are then analyzed using the user-friendly web-based platform Pathogenwatch, which facilitates species identification, molecular typing, and antimicrobial resistance (AMR) prediction, all while requiring minimal bioinformatics expertise. The efficacy of RapidONT was evaluated using nine clinically relevant pathogens, encompassing a total of 90 gram-positive and gram-negative bacterial strains. The workflow demonstrated high accuracy in critical tasks such as multilocus sequence typing (MLST) and AMR identification, using only ONT R9.4.1 flowcell data. Notably, limitations were observed with Salmonella spp. and Neisseria gonorrhoeae. Furthermore, RapidONT enabled the generation of genomic information for 48 bacterial isolates by using a single flow cell, significantly reducing sequencing costs. This approach eliminates the need for extensive experimentation in obtaining crucial genomic information. This workflow facilitates broader WGS implementation in clinical pathogen analysis and diagnostics.}, }
@article {pmid39977545, year = {2025}, author = {Gandin, V and Kim, J and Yang, LZ and Lian, Y and Kawase, T and Hu, A and Rokicki, K and Fleishman, G and Tillberg, P and Castrejon, AA and Stringer, C and Preibisch, S and Liu, ZJ}, title = {Deep-tissue transcriptomics and subcellular imaging at high spatial resolution.}, journal = {Science (New York, N.Y.)}, volume = {388}, number = {6744}, pages = {eadq2084}, pmid = {39977545}, issn = {1095-9203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Mice ; Embryo, Mammalian/metabolism ; Fibroblasts/metabolism ; *Gene Expression Profiling/methods ; Hippocampus/metabolism/cytology ; Imaging, Three-Dimensional/methods ; *Microscopy, Fluorescence/methods ; *Molecular Imaging/methods ; *RNA/analysis ; Transcriptome ; *In Situ Hybridization, Fluorescence/methods ; }, abstract = {Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. We introduce cycle hybridization chain reaction (cycleHCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.}, }
@article {pmid39975614, year = {2025}, author = {Bhowmik, B and Dey, B and Das, S and Barman, GD and Chanda, S and Mondal, R}, title = {Morphological, ultrastructure and molecular characterization of Unionicola chelata (Acari: Hydrachnida: Unionicolidae) isolated from Bellamya bengalensis, West Bengal, India.}, journal = {Journal of parasitic diseases : official organ of the Indian Society for Parasitology}, volume = {49}, number = {1}, pages = {37-44}, pmid = {39975614}, issn = {0971-7196}, abstract = {Unionicola spp. is a parasitic aquatic mite known to infect freshwater aquatic organisms, especially the marine and freshwater molluscs and few species of sponges. Unionicola chelata (Acari: Hydrachnida: Unionicolidae) generally infect the freshwater bivalves of the Genus Unio sp. They are usually facultative in nature and can be parasitic at any stage of their life cycle. They cause damage to the gills of the host which harms their normal respiration process. The present work portraits the morphological characters, ultrastructure and DNA barcoding of its mitochondrial gene Cytochrome Oxidase I (COI)(mtCOI), and its taxonomic position was justified by obtaining a phylogenetic tree. The description regarding its morphological characters, ultrastructure and molecular characterization has been presented here. This paper holds the report of a parasitic aquatic mite Unionicola chelata for the first time from a gastropod molluscan host Bellamya bengalensis (Lamarck, 1882), from Diamond Harbour, South 24 Parganas, West Bengal, India.}, }
@article {pmid39975479, year = {2024}, author = {Sadler, JM and Simkin, A and Tchuenkam, VPK and Gerdes Gyuricza, I and Fola, AA and Wamae, K and Assefa, A and Niaré, K and Thwai, K and White, SJ and Moss, WJ and Dinglasan, RR and Nsango, SE and Tume, CB and Parr, JB and Ali, IM and Bailey, JA and Juliano, JJ}, title = {Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.}, journal = {Frontiers in parasitology}, volume = {3}, number = {}, pages = {1509261}, pmid = {39975479}, issn = {2813-2424}, support = {R01 AI165537/AI/NIAID NIH HHS/United States ; R01 AI177791/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; R01 AI155730/AI/NIAID NIH HHS/United States ; R01 AI156267/AI/NIAID NIH HHS/United States ; K24 AI134990/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing.<br><br>METHODS: Plasmodium falciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach.<br><br>RESULTS: We evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf-SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf-SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed.<br><br>CONCLUSION: Overall, Pf-SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible.}, }
@article {pmid39973970, year = {2024}, author = {Yang, Z and Chen, J and Xiao, Y and Yang, C and Zhao, CX and Chen, D and Weitz, DA}, title = {Digital Barcodes for High-Throughput Screening.}, journal = {Chem &amp; bio engineering}, volume = {1}, number = {1}, pages = {2-12}, pmid = {39973970}, issn = {2836-967X}, abstract = {High-throughput screening is an indispensable technology in drug discovery, cancer therapy, and disease diagnosis, and it could greatly reduce time cost, reagent consumption, and labor expense. Here, four high-throughput screening methods with high sensitivity and accessibility are discussed in detail. Fluorescence, DNA, heavy metal, and nonmetal isotope barcodes, which generally label antibodies, proteins, and saccharides to identify cells, are detected by flow cytometry, second-generation DNA sequencing, mass cytometry, and second-ion mass spectrometry, respectively. Encoding binary information in barcodes, labeling individual cells by barcodes, performing the characterization of cells together, and identifying the result belonging to individual cells via barcodes are the main steps for high-throughput screening. Applications of the four digital barcodes in high-throughput screening for both in vitro and in vivo tests are described in detail, and their advantages and disadvantages are also summarized. High-throughput screening has provided a powerful platform widely accessible for multidisciplinary studies and has greatly sped up the progress of drug discovery, disease diagnosis, and cancer therapy.}, }
@article {pmid39972899, year = {2025}, author = {Mohanta, D and Dvirnas, A and Ambjörnsson, T}, title = {Random sampling of ligand arrangements on a one-dimensional lattice.}, journal = {Physical review. E}, volume = {111}, number = {1-1}, pages = {014412}, doi = {10.1103/PhysRevE.111.014412}, pmid = {39972899}, issn = {2470-0053}, abstract = {We introduce a transfer-matrix-based sequential sampling scheme for generating random samples of ligand arrangements on one-dimensional templates. The number of ligand types is arbitrary, the binding constants can have positional dependence, and cooperativity parameters are included. From the random arrangements, any (linear or nonlinear) observable can be calculated using sample averaging. As an example case study, we investigate the competitive binding of three ligand types (the sequence-specific binder netropsin, YOYO-1, and ethidium bromide) to a DNA molecule. We also employ our random sampling method of ligands to determine the quality of synthetically generated DNA barcodes as a function of concentration of a ligand (e.g., netropsin) in optical DNA mapping (ODM) experiments. We provide publically available softwares, with a computational time that scales linearly with the lattice size, for generating random ligand arrangements and for generating synthetic barcodes.}, }
@article {pmid39972011, year = {2025}, author = {Marsh, WA and Hall, A and Barnes, I and Price, B}, title = {Facilitating high throughput collections-based genomics: a comparison of DNA extraction and library building methods.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6013}, pmid = {39972011}, issn = {2045-2322}, mesh = {*DNA/isolation &amp; purification/genetics ; *Gene Library ; *Genomics/methods ; Museums ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {While DNA barcoding methods are an increasingly important tool in biological conservation, the resource requirements of constructing reference libraries frequently reduce their efficacy. One efficient way of sourcing taxonomically validated DNA for reference libraries is to use museum collections. However, DNA degradation intrinsic to historical museum specimens can, if not addressed in the wet lab, lead to low quality data generation and severely limit scientific output. Several DNA extraction and library build methods that are designed to work with degraded DNA have been developed, although the ability to implement these methods at scale and at low cost has yet to be formally addressed. Here, the performance of widely used DNA extraction and library build methods are compared using museum specimens. We find that while our selected DNA extraction methods do not significantly differ in DNA yield, the Santa Cruz Reaction (SCR) library build method is not only the most effective at retrieving degraded DNA from museum specimens but also easily implemented at high throughput for low cost. Results highlight the importance of lab protocol on data yield. An optimised "sample to sequencing" high-throughput protocol which incorporates SCR is included to allow for easy uptake by the wider scientific community.}, }
@article {pmid39970179, year = {2025}, author = {Yang, J and Kim, SC}, title = {Hosta clausa (Asparagaceae) in East Asia: Intraspecific chloroplast genome variation and its phylogenomic implications.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0317884}, pmid = {39970179}, issn = {1932-6203}, mesh = {*Phylogeny ; *Genome, Chloroplast ; *Genetic Variation ; Asia, Eastern ; }, abstract = {Hosta species are abundant in northeastern Asia, offering significant ornamental and horticultural value due to their diverse foliage colors and textures, as well as their showy, fragrant flowers. Among the eight taxa naturally distributed in Korea, H. clausa is found in central and northern Korea, as well as northeastern China, providing valuable resources for developing and improving new varieties. Currently, four intraspecific taxa of H. clausa are recognized at the variety level based on reproductive (opened vs. closed perianth), vegetative (leaf shape), and habitat characteristics: var. clausa, var. normalis, var. ensata, and var. geumgangensis. Despite its horticultural and taxonomic importance, little is known about the degree of intraspecific chloroplast genome variation and relationships among the varieties of H. clausa. This could provide some valuable information for marker-assisted breeding programs and molecular cultivar identification. In this study, we investigated the complete plastid genome of 14 accessions of H. clausa, covering its native distribution range. We characterized genome size and features and performed comparative plastome analyses (frequency of codon usage, nucleotide diversity, mutation hotspots). Our analysis revealed highly conserved structures and gene content organization in H. clausa, along with significantly (two to three times) lower nucleotide diversity compared to intraspecific herbaceous and woody species. The phylogenetic analysis did not support the recognition of intraspecific taxa as currently delimited, and a broad-scale geographical structure of complete plastomes was not apparent. The asexual reproductive mode of H. clausa appears to contribute to the low plastome genetic diversity. A total of 72 polymorphic sites identified among 14 accessions of H. clausa and their phylogenetic relationships, in conjunction with their geographical distribution and morphological characteristics, will be a valuable resource for barcoding study, marker-assisted breeding programs, and developing conservation strategies for hosta species in East Asia.}, }
@article {pmid39970170, year = {2025}, author = {Almuteri, JS and Al Wahaibi, MS and Mustafa, AEM and Alshaqhaa, MA and Afzal, M and Alshehri, MD}, title = {Morphological characterization and DNA barcoding of Ruellia sp. in Saudi Arabia.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0315827}, pmid = {39970170}, issn = {1932-6203}, mesh = {*DNA Barcoding, Taxonomic/methods ; Saudi Arabia ; Phylogeny ; *DNA, Plant/genetics ; Flowers/genetics/anatomy &amp; histology ; }, abstract = {The genus Ruellia L. belongs to this family and its plants are herbs or shrubs. This genus was first detected in the tropical and subtropical regions. The primary objective this study is to identify the various species within the genus Ruellia using both morphological characteristics and DNA barcoding methods. For this purpose, plant samples were meticulously collected from eight distinct natural habitats across the region. All vegetative and floral parts were examined using a binocular microscope. All parts are measured and photographed. To ensure accurate identification and characterization, four molecular barcoding markers were employed: Psbk-psbi, trnH-psbA, rbcL, and AtpF-AtpH. Eight Ruellia species were identified from different regions: Abha, Aseer (24651), Jazan (24652), Malacosperma, Patula, Taif (24650 rose), Taif (24650 violet), and Taif (24650 white). The species were confirmed using specimens from the King Saud University herbarium. Notably, the samples collected from Taif, which had flowers of different colors, were determined to represent a single species with different genotypes. The use of four DNA barcode markers (Psbk-psbi, trnH-psbA, rbcL, and AtpF-AtpH) facilitated the identification of five distinct species: R. tweediana, R. sp. SH2010, R. carolinensis, R. simplex, and R. patula. These findings confirmed the dominant Ruellia species in Saudi Arabia and demonstrated the reliability of DNA barcode markers for species identification. Further assessment of these species' adaptability, molecular genetics, and functional genomics is necessary for their commercial utilization in the region. These species are recorded for the first time in Saudi Arabia and represent the first record.}, }
@article {pmid39968047, year = {2024}, author = {Ling, M and Szarvas, J and Kurmauskaitė, V and Kiseliovas, V and Žilionis, R and Avot, B and Munk, P and Aarestrup, FM}, title = {High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1516656}, pmid = {39968047}, issn = {1664-302X}, abstract = {Single-cell sequencing may serve as a powerful complementary technique to shotgun metagenomics to study microbiomes. This emerging technology allows the separation of complex microbial communities into individual bacterial cells, enabling high-throughput sequencing of genetic material from thousands of singular bacterial cells in parallel. Here, we validated the use of microfluidics and semi-permeable capsules (SPCs) technology (Atrandi) to isolate individual bacterial cells from sewage and pig fecal samples. Our method involves extracting and amplifying single bacterial DNA within individual SPCs, followed by combinatorial split-and-pool single-amplified genome (SAG) barcoding and short-read sequencing. We tested two different sequencing approaches with different numbers of SPCs from the same sample for each sequencing run. Using a deep sequencing approach, we detected 1,796 and 1,220 SAGs, of which 576 and 599 were used for further analysis from one sewage and one fecal sample, respectively. In shallow sequencing data, we aimed for 10-times more cells and detected 12,731 and 17,909 SAGs, of which we used 2,456 and 1,599 for further analysis for sewage and fecal samples, respectively. Additionally, we identified the top 10 antimicrobial resistance genes (ARGs) in both sewage and feces samples and linked them to their individual host bacterial species.}, }
@article {pmid39967725, year = {2025}, author = {Islam, S}, title = {Commentary on "Preliminary Species Hypotheses" in Entomological Taxonomy: A Global Data and FAIR Infrastructure Perspective.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e141562}, pmid = {39967725}, issn = {1314-2828}, abstract = {What if early taxonomic findings were treated like preprints, open to iterative improvement or managed with practices from the open-source community, such as Git branching, merging and patch management? Prompted by Buckley's article Charting a Future for Entomological Taxonomy in New Zealand (2024), this commentary explores these possibilities in the context of biodiversity informatics. In response to the need for rapid, scalable biodiversity monitoring, Buckley introduces preliminary species hypotheses (PSH) as a bridge between quick identification tools and the rigorous Linnaean system, leveraging DNA barcoding and AI-assisted image recognition to produce provisional classifications that can later be validated. Expanding on Buckley's framework, this commentary emphasises the critical role of data linking, versioning and integration to support evolving taxonomic data. Borrowing from software and open-source practices, I explore the idea of managing PSH with an infrastructure that treats each taxonomic update as a versioned "commit", which can be tracked, refined and integrated over time. Drawing insights from FAIR (Findable, Accessible, Interoperable, Reusable) principles and Digital Extended Specimens, I identify infrastructure requirements for PSH, including robust data standards, persistent identifiers and interoperability to support global biodiversity repositories. Additionally, Taxonomic Data Objects offer a model for dynamically integrating PSH into adaptable taxonomies that can evolve with new data and tools. By positioning PSH within an open, infrastructure-focused framework, this commentary advocates for scalable, hypothesis-driven biodiversity data that meets modern conservation needs, bridging traditional and emerging practices in taxonomy.}, }
@article {pmid39966379, year = {2025}, author = {Schubert, C and Nguyen, BD and Sichert, A and Näpflin, N and Sintsova, A and Feer, L and Näf, J and Daniel, BBJ and Steiger, Y and von Mering, C and Sauer, U and Hardt, WD}, title = {Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1735}, pmid = {39966379}, issn = {2041-1723}, support = {10.001.588//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_19256//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; SCHU 3606/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Salmonella typhimurium/metabolism/genetics/growth &amp; development ; Mice ; *Gastrointestinal Microbiome ; Cecum/microbiology/metabolism ; *Monosaccharides/metabolism ; Glucose/metabolism ; Fructose/metabolism ; Mice, Inbred C57BL ; Galactose/metabolism ; Salmonella Infections/microbiology/metabolism ; Female ; Mannose/metabolism ; }, abstract = {The carbohydrates that fuel gut colonization by S. Typhimurium are not fully known. To investigate this, we designed a quality-controlled mutant pool to probe the metabolic capabilities of this enteric pathogen. Using neutral genetic barcodes, we tested 35 metabolic mutants across five different mouse models with varying microbiome complexities, allowing us to differentiate between context-dependent and context-independent nutrient sources. Results showed that S. Typhimurium uses D-mannose, D-fructose and likely D-glucose as context-independent carbohydrates across all five mouse models. The utilization of D-galactose, N-acetylglucosamine and hexuronates, on the other hand, was context-dependent. Furthermore, we showed that D-fructose is important in strain-to-strain competition between Salmonella serovars. Complementary experiments confirmed that D-glucose, D-fructose, and D-galactose are excellent niches for S. Typhimurium to exploit during colonization. Quantitative measurements revealed sufficient amounts of carbohydrates, such as D-glucose or D-galactose, in the murine cecum to drive S. Typhimurium colonization. Understanding these key substrates and their context-dependent or -independent use by enteric pathogens will inform the future design of probiotics and therapeutics to prevent diarrheal infections such as non-typhoidal salmonellosis.}, }
@article {pmid39965776, year = {2025}, author = {Wang, K and Xu, Y and Lin, R and Yang, S and Wang, Z and Cui, K and Chen, S and Wang, Z and Chen, S and Wang, Z and Zhang, W and Zhu, C and Gao, Z}, title = {Spatiotemporal Control of Photoisomerization Dynamics via Domino Barriers for Programmatically Responsive Heterostructures.}, journal = {ACS nano}, volume = {19}, number = {8}, pages = {7718-7727}, doi = {10.1021/acsnano.4c12005}, pmid = {39965776}, issn = {1936-086X}, abstract = {Controlling the photoisomerization reaction at the micro-/nanoscale is important for the realization of high-end photonic components. Unfortunately, spatiotemporal manipulation of the photoisomerization dynamics still faces a significant challenge. Here, we propose an effective strategy to control the photoisomerization reaction spatiotemporally through introducing a steric-hindrance effect by the aid of alloy engineering. The external guest molecules behave like domino barriers and efficiently regulate the photoisomerization dynamics. Moreover, the flexible assembly of the organic heterostructures with different steric-hindrance degrees enabled us to spatiotemporally modulate the photoisomerization dynamics in 1D, 2D, and even annular morphologies. Interestingly, the photoisomerization reaction exhibits anisotropic change characteristics in 2D microcrystals. Our work provides deep insight into the modulation of the photoisomerization reaction and would promote the development of smart responsive barcodes with improved security level toward advanced anti-counterfeiting applications.}, }
@article {pmid39963517, year = {2025}, author = {Wang, C and Lu, Z and She, G and Chen, K and Zhou, H and Zhan, X and Yu, H and Pi, L and Zuo, L and Che, D}, title = {The Identification of FN1 as an Early Diagnostic Marker for Recurrent Abortion by Single-Exosome Profiling.}, journal = {International journal of general medicine}, volume = {18}, number = {}, pages = {691-702}, pmid = {39963517}, issn = {1178-7074}, abstract = {PURPOSE: Recurrent abortion(RA) is a prevalent adverse pregnancy event. Exosomes, secreted by various body fluids, are known to play a role in disease diagnosis and serve as biomarkers through intercellular communication. This study aims to analyze single exosomes in patients with recurrent abortion to identify new biomarkers that may significantly contribute to recurrent abortion, providing new directions for its treatment.<br><br>PATIENTS AND METHODS: A total of 244 serum exosomes were collected, including 216 patients with recurrent abortion of varying outcomes and 28 normal pregnancies. We performed the proximity barcoding assay (PBA) to analyze single exosome surface proteins, which allowed us to identify individual exosomes related to the development of RA as well as the major subpopulations of exosomes. After PBA treatment, samples were analyzed for single exosomes, and exosomes from each group were compared using volcano plots, dot plots, and ROC curves.<br><br>RESULTS: By intersecting all significantly differentially expressed genes obtained from comparisons between the normal pregnancy control group and the recurrent abortion group, including the RA before abortion, RA after abortion, and RA non-pregnancy groups, we identified seven shared differential genes: FN1, APIPOQ, CDH13, DSG1, CLDN4, CD36, and ULBP3. Among these, FN1 was the most significantly differentially expressed gene in exosomes, with FN1 | log2 (fold change) |>1.5 and an AUC of 0.7414. In addition, exosome subpopulation analyses showed that cluster 11 accounted for the largest proportion of the total 16 subpopulations, and FN1 was the marker with the highest concentration of cluster 11.<br><br>CONCLUSION: Single-exosome profiling and exosome subpopulations of RA by PBA yielded significant differential gene FN1, which provides new possibilities for diagnostic screening of RA.}, }
@article {pmid39963510, year = {2025}, author = {Corvalán, LCJ and de Melo-Ximenes, AA and Carvalho, LR and E Silva-Neto, CM and Diniz-Filho, JAF and Telles, MPC and Nunes, R}, title = {Is There a Key Primer for Amplification of Core Land Plant DNA Barcode Regions (rbcL and matK)?.}, journal = {Ecology and evolution}, volume = {15}, number = {2}, pages = {e70961}, pmid = {39963510}, issn = {2045-7758}, abstract = {The DNA barcode is a technique for molecular identification of species. Two core genes, matK and rbcL, are widely used for land plants. In this technique, the selection of primers is a fundamental step for the success of amplification. Then, we aim to evaluate the primer amplification capability for the DNA barcode regions rbcL and matK. We extracted primer sequences from DNA barcode studies in the Web of Science and used chloroplast genome sequences from NCBI for in silico PCR tests using OpenprimeR. Physicochemical properties of in silico PCR were evaluated using OpenprimeR. Our literature review resulted in 366 and 489 different rbcL and matK primers. These were tested in 8665 sequences, 8463 species from 98 orders. Evaluating only the primer and sequence match, the primers with the highest number of sequences covered were 96.39% and 93.81% forward and reverse for rbcL, and 91.56% and 61.62% forward and reverse for matK. No universal primer for all land plants was found, but two rbcL primer pairs could amplify > 99% of the sequences. In contrast to the results obtained for the matK region, the 10 pairs optimized for the greatest coverage of sequences were not covered by > 85% of the sequences. Therefore, it is advisable to pay attention when selecting primers for the matK region and the need to develop new primers. Here, we recommend a set of primers to cover the largest number of sequences and orders.}, }
@article {pmid39963041, year = {2025}, author = {Lima-Cordón, R and Mohabir, JT and Sooklall, M and Zurita, AM and Shieh, M and Knox, C and Gobran, S and Johnson, Z and Laws, M and Panchal, R and Niles-Robin, R and Cox, H and Grillet, ME and Moreno, JE and Herrera, S and Quinones, M and Early, AM and Tennessen, JA and Neafsey, DE}, title = {A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.}, journal = {Molecular ecology resources}, volume = {25}, number = {6}, pages = {e14088}, pmid = {39963041}, issn = {1755-0998}, support = {U19 AI110818/AI/NIAID NIH HHS/United States ; U19AI110818//National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services/ ; INV-009416/GATES/Gates Foundation/United States ; INV-009416/GATES/Gates Foundation/United States ; }, mesh = {Animals ; *Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Sequence Analysis, DNA/methods ; *Diptera/genetics/classification ; *Insect Vectors/classification/genetics/parasitology ; Anopheles/genetics/parasitology/classification ; Humans ; *Disease Vectors ; }, abstract = {Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.}, }
@article {pmid39961041, year = {2025}, author = {Kim, IK and Kim, CJ and Choi, JH and Kang, HJ and Choi, MB}, title = {Stylopization by Xenos spp. (Xenidae, Strepsiptera) in invasive alien hornet, Vespa velutina, in South Korea.}, journal = {Parasite (Paris, France)}, volume = {32}, number = {}, pages = {10}, pmid = {39961041}, issn = {1776-1042}, support = {KNA1-2-44-23-2//Korea National Arboretum/ ; }, mesh = {Animals ; Republic of Korea ; Male ; *Introduced Species ; *Wasps/parasitology ; Female ; Pupa/parasitology ; Larva/parasitology ; Host-Parasite Interactions ; *Insecta/physiology ; }, abstract = {The invasive hornet Vespa velutina Lepeletier, which first invaded South Korea in 2003, has spread throughout the country, significantly affecting apiaries, ecosystems, and human health. Xenos spp. (Xenidae, Strepsiptera) are primarily parasitic to social wasps, with V. analis being the only known host in Korea. Until recently, no parasites or parasitoids on V. velutina had been discovered. In 2020, strepsipteran parasites were discovered on 11 hornet workers in Andong City, South Korea. These parasites, comprising four larvae and seven pupae, were all male, except for one individual of an undetermined sex. Molecular analysis and morphological examination identified the parasites as Xenos moutoni (du Buysson, 1903) and X. oxyodontes Nakase &amp; Kato, 2013. This marks the first recorded instance of strepsipteran parasites on V. velutina in regions invaded by this hornet. Although the exact infection rate of these parasites could not be determined, it appears that native strepsipteran parasites have adapted to a non-native Vespa species. Stylopization, the condition caused by these parasites, is known to negatively affect hornet colonies: infected workers do not contribute to nest activities, hindering nest development, and infected reproductive individuals (males and new queens) do not mate, which impedes the establishment of new colonies. However, due to the hornet's high reproductive rate and compensatory mechanisms, the overall control effect of the parasites is likely to be minor.}, }
@article {pmid39959867, year = {2025}, author = {Hernández, M and Michel, M and García, J and Dueñas, G and Moncada, M and Amaya, K and Yánez, Y and Pinto, A and Matamoros, G and Zamora, A and Fontecha, G}, title = {Diversity of beetles (Arthropoda, Insecta, Coleoptera) associated with coniferous forests in Honduras.}, journal = {ZooKeys}, volume = {1226}, number = {}, pages = {101-119}, pmid = {39959867}, issn = {1313-2989}, abstract = {Bark beetles are among the primary drivers of tree mortality in coniferous forests worldwide. Individuals belonging to the order Coleoptera were identified across different forest areas in Honduras. Descriptive statistics were used to calculate the number of families, subfamilies, genera, and species collected per department. Moreover, the barcoding approach was used by amplifying and sequencing the mitochondrial COI gene. The intraspecific genetic diversity of Ipsapache was also analyzed. 1,131 individuals were examined and 27 genera were identified. Most of the specimens were identified as belonging to the genus Ips, accounting for 53.2% of the total. Xyleborus accounted for 16.5% and Temnoscheila accounted for 10%. Fewer than four individuals were found for fifteen genera. 68% of the specimens were identified to the species level, and all the specimens were identified to the genus level. Ips, Temnoscheila, Xyleborus, Hypothenemus, and Pityophthorus exhibited the most extensive geographic distribution among the sampled sites. At the genus level, Olancho, El Paraíso, and Copán displayed the highest diversity. This study also marks the first report of the genera Xylomeira and Stephanopachys in Honduran pine forests. Within I.apache, evidence of intraspecific genetic diversity was observed, although no population structure was detected. While this research provides an updated inventory of beetle species associated with Honduran coniferous forests, further taxonomic surveys and ecological studies are essential to better understand the spread and impact of bark beetles in pine ecosystems.}, }
@article {pmid39959861, year = {2025}, author = {Betancourth-Cundar, M and Ríos-Orjuela, JC and Crawford, AJ and Cannatella, DC and Tarvin, RD}, title = {Honoring the Afro-Colombian musical culture with the naming of Epipedobatescurrulao sp. nov. (Anura, Dendrobatidae), a frog from the Pacific rainforests.}, journal = {ZooKeys}, volume = {1226}, number = {}, pages = {139-170}, pmid = {39959861}, issn = {1313-2989}, abstract = {The number of amphibian species described yearly shows no signs of slowing down, especially in tropical regions, implying that the biodiversity of amphibians remains woefully underestimated. A new species of poison frog is described from the Pacific lowlands of southwestern Colombia: Epipedobatescurrulao sp. nov., named for the Pacific music and dance genre known as "currulao" or "bambuco viejo". This species inhabits lowland forests from 0-260 m a.s.l. This taxon differs from congeners by having a combination of bright yellow blotches in the dorsal anterior region of the thigh and upper arm, homogenous dark-brown dorsal coloration, and advertisement calls of long duration and many pulses. We also describe the courtship call of E.currulao sp. nov., which is lower in frequency and shorter in duration than its advertisement call. Molecular phylogenetic analyses confirm the monophyly of the populations sampled and its position as the sister species of Epipedobatesnarinensis, which occurs in southwestern Colombia. Among species of Epipedobates, the new species has been previously confused with E.boulengeri, but the two species are allopatric and represent two divergent clades (1.77% divergent for 12S-16S and 5.39% for CYTB). These species can be distinguished by the presence of a bright yellow blotch on the dorsal anterior region of the thigh and on the upper arm of E.currulao sp. nov., blotches that are either more white than yellow or absent in E.boulengeri. In addition, the advertisement calls are distinct, with E.currulao sp. nov. having a single but long call in each call series while E.boulengeri has 2-6 calls in a series with each call being much shorter in length. Epipedobatescurrulao sp. nov. is the most northern species of Epipedobates, which extends southwards along the western edge of the Andes. Known as the Chocó, this biogeographic region has been largely converted to agriculture in Ecuador and is experiencing widespread transformation in Colombia, which may endanger E.currulao sp. nov. and biodiversity in the region. A Spanish translation of the main text is available in Suppl. material 8.}, }
@article {pmid39958907, year = {2025}, author = {Liang, Y and Liu, J and Yin, H and Xu, X}, title = {On new spider species of the genus Episinus (Araneae, Theridiidae) from China and proposal of five species groups.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e144222}, pmid = {39958907}, issn = {1314-2828}, abstract = {BACKGROUND: Currently, the genus Episinus Walckenaer, 1809 includes 64 described species mainly being distributed in Asia, Africa and the Americas, with 16 described species in China. During the recent surveys across various regions of China, we found three previously undescribed species which have been identified as belonging to Episinus.<br><br>NEW INFORMATION: Three new species of Episinus Walckenaer, 1809 are described: Episinusanfu sp. nov. (&#x2640;) from Jiangxi Province, E.implicatus sp. nov. (&#x2640;) from Yunnan Province and E.pseudonubilus sp. nov. (&#x2642;&#x2640;) from Shaanxi Province. Based on morphological characteristics and previous studies, we further propose five species groups to accommodate the Chinese Episinus, including two species groups proposed by Liu et al. (2022). Detailed descriptions, photographs, hand drawings, DNA barcodes and a distribution map of the three new species are provided.}, }
@article {pmid39956942, year = {2025}, author = {Meier, R and Srivathsan, A and Oliveira, SS and Balbi, MIPA and Ang, Y and Yeo, D and Kjærandsen, J and Amorim, DS}, title = {"Dark taxonomy": A new protocol for overcoming the taxonomic impediments for dark taxa and broadening the taxon base for biodiversity assessment.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {41}, number = {2}, pages = {223-238}, pmid = {39956942}, issn = {1096-0031}, mesh = {*Biodiversity ; *Classification/methods ; Phylogeny ; *Fungi/classification/genetics ; Singapore ; }, abstract = {We are entering the sixth mass extinction with little data for "dark taxa", although they comprise most species. Much of the neglect is due to the fact that conventional taxonomic methods struggle with handling thousands of specimens belonging to hundreds of species. We thus here propose a new strategy that we call "dark taxonomy". It addresses (i) taxonomic impediments, (ii) the lack of biodiversity baselines and (iii) the low impact of revisionary research. Taxonomic impediments are reduced by carrying out revisions at small geographic scales to keep the number of specimens low. The risk of taxonomic error is reduced by delimiting species based on two types of data. We furthermore show that dark taxonomy can yield important biodiversity baseline data by using samples obtained with biomonitoring traps. Lastly, we argue that the impact of revisionary research can be improved by publishing two papers addressing different readerships. The principles of dark taxonomy are illustrated by our taxonomic treatment of Singapore's fungus gnats (Mycetophilidae) based only on Malaise trap samples. We show that a first batch of specimens (N = 1454) contains 120 species, of which 115 are new to science, thus reducing taxonomic impediments by increasing the number of described Oriental species by 25%. Species delimitation started with using DNA barcodes to estimate the number of Molecular Operational Taxonomic Units (MOTUs) before "LIT" (Large-scale Integrative Taxonomy) was used to obtain the species boundaries for the 120 species by integrating morphological and molecular data. To test the taxonomic completeness of the revision, we next analysed a second batch of 1493 specimens and found that >97% belonged to the 120 species delimited based on the first batch. Indeed, the second batch only contained 18 new and rare MOTUs, i.e. our study suggests that a single revision can simultaneously yield the names for all important species and relevant biodiversity baseline data. Overall, we believe that "dark taxonomy" can quickly ready a large unknown taxon for biomonitoring.}, }
@article {pmid39955482, year = {2025}, author = {Wang, M and Yang, J and Hou, Z and Li, C and Niu, Z and Zhang, B and Xue, Q and Liu, W and Ding, X}, title = {The multi-chromosomal structure of mitogenomes provided new insights into the accurate authentication of medicinal Dendrobium species.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {202}, pmid = {39955482}, issn = {1471-2229}, support = {32070353//National Natural Science Foundation of China/ ; (LYKJ[2021]12//Forestry Science and Technology Innovation and Promotion Project of Jiangsu Province/ ; 2024QL061//Youth Science and Technology Innovation Leading Talent Project of Ningbo, China/ ; 2024S110//the Public Welfare Project of Ningbo, China/ ; }, mesh = {*Dendrobium/genetics/classification ; *Plants, Medicinal/genetics/classification ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Chromosomes, Plant/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: The global prevalence of herbal-based health care rapidly promoted requirements for medicinal plant resources. Accurate classification and identification are crucial to assuring the safety of these herbal sources.<br><br>RESULTS: Here, we took Dendrobium (Orchidaceae), a famous horticultural and medicinal plant taxon, as the study focus to establish an effective authentication approach for medicinal plants based on new mtDNA barcodes. We first de novo assembled three complete mitogenomes using Illumina and Nanopore data. These three mitogenomes were 635,454&#xa0;bp-831,745&#xa0;bp long with multichromosomal structures. Moreover, the three mitogenomes were compared to the other four published Dendrobium mitogenomes. The results revealed great variations of the structure and repeat contents among these mitogenomes, while gene contents and genomic sequences were relatively conserved. The analysis of mutational hotspots showed eight mitochondrial DNA regions with high sequence variability (>&#x2009;5%) at the interspecific level, which could provide abundant informatic loci for phylogeny, genetic diversity, and identification analyses. We also newly obtained mitochondrial sequences of 45 individuals from 15 Dendrobium species for authentication analysis. These 15 Dendrobium species were successfully identified by the whole mitogenome sequences and the isoform combination (Mt17&#x2009;+&#x2009;Mt19) respectively.<br><br>CONCLUSIONS: Our findings revealed that mitochondrial isoforms (chromosomes) could be used as super-barcodes for Dendrobium species authentication. The multi-chromosomal structure of mitogenomes provided new insights into the accurate authentication of medical plants.}, }
@article {pmid39955017, year = {2025}, author = {Diekmann, I and Krücken, J and Kuzmina, TA and Bredtmann, CM and Louro, M and Kharchenko, VA and Tzelos, T and Matthews, JB and Madeira de Carvalho, LM and von Samson-Himmelstjerna, G}, title = {Comparative phylogenetic and sequence identity analysis of internal transcribed spacer 2 and cytochrome c oxidase subunit I as DNA barcode markers for the most common equine Strongylidae species.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {129}, number = {}, pages = {105729}, doi = {10.1016/j.meegid.2025.105729}, pmid = {39955017}, issn = {1567-7257}, mesh = {Animals ; *Phylogeny ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Horses/parasitology ; *DNA, Ribosomal Spacer/genetics ; *Horse Diseases/parasitology ; Sequence Analysis, DNA ; }, abstract = {Morphologically, 64 strongylid species have been described in equines. Co-infections are common, with up to 29 species reported in a single horse. Morphological identification of these species is time consuming and requires expert knowledge due to their similar appearance. Therefore, non-invasive identification methods are needed. DNA barcoding offers a rapid and reliable tool for species identification and the discovery of cryptic species for these most common parasitic nematodes of equines. In total, 269 cytochrome c oxidase subunit I (COI) gene and 312 internal transcribed spacer 2 (ITS-2) sequences from 27 equine Strongylidae species, including sequences from two uncharacterised species, Coronocyclus sagittatus and Triodontophorus tenuicollis, were generated and combined with COI and ITS-2 sequences data from six Cyathostominae species from previous studies. This study represents a comprehensive DNA barcoding analysis of 22 Cyathostominae and six Strongylinae species using mitochondrial COI gene and ITS-2 sequences. Maximum likelihood phylogenetic trees were constructed and the intra- and interspecific genetic distances for both markers were compared. Analysis revealed complex phylogenetic relationships. Para- and polyphyletic relationships were observed among most genera within Strongylinae and Cyathostominae. This challenges current morphological classifications. Although both markers showed overlapping pairwise identities in intra- and inter-species comparisons, COI had higher discriminatory power than ITS-2. Expanding the COI and ITS-2 reference database, including the first sequences for Coronocyclus sagittatus and Triodontophorus tenuicollis, improve a reliable species identification and advanced studies on Strongylinae and Cyathostominae diversity using barcoding and metabarcoding.}, }
@article {pmid39953951, year = {2025}, author = {Ametrano, CG and Jensen, J and Lumbsch, HT and Grewe, F}, title = {UnFATE: A Comprehensive Probe Set and Bioinformatics Pipeline for Phylogeny Reconstruction and Multilocus Barcoding of Filamentous Ascomycetes (Ascomycota, Pezizomycotina).}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syaf011}, pmid = {39953951}, issn = {1076-836X}, abstract = {The subphylum Pezizomycotina (filamentous ascomycetes) is the largest clade within Ascomycota. Despite the importance of this group of fungi, our understanding of their evolution is still limited due to insufficient taxon sampling. Although next-generation sequencing technology allows us to obtain complete genomes for phylogenetic analyses, generating complete genomes of fungal species can be challenging, especially when fungi occur in symbiotic relationships or when the DNA of rare herbarium specimens is degraded or contaminated. Additionally, assembly, annotation, and gene extraction of whole-genome sequencing data require bioinformatics skills and computational power, resulting in a substantial data burden. To overcome these obstacles, we designed a universal target enrichment probe set to reconstruct the phylogenetic relationships of filamentous ascomycetes at different phylogenetic levels. From a pool of single-copy orthologous genes extracted from available Pezizomycotina genomes, we identified the smallest subset of genetic markers that can reliably reconstruct a robust phylogeny. We used a clustering approach to identify a sequence set that could provide an optimal trade-off between potential missing data and probe set cost. We incorporated this probe set into a user-friendly wrapper script named UnFATE (https://github.com/claudioametrano/UnFATE) that allows phylogenomic inferences without requiring expert bioinformatics knowledge. In addition to phylogenetic results, the software provides a powerful multilocus alternative to ITS-based barcoding. Phylogeny and barcoding approaches can be complemented by an integrated, pre-processed, and periodically updated database of all publicly available Pezizomycotina genomes. The UnFATE pipeline, using the 195 selected marker genes, consistently performed well across various phylogenetic depths, generating trees consistent with the reference phylogenomic inferences. The topological distance between the reference trees from literature and the best tree produced by UnFATE ranged between 0.10 and 0.14 (nRF) for phylogenies from family to subphylum level. We also tested the in vitro success of the universal baits set in a target capture approach on 25 herbarium specimens from ten representative classes in Pezizomycotina, which recovered a topology congruent with recent phylogenomic inferences for this group of fungi. The discriminating power of our gene set was also assessed by the multilocus barcoding approach, which outperformed the barcoding approach based on ITS. With these tools, we aim to provide a framework for a collaborative approach to build robust, conclusive phylogenies of this important fungal clade.}, }
@article {pmid39952916, year = {2025}, author = {Zhang, TH and Shi, Y and Komarova, NL and Wordaz, D and Kostelny, M and Gonzales, A and Abbaali, I and Chen, H and Bresson-Tan, G and Dimapasoc, M and Harvey, W and Oh, C and Carmona, C and Seet, C and Du, Y and Sun, R and Zack, JA and Kim, JT}, title = {Barcoded HIV-1 reveals viral persistence driven by clonal proliferation and distinct epigenetic patterns.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1641}, pmid = {39952916}, issn = {2041-1723}, support = {UM1 AI164568/AI/NIAID NIH HHS/United States ; R01 AI161803/AI/NIAID NIH HHS/United States ; AI155232//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; AI164568//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UL1TR001881//U.S. Department of Health &amp; Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; AI127410//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; UL1 TR001881/TR/NCATS NIH HHS/United States ; 2152155//National Science Foundation (NSF)/ ; P30 AI152501/AI/NIAID NIH HHS/United States ; K08 AI155232/AI/NIAID NIH HHS/United States ; }, mesh = {*HIV-1/genetics/physiology ; *HIV Infections/virology/drug therapy/genetics ; *Epigenesis, Genetic ; Proviruses/genetics ; Humans ; Animals ; Mice ; Cell Proliferation ; Virus Latency/genetics ; RNA, Viral/genetics ; Viremia/virology ; Viral Load ; Genetic Variation ; }, abstract = {The HIV reservoir consists of infected cells in which the HIV-1 genome persists as provirus despite effective antiretroviral therapy (ART). Studies exploring HIV cure therapies often measure intact proviral DNA levels, time to rebound after ART interruption, or ex vivo stimulation assays of latently infected cells. This study utilizes barcoded HIV to analyze the reservoir in humanized mice. Using bulk PCR and deep sequencing methodologies, we retrieve 890 viral RNA barcodes and 504 proviral barcodes linked to 15,305 integration sites at the single RNA or DNA molecule in vivo. We track viral genetic diversity throughout early infection, ART, and rebound. The proviral reservoir retains genetic diversity despite cellular clonal proliferation and viral seeding by rebounding virus. Non-proliferated cell clones are likely the result of elimination of proviruses associated with transcriptional activation and viremia. Elimination of proviruses associated with viremia is less prominent among proliferated cell clones. Proliferated, but not massively expanded, cell clones contribute to proviral expansion and viremia, suggesting they fuel viral persistence. This approach enables comprehensive assessment of viral levels, lineages, integration sites, clonal proliferation and proviral epigenetic patterns in vivo. These findings highlight complex reservoir dynamics and the role of proliferated cell clones in viral persistence.}, }
@article {pmid39952465, year = {2025}, author = {Godfrey, TE and Kintsurashvili, E and Rasic, G and Kaur, J and D'Amato, C and Meltzer, RH}, title = {Single-Tube, Switched Temperature Amplicon Barcoding for Multiplex Detection of Rare Mutations in Circulating Tumor DNA.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {27}, number = {4}, pages = {237-246}, pmid = {39952465}, issn = {1943-7811}, mesh = {*Circulating Tumor DNA/genetics/blood ; Humans ; *Mutation ; High-Throughput Nucleotide Sequencing/methods ; Biomarkers, Tumor/genetics ; *DNA Barcoding, Taxonomic/methods ; *Multiplex Polymerase Chain Reaction/methods ; Temperature ; Neoplasms/genetics/diagnosis ; DNA Mutational Analysis/methods ; }, abstract = {Detection and analysis of circulating tumor DNA (ctDNA) as a biomarker for cancer is a promising approach. Applications for ctDNA analysis include screening, diagnosis, treatment selection, treatment monitoring, minimal residual disease detection, and recurrence monitoring. Detection of ctDNA is challenging and requires highly sensitive methods. Approaches such as digital PCR are appropriate when only a small number of targets is being interrogated, whereas next-generation sequencing (NGS) is typically used when more targets are being analyzed. There are several NGS methods available, some of which are published and can be implemented in laboratories with the required expertise while other, commercial approaches are proprietary and are only available as a service. Of the published methods, most use some kind of unique molecular identifiers (or barcodes) to facilitate NGS error correction and detection of rare mutations at mutant allele frequencies of <0.1%. However, incorporation of barcodes and amplification of the resulting libraries are not trivial and typically require multiple steps and considerable hands-on time by an experienced molecular biologist. Herein, a novel approach for switched temperature amplicon barcoding was used, in which barcoding and library amplification were performed in the same tube using a two-stage PCR protocol with no additional manipulation. Total hands-on time was 10 to 15 minutes for reaction setup; the library was then cleaned and was ready for sequencing.}, }
@article {pmid39951365, year = {2025}, author = {Fernandes, MB and Bitencourt, JA and da Silva, AT and Vicari, MR and Azambuja, M and Affonso, PRAM}, title = {Small Fishes, Big Issues: Species Delimitation in Hemigrammus Marginatus, Gill, 1958 (Acestrorhamphidae: Pristellinae) from Brazilian Coastal Basins Based on Integrative Genetics.}, journal = {Zebrafish}, volume = {22}, number = {2}, pages = {46-58}, doi = {10.1089/zeb.2024.0174}, pmid = {39951365}, issn = {1557-8542}, mesh = {Animals ; Brazil ; Electron Transport Complex IV/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Rivers ; *Characiformes/genetics/classification ; }, abstract = {The small characins represent a systematic puzzle in the Neotropical ichthyofauna as a result of independent miniaturization processes, adaptive convergence and lack of diagnostic characters for several genera. In order to diminish the taxonomic uncertainties and the evolutionary pathways in Hemigrammus, we carried out an integrative genetic analysis in the putatively widespread Hemigrammus marginatus Ellis, 1958 by combining cytogenetic and molecular data based on the mitochondrial Cytochrome C Oxidase subunit I (COI). Specimens of H. marginatus from the type locality in Itapicuru River basin and other two populations from coastal rivers in northeastern Brazil were analyzed and compared with the available data from other regions in South America. Conspicuous macro and microkaryotypic differences were detected between the samples from northeastern and southern Brazil (Upper Paraná River basin). Likewise, the DNA barcoding and species delimitation analyses recovered distinct Molecular Operational Taxonomical Units within H. marginatus. Therefore, the population from the type locality should be referred to as H. marginatus stricto sensu, representing a restricted characin taxon from coastal drainages (including the São Francisco River basin) along northeastern Brazil, while other populations of this small characin fish need to be taxonomically revised and managed as unique lineages.}, }
@article {pmid39951198, year = {2025}, author = {Senggagau, B and Bond, MM and Saputra, S and Pantjara, B and Sholichah, L}, title = {Evaluation of antioxidant activity of brown macroalgae found in Lampung Bay, Indonesia and molecular identification using DNA barcode cox1 BLAST.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {231}, pmid = {39951198}, issn = {1573-4978}, support = {B-3840/II.7.5/FR.06.00/11/2023//RIIM-LPDP/ ; }, mesh = {*Antioxidants/pharmacology/metabolism ; *DNA Barcoding, Taxonomic/methods ; *Seaweed/genetics/metabolism/classification/chemistry ; *Phaeophyceae/genetics ; Bays ; Sargassum/genetics ; Free Radical Scavengers ; }, abstract = {BACKGROUND: The study on identifying of brown macroalgae species, particularly those on the southern coast of Lampung Bay-Indonesia, at the molecular level and their antioxidant activity has never been conducted, so we examined it as our purpose study.<br><br>METHOD AND RESULTS: The research uses DPPH free radical scavenging activity and molecular identification using DNA barcode cox1 BLAST. Fifteen samples of fresh brown macroalgae with five samples, respectively, were collected from Sebalang Beach, Kalianda and Pesawaran, South Lampung. The DNA was first purified, and then the gene product was amplified using specific primers, cox1F1 primer and cox1R1 primer. The DNA sequence was checked and traced using the Basic Local Alignment Search Tool (BLAST). The three most dominant species of brown macroalgae were identified, namely Sargassum plagiophyllum, Sargassum ilicifolium and Hormophysa cuneiformis. The base length obtained ranged from 1164 to 1212&#xa0;bp, with a similarity percentage of 98.36% to 100%. The three types of brown macroalgae have the ability to scavenge DPPH free radicals. Ethanol solvent and extract fractions significantly influence the reduction of DPPH free radicals. The ethanolic extract fraction of S. ilicifolium exhibited the lowest EC50 value (64.17&#x2009;&#xb1;&#x2009;1.23&#xa0;mg L[-1]) and has the strongest antioxidant activity, followed by H. cuneiformis (75.88&#x2009;&#xb1;&#x2009;0.34&#xa0;mg L[-1]), and S. plagiophyllum (82.97&#x2009;&#xb1;&#x2009;1.30&#xa0;mg L[-1]).<br><br>CONCLUSION: The difference in species of brown macroalgae had no significant effect on the EC50 activity, and all three had robust antioxidant activity because their concentrations ranged between 50 and 100&#xa0;mg L[-1].}, }
@article {pmid39949805, year = {2025}, author = {Xiang, R and Wan, H and Sun, W and Duan, B and Chen, W and Cao, X and Wang, S and Song, C and Chen, S and Wang, Y and Wahab, AT and Iqbal Choudhary, M and Meng, X}, title = {TPMGD: A genomic database for the traditional medicines in Pakistan.}, journal = {Chinese herbal medicines}, volume = {17}, number = {1}, pages = {87-93}, pmid = {39949805}, issn = {2589-3610}, abstract = {OBJECTIVE: In Pakistan, traditional medicines are an important component of the medical system, with numerous varieties and great demands. However, due to the scattered resources and the lack of systematic collection and collation, adulteration of traditional Pakistani medicine (TPM) is common, which severely affects the safety of their medicinal use and the import and export trades. Therefore, it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of TPM.<br><br>METHODS: We collected and organized the information on 128 TPMs with regard to their medicinal parts, efficacy, usage, and genetic material, based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine: Pharmaceutical Codex. The genetic information of TPM is summarized from national center for biotechnology information (NCBI) and global pharmacopoeia genome database (GPGD). Furthermore, we utilized bioinformatics technology to supplement the chloroplast genome (cp-genome) data of 12 TPMs. To build the web server, we used the Linux&#xa0;+&#xa0;Apache&#xa0;+&#xa0;MySQL&#xa0;+&#xa0;PHP (LAMP) system and constructed the webpage on a PHP: Hypertext Preprocessor (PHP) model view controller (MVC) framework.<br><br>RESULTS: We constructed a new genomic database, the traditional Pakistani medicine genomic database (TPMGD). This database comprises five entries, namely homepage, medicinal species, species identification, basic local alignment search tool (BLAST), and download. Currently, TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs, including 140 cytochrome c oxidase subunit I (COI) sequences and 119 mitochondrial genome sequences from Bombyx mori, 1 396 internal transcribed spacer 2 (ITS2) sequences and 1 074 intergenic region (psbA-trnH) sequences specific to 92 and 83 plant species, respectively. Additionally, TPMGD includes 199 cp-genome sequences of 82 TPMs.<br><br>CONCLUSION: TPMGD is a multifunctional database that integrates species description, functional information inquiry, genetic information storage, molecular identification of TPM, etc. The database not only provides convenience for TPM information queries but also establishes the scientific basis for the medication safety, species identification, and resource protection of TPM.}, }
@article {pmid39949130, year = {2025}, author = {Titus, M and Varetto, I and Grosser, C and Russo, E and Davinack, A}, title = {First molecular characterization of Proctoeces maculatus (Looss, 1901) (Digenea: Fellodistomidae) infecting blue mussels (Mytilus edulis) from the northeastern USA.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e25}, doi = {10.1017/S0022149X25000021}, pmid = {39949130}, issn = {1475-2697}, mesh = {Animals ; *Mytilus edulis/parasitology ; Phylogeny ; *Trematoda/genetics/classification/isolation &amp; purification ; *Genetic Variation ; Haplotypes ; RNA, Ribosomal, 28S/genetics ; New England ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The digenetic trematode Proctoeces maculatus is a cosmopolitan parasite that infects various invertebrates and fish hosts, including the blue mussel, Mytilus edulis, along the northeastern U.S. coast. Despite its impact on mussel fitness and the region's aquaculture, little is known about the genetic diversity and connectivity of P. maculatus in this region. This study provides the first genetic characterization of P. maculatus populations in New England using the D1-D3 region of the 28S ribosomal RNA gene. Bayesian phylogenetic analysis and a haplotype network were used to assess genetic variation and connectivity across six localities in Maine, New York, and southern New England, and to compare these populations to global samples. Our results revealed distinct geographic structuring of P. maculatus haplotypes. The ME1 haplotype, unique to Maine, reflects either recent range expansion or isolation driven by environmental and biogeographic factors, such as Cape Cod's role as a phylogeographic barrier. The most common haplotype, US1, was shared by populations in southern New England, New York, and a single specimen from Tunisia, indicating possible historical or anthropogenic connectivity. Two divergent haplotypes from Mississippi and Chile likely represent misidentifications or cryptic species. These findings support the hypothesis that P. maculatus is likely a cryptic species complex. Molecular evidence suggests connectivity across distant regions, emphasizing the role of host movement in parasite dispersal. Continued genetic studies, particularly from under-sampled regions, are needed to unravel the diversity and biogeography of P. maculatus and its potential impact on declining mussel populations.}, }
@article {pmid39948460, year = {2025}, author = {Keukeleire, P and Rosen, JD and Göbel-Knapp, A and Salomon, K and Schubach, M and Kircher, M}, title = {Using individual barcodes to increase quantification power of massively parallel reporter assays.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {52}, pmid = {39948460}, issn = {1471-2105}, support = {UM1 HG011966/HG/NHGRI NIH HHS/United States ; 1UM1HG011966//Impact of Genomic Variation on Function (IGVF)/ ; 1UM1HG012003//Impact of Genomic Variation on Function (IGVF)/ ; }, mesh = {*Genes, Reporter ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Humans ; }, abstract = {BACKGROUND: Massively parallel reporter assays (MPRAs) are an experimental technology for measuring the activity of thousands of candidate regulatory sequences or their variants in parallel, where the activity of individual sequences is measured from pools of sequence-tagged reporter genes. Activity is derived from the ratio of transcribed RNA to input DNA counts of associated tag sequences in each reporter construct, so-called barcodes. Recently, tools specifically designed to analyze MPRA data were developed that attempt to model the count data, accounting for its inherent variation. Of these tools, MPRAnalyze and mpralm are most widely used. MPRAnalyze models barcode counts to estimate the transcription rate of each sequence. While it has increased statistical power and robustness against outliers compared to mpralm, it is slow and has a high false discovery rate. Mpralm, a tool built on the R package Limma, estimates log fold-changes between different sequences. As opposed to MPRAnalyze, it is fast and has a low false discovery rate but is susceptible to outliers and has less statistical power.<br><br>RESULTS: We propose BCalm, an MPRA analysis framework aimed at addressing the limitations of the existing tools. BCalm is an adaptation of mpralm, but models individual barcode counts instead of aggregating counts per sequence. Leaving out the aggregation step increases statistical power and improves robustness to outliers, while being fast and precise. We show the improved performance over existing methods on both simulated MPRA data and a lentiviral MPRA library of 166,508 target sequences, including 82,258 allelic variants. Further, BCalm adds functionality beyond the existing mpralm package, such as preparing count input files from MPRAsnakeflow, as well as an option to test for sequences with enhancing or repressing activity. Its built-in plotting functionalities allow for easy interpretation of the results.<br><br>CONCLUSIONS: With BCalm, we provide a new tool for analyzing MPRA data which is robust and accurate on real MPRA datasets. The package is available at https://github.com/kircherlab/BCalm .}, }
@article {pmid39946438, year = {2025}, author = {Somma, E and Costantini, M and Pennesi, C and Ruocco, N and De Castro, O and Terlizzi, A and Zupo, V}, title = {Identification of Cocconeis neothumensis var. marina using a polyphasic approach including ultrastructure and gene annotation.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0317360}, pmid = {39946438}, issn = {1932-6203}, mesh = {*Diatoms/genetics/ultrastructure/classification ; Phylogeny ; DNA Barcoding, Taxonomic ; RNA, Ribosomal, 18S/genetics ; Molecular Sequence Annotation ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {Several microalgae, including marine diatoms, significantly contribute to the global primary production and play a vital role in the food webs of benthic and planktonic ecosystems. Diatoms of the genus Cocconeis frequently inhabit benthic substrates, including the leaves of seagrasses. They are seasonally dominant in the leaf epiphytic layer of the Mediterranean seagrass Posidonia oceanica L. Delile, and have been proposed as model organisms for chemical ecology studies. However, the genome of Cocconeis spp. has not been sequenced. Consequently, their low-level molecular identification is currently impossible, besides a few examples. To address this gap, a polyphasic identification of C. neothumensis has been employed, combining ultra-morphological data with DNA barcoding markers. A strain of diatoms was isolated from P. oceanica leaves. It has been cultured in the laboratory and examined under Scanning Electron Microscopy (SEM). The 18S ribosomal RNA gene (18S rRNA, nrDNA) and the ribulose 1,5-biphosphate carboxylase (rbcL, cpDNA) gene were analysed for DNA barcoding characterisation. Since ultra-morphology data unambiguously identified the isolated strain as C. neothumensis Krammer, 1991, the molecular sequences herein reported will facilitate its rapid and accurate identification. In addition, our comparative analyses will facilitate the evaluation of these molecular markers for identification of closely related benthic diatoms.}, }
@article {pmid39945940, year = {2025}, author = {Celante, GL and Domahovski, AC and Jahyny, BJB and Martins, AL}, title = {Taxonomy and Biological Aspects of Gonatopus Ljungh (Hymenoptera: Dryinidae): Description of a New Species, Sexual Association and Record of Host from Northeast Brazil.}, journal = {Neotropical entomology}, volume = {54}, number = {1}, pages = {38}, pmid = {39945940}, issn = {1678-8052}, support = {A.L.M. (process 151844/2022-4)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; and G.L.C. (process n&#xba;130692/2023-9)//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; ACD (FAPERJ//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; proc. E-26/204.206/2021)//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, mesh = {Animals ; Brazil ; Female ; Male ; *Hymenoptera/classification/anatomy &amp; histology/physiology ; *Hemiptera/parasitology ; Host-Parasite Interactions ; Nymph/parasitology ; Sex Characteristics ; Larva ; *Wasps/classification/anatomy &amp; histology/physiology ; }, abstract = {Gonatopus Ljungh is recognized as the third most diverse genus within Dryinidae (Hymenoptera: Aculeata) and exhibits a pronounced sexual dimorphism. Due to its extensive diversity, species recognition for both sexes are challenging without the use of specimens obtained through rearing or the application of molecular techniques such as DNA barcoding. In Brazil, the knowledge of Gonatopus fauna is limited, with the Northeast region being particularly under-studied. The objective of this study was to gather comprehensive information about the biology of Gonatopus through the rearing of parasitized leafhoppers (Hemiptera: Cicadellidae). This approach allowed for the recognition and description of a new species, G. cambitos Martins &amp; Celante sp. nov. Furthermore, the study facilitated the association of sexes through the parasitism performed by females of the new species on nymphs of Frequenamia confusa (Linnavuori) (Cicadellidae, Deltocephalinae). Additionally, the research provided insights into predation and parasitism behavior, detailing the developmental stages from larva to adult and we provided a discussion about the distribution of Gonatopus in the Northeast Region of Brazil. In addition to these findings, is provided a discussion about the previous of Gonatopus in the Northeast region of Brazil, based on distribution records.}, }
@article {pmid39945845, year = {2025}, author = {Dubey, S and Pellaud, S and Furrer, S and Dufresnes, C}, title = {Unsuspected diversity and multiple origins of the frog legs imported to Switzerland for human consumption, as determined by DNA barcoding and morphology.}, journal = {Die Naturwissenschaften}, volume = {112}, number = {2}, pages = {17}, pmid = {39945845}, issn = {1432-1904}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Switzerland ; Humans ; *Ranidae/anatomy &amp; histology/genetics/classification ; Phylogeography ; *Biodiversity ; }, abstract = {The frog leg industry relies on a global, largely underregulated market with potentially important ecological impact such as the uncontrolled harvest of declining wild populations and the introduction of invasive species. Here, we inferred the taxonomic nature and geographic origins of frog legs imported to Switzerland by DNA barcoding. Out of 34 samples, we retrieved eight distinct lineages attributed to five species from four genera, namely Hoplobatrachus rugulosus from Vietnam, Fejervarya cancrivora from Indonesia (invasive on several Pacific islands), two phylogeographic lineages of Limnonectes macrodon from Western and Central Java, L. kadarsani from eastern Indonesia, and three phylogeographic lineages of Pelophylax ridibundus from northern and central southern Turkey (invasive in Western Europe). Only the first two species were correctly declared, which is particularly problematic to track down harvests of the declining and geographically restricted Limnonectes taxa. In this respect, we show that the three Asian genera can be reliably distinguished by basic measurements of the frog legs, which could be used in future forensic controls. Our study calls for more stringent international regulations of the frog trade, including shipment monitoring to document the relative abundance of harvested species and ensure the sustainability of their wild populations.}, }
@article {pmid39945742, year = {2025}, author = {Hotinger, JA and Campbell, IW and Hullahalli, K and Osaki, A and Waldor, MK}, title = {Quantification of Salmonella enterica serovar Typhimurium population dynamics in murine infection using a highly diverse barcoded library.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39945742}, issn = {2050-084X}, support = {R01 AI042347/AI/NIAID NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; F31 AI156949/AI/NIAID NIH HHS/United States ; T32 DK007477/DK/NIDDK NIH HHS/United States ; P30 CA006516/CA/NCI NIH HHS/United States ; T32 DK007477-37/DK/NIDDK NIH HHS/United States ; }, mesh = {*Salmonella enterica/classification/drug effects/genetics/growth &amp; development ; *Serogroup ; *Salmonella Infections, Animal/microbiology ; Animals ; *DNA Barcoding, Taxonomic ; *Gene Library ; *Genetic Variation ; Streptomycin/pharmacology ; Intestines/microbiology/pathology ; Bile/microbiology ; Gallbladder/microbiology/pathology ; Male ; Female ; Mice, Inbred C57BL ; }, abstract = {Murine models are often used to study the pathogenicity and dissemination of the enteric pathogen Salmonella enterica serovar Typhimurium. Here, we quantified S. Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverse S. Typhimurium barcoded library containing ~55,000 unique strains distinguishable by genomic barcodes by enumerating S. Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen's colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed that Salmonella re-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding of Salmonella population dynamics.}, }
@article {pmid39943127, year = {2025}, author = {Klimov, PB and Kolesnikov, VB and Khaustov, AA and Khaustov, VA and Merckx, J and Duarte, MVA and Vangansbeke, D and Geudens, I and Pepato, A}, title = {Typification of the Economically Important Species Thyreophagus entomophagus (Acari: Astigmata: Acaridae) Used for the Industrial Production of Predatory Mites: The Designation of a Neotype with Detailed Morphological and DNA Sequence Data.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, pmid = {39943127}, issn = {2076-2615}, support = {&#x2116; 075-15-2021-1345, unique identifier RF-193021X0012//Ministry of Science and Higher Education of the Russian Federation within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027/ ; }, abstract = {The mite Thyreophagus entomophagus is a cosmopolitan species of significant economic importance in biocontrol applications, serving as a factitious prey for the mass rearing of predatory mites. This species has been reported from a variety of habitats. However, the taxonomic reliability of its name is questionable due to inconsistencies in historical species identifications, the absence of type specimens, and misidentified GenBank sequences. Here, to address these issues and to standardize the nomenclature, we redescribe Thyreophagus entomophagus based on a commercial culture with known COX1 barcoding sequence data and designate a neotype from this culture. As part of delimiting the species boundaries of Th. entomophagus, the question of whether this species forms heteromorphic deutonymphs is particularly important. While the literature suggests that most populations lack them, at least one population in Germany has been reported to produce heteromorphic deutonymphs. However, after careful examination, we identified this population as a new species, Thyreophagus holda, indicating that previous identifications of this population as Th. entomophagus were incorrect. The absence of the heteromorphic deutonymphal stage is a beneficial trait for mass production, as it simplifies the life cycle by eliminating the energetically costly heteromorphic deutonymph. Our preliminary molecular phylogenetic analyses of Th. entomophagus and other species of Thyreophagus indicate that the loss of heteromorphic deutonymphs and the emergence of asexual reproduction (another beneficial trait for mass production) are derived traits that arose after the divergence of the most recent common ancestor of Thyreophagus. These insights enhance our understanding of the evolutionary traits that increase the effectiveness of Th. entomophagus and related species in biocontrol settings. Our study points to the need for additional bioprospecting efforts to identify new candidate species for biocontrol that possess both asexual reproduction and the absence of heteromorphic deutonymphs.}, }
@article {pmid39941137, year = {2025}, author = {Xu, J and Zhang, H and Yang, F and Zhu, W and Li, Q and Cao, Z and Song, Y and Xin, P}, title = {Phylogeny of Camphora and Cinnamomum (Lauraceae) Based on Plastome and Nuclear Ribosomal DNA Data.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, pmid = {39941137}, issn = {1422-0067}, support = {123456789//Yunnan Province landscape architecture first-class discipline construction fund/ ; No. 202302AE090018//Key Technologies Research for the Germplasm of Important Woody Flowers in Yunnan Province/ ; Nos. 32260060//National Natural Science Foundation of China/ ; Nos. 32060710//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *DNA, Ribosomal/genetics ; *Plastids/genetics ; *Cinnamomum/genetics/classification ; DNA, Plant/genetics ; *Cinnamomum camphora/genetics/classification ; Evolution, Molecular ; Microsatellite Repeats ; }, abstract = {Camphora Fabr. is a genus in the family Lauraceae, comprising over 20 tropical and subtropical tree species. Since the genera Camphora and Cinnamomum Schaeff. were described, there has been a long-lasting controversy regarding the phylogenetic relationships among taxa in both genera. In particular, phylogenetic inferences derived from plastid data remain debated, with varying hypotheses proposed and occasional disputes concerning the monophyly of Camphora taxa. To further investigate the relationships, We analyzed plastomes and nuclear ribosomal cistron sequences (nrDNA) of 22 Camphora taxa, 15 Cinnamomum taxa, and 13 representative taxa of related genera. The Camphora plastomes range from 152,745 to 154,190 bp, with a GC content of 39.1% to 39.2%. A total of 128 genes were identified in the Camphora plastomes, including 84 protein-coding genes, 8 rRNA genes, and 36 tRNA genes. A total of 1130 SSR loci were detected from plastomes of Camphora, and A/T base repeats looked like the most common. Comparative analyses revealed that the plastomes of Camphora exhibit high similarity in overall structure. The loci ycf1, ycf2, trnK (UUU), psbJ-psbL, and ccsA-ndhD were identified as candidate DNA barcodes for these taxa. Plastome phylogenetic analysis revealed that Camphora is not monophyletic, whereas the nrDNA dataset supported the monophyly of Camphora. We propose that intergeneric hybridization may underlie the observed discordance between plastid and nuclear data in Camphora, and we recommend enhanced taxonomic sampling and precise species identification to improve phylogenetic resolution and accuracy.}, }
@article {pmid39939719, year = {2025}, author = {Olsen, TR and Talla, P and Sagatelian, RK and Furnari, J and Bruce, JN and Canoll, P and Zha, S and Sims, PA}, title = {Scalable co-sequencing of RNA and DNA from individual nuclei.}, journal = {Nature methods}, volume = {22}, number = {3}, pages = {477-487}, pmid = {39939719}, issn = {1548-7105}, support = {R01 NS103473/NS/NINDS NIH HHS/United States ; R01 CA275184/CA/NCI NIH HHS/United States ; U54CA274506//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; P30 CA013696/CA/NCI NIH HHS/United States ; P30 DK132710/DK/NIDDK NIH HHS/United States ; R01NS103473//U.S. Department of Health &amp; Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; R01CA275184//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; U54 CA274506/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Cell Nucleus/genetics ; *DNA/genetics ; Nucleosomes/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Sequence Analysis, RNA/methods ; Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA/methods ; Single-Cell Analysis/methods ; *RNA/genetics ; RNA, Messenger/genetics ; }, abstract = {The ideal technology for directly investigating the relationship between genotype and phenotype would analyze both RNA and DNA genome-wide and with single-cell resolution; however, existing tools lack the throughput required for comprehensive analysis of complex tumors and tissues. We introduce a highly scalable method for jointly profiling DNA and expression following nucleosome depletion (DEFND-seq). In DEFND-seq, nuclei are nucleosome-depleted, tagmented and separated into individual droplets for messenger RNA and genomic DNA barcoding. Once nuclei have been depleted of nucleosomes, subsequent steps can be performed using the widely available 10x Genomics droplet microfluidic technology and commercial kits. We demonstrate the production of high-complexity mRNA and gDNA sequencing libraries from thousands of individual nuclei from cell lines, fresh and archived surgical specimens for associating gene expression with both copy number and single-nucleotide variants.}, }
@article {pmid39939455, year = {2025}, author = {Suetsugu, K and Yagi, R and Okada, H and Matsubayashi, J}, title = {The tiny-leaved orchid Disperis neilgherrensis primarily obtains carbon from decaying litter via saprotrophic Ceratobasidium.}, journal = {Mycorrhiza}, volume = {35}, number = {1}, pages = {9}, pmid = {39939455}, issn = {1432-1890}, support = {JPMJPR21D6//Precursory Research for Embryonic Science and Technology/ ; 21H04784//Japan Society for the Promotion of Science/ ; }, mesh = {*Orchidaceae/microbiology/metabolism ; *Carbon/metabolism ; *Mycorrhizae/physiology/metabolism ; *Basidiomycota/physiology/metabolism ; Plant Leaves/microbiology/metabolism ; Carbon Isotopes/analysis ; Japan ; }, abstract = {While most green orchids establish associations with non-ectomycorrhizal rhizoctonias belonging to Ceratobasidiaceae, Tulasnellaceae, and Serendipitaceae, fully mycoheterotrophic orchids-excluding albino mutants-primarily depend on either ectomycorrhizal fungi or saprotrophic non-rhizoctonia fungi. This suggests that non-ectomycorrhizal rhizoctonias may be unable to meet the carbon demands of adult orchids that exhibit a high degree of mycoheterotrophy. To understand the physiological ecology of Disperis neilgherrensis, an orchid species with reduced leaves growing in decaying litter from non-ectomycorrhizal trees, we employed molecular and stable isotope analyses to identify its mycorrhizal partners and ultimate nutritional sources at two populations on Ishigaki Island, Japan. Molecular barcoding techniques revealed that D. neilgherrensis forms exclusive associations with non-ectomycorrhizal Ceratobasidiaceae fungi. The Disperis specimens exhibited δ[13]C and δ[15]N isotopic values similar to those found in fully mycoheterotrophic orchids that exploit litter-decaying fungi. Furthermore, the pelotons of D. neilgherrensis showed significantly elevated δ[13]C values similar to saprotrophic non-rhizoctonia fungi. Our findings indicate that D. neilgherrensis primarily obtains its carbon from decaying litter through a specialized relationship with non-ECM Ceratobasidiaceae. Given that saprotrophic Ceratobasidiaceae facilitate nearly fully mycoheterotrophic growth in D. neilgherrensis, at least under warm and humid conditions, it is plausible that other (nearly) fully mycoheterotrophic tropical orchids also meet their carbon requirements through associations with saprotrophic rhizoctonias.}, }
@article {pmid39939320, year = {2025}, author = {Kim, W and Chon, M and Koh, Y and Choi, H and Choi, E and Park, H and Jung, Y and Ryu, T and Kwon, S and Choi, Y}, title = {Oligonucleotide subsets selection by single nucleotide resolution barcode identification.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1586}, pmid = {39939320}, issn = {2041-1723}, support = {RS-2024-00440370//National Research Foundation of Korea (NRF)/ ; NRF-2022M3C1A3081366//National Research Foundation of Korea (NRF)/ ; RS-2023-00302766//National Research Foundation of Korea (NRF)/ ; }, mesh = {Gene Library ; *Oligonucleotides/genetics ; Polymerase Chain Reaction/methods ; DNA Primers/genetics ; *Nucleotides/genetics ; *DNA Barcoding, Taxonomic/methods ; }, abstract = {Effective subset selection from complex oligonucleotide libraries is crucial for genomics, synthetic biology, and DNA data storage. The polymerase chain reaction, foundational for amplifying target subsets is limited by primer design and length for specificity, which constrains the scalability of oligo libraries and increases the synthesis burden for primers. We introduce an oligo subset selection methodology that utilizes sequence-specific cyclic nucleotide synthesis and blocking of the template oligos. This approach eliminates the need for primers for selective hybridization and enables the encoding and selection of hundreds of subsets with barcode lengths of fewer than five nucleotides. Moreover, cyclic selection enables a hierarchical data structure in the oligo library, enhancing the programmability. This advancement offers a scalable and cost-effective solution for handling complex oligo libraries.}, }
@article {pmid39937412, year = {2025}, author = {Liu, G and Wang, X and Su, X and Ji, S and Ma, Z and Gao, Y and Song, X}, title = {The Development Potential of AuNPs-Based Lateral Flow Technology Combined with Other Advanced Technologies in POCT.}, journal = {Applied biochemistry and biotechnology}, volume = {197}, number = {5}, pages = {2867-2886}, pmid = {39937412}, issn = {1559-0291}, support = {No.20240304070SF//Science and Technology Development Plan Project of Jilin Province/ ; }, mesh = {*Metal Nanoparticles/chemistry ; *Gold/chemistry ; *Point-of-Care Testing ; Humans ; Spectrum Analysis, Raman ; Point-of-Care Systems ; }, abstract = {Currently, there is a demand for rapid, sensitive, low-cost, portable, and visualized testing technologies for point-of-care testing (POCT). However, most traditional testing methods face challenges such as long testing times, complicated operations, and high costs, limiting their implementation in resource-limited areas and hindering the fulfillment of POCT demands. Lateral flow assay (LFA) has emerged as an ideal detection technique for POCT, particularly when utilizing gold nanoparticles (AuNPs) as labels. This approach not only enables visualization with the naked eye but also reduces the need for expensive reading instruments. The technologies reviewed in this paper encompass integrated detection technology utilizing amplification technique and LFA, integrated detection technology utilizing clustered regularly interspaced short palindromic repeats (CRISPR) system and LFA, the utilization of surface-enhanced Raman spectroscopy (SERS) in LFA detection technique, the utilization of aptamers in LFA detection technique, and the utilization of DNA barcodes in LFA detection technique. By integrating these advanced techniques, there is significant potential to overcome the limitations of LFA, including low sensitivity, poor specificity, inability to quantify, and false positives, thereby enabling broader applications in resource-constrained settings. Additionally, this article comprehensively evaluates the strengths and weaknesses of each approach, underscoring the immense developmental potential of AuNPs-based LFA in point-of-care testing (POCT).}, }
@article {pmid39929864, year = {2025}, author = {Khan, MA and Latif, M and Mansha, M and Hussain, T and Bin Jardan, YA and Metouekel, A and Dauelbait, M and Belkahia, H and Iqbal, F and Said, MB}, title = {Genetic characterization and phylogenetic analysis of common house crows (Corvus splendens).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4871}, pmid = {39929864}, issn = {2045-2322}, mesh = {Animals ; *Crows/genetics/classification ; *Phylogeny ; *Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Pakistan ; Genetic Variation ; }, abstract = {The Common House Crow (Corvus splendens) exhibits remarkable ecological adaptability, enabling its rapid expansion across continents. However, despite its wide distribution, there is a need for genetic studies to clarify its evolutionary history and population structure. This research employs DNA barcoding, focusing on the mitochondrial gene cytochrome oxidase subunit I (Cox1), which is effective for species identification and phylogenetic analysis. Blood samples were collected from 70 C. splendens specimens across seven cities in Punjab, Pakistan: Lahore, Kasur, Sialkot, Narowal, Pakpattan, Gujranwala, and Bahawalpur. Genomic DNA extraction was performed, and a partial sequence of the COX1 gene was amplified using PCR techniques. Sequencing of the Cox1 marker from 10 randomly selected specimens revealed nine distinct genetic variants. Interspecific analysis positioned our C. splendens sequences alongside various Corvus species available in GenBank, while intraspecific analysis identified a total of 15 genetic variants. These variants showed nucleotide identity rates ranging from 98.7 to 99.8%, with genetic distances between 0.002 and 0.013. The analysis indicated that the C. splendens group consists of a single heterogeneous clade with variants from multiple countries, including Pakistan, Tanzania, Nepal, South Africa, Malaysia, Sri Lanka, Bangladesh, Kenya, Australia, and Singapore. This study significantly enhances our understanding of genetic diversity and evolutionary relationships within C. splendens populations, highlighting the necessity of genetic research to inform conservation strategies. Further research employing advanced molecular techniques and broader geographic sampling is essential to assess the genetic diversity and population dynamics of this adaptable species.}, }
@article {pmid39924908, year = {2025}, author = {Gao, Y and Ang, YS and Yung, LL}, title = {CRISPR-Cas12a-Assisted DNA Circuit for Nonmicroscopic Detection of Cell Surface Receptor Clustering.}, journal = {ACS sensors}, volume = {10}, number = {2}, pages = {977-985}, doi = {10.1021/acssensors.4c02770}, pmid = {39924908}, issn = {2379-3694}, support = {U54 HG006097/HG/NHGRI NIH HHS/United States ; U54 HL127365/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *CRISPR-Cas Systems ; *DNA/genetics/chemistry/metabolism ; Cell Line, Tumor ; *Receptor, ErbB-2/metabolism ; *Endodeoxyribonucleases/metabolism/genetics ; *CRISPR-Associated Proteins/metabolism/genetics ; Receptor, ErbB-3/metabolism ; *Bacterial Proteins/genetics/metabolism ; }, abstract = {Protein-protein interactions (PPIs) on the cell surface have been of great interest due to their high clinical relevance and significance; however, the methods for detecting PPIs heavily rely on microscopic instruments. In this work, we designed a Cas12a-assisted DNA circuit for detecting cell surface receptor clustering events without a dependence on microscopy. This nonmicroscopic approach is based on the proximity principle, where localized protein-protein interactions such as receptor clustering are converted into DNA barcodes. These barcodes can then be identified by Cas12a for signal generation in the bulk. The compatibility of the circuit with Cas12a was first experimentally verified. Several leak reactions were identified and minimized. Lastly, we implemented this design in human breast cancer cell line models to distinguish the different levels of human epidermal growth factor receptor 2 (HER2) homodimers and heterodimers with HER1 and HER3 semiquantitatively without the use of a microscope. Overall, our proposed Cas12a-assisted DNA circuit for detecting cell surface receptor clustering shows the potential for fast screening in diagnostic applications and drug discovery, demonstrating the promising use of enzymatic DNA circuits in biological applications.}, }
@article {pmid39922091, year = {2025}, author = {Zhu, Q and Wang, H and Hu, Y and Wei, Y and Wang, Y and Hou, T and Shan, T and Zhang, X and Yang, C and Cai, Y and Wang, Y and Zhang, J}, title = {Investigation into the genotyping performance of a unique molecular identifier based microhaplotypes MPS panel in complex DNA mixture.}, journal = {Forensic science international. Genetics}, volume = {76}, number = {}, pages = {103236}, doi = {10.1016/j.fsigen.2025.103236}, pmid = {39922091}, issn = {1878-0326}, mesh = {Humans ; DNA Probes ; *Forensic Genetics/methods ; Gene Library ; *Genotyping Techniques/methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Polymorphism, Genetic ; *Sequence Analysis, DNA/methods ; DNA Fingerprinting ; }, abstract = {In forensic science, genotyping mixed DNA is a critical and complex task. Sequencing errors and allele sharing complicate the analysis, particularly in cases involving unbalanced mixtures, multiple contributors, and kinship relationships. Massively parallel sequencing (MPS) panels comprising highly polymorphic microhaplotypes (MHs) offer a promising approach for detecting unique alleles in mixtures with a mixture ratio greater than 10:1, involving more than two contributors or contributors with kinship. However, sequencing errors such as base substitution and InDels on the MPS platform remain a significant challenge in genotyping complex mixed DNA. The barcoding approach has been introduced to MPS to distinguish true alleles from sequencing errors. This method employs unique molecular identifiers (UMIs) to tag individual DNA molecules, allowing for the identification and correction of random sequencing errors. By generating consensus sequences from read replicates associated with the same UMI, this approach enhances the accuracy of allele detection. In this study, UMIs were incorporated into developing a highly polymorphic panel consisting of 105 MHs, with an average effective number of alleles (Ae) of 6.9. Various types of mixed DNA samples were prepared, including unbalanced mixtures with ratios ranging from 1:1-160:1, multi-contributor mixtures with 2-6 contributors, and kinship-involved mixtures with parent-offspring to fourth-degree relatives contributors. Unique alleles were quantified, and mixture proportions (Mx) were calculated separately using sequencing reads and the number of UMI families with more than 10 members. The results demonstrated that UMI played a critical role in identifying sequencing errors and enhancing the accuracy of allele genotyping in unbalanced mixtures. A strong correlation (R[2] = 0.96) between UMI count and DNA template amount demonstrated that DNA template amount could be inferred from UMI count. Mx values derived from the number of UMIs were consistent across loci and showed a high correlation with mixture ratios (R[2] = 0.85). Additionally, the panel efficiently detected unique alleles across all three types of complex DNA mixtures. Overall, this study underscores the importance of UMIs in mitigating PCR and sequencing biases, thereby improving the performance of the MH-MPS panel for genotyping complex DNA mixtures. UMIs represent a valuable tool for mixed DNA genotyping and hold potential for boarder applications in probabilistic genotyping.}, }
@article {pmid39921565, year = {2025}, author = {Harris, DT and Jan, CH}, title = {CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR.}, journal = {Nucleic acids research}, volume = {53}, number = {4}, pages = {}, pmid = {39921565}, issn = {1362-4962}, support = {//Calico Life Sciences LLC/ ; }, mesh = {*RNA Polymerase III/genetics/metabolism ; *TOR Serine-Threonine Kinases/metabolism/genetics ; Humans ; *Ribonucleoproteins/genetics/metabolism ; *Stress, Physiological/genetics ; RNA, Transfer/genetics/metabolism/biosynthesis ; *Transcription, Genetic ; Mechanistic Target of Rapamycin Complex 1/metabolism/genetics ; CRISPR-Cas Systems ; Repressor Proteins/metabolism/genetics ; Protein Biosynthesis ; }, abstract = {Genetic screens using CRISPR (Clustered Regularly Interspaced Palindromic Repeats) provide valuable information about gene function. Nearly all pooled screening technologies rely on the cell to link genotype to phenotype, making it challenging to assay mechanistically informative, biochemically defined phenotypes. Here, we present CRISPuRe-seq (CRISPR PuRification), a novel pooled screening strategy that expands the universe of accessible phenotypes through the purification of ribonucleoprotein complexes that link genotypes to expressed RNA barcodes. While screening for regulators of the integrated stress response (ISR), we serendipitously discovered that the ISR represses transfer RNA (tRNA) production under conditions of reduced protein synthesis. This regulation is mediated through inhibition of mTORC1 and corresponding activation of the RNA polymerase III inhibitor MAF1. These data demonstrate that coherent downregulation of tRNA expression and protein synthesis is achieved through cross-talk between the ISR and mTOR, two master integrators of cell state.}, }
@article {pmid39920599, year = {2025}, author = {Kalumbilo, M and Chuba, D and Banda, A and Smid, EJ and Schoustra, SE and De Deyn, GB}, title = {Characterization and DNA barcoding of Zambian plant species used as inoculum in the traditional fermentation of Munkoyo; a cereal-based beverage.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {166}, pmid = {39920599}, issn = {1471-2229}, mesh = {*DNA Barcoding, Taxonomic ; Zambia ; Fermentation ; Plant Roots/genetics ; Soil/chemistry ; *Beverages ; *Vigna/genetics ; Edible Grain ; *Fabaceae/genetics/classification ; Phylogeny ; DNA, Plant/genetics ; }, abstract = {BACKGROUND: Munkoyo, a non-alcoholic fermented beverage, is traditionally prepared in Zambia and neighbouring countries using cooked grains and the uncooked roots of wild plant species, collectively called 'Munkoyo' plants. The drink, valued for its refreshing taste and nutritional contribution, is made using roots of several wild plant species resulting in variations in the taste and quality of the beverage. However, comprehensive information on the specific plant species used in different regions of Zambia, as well as their occurrence in terms of habitat and soil type, is missing. This gap limits our understanding of the factors contributing to Munkoyo's heterogeneity. The present study sought to identify the Zambian plant species used as an inoculum in Munkoyo fermentation and to characterize the soil in which they occur.<br><br>RESULTS: Plant and soil samples were collected from four districts in Zambia known for Munkoyo production. Using morphological taxonomy, three Fabaceae species were identified as commonly used Munkoyo plants: Rhynchosia insignis (O.Hoffm.) R.E.Fr., Rhynchosia heterophylla Hauman, and Eminia holubii (Hemsl.) Taub. Root colour differed among these species, with the Rhynchosia species having yellowish roots and E. holubii having whitish roots. To validate their identification, we evaluated three DNA barcoding markers (matK, rbcL, and ITS2) for species discrimination. All markers showed 100% PCR amplification and sequencing success rates, with ITS2 displaying the highest genetic variability and species-level resolution. Phylogenetic analyses further confirmed ITS2 as the most effective marker. Validation using samples from a fifth district reaffirmed ITS2's suitability for species-level discrimination. Soil analysis revealed significant associations between soil texture and plant occurrence: R. insignis and E. holubii were prevalent in sandy soils, while R. heterophylla was more prevalent in soils with lower sand content.<br><br>CONCLUSIONS: This study identified three common Munkoyo plant species and demonstrated ITS2 as a robust DNA barcode for their identification. It also established the influence of soil texture on the distribution of these plants, contributing to the understanding of Munkoyo production's biological and environmental determinants.}, }
@article {pmid39915438, year = {2025}, author = {van der Horst, SC and Kollenstart, L and Batté, A and Keizer, S and Vreeken, K and Pandey, P and Chabes, A and van Attikum, H}, title = {Replication-IDentifier links epigenetic and metabolic pathways to the replication stress response.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1416}, pmid = {39915438}, issn = {2041-1723}, support = {Vici 182.052//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*DNA Replication/genetics/drug effects ; *Saccharomyces cerevisiae/genetics/metabolism/drug effects ; Saccharomyces cerevisiae Proteins/metabolism/genetics ; *Epigenesis, Genetic ; *Metabolic Networks and Pathways/genetics ; Hydroxyurea/pharmacology ; DNA Polymerase II/metabolism/genetics ; Gene Expression Regulation, Fungal ; Stress, Physiological/genetics ; Ubiquitination ; DNA Damage ; Histones/metabolism ; Transcription Factors/metabolism/genetics ; }, abstract = {Perturbation of DNA replication, for instance by hydroxyurea-dependent dNTP exhaustion, often leads to stalling or collapse of replication forks. This triggers a replication stress response that stabilizes these forks, activates cell cycle checkpoints, and induces expression of DNA damage response genes. While several factors are known to act in this response, the full repertoire of proteins involved remains largely elusive. Here, we develop Replication-IDentifier (Repli-ID), which allows for genome-wide identification of regulators of DNA replication in Saccharomyces cerevisiae. During Repli-ID, the replicative polymerase epsilon (Pol ε) is tracked at a barcoded origin of replication by chromatin immunoprecipitation (ChIP) coupled to next-generation sequencing of the barcode in thousands of hydroxyurea-treated yeast mutants. Using this approach, 423 genes that promote Pol ε binding at replication forks were uncovered, including LGE1 and ROX1. Mechanistically, we show that Lge1 affects replication initiation and/or fork stability by promoting Bre1-dependent H2B mono-ubiquitylation. Rox1 affects replication fork progression by regulating S-phase entry and checkpoint activation, hinging on cellular ceramide levels via transcriptional repression of SUR2. Thus, Repli-ID provides a unique resource for the identification and further characterization of factors and pathways involved in the cellular response to DNA replication perturbation.}, }
@article {pmid39912668, year = {2025}, author = {Weigl, S and Dabernig-Heinz, J and Granitz, F and Lipp, M and Ostermann, L and Harmsen, D and Trinh, TT and Steinmetz, I and Wagner, GE and Lichtenegger, S}, title = {Improving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like Burkholderia pseudomallei.}, journal = {Journal of clinical microbiology}, volume = {63}, number = {3}, pages = {e0156924}, pmid = {39912668}, issn = {1098-660X}, support = {"Individual Research Grant", 2024//European Society of Clinical Microbiology and Infectious Diseases (ESCMID)/ ; }, mesh = {*Burkholderia pseudomallei/genetics/classification ; *Multilocus Sequence Typing/methods ; Humans ; *Genome, Bacterial ; *Nanopore Sequencing/methods ; *Infection Control/methods ; *Melioidosis/microbiology ; Base Composition ; }, abstract = {UNLABELLED: Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor cost-efficiency of short-read (SR) sequencing. Oxford Nanopore long-read sequencing (ONT-LR), which allows fast on-site analysis with comparatively low costs, could provide an alternative. Despite ONT-LR raw read accuracy improvement, evidence for methylation-based errors accumulates. PCR-based library preparation, suggested as a solution, presumably poses difficulties for GC-rich bacteria. We challenged ONT-LR-based cgMLST using the highly GC-rich pathogen Burkholderia pseudomallei to develop a clinically applicable workflow. Our B. pseudomallei cgMLST scheme was applied to ONT-LR data, and the results were validated against SR data. Native, rapid, and PCR-based library preparation was performed and combined with different basecalling models (SUP@bacterial-methylation, SUP@v4.2, SUP@v4.3, and SUP@v5.0) and polishing strategies (medaka_consensus, medaka_variant, r103_min_high_g360). To ensure reliability across genotypes, we included 14 sequence types and 27 genotypes. The recommended ONT-LR workflow at study initiation (SUP@v4.2, medaka_consensus) showed nearly 200 allele differences compared with the reference for specific strains. PCR-based library preparation resulted in missing targets and typing errors of up to 21 alleles. Native barcoding with SUP@v5.0 basecalling and r103_min_high_g360 polishing outperformed the PCR-based approach in all parameters reducing the error rate to a maximum of two allele differences. The optimized ONT-LR-based cgMLST workflow for B. pseudomallei integrates high resolution and ease of implementation with enhanced cost-efficiency for rapid diagnostics. The developed protocol might serve as a guideline for other GC-rich pathogens.<br><br>IMPORTANCE: This study highlights a significant advancement in genomic surveillance of bacterial pathogens, specifically addressing the challenges posed by the GC-rich species Burkholderia pseudomallei. Core genome multilocus sequence typing (cgMLST) is widely used for bacterial typing as it combines high resolution with simple implementation and standardization. To improve cost efficiency and thus accessibility, we changed the sequencing approach from Illumina short-read (SR) to Oxford Nanopore long-read sequencing (ONT-LR). ONT-LR-based cgMLST showed a very high error rate compared with SR-based cgMLST, most likely due to methylation-associated errors. PCR-based library preparation, which is proposed to correct these errors, did not achieve the required accuracy. In contrast, native barcoding with advanced basecalling and polishing strategies massively reduces allelic differences. This optimized ONT-LR cgMLST workflow provides a transformative solution for cost-efficient, high-resolution typing of B. pseudomallei. Furthermore, this study can serve as a guide for similarly challenging bacteria.}, }
@article {pmid39912533, year = {2025}, author = {Emerson, BC}, title = {Delimiting Species-Prospects and Challenges for DNA Barcoding.}, journal = {Molecular ecology}, volume = {34}, number = {5}, pages = {e17677}, pmid = {39912533}, issn = {1365-294X}, support = {PID2020-116788GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Arthropods/genetics/classification ; *Biodiversity ; Sequence Analysis, DNA ; Phylogeny ; }, abstract = {Discovering, describing and cataloguing global species diversity remains a fundamental challenge both for biodiversity research and for the management and conservation of biodiversity. Among animals, the challenge is particularly acute within the arthropods, which comprise approximately 85% of all described animals, with approximately 1 million described species. The true number of arthropod species is estimated to be in excess of 10 million species. This estimate is likely to be revised upward in the light of global DNA barcode sequencing initiatives that are cataloguing unprecedented levels of cryptic or overlooked diversity. The scale of diversity that is being recovered with barcode sequencing places further strain on a taxonomic system confronted by ever-limited global taxonomic capacity to verify and describe new species. It is predicted that the number of novel operational taxonomic units delimited by barcode sequencing is likely to eclipse the number of species described by Linnean taxonomy by as early as 2029. Unless addressed, this may see an increasing proportion of arthropod species falling outside of protective legislative frameworks as a consequence of their lack of formal description. Confronted with this challenge, there is increasing, but controversial, acceptance of species delimitation and species description based on barcode sequence clustering thresholds. In response to the evolving controversy surrounding this issue, it is both timely and important to identify and clarify prospects and challenges for DNA barcoding, with a specific focus on species delimitation to address important shortfalls and impediments in biodiversity research.}, }
@article {pmid39908076, year = {2025}, author = {Blanco Mendana, J and Donovan, M and O'Brien, LG and Auch, B and Garbe, J and Gohl, DM}, title = {Deterministic genetic barcoding for multiplexed behavioral and single-cell transcriptomic studies.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {39908076}, issn = {2050-084X}, support = {P40 OD018537/OD/NIH HHS/United States ; }, mesh = {Animals ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; *Drosophila melanogaster/genetics ; *Transcriptome ; *Gene Expression Profiling/methods ; Drosophila/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Advances in single-cell sequencing technologies have provided novel insights into the dynamics of gene expression and cellular heterogeneity within tissues and have enabled the construction of transcriptomic cell atlases. However, linking anatomical information to transcriptomic data and positively identifying the cell types that correspond to gene expression clusters in single-cell sequencing data sets remains a challenge. We describe a straightforward genetic barcoding approach that takes advantage of the powerful genetic tools in Drosophila to allow in vivo tagging of defined cell populations. This method, called Targeted Genetically-Encoded Multiplexing (TaG-EM), involves inserting a DNA barcode just upstream of the polyadenylation site in a Gal4-inducible UAS-GFP construct so that the barcode sequence can be read out during single-cell sequencing, labeling a cell population of interest. By creating many such independently barcoded fly strains, TaG-EM enables positive identification of cell types in cell atlas projects, identification of multiplet droplets, and barcoding of experimental timepoints, conditions, and replicates. Furthermore, we demonstrate that TaG-EM barcodes can be read out using next-generation sequencing to facilitate population-scale behavioral measurements. Thus, TaG-EM has the potential to enable large-scale behavioral screens in addition to improving the ability to multiplex and reliably annotate single-cell transcriptomic experiments.}, }
@article {pmid39908038, year = {2025}, author = {Gevers, J and Beamish, E and Voorspoels, A and Botermans, W and Fauvart, M and Martens, K and Van Dorpe, P}, title = {Impact of Translocation Dynamics and Bandwidth on the Readout of DNA Structural Barcodes with Membrane-Based Solid-State Nanopores.}, journal = {ACS nano}, volume = {19}, number = {6}, pages = {6058-6068}, doi = {10.1021/acsnano.4c12111}, pmid = {39908038}, issn = {1936-086X}, mesh = {*Nanopores ; *DNA/chemistry ; Nucleic Acid Conformation ; }, abstract = {Recent advances in nanopore technology have promoted significant progress in single-molecule detection and analysis. In particular, membrane-based solid-state nanopores show promise as highly scalable readout platforms. This study explores the detection performance of this class of nanopores, with a focus on their application in molecular sensing schemes using DNA structural barcodes. The barcode structures, here specifically a series of dumbbell-shaped hairpins, encode information in a dumbbell-bit, which modulates the nanopore ionic current during translocation for readout. Our experiments evaluate the detection capabilities of membrane-based solid-state nanopores with a diameter of ∼15 nm. We investigate the detection success rates of individual dumbbell-bits with lengths ranging from 5 dumbbells (∼35 nm) to 29 dumbbells (∼195 nm) and with varying transmembrane potential. Longer dumbbell-bits exhibit a quasi-constant detection rate, whereas shorter bits show a significant decrease in the detection rate with increasing voltage. The observed dependencies are shown to be due to the increasing translocation velocity with voltage, in combination with the temporal resolution limit of the measurement system. Moreover, we show that a local increase of the effective charge at the dumbbell-bits leads to a proportionally increased local translocation velocity. This local velocity increase further degrades the detection success rate for dumbbell-bits. The findings in this study enhance our understanding of the fundamental limitations and capabilities of nanopore technology in high-throughput biosensing applications and have important implications for the design and optimization of future molecular assays and solid-state nanopore readout platforms.}, }
@article {pmid39905314, year = {2025}, author = {Nguyen, PL and Jung, JK and Park, JS and Sim, SC}, title = {Low-density SNP marker sets for genetic variation analysis and variety identification in cultivated citrus.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {146}, pmid = {39905314}, issn = {1471-2229}, support = {320040052HD060//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; }, mesh = {*Polymorphism, Single Nucleotide/genetics ; *Citrus/genetics/classification ; *Genetic Variation ; Genetic Markers ; Genotype ; Principal Component Analysis ; }, abstract = {BACKGROUND: The Citrus species are major fruit crops cultivated in the world and have complex genetic relationships due to sexual comparability between Citrus and related genera. Of these, satsuma mandarin (C. unshiu (Mak.) Marc.) and sweet orange (C. sinensis (L.) Osb.) are widely grown diploid species. In this study, genotyping by sequencing (GBS) was conducted to identify single nucleotide polymorphisms (SNPs) for investigating genetic variation in a citrus collection.<br><br>RESULTS: A total of 26,903 high-quality SNPs were detected across nine chromosomes in the 144 citrus varieties, consisting of 70 C. unshiu, 40 C. sinensis, 22 interspecific hybrids, and 12 others. Of these, a core set of 481 SNPs was filtered based on polymorphism information content and genome distribution. Both principal component analysis (PCA) and model-based clustering showed genetic differentiation between C. unshiu and C. sinensis. For interspecific hybrids, these were separated from two species in PCA, but were mixed with each species in model-based clustering. Significant genetic differentiations between three populations were also found using the pairwise Fst. In addition, interspecific hybrids showed higher level of genetic diversity relative to the C. unshiu and C. sinensis populations. With the 481 SNPs, four subsets (192, 96, 48, and 24 SNPs) were generated to evaluate their performance for variety identification. Both 192 and 96 SNP sets distinguished all 144 varieties, while the 48 and 24 SNP sets separated 134 (93.1%) and 110 (76.4%), respectively.<br><br>CONCLUSIONS: The GBS-based SNP discovery led to robust and cost-effective molecular marker sets to assess genetic variation in the cultivated citrus species with narrow genetic bases. The resulting SNP sets are a resource to enhance the phenotype-based DUS testing by developing a DNA barcode system and thus facilitate new variety breeding and protection in citrus.}, }
@article {pmid39905266, year = {2025}, author = {Tan, JH and Fraser, AG}, title = {Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39905266}, issn = {1546-1696}, support = {PJT183712//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; }, abstract = {Here we report a method, smol-seq (small-molecule sequencing), using structure-switching aptamers (SSAs) and DNA sequencing to quantify metabolites. In smol-seq, each SSA detects a single target molecule and releases a unique DNA barcode on target binding. Sequencing the released barcodes can, thus, read out metabolite levels. We show that SSAs are highly specific and can be multiplexed to detect multiple targets in parallel, bringing the power of DNA sequencing to metabolomics.}, }
@article {pmid39905157, year = {2025}, author = {Yong, Q and Li, M and Li, Z and Luo, C and Zhang, J and Bai, X}, title = {Complete chloroplast genomes of 13 species of the Impatiens genus for genomic features and phylogenetic relationships studies.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4258}, pmid = {39905157}, issn = {2045-2322}, support = {(2022-36)//Guizhou University Talent Introduction Research Project: Systematic Evolution and Genetic Diversity of Wild Impatiens in Guizhou/ ; [2023]25//Guizhou University Cultivation Project: Molecular Mechanism of Phylogenetic Development of Wild Impatiens in Karst Regions/ ; No.32201282//National Natural Science Foundation of China: Leaf photophobic drooping is a unique mechanism to avoid photooxidation against sunflecks in karst-dwelling Impatiens hainanensis/ ; No. 322QN249//National Natural Science Foundation of Hainan: Physiological and ecological mechanisms adapt to different water conditions in karst-dwelling of Impatiens hainanensis/ ; Qiankehe Foundation-ZK [2023] General 102//Guizhou Provincial Science and Technology Projects: Taxonomic studies of wild Impatiens L. in Guizhou Province/ ; Qiankehefuqi [2024.013]//the Special fund for innovation capacity construction of Guizhou research institution/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; *Impatiens/genetics/classification ; Microsatellite Repeats ; China ; Genomics/methods ; Codon Usage ; }, abstract = {Impatiens spp. are well-known ornamental and medicinal plants that are widely distributed in the highlands and mountains of southwestern China. This area is one of the hotspots for the distribution of Impatiens species, with typical karst landforms and abundant wild resources. Many of these species are endemic to a narrow distribution area, but their classification and relationships are relatively unclear because of insufficient field investigations, diverse morphological characteristics and lack of molecular information. In this study, chloroplast genome analysis of 13 species (including 2 synonyms) in karst habitats was conducted to study their characteristics and phylogenetic relationships. The results revealed that these chloroplast genomes all had double-stranded tetrad structures ranging in length from 151,284 bp to 152,421 bp, including a total of 113 genes, including 80 protein-coding genes, 29 transfer RNAs, and 4 ribosomal RNAs. SSRs mainly consist of A/T repeats and AT/AT repeats, while INEs mainly consist of positive repeats and palindromic repeats. The frequency of codon usage was essentially the same, with a total of 31 high-frequency codons detected, the vast majority ending in A/U. Five mutation hotspots were detected: rps16-trnQ-UUG, ndhF, ccsA-ndhD, ycf1, and trnN-GUU, among which ycf1 had the highest Pi value and the greatest potential as a DNA barcode marker. Our phylogenetic tree shows that all 13 species belong to Section Impatiens. And supported the classification of I. reptans and I. rhombifolia should as synonyms (BS = 100/PP = 1.00). This study comprehensively analyzed the cp genomes of different taxa, sheds light on the taxonomic intricacies of Impatiens species, provide valuable information into its phylogenetic and taxonomy.}, }
@article {pmid39903394, year = {2025}, author = {Rodrigues, P and Teixeira, C and Guimarães, L and Ferreira, NGC}, title = {Barcoding the Caatinga biome bees: a practical review.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {196}, pmid = {39903394}, issn = {1573-4978}, mesh = {Bees/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; Brazil ; Ecosystem ; Pollination/genetics ; Phylogeny ; }, abstract = {Bees play a critical role as pollinators in ecosystem services, contributing significantly to the sexual reproduction and diversity of plants. The Caatinga biome in Brazil, home to around 200 bee species, provides an ideal habitat for these species due to its unique climate conditions. However, this biome faces threats from anthropogenic processes, making it urgent to characterise the local bee populations efficiently. Traditional taxonomic surveys for bee identification are complex due to the lack of suitable keys and expertise required. As a result, molecular barcoding has emerged as a valuable tool, using genome regions to compare and identify bee species. However, little is known about Caatinga bees to develop these molecular tools further. This study addresses this gap, providing an updated list of 262 Caatinga bee species across 86 genera and identifying ~ 40 primer sets to aid in barcoding these species. The findings highlight the ongoing work needed to fully characterise the Caatinga biome's bee distribution and species or subspecies to support more effective monitoring and conservation efforts.}, }
@article {pmid39903046, year = {2025}, author = {Pinder, MIM and Andersson, B and Blossom, H and Svensson, M and Rengefors, K and Töpel, M}, title = {Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes.}, journal = {Molecular ecology resources}, volume = {25}, number = {4}, pages = {e14067}, pmid = {39903046}, issn = {1755-0998}, support = {2016-00594//Svenska Forskningsr&#xe5;det Formas/ ; 2017-00466//Svenska Forskningsr&#xe5;det Formas/ ; 2018-04555//Vetenskapsr&#xe5;det/ ; FO2018-0042//Stiftelsen Oscar och Lili Lamms Minne/ ; }, mesh = {*Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Diatoms/genetics/classification ; *Chlamydomonas reinhardtii/genetics/classification ; Polymorphism, Single Nucleotide ; }, abstract = {Evolutionary changes in populations of microbes, such as microalgae, cannot be traced using conventional metabarcoding loci as they lack intraspecific resolution. Consequently, selection and competition processes among strains of the same species cannot be resolved without elaborate isolation, culturing, and genotyping efforts. Bamboozle, a new bioinformatic tool introduced here, scans the entire genome of a species and identifies allele-rich barcodes that enable direct identification of different genetic strains from a population using amplicon sequencing of a single DNA sample. We demonstrate its usefulness by identifying hypervariable barcoding loci (< 500 bp) from genomic data in two microalgal species, the diploid diatom Skeletonema marinoi and the haploid chlorophyte Chlamydomonas reinhardtii. Across the two genomes, four and twenty-two loci, respectively, were identified that could in silico resolve all analysed genotypes. All of the identified loci are within protein-coding genes with various metabolic functions. Single nucleotide polymorphisms (SNPs) provided the most reliable genetic markers, and among 54 strains of S. marinoi, three 500 bp loci contained, on average, 46 SNPs, 103 strain-specific alleles, and displayed 100% heterozygosity. This high level of heterozygosity was identified as a novel opportunity to improve strain quantification and detect false positive artefacts during denoising of amplicon sequences. Finally, we illustrate how metabarcoding of a single genetic locus can be used to track abundances of S. marinoi strains in an artificial selection experiment. As future genomic datasets become available and DNA sequencing technologies develop, Bamboozle has flexible user settings enabling optimal barcodes to be designed for other species and applications.}, }
@article {pmid39902320, year = {2025}, author = {Maldonado-Carrizales, J and Valdez-Mondragón, A and Jiménez-Jiménez, ML and Ponce-Saavedra, J}, title = {Three new species of the spider genus Naphrys Edwards (Araneae, Salticidae) under morphology and molecular data with notes in the distribution of Naphrys acerba (Peckham &amp; Peckham) from Mexico.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18775}, pmid = {39902320}, issn = {2167-8359}, mesh = {Animals ; *Spiders/classification/genetics/anatomy &amp; histology ; Mexico ; Phylogeny ; Female ; Male ; Bayes Theorem ; }, abstract = {Herein, we describe three new species of the spider genus Naphrys Edwards, 2003 from Mexico: Naphrys echeri sp. nov., Naphrys tecoxquin sp. nov., and Naphrys tuuca sp. nov. An integrative taxonomic approach was applied, utilizing data from morphology, ultra-morphology, the mitochondrial gene COI, and distribution records. Four molecular methods for species delimitation were implemented under the corrected p-distance Neighbor-Joining (NJ) criteria: (1) Assemble Species by Automatic Partitioning (ASAP); (2) general mixed Yule coalescent (GMYC); (3) Bayesian Poisson tree process (bPTP); and (4) multi-rate Poisson tree process (mPTP). Both morphological and molecular data supported the delimitation and recognition of the three new species. The average interspecific genetic distance (p-distance) within the genus Naphrys is 14%, while the intraspecific genetic distances (p-distance) is <2% for most species. We demonstrate that the natural distribution of Naphrys is not restricted to the Nearctic region. Furthermore, the reported localities herein represent the first with precise locations in the country for Naphrys acerba. In addition, a taxonomic identification key is provided for the species in the genus.}, }
@article {pmid39902286, year = {2024}, author = {Gurjão, L and Brito, L and Dias, O and Neto, J and Iñiguez, AM}, title = {Integrating paleoparasitological, paleogenetic, and archaeological data to understand the paleoecological scenario of pre-Columbian archaeological site Gruta do Gentio II, Brazil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1505059}, pmid = {39902286}, issn = {1664-302X}, abstract = {Paleoparasitology and paleogenetics is the study parasites in ancient remains from latrines, mummified individuals, and coprolites, that is fossilized or desiccated feces. Paleoparasitological studies in Brazil began with analyses of coprolites from the Gruta do Gentio II (GGII) archaeological site, the oldest site related to the Una ceramist tradition (12,000 to 410 BP), Brazil. The GGII archaeological site contained numerous human burials, lithics, and cultural artifacts such as basketry, ceremonial ornaments, and unique pottery of the Una tradition. Coprolites of GGII were submitted to paleoparasitological, and paleogenetic analyses for parasite identification and coprolite origin. In addition, the archaeological characterization of the GGII site was integrated into paleo analyses for proposing a paleoecological scenario. Five taxa of parasites, including Ancylostomidae, Echinostoma sp., Spirometra sp., and Trichostrongylus sp., and three different morphotypes of Capillariidae were recognized in multiple coprolites that were distributed heterogeneously in several stratigraphical layers. The origin of coprolites was genetically defined as five species of mammals, humans, felines as Panthera onca and Leopardus pardalis, and marsupials as Didelphis albiventris and Philander opossum. This is the first study in Brazil that identified both, parasites and species of animals in Pleistocene/Holocene producers of coprolites with geographical and temporal information. The integration of paleoparasitology, paleogenetics, and archaeology is essential to propose paleoecological scenarios from the past of Brazil.}, }
@article {pmid39901058, year = {2025}, author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {527-540}, pmid = {39901058}, issn = {2058-5276}, support = {HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; MCB-2025515//National Science Foundation (NSF)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; U54 CA272220/CA/NCI NIH HHS/United States ; DGE-1644869//National Science Foundation (NSF)/ ; R01 DK118044/DK/NIDDK NIH HHS/United States ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Microbial Consortia/genetics ; Metagenome ; Inulin ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.}, }
@article {pmid39896656, year = {2025}, author = {Andrianiaina, AF and Andry, S and Kettenburg, G and Ranaivoson, HC and Lacoste, V and Dussart, P and Heraud, JM and Laverty, TM and Guth, S and Young, KI and Andrianarimisa, A and Brook, CE}, title = {Diversity and seasonality of ectoparasite burden on two species of Madagascar fruit bat, Eidolon dupreanum and Rousettus madagascariensis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39896656}, issn = {2692-8205}, support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Bats are important reservoir hosts for a variety of microparasites, some of which are transmitted by ectoparasite vectors that include mites, fleas, lice, ticks, and bat flies (families Nycteribiidae and Streblidae). All of these ectoparasite taxa are known to parasitize two endemic fruit bats of Madagascar, Eidolon dupreanum and Rousettus madagascariensis. We aimed to describe the diversity of ectoparasite infestation for both bat species through morphological observation and DNA barcoding and elucidate ecological and climatic correlates of seasonal nycteribiid parasitism of these hosts.<br><br>METHODS: Live E. dupreanum and R. madagascariensis fruit bats were captured monthly in northern and central-eastern Madagascar from 2013-2020. Ectoparasites on all captured bats were counted and identified in the field, then collected into ethanol. Field identification of a subset of samples were confirmed via microscopy and DNA barcoding of the cytochrome C oxidase subunit 1 (COI) and 18S genes. The seasonal abundance of nycteribiid bat flies on both host bats was analyzed using generalized additive models, and the role of climate in driving this seasonality was assessed via cross-correlation analysis combined with generalized linear models. Phylogenetic trees were generated to compare COIand 18S sequences of Madagascar nycteribiid and streblid bat flies with available reference sequences from GenBank.<br><br>RESULTS: Ectoparasites corresponding to four broad taxa (mites, ticks, fleas, and bat flies) were recovered from 628 of 873 E. dupreanum and 831 of 862 R. madagascariensis. E. dupreanum were most commonly parasitized by Cyclopodia dubia nycteribiids and R. madagascariensis by Eucampsipoda madagascariensis nycteribiids or Megastrebla wenzeli streblids. We observed significant seasonality in nycteribiid abundance on both bat hosts, which varied by bat sex and was positively correlated with lagged temperature, precipitation, and humidity variables. Barcoding sequences recovered for all three bat fly species grouped with previously reported sequences, confirming morphological species identification. Our study contributes the first DNA barcodes of any kind reported for M. wenzeli and the first 18S barcodes for C. dubia.<br><br>CONCLUSION: This study explores the diversity and abundance of ectoparasite burdens in two Malagasy fruit bat species, highlighting the importance of seasonal ecology and the influence of climate variables on parasitism, which correlates with resource availability.}, }
@article {pmid39896473, year = {2025}, author = {Gardner, AL and Zheng, L and Howland, K and Saunders, A and Ramirez, A and Parker, P and Iloegbunam, C and Morgan, D and Jost, TA and Brock, A}, title = {Mapping cell-cell fusion at single-cell resolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39896473}, issn = {2692-8205}, support = {F31 CA268833/CA/NCI NIH HHS/United States ; R01 CA226258/CA/NCI NIH HHS/United States ; R01 CA255536/CA/NCI NIH HHS/United States ; U01 CA253540/CA/NCI NIH HHS/United States ; }, abstract = {Cell-cell fusion is a tightly controlled process in the human body known to be involved in fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first in a whole-genome doubled state, which may be followed by the generation of aneuploidies; these genomic alterations are known drivers of tumor evolution. The role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events. To meet this need, we developed a molecular toolkit to map the origins and outcomes of individual cell fusion events within a tumor cell population. This platform, ClonMapper Duo ('CMDuo'), identifies cells that have undergone cell-cell fusion through a combination of reporter expression and engineered fluorescence-associated index sequences paired to randomly generated nucleotide barcodes. scRNA-seq of the indexed barcodes enables the mapping of each set of parental cells and fusion progeny throughout the cell population. In triple-negative breast cancer cells CMDuo uncovered subclonal transcriptomic hybridization and unveiled distinct cell-states which arise in direct consequence of homotypic cell-cell fusion. CMDuo is a platform that enables mapping of cell-cell fusion events in high-throughput single cell data and enables the study of cell fusion in disease progression and therapeutic response.}, }
@article {pmid39896240, year = {2025}, author = {Queirós, J and Silva, R and Pinho, CJ and Vale-Gonçalves, HM and Pita, R and Alves, PC and Beja, P and Paupério, J and Porto, M}, title = {The InBIO Barcoding Initiative Database: contribution to the knowledge of DNA barcodes of the vascular plants of north-eastern Portugal.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e142020}, pmid = {39896240}, issn = {1314-2828}, abstract = {BACKGROUND: Metabarcoding is invaluable for understanding trophic interactions, enabling high-resolution and rapid dietary assessments. However, it requires a robust DNA barcode reference library for accurate taxa identification. This dataset has been generated in the framework of the InBIO Barcoding Initiative (IBI) and Agrivole project. The integration of these two projects was crucial, as Agrivole aimed to investigate the trophic niche of small mammals in Trás-os-Montes Region through DNA metabarcoding, which required a reliable plant DNA barcode library for this same region. Given the large number of species not yet represented in international databases, a survey of local plants was essential to fill this gap. Thus, this study created an accurate DNA reference database for the plants of the Trás-os-Montes Region of Portugal.<br><br>NEW INFORMATION: The current DNA reference database contains 632 vascular plant samples, all morphologically identified and belonging to 435 species. This represents 14% and 38.7% of the total known plant species for Portugal and the study area, respectively.Of the 1781 barcode sequences provided in this dataset, 1099 contain new information (61.7%) at different levels: 254 (13.6%, ITS2: 41, trnL-ef: 126, trnL-gh: 87) are completely new to GenBank and/or BOLD databases at the time of publication, 438 (24.6%, ITS2: 59, trnL-ef: 173, trnL-gh: 206) are new records for a given species and 407 (22.9%, ITS2: 187, trnL-ef: 206, trnL-gh: 14) provide additional information (e.g. different bp length, intraspecific genetic variability); the remaining 682 sequences (38.3%) are equal (100% identity) to sequences already publicly available for the identified species. Overall, this dataset represents a significant contribution to the genetic knowledge of vascular plants represented in public libraries. This is one of the public releases of the IBI database, which provides genetic and distributional data for several taxa.All vouchers are deposited in the Herbarium of the Museum of Natural History and Science of the University of Porto (MHNC-UP) and their DNA barcodes are publicly available in the Barcode of Life Data System (BOLD), NCBI GenBank online databases and International Nucleotide Sequence Database Collaboration (INSDC).}, }
@article {pmid39895457, year = {2025}, author = {Naranjo-Orrico, D and Ovaskainen, O and Furneaux, B and Purhonen, J and Arancibia, PA and Burg, S and Moser, N and Niku, J and Tikhonov, G and Zakharov, E and Monkhouse, N and Abrego, N}, title = {Wind Is a Primary Driver of Fungal Dispersal Across a Mainland-Island System.}, journal = {Molecular ecology}, volume = {34}, number = {5}, pages = {e17675}, doi = {10.1111/mec.17675}, pmid = {39895457}, issn = {1365-294X}, support = {856506//H2020 European Research Council/ ; 336212//Research Council of Finland/ ; 342374//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 346492//Research Council of Finland/ ; //Department of Biological and Environmental Sciences, University of Jyv&#xe4;skyl&#xe4;/ ; }, mesh = {*Wind ; Finland ; *Fungi/genetics/classification ; Phylogeny ; Islands ; Spores, Fungal ; DNA Barcoding, Taxonomic ; Lakes/microbiology ; Biodiversity ; Ecosystem ; DNA, Fungal/genetics ; }, abstract = {Dispersal is one of the main processes shaping ecological communities. Yet, for species-rich communities in natural systems, the role of dispersal in community assembly remains relatively less studied compared to other processes. This is the case for fungal communities, for which predictable knowledge about where and how the dispersal propagules move across space is largely lacking. We sampled fungal communities at their dispersal stage in a lake mainland-island system in Finland, using a regular grid of 18 × 18 km, including sites on the mainland, islands and over the water. Fungal communities were screened by applying DNA barcoding to air samples. To assess the factors determining fungal dispersal, we modelled aerial fungal communities with a joint species distribution model, including spore traits, weather-related predictors, and spatial predictors. We found that the probability of occurrence of most species (and consequently species richness measured as the number of OTUs per sample) was lower in low-connectivity sites (water and isolated islands) compared to high-connectivity sites (mainland). There was a strong phylogenetic signal in how the fungal species responded to connectivity, indicating that some taxonomic groups are more dispersal limited than others, although such responses were not structured by their trophic guilds. Furthermore, wind speed influenced how species with different spore sizes responded to connectivity: in low-connectivity sites, species with large sexual spores were detected especially when wind was high, whereas, in high-connectivity sites, they were detected especially when wind was low. This study demonstrates that air fungal dispersal might be more predictable than previously considered and contributes to the mechanistic understanding of fungal air dispersal.}, }
@article {pmid39893778, year = {2025}, author = {Shang, Y and Liu, S and Liang, C and Tuliebieke, T and Chen, S and Du, K and Tian, X and Li, J and He, J and Jin, H and Chang, Y}, title = {A strategy integrated DNA barcoding with metabolomics for screening distinguishable combinatorial chemical quality marker between Pheretima aspergillum and Pheretima vulgaris Chen.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {257}, number = {}, pages = {116716}, doi = {10.1016/j.jpba.2025.116716}, pmid = {39893778}, issn = {1873-264X}, mesh = {*Metabolomics/methods ; *DNA Barcoding, Taxonomic/methods ; Quality Control ; Animals ; Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/chemistry/standards ; Biomarkers ; Species Specificity ; }, abstract = {Pheretima is an animal-derived traditional Chinese medicines (TCMs). The chemical quality markers of Pheretima used to distinguish different species are still ambiguous. Under this premise, a strategy integrated DNA barcoding with metabolomics is promoted for identifying Pheretima and screening distinguishable combinatorial chemical quality marker (DCQ-marker) between Pheretima aspergillum (P. aspergillum) and Pheretima vulgaris Chen (P. vulgaris). As a result, adenosine, adenine, L-phenylalanine and uridine are successfully selected as DCQ-markers between P. aspergillum and P. vulgaris. This study provides convenient strategy for quickly screening DCQ-marker between P. aspergillum and P. vulgaris. It will be meaningful for further promoting quality control on Pheretima and providing a reference for the quality evaluation of other animal-derived TCMs.}, }
@article {pmid39890856, year = {2025}, author = {Parihar, TJ and Naik, M and Mehraj, S and Inam Ul Haq, S and Perveen, M and Malla, IA and Abid, T and Gul, N and Masoodi, KZ}, title = {Emergence of Fusarium incarnatum and Fusarium avenaceum in wilt affected solanaceous crops of the Northern Himalayas.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3855}, pmid = {39890856}, issn = {2045-2322}, support = {PURSE Grant- SR/PURSE/2022/124//Department of Science and Technology, Ministry of Science and Technology, India/ ; CRG/2022/000207//Anusandhan national research foundation/ ; }, mesh = {*Fusarium/genetics/pathogenicity/classification/isolation &amp; purification ; *Plant Diseases/microbiology ; India ; Phylogeny ; *Crops, Agricultural/microbiology ; Solanum lycopersicum/microbiology ; Himalayas ; }, abstract = {The objective of this study was to identify and characterize the fungal pathogens responsible for wilt diseases in solanaceous crops, specifically tomato, brinjal, and chili, in the Kashmir valley. Through both morphological and molecular analyses, including DNA barcoding of the ITS, TEF, RPB1, and RPB2 genomic regions, Fusarium incarnatum and Fusarium avenaceum were identified as the primary causal agents of wilt in tomato and brinjal, and chili, respectively. Pathogenicity tests confirmed the virulence of these pathogens, with typical wilt symptoms observed upon inoculation. This represents the first report of F. incarnatum and F. avenaceum as wilt pathogens in solanaceous crops in India. Phylogenetic analysis further confirmed the genetic variability of these pathogens, revealing their expanding host range. The findings underscore the growing adaptability of these Fusarium species to diverse agricultural systems and highlight the urgent need for targeted disease management strategies to mitigate the significant yield losses caused by Fusarium wilt in solanaceous vegetable production.}, }
@article {pmid39887239, year = {2025}, author = {Chen, P-R and Wei, Y and Li, X and Yu, H-Y and Wang, S-G and Yuan, X-Z and Xia, P-F}, title = {Precision engineering of the probiotic Escherichia coli Nissle 1917 with prime editing.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {2}, pages = {e0003125}, pmid = {39887239}, issn = {1098-5336}, support = {22278246//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022HWYQ-017//Department of Science and Technology of Shandong Province/ ; ZR2021ME066//Natural Science Foundation of Shandong Province/ ; Qilu Young Scholar Program//Shandong University (SDU)/ ; NO. tstp20230604//Taishan Scholar Project of Shandong Province/ ; U20A20146, 22378233//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Escherichia coli/genetics ; *Probiotics ; *Gene Editing/methods ; *CRISPR-Cas Systems ; }, abstract = {CRISPR-Cas systems are transforming precision medicine with engineered probiotics as next-generation diagnostics and therapeutics. To promote human health and treat disease, engineering probiotic bacteria demands maximal versatility to enable non-natural functionalities while minimizing undesired genomic interferences. Here, we present a streamlined prime editing approach tailored for probiotic Escherichia coli Nissle 1917 utilizing only essential genetic modules, including Cas9 nickase from Streptococcus pyogenes, a codon-optimized reverse transcriptase, and a prime editing guide RNA, and an optimized workflow with longer induction. As a result, we achieved all types of prime editing in every individual round of experiments with efficiencies of 25.0%, 52.0%, and 66.7% for DNA deletion, insertion, and substitution, respectively. A comprehensive evaluation of off-target effects revealed a significant reduction in unintended mutations, particularly in comparison to two different base editing methods. Leveraging the prime editing system, we inserted a unique DNA sequence to barcode the edited strain and established an antibiotic-resistance-gene-free platform to enable non-natural functionalities. Our prime editing strategy presents a CRISPR-Cas system that can be readily implemented in any laboratories with the basic CRISPR setups, paving the way for future innovations in engineered probiotics.IMPORTANCEOne ultimate goal of gene editing is to introduce designed DNA variations at specific loci in living organisms with minimal unintended interferences in the genome. Achieving this goal is especially critical for creating engineered probiotics as living diagnostics and therapeutics to promote human health and treat diseases. In this endeavor, we report a customized prime editing system for precision engineering of probiotic Escherichia coli Nissle 1917. With such a system, we developed a barcoding system for tracking engineered strains, and we built an antibiotic-resistance-gene-free platform to enable non-natural functionalities. We provide not only a powerful gene editing approach for probiotic bacteria but also new insights into the advancement of innovative CRISPR-Cas systems.}, }
@article {pmid39887112, year = {2025}, author = {Maduenyane, M and Dos Santos, QM and Avenant-Oldewage, A}, title = {Multifaceted taxonomy of two Dactylogyrus species on Enteromius paludinosus: Integrating light microscopy, scanning electron microscopy and molecular approaches.}, journal = {Parasite (Paris, France)}, volume = {32}, number = {}, pages = {5}, pmid = {39887112}, issn = {1776-1042}, support = {Doctoral grant//National Research Foundation, South Africa/ ; Post doctoral fellowship//Ernest Oppenheimer Memorial Trust/ ; SRUG22052013241//National Research Foundation, South Africa/ ; University Research Committee and Faculty Research Committee//University of Johannesburg/ ; }, mesh = {Animals ; Microscopy, Electron, Scanning/veterinary ; Phylogeny ; *Fish Diseases/parasitology ; South Africa ; DNA, Helminth/genetics/chemistry/isolation &amp; purification ; *Trematode Infections/veterinary/parasitology/epidemiology ; DNA, Mitochondrial/genetics/chemistry ; *Cyprinidae/parasitology ; Microscopy ; *Trematoda/classification/genetics/ultrastructure/isolation &amp; purification ; Rivers ; }, abstract = {Dactylogyrus Diesing, 1850 is the most speciose genus of platyhelminths with more than 900 species, and over a hundred species recorded from Africa. Of the latter, six are from the straightfin barb, Enteromius paludinosus (Peters). Dactylogyrus teresae Mashego, 1983 and Dactylogyrus dominici Mashego, 1983 were collected from E. paludinosus in the Vaal River system, Gauteng, South Africa and their taxonomic data revised using standard protocols and modern approaches, alongside the type material. Whole worms were mounted on glass slides with glycerine ammonium picrate (GAP) and studied using light microscopy (LM). For scanning electron microscopy (SEM), whole worms were placed on concavity slides and the soft tissue digested to release the sclerotised copulatory organs and haptoral sclerites. A combination of these approaches (LM and SEM) was employed for the first time to study the sclerotised structures of GAP-mounted material. Soft tissues of SEM analysed specimens were genetically characterised using CO1 mtDNA, 18S-ITS1-5.8S rDNA and partial 28S rDNA fragments. Phylogenetic topologies were constructed using Bayesian inference. Results confirmed the morphologic and genetic distinctness of D. dominici and D. teresae, highlighting the importance of studying the varying orientations of specifically the vagina and transverse bar. This study presents a new locality record, the first SEM study of isolated sclerotised structures, as well as the first molecular data for the Dactylogyrus afrobarbae-like species. The multifaceted approaches applied to the same specimen in this study enabled improved resolution of individual specimens, showing promise for studies where limited specimens are available.}, }
@article {pmid39885425, year = {2025}, author = {Yu, W and Li, XJ and Lv, Z and Yang, LE and Peng, DL}, title = {The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {93}, pmid = {39885425}, issn = {1471-2164}, support = {GZY24006//the Project for Fundamental Research of Guangxi Institute of Botany/ ; 31900185, 32360057//National Natural Science Foundation of China/ ; 202001AU070092//Natural Science Foundation of Yunnan Province/ ; }, mesh = {*Genome, Chloroplast ; Phylogeny ; Microsatellite Repeats ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Pseudogalium is a new monotypic genus with two subspecies in China and one in Japan, which holds a distinctive phylogenetic position and ecological significance within the tribe Rubieae. Chloroplast genomes contain abundant information for resolving phylogenetic relationships. To investigate the phylogenetics of P. paradoxum and its related genera, we first sequenced, assembled, and annotated the chloroplast genome of two subspecies of P. paradoxum in China and reconstructed the phylogenetic trees. Due to the lack of samples of P. paradoxum subsp. franchetianum from Japan, this study only analyzed and discussed P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei.<br><br>RESULTS: This study had shown that the complete chloroplast genomes of Pseudogalium ranged from 153,093&#xa0;bp to 153,333&#xa0;bp in length with 130 genes in total, all of which had typical circular structures consisting of a large single-copy region, a small single-copy region and a pair of inverted repeat regions. The comparative analysis showed that the chloroplast genome of P. paradoxum was conserved in the inverted repeat regions. Additionally, we identified 60 dispersed repeat sequences, 61-63 simple sequence repeats, and 30 codons within the 82 protein-coding genes that exhibited RSCU values greater than one. Furthermore, we detected highly divergent regions that hold potential as new DNA barcodes for species identification. Compared with Pseudogalium, the gene number, gene length, and GC content in the chloroplast genomes of Galium and Rubia exhibited differential characteristics, and the dispersed repeat sequences and SSRs in Galium and Rubia were significantly different. Phylogenetic analysis based on the whole chloroplast genomes showed that Pseudogalium can be treated as a new genus, with P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei considered as two distinct subspecies of P. paradoxum.<br><br>CONCLUSIONS: The complete chloroplast genomes of P. paradoxum were first reported in this study, which provided a new insight into phylogeny and taxonomy of this genus. Phylogenetic analyses strongly supported the following proposals: (1) P. paradoxum can be isolated as a genus closely related to Galium; (2) P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei form distinct clades, both of which can be considered as subspecies of P. paradoxum.}, }
@article {pmid39884748, year = {2025}, author = {Munro, R and Payne, A and Holmes, N and Moore, C and Cahyani, I and Loose, M}, title = {Enhancing nanopore adaptive sampling for PromethION using readfish at scale.}, journal = {Genome research}, volume = {35}, number = {4}, pages = {877-885}, pmid = {39884748}, issn = {1549-5469}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Nanopore Sequencing/methods ; *Nanopores ; Genome, Human ; DNA Copy Number Variations ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {A unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling all features for the industrial scale PromethION sequencer, including standard and "barcode-aware" adaptive sampling. We demonstrate effective coverage enrichment and assessment of multiple human genomes for copy number and structural variation on a single PromethION flow cell.}, }
@article {pmid39883237, year = {2025}, author = {González, MA and Barceló, C and Rodríguez-López, A and Figuerola, J and Miranda, M&#xc1;}, title = {Human-biting behaviour of Leptoconops irritans (Diptera: Ceratopogonidae) in a touristic area of the Balearic Islands (Spain).}, journal = {Parasitology research}, volume = {124}, number = {2}, pages = {15}, pmid = {39883237}, issn = {1432-1955}, support = {HR22-00123//Fundaci&#xf3;n "La Caixa" through the project ARBOPREVENT/ ; }, mesh = {Animals ; Spain ; Humans ; *Ceratopogonidae/physiology/anatomy &amp; histology/classification/genetics ; *Insect Bites and Stings/epidemiology ; Male ; Female ; DNA Barcoding, Taxonomic ; Adult ; *Feeding Behavior ; Ecosystem ; Tourism ; }, abstract = {Biting midges of genus Leptoconops Skuse 1889 are small blood-feeding insects recognized as highly irritating diurnal pests in certain regions around the globe. In Europe, their presence is poorly documented, except in France and Italy. Following reports of human discomfort in a tourist area of Menorca, Balearic Islands (Spain), a small-scale study was conducted to identify the biting species and assess their preferred biting sites using a human-landing assay along a habitat gradient in a coastal dune area. Leptoconops irritans (Noé, 1905) was identified based on morphological features and DNA barcoding. This species reached high densities (average rates of 3.3 landings/min), particularly near coastal dune vegetation. No statistically significant differences were found among the four main body sites for landings of L. irritans (F3,6.023 = 1.80, p = 0.250): head (n = 91, 53.8%), lower extremities (n = 39, 23.1%), upper extremities (n = 37, 21.9%), and other covered areas (n = 2, 1.2%). Landing preferences varied among the three volunteers, and bites progressed differently. This study represents the second documented case of Leptoconops midges causing human discomfort in Spain. We hope this research will stimulate further interest in this understudied genus, which has been largely overlooked across much of Europe.}, }
@article {pmid39881664, year = {2025}, author = {Nečas, T and Badjedjea, G and Czurda, J and Gvoždík, V}, title = {An eastern Congolian endemic, or widespread but secretive? New data on the recently described Afrixaluslacustris (Anura, Hyperoliidae) from the Democratic Republic of the Congo.}, journal = {ZooKeys}, volume = {1224}, number = {}, pages = {55-68}, pmid = {39881664}, issn = {1313-2989}, abstract = {The Great Lakes spiny reed frog (Afrixaluslacustris) was recently described from transitional (submontane) forests at mid-elevations of the Albertine Rift mountains in the eastern Congolian region. Previously, because of its similarity, it had been understood to represent eastern populations of the unrelated A.laevis, which is known mainly from Cameroon. Based on DNA barcoding, we document the westward extension of the known range of A.lacustris within lowland rainforests in the Northeastern and Central Congolian Lowland Forests. One sample was represented by a larva found in a clutch in a folded leaf, a typical oviposition type for most Afrixalus species, contrary to oviposition on an unfolded leaf surface in the similar A.laevis and closely related A.dorsimaculatus and A.uluguruensis. Comparison of the advertisement call of A.lacustris from Salonga National Park, Democratic Republic of the Congo, indicates similarity to its sister species from montane areas of the Albertine Rift, the ghost spiny reed frog (A.phantasma). Phylogeographic analysis suggests that A.phantasma and A.lacustris speciated allopatrically during the Early Pleistocene, with the former having refugia in montane forests and the latter in transitional and also lowland forests. The lowland populations of A.lacustris represent distinct evolutionary lineages, which diversified probably in isolated forest refugia during the Middle Pleistocene.}, }
@article {pmid39881498, year = {2025}, author = {Gião, T and Müller, MI and Yamada, F and Freitas, F and Leite, L and da Silva, RJ and de Azevedo, R and Abdallah, V}, title = {Morphological and molecular phylogeny of Clinostomum sp. (Digenea: Clinostomidae) metacercariae, using DNA barcode from a South American freshwater fish.}, journal = {Journal of helminthology}, volume = {99}, number = {}, pages = {e13}, doi = {10.1017/S0022149X24000993}, pmid = {39881498}, issn = {1475-2697}, support = {3005/2010//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 174814/2023-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Phylogeny ; *Trematoda/genetics/classification/anatomy &amp; histology/isolation &amp; purification ; *Metacercariae/genetics/classification/anatomy &amp; histology/isolation &amp; purification ; DNA Barcoding, Taxonomic ; Fresh Water ; Brazil ; *Fish Diseases/parasitology ; Electron Transport Complex IV/genetics ; *Trematode Infections/parasitology/veterinary ; *Fishes/parasitology ; DNA, Helminth/genetics/chemistry ; Sequence Analysis, DNA ; South America ; }, abstract = {Here, we present a comprehensive morphological and molecular phylogenetic analysis of Clinostomum sp. (Digenea: Clinostomidae) metacercariae parasitizing two freshwater fish species from Southeast Brazil: Serrasalmus spilopleura (piranha) and Callichthys callichthys (tambuatá). The morphological examination revealed distinct characteristics of metacercariae in each host. Using the cytochrome c oxidase I (COI) gene barcode region, we obtained DNA sequences that allowed for accurate phylogenetic placement. Phylogenetic analyses revealed that Clinostomum sp. HM41 (metacercariae), isolated from S. spilopleura, exhibited 86% similarity to Ithyoclinostomum yamagutii, while Clinostomum sp. HM125 (metacercariae), from C. callichthys, showed 98.7% similarity to Clinostomum sp. Cr_Ha1. The phylogenetic trees constructed through Bayesian Inference and Maximum Likelihood methods indicated high biodiversity within the Clinostomum genus and strong support for distinct lineages. These findings enhance our understanding of the diversity and ecological distribution of Clinostomum species in South American freshwater environments.}, }
@article {pmid39880590, year = {2025}, author = {Pryszcz, LP and Diensthuber, G and Llovera, L and Medina, R and Delgado-Tejedor, A and Cozzuto, L and Ponomarenko, J and Novoa, EM}, title = {Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger.}, journal = {Genome research}, volume = {35}, number = {4}, pages = {956-966}, pmid = {39880590}, issn = {1549-5469}, mesh = {*Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; *Software ; Gene Library ; *RNA/genetics ; Humans ; Nanopores ; }, abstract = {Nanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding of multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, are not compatible with newer RNA chemistry flowcells and the latest generation of graphics processing units (GPUs). To overcome these limitations, we introduce SeqTagger, a rapid and robust method that can demultiplex DRS data sets with 99% precision and 95% recall. We demonstrate the applicability of SeqTagger in both RNA002/R9.4 and RNA004/RNA chemistries and show its robust performance both for long and short RNA libraries, including custom libraries that do not contain standard poly(A) tails, such as Nano-tRNAseq libraries. Finally, we demonstrate that increasing the multiplexing up to 96 barcodes yields highly accurate demultiplexing models. SeqTagger can be executed in a standalone manner or through the MasterOfPores NextFlow workflow. The availability of an efficient and simple multiplexing strategy improves the cost-effectiveness of this technology and facilitates the analysis of low-input biological samples.}, }
@article {pmid39877676, year = {2025}, author = {Vargas, HA}, title = {Keiferiaazapaensis sp. nov., the first representative of the New World micromoth genus Keiferia Busck (Lepidoptera, Gelechiidae) associated with a member of Asteraceae.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e141827}, pmid = {39877676}, issn = {1314-2828}, abstract = {BACKGROUND: The New World micromoth genus Keiferia Busck, 1939 (Lepidoptera, Gelechiidae, Gelechiinae, Gnorimoschemini) includes 21 described species, ten of which occur in South America. Like the tomato pinworm, K.lycopersicella (Walsingham, 1897), all the species of Keiferia, whose host plants have been documented, are associated exclusively with members of the family Solanaceae.<br><br>NEW INFORMATION: Keiferiaazapaensis sp. nov. is described and illustrated, based on adults reared from leaf miner larvae collected on the shrub Trixiscacalioides (Kunth) D. Don (Asteraceae) in the Atacama Desert, northern Chile. Despite this unusual host plant, a Maximum Likelihood analysis, based on mitochondrial DNA sequences, placed the new species within a well-supported Keiferia clade. The discovery of the trophic association between K.azapaensis sp. nov. and T.cacalioides represents the first record of a member of Asteraceae as a host plant for the micromoth genus Keiferia.}, }
@article {pmid39877055, year = {2025}, author = {Seid, CA and Hiley, AS and McCowin, MF and Carvajal, JI and Cha, H and Ahyong, ST and Ashford, OS and Breedy, O and Eernisse, DJ and Goffredi, SK and Hendrickx, ME and Kocot, KM and Mah, CL and Miller, AK and Mongiardino Koch, N and Mooi, R and O'Hara, TD and Pleijel, F and Stiller, J and Tilic, E and Valentich-Scott, P and Warén, A and Wicksten, MK and Wilson, NG and Cordes, EE and Levin, LA and Cortés, J and Rouse, GW}, title = {A faunal inventory of methane seeps on the Pacific margin of Costa Rica.}, journal = {ZooKeys}, volume = {1222}, number = {}, pages = {1-250}, pmid = {39877055}, issn = {1313-2989}, abstract = {The methane seeps on the Pacific margin of Costa Rica support extensive animal diversity and offer insights into deep-sea biogeography. During five expeditions between 2009 and 2019, we conducted intensive faunal sampling via 63 submersible dives to 11 localities at depths of 300-3600 m. Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. In total 488 morphospecies were identified, representing the highest number of distinct morphospecies published from a single seep or vent region to date. Of these, 131 are described species, at least 58 are undescribed species, and the remainder include some degree of taxonomic uncertainty, likely representing additional undescribed species. Of the described species, 38 are known only from the Costa Rica seeps and their vicinity. Fifteen range extensions are also reported for species known from Mexico, the Galápagos seamounts, Chile, and the western Pacific; as well as 16 new depth records and three new seep records for species known to occur at vents or organic falls. No single evolutionary narrative explains the patterns of biodiversity at these seeps, as even morphologically indistinguishable species can show different biogeographic affinities, biogeographic ranges, or depth ranges. The value of careful molecular taxonomy and comprehensive specimen-based regional inventories is emphasized for biodiversity research and monitoring.}, }
@article {pmid39873746, year = {2025}, author = {Nammoku, Y and Nikkeshi, A and Terai, Y and Ushimaru, A and Kinoshita, M}, title = {Morphological and DNA analysis of pollen grains on butterfly individuals reveal their flower visitation history.}, journal = {Die Naturwissenschaften}, volume = {112}, number = {1}, pages = {13}, pmid = {39873746}, issn = {1432-1904}, mesh = {Animals ; *Butterflies/physiology/anatomy &amp; histology ; *Pollen/genetics/anatomy &amp; histology ; *Pollination/physiology ; *Flowers/physiology ; DNA, Plant/genetics ; }, abstract = {Many butterfly species are conspicuous flower visitors. However, understanding their flower visitation patterns in natural habitats remains challenging due to the difficulty of tracking individual butterflies. Therefore, we aimed at establishing a protocol to solve the problem using the Common five-ring butterfly, Ypthima argus (Nymphalidae: Satyrinae). Focusing on the pollen grains attached the butterfly's body surface, we examined validities of two pollen analyses based on pollen morphology and DNA markers (ITS1 and ITS2), in addition to the classical route census method. We captured thirty-nine butterflies from mid-April to early July and collected pollen grains from each individual. Morphological and DNA analyses of collected pollens identified eighteen and thirty-four taxa of insect pollinated plants respectively, including woody plants such as Castanopsis. The DNA analysis detected as many as thirteen plant taxa from a single butterfly, indicating its high sensitivity for detecting flower visitation. We detected more plant taxa in May when many individuals were flying. This is assumingly related to the post emergence days of the butterflies with more foraging experience. We also found that fluctuations of pollen grain numbers of Leucanthemum vulgare and Erigeron philadelphicus on individual butterflies depend on their flowering periods overlapping partly. Consequently, we conclude that pollen morphology and DNA barcoding analysis, and field observations are mutually complementary techniques, providing an integrated pollen analysis method to study the pollination ecology of butterflies.}, }
@article {pmid39872901, year = {2025}, author = {Thurman, CL and McNamara, JC and Shih, HT and Capparelli, MV}, title = {Fiddler Crabs (Crustacea: Decapoda: Ocypodidae) From Coastal Ecuador and the Galápagos Islands: Species Descriptions and DNA Barcodes.}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70646}, pmid = {39872901}, issn = {2045-7758}, abstract = {Neotropical regions near the equator are recognized as speciation "hot spots" reflecting their abundant biodiversity. In western South America, the coasts of Panama, Colombia, Ecuador, the Galápagos Archipelago, and northern Peru form the Tropical Eastern Pacific biome. This area has the greatest heterogeneity of sympatric fiddler crab species of any portion of the planet. Since the coastal fauna has not been assessed for almost 50 years, we studied fiddler crab species diversity in Ecuador and on the Galápagos Archipelago. Preserved collecting records for various species were examined at the U.S. National Museum of Natural History, Washington, DC, the American Museum of Natural History, New York, and the Naturalis Biodiversity Center, Leiden, the Netherlands. During a field study, 51 locations were collected resulting in over 870 preserved specimens (120 lots) along the 2237-km (1390 mi) coast of Ecuador and on three Galápagos Islands. A neighbor-joining tree was constructed using the Kimura 2-parameter model with a partial DNA sequence of the cytochrome oxidase-subunit 1 gene (COI) for a barcoding study. Twenty-five taxa were collected during the surveys, while two more were noted from the literature and museum collections. Five published species are new to Ecuador. The species assemblage was divided among four genera: Uca, Leptuca, Minuca, and Petruca. Morphological definitions and photographic images are given for 27 species. COI sequences were obtained for 27 operational taxonomic units from Ecuador, with three morphologically indistinguishable cryptic or pseudocryptic taxa also revealed. Based on species distributions, it appears that the area between Cabo San Lorenzo and Punta Santa Elena serves as a weak barrier separating some "northern" from "southern" taxa. Since coastal Ecuador is undergoing rapid economic development, the construction of maricultural facilities and the deforestation of mangroves promote wholesale habitat destruction. As habitat diversity is reduced, it is expected that there will be, in general, a local decline in fiddler crab species diversity with some taxa becoming rare or extinct.}, }
@article {pmid39872206, year = {2024}, author = {Dhyani, A and Kasana, S and Uniyal, PL}, title = {From barcodes to genomes: a new era of molecular exploration in bryophyte research.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1500607}, pmid = {39872206}, issn = {1664-462X}, abstract = {Bryophytes represent a diverse and species-rich group of plants, characterized by a remarkable array of morphological variations. Due to their significant ecological and economic roles worldwide, accurate identification of bryophyte taxa is crucial. However, the variability in morphological traits often complicates their proper identification and subsequent commercial utilization. DNA barcoding has emerged as a valuable tool for the precise identification of bryophyte taxa, facilitating comparisons at both interspecific and intraspecific levels. Recent research involving plastomes, mitogenomes, and transcriptomes of various bryophyte species has provided insights into molecular changes and gene expression in response to environmental stressors. Advances in molecular phylogenetics have shed light on the origin and evolutionary history of bryophytes, thereby clarifying their phylogenetic relationships. Despite these advancements, a comprehensive understanding of the systematic relationships within bryophytes is still lacking. This review synthesizes current molecular studies that have been instrumental in unraveling the complexity of bryophyte taxonomy and systematics. By highlighting key findings from recent genetic and genomic research, we underscore the importance of integrating molecular data with traditional morphological approaches. Such integration is essential for refining the classification systems of bryophytes and for understanding their adaptive strategies in various ecological niches. Future research should focus on expanding the molecular datasets across underrepresented bryophyte lineages and exploring the functional significance of genetic variations under different environmental conditions. This will not only enhance our knowledge of bryophyte evolution, but also inform conservation strategies and potential applications in biotechnology.}, }
@article {pmid39870862, year = {2025}, author = {Ramezani, M and Weisbart, E and Bauman, J and Singh, A and Yong, J and Lozada, M and Way, GP and Kavari, SL and Diaz, C and Leardini, E and Jetley, G and Pagnotta, J and Haghighi, M and Batista, TM and Pérez-Schindler, J and Claussnitzer, M and Singh, S and Cimini, BA and Blainey, PC and Carpenter, AE and Jan, CH and Neal, JT}, title = {A genome-wide atlas of human cell morphology.}, journal = {Nature methods}, volume = {22}, number = {3}, pages = {621-633}, pmid = {39870862}, issn = {1548-7105}, support = {DP2 GM146252/GM/NIGMS NIH HHS/United States ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 1DP2GM146252//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Humans ; *Genome, Human ; CRISPR-Cas Systems ; Phenotype ; *Genomics/methods ; Membrane Proteins/genetics ; Genome-Wide Association Study/methods ; }, abstract = {A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-wide genotype-phenotype maps comprising CRISPR-Cas9-based knockouts of >20,000 genes in >30 million cells. Our optical pooled cell profiling platform (PERISCOPE) combines a destainable high-dimensional phenotyping panel (based on Cell Painting) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This perturbation atlas comprises high-dimensional phenotypic profiles of individual cells with sufficient resolution to cluster thousands of human genes, reconstruct known pathways and protein-protein interaction networks, interrogate subcellular processes and identify culture media-specific responses. Using this atlas, we identify the poorly characterized disease-associated TMEM251/LYSET as a Golgi-resident transmembrane protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes. In sum, this perturbation atlas and screening platform represents a rich and accessible resource for connecting genes to cellular functions at scale.}, }
@article {pmid39870610, year = {2025}, author = {Schlüter, HM and Uhler, C}, title = {Integrating representation learning, permutation, and optimization to detect lineage-related gene expression patterns.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1062}, pmid = {39870610}, issn = {2041-1723}, support = {DP2 AT012345/AT/NCCIH NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; N00014-22-1-2116//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; 1DP2AT012345//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; }, mesh = {Animals ; Mice ; Caenorhabditis elegans/genetics/embryology ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Lung Neoplasms/genetics/pathology ; *Gene Expression Profiling/methods ; Embryonic Development/genetics ; Sequence Analysis, RNA ; RNA-Seq ; Humans ; }, abstract = {Recent barcoding technologies allow reconstructing lineage trees while capturing paired single-cell RNA-sequencing (scRNA-seq) data. Such datasets provide opportunities to compare gene expression memory maintenance through lineage branching and pinpoint critical genes in these processes. Here we develop Permutation, Optimization, and Representation learning based single Cell gene Expression and Lineage ANalysis (PORCELAN) to identify lineage-informative genes or subtrees where lineage and expression are tightly coupled. We validate our method using synthetic data and apply it to recent paired lineage and scRNA-seq data of lung cancer in a mouse model and embryogenesis of mouse and C. elegans. Our method pinpoints subtrees giving rise to metastases or new cell states, and genes identified as most informative about lineage overlap with known pathways involved in lung cancer progression. Furthermore, our method highlights differences in how gene expression memory is maintained through divisions in cancer and embryogenesis, thereby providing a tool for studying cell state memory through divisions across biological systems.}, }
@article {pmid39869770, year = {2025}, author = {Katalinić, J and Richards, M and Auyang, A and Millett, JH and Kogenaru, M and Windbichler, N}, title = {Do the Shuffle: Expanding the Synthetic Biology Toolkit for Shufflon-like Recombination Systems.}, journal = {ACS synthetic biology}, volume = {14}, number = {2}, pages = {363-372}, pmid = {39869770}, issn = {2161-5063}, mesh = {*Synthetic Biology/methods ; Escherichia coli/genetics/metabolism ; Plasmids/genetics ; *Recombination, Genetic/genetics ; }, abstract = {Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation in prokaryotes. Shufflon invertase (SI) Rci from plasmid R64, recognizing asymmetric sfx sites, has been adopted as a tool for synthetic biology. However, the availability of a single enzyme with moderate rates of recombination has hampered the more widespread use of SIs. We identified 14 previously untested SI genes and their sfx sites in public databases. We established an assay based on single-molecule sequencing that allows the quantification of the inversion rates of these enzymes and determined cross-recognition to identify orthogonal SI/sfx pairs. We describe SI enzymes with substantially improved shuffling rates when expressed in an inducible manner in E. coli. Our findings will facilitate the use of SIs in engineering biology where synthetic shufflons enable the generation of millions of sequence variants in vivo for applications such as barcoding or experimental selection.}, }
@article {pmid39869133, year = {2025}, author = {An, K and Yin, G and Wang, X and Shi, Y and Zhang, X and He, G and Amu, L and Chen, W and Wang, B and Hu, X and Wang, X and Wei, S}, title = {Intraspecific identification and genetic diversity analysis of Paeonia lactiflora based on chloroplast genes rpoB and psbK-psbI.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {165}, pmid = {39869133}, issn = {1573-4978}, support = {2020110031009381//molecular anti-counterfeiting technology of 2 precision medicinal materials of Atractylodes chinensis and P. lactiflora/ ; }, mesh = {*Paeonia/genetics/classification ; Genetic Variation/genetics ; Phylogeny ; China ; *Genes, Chloroplast/genetics ; Haplotypes/genetics ; Chloroplasts/genetics ; Genome, Chloroplast/genetics ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Paeonia lactiflora Pall., a member of Paeoniaceae family, is a medicinal herb widely used in traditional Chinese medicine. Chloroplasts are multifunctional organelles containing distinct genetic material. This study provides a foundation for identifying P. lactiflora, protecting and utilizing germplasm resources, and supporting molecular breeding efforts.<br><br>RESULTS AND CONCLUSION: In this study, five complete chloroplast genome sequences of P. lactiflora samples originating from different regions in China were sequenced using the Illumina NovaSeq 4000 platform. All five P. lactiflora chloroplasts had a typical cyclic tetrameric structure with 130 genes annotated. Comparative genomic analysis indicated that rpoB and psbK-psbI function as the&#xa0;potential specific DNA barcodes for intraspecific identification of P. lactiflora. PCR amplification of rpoB and psbK-psbI was performed on 246 samples from 7 production areas, achieving 100% amplification efficiency. Sequence analysis revealed that 5 and 10 haplotypes were identified based on rpoB and psbK-psbI, respectively. The joint analysis of two sequences identified 15 haplotypes named Hap1&#x2009;~&#x2009;Hap15. Hap5 emerged as the most prevalent and geographically widespread haplotype across China. Haplotypic diversity (Hd) was 0.786, and nucleotide diversity was 0.00281, suggesting that P. lactiflora had high genetic diversity at the species level. The Neighbor-Joining tree showed that the 15 haplotypes were clustered into two branches, indicating extensive genetic exchange between clusters. The introduction of new individuals or rare genes into different clusters through gene flow increased genetic variation within clusters, enriching P. lactiflora genetic diversity.}, }
@article {pmid39868307, year = {2025}, author = {Adler, KM and Xu, H and Gladstein, AC and Irizarry-Negron, VM and Robertson, MR and Doerig, KR and Petrov, DA and Winslow, MM and Feldser, DM}, title = {Tumor suppressor genotype influences the extent and mode of immunosurveillance in lung cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.15.633175}, pmid = {39868307}, issn = {2692-8205}, abstract = {UNLABELLED: The impact of cancer driving mutations in regulating immunosurveillance throughout tumor development remains poorly understood. To better understand the contribution of tumor genotype to immunosurveillance, we generated and validated lentiviral vectors that create an epi-allelic series of increasingly immunogenic neoantigens. This vector system is compatible with autochthonous Cre-regulated cancer models, CRISPR/Cas9-mediated somatic genome editing, and tumor barcoding. Here, we show that in the context of KRAS-driven lung cancer and strong neoantigen expression, tumor suppressor genotype dictates the degree of immune cell recruitment, positive selection of tumors with neoantigen silencing, and tumor outgrowth. By quantifying the impact of 11 commonly inactivated tumor suppressor genes on tumor growth across neoantigenic contexts, we show that the growth promoting effects of tumor suppressor gene inactivation correlate with increasing sensitivity to immunosurveillance. Importantly, specific genotypes dramatically increase or decrease sensitivity to immunosurveillance independently of their growth promoting effects. We propose a model of immunoediting in which tumor suppressor gene inactivation works in tandem with neoantigen expression to shape tumor immunosurveillance and immunoediting such that the same neoantigens uniquely modulate tumor immunoediting depending on the genetic context.<br><br>ONE SENTENCE SUMMARY: Here we uncover an under-appreciated role for tumor suppressor gene inactivation in shaping immunoediting upon neoantigen expression.}, }
@article {pmid39867691, year = {2025}, author = {Li, Q and Haqnawaz, M and Niazi, AR and Khalid, AN}, title = {Phylogenetic studies on the genus Candolleomyces (Psathyrellaceae, Basidiomycota) occurring in the bed of the Indus River, Punjab, Pakistan, reveal three new species.}, journal = {MycoKeys}, volume = {112}, number = {}, pages = {165-182}, pmid = {39867691}, issn = {1314-4049}, abstract = {During macrofungal surveys in 2019-2024, several specimens belonging to the family Psathyrellaceae were collected from the bed of the Indus River, Punjab, Pakistan. Phylogenetic analyses, based on ITS, LSU, and tef-1α sequences and morpho-anatomical study, confirmed the novelty and placement of three taxa in the genus Candolleomyces. They are described as Candolleomycescrenatus, C.undulatus, and C.virgatus. For distinguishing characters, C.crenatus has crenate cap margins, small basidiospores, and a marginate base of stipe. Candolleomycesundulatus has parabolic to campanulate, wavy margins, light purplish gray with a light brownish gray center of pileus, and an appendiculate, pendant annulus. Candolleomycesvirgatus has a parabolic to plane, distinct umbo, a virgate surface of pileus, 1-7 tiers, forking lamellae, and longitudinal striation on the surface of the stipe. Currently, Candolleomyces comprises 60 formally recognized species worldwide. However, with the inclusion of these three species, the total number rises to 63. Detailed descriptions, a phylogenetic estimate, morphological comparisons, and illustrations are provided.}, }
@article {pmid39867668, year = {2025}, author = {Hu, H and Zhou, F and Ma, X and Brokstad, KA and Kolmar, L and Girardot, C and Benes, V and Cox, RJ and Merten, CA}, title = {Targeted barcoding of variable antibody domains and individual transcriptomes of the human B-cell repertoire using Link-Seq.}, journal = {PNAS nexus}, volume = {4}, number = {1}, pages = {pgaf006}, pmid = {39867668}, issn = {2752-6542}, abstract = {Here, we present Link-Seq, a highly efficient droplet microfluidic method for combined sequencing of antibody-encoding genes and the transcriptome of individual B cells at large scale. The method is based on 3' barcoding of the transcriptome and subsequent single-molecule PCR in droplets, which freely shift the barcode along specific gene regions, such as the antibody heavy- and light-chain genes. Using the immune repertoire of COVID-19 patients and healthy donors as a model system, we obtain up to 91.7% correctly paired immunoglobulin heavy and light chains. Furthermore, we map the V(D)J usage and obtain sensitivities comparable with the current gold-standard 10× Genomics commercial systems while offering full flexibility in experimental setup and significant cost savings. A further unique feature of Link-Seq is the possibility of barcoding multiple target genes in a site-specific manner. Based on the open character of the platform and its conceptual advantages, we expect Link-Seq to become a versatile tool for single-cell analysis, especially for applications requiring additional processing steps that cannot be implemented on commercially available platforms.}, }
@article {pmid39865877, year = {2025}, author = {Venugopal Menon, N and Lee, J and Tang, T and Lim, CT}, title = {Microfluidics for morpholomics and spatial omics applications.}, journal = {Lab on a chip}, volume = {25}, number = {5}, pages = {752-763}, doi = {10.1039/d4lc00869c}, pmid = {39865877}, issn = {1473-0189}, mesh = {Humans ; *Microfluidic Analytical Techniques/instrumentation ; *Single-Cell Analysis/instrumentation ; Animals ; *Lab-On-A-Chip Devices ; *Microfluidics ; }, abstract = {Creative designs, precise fluidic manipulation, and automation have supported the development of microfluidics for single-cell applications. Together with the advancements in detection technologies and artificial intelligence (AI), microfluidic-assisted platforms have been increasingly used for new modalities of single-cell investigations and in spatial omics applications. This review explores the use of microfluidic technologies for morpholomics and spatial omics with a focus on single-cell and tissue characterization. We emphasize how various fluid dynamic principles and unique design integrations enable highly precise fluid manipulation, enhancing sample handling in morpholomics. Additionally, we examine the use of microfluidics-assisted spatial barcoding with micrometer resolutions for the spatial profiling of tissue specimens. Finally, we discuss how microfluidics can serve as a bridge for integrating multiple unique fields in omics research and outline key challenges that these technologies may face in practical translation.}, }
@article {pmid39862392, year = {2025}, author = {Biernat, B and Gładysz, P and Kuna, A and Sulima, M and Bykowska-Tumasz, M and Sontag, E}, title = {Myiasis by Cordylobia anthropophaga and C. rodhaini (Diptera: Calliphoridae) in Polish travelers to Africa with new molecular data.}, journal = {Journal of medical entomology}, volume = {62}, number = {2}, pages = {471-474}, pmid = {39862392}, issn = {1938-2928}, support = {//Division of Tropical Parasitology/ ; //Department of Tropical Medicine and Parasitology/ ; //Institute of Maritime and Tropical Medicine/ ; //Medical University of Gda&#x144;sk/ ; }, mesh = {Animals ; *Myiasis/parasitology ; Poland ; Larva/genetics/growth &amp; development/classification ; *Calliphoridae/genetics/growth &amp; development/classification ; Humans ; Electron Transport Complex IV/genetics ; Male ; Travel ; Female ; *Diptera/genetics/growth &amp; development ; Africa ; }, abstract = {Myiasis is a parasitic infestation of soft vertebrate tissues by larval stages of Diptera. We briefly described the lesion-causing genus Cordylobia Grünberg (Diptera: Calliphoridae). Three Polish travelers to Uganda, Gambia, and Senegal returned with furuncular myiasis. To identify the third-instar larvae removed from their skin, we examined the morphological features of the 3 specimens and sequenced a 5' barcoding fragment of the cytochrome c oxidase subunit I gene (COI-5P). One larva was identified as C. rodhaini Gedoelst, and 2 larvae were identified as C. anthropophaga (Blanchard). We were the first to submit the COI-5P of C. rodhaini to GenBank and the Barcode of Life Database. This is the first record of the importation of C. anthropophaga and the second record of the importation of C. rodhaini to Poland.}, }
@article {pmid39861914, year = {2025}, author = {Ranabhat, NB and Fellers, JP and Bruce, MA and Rupp, JLS}, title = {High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management.}, journal = {Viruses}, volume = {17}, number = {1}, pages = {}, pmid = {39861914}, issn = {1999-4915}, support = {USDA-ARS CRIS, 3020-21000-011-000-D//United States Department of Agriculture/ ; startup fund//Kansas State University/ ; }, mesh = {*Triticum/virology ; *Plant Diseases/virology ; *Nanopore Sequencing/methods ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Kansas ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; RNA, Viral/genetics ; Plant Leaves/virology ; }, abstract = {Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021. Wheat leaves exhibiting virus-like symptoms were collected, total RNA was extracted, and cDNA libraries were prepared using a PCR-cDNA barcoding kit, then loaded onto ONT MinION flow cells. Sequencing reads aligned with cereal virus references identified eight wheat virus species. Tritimovirus tritici (wheat streak mosaic virus, WSMV), Poacevirus tritici (Triticum mosaic virus, TriMV), Bromovirus BMV (brome mosaic virus, BMV), as well as Emaravirus tritici, Luteovirus pavhordei, L. sgvhordei, Bymovirus tritici, and Furovirus tritici. Mixed infections involving two to five viruses in a single sample were common, with the most prevalent being WSMV + TriMV at 16.7% and WSMV + TriMV + BMV at 11.9%. Phylogenetic analysis revealed a wide distribution of WSMV isolates, including European and recombinant variants. A phylogenetic analysis of Emaravirus tritici based on RNA 3A and 3B segments and whole-genome characterization of Furovirus tritici were also conducted. These findings advance understanding of genetic variability, phylogenetics, and viral co-infections, supporting the development of sustainable management practices through host genetic resistance.}, }
@article {pmid39859664, year = {2025}, author = {Barták, M and Kozánek, M and Belcari, A and Tóthová, A&#x160;}, title = {New Species of Empidinae (Diptera) from San Rossore National Park, Italy, with the First Report on Leg Polymorphism in the Genus Hilara Meigen and Their DNA Barcoding Evidence.}, journal = {Insects}, volume = {16}, number = {1}, pages = {}, pmid = {39859664}, issn = {2075-4450}, abstract = {Altogether three species of Empidinae are described from San Rossore National Park, Italy: Empis (Euempis) sanrossorensis Barták sp. nov., Hilara polymorpha Barták sp. nov., and Rhamphomyia (Megacyttarus) sanrossorensis Barták sp. nov. Polymorphism in the shape of foreleg in Hilara is reported for the first time. The COI sequences for barcoding purposes and upcoming studies are provided.}, }
@article {pmid39859622, year = {2025}, author = {Wu, J and Zhao, TT and Geng, H and Jin, GZ and Han, HL}, title = {Guium nebulum gen. et sp. nov., a New Cup Moth from Southern China Based on Morphological and Molecular Analysis (Lepidoptera: Zygaenoidea: Limacodidae).}, journal = {Insects}, volume = {16}, number = {1}, pages = {}, pmid = {39859622}, issn = {2075-4450}, support = {No. 31572294//National Nature Science Foundation of China/ ; No. 415486//the financial assistance under Heilongjiang Postdoctoral Fund/ ; No. 415895//Full-time Postdoctoral Support Program/ ; NABRI202303; 2572022DS09//Northeast Asia Biodiversity Research Center/ ; }, abstract = {A new genus and species of Limacodidae, Guium nebulum gen. et sp. nov., is described based on specimens collected from Guangxi Autonomous Region and Jiangxi Province in China. The new genus shares certain morphological features, such as a well-developed labial palpus, with related genera like Tanvia Solovyev &amp; Witt, 2009; Scopelodes Westwood, 1841; Hyphorma Walker, 1865; and Monema Walker, 1855. However, the new genus can be separated from them by the wing venation and the male genital characteristics. COI molecular marker analysis further supports the monophyly of this new genus, indicating a close relationship with Scopelodes.}, }
@article {pmid39859606, year = {2024}, author = {Yang, F and Xiao, J and Zhang, X and Shang, Y and Guo, Y}, title = {First Report and Phylogenetic Analysis of Mitochondrial Genomes of Chrysomya villeneuvi and Sarcophaga genuforceps.}, journal = {Insects}, volume = {16}, number = {1}, pages = {}, pmid = {39859606}, issn = {2075-4450}, support = {82072114//National Natural Science Foundation of China/ ; }, abstract = {The mitochondrial genome, highly conserved across species, is crucial for species identification, phylogenetic analysis, and evolutionary research. Chrysomya villeneuvi and Sarcophaga genuforceps, two species with significant forensic value, have been understudied in terms of genetic data. In this study, the complete mitochondrial genomes of C. villeneuvi (15,623 bp) and S. genuforceps (15,729 bp) were sequenced and analyzed. All thirteen protein-coding genes (PCGs) exhibited Ka/Ks ratios below one, indicating purifying selection and supporting their utility as barcoding markers. Phylogenetic analysis and genetic distance calculations based on PCGs showed that C. villeneuvi is closely related to Chrysomya rufifacies and Chrysomya albiceps, and S. genuforceps aligns more closely with Sarcophaga kentejana and Sarcophaga schuetzei. This research is the first to provide mitochondrial genome data for C. villeneuvi and S. genuforceps, expanding the genetic resources available for Calliphoridae and Sarcophagidae and offering a foundation for further forensic and evolutionary studies.}, }
@article {pmid39858563, year = {2024}, author = {Wang, M and Lin, H and Lin, H and Du, P and Zhang, S}, title = {From Species to Varieties: How Modern Sequencing Technologies Are Shaping Medicinal Plant Identification.}, journal = {Genes}, volume = {16}, number = {1}, pages = {}, pmid = {39858563}, issn = {2073-4425}, mesh = {*Plants, Medicinal/genetics/classification ; *High-Throughput Nucleotide Sequencing/methods ; *DNA Barcoding, Taxonomic/methods ; Genomics/methods ; Sequence Analysis, DNA/methods ; Genome, Plant ; }, abstract = {BACKGROUND/OBJECTIVES: Modern sequencing technologies have transformed the identification of medicinal plant species and varieties, overcoming the limitations of traditional morphological and chemical approaches. This review explores the key DNA-based techniques, including molecular markers, DNA barcoding, and high-throughput sequencing, and their contributions to enhancing the accuracy and reliability of plant identification. Additionally, the integration of multi-omics approaches is examined to provide a comprehensive understanding of medicinal plant identity.<br><br>METHODS: The literature search for this review was conducted across databases such as Google Scholar, Web of Science, and PubMed, using keywords related to plant taxonomy, genomics, and biotechnology. Inclusion criteria focused on peer-reviewed studies closely related to plant identification methods and techniques that contribute significantly to the field.<br><br>RESULTS: The review highlights that while sequencing technologies offer substantial improvements, challenges such as high costs, technical expertise, and the lack of standardized protocols remain barriers to widespread adoption. Potential solutions, including AI-driven data analysis and portable sequencers, are discussed.<br><br>CONCLUSIONS: This review provides a comprehensive overview of molecular techniques, their transformative impact, and future perspectives for more accurate and efficient medicinal plant identification.}, }
@article {pmid39856575, year = {2025}, author = {Mitra, A and Mitra, P and Mahadani, P and Trivedi, S and Banerjee, D and Das, M}, title = {Application of character based DNA barcode: a novel approach towards identification of fruit fly (Diptera: Tephritidae) species from cucurbit crops.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {70}, pmid = {39856575}, issn = {1471-2164}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Tephritidae/genetics/classification ; Phylogeny ; *Crops, Agricultural/parasitology ; *Cucurbitaceae/parasitology ; Species Specificity ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: The Tephritidae family, commonly referred to as true fruit flies, comprises of a substantial group within order Diptera. Numerous species within this family are major agricultural pests, with a tendency to infest a wide array of fruits and vegetables in tropical and sub- tropical regions, leading to considerable damage and consequent reductions in the market value of the crops.<br><br>METHODS AND RESULTS: The current study was aimed to propose a promising solution to the menace posed by fruit flies by offering rapid, accurate and reliable species identification by using character-based DNA barcode methodology. The Tephritid specimens were collected from Cucurbitaceous plants of southern parts of West Bengal, India, and a total of eight species from Tephritidae family were obtained belonging to three genera, namely Bactrocera (Macquart, 1835), Dacus (Fabricius, 1805) and Zeugodacus (Hendel, 1927). Their morphological features were meticulously studied based on available literature, along with genetic analysis based on mitochondrial COI and ND1 gene sequences. A total of 30 uniquely variable sites at nucleotide position 42,48,51,60,66,72, 105,111,144,198,207,243, 273,297,307,318,345,357, 375,378,381,387,399,400, 402,436,444,450,453 and 460 in COI gene were discerned among Tephritid species in the present study.<br><br>CONCLUSIONS: The character-based DNA barcode holds the potential to differentiate closely related species of fruit flies and morphologically look-a-like ones. The novel method will be very significant in terms of rapid, precise and reliable species identification and might be extremely essential for early detection during pest outbreaks by facilitating timely intervention strategies to mitigate crop damage.}, }
@article {pmid39853537, year = {2025}, author = {Ramezankhani, R and De Smedt, J and Toprakhisar, B and van der Veer, BK and Tricot, T and Vanmarcke, G and Balaton, B and van Grunsven, L and Vosough, M and Chai, YC and Verfaillie, C}, title = {Identification of Cell Fate Determining Transcription Factors for Generating Brain Endothelial Cells.}, journal = {Stem cell reviews and reports}, volume = {21}, number = {3}, pages = {744-766}, pmid = {39853537}, issn = {2629-3277}, support = {G0B5819N//Fonds Wetenschappelijk Onderzoek/ ; S001221N//Fonds Wetenschappelijk Onderzoek/ ; 1280923N//Fonds Wetenschappelijk Onderzoek/ ; 11E7920N//Fonds Wetenschappelijk Onderzoek/ ; PDMT2/23/083//KU Leuven postdoctoral mandate/ ; }, mesh = {Humans ; *Endothelial Cells/metabolism/cytology ; *Transcription Factors/metabolism/genetics ; *Brain/cytology/metabolism ; *Cell Differentiation/genetics ; Blood-Brain Barrier/metabolism/cytology ; Transcriptome ; Pluripotent Stem Cells/cytology/metabolism ; *Cell Lineage/genetics ; }, abstract = {Reliable models of the blood-brain barrier (BBB), wherein brain microvascular endothelial cells (BMECs) play a key role in maintenance of barrier function, are essential tools for developing therapeutics and disease modeling. Recent studies explored generating BMEC-like cells from human pluripotent stem cells (hPSCs) by mimicking brain-microenvironment signals or genetic reprogramming. However, due to the lack of comprehensive transcriptional studies, the exact cellular identity of most of these cells remains poorly defined. In this study we aimed to identify the most likely master transcription factors (TFs) for inducing brain endothelial cell (EC) fate and assess the transcriptomic changes following their introduction into immature ECs. Therefore, we first generated PSC-derived immature ECs by transient overexpression of the TF, ETV2. Subsequently, by performing an extensive meta-analysis of transcriptome studies of brain and non-brain ECs, 12 candidate TFs were identified, which might fate immature ECs towards cells with brain EC features. Following combinatorial overexpression of these 12 TFs tagged with unique barcodes, single cell transcriptomics identified a subset of transduced cells that resembled mid-gestational human brain ECs. Assessment of the TF barcodes present in these cells revealed significant enrichment of the TFs ZIC3, TFAP2C, TFAP2A, and DLX2. These TFs might be useful to fate PSC-EC to BMEC-like cells, which could be incorporated in human in vitro BBB models.}, }
@article {pmid39852453, year = {2025}, author = {Psurtseva, NV and Kiyashko, AA and Senik, SV and Pham, THG}, title = {Ex Situ Conservation, DNA Barcoding and Enzymatic Potential Evaluation of Macrofungi (Basidiomycota, Ascomycota) from Vietnam.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, pmid = {39852453}, issn = {2309-608X}, support = {075-15-2021-1056//Ministry of Education and Science of the Russian Federation/ ; 124013100829-3//State Assignment of BIN RAS/ ; E1.5//Joint Vietnam - Russia Tropical Science and Technology Research Centre/ ; }, abstract = {The diversity and resource potential of macroscopic fungi in tropical regions remain understudied. Vietnam, being in a biodiversity hotspot, has a large number of new fungal species that are of interest for biotechnology and medicine. The presence of a large number of protected areas in Vietnam creates favorable opportunities for the study and ex situ conservation of tropical biodiversity. From 2012 to 2023, 785 strains of macrofungi from National Parks of Vietnam were preserved in the LE-BIN collection, 327 of which were barcoded with the sequences deposited in the NCBI GenBank. A taxonomic analysis demonstrated that many of the preserved isolates are potentially new or poorly studied species, representing a useful resource for taxonomical studies and a search for new medicinal mushrooms. More than 180 strains were studied for the first time for growth rate and enzymatic activities. Of these, 53 strains showed high growth rate, 43-high cellulolytic activity, 73-high oxidative enzymes activity, and 27 showed high proteolytic activity, making them promising candidates for biotechnological and medical applications and opening new opportunities for sustainable biomass management, discovery of new enzymes and bioactive substances, development of new drugs and efficient plant waste treatment technologies. The results confirm the importance of the ex situ conservation of fungal diversity in tropical regions as a valuable source for scientific and commercial applications and suggest certain new active strains for biotechnological study.}, }
@article {pmid39849649, year = {2025}, author = {Hornok, S and Kontschán, J and Keve, G and Takács, N and Van Nguyen, D and Ho, KNP and Görföl, T and Wang, Y and Farkas, R and Dao, TTH}, title = {First report of Haemaphysalis bispinosa, molecular-geographic relationships of Ixodes granulatus and a new Dermacentor species from Vietnam.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {21}, pmid = {39849649}, issn = {1756-3305}, support = {1500107//HUN-REN Office for Supported Research Groups/ ; FK137778//NKFIH/ ; 2019-2.1.12-T&#xc9;T VN-2020-00012//NKFIH/ ; }, mesh = {Animals ; Vietnam/epidemiology ; Phylogeny ; Female ; RNA, Ribosomal, 16S/genetics ; *Ixodidae/classification/genetics/anatomy &amp; histology ; *Dermacentor/classification/genetics/anatomy &amp; histology ; Dogs ; *Tick Infestations/veterinary/parasitology/epidemiology ; Male ; Electron Transport Complex IV/genetics ; Sequence Analysis, DNA ; Dog Diseases/parasitology ; }, abstract = {BACKGROUND: Vietnam and its region are regarded as an ixodid tick biodiversity hotspot for at least two genera: Haemaphysalis and Dermacentor. To contribute to our knowledge on the tick fauna of this country, ticks from these two genera as well as an Ixodes species were analyzed morphologically and their molecular-phylogenetic relationships were examined in taxonomic and geographical contexts.<br><br>METHODS: For this study, seven Haemaphysalis sp. ticks were removed from dogs and collected from the vegetation. These showed morphological differences from congeneric species known to occur in Vietnam. In addition, three Ixodes sp. ticks were collected from pygmy slow lorises (Xanthonycticebus pygmaeus), and a Dermacentor female had been previously collected from the vegetation. After DNA extraction, these were molecularly or phylogenetically analyzed based on the cytochrome c oxidase subunit I (cox1) and 16S rRNA genes.<br><br>RESULTS: The three species were morphologically identified as (i) Ixodes granulatus, which had nearly or exactly 100% sequence identities to conspecific ticks reported from large (approximately 2000&#xa0;km) geographical distances but was more different (having lower, only 94.2% cox1 and 96.7% 16S rRNA sequence identity) from samples collected within 1000&#xa0;km of Vietnam in Southern China and Malaysia, respectively; (ii) Haemaphysalis bispinosa, which showed 100% sequence identity to samples reported within both narrow and broad geographical ranges; and (iii) a new species, Dermacentor pseudotamokensis Hornok sp. nov., described here morphologically and shown to be phylogenetically&#xa0;a sister species to Dermacentor tamokensis.<br><br>CONCLUSIONS: Haemaphysalis bispinosa shows genetic homogeneity in the whole of South and Southeast Asia, probably owing to its frequent association with domestic ruminants and dogs (i.e. frequently transported hosts). However, I. granulatus, the Asian rodent tick, has a mixed geographical pattern of haplotypes, probably because it may associate with either synanthropic or wild-living rodents as primary hosts. This tick species is recorded here, for the first time to our knowledge, as parasitizing lorises in Vietnam and its region. Based on phylogenetic analyses, D. pseudotamokensis Hornok&#xa0;sp. nov., recognized and described here for the first time, was almost certainly misidentified previously as Dermacentor steini, drawing attention to the need to barcode all Dermacentor spp. in Southern Asia.}, }
@article {pmid39845798, year = {2024}, author = {He, G and Man, J and Chen, Y and Zhang, X and Wang, X and An, K and Amu, L and Chen, W and Wang, B and Shi, Y and Wang, X and Wei, S}, title = {Identification of Salvia miltiorrhiza germplasm resources based on metabolomics and DNA barcoding.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1518906}, pmid = {39845798}, issn = {1663-9812}, abstract = {INTRODUCTION: Salvia miltiorrhiza radix et rhizoma (Danshen) is a crucial medicinal material for treating cardiovascular and cerebrovascular diseases. However, the presence of adulterants and intraspecific variability poses challenges to its clinical safety.<br><br>METHODS: This study collected samples of S. miltiorrhiza from various regions and commonly encountered adulterants. The composition differences of S. miltiorrhiza radix and its adulterants were analyzed by fingerprint and broad-target metabolomics. Chloroplast genome was used to distinguish intra-genus species and DNA barcoding was used to identify germplasm sources.<br><br>RESULTS: The fingerprinting analysis proved that there is no chemical composition consistency between S. miltiorrhiza radix and its adulterants. Broad-targeted metabolomics can distinguish S. miltiorrhiza radix from Salvia yunnanensis radix, Dipsacus asperoides radix, and Arctium lappa radix. Additionally, comparative chloroplast genome analysis indicated that atpF and rps4-trnT-UGU were the potential DNA barcodes for S. miltiorrhiza. 259 samples from 13 provinces and 21 origins were amplified and sequenced, resulting in the identification of 62 haplotypes. The unique haplotypes found in Shanxi Luoyang, Shandong Qingdao and other places can be used as molecular geographic markers for the identification of the germplasm source of S. miltiorrhiza.<br><br>DISCUSSION: This study systematically differentiates S. miltiorrhiza from its adulterants and highlights the potential of unique haplotypes as markers for sourcing. The findings provide strong scientific evidence for the clinical safety of S. miltiorrhiza, emphasizing the importance of proper cultivation, selection, and breeding of varieties.}, }
@article {pmid39845644, year = {2025}, author = {Yu, Z and Qi, Y and Wei, Y and Zhuang, G and Li, Y and Wang, B and Akbar, S and Xu, Y and Hua, X and Xu, Q and Deng, Z and Zhang, J and Huang, Y and Yu, F and Zhou, J}, title = {A cost-effective oligo-based barcode system for chromosome identification in longan and lychee.}, journal = {Horticulture research}, volume = {12}, number = {1}, pages = {uhae278}, pmid = {39845644}, issn = {2662-6810}, abstract = {Oligonucleotide (Oligo)-based fluorescence in situ hybridization (FISH) represents a highly effective methodology for identifying plant chromosomes. Longan is a commercially significant fruit species, yet lacking basic chromosomal markers has hindered its cytogenetic research. In this study, we developed a cost-effective oligo-based system for distinguishing chromosomes of longan (Dimocarpus longan Lour., 2n = 2x = 30). For this system, each synthesized oligo contained two chromosome-specific sequences that spanned a distance of over 200 kb, and a PCR-based flexible amplification method coupled with nested primers was used for probe labeling. The use of these oligo-based barcodes enabled the marking of 36 chromosomal regions, which allowed for the unambiguous distinction of all 15 chromosomes in both longan and lychee (Litchi chinensis Sonn., 2n = 2x = 30) species. Based on the identification of individual chromosomes, we constructed karyotypes and detected genome assembly errors involving the 35S ribosomal RNA gene (35S rDNA) in longan and lychee. Developing oligo-based barcodes offers considerable promise for advancing cytogenetic research in longan, lychee, and their related species. Furthermore, this cost-effective synthesis system can be referred to the development of new oligo libraries among other species.}, }
@article {pmid39845497, year = {2025}, author = {Lee, DJ and Kim, J and Euo, SS and Lee, JS and Lee, H and Roh, SJ}, title = {A new species of the genus Oiketicoides Heylaerts, 1885 (Lepidoptera, Psychidae) from Korea with its natural parasitoid enemy.}, journal = {ZooKeys}, volume = {1223}, number = {}, pages = {311-317}, pmid = {39845497}, issn = {1313-2989}, abstract = {Oiketicoidesgohadoensis Roh &amp; Lee, sp. nov. is described as new to science. The morphology of male adult, including genitalia, is described, and DNA barcodes for precise identification of the species are provided. A parasitoid, Neophryxepsychidis Townsend, 1916 (Diptera, Tachinidae) of O.gohadoensis is also reported for the first time in Korea, together with its DNA barcode sequence.}, }
@article {pmid39843438, year = {2025}, author = {Lin, C and Liu, C and Chen, L and Cheng, H and Ashfaq, M and Hebert, PDN and Gao, Y}, title = {Data on insect biodiversity in a Chinese potato agroecosystem from DNA metabarcoding.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {131}, pmid = {39843438}, issn = {2052-4463}, support = {59-0212-9-001-F//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; }, mesh = {Animals ; *Biodiversity ; China ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Insecta/classification/genetics ; *Solanum tuberosum ; }, abstract = {Potato (Solanum tuberosum) is a staple crop important in global food security. As a leading potato producer, China faces significant challenges from insect pest infestations that compromise yield and quality. However, insect communities within Chinese potato fields remain poorly characterized. This study aimed to explore insect diversity in potato fields in Yunnan Province. From autumn 2021 to summer 2022, five Malaise traps were strategically deployed to capture insect samples. In total, 245 samples were collected over 49 weeks, and DNA metabarcoding was performed on bulk samples. The generated sequences were curated and analyzed using the Barcode of Life Data System and the Multiplex Barcode Research and Visualization Environment. The analysis assigned sequences to 1,688 Barcode Index Numbers (BINs) as species proxies derived from the Global Insecta Library, along with 166 BINs from the China Insecta dataset. This research provides valuable insights for barcoding local biodiversity and developing regional reference libraries and presents a comprehensive dataset of insect biodiversity within potato agroecosystems, encompassing 1,707 BINs linked to known insect taxa.}, }
@article {pmid39838754, year = {2025}, author = {Zhang, D and Zhou, Y and Li, X and Luan, Q}, title = {CRISPR/Cas13a-Enhanced Porous Hydrogel Encapsulated Photonic Barcodes for Multiplexed Detection of Virus.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {21}, number = {8}, pages = {e2408725}, doi = {10.1002/smll.202408725}, pmid = {39838754}, issn = {1613-6829}, support = {82102511//National Natural Science Foundation of China/ ; 82102181//National Natural Science Foundation of China/ ; BK20210021//National Natural Science Foundation of China/ ; BK20210009//National Natural Science Foundation of China/ ; M2021031//Research Project of&#xa0;Jiangsu Province Health Committee/ ; 2024-LCYJ-MS-15//Medical School of Nanjing University/ ; (YKK23068)//Nanjing Medical Science and Technique Development Foundation YKK23068/ ; }, mesh = {*Hydrogels/chemistry ; *SARS-CoV-2/genetics/isolation &amp; purification ; *CRISPR-Cas Systems/genetics ; Humans ; Porosity ; COVID-19/diagnosis/virology ; Photons ; RNA, Viral/genetics ; Nucleic Acid Hybridization ; }, abstract = {In this study, we present an ultrasensitive and specific multiplexed detection method for SARS-CoV-2 and influenza (Flu) utilizing CRISPR/Cas13a technology combined with a hydrogel-encapsulated photonic crystal (PhC) barcode integrated with hybridization chain reaction (HCR). The barcodes, characterized by core-shell structures, are fabricated through partial replication of periodically ordered hexagonally close-packed silicon dioxide beads. Consequently, the opal hydrogel shell of these barcodes features abundant interconnected pores that provide a substantial surface area for probe immobilization. Furthermore, the inherent structural colors remain stable during detection events due to the robust mechanical strength of the barcode cores. This integration of CRISPR/Cas13a and HCR leverages both the highly specific RNA recognition capabilities and trans-cleavage activity of Cas13a while employing HCR to enhance sensitivity. Upon encountering target RNA, Cas13a cleaves a hairpin probe, thereby initiating subsequent HCR amplification for enhanced detection sensitivity. Our method demonstrates high accuracy and sensitivity in multiplexed detection of SARS-CoV-2, Flu A and Flu B RNA with a limit-of-detection as low as 200 aM. Importantly, this assay also exhibits acceptable accuracy in repeated clinical sample testing. Thus, our platform represents a promising strategy for highly sensitive multiplexed virus detection in clinical.}, }
@article {pmid39837566, year = {2025}, author = {Zhuoma, D and Tingyin, D and Jun, L and Pei, Q and Duoji, C and Feng, D and Fang, D and Yan, Z}, title = {Study on Quality Evaluation of Tibetan Dracocephali tangutici Herba Based on DNA Barcode and HPLC Fingerprinting.}, journal = {Phytochemical analysis : PCA}, volume = {36}, number = {4}, pages = {1202-1211}, doi = {10.1002/pca.3503}, pmid = {39837566}, issn = {1099-1565}, support = {XZ202101ZD0024G//Project of Science and Technology Programme of Tibet Autonomous Region/ ; }, mesh = {Chromatography, High Pressure Liquid/methods ; *DNA Barcoding, Taxonomic/methods ; Principal Component Analysis ; Quality Control ; *Lamiaceae/genetics/chemistry ; *Drugs, Chinese Herbal/chemistry ; Discriminant Analysis ; *DNA Fingerprinting/methods ; Tibet ; }, abstract = {OBJECTIVES: The quality of 30 batches of the Tibetan Dracocephali tangutici Herba was evaluated using HPLC fingerprinting and DNA sequences.<br><br>METHODS: Botanical identification of 30 batches of D. tangutici herba was conducted using the DNA barcoding approach, specifically analyzing the ITS and rbcL sequences. HPLC fingerprints of Tibetan Dracocephali tangutici Herba were established. The quality of 30 batches of D. tangutici herba was comprehensively evaluated using principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and entropy weighting method (EWM) combined with grey relation analysis (GRA).<br><br>RESULTS: The botanical provenance of all 30 batches of herbs was proven to be Dracocephali tangutici Maxim. using DNA barcoding techniques, namely, ITS sequence and rbcL sequence testing. A total of 17 common peaks were chosen from the HPLC fingerprinting analysis. Among these, three peaks were recognized by comparing them with three reference standards: chlorogenic acid, cryptochlorogenic acid, and salvianolic acid B. The similarity scores of the 30 batches of D. tangutici herba varied between 0.846 and 0.991. The 30 batches of samples were categorized into two groups using PCA. The findings from OPLS-DA indicated that chlorogenic acid and four flavonoids could be the crucial components for evaluating the quality of D. tangutici herba. Additionally, the combined evaluation results of EWM and GRA suggested that the quality of the 30 batches of samples varied significantly.<br><br>CONCLUSION: The results of this study can provide a reference basis for the development of quality standards for D. tangutici herba in Tibet.}, }
@article {pmid39834682, year = {2025}, author = {}, title = {Correction to "Species Identification of Livefood Flightless Fly (Torinido-Shoujoubae) Through DNA Barcoding".}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70864}, doi = {10.1002/ece3.70864}, pmid = {39834682}, issn = {2045-7758}, abstract = {[This corrects the article DOI: 10.1002/ece3.11622.].}, }
@article {pmid39831564, year = {2025}, author = {Mariz, J and Nawaz, A and Bösch, Y and Wurzbacher, C}, title = {Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14055}, pmid = {39831564}, issn = {1755-0998}, support = {WU 890/2-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *Biodiversity ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA, Fungal/genetics/chemistry ; *Single-Cell Analysis/methods ; Sequence Analysis, DNA ; *Environmental Microbiology ; }, abstract = {Known for its remarkable diversity and ecological importance, the fungal kingdom remains largely unexplored. In fact, the number of unknown and undescribed fungi is predicted to exceed the number of known fungal species by far. Despite efforts to uncover these dark fungal taxa, we still face inherent sampling biases and methodological limitations. Here, we present a framework that combines taxonomic knowledge, molecular biology and data processing to explore the fungal biodiversity of enigmatic aquatic fungal lineages. Our work is based on serial screening of environmental fungal cells to approach unknown fungal taxa. Microscopic documentation is followed by DNA analysis of laser micro-dissected cells, coupled with a ribosomal operon barcoding step realised by long-read sequencing, followed by an optional whole genome sequencing step. We tested this approach on a range of aquatic fungal cells mostly belonging to the ecological group of aquatic hyphomycetes derived from environmental samples. From this initial screening, we were able to identify 60 potentially new fungal taxa in the target dataset. By extending this methodology to other fungal lineages associated with different habitats, we expect to increasingly characterise the molecular barcodes of dark fungal taxa in diverse environmental samples. This work offers a promising solution to the challenges posed by unknown and unculturable fungi and holds the potential to be applied to the diverse lineages of undescribed microeukaryotes.}, }
@article {pmid39831278, year = {2025}, author = {Nguyen, AD and Vu, TTT and Nguyen, TT}, title = {Mountainous millipedes in Vietnam. III. Two new dragon millipedes from limestone mountains in northern Vietnam (Polydesmida, Paradoxosomatidae, Hylomus), with an identification key to Vietnamese Hylomus species.}, journal = {ZooKeys}, volume = {1223}, number = {}, pages = {247-262}, pmid = {39831278}, issn = {1313-2989}, abstract = {Two new species of the dragon millipede genus Hylomus Cook &amp; Loomis, 1924 are described from mountainous areas in northern Vietnam, namely Hylomuspiccolo sp. nov. and Hylomusborealis sp. nov. The COI barcodes are provided for these species, and an identification key is presented to all Vietnamese Hylomus species.}, }
@article {pmid39830292, year = {2024}, author = {Crous, PW and Wingfield, MJ and Jurjević, &#x17d; and Balashov, S and Osieck, ER and Marin-Felix, Y and Luangsa-Ard, JJ and Mejía, LC and Cappelli, A and Parra, LA and Lucchini, G and Chen, J and Moreno, G and Faraoni, M and Zhao, RL and Weholt, &#xd8; and Borovička, J and Jansen, GM and Shivas, RG and Tan, YP and Akulov, A and Alfenas, AC and Alfenas, RF and Altés, A and Avchar, R and Barreto, RW and Catcheside, DEA and Chi, TY and Esteve-Raventós, F and Fryar, SC and Hanh, LTM and Larsbrink, J and Oberlies, NH and Olsson, L and Pancorbo, F and Raja, HA and Thanh, VN and Thuy, NT and Ajithkumar, K and Akram, W and Alvarado, P and Angeletti, B and Arumugam, E and Khalilabad, AA and Bandini, D and Baroni, TJ and Barreto, GG and Boertmann, D and Bose, T and Castañeda Ruiz, RF and Couceiro, A and Cykowska-Marzencka, B and Dai, YC and Darmostuk, V and da Silva, SBG and Dearnaley, JDW and de Azevedo Santiago, ALCM and Declercq, B and de Freitas, LWS and De la Peña-Lastra, S and Delgado, G and de Lima, CLF and Dhotre, D and Dirks, AC and Eisvand, P and Erhard, A and Ferro, LO and García, D and García-Martín, A and Garrido-Benavent, I and Gené, J and Ghobad-Nejhad, M and Gore, G and Gunaseelan, S and Gusmão, LFP and Hammerbacher, A and Hernández-Perez, AT and Hernández-Restrepo, M and Hofmann, TA and Hubka, V and Jiya, N and Kaliyaperumal, M and Keerthana, KS and Ketabchi, M and Kezo, K and Knoppersen, R and Kolarczyková, D and Kumar, TKA and Læssøe, T and Langer, E and Larsson, E and Lodge, DJ and Lynch, MJ and Maciá-Vicente, JG and Mahadevakumar, S and Mateos, A and Mehrabi-Koushki, M and Miglio, BV and Noor, A and Oliveira, JA and Pereira, OL and Piątek, M and Pinto, A and Ramírez, GH and Raphael, B and Rawat, G and Renuka, M and Reschke, K and Mateo, AR and Saar, I and Saba, M and Safi, A and Sánchez, RM and Sandoval-Denis, M and Savitha, AS and Sharma, A and Shelke, D and Sonawane, H and Souza, MGAP and Stryjak-Bogacka, M and Thines, M and Thomas, A and Torres-Garcia, D and Traba, JM and Vauras, J and Vermaas, M and Villarreal, M and Vu, D and Whiteside, EJ and Zafari, D and Starink-Willemse, M and Groenewald, JZ}, title = {Fungal Planet description sheets: 1697-1780.}, journal = {Fungal systematics and evolution}, volume = {14}, number = {}, pages = {325-577}, pmid = {39830292}, issn = {2589-3831}, support = {P01 CA125066/CA/NCI NIH HHS/United States ; }, abstract = {Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Wingfield MJ, Jurjević Ž, et al. (2024). Fungal Planet description sheets: 1697-1780. Fungal Systematics and Evolution 14: 325-577. doi: 10.3114/fuse.2024.14.19.}, }
@article {pmid39825896, year = {2025}, author = {Ellisor, D and Gregg, M and Folz, A and Possolo, A}, title = {Robust discrimination between closely related species of salmon based on DNA fragments.}, journal = {Analytical and bioanalytical chemistry}, volume = {417}, number = {12}, pages = {2579-2588}, pmid = {39825896}, issn = {1618-2650}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *DNA Barcoding, Taxonomic/methods ; Species Specificity ; *Salmon/genetics/classification ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing/methods ; Salmo salar/genetics/classification ; *Oncorhynchus kisutch/genetics/classification ; }, abstract = {Closely related species of Salmonidae, including Pacific and Atlantic salmon, can be distinguished from one another based on nucleotide sequences from the cytochrome c oxidase sub-unit 1 mitochondrial gene (COI), using ensembles of fragments aligned to genetic barcodes that serve as digital proxies for the relevant species. This is accomplished by exploiting both the nucleotide sequences and their quality scores recorded in a FASTQ file obtained via Next Generation (NextGen) Sequencing of mitochondrial DNA extracted from Coho salmon caught with hook and line in the Gulf of Alaska. The alignment is done using MUSCLE (Muscle 5.2) [1], applied to multiple versions of each fragment perturbed according to the nucleobase identification error probabilities underlying the quality scores. The Damerau-Levenshtein distance was used to determine the genetic barcode of the candidate species that is closest to each aligned, perturbed fragment. The "votes" that the sampled fragments cast for the different candidate species are then pooled and converted into identification probabilities, using weights determined by the entropy of the fragment-specific identification probability distributions. This novel approach to quantify the uncertainty associated with measurements made using NextGen Sequencing can be applied to discriminate closely related species, hence to value-assignment for reference materials supporting determinations of the authenticity of seafood, for example, NIST Reference Materials 8256 and 8257 (Coho salmon) [2].}, }
@article {pmid39824859, year = {2025}, author = {Holmes, CL and Dailey, KG and Hullahalli, K and Wilcox, AE and Mason, S and Moricz, BS and Unverdorben, LV and Balazs, GI and Waldor, MK and Bachman, MA}, title = {Patterns of Klebsiella pneumoniae bacteremic dissemination from the lung.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {785}, pmid = {39824859}, issn = {2041-1723}, support = {K99 AI175481/AI/NIAID NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; AI042347//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI042347/AI/NIAID NIH HHS/United States ; K99A1175481//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/physiology ; *Bacteremia/microbiology ; *Klebsiella Infections/microbiology/pathology ; *Lung/microbiology/pathology ; Animals ; Humans ; Mice ; Male ; Female ; Mice, Inbred C57BL ; }, abstract = {Bacteremia, a leading cause of death, generally arises after bacteria establish infection in a particular tissue and transit to secondary sites. Studying dissemination from primary sites by solely measuring bacterial burdens does not capture the movement of individual clones. By barcoding Klebsiella pneumoniae, a leading cause of bacteremia, we track pathogen dissemination following pneumonia. Variability in organ bacterial burdens is attributable to two distinct dissemination patterns distinguished by the degree of similarity between the lung and systemic sites. In metastatic dissemination, lung bacterial clones undergo heterogeneous expansion and the dominant clones spread to secondary organs, leading to greater similarity between sites. In direct dissemination, bacterial clones exit the lungs without clonal expansion, leading to lower burdens in systemic sites and more dissimilarity from the lung. We uncover bacterial and host factors that influence the dynamics of clonal sharing and expansion. Here, our data reveal unexpected heterogeneity in Klebsiella bacteremia dynamics and define a framework for understanding within-host bacterial dissemination.}, }
@article {pmid39823405, year = {2025}, author = {Miller, D and Dziulko, A and Levy, S}, title = {Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0299440}, pmid = {39823405}, issn = {1932-6203}, support = {R01 AI164530/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *SARS-CoV-2/metabolism/physiology/genetics ; *COVID-19/virology/metabolism ; *Host-Pathogen Interactions ; *Protein Interaction Mapping/methods ; *Protein Interaction Maps ; HEK293 Cells ; }, abstract = {Protein-Protein Interactions (PPIs) are a key interface between virus and host, and these interactions are important to both viral reprogramming of the host and to host restriction of viral infection. In particular, viral-host PPI networks can be used to further our understanding of the molecular mechanisms of tissue specificity, host range, and virulence. At higher scales, viral-host PPI screening could also be used to screen for small-molecule antivirals that interfere with essential viral-host interactions, or to explore how the PPI networks between interacting viral and host genomes co-evolve. Current high-throughput PPI assays have screened entire viral-host PPI networks. However, these studies are time consuming, often require specialized equipment, and are difficult to further scale. Here, we develop methods that make larger-scale viral-host PPI screening more accessible. This approach combines the mDHFR split-tag reporter with the iSeq2 interaction-barcoding system to permit massively-multiplexed PPI quantification by simple pooled engineering of barcoded constructs, integration of these constructs into budding yeast, and fitness measurements by pooled cell competitions and barcode-sequencing. We applied this method to screen for PPIs between SARS-CoV-2 proteins and human proteins, screening in triplicate >180,000 ORF-ORF combinations represented by >1,000,000 barcoded lineages. Our results complement previous screens by identifying 74 putative PPIs, including interactions between ORF7A with the taste receptors TAS2R41 and TAS2R7, and between NSP4 with the transmembrane KDELR2 and KDELR3. We show that this PPI screening method is highly scalable, enabling larger studies aimed at generating a broad understanding of how viral effector proteins converge on cellular targets to effect replication.}, }
@article {pmid39823165, year = {2025}, author = {Ivanova, A and Chalupska, R and Louro, AF and Firth, M and González-King Garibotti, H and Hultin, L and Kohl, F and Lázaro-Ibáñez, E and Lindgren, J and Musa, G and Oude Blenke, E and Silva, AM and Szeponik, L and Taylor, A and Viken, I and Wang, X and Jennbacken, K and Wiseman, J and Dekker, N}, title = {Barcoded Hybrids of Extracellular Vesicles and Lipid Nanoparticles for Multiplexed Analysis of Tissue Distribution.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {10}, pages = {e2407850}, pmid = {39823165}, issn = {2198-3844}, support = {825828//European Union's Horizon 2020 Research and Innovation Programme/ ; }, mesh = {*Extracellular Vesicles/metabolism ; Animals ; Mice ; *Nanoparticles/chemistry/metabolism ; Tissue Distribution ; Humans ; Drug Delivery Systems/methods ; *Lipids/chemistry ; Liposomes ; }, abstract = {Targeted delivery of therapeutic agents is a persistent challenge in modern medicine. Recent efforts in this area have highlighted the utility of extracellular vesicles (EVs) as drug carriers, given that they naturally occur in bloodstream and tissues, and can be loaded with a wide range of therapeutic molecules. However, biodistribution and tissue tropism of EVs remain difficult to study systematically. Here, a multiplexed approach is developed for simultaneous tracking of EVs from various cell lines within a single in vivo experiment. EVs are used from 16 different cell lines, and through controlled fusion with lipid nanoparticles (LNPs) carrying single-stranded DNA barcodes, uniquely barcoded hybrid EV particle (hEV) library is generated. These hEVs are combined for a multiplexed in vivo biodistribution profiling in mice, and discovered that HAP1-derived hEVs demonstrated lung tropism, suggesting that these hEVs may be used for targeted drug delivery into lung tissue. To examine this possibility further, it is shown that HAP1 hEV loaded with Cre mRNA displayed functional delivery to the lungs. Overall, the barcoded hEV technology enables rapid profiling of biodistribution across EV cell sources, which is poised to improve throughput and extent of EV studies, while reducing the number of animals required for research.}, }
@article {pmid39821740, year = {2025}, author = {Dou, HY and Huang, TS and Wu, HC and Hsu, CH and Chen, FJ and Liao, YC}, title = {Targeted sputum sequencing for rapid and broad drug resistance of Mycobacterium tuberculosis.}, journal = {Infection}, volume = {53}, number = {4}, pages = {1413-1423}, pmid = {39821740}, issn = {1439-0973}, support = {IV-111-PP-23//National Health Research Institutes, Taiwan/ ; PH-112-PP-05//National Health Research Institutes, Taiwan/ ; 110-2314-B-400-038//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Mycobacterium tuberculosis/genetics/drug effects/isolation &amp; purification ; *Sputum/microbiology ; Humans ; Antitubercular Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Multiplex Polymerase Chain Reaction/methods ; Tuberculosis, Multidrug-Resistant/microbiology/diagnosis ; Microbial Sensitivity Tests ; DNA, Bacterial/genetics ; Nanopore Sequencing/methods ; }, abstract = {PURPOSE: Rapid detection of drug resistance in Mycobacterium tuberculosis (Mtb) from clinical samples facilitates the timely provision of optimal treatment regimens for tuberculosis (TB) patients.<br><br>METHODS: In November, 2023, the WHO released its second catalogue of resistance-conferring mutations in Mtb. Utilizing this information, we developed a single 17-plex PCR assay covering 16 key resistance genes and modified thermo-protection buffer to amplify 30 kbp DNA directly from sputum samples for nanopore sequencing. We implemented our protocol using rapid barcoding for sequencing with both a Flongle and a MinION flow cell.<br><br>RESULTS: The single multiplex PCR assay was successfully validated on clinical sputum samples using the thermo-protection buffer. The protocol was applied to both Flongle and MinION flow cells, analyzing 12 and 40 samples, respectively. Data analysis suggested that optimal performance could be achieved by processing 6 and 12 samples with similar microscope staining scores on these two platforms. This approach facilitated rapid antimicrobial resistance (AMR) predictions directly from sputum on the day of collection or the following day, with a cost of less than $35 per sample. Compared to AMR predictions based on whole-genome sequencing (WGS) using Mykrobe and TBProfiler, our amplicon-based analysis tool, ARapidTb, demonstrated superior resistance detection capabilities. When analyzing publicly available nanopore WGS datasets for 442 isolates, ARapidTb achieved agreement rates of 95.8% and 98.0%, outperforming Mykrobe (89.4% and 98.3%) and TBProfiler (75.6% and 89.8%).<br><br>CONCLUSIONS: Our study significantly reduces the time required for drug resistance detection, enabling quicker initiation of appropriate treatments and potentially improving patient outcomes and TB management.}, }
@article {pmid39821447, year = {2025}, author = {Zhang, C and Li, J and Yan, F and Wang, Z and Zeng, X and Zhang, J}, title = {Comparative analysis of the complete chloroplast genome of seven Wikstroemia taxa (Thymelaeaceae) provides insights into the genome structure and phylogenetic relationships.}, journal = {Planta}, volume = {261}, number = {2}, pages = {40}, pmid = {39821447}, issn = {1432-2048}, support = {2022QB-153//Science Fund for Distinguished Young Scholars of Gansu Province/ ; KYQD2022013//Doctoral Start-up Foundation of Hexi University/ ; 22JR11RG225//the Natural Science Foundation of Gansu Province, China/ ; 202210740073//National College Students Innovation and Entrepreneurship Training Program/ ; 22CX8NA071//the Technology Innovation Guidance Program Project of Gansu Provincial "Research and Popularization of Ecological Planting Techniques for Economic Shrubs Daphne tangutica Maxim. in Qilian Mountains"/ ; No. 32260472//the National Natural Science Foundation of China/ ; }, mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; Base Composition/genetics ; }, abstract = {New insights into the phylogeny of species in the family Thymelaeaceae and support of the recognition of D. genkwa and D. aurantiaca as species in the genus Wikstroemia are provided. Wikstroemia (Thymelaeaceae) is an economically important genus because some of its species are used in traditional medicine and also contribute to pulp production. The morphological characteristics of Wikstroemia species exhibit continuous natural variation, posing a challenge in accurately distinguishing this genus from its sister genera solely based on morphological traits. Consequently, the classification of, and phylogenetic relationships between, Wikstroemia and its sister genera, as inferred from morphological characteristics, remain contentious. Chloroplast genome information has proven to be a valuable tool in plant phylogeny. Here, we performed a comparative analysis of the chloroplast genomes of 15 species in the genus Wikstroemia, all of which exhibited typical quadripartite structures, with sizes ranging from 150,054 bp to 175,898bp. These genomes encoded 122-143 genes, including 79-95 protein-coding genes, 36-40 tRNA genes, and 8 rRNA genes. The overall GC content displayed minimal variation, ranging from 36.6% to 37.47%. The distributions of SSRs and codon bias exhibited similarities among Wikstroemia species. High variability hotspots were found in 15 intergenic spacers and 5 genes. Phylogenetic analyses consistently grouped all Wikstroemia species into a single clade. Notably, Daphne genkwa and D. aurantiaca were found to be nested within Wikstroemia, rather than being closely related to other Daphne species. Furthermore, phylogenetic analyses suggested that Wikstroemia is paraphyletic relative to Stellera chamaejasme. These findings provide new insights into the phylogeny of Wikstroemia and Daphne within the Thymelaeaceae, contributing to improved species identification and increasing the taxonomic and phylogenetic resolution of Wikstroemia.}, }
@article {pmid39821021, year = {2025}, author = {Merle, C and Fre, S}, title = {Recording Lineage History with Cellular Barcodes in the Mammary Epithelium and in Breast Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1464}, number = {}, pages = {77-94}, pmid = {39821021}, issn = {0065-2598}, mesh = {Humans ; *Breast Neoplasms/pathology/genetics/metabolism ; *Cell Lineage ; Female ; Animals ; Single-Cell Analysis/methods ; *Mammary Glands, Human/pathology/metabolism/cytology ; *DNA Barcoding, Taxonomic/methods ; }, abstract = {Lineage tracing methods have extensively advanced our understanding of physiological cell behaviour in vivo and in situ and have vastly contributed to decipher the phylogeny and cellular hierarchies during normal and tumour development. In recent years, increasingly complex systems have been developed to track thousands of cells within a given tissue or even entire organisms. Cellular barcoding comprises all techniques designed to genetically label single cells with unique DNA sequences or with a combination of fluorescent proteins, in order to trace their history and lineage production in space and time. We distinguish these two types of cellular barcoding as genetic or optical barcodes. Furthermore, transcribed cellular barcodes can integrate the lineage information with single-cell profiling of each barcoded cell. This enables the potential identification of specific markers or signalling pathways defining distinct stem cell states during development, but also signals promoting tumour growth and metastasis or conferring therapy resistance.In this chapter, we describe recent advances in cellular barcoding technologies and outline experimental and computational challenges. We discuss the biological questions that can be addressed using single-cell dynamic lineage tracing, with a focus on the study of cellular hierarchies in the mammary epithelium and in breast cancer.}, }
@article {pmid39820073, year = {2025}, author = {Yeh, YH and Kirschner, R}, title = {Study of endophytic fungi of Ipomoea pes-caprae reveals the superiority of in situ plant conservation over ex situ conservation from a mycological view.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2040}, pmid = {39820073}, issn = {2045-2322}, support = {NSTC 110-2811-B-002-568//National Science and Technology Council/ ; NSTC 111-2811-B-002-092//National Science and Technology Council/ ; NSTC 112-2811-B-002-150//National Science and Technology Council/ ; MOST 108-2621-B-002-007//National Science and Technology Council/ ; 109-2621-B-002-004//National Science and Technology Council/ ; 110-2621-B-002-001-MY2//National Science and Technology Council/ ; }, mesh = {*Endophytes/genetics/classification/isolation &amp; purification ; *Ipomoea/microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Conservation of Natural Resources ; Biodiversity ; Phylogeny ; Taiwan ; Principal Component Analysis ; }, abstract = {In nature conservation, ex situ and in situ conservation strategies are discussed for protecting endangered species of plants and animals. However, the impacts of these strategies on the microbes associated with these species are rarely considered. In our study, we chose the endophytic fungi of the pantropical creeping plant Ipomoea pes-caprae as representative coastal plant in two natural coastal populations and two botanical gardens in Taiwan as collection sites in order to investigate the potential effect of ex situ plantation on the biodiversity of microbes intimately associated with this plant. In a culture-dependent approach, endophytic fungi were isolated under axenic conditions and identified to species, genus, or higher taxonomic ranks with DNA barcodes and morphology. In addition to yielding ca. 800 strains and over 100 morphospecies, a principal component analysis (PCA) of the distribution of the dominant fungal species showed clear differences in the composition of endophytic fungal species depending on the sampling sites. We conclude that the endophytic fungi from the original site are replaced by other species in the ex situ plantations. Due to the limitations of ex situ conservation of microbes and from a mycological and microbial perspective, in situ conservation should outweigh ex situ approaches.}, }
@article {pmid39819888, year = {2025}, author = {Sun, J and Philpott, M and Loi, D and Hoffman, G and Robson, J and Mehta, N and Calcutt, E and Gamble, V and Brown, T and Brown, T and Oppermann, U and Cribbs, AP}, title = {Enhancing single-cell transcriptomics using interposed anchor oligonucleotide sequences.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {67}, pmid = {39819888}, issn = {2399-3642}, support = {MR/V010182/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {*Single-Cell Analysis/methods ; *Oligonucleotides/genetics ; *Gene Expression Profiling/methods ; *Transcriptome ; Humans ; RNA, Messenger/genetics ; Sequence Analysis, RNA/methods ; }, abstract = {Single-cell transcriptomics, which utilises barcodes and unique molecular identifiers (UMIs) for polyA+ mRNA capture, is compromised by oligonucleotide synthesis errors. To address this, we modified the oligonucleotide capture design and integrated an interposed anchor between the barcode and the UMI. This design significantly reduces the need to discard reads due to synthesis inaccuracies. Our results demonstrate that this anchor-enhanced design substantially improves gene expression profiles in droplet-based single-cell sequencing analyses.}, }
@article {pmid39819789, year = {2025}, author = {Chaumeau, V and Sawasdichai, S and Min, TZMMM and Kularbkeeree, T and Jaruwan, N and Gloria, N and Lee, NY and Trackoolchengkaew, M and Phanaphadungtham, M and Rongthong, P and Inta, A and Watthanaworawit, W and Nosten, F}, title = {Identification of Southeast Asian Anopheles mosquito species with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a cross-correlation approach.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {8}, pmid = {39819789}, issn = {1756-3305}, support = {/WT_/Wellcome Trust/United Kingdom ; 220211/WT_/Wellcome Trust/United Kingdom ; OPP1177406//Bill and Melinda Gates Foundation/ ; }, mesh = {Animals ; *Anopheles/classification/genetics/chemistry ; DNA Barcoding, Taxonomic ; Myanmar ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; }, abstract = {BACKGROUND: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is proposed for mosquito species identification. The absence of public repositories sharing mass spectra and open-source data analysis pipelines for fingerprint matching to mosquito species limits the widespread use of this technology. The objective of this study was to develop a free open-source data analysis pipeline for Anopheles species identification with MALDI-TOF MS.<br><br>METHODS: Anopheles mosquitoes were captured in 33 villages in Karen (Kayin) state in Myanmar. A subset of 403 specimens was selected for inclusion in either the reference or the test panel (270 and 133 specimens, respectively). Three hundred fifty-nine specimens could be identified with DNA barcodes and were assigned to 21 sensu stricto species and five sibling species pairs or complexes. A total of 3584 mass spectra of the head of these specimens identified with DNA barcoding were acquired and the similarity between mass spectra was quantified using a cross-correlation approach adapted from the published literature. A reference mass spectra database was created using all spectra of the PCR-identified specimens assigned to the reference panel. A simulation experiment was carried out by querying the reference database with the spectra of the test panel to evaluate the performance of species identification with MALDI-TOF MS at varying thresholds of the cross-correlation index for the algorithm to output an identification result and with varying numbers of technical replicates for the tested specimens, considering PCR identification results as the reference.<br><br>RESULTS: With one spot and a threshold value of -14 for the cross-correlation index on the log scale, the sensitivity was 0.99 [95% credible interval (CrI): 0.98-1.00], the predictive positive value was 0.99 (95% CrI: 0.98-0.99), and the accuracy was 0.98 (95% CrI: 0.97-0.99). It was not possible to directly estimate the sensitivity and negative predictive value because there was no true negative (i.e., queries of species not referenced in the database) in the assessment.<br><br>CONCLUSIONS: The cross-correlation approach can be used to match mass spectral fingerprints to predefined taxa. MALDI-TOF MS is a valuable tool for rapid, accurate, and affordable identification of Anopheles species.}, }
@article {pmid39816673, year = {2025}, author = {Marquisseau, A and Canale-Tabet, K and Labarthe, E and Pascal, G and Klopp, C and Pornon, A and Escaravage, N and Rudelle, R and Vignal, A and Ouin, A and Ollivier, M and Pichon, M}, title = {Building a reliable 16S mini-barcode library of wild bees from Occitania, south-west of France.}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e137540}, pmid = {39816673}, issn = {1314-2828}, abstract = {BACKGROUND: DNA barcoding and metabarcoding are now powerful tools for studying biodiversity and especially the accurate identification of large sample collections belonging to diverse taxonomic groups. Their success depends largely on the taxonomic resolution of the DNA sequences used as barcodes and on the reliability of the reference databases. For wild bees, the barcode sequences coverage is consistently growing in volume, but some incorrect species annotations need to be cared for. The COI (Cytochrome Oxydase subunit 1) gene, the most used in barcoding/metabarcoding of arthropods, suffers from primer bias and difficulties for covering all wild bee species using the classical Folmer primers.<br><br>NEW INFORMATION: We present here a curated database for a 250 bp mini-barcode region of the 16S rRNA gene, suitable for low-cost metabarcoding wild bees in applications, such as eDNA analysis or for sequencing ancient or degraded DNA. Sequenced specimens were captured in Occitania (south-west of France) and morphologically identified by entomologists, with a total of 530 individuals belonging to 171 species and 19 genera. A customised workflow including distance-tree inferences and a second round of entomologist observations, when necessary, was used for the validation of 348 mini-barcodes covering 148 species. Amongst them, 93 species did not have any 16S reference barcode available before our contribution. This high-quality reference library data are freely available to the scientific community, with the aim of facilitating future large-scale characterisation of wild bee communities in a context of pollinators' decline.}, }
@article {pmid39814875, year = {2025}, author = {Elzain, IA and Idris, AB and Karim, AA and Ahmed, NM and Elzaki, SG and Yılmaz, S and Hassan, MA and Abdalla, HS}, title = {Analysis of DNA cox1 barcoding revealed novel haplotype in Schistosoma haematobium isolated from Western Sudan.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2062}, pmid = {39814875}, issn = {2045-2322}, mesh = {*Schistosoma haematobium/genetics/isolation &amp; purification ; Sudan/epidemiology ; Humans ; Child ; Animals ; Adolescent ; *Haplotypes ; *Schistosomiasis haematobia/parasitology/epidemiology ; *Cyclooxygenase 1/genetics ; *DNA Barcoding, Taxonomic/methods ; Male ; Female ; Phylogeny ; Cross-Sectional Studies ; Child, Preschool ; Young Adult ; Feces/parasitology ; Genetic Variation ; }, abstract = {Schistosomiasis poses a significant global health threat, particularly in tropical and subtropical regions like Sudan. Although numerous epidemiological studies have examined schistosomiasis in Sudan, the genetic diversity of Schistosoma haematobium populations, specifically through analysis of the mtcox1 gene, remains unexplored. This study aimed to investigate the risk factors associated with urogenital schistosomiasis among school pupils in El-Fasher, Western Sudan, as well as the mtcox1 genetic diversity of human S. haematobium in this region. A cross-sectional study was conducted among school pupils aged 4 to 19 years. In total, 196 urine samples and 196 fecal samples were collected from participants across schools, health centers, and refugee camps in El-Fasher. Samples were examined using simple centrifugation/sedimentation technique and formol-ether concentration method to detect S. haematobium and S. mansoni eggs, respectively. S. haematobium mtcox1 partial gene was amplified and sequenced by the Sanger technique. A neighbor-joining phylogenetic tree was generated by MEGA software, and a haplotype network was constructed using PopART v.1.7 with the median-joining network method. In this study, S. haematobium was detected in 6.1% (12/196) of the participants while no S. mansoni ova were observed in fecal samples. The infection was more common among those who relied on indirect water supply like tankers (6, 50%). No infection was observed among residents of refugee camps. Only eight samples were PCR-positive, which were successfully sequenced, and included in the genetic diversity analysis. A unique haplotype (Hap_1) with no sequence diversity was found among cox1 sequences from El-Fasher strains. Both El-Fasher S. haematobium haplotype (Hap_1) and Gezira haplotype (Hap_31) fall within the mainland Africa group (group 1). In conclusion, this study identified a novel S. haematobium strain and provides insights into the evolutionary history and phylogeography of S. haematobium in Sudan, particularly in the western region. This genetic data could help in the control and monitoring of urogenital schistosomiasis in this region. For the first time, we utilized the DNA mtcox1 barcoding to investigate S. haematobium haplotypes in Western Sudan.}, }
@article {pmid39814794, year = {2025}, author = {Yassin, S and Elsohafy, SM and El-Hawiet, A and Abdel-Kader, MS and Ghareeb, DA and Darwish, FA and Amer, ME}, title = {Comparative phytochemical and pharmacological analysis of two cultivars of Annona squamosa L. cultivated in Egypt.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {8}, pmid = {39814794}, issn = {2396-8370}, abstract = {This study compared two Annona squamosa L. cultivars, Abdelrazik (Annona A.) and Balady (Annona B.), in terms of their chemical profile, in vitro cytotoxicity against HCT-116 and A549 cell lines, and total acetogenin. In addition, the two cultivars pulp were compared regarding carbohydrates and magnesium ions content and immunomodulating activity. The two cultivars were also differentiated genetically by DNA barcoding using the universal primer matK and the specific primer Annona squamosa matK. The results showed that Annona A. seeds had higher acetogenin content and exhibited more potent cytotoxic activity against the two cell lines. In contrast, Annona B. pulp had higher carbohydrate content and lower magnesium ions content. The splenic lymphocyte proliferation assay revealed that Annona A. pulp extract was slightly more active as an immunostimulant. The specific primer used for DNA barcoding was more effective for species identification, while the universal primer was better for cultivar differentiation. Overall, our findings indicate the potential for using active compounds of Annona squamosa L. cultivars to develop new therapeutic agents for cancer therapy and immune enhancement.}, }
@article {pmid39813480, year = {2025}, author = {Câmara, PEAS and Pellizzari, FM and Lopes, FAC and Amorim, ET and Bones, FLV and Anjos, DA and Carvalho-Silva, M and Convey, P and Rosa, LH}, title = {DNA metabarcoding reveal hidden diversity of periphytic eukaryotes on marine Antarctic macroalgae.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {96}, number = {suppl 2}, pages = {e20240570}, doi = {10.1590/0001-3765202420240570}, pmid = {39813480}, issn = {1678-2690}, mesh = {Antarctic Regions ; *DNA Barcoding, Taxonomic/methods ; *Seaweed/classification/genetics ; *Biodiversity ; *Eukaryota/genetics/classification ; Rhodophyta/classification/genetics ; Phaeophyceae/classification/genetics ; Chlorophyta/classification/genetics ; }, abstract = {Polar marine macroalgae thrive in extreme conditions, often displaying geographic isolation and high degree of endemism. The "phycosphere" refers to the zone around the algae inhabited by microrganisms. Our study used DNA metabarcoding to survey the eukaryotic communities associated with seven seaweed species obtained at King George Island (South Shetland Islands, maritime Antarctic), including two Rhodophyta, two Chlorophyta and three Phaeophyceae. The ITS2 region was used as a barcode and our analysis yielded 77 eukaryotic ASVs spanning five Kingdoms (Fungi, Metazoa, Chromista, Protozoa, and Viridiplantae) and ten phyla (Ascomycota, Basidiomycota, Cercozoa, Ciliophora, Ochrophyta, Amebozoa, Chlorophyta, Rhodophyta, Bryophyta and Cnidaria). Additionally, we identified 14 potential new occurrence records for Antarctica. Ciliates and green algae were the most species-rich groups. The most abundant assigned associated species was Monostroma angicava (Chrorophyta). Within the macroalgal, the Chlorophyceans Ulothrix sp. hosted the greatest number of taxa, followed by Monostroma hariotii. Our data suggested that Antarctic macroalgae host a rich diversity of associated organisms and the biodiversity associated with the phycosphere remains underestimated.}, }
@article {pmid39813353, year = {2025}, author = {Trende, R and Darling, TL and Gan, T and Wang, D and Boon, ACM}, title = {Barcoded SARS-CoV-2 viruses define the impact of duration and route of exposure on the transmission bottleneck in a hamster model.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eads2927}, pmid = {39813353}, issn = {2375-2548}, support = {75N93021C00016/AI/NIAID NIH HHS/United States ; R01 AI169022/AI/NIAID NIH HHS/United States ; U01 AI151810/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *SARS-CoV-2/genetics ; *COVID-19/transmission/virology ; Cricetinae ; Disease Models, Animal ; Lung/virology ; Humans ; Mesocricetus ; Trachea/virology ; *DNA Barcoding, Taxonomic ; }, abstract = {The transmission bottleneck, defined as the number of viruses shed from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission bottleneck remains poorly characterized. We adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes, infected donor hamsters with this pool, and exposed contact hamsters to paired infected donors, varying the duration and route of exposure. Following exposure, the nasal turbinates, trachea, and lungs were collected and the number of barcodes in each tissue was enumerated. We found that longer and more direct exposures increased the transmission bottleneck and that the upper airway is the primary source of transmitted virus in this model. Together, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission.}, }
@article {pmid39811811, year = {2024}, author = {Duan, HN and Jiang, YZ and Yang, JB and Cai, J and Zhao, JL and Li, L and Yu, XQ}, title = {Skmer approach improves species discrimination in taxonomically problematic genus Schima (Theaceae).}, journal = {Plant diversity}, volume = {46}, number = {6}, pages = {713-722}, pmid = {39811811}, issn = {2468-2659}, abstract = {Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants. However, conserved DNA barcoding markers, including complete plastid genome and nuclear ribosomal DNA (nrDNA) sequences, are inadequate for accurate species identification. Skmer, a recently proposed approach that estimates genetic distances among species based on unassembled genome skims, has been proposed to effectively improve species discrimination rate. In this study, we used Skmer to identify species based on genomic skims of 47 individuals representing 10 out of 13 species of Schima (Theaceae) from China. The unassembled reads identified six species, with a species identification rate of 60%, twice as high as previous efforts that used plastid genomes (27.27%). In addition, Skmer was able to identify Schima species with only 0.5× sequencing depth, as six species were well-supported with unassembled data sizes as small as 0.5 Gb. These findings demonstrate the potential for Skmer approach in species identification, where nuclear genomic data plays a crucial role. For taxonomically difficult taxa such as Schima, which have diverged recently and have low levels of genetic variation, Skmer is a promising alternative to next generation barcodes.}, }
@article {pmid39811021, year = {2025}, author = {Mutafchiev, Y and Roman, Y and Griffiths, K and Kenderov, L and Michalski, ML}, title = {DNA-elucidated life cycle of a highly pathogenic avian nematode: Streptocara incognita (Spirurida: Acuariidae) and its morphological development from infective third-stage larva to adult.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {7}, number = {}, pages = {100238}, pmid = {39811021}, issn = {2667-114X}, abstract = {Streptocara incognita Gibson, 1968 is an acuariid nematode associated with lethal cases of streptocarosis of diverse aquatic birds in North America and Europe. This study reports S. incognita as an agent causing severe and fatal necrosis of the oesophagus and proventriculus of anatids, i.e. Somateria mollissima (L.), Marmaronetta angustirostris (Ménétriés), Tadorna tadorna (L.) and Spatula querquedula (L.), kept in open pens in the Zoological Park, Clères, France. Comparative analysis of 12S rRNA gene sequences revealed that third-stage infective nematode larvae found in the amphipod Gammarus pulex pulex (L.) in the river passing through the pens belong to S. incognita thus elucidating the life cycle of this species. A partial sequence of the cox1 gene was also generated. To complement the brief original description of S. incognita, a detailed morphological description of the adult stages is provided based on light and scanning electron microscopy. Additionally, morphological data on the developing third- and fourth-stage larvae found in the definitive host and third-stage infective nematode larvae found in G. pulex pulex are also provided. This is the first record of an intermediate host of S. incognita. Somateria mollissima, M. angustirostris and S. querquedula are new host records.}, }
@article {pmid39809848, year = {2025}, author = {Kniesz, K and Hoffman, L and Martínez Arbizu, P and Kihara, TC}, title = {High genomic connectivity within Anatoma at hydrothermal vents along the Central and Southeast Indian Ridge.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1971}, pmid = {39809848}, issn = {2045-2322}, mesh = {*Hydrothermal Vents ; Animals ; *Gastropoda/genetics/classification ; India ; Phylogeny ; Ecosystem ; Genomics ; Gene Flow ; }, abstract = {Hydrothermal vents are ecosystems inhabited by a highly specialized fauna. To date, more than 30 gastropod species have been recorded from vent fields along the Central and Southeast Indian Ridge and all of them are assumed to be vent-endemic. During the INDEX project, 701 representatives of the genus Anatoma (Mollusca: Vetigastropoda) were sampled from six abyssal hydrothermal vent fields. Traditional morphology and COI barcoding of Hoffman et al. (Eur J Taxon 826:135-162, 2022) were combined with 2b-RAD sequencing to investigate the anatomid community structure and connectivity between the different vent fields. Consequently, 2b-RAD sequencing supported the primary species hypothesis (based on morphology) for 125 individuals of the recently described taxa A. discapex, A. declivis, A. laevapex and A. paucisculpta. We assigned 22 additional specimens to species with 2b-RAD sequencing and updated the community analyses that confirmed the pattern of expanding populations. Population structure and FST values indicated high connectivity along the six sampled vent fields for the three most abundant species. High levels of gene flow are suggested, pointing to high dispersal potential of the target species along the study area. However, low levels of heterozygosity revealed a small gene pool and therefore an increased vulnerability towards environmental change. Our results demonstrate that 2b-RAD sequencing, in combination with other molecular methods, can accurately characterise macrobenthic mollusc communities. Sequencing technology is an essential tool for ongoing monitoring. Furthermore, we highlight that the inferred molecular and ecological patterns provide valuable insights into hydrothermal vent ecosystems, which are crucial for the successful conservation of these ecosystems.}, }
@article {pmid39809825, year = {2025}, author = {Eroğlu, M and Çelik, I and Düşükcan, M and Ünal, EM and Çoban, MZ and Gündüz, F and Keskin, E}, title = {DNA barcoding of invasive Gambusia holbrooki Girard, 1859 and Atherina boyeri Risso, 1810 inhabiting Upper Euphrates River Basin, Türkiye.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1907}, pmid = {39809825}, issn = {2045-2322}, support = {SUF-16.13//F&#x131;rat University Scientific Research Projects Coordination Office/ ; }, mesh = {Animals ; *Introduced Species ; *Cyprinodontiformes/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Rivers ; Electron Transport Complex IV/genetics ; Phylogeny ; }, abstract = {The main contributor to Türkiye's abundant freshwater fish biodiversity is its geographic location. This fauna consists of endemic, native, and non-native fish species. The introduction of Gambusia holbrooki Girard, 1859 to Lake Amik in the 1920s for the biological control of malaria was the first introduction of nonnative species to Türkiye. Atherina boyeri Risso, 1810 and other nonnative fish species have recently been introduced to Türkiye's freshwaters. In this research, the first records of invasive Gambusia holbrooki (Keban Dam Lake, in Elazığ Province) and Atherina boyeri (Karakaya Dam Lake, in Elazığ Province) are cited from the Upper Euphrates River Basin in the Eastern Anatolia Region of Türkiye. In situ electrofishing equipment was used to gather the specimens. Fish muscle samples were used to extract genomic DNA, which was then used to barcode the mitochondrial cytochrome c oxidase subunit I (COI) gene to identify different species of fish. The identification of invasive fish species using DNA barcoding is an effective technique, as evidenced by the comparison of amplified COI sequences to the BLAST database.}, }
@article {pmid39807677, year = {2025}, author = {Lin, YC and Lee, LR and Tsai, TH and Lin, J and Hsu, YS and Kesavan, M and Lin, YL and Chen, YF and Chen, JT}, title = {A Streamlined Approach to Anticounterfeiting Technologies: Patterned AAO Membranes Based on Photonic Crystal Effects with Tunable Color Shifts and pH Responsiveness.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {21}, number = {8}, pages = {e2409919}, pmid = {39807677}, issn = {1613-6829}, support = {//Center for Emergent Functional Matter Science of National Yang Ming Chiao Tung University/ ; NSTC 112-2628-E-A49-012//National Science and Technology Council/ ; NSTC 113-2628-E-A49-006//National Science and Technology Council/ ; NSTC113-2740-M-007-001//National Science and Technology Council/ ; }, abstract = {Anticounterfeiting technologies have become increasingly crucial due to the growing issue of counterfeit goods, particularly in high-value industries. Traditional methods such as barcodes and holograms are prone to replication, prompting the need for advanced, cost-effective, and efficient solutions. In this work, a practical application of anodic aluminum oxide (AAO) membranes are presented for anticounterfeiting, which addresses the challenges of high production costs and complex fabrication processes. Unlike previous approaches requiring metal coatings for color generation, this method uses commercial aluminum foils to produce colorful AAO membranes without metal layers. Elemental mapping suggests that impurities on the aluminum surface contribute to enhanced reflectivity, aiding photonic crystal formation. A two-step anodization process that creates patterned AAO membranes is further introduced, with the pattern clarity controlled by anodization time. Additionally, a pH-responsive film composed of 2-anilino-6-dibutylaminofluoran (ODB-2) and thermoplastic polyurethane (TPU) is integrated, enabling dynamic color changes under varying pH conditions, further enhancing the anticounterfeiting functionality. This streamlined approach provides a scalable and cost-effective solution for developing versatile AAO membranes for industrial anticounterfeiting applications.}, }
@article {pmid39805772, year = {2024}, author = {Chen, ZY and Hua, ZY and Yuan, Y}, title = {[Establishment and application of chloroplast genome database with the largest number of species in world].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {23}, pages = {6257-6263}, doi = {10.19540/j.cnki.cjcmm.20240909.101}, pmid = {39805772}, issn = {1001-5302}, mesh = {*Genome, Chloroplast ; *Plants/genetics/classification ; *Databases, Genetic ; Phylogeny ; *Chloroplasts/genetics ; }, abstract = {The chloroplast genome is an important tool for studying plant classification, evolution, and the heterologous production of secondary metabolites and protein drugs. With advancements in sequencing technology and reductions in sequencing costs, chloroplast genome data have rapidly accumulated. However, existing chloroplast genome databases suffer from issues such as incomplete data, inadequate management, and inconsistent, inaccurate information, posing significant challenges for the development and utilization of the chloroplast genome. Therefore, it is urgently necessary to establish a database that provides comprehensive and reliable chloroplast genome information. This article provides a brief introduction to the Chloroplast Genome Information Resource(CGIR), the most comprehensive chloroplast genome database globally in terms of species coverage. The database, consisting of five modules, i.e.,(1) genomes,(2) genes,(3) simple sequence repeats(SSRs),(4) DNA barcodes, and(5) DNA signature sequences(DSSs), currently includes 34 923 chloroplast genome assemblies from 16 717 species. Based on the functionalities of these modules, the article systematically summarizes the progress in the application of the database in plant phylogenetic analysis, species identification, and chloroplast genetic engineering. The chloroplast genome database will be continuously updated in the future to provide a solid and reliable data foundation for chloroplast genome research, further promoting studies on traditional Chinese medicine(TCM)identification, resource conservation, and germplasm innovation.}, }
@article {pmid39805757, year = {2024}, author = {Li, XY and Guo, H and Ma, MX and Xu, LW and Huang, YH and Zhang, Y and Yang, CP and He, F and Tian, XX}, title = {[Mini-barcode combined with ITS2 for identification of bulk Artemisiae Scopariae Herba].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {24}, pages = {6685-6691}, doi = {10.19540/j.cnki.cjcmm.20240912.101}, pmid = {39805757}, issn = {1001-5302}, mesh = {*Artemisia/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA, Plant/genetics ; *DNA, Ribosomal Spacer/genetics ; }, abstract = {Artemisiae Scoporiae Herba is derived from Artemisia scoparia or A. capillaris. The accurate identification of the herbs, particularly when dealing with bulk samples, is critical for ensuring the quality and efficacy of the medicinal product. This study aimed to establish a comprehensive molecular approach by combining multiple markers for the precise identification of Artemisiae Scoporiae Herba. The ITS2 from A. scoparia, A. capillaris, and other common Artemisia species were retrieved from GenBank. MEGA was used to build a phylogenetic tree with these sequences, and the effectiveness of ITS2 in species identification was assessed. The analysis revealed that while ITS2 could distinguish Artemisiae Scoporiae Herba from other closely related species of Artemisia, it was insufficient to differentiate between A. scoparia and A. capillaris. To address this limitation, the chloroplast genome of A. capillaris was assembled and compared with the published chloroplast genomes of A. scoparia and A. capillaris, on the basis of which a DNA mini-barcode was developed. The rpoA-rps11 region was selected as the target for the development of mini-barcode due to its potential for distinguishing between these two species. Specific primers were designed to differentiate A. scoparia from A. capillaris. The ITS2 sequences and the newly developed mini-barcode were used together for Sanger sequencing to identify individual samples of Artemisiae Scoporiae Herba, while DNA metabarcoding was employed for the identification of bulk samples. The identification results of representative individual samples and bulk samples from different regions consistently confirmed A. capillaris. This study established a method that combined ITS2 and mini-barcode to identify bulk samples of Artemisiae Scoporiae Herba from different regions. This approach overcomes the limitations of morphological and chemical methods, enhancing species identification accuracy and supporting a stable supply of medicinal materials.}, }
@article {pmid39803186, year = {2025}, author = {Yao, J and Zheng, Z and Xu, T and Wang, D and Pu, J and Zhang, Y and Zha, L}, title = {Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum.}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70831}, pmid = {39803186}, issn = {2045-7758}, abstract = {The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of Polygonatum medicinal plants (P. zanlanscianense, P. kingianum, P. sibiricum, P. cyrtonema, P. filipes, and P. odoratum, respectively) to explore their interspecific relationships. The sequence length (154, 578-155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. Among the 127-131 genes contained in the genomes, 84-85 are protein-coding genes, 37-38 are transfer RNA genes, and 6-8 are ribosomal RNA genes. The genomes contained 64-76 simple sequence repeats (SSRs) and 36-62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In 30 types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty-one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. Furthermore, a phylogenetic analysis encompassing these and 53 other chloroplast genomes of Polygonatum species revealed that P. cyrtonema, P. odoratum, and P. filipes clustered together on one clade, whereas P. kingianum and P. zanlanscianense formed separate clades. Notably, P. sibiricum emerged as a standalone clade, and our phylogenetic tree reinforces the classification of P. sibiricum as forming a monophyly. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.}, }
@article {pmid39802739, year = {2025}, author = {Meng, Z and Zheng, Q and Wang, W and Zhu, Y and Li, Y and Dong, F and Luo, W and Zhang, Z and Wang, F and Shen, H and Xie, Q and Li, H}, title = {Oligo-FISH barcode chromosome identification system provides novel insights into the natural chromosome aberrations propensity in the autotetraploid cultivated alfalfa.}, journal = {Horticulture research}, volume = {12}, number = {1}, pages = {uhae266}, pmid = {39802739}, issn = {2662-6810}, abstract = {Alfalfa is one of the most economically valuable forage crops in the world. However, molecular cytogenetic studies in alfalfa lag far behind other cash crops and have reached a bottleneck. Here, we developed a novel chromosome identification system by designing 21 oligo probes in specific regions of each chromosome, which can be used as a barcode to simultaneously distinguish all chromosomes in a cell. Using this system, we revealed the chromosome karyotype features and evolutionary differences among 10 cultivated alfalfa varieties. Interestingly, we also found two chromosomal variation types, i.e. aneuploidy and large chromosomal segment deletions in the seeds of three alfalfa varieties. Variation frequency analysis showed that only 7/173 seeds in those three alfalfa varieties had chromosome aberrations, which indicated that the inheritance and meiosis of alfalfa had evolved to a relatively stable state. Remarkably, 4/7 variation seeds were chromosome 2 aberrations, suggesting that chromosome 2 appears to be more susceptible to natural chromosomal aberrations than other chromosomes during inheritance. DNA sequence variation analysis showed that the difference of presence and absence variations (PAVs) among homologous copies of chromosome 2 was larger than that of the other seven chromosomes. We suggest that such large PAV divergence among homologous copies may provide the physical basis for natural chromosome 2 aberrations propensity. Our study provides a valuable and efficient tool for alfalfa's molecular cytogenetics and sheds new insights into the propensity for natural chromosome aberrations during autopolyploid inheritance.}, }
@article {pmid39801509, year = {2025}, author = {Hao, L and Yu, K and Zhang, F}, title = {Description of five new species from southern China, with note on the type species of Latouchia Pocock, 1901 (Araneae, Halonoproctidae).}, journal = {Biodiversity data journal}, volume = {13}, number = {}, pages = {e137852}, pmid = {39801509}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Latouchia Pocock, 1901 previously included 25 known species and one subspecies from Asia, 12 species and one subspecies were reported in China.<br><br>NEW INFORMATION: Five new species of Latouchia Pocock, 1901 from southern China are described: L.calcicola sp. nov. (&#x2642;&#x2640;) from Hainan, L.jinyun sp. nov. (&#x2642;&#x2640;) from Chongqing, L.linmufu sp. nov. (&#x2642;&#x2640;) from Hunan, L.wenchuan sp. nov. (&#x2642;) from Sichuan and L.yaoi sp. nov. (&#x2642;&#x2640;) from south part of Shaanxi. DNA barcodes of the new species described herein are provided. The potential error in the previous illustrations of the alleged male of L.fossoria Pocock, 1901 (type species of the genus) is pointed out.}, }
@article {pmid39799216, year = {2025}, author = {Shi, C and Guo, Y and Yao, L and Xu, Y and Zhou, J and Hua, M}, title = {Development of a mitochondrial mini-barcode and its application in metabarcoding for identification of leech in traditional Chinese medicine.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1698}, pmid = {39799216}, issn = {2045-2322}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Leeches/genetics/classification ; *Medicine, Chinese Traditional ; RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; }, abstract = {In Traditional Chinese Medicine (TCM), the medicinal leech is vital for treatments to promote blood circulation and eliminate blood stasis. However, the prevalence of counterfeit leech products in the market undermines the quality and efficacy of these remedies. Traditional DNA barcoding techniques, such as the COI barcode, have been limited in their application due to amplification challenges. This study identified high variability in the 16 S rRNA gene within the mitochondrial genome across five leech species, leading to the development of a novel 219 bp mini-barcode. Compared with the traditional COI barcode, our mini-barcode showed remarkable identification efficiency, classifying 142 out of 147 leech samples from fresh and processed materials. In contrast, the COI barcode could only successfully identify 79 out of the 147 samples. In the case of seven batches of leech decoction pieces, the mini-barcode identified six, whereas the COI barcode only recognized one. Additionally, the mini-barcode effectively discerned five leech species within Chinese patent medicines when combined with metabarcoding technology. These results confirm the mini-barcode's potential as a reliable tool for rapidly and precisely identifying leech species in TCM products.}, }
@article {pmid39795359, year = {2025}, author = {Jiamahate, A and Bozorov, TA and Wang, J and Zhang, J and Zhang, H and Wang, X and Yang, H and Zhang, D}, title = {Insights from DNA Barcodes-Based Phylogenetic Analysis of Medicinal Plants and Estimation of Their Conservation Status: A Case Study in the Tianshan Wild Forest, China.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, pmid = {39795359}, issn = {2223-7747}, support = {Grant No.2021xjkk0500//Third Xinjiang Scientific Expedition Program/ ; 2021-XBQNXZ-015//the West Light Talents Cultivation Program of the Chinese Academy of Sciences/ ; Grant No. 31700289//the National Natural Science Foundation of China/ ; 2022D01A354//the Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; ZDBS-LY-SM009//Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; 2022TSYCLJ0049//Leading Talents in Technological Innovation programme/ ; }, abstract = {The Tianshan wild fruit forest region is a vital repository of plant biodiversity, particularly rich in the unique genetic resources of endemic medicinal plants in this ecological niche. However, human activities such as unregulated mining and excessive grazing have led to a significant reduction in the diversity of these medicinal plants. This study represents the first application of DNA barcoding to 101 medicinal plants found in the Tianshan wild fruit forests, using three genetic loci along with morphological identification methods. A phylogenetic analysis was performed to delineate species relationships. The results indicate that the internal transcribed spacer (ITS) region has been identified as the most reliable barcode for species identification across different families, while combining data from multiple gene segments can improve species detection. Moreover, the Analytical Hierarchy Process (AHP) was employed to assess and prioritize the 101 medicinal plants, highlighting 23 species as candidates for urgent conservation efforts in the region. The approaches and insights from this study provide a significant benchmark for DNA barcoding studies on medicinal plants with local significance and establish an evaluative framework for the conservation of biodiversity and the surveillance of genetic resources among medicinal plants in the Tianshan wild fruit forest area.}, }
@article {pmid39794360, year = {2025}, author = {Maulding, ND and Zou, J and Zhou, W and Metcalfe, C and Stuart, JM and Ye, X and Hafner, M}, title = {Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer.}, journal = {NPJ systems biology and applications}, volume = {11}, number = {1}, pages = {5}, pmid = {39794360}, issn = {2056-7189}, support = {U24 CA210990/CA/NCI NIH HHS/United States ; U24 CA264009/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Breast Neoplasms/genetics/drug therapy/metabolism/pathology ; Female ; *Drug Resistance, Neoplasm/genetics ; Gene Expression Regulation, Neoplastic/drug effects ; Piperazines/pharmacology ; Pyridines/pharmacology ; Cell Line, Tumor ; Single-Cell Analysis ; Deep Learning ; Gene Expression Profiling ; }, abstract = {Understanding transcriptional heterogeneity in cancer cells and its implication for treatment response is critical to identify how resistance occurs and may be targeted. Such heterogeneity can be captured by in vitro studies through clonal barcoding methods. We present TraCSED (Transformer-based modeling of Clonal Selection and Expression Dynamics), a dynamic deep learning approach for modeling clonal selection. Using single-cell gene expression and the fitness of barcoded clones, TraCSED identifies interpretable gene programs and the time points at which they are associated with clonal selection. When applied to cells treated with either giredestrant, a selective estrogen receptor (ER) antagonist and degrader, or palbociclib, a CDK4/6 inhibitor, pathways dynamically associated with resistance are revealed. For example, ER activity is associated with positive selection around day four under palbociclib treatment and this adaptive response can be suppressed by combining the drugs. Yet, in the combination treatment, one clone still emerged. Clustering based on partial least squares regression found that high baseline expression of both SNHG25 and SNCG genes was the primary marker of positive selection to co-treatment and thus potentially associated with innate resistance - an aspect that traditional differential analysis methods missed. In conclusion, TraCSED enables associating features with phenotypes in a time-dependent manner from scRNA-seq data.}, }
@article {pmid39792883, year = {2025}, author = {Park, JW and Park, K and Kwak, IS}, title = {First report of a major management target species, chironomid Paratanytarsus grimmii (Diptera: Chironomidae) larvae, in drinking water treatment plants (DWTPs) in South Korea.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0315390}, pmid = {39792883}, issn = {1932-6203}, mesh = {Animals ; *Chironomidae/genetics/classification ; *Larva/genetics ; Republic of Korea ; Drinking Water ; Water Purification ; Phylogeny ; }, abstract = {Ensuring the supply of safe and high-quality drinking water can be compromised by the presence of chironomid larvae in drinking water treatment plants (DWTPs), which may contaminate municipal water systems through freshwater resources. Chironomids are dominant species known for their resilience to a broad range of extreme aquatic environments. This study aimed to identify the morphological characteristics and obtain genetic information of the chironomid Paratanytarsus grimmii found in the water intake source and freshwater resource of DWTPs in Korea, highlighting the potential possibility of a parthenogenetic chironomid outbreak within DWTP networks. The distribution of chironomid larvae at the water intake source site (DY) of the Danyang DWTP and the freshwater resource (ND) of the Nakdong River was investigated. A total of 180 chironomid individuals, encompassing three subfamilies and six species from six 6 genera were identified at the DY site, with Procladius nigriventris being the dominant species. At the ND site, fifty chironomid individuals, encompassing two subfamilies and six species from six genera, were identified, with Cricotopus sylvestris being the dominant species. The morphological characteristics of the head capsule, mentum, mandible, and antennae of six P. grimmii larvae collected from the DY and ND sites were characterized. DNA barcoding and phylogenetic analysis revealed distinct mitochondrial diversities between the P. grimmii larvae from DY and those from ND. These results provide crucial information for the morphological identification and DNA barcoding of the key management target chironomid P. grimmii larvae, which can be used to detect the occurrence of this chironomid species in DWTPs.}, }
@article {pmid39791888, year = {2025}, author = {Manmana, Y and Kinugasa, S and Hiruta, Y and Citterio, D}, title = {Development of a Semiquantitative Barcode Readout Approach for Paper-Based Analytical Devices (PADs) for Enzymatic H2O2 and Glucose Detection.}, journal = {Analytical chemistry}, volume = {97}, number = {3}, pages = {1500-1506}, pmid = {39791888}, issn = {1520-6882}, mesh = {*Hydrogen Peroxide/analysis/metabolism ; *Paper ; Horseradish Peroxidase/metabolism/chemistry ; *Glucose/analysis ; Smartphone ; 3,3'-Diaminobenzidine/chemistry/metabolism ; *Biosensing Techniques/instrumentation ; Humans ; }, abstract = {The integration of barcode technology with smartphones on paper-based analytical devices (PADs) presents a promising approach to bridging manual detection with digital interpretation and data storage. However, previous studies of 1D barcode approaches have been limited to providing only a "yes/no" response for analyte detection. Herein, a method of using barcode readout for semiquantitative signal detection on PADs has been achieved through the integration of barcode technology with a distance-based measurement concept on PADs. To demonstrate the feasibility of this concept, a PAD fabrication strategy incorporating barcodes was explored, using the enzymatic reaction between horseradish peroxidase (HRP), 3,3'-diaminobenzidine (DAB), and H2O2 as a model system. The enzyme-catalyzed polymerization of DAB to polyDAB in the presence of hydrogen peroxide results in the appearance of color observable by the naked eye inside a paperfluidic channel, with the color-changed length depending on the H2O2 concentration. At the same time, the barcode pattern displayed as a result of this distance-based color evolution overlaid with a paper-based barcode layer can be read using a smartphone application. Parameters affecting the signal readout performance were studied. The developed device can be used to detect H2O2 concentrations in the range of 0.25 to 10 mM within 90 min with 79.6% of barcode signals correctly readable. Additionally, results from different smartphone models showed a consistent reading performance (78.4-79.6%). Finally, the quantification of glucose levels in artificial urine samples was demonstrated. This developed PAD signaling strategy offers end-users more simplicity and can be used as a standalone device or in conjunction with other digital devices.}, }
@article {pmid39789982, year = {2025}, author = {Xu, Y and Chan, MTJ and Yang, M and Meng, H and Chen, CH}, title = {Time-resolved single-cell secretion analysis via microfluidics.}, journal = {Lab on a chip}, volume = {25}, number = {5}, pages = {1282-1295}, doi = {10.1039/d4lc00904e}, pmid = {39789982}, issn = {1473-0189}, mesh = {*Single-Cell Analysis/instrumentation/methods ; *Microfluidic Analytical Techniques/instrumentation/methods ; Humans ; Animals ; Time Factors ; Lab-On-A-Chip Devices ; }, abstract = {Revealing how individual cells alter their secretions over time is crucial for understanding their responses to environmental changes. Key questions include: When do cells modify their functions and states? What transitions occur? Insights into the kinetic secretion trajectories of various cell types are essential for unraveling complex biological systems. This review highlights seven microfluidic technologies for time-resolved single-cell secretion analysis: 1. Microwell real-time electrical detection: uses microelectrodes for precise, cell-specific, real-time measurement of secreted molecules. 2. Microwell real-time optical detection: employs advanced optical systems for real-time, multiplexed monitoring of cellular secretions. 3. Microvalve real-time optical detection: dynamically analyzes secretions under controlled in situ stimuli, enabling detailed kinetic studies at the single-cell level. 4. Droplet real-time optical detection: provides superior throughput by generating droplets containing single cells and sensors for high-throughput screening. 5. Microwell time-barcoded optical detection: utilizes sequential barcoding techniques to facilitate scalable assays for tracking multiple secretions over time. 6. Microvalve time-barcoded optical detection: incorporates automated time-barcoding via micro-valves for robust and scalable analysis. 7. Microwell time-barcoded sequencing: captures and labels secretions for sequencing, enabling multidimensional analysis, though currently limited to a few time points and extended intervals. This review specifically addresses the challenges of achieving high-resolution timing measurements with short intervals while maintaining scalability for single-cell screening. Future advancements in microfluidic devices, integrating innovative barcoding technologies, advanced imaging technologies, artificial intelligence-powered decoding and analysis, and automations are anticipated to enable highly sensitive, scalable, high-throughput single-cell dynamic analysis. These developments hold great promise for deepening our understanding of biosystems by exploring single-cell timing responses on a larger scale.}, }
@article {pmid39787166, year = {2025}, author = {Guarniero, I and Stancampiano, L and Franch, R and Armaroli, E and Macchioni, F and Negrisolo, E}, title = {Genetic variability and population structure analysis of Protostrongylus oryctolagi (Nematoda: Protostrongylidae) in Lepus europaeus from Central and Northern Italy.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0313998}, pmid = {39787166}, issn = {1932-6203}, mesh = {Animals ; Italy ; *Genetic Variation ; *Haplotypes ; Hares/genetics/parasitology ; Phylogeny ; Genetics, Population ; }, abstract = {Nematodes are abundant and ubiquitous animals which are poorly known at intraspecific level. This work represents the first attempt to fill the gap on basic knowledge of genetic variability and differentiation in Protostrongylus oryctolagi, a nematode parasite of lagomorphs. 68 cox1 sequences were obtained from brown hares collected in five locations in Northern and Central Italy, highlighting the presence of a high amount of genetic variation inside this species. The eleven haplotypes identified (Haplotype diversity equal to 0.702) were split into two lineages: lineage A (comprising six different haplotypes, A1-A6) and lineage B (B1-B5). The mean intra-lineage amount of genetic variation was 0.3%, whereas the inter-lineage percentage of variation was ten-fold higher (3%). These two lineages were non-randomly distributed in the investigated areas. Lineage A showed a preference for Central Italy (Tuscany) even if it was sporadically found also in northern territories (Emilia-Romagna), while B-haplotypes were present exclusively in Emilia-Romagna. The analysis of molecular variance identified two main barriers to gene flow: (i) a strong major one which separate samples of Central Italy (PIA and GR7) from the northern ones (RE1, RE3 and MO1; ΦST = 0.750, P = 0.00); (ii) a secondary faint barrier which separates Pianosa island from Grosseto (ΦST = 0.133, P = 0.00). Any difference was found among northern samples (ΦST = 0.009, P = 0.00). The observed data may be explained by several factors ranging from the parasite's biology (presence of a narrow host spectrum), the final host's behaviour (small home range), the natural dispersion of the host-parasite dyad occurred in past or the recent passive men-mediated migration. Finally, the presence of unconventional shortened amplicons revealed the presence of NUMTs (nuclear copy of mitochondrial genes) in the P. oryctolagi nuclear genome, suggesting caution when using DNA barcode as unique marker for the identification of species belonging to this genus. "In short, if all the matter in the universe except the nematodes were swept away, our world would still be dimly recognizable". Nathan Augustus Cobb, from "Nematodes and Their Relationships", 1915.}, }
@article {pmid39781258, year = {2025}, author = {Fernando, MATM and Fu, J and Adamowicz, SJ}, title = {Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation.}, journal = {Ecology and evolution}, volume = {15}, number = {1}, pages = {e70817}, pmid = {39781258}, issn = {2045-7758}, abstract = {Advancements in DNA sequencing technology have facilitated the generation of a vast number of DNA sequences, posing opportunities and challenges for constructing large phylogenetic trees. DNA barcode sequences, particularly COI, represent extensive orthologous sequences suitable for phylogenetic analysis. Phylogenetic placement analysis offers a promising method to integrate COI data into tree-building efforts, yet the impacts of backbone tree completeness and species composition remain under-explored. Using a dataset comprising 27 genes and 4520 species of bony fishes, we assessed the accuracy of phylogenetic inference by "placing" COI sequences onto backbone trees. The backbone tree completeness was varied by subsampling 20%, 40%, 60%, 80%, and 99% of the total species separately, followed by placement of those missing species based on their COI sequences using software packages EPA-ng and APPLES. We also compared the effects of biased, random, and stratified sampling strategies; the latter ensured the representation of all major lineages (Family) of bony fish. Our findings indicate that the placement accuracy is consistently high across all levels of backbone tree completeness, where 70%-78% missing species are correctly placed (by EPA-ng) in the same locations as the reference tree derived from the complete data. High completeness produces slightly high placement accuracy, although in many cases the differences are nonsignificant. For example, at the 99% completeness level with stratified sampling, EPA-ng placed 78% missing species correctly, and when only considering placement with high confidence (LWR > 0.9), the percentage is 87%. Additionally, stratified sampling outperforms random sampling in most cases, and biased sampling has the worst performance. The likelihood-based EPA-ng consistently provide higher accurate placements than the distance-based APPLES. In conclusion, COI-based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees.}, }
@article {pmid39776788, year = {2025}, author = {Sander, PN and Gillen Miller, JT and Lairson, LL}, title = {Induced cell phenotype activity recording of DNA-tagged ligands.}, journal = {RSC chemical biology}, volume = {6}, number = {2}, pages = {273-280}, pmid = {39776788}, issn = {2633-0679}, abstract = {Based on their ability to canvas vast genetic or chemical space at low cost and high speed, DNA-encoded libraries (DEL) have served to enable both genomic and small molecule discovery. Current DEL chemical library screening approaches focus primarily on in vitro target-based affinity or activity. Here we describe an approach to record the phenotype-based activity of DNA-encoded small molecules on their cognate barcode in living cells. We transfected chloroalkane-derivatized DNA barcodes carrying photoreleasable small molecules into cells. Following photorelease, bioactive compounds induced expression of a reporter gene cassette containing self-labeling HaloTag protein that becomes covalently modified by encoding barcodes. We demonstrate that we can recover activity information from cells that received active compound following immunoprecipitation-based enrichment. This generalizable approach should enable future strategies that facilitate phenotype-based screens of DNA-encoded chemical libraries in complex cellular or organism level systems.}, }
@article {pmid39775746, year = {2024}, author = {de Freitas, EA and Dos Santos, DB and Moraes Ferreira, CS and Silva-Oliveira, C and Evangelista-Gomes, GF and Veneza, IB}, title = {Integrative use of DNA barcode and morphology reveal high level of diversity in the ornamental fish on the lower Amazon basin.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0316455}, pmid = {39775746}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Electron Transport Complex IV/genetics ; Brazil ; Phylogeny ; Rivers ; Lakes ; Characiformes/genetics/classification ; }, abstract = {The Amazon basin is the world's largest hydrographic basin, in terms of both its total area and its species diversity, with more than 2,700 species of fish. Despite this diversity, the data available on the fish fauna of the Amazon basin are still relatively scant and incomplete, in particular from the streams and floodplain lakes of the lower Amazon, which may contain a large proportion of the still undescribed species of the basin. Many of these species are expected to be of interest to the ornamental fish market. The investigation of the diversity of potential ornamental fish using molecular tools is even more limited. Given this scenario, the present study employed DNA barcoding to investigate the diversity of ornamental fish found in two streams and a floodplain lake of the lower Amazon. The mitochondrially encoded cytochrome c oxidase I (MT-CO1) molecular marker was used to identify the taxa, in combination with morphological keys. A total of 51 ornamental species were identified, representing 13 families and three orders. A majority of the species were found at only one of the sampling points, which indicates that the distribution of the species is influenced by ecological factors. The most speciose order was the Characiformes, followed by the Cichliformes and Siluriformes, while the family with the greatest diversity of species was the Acestrorhamphidae (31.3% of the total number of species), followed by the Cichlidae (27.4%), and the Lebiasinidae (9.8%). One specie was registered in the region of the lower Amazon for the first time, and evidence was found of the possible existence of species not formally described of Aphyocharax, Astyanax, Apareiodon and Hemigrammus.}, }
@article {pmid39774107, year = {2025}, author = {Dufresnes, C and Jablonski, D and Ambu, J and Prasad, VK and Bala Gautam, K and Kamei, RG and Mahony, S and Hofmann, S and Masroor, R and Alard, B and Crottini, A and Edmonds, D and Ohler, A and Jiang, J and Khatiwada, JR and Gupta, SK and Borzée, A and Borkin, LJ and Skorinov, DV and Melnikov, DA and Milto, KD and Konstantinov, EL and Künzel, S and Suchan, T and Arkhipov, DV and Trofimets, AV and Nguyen, TV and Suwannapoom, C and Litvinchuk, SN and Poyarkov, NA}, title = {Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus).}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {298}, pmid = {39774107}, issn = {2041-1723}, support = {RFIS 3211101356//National Natural Science Foundation of China (National Science Foundation of China)/ ; SPP1991 VE247/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Bufonidae/genetics/classification ; *Introduced Species ; Phylogeny ; Genetic Speciation ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Madagascar ; Phylogeography ; Asia, Southeastern ; India ; }, abstract = {Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biological invasions (Wallacea and Madagascar). The results emphasize a complex diversification shaped by speciation and mitochondrial introgression that comprises two distinct species. One species (true D. melanostictus) is distributed in the Indian subcontinent and is invasive in Wallacea. The other species, whose nomenclature remains unsettled, diverged from D. melanostictus in the Miocene era (~7 Mya) and diversified across Southeast Asia, from where it was introduced to Madagascar. Remarkably, the Indonesian population of D. melanostictus was recently established from India, which suggests historical, possibly human-assisted dispersal across the Bay of Bengal, reflecting the centuries-old connection between these regions.}, }
@article {pmid39774015, year = {2025}, author = {Appleyard, SA and Ward, RD and Pogonoski, JJ and Graham, A and Last, PR and Deagle, BE and Holmes, B and Gomon, MF and Bray, DJ and Johnson, JW and Hay, AC and Moore, GI and Hammer, MP and Russell, B and Graham, KJ}, title = {Australia's marine fishes DNA barcode reference library for integrated taxonomy, metabarcoding &amp; eDNA research.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {21}, pmid = {39774015}, issn = {2052-4463}, mesh = {Animals ; *Aquatic Organisms/genetics/classification ; Australia ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Fishes/genetics/classification ; *Gene Library ; }, abstract = {Over 15 000 species of fishes are found globally in the marine environment and DNA barcodes are used extensively to describe, catalogue, understand and manage this diversity. The dataset outlined here represents a DNA barcode reference library of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) from 9767 voucher specimens (representing at least 2220 species and 288 families) of marine fishes. This publicly available dataset in the Barcode of Life Data System (BOLD) represents 17 years (2005-2022) of barcoding of marine fishes identified from Australian territorial waters. Tissues targeted for sequencing with their matching physical specimens (and extracted DNA), obtained via a multi-agency sampling effort, are mostly maintained and curated by the CSIRO Australian National Fish Collection (ANFC) in Hobart, Australia. Species-level integrated taxonomy (assigned after combined morphological and genetic assessment) has been determined for 91% of the dataset. The library represents the most complete COI barcode reference dataset for marine fishes from Australian waters and is currently utilised for integrated taxonomy, (meta)barcoding and eDNA studies.}, }
@article {pmid39771256, year = {2024}, author = {Fedosov, VE and Pisarenko, OY and Fedorova, AV and Afonina, OM and Ignatova, EA}, title = {On the Cryptic Speciation in the Mosses with East Asia-East North America Disjunction: A Case Study of Two Poorly Understood Mosses from the Southern Extremity of the Russian Far East.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, pmid = {39771256}, issn = {2223-7747}, support = {23-14-00043//Russian scientific foundation/ ; }, abstract = {A survey of the moss flora of the southernmost part of the Russian Primorsky Territory yielded several intriguing taxa, whose identity is assessed herein based on an integrative morpho-molecular approach. Bellibarbula recurva was previously known in inland Asia only from the Sino-Himalayan region and the new locality is distant from the earlier known ones to ca. 3000 km. Despite the morphological uniformity, Russian specimens are remarkably distinct in sequences of all three obtained DNA markers, approaching an American specimen in the rps4 sequence. Another probable relic, Symblepharis cf. crispifolia, appeared to be fairly common in the southern part of the Primorsky Territory, where low mountains are covered with hard-leaved forests. Russian specimens of Symblepharis cf. crispifolia var. brevipes show significant divergence from S. crispifolia s.str., which also has complex phylogenetic structure, obscuring further taxonomic implications. The description and illustrations of both taxa based on Russian specimens are provided, and the area, where both species occur, is briefly characterized; it includes numerous thermophilous species, which are rare or do not occur northwards. Our case study uncovers the problem of cryptic speciation within species distributed in temperate climate and is considered to represent relics of Arcto-Tertiary flora.}, }
@article {pmid39771168, year = {2024}, author = {Li, X and Jia, H and Liu, D and Zhou, X and Wu, K}, title = {Potential Regional Pollination Services of Spodoptera litura (Lepidoptera: Noctuidae) Migrants as Evidenced by the Identification of Attached Pollen.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, pmid = {39771168}, issn = {2223-7747}, support = {2023FY100500//Science &amp; Technology Fundamental Resources Investigation Program/ ; }, abstract = {Many species of noctuid moths exhibit long-distance migratory behavior and have an important pollination service function in terrestrial ecosystems. Spodoptera litura (Fabricius) is a globally distributed insect; however, its role in pollination remains underexplored. In this study, the feeding preferences and inter regional pollination of S. litura adults were explored. We conducted pollen analysis on 1253 S. litura migrants captured from 2018 to 2021 on Beihuangcheng Island in the Bohai Strait of China, which is located in the East Asian insect migration path. The results show that an average of 51.1% of S. litura migrants carry plant pollen each year, and the carrying rate shows fluctuations based on sex, year, and season. By combining morphological identification and DNA barcoding, pollen species were identified from 40 species of plants, representing 21 families and 26 genera, mainly from angiosperms of Dicotyledoneae, with Asteraceae, Apocynaceae, and Amaranthaceae being the dominant taxa. The geographical distribution range of Chrysanthemum zawadskii and Adenophora trachelioides and a migration trajectory simulation analysis indicate that S. litura predominantly migrate from Liaoning Province in Northeast China to North China over the Bohai Sea in autumn. These findings indicate the potential pollination activities of S. litura in North China and Northeast China, enriching our understanding of the interaction between S. litura and the plants it pollinates.}, }
@article {pmid39769939, year = {2024}, author = {Wu, Z and Yu, W and Luo, F and Jin, Y and Pan, L and Deng, Q and Wang, Q and Yu, M}, title = {Construction of Heterogeneous Aggregation-Induced Emission Microspheres with Enhanced Multi-Mode Information Encryption.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {24}, pages = {}, pmid = {39769939}, issn = {1420-3049}, abstract = {Traditional organic light-emitting materials hinder their anti-counterfeiting application in solid state due to their aggregation-caused quenching effect. A facile and straightforward method was reported to introduce AIE molecules into microspheres and manipulate different reaction parameters to prepare AIE microspheres with different morphologies. In this strategy, fluorescent microspheres with spherical, apple-shaped, and hemoglobin-like types were synthesized. Driven by the photocyclization and oxidation of tetraphenylethene, microspheres can be used as an aqueous fluorescence ink with erasable properties. The fluorescent patterns printed by microsphere ink on paper can be irreversibly erased by prolonged exposure to ultraviolet light (365 nm, 60 mw/cm[2]). Moreover, the multi-morphology microspheres can be further arranged for multiple-information encryption and anti-counterfeiting of barcodes and two-dimensional codes, in which double validation was carried out through fluorescence spectroscopy and laser confocal microscopy. This approach provides a new method for more reliable anti-counterfeiting and information encryption.}, }
@article {pmid39769610, year = {2024}, author = {Ye, C and Tang, X and Yang, F and Zhang, X and Shang, Y and Xia, Y and Wang, Y and Guo, S and Zha, L and Guo, Y and Wen, D}, title = {Rapid and Accurate Detection of Chrysomya megacephala (Diptera: Calliphoridae) Using Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, pmid = {39769610}, issn = {2075-4450}, support = {No. 82072114//National Natural Science Foundation of China/ ; }, abstract = {Estimating the postmortem interval (PMI) is critical in the field of forensic science, and necrophagous insects play a significant role in this process. Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae) is a common necrophagous insect species, making its rapid and accurate identification essential. However, commonly used molecular biology methods, such as DNA barcode, still have some limitations in identifying necrophagous insects as they are often complex, time-consuming, and reliant on laboratory instruments. Therefore, in this study, we have developed an innovative detection system for the rapid and accurate identification of C. megacephala based on the Cytochrome b gene using recombinase polymerase amplification (RPA) and lateral flow dipstick (LFD) in combination. The developed RPA-LFD detection system achieved complete amplification in just 15 min at 37 °C with good sensitivity and specificity. Only 7.8 × 10[-4] ng or more of target DNA fragments were required, and a positive detection rate of 100% was achieved in 18 C. megacephala samples from actual cases. In addition, the ability of the developed RPA-LFD detection system in combination with rapid DNA extraction methods to enable on-site detection was preliminarily explored. The results suggested that when the RPA-LFD detection system was combined with the grinding ddH2O extraction method (a rapid DNA extraction method), the process from species acquisition to visualization of detection results could be completed in less than 20 min. In conclusion, this innovative RPA-LFD detection system outperforms commonly used molecular biology methods for C. megacephala identification in terms of speed, sensitivity and convenience, making it suitable for direct application at crime scenes, promising to provide important assistance in estimating PMI and expanding the impact of forensic entomological evidence.}, }
@article {pmid39769570, year = {2024}, author = {Han, Y and Achterberg, KV and Chen, X}, title = {DNA Barcodes and Morphology Reveal Two New Species of the Genus Prochas Walkley, 1959 (Ichneumonidae, Campopleginae), from China.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, pmid = {39769570}, issn = {2075-4450}, support = {31920103005//the Key International Joint Research Program of the Na-325 tional Natural Science Foundation of China/ ; 32070467//the National Natural Science Founda-326 tion of China/ ; 2017YFD0200101//the National Key Research and Development Plan/ ; 2019YFD0300104//the National Key Research and Development Plan/ ; 2018R51004//the Fundamental Research Funds for the Central Universities, the Special Re-328 search Fund for Distinguished Scholars of Zhejiang Province, China/ ; 2023qd31//the Scien-329 tific Research Starting Foundation of Chuzhou University, China/ ; }, abstract = {DNA barcoding is an effective modern tool in taxonomy, evolutionary biology, and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. We combined morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene using the automatic barcode gap discovery (ABGD) to investigate species boundaries. The genus Prochas Walkley (Hymenoptera, Ichneumonidae, Campopleginae) was first reported from China and is new for the Oriental and Eastern Palearctic regions. Using an integrative taxonomy method, two new species P. rugipunctata sp. nov. and P. striata sp. nov. are hereby described and illustrated. A key to the world species and a distribution map are provided.}, }
@article {pmid39769553, year = {2024}, author = {Enguídanos García, A and Galià-Camps, C and Pérez-González, CM and Víquez, D and Mateos, E}, title = {Expanding Soil Invertebrate Knowledge in Panama: The Genus Lepidocyrtus (Collembola, Entomobryidae) in the Parque Natural Metropolitano as a Study Case.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, pmid = {39769553}, issn = {2075-4450}, support = {2023-GEBI-Panama//European Society of Evolutionary Biology/ ; 2023-Linn&#xe9;Sys-Panama//Linnean Society of London &amp; Systematics Association/ ; Internacionalitzaci&#xf3;UB-Panama//Universitat de Barcelona/ ; 2021SGR689//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; 2021SGR1271//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {Panama, located in the heart of the Mesoamerican hotspot, harbors an extraordinary species diversity across the Tree of Life. The Collembola species of the genus Lepidocyrtus play an important role in soil biological processes such as decomposition, being used to monitor soil health and functional parameters. However, the limitation of morphological characters and molecular resources hampers the evaluation of local soil diversity. Here, using 30 Lepidocyrtus specimens collected in the Parque Natural Metropolitano (PNM), we unravel the diversity of this Panamanian protected area through molecular tools and new taxonomic traits. Our phylogenies, in combination with species delimitation analyses, indicate that the PNM harbors an extremely rich community of Lepidocyrtus species, two of them cited in Panama for the first time, and three of them potentially new to science. We highlight that the presence of the dental tubercle and pseudopores on the BP4 region are not monophyletic and, therefore, can be used as supplementary characters to morphologically resolve species complexes. Overall, this study sheds light on the Lepidocyrtus richness of the PNM, which acts as a shelter for Panamanian and the Mesoamerican hotspot species.}, }
@article {pmid39769528, year = {2024}, author = {Chen, H and van Achterberg, C and Li, Y and Liu, Z and Wang, J and Luo, S}, title = {Parasitoids of Insect Pests Feeding on Scaevola taccada (Goodeniaceae) from Yongxing Island in South China Sea.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, pmid = {39769528}, issn = {2075-4450}, abstract = {Scaevola taccada (Goodeniaceae) is an important evergreen coastal plant on islands in the South China Sea, which shows excellent tolerance for salty and drought conditions. Nevertheless, the growth of S. taccada populations on these islands in the South China Sea has been threatened by a few serious insect pests. However, we know little about the biology of these pests. In this study, we surveyed and identified the parasitoids of two main pests (Herpetogramma submarginale (Swinhoe, 1901) and Ophiomyia scaevolana Shiao and Wu, 1996) of S. taccada communities on Yongxing Island in the South China Sea, with the aim to assess their potential in biological control. Dolichogenidea stantoni (Ashmead, 1904) is a gregarious endoparasitoid of the larva of H. submarginale and contributes an average 48.9% parasitism rate on H. submarginale. Opius biroi, Fischer, 1960 and Euderus albitarsis (Zetterstedt, 1838) are both solitary endoparasitoids of the larva of O. scaevolana, with a respective 5.8% and 64.4% parasitism rate on O. scaevolana. We summarize the species diagnosis, biology, and distribution of the three parasitoid species. The potential of these parasitoids used in biological control is also discussed.}, }
@article {pmid39769523, year = {2024}, author = {Lei, T and Gu, J and Zhao, M and Chen, Y and Song, C and Qi, X}, title = {Seasonal Dynamics of Non-Biting Midges (Diptera: Chironomidae) and Relevant Environmental Factors.}, journal = {Insects}, volume = {15}, number = {12}, pages = {}, pmid = {39769523}, issn = {2075-4450}, support = {32070481//National Natural Science Foundation of China/ ; 32100353//National Natural Science Foundation of China/ ; LY22C040003//Zhejiang Provincial Natural Science Foundation/ ; }, abstract = {The family Chironomidae is speciose and is present in almost all freshwater habitats. Adult non-biting midges emerge from waterbodies and swarm in high numbers, occasionally disrupting people's outdoor activities. In order to understand the seasonal dynamics of species composition, a continuous observation of non-biting midge diversity was performed. Adult non-biting midges were collected using light traps from the autumn of 2022 to the summer of 2023 in an urban wetland park. Species were identified based on morphological characteristics and DNA barcodes. Alpha diversity was evaluated using Margalef, Pielou, and Shannon-Wiener indexes. Beta diversity was evaluated using unconstrained NMDS analysis and constrained CCA. The impacts of environmental factors, including barometric pressure, temperature, relative humidity, and wind speed, on the variation in species composition were estimated in the constrained analyses. A total of 42 species were identified, with 29 species belonging to Chironominae, 9 species belonging to Orthocladiinae, and 4 species belonging to Tanypodinae. The species composition varied across different seasons. Summer sites and autumn sites shared the highest similarity in diversity, and spring sites presented the lowest diversity. The variation was significantly correlated with environmental conditions. The results showed that seasonality is a factor influencing the diversity of adult non-biting midges.}, }
@article {pmid39765491, year = {2024}, author = {Chen, H and Olmi, M and Wang, J and Sun, Q and Luo, S}, title = {DNA Barcoding Reveals Species Diversity and Host Associations of Dryinidae Wasps (Insecta, Hymenoptera): A Case Study from the Xisha Islands in the South China Sea.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {24}, pages = {}, pmid = {39765491}, issn = {2076-2615}, abstract = {Dryinidae is a cosmopolitan wasp family, with over 1900 species found worldwide [...].}, }
@article {pmid39764454, year = {2024}, author = {Jiang, S and Zhao, G and Ding, Y and Ye, S and Li, Z and You, C and Yin, Y and Guo, X}, title = {Deciphering dengue: novel RNA barcoding segments for enhanced serotype-specific identification and global surveillance of dengue viruses.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1474406}, pmid = {39764454}, issn = {1664-302X}, abstract = {INTRODUCTION: Dengue viruses (DENVs), the causative agents of dengue hemorrhagic fever and dengue shock syndrome, undergo genetic mutations that result in new strains and lead to ongoing global re-infections.<br><br>OBJECTIVES: To address the growing complexity of identifying and tracking biological samples, this study screened RNA barcode segments for the four DENV serotypes, ensuring high specificity and recall rates for DENV identification using segments.<br><br>RESULTS: Through analyzing complete genome sequences of DENVs, we screened eight barcode segments for DENV, DENV-1, DENV-2, DENV-3, and DENV-4 identification. Comparing the screened barcode segments to sequences of known strains and determining the proportion of correctly or incorrectly identified nucleotides, these segments demonstrated an average recall rate at nucleotide level of 91.34% for four DENV serotypes, a specificity of 99.50% at species level within the Flaviviridae family, and a precision rate of 100% for identifying DENVs. For arboviruses, the nucleotide-level specificity was 63.58%. We designed and used the "Barcoding" software to streamline segment design, integrating automated sequence preprocessing, evaluation of barcode segments, and primer design, significantly reducing manual intervention and enhancing overall efficiency. We also established an online database called "Barcodes" for storing and preparing barcode segments.<br><br>CONCLUSION: This work established a standard framework for DENV identification and barcode segment selection, promising significant advancements in the real-time management and control of DENVs, thereby enhancing surveillance capabilities and facilitating targeted interventions in dengue outbreak-prone regions.}, }
@article {pmid39764013, year = {2025}, author = {Comstock, WJ and Navarro, MV and Maybee, DV and Rho, Y and Wagner, M and Wang, Y and Smolka, MB}, title = {Proteomic Sensors for Quantitative, Multiplexed and Spatial Monitoring of Kinase Signaling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.12.16.628391}, pmid = {39764013}, issn = {2692-8205}, support = {R35 GM141159/GM/NIGMS NIH HHS/United States ; }, abstract = {Understanding kinase action requires precise quantitative measurements of their activity in vivo . In addition, the ability to capture spatial information of kinase activity is crucial to deconvolute complex signaling networks, interrogate multifaceted kinase actions, and assess drug effects or genetic perturbations. Here we developed a proteomic kinase activity sensor platform (ProKAS) for the analysis of kinase signaling using mass spectrometry. ProKAS is based on a tandem array of peptide sensors with amino acid barcodes that allow multiplexed analysis for spatial, kinetic, and screening applications. We engineered a ProKAS module to simultaneously monitor the activities of the DNA damage response kinases ATR, ATM, and CHK1 in response to genotoxic drugs, while also uncovering differences between these signaling responses in the nucleus, cytosol, and replication factories. Furthermore, we developed an in silico approach for the rational design of specific substrate peptides expandable to other kinases. Overall, ProKAS is a novel versatile system for systematically and spatially probing kinase action in cells.}, }
@article {pmid39763829, year = {2024}, author = {Feng, Y and Chen, D and Applegate, CC and Gonzalez Medina, NY and Kuo, CW and Arogundade, OH and Wright, CL and Xu, F and Drnevich, J and Smith, AM}, title = {Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.12.16.628827}, pmid = {39763829}, issn = {2692-8205}, support = {R01 DK112251/DK/NIDDK NIH HHS/United States ; R01 DK131782/DK/NIDDK NIH HHS/United States ; R01 DK127531/DK/NIDDK NIH HHS/United States ; R35 HL167143/HL/NHLBI NIH HHS/United States ; R01 DK124290/DK/NIDDK NIH HHS/United States ; }, abstract = {Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling across heterogeneous cell populations. Here, we introduce Nanocoding using lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by dissolution. In cultured cell lines and heterogeneous cells from tissue digests, Nanocoding occurs in 40 minutes with stability after sample mixing and requires only commercially available reagents without novel chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples containing lipid-rich debris and heterogeneous cells from adipose tissue of obese rodents show more than 95% labeling with all known subtypes identified. Using Nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. This ease of generating and tuning these constructs may afford efficient and robust whole-sample multiplexing with minimal sample crosstalk.}, }
@article {pmid39762652, year = {2025}, author = {Hong, SJ and Resnick, SJ and Iketani, S and Cha, JW and Albert, BA and Fazekas, CT and Chang, CW and Liu, H and Dagan, S and Abagyan, MR and Fajtová, P and Culbertson, B and Brace, B and Reddem, ER and Forouhar, F and Glickman, JF and Balkovec, JM and Stockwell, BR and Shapiro, L and O'Donoghue, AJ and Sabo, Y and Freundlich, JS and Ho, DD and Chavez, A}, title = {A multiplex method for rapidly identifying viral protease inhibitors.}, journal = {Molecular systems biology}, volume = {21}, number = {2}, pages = {158-172}, pmid = {39762652}, issn = {1744-4292}, support = {1U19AI1711401//HHS | National Institutes of Health (NIH)/ ; 1017195.01//Burroughs Wellcome Fund (BWF)/ ; N/A//jack ma foundation/ ; DGE-2038238//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; }, mesh = {*High-Throughput Screening Assays/methods ; *Viral Protease Inhibitors/pharmacology/chemistry ; Humans ; *Antiviral Agents/pharmacology/chemistry ; SARS-CoV-2/enzymology/drug effects ; Biosensing Techniques/methods ; Drug Discovery/methods ; *Viral Proteases/metabolism ; }, abstract = {With current treatments addressing only a fraction of pathogens and new viral threats constantly evolving, there is a critical need to expand our existing therapeutic arsenal. To speed the rate of discovery and better prepare against future threats, we establish a high-throughput platform capable of screening compounds against 40 diverse viral proteases simultaneously. This multiplex approach is enabled by using cellular biosensors of viral protease activity combined with DNA-barcoding technology, as well as several design innovations that increase assay sensitivity and correct for plate-to-plate variation. Among >100,000 compound-target interactions explored within our initial screen, a series of broad-acting inhibitors against coronavirus proteases were uncovered and validated through orthogonal assays. A medicinal chemistry campaign was performed to improve one of the inhibitor's potency while maintaining its broad activity. This work highlights the power of multiplex screening to efficiently explore chemical space at a fraction of the time and costs of previous approaches.}, }
@article {pmid39758945, year = {2024}, author = {Senofsky, SR and Zamudio, I and Pan, B and McFadden, CS}, title = {Efficacy of the 28S rDNA barcode in differentiating Caribbean octocorals.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e140454}, pmid = {39758945}, issn = {1314-2828}, abstract = {The ecological landscape of Caribbean reefs is rapidly changing as octocorals fill the void left by declining scleractinian populations. Effective molecular barcodes are necessary to accurately identify these octocorals and monitor this shifting ecosystem. We tested the efficacy of the 28S rDNA as a barcode compared to the most commonly used mtMutS barcode on a collection of octocorals from across the Caribbean. Based on pairwise genetic distance values, 28S appeared to be more effective at differentiating species within the families Plexauridae and Gorgoniidae, while mtMutS was slightly more effective at distinguishing species of Pterogorgiidae. However, the standard 28S rDNA primers did not amplify all species as effectively as mtMutS, especially those belonging to the genus Eunicea. A shorter 28S barcode developed for eDNA applications distinguished species as effectively as the complete 28S barcode.}, }
@article {pmid39758943, year = {2024}, author = {Boóz, B and Kovács, Z and Bartalovics, B and Boda, P and Miliša, M and Pernecker, B and Pařil, P and Rewicz, T and Simon, AB and Csabai, Z and Móra, A}, title = {Chironomids (Diptera) from Central European stream networks: new findings and taxonomic issues.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e136241}, pmid = {39758943}, issn = {1314-2828}, abstract = {BACKGROUND: Chironomidae, with over 7,300 described species, are amongst the most diverse and abundant insect families in freshwater ecosystems worldwide. Chironomids are known for their widespread distribution from various water types. The level of documentation of chironomid fauna varies considerably amongst European countries, with more comprehensive knowledge for Western Europe compared to other regions. Despite the recent extensive sampling effort and the increasing number of available data, the chironomid fauna of Central European countries still remains poorly known.<br><br>NEW INFORMATION: This study contributes to the knowledge of chironomid fauna in three river catchments in Croatia, Hungary and Czechia. A combination of morphological and molecular techniques was employed, with a focus on larvae, although pupae and exuviae were also examined. We found 207 taxa, amongst which 170 were identified to species level. In Croatia, 14 species were recorded for the first time and two species were newly recorded in Czechia. DNA barcoding of 31 specimens resulted in 23 BINs, including eight new ones to BOLD. We provided detailed notes on taxa with taxonomic problems and/or morphological peculiarities. Our results highlight that extensive studies conducted in relatively small areas and a limited range of habitats (only streams in hilly regions) can remarkably contribute to the local and global knowledge on Chironomidae fauna, especially when the taxonomically difficult and often problematic larvae are investigated.}, }
@article {pmid39753672, year = {2025}, author = {Acford-Palmer, H and Andrade, AO and Phelan, JE and Santana, RA and Lopes, SCP and Medeiros, JF and Clark, TG and Araujo, MS and Campino, S}, title = {Application of a targeted amplicon sequencing panel to screen for insecticide resistance mutations in Anopheles darlingi populations from Brazil.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {731}, pmid = {39753672}, issn = {2045-2322}, support = {CON-80002357//ICEMR/ ; BB/X018156/1//UK Research and Innovation/ ; INV-003970/GATES/Gates Foundation/United States ; 442653/2019-0//Brazilian Ministry of Health/DECIT/CNPq N&#xb0; 23/2019/ ; INV-003970/GATES/Gates Foundation/United States ; 304830/2022-4//CNPq productivity grant/ ; no. 261868591//British Council, Newton Institutional Links Grant/ ; }, mesh = {Animals ; *Anopheles/genetics/drug effects ; *Insecticide Resistance/genetics ; Brazil ; *Mosquito Vectors/genetics/drug effects ; High-Throughput Nucleotide Sequencing/methods ; Insecticides/pharmacology ; Mutation ; Malaria/transmission/prevention &amp; control ; }, abstract = {Large-scale surveillance and informed vector control approaches are urgently needed to ensure that national malaria programs remain effective in reducing transmission and, ultimately, achieving malaria elimination targets. In South America, Anopheles darlingi is the primary malaria vector and is responsible for the majority of Plasmodium species transmission. However, little is known about the molecular markers associated with insecticide resistance in this species. In this study, we developed a low-cost, high throughput amplicon sequencing ("amp-seq") panel, consisting of 11 amplicons targeting genes linked to mosquito species identification (cox-1 and its2) and insecticide resistance (ace-1, GSTe2, vgsc and rdl). When used in tandem with dual-index barcoding of amplicons, this approach permits high numbers of loci and samples to be sequenced in single runs, thereby decreasing costs and increasing efficiency. By screening 200 An. darlingi mosquitoes collected in Brazil, our amp-seq approach identified 10 point mutations leading to amino acid changes in ace-1 (V243I, N294H, S673N, S674N/T) and GSTe2 genes (I114V, D128E, T166I, T179I, and T205A). Overall, our work has demonstrated the utility of amp-seq to provide insights into the genetic diversity of An. darlingi mosquitoes. The amp-seq approach can be applied as a wide-scale insecticide-resistance surveillance technique to better inform vector-control methods.}, }
@article {pmid39752373, year = {2025}, author = {, }, title = {Correction: Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0317172}, pmid = {39752373}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0275090.].}, }
@article {pmid39748949, year = {2024}, author = {Cabrera-Sosa, L and Safarpour, M and Kattenberg, JH and Ramirez, R and Vinetz, JM and Rosanas-Urgell, A and Gamboa, D and Delgado-Ratto, C}, title = {Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1488109}, pmid = {39748949}, issn = {1664-8021}, support = {U19 AI089681/AI/NIAID NIH HHS/United States ; }, abstract = {INTRODUCTION: Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control programs. We previously designed AmpliSeq assays for MMS, which include different traits of interest (resistance markers and pfhrp2/3 deletions), and SNP barcodes to provide population genetics estimates of Plasmodium vivax and Plasmodium falciparum parasites in the Peruvian Amazon. The present study compares the genetic resolution of the barcodes in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate population genetics of Amazonian malaria parasites.<br><br>METHODS: We analyzed 51&#xa0;P. vivax and 80&#xa0;P. falciparum samples from three distinct areas in the Loreto region of the Peruvian Amazon: Nueva Jerusal&#xe9;n (NJ), Mazan (MZ), and Santa Emilia (SE). Population genetics estimates and costs were compared using the SNP barcodes (P. vivax: 40 SNPs and P. falciparum: 28 SNPs) and MS panels (P. vivax: 16 MS and P. falciparum: 7 MS).<br><br>RESULTS: The P. vivax genetic diversity (expected heterozygosity, He) trends were similar for both markers: He MS = 0.68-0.78 (p > 0.05) and He SNP = 0.36-0.38 (p > 0.05). P. vivax pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04-0.14 and FST-SNP = 0.03-0.12 (pairwise p > 0.05). In addition, P. falciparum genetic diversity trends (He MS = 0-0.48, p < 0.05; He SNP = 0-0.09, p < 0.05) and pairwise FST comparisons (FST-MS = 0.14-0.65, FST-SNP = 0.19-0.61, pairwise p > 0.05) were concordant between both panels. For P. vivax, no geographic clustering was observed with any panel, whereas for P. falciparum, similar population structure clustering was observed with both markers, assigning most parasites from NJ to a distinct subpopulation from MZ and SE. We found significant differences in detecting polyclonal infections: for P. vivax, MS identified a higher proportion of polyclonal infections than SNP (69% vs. 33%, p = 3.3 &#xd7; 10[-5]), while for P. falciparum, SNP and MS detected similar rates (46% vs. 31%, p = 0.21). The AmpliSeq assay had a higher estimated per-sample cost compared to MS ($183 vs. $27-49).<br><br>DISCUSSION: The SNP barcodes in the AmpliSeq assays offered comparable results to MS for investigating population genetics in P. vivax and P. falciparum populations, despite some discrepancies in determining polyclonality. Given both panels have their respective advantages and limitations, the choice between both should be guided by research objectives, costs, and resource availability.}, }
@article {pmid39747844, year = {2025}, author = {Coulombe, P and Tomellini, E and Chagraoui, J and Mayotte, N and Sauvageau, G}, title = {Deciphering the effect of UM171 on human hematopoietic progenitor cell fate through clonal analysis.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {195}, pmid = {39747844}, issn = {2041-1723}, support = {PJT-178113//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; FDN-143286//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; HZN-C4R1-1//Stem Cell Network (Le R&#xe9;seau de cellules souches)/ ; }, mesh = {*Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Animals ; *Cell Differentiation ; Mice ; *Mast Cells/cytology/metabolism/drug effects ; Cell Proliferation ; Cell Lineage ; Cell Self Renewal/drug effects ; Hematopoietic Stem Cell Transplantation ; Signal Transduction ; }, abstract = {Ex vivo expansion of hematopoietic stem cells (HSC) requires the maintenance of a stemness state while cells are proliferating. This can be achieved via exposure to UM171 which leads to the degradation of chromatin modifiers and prevents the loss of key epigenetic marks. However, the chromatin landscape varies across populations within the hematopoietic system and the effect of UM171 on self-renewal and differentiation potential of different hematopoietic progenitor cells is less characterized. To address this, we use the CellTag barcoding approach to track the fate of individual stem and progenitor cells during in vitro expansion. We show that, in addition to its HSC self-renewing property, UM171 specifically modulates cell fate of a precursor common to erythroid, megakaryocytic, and mast cells in favor of self-renewal and a mast-bias differentiation trajectory. This differentiation bias can be driven by pro-inflammatory signaling pathways that are activated downstream of UM171 and results in an abundant mast cell population that can be transplanted as part of the graft to populate mice tissues in xenotransplantation studies.}, }
@article {pmid39747602, year = {2025}, author = {Cho, S and Martino, N and Yun, SH}, title = {Half-wave nanolasers and intracellular plasmonic lasing particles.}, journal = {Nature nanotechnology}, volume = {20}, number = {3}, pages = {404-410}, pmid = {39747602}, issn = {1748-3395}, support = {Fund for Medical Discovery fundamental research fellowship award//Massachusetts General Hospital (MGH)/ ; R01 EB034687/EB/NIBIB NIH HHS/United States ; R01-EB033155//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01-EB034687//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 EB033155/EB/NIBIB NIH HHS/United States ; }, abstract = {The ultimate limit for laser miniaturization would be achieving lasing action in the lowest-order cavity mode within a device volume of ≤(λ/2n)[3], where λ is the free-space wavelength and n is the refractive index. Here we highlight the equivalence of localized surface plasmons and surface plasmon polaritons within resonant systems, introducing nanolasers that oscillate in the lowest-order localized surface plasmon or, equivalently, half-cycle surface plasmon polariton. These diffraction-limited single-mode emitters, ranging in size from 170 to 280 nm, harness strong coupling between gold and InxGa1-xAs1-yPy in the near-infrared (λ = 1,000-1,460 nm), away from the surface plasmon frequency. This configuration supports only the lowest-order dipolar mode within the semiconductor's broad gain bandwidth. A quasi-continuous-level semiconductor laser model explains the lasing dynamics under optical pumping. In addition, we fabricate isolated gold-coated semiconductor discs and demonstrate higher-order lasing within live biological cells. These plasmonic nanolasers hold promise for multi-colour imaging and optical barcoding in cellular applications.}, }
@article {pmid39745647, year = {2025}, author = {Raj, B}, title = {Single-Cell Profiling of Lineages and Cell Types in the Vertebrate Brain.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {299-310}, pmid = {39745647}, issn = {1940-6029}, support = {DP2 NS131787/NS/NINDS NIH HHS/United States ; R00 HD098298/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Single-Cell Analysis/methods ; *Brain/cytology/metabolism ; *Zebrafish/genetics ; *CRISPR-Cas Systems ; *Cell Lineage/genetics ; *Gene Editing/methods ; Transcriptome ; Gene Expression Profiling/methods ; }, abstract = {CRISPR-Cas tools have recently been adapted for cell lineage tracing during development. Combined with single-cell RNA sequencing, these methods enable scalable lineage tracing with single-cell resolution. Here, I describe, scGESTALTv2, which combines cumulative CRISPR-Cas9 editing of a lineage barcode array with transcriptional profiling via droplet-based single-cell RNA sequencing (scRNA-seq). The technique is applied in developing zebrafish brains to generate mutations in the barcode array during development. The recorded lineages along with cellular transcriptomes are then extracted via scRNA-seq to define cell relationships among thousands of profiled brain cells and dozens of cell types.}, }
@article {pmid39745646, year = {2025}, author = {Bowling, S and Camargo, FD}, title = {CARLIN: A Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {281-298}, pmid = {39745646}, issn = {1940-6029}, mesh = {Animals ; Mice ; *Cell Lineage/genetics ; *DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Single-Cell Analysis/methods ; CRISPR-Cas Systems ; Gene Editing/methods ; Gene Expression/genetics ; }, abstract = {The CRISPR-activated repair lineage tracing (CARLIN) mouse line uses DNA barcoding to enable high-resolution tracing of cell lineages in vivo (Bowling et al, Cell 181, 1410-1422.e27, 2020). CARLIN mice contain expressed barcodes that allow simultaneous interrogation of lineage and gene expression information from single cells. Furthermore, barcode editing is fully inducible, resulting in cell lineage labeling that can be performed at any time point in development or adulthood. This chapter details the protocols followed for maintaining CARLIN mice, inducing barcoding, and amplifying the CARLIN barcode from DNA, RNA, and single-cell RNA-sequencing libraries for next-generation sequencing.}, }
@article {pmid39745644, year = {2025}, author = {Spanjaard, B and Junker, JP}, title = {LINNAEUS: Simultaneous Single-Cell Lineage Tracing and Cell Type Identification.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {243-263}, pmid = {39745644}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Animals ; Gene Editing/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Humans ; }, abstract = {A key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469-473. https://doi.org/10.1038/nbt.4124 , 2018; Hu et al, Nat Genet 54:1227-1237. https://doi.org/10.1038/s41588-022-01129-5 , 2022) (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.}, }
@article {pmid39745643, year = {2025}, author = {Baron, CS and Alemany, A}, title = {Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {221-241}, pmid = {39745643}, issn = {1940-6029}, mesh = {Animals ; *Zebrafish/genetics ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; *CRISPR-Cas Systems ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; Embryo, Nonmammalian/metabolism ; }, abstract = {ScarTrace is a CRISPR/Cas9-based genetic lineage tracing method that allows for uniquely barcoding the DNA of single cells at a target GFP sequence during developing zebrafish embryos. Single cells from barcoded adult zebrafish can be isolated from various tissues (e.g., marrow, brain, eyes, fins), and their transcriptome and barcode sequences are captured by single-cell cDNA amplification and genomic DNA nested PCR, respectively. Computationally, cell type and barcode identification permit clone tracing and lineage tree reconstruction of tissues to unravel fate decisions during embryogenesis.}, }
@article {pmid39745641, year = {2025}, author = {Fang, W and Yang, Y and Ji, H and Kalhor, R}, title = {Reconstructing Progenitor State Hierarchy and Dynamics Using Lineage Barcoding Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {177-199}, pmid = {39745641}, issn = {1940-6029}, support = {R01 HG010889/HG/NHGRI NIH HHS/United States ; R01 HG012357/HG/NHGRI NIH HHS/United States ; U01 HL156056/HL/NHLBI NIH HHS/United States ; }, mesh = {*Cell Lineage/genetics ; *Algorithms ; Animals ; Phylogeny ; Cell Differentiation/genetics ; Stem Cells/cytology/metabolism ; Single-Cell Analysis/methods ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Software ; Humans ; }, abstract = {Measurements of cell phylogeny based on natural or induced mutations, known as lineage barcodes, in conjunction with molecular phenotype have become increasingly feasible for a large number of single cells. In this chapter, we delve into Quantitative Fate Mapping (QFM) and its computational pipeline, which enables the interrogation of the dynamics of progenitor cells and their fate restriction during development. The methods described here include inferring cell phylogeny with the Phylotime model, and reconstructing progenitor state hierarchy, commitment time, population size, and commitment bias with the ICE-FASE algorithm. Evaluation of adequate sampling based on progenitor state coverage statistics is emphasized for interpreting the QFM results. Overall, this chapter describes a general framework for characterizing the dynamics of cell fate changes using lineage barcoding data.}, }
@article {pmid39745638, year = {2025}, author = {Ratz, M and von Berlin, L}, title = {Clonal Tracking in the Mouse Brain with Single-Cell RNA-Seq.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {103-137}, pmid = {39745638}, issn = {1940-6029}, mesh = {Animals ; Mice ; *Single-Cell Analysis/methods ; *Brain/metabolism/cytology/embryology ; RNA-Seq/methods ; Cell Lineage/genetics ; Cell Tracking/methods ; Lentivirus/genetics ; Sequence Analysis, RNA/methods ; Single-Cell Gene Expression Analysis ; }, abstract = {Lineage tracing methods enable the identification of all progeny generated by a single cell. High-throughput lineage tracing in the mammalian brain involves parallel labeling of thousands of progenitor cells with genetic barcodes in vivo followed by single-cell RNA-seq of lineage relations and cell types. Here we describe the generation of barcoded lentivirus, microinjections into the embryonic day 9.5 mouse forebrain, dissociation of 2-week-old mouse brain tissue, single-cell RNA-seq library preparation, and data analysis using a custom software. Compared to traditional methods based on sparse fluorophore labeling of progenitor cells, lineage tracing with genetic barcodes and single-cell RNA-seq has a >100-fold higher throughput while using >10 times fewer mice.}, }
@article {pmid39745637, year = {2025}, author = {Gentile, E and Maynard, A and He, Z and Treutlein, B}, title = {Lineage Recording in Human Brain Organoids with iTracer.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {85-101}, pmid = {39745637}, issn = {1940-6029}, mesh = {Humans ; *Organoids/cytology/metabolism ; *Brain/cytology ; *Induced Pluripotent Stem Cells/cytology/metabolism ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; *CRISPR-Cas Systems ; Transcriptome ; Cell Differentiation ; }, abstract = {Induced pluripotent stem cell (iPSC)-derived organoids provide models to study human organ development. Single-cell transcriptomics enables highly resolved descriptions of cell states within these systems; however, approaches are needed to directly determine the lineage relationship between cells. Here we provide a detailed protocol (Fig. 1) for the application of iTracer (He Z, Maynard A, Jain A, et al., Nat Methods 19:90-99, 2022), a recently published lineage recorder that combines reporter barcodes with inducible CRISPR-Cas9 scarring and is compatible with single-cell and spatial transcriptomics. iTracer is used to explore clonality and lineage dynamics during brain organoid development. More broadly, iTracer can be adapted to any iPSC-derived culture system to dissect lineage dynamics during normal or perturbed development.}, }
@article {pmid39745636, year = {2025}, author = {Rodriguez Fraticelli, AE and Sánchez, PS}, title = {Single-Cell Lineage Tracing and Clonal State-Fate Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2886}, number = {}, pages = {65-84}, pmid = {39745636}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Humans ; Cell Differentiation ; Animals ; Clone Cells/cytology ; DNA Barcoding, Taxonomic/methods ; Lentivirus/genetics ; Cell Tracking/methods ; }, abstract = {Lineage tracing has significantly advanced our comprehension in many areas of biology, such as development or immunity, by precisely measuring cellular processes like migration, division, or differentiation across labeled cells and their progeny. Traditional recombinase-based prospective lineage tracing is limited by the need for a priori cell type information and is constrained in the numbers of clones it can simultaneously track. In this sense, clonal lineage tracing with integrated random barcodes offers a robust alternative, enabling researchers to label and track a vast array of cells and their progeny over time. Moreover, clonal lineage tracing can be combined with single-cell omics technologies to study cell states and their maintenance over time. Key steps in these protocols include stable barcode integration, cell division to expand clones, and simultaneous capture of cellular properties with barcode information. Here, we comment on those steps and summarize important parameters to take into account during the design of single-cell lineage tracing experiments. Also, we present the main features for various available lentiviral libraries of expressed barcodes than can be captured alongside the transcriptome of individual cells. We cover other crucial aspects of experimental design, such as the optimization of cellular sampling, library diversity, and the minimization of clonal dropouts. Regarding sequencing data analysis, we provide some tips based on our experience, as well as available computational tools for the assignment of clonal identities and the identification of fate determinants. We finally discuss limitations of current methodologies and use an example step-by-step protocol to illustrate key points during the process. In sum, we provide a roadmap for considering and implementing single-cell lineage tracing studies to comprehensively explore fate determinants and their mechanisms.}, }
@article {pmid39745115, year = {2025}, author = {González-Peña, R and Laredo-Tiscareño, SV and Huerta, H and Hernández-Triana, LM and DE Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and García-Rejón, JE and Hidalgo-Martínez, DO and Garza-Hernández, JA}, title = {FIRST STATE AND NATIONAL RECORDS OF CULICOIDES DEBILIPALPIS AND CULICOIDES REEVESI IN CHIHUAHUA, MEXICO.}, journal = {Journal of the American Mosquito Control Association}, volume = {41}, number = {1}, pages = {39-42}, doi = {10.2987/24-7207}, pmid = {39745115}, issn = {1943-6270}, mesh = {Animals ; Mexico ; *Ceratopogonidae/classification/physiology ; Female ; *Animal Distribution ; }, abstract = {In July 2022, adult female Culicoides were collected from San Buenaventura (54 specimens) and Urique (3 specimens) in Chihuahua, Mexico. Culicoides reevesi and Culicoides debilipalpis were new records for the state, with C. reevesi also being a first for Mexico. The study highlights DNA barcode identification challenges and emphasizes the need for ongoing surveillance along the Mexico-USA border.}, }
@article {pmid39745059, year = {2025}, author = {Huang, Z and Xie, X and Wu, Y and Liu, R and Lv, Y}, title = {Breaking Barcode Limits: Metal Nanoparticle Lego Brick Self-Assembly for High-Throughput Screening.}, journal = {Journal of the American Chemical Society}, volume = {147}, number = {6}, pages = {4904-4914}, doi = {10.1021/jacs.4c13706}, pmid = {39745059}, issn = {1520-5126}, mesh = {*Metal Nanoparticles/chemistry ; *High-Throughput Screening Assays/methods ; Humans ; Biomarkers, Tumor/analysis ; Immunoassay ; Biotin/chemistry ; }, abstract = {As precision medicine increasingly reveals the biological diversity among individuals, the demand for higher-throughput screening techniques, particularly suspension array technologies capable of more multiplexing from smaller samples in a single run, is intensifying. However, advancements in the multiplexing capability of current suspension platforms have lagged with limited alleviation, necessitating breakthroughs for innovative solutions that enable larger-scale measurements. Here, we introduce such a breakthrough with a novel mass-cytometric barcode engineering by metal nanoparticle-based "Lego Brick"-like self-assembly for high-throughput barcode design and capacity amplification. The suspension array capacity can be expanded to over 20,500 unique barcodes by flexibly assembling just 10 types of barcoding units (metal nanoparticles) onto the surface of the barcoding center (magnetic spheres) through a universal biotin-streptavidin binding template, significantly enhancing both throughput and versatility. Further multiplexed immunoassay, termed MassMAP, demonstrates high-throughput profiling of cancer biomarkers, highlighting the revolutionary potential of Lego Brick self-assembly in massive cytometric screening for higher-throughput applications.}, }
@article {pmid39742275, year = {2024}, author = {Ado, S and Dong, C and Attaf, N and Moussa, M and Carrier, A and Milpied, P and Navarro, JM}, title = {FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1505971}, pmid = {39742275}, issn = {1664-3224}, mesh = {Animals ; *Single-Cell Analysis/methods ; *Antibodies, Monoclonal/immunology/genetics ; *B-Lymphocytes/immunology/metabolism ; Mice ; Receptors, Antigen, B-Cell/genetics/immunology ; Gene Library ; Flow Cytometry/methods ; Sequence Analysis, RNA/methods ; Humans ; Transcriptome ; }, abstract = {Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. However, in most cases, the specificity and affinity of the B cell antigen receptor cannot be inferred from its sequence. Antibody cloning and expression from single B cells is then required for functional assays. Here we propose a method that integrates FACS-based 5'-end single-cell RNA sequencing (FB5P-seq) and monoclonal antibody cloning for integrative analysis of single B cells. Starting from a cell suspension, single B cells are FACS-sorted into 96-well plates for reverse transcription, cDNA barcoding and amplification. A fraction of the single-cell cDNA is used for preparing 5'-end RNA-seq libraries that are sequenced for retrieving transcriptome-wide gene expression and paired BCR sequences. The archived cDNA of selected cells of interest is used as input for cloning heavy and light chain variable regions into antibody expression plasmid vectors. The corresponding monoclonal antibodies are produced by transient transfection of a eukaryotic producing cell line and purified for functional assays. We provide detailed step-by-step instructions and describe results obtained on ovalbumin-specific murine germinal center B cells after immunization. Our method is robust, flexible, cost-effective, and applicable to different B cell types and species. We anticipate it will be useful for mapping antigen specificity and affinity of rare B cell subsets characterized by defined gene expression and/or antigen receptor sequence.}, }
@article {pmid39741786, year = {2024}, author = {Haverinen, R and Pototski, A and Mutanen, M and Mikalauskas, D and Yakovlev, RV and Müller, GC and Prozorov, AM and Saldaitis, A}, title = {Integrative review of Xylomoiastrix, X.retinax and X.stangelmaieri (Lepidoptera, Noctuidae, Xyleninae, Apameini).}, journal = {ZooKeys}, volume = {1221}, number = {}, pages = {309-342}, pmid = {39741786}, issn = {1313-2989}, abstract = {The relationship of Xylomoiastrix Mikkola, 1980; Xylomoiaretinax Mikkola, 1998; and Xylomoiastangelmaieri Mikkola, 1998 is reconsidered based on 59 genitalia slides (37 males and 22 females) and 40 barcodes of adults collected from the type localities and areas in-between. Due to lack of stable morphologic differences, apart from the wing coloration of X.retinax, and low genetic distance between the three, they are considered as three subspecies of X.strix: the nominotypical one X.strixstangelmaieri stat. nov. and X.strixretinax stat. nov. Included are photographs of all specimens covering 37 adults, and 28 male and 18 female genitalia, as well as a phylogenetic tree and a map showing collecting localities.}, }
@article {pmid39739757, year = {2025}, author = {Ramaprasad, A and Blackman, MJ}, title = {A scaleable inducible knockout system for studying essential gene function in the malaria parasite.}, journal = {Nucleic acids research}, volume = {53}, number = {4}, pages = {}, pmid = {39739757}, issn = {1362-4962}, support = {CC2129/CRUK_/Cancer Research UK/United Kingdom ; 751865//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 220318/A/20/Z/WT_/Wellcome Trust/United Kingdom ; CC2129/WT_/Wellcome Trust/United Kingdom ; //European Society of Clinical Microbiology and Infectious Diseases/ ; }, mesh = {*Gene Knockout Techniques/methods ; *Genes, Essential ; *Plasmodium falciparum/genetics ; Frameshift Mutation ; Protozoan Proteins/genetics/metabolism ; Animals ; Erythrocytes/parasitology ; Humans ; }, abstract = {The malaria parasite needs nearly half of its genes to propagate normally within red blood cells. Inducible ways to interfere with gene expression like the DiCre-lox system are necessary to study the function of these essential genes. However, existing DiCre-lox strategies are not well-suited to be deployed at scale to study several genes simultaneously. To overcome this, we have developed SHIFTiKO (frameshift-based trackable inducible knockout), a novel scaleable strategy that uses short, easy-to-construct, barcoded repair templates to insert loxP sites around short regions in target genes. Induced DiCre-mediated excision of the flanked region causes a frameshift mutation resulting in genetic ablation of gene function. Dual DNA barcodes inserted into each mutant enables verification of successful modification and induced excision at each locus and collective phenotyping of the mutants, not only across multiple replication cycles to assess growth fitness but also within a single cycle to identify specific phenotypic impairments. As a proof of concept, we have applied SHIFTiKO to screen the functions of malarial rhomboid proteases, successfully identifying their blood stage-specific essentiality. SHIFTiKO thus offers a powerful platform to conduct inducible phenotypic screens to study essential gene function at scale in the malaria parasite.}, }
@article {pmid39739202, year = {2025}, author = {Bard, NW and Davies, TJ and Cronk, QCB}, title = {Teknonaturalist: A Snakemake Pipeline for Assessing Fungal Diversity From Plant Genome Bycatch.}, journal = {Molecular ecology resources}, volume = {25}, number = {3}, pages = {e14056}, pmid = {39739202}, issn = {1755-0998}, support = {RGPIN-2019-04041//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2020-04439//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *Plants/microbiology ; DNA, Ribosomal Spacer/genetics/chemistry ; *Computational Biology/methods ; DNA, Fungal/genetics/chemistry ; *DNA Barcoding, Taxonomic/methods ; *Genome, Plant ; Endophytes/classification/genetics ; *Biodiversity ; Sequence Analysis, DNA ; }, abstract = {Relatively little is known of the host associations and compatibility of fungal plant pathogens and endophytes. Publicly available plant genomic DNA can be mined to detect incidental fungal DNA, but taxonomic assignment can be challenging due to short lengths and variable discriminative power among different genomic regions and taxa. Here, we introduce a computationally lightweight and accessible Snakemake pipeline for rapid detection and classification (identification and assignment to taxonomic rank) of pathogenic and endophytic fungi (and other fungi associated with plants) that targets the internal transcribed spacer (ITS) region, a fungal barcode standard. We include methods for maximising query sequence length, which gives higher support for ITS1 and ITS2 taxonomic classifications by extending to other fragments of the ITS region and providing taxon-specific local cut-off and confidence scores. We demonstrate our pipeline with a case study using public genomic sequence data for six diverse plant species, including four species within Betula, an ecologically and economically important broadleaved forest tree genus, a shrub and a grass. Our pipeline classified fungi within minutes to a few hours per host individual, with 204 different fungal genera identified at high confidence (≥ 70%). Our pipeline detected and classified pathogenic and endophytic genera known to associate with Betula, and many others with no prior record of association. Our pipeline, leveraging existing sequence data, has several potential applications, including detecting cryptic fungal pathogens and helping characterise the endophytic fungal microbiome, bioprospecting commercially useful fungal species, and determining the plant host range of fungi.}, }
@article {pmid39736908, year = {2024}, author = {Nguyen, QH and Van Nguyen, T and Vi, TTX and Vu, TTT and Nguyen, LTN and Nguyen, YTH and Nguyen, HD and Tu, TQ and Chu, MH}, title = {Dataset on ITS and some chloroplast DNA regions of Boehmeria holosericea Blume in Vietnam.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111193}, pmid = {39736908}, issn = {2352-3409}, abstract = {Species of the Boehmeria genus have the potential to be natural medicines and have industrial fibre production uses. Many species of this genus are morphologically similar and are difficult to distinguish, especially when their morphology is distorted. This dataset includes sequence information of several DNA regions isolated from the genome of Boehmeria holosericea, namely ITS (from the nuclear genome), matK, trnL-trnF, trnH-psbA, and rpoC1 (from the chloroplast genome) and phylogenetic analysis results based on the isolated sequences. On the phylogenetic tree based on the matK gene sequence, B. holosericea is grouped with B. umbrosa, B. clidemioides, B. spicata, and B. macrophylla with a bootstrap coefficient of 100%. In the phylogenetic tree based on the trnH-psbA spacer region sequences, B. holosericea was grouped with B. clidemioides (a bootstrap coefficient of 96%). In the phylogenetic tree based on the rpoC1 gene sequences, B. holosericea was grouped with B. spicata (a bootstrap coefficient of 100%). In the phylogenetic tree based on the ITS region sequences, B. holosericea was grouped with B. macrophylla (a bootstrap coefficient of 73%), and based on the trnL-trnF spacer region, B. holosericea was grouped with B. pilociuscula (a bootstrap coefficient of 16%). Two genes, matK and rpoC1 and the trnH-psbA region from the chloroplast genome, are potential DNA barcode candidates that could aid in the species identification of B. holosericea. This dataset the first report on the ITS, matK, trnL-trnF, trnH-psbA, and rpoC1 sequences and the phylogeny of B. holosericea.}, }
@article {pmid39732835, year = {2024}, author = {Eastburn, DJ and White, KS and Jayne, ND and Camiolo, S and Montis, G and Ha, S and Watson, KG and Yeakley, JM and McComb, J and Seligmann, B}, title = {High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31285}, pmid = {39732835}, issn = {2045-2322}, support = {R43 GM140771/GM/NIGMS NIH HHS/United States ; R44 GM140771/GM/NIGMS NIH HHS/United States ; R44GM140771/GF/NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; Animals ; *Brain/metabolism ; *Kidney/metabolism/cytology ; *Lung/metabolism/cytology ; *Gene Expression Profiling/methods ; Mice ; Transcriptome ; Humans ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000 + cells per sample. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC offers a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has a multiplet rate of less than 1.1% and a cell capture rate of ~ 50%. Although the assay can accurately profile the whole transcriptome (19,683 human, 21,400 mouse and 21,119 rat genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest - thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of more than 90,000 cells across multiple species and sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate more than 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies with high data quality.}, }
@article {pmid39731283, year = {2024}, author = {Nieto-Clavijo, C and Morales, L and Delgado-Aldana, A and Hernández, PC and Torres-Molina, I and Gonzalez-Cuiza, A and Cortés-Muñoz, F and Chaparro-Olaya, J}, title = {Enhanced Blastocystis subtyping from stool samples using semi-nested barcode PCR: validation with an NGS-based approach.}, journal = {BioTechniques}, volume = {76}, number = {12}, pages = {581-591}, doi = {10.1080/07366205.2024.2442835}, pmid = {39731283}, issn = {1940-9818}, mesh = {*Blastocystis/genetics/classification/isolation &amp; purification ; *Feces/parasitology ; Humans ; *Polymerase Chain Reaction/methods ; *High-Throughput Nucleotide Sequencing/methods ; *DNA Barcoding, Taxonomic/methods ; Blastocystis Infections/parasitology/diagnosis ; RNA, Ribosomal, 18S/genetics ; DNA, Protozoan/genetics ; }, abstract = {In 2006, a PCR method was introduced to subtype Blastocystis by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non-Blastocystis sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from Blastocystis cultures, limiting its sensitivity when used directly with stool samples. As a result, barcoding-PCR can sometimes yield negative results for stool samples confirmed as Blastocystis-positive by microscopy. To improve subtyping from stool-derived DNA, we developed a Semi-Nested barcode PCR that amplifies the barcoding region in a second reaction. Our study shows that this Semi-Nested approach outperforms classical barcoding-PCR, detecting Blastocystis more reliably from stool samples with stronger gel signals and no false positives. This was confirmed by near-complete concordance (68/70 samples) with the Santin-PCR coupled to Next-Generation Sequencing (NGS) as reference standard for Blastocystis subtyping. Of particular interest, one amplicon matched the only previous report of ST35, marking this as the second global detection of ST35 and the first in Colombia. Overall, Semi-Nested barcoded PCR offers a more robust and sensitive alternative compared to classical barcoding-PCR for subtyping Blastocystis directly from stool samples.}, }
@article {pmid39730712, year = {2024}, author = {Nurtaza, A and Dyussembekova, D and Islamova, S and Samatova, I and Zhanybekova, Z and Umirzakova, A and Magzumova, G and Muranets, A and Kakimzhanova, A}, title = {In Vitro conservation and genetic diversity analysis of rare species Ribes janczewskii.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31117}, pmid = {39730712}, issn = {2045-2322}, support = {AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; AP14869409//Ministry of Education and Science of the Republic of Kazakhstan/ ; }, mesh = {*Genetic Variation ; Genotype ; Fruit/genetics/growth &amp; development ; DNA Barcoding, Taxonomic ; Conservation of Natural Resources ; }, abstract = {Ribes janczewskii is a rare and valuable plant known for its resistance to spring frosts, pests, and diseases. It is used in hybridization to develop resistant currant varieties but is on the verge of extinction, listed in Kazakhstan Red Book. This study developed a micropropagation and slow-growth storage protocol for conservation. Genotypes were identified through DNA barcode analysis (rbcL, ITS, and matK) and sequences uploaded to the National Center for Biotechnology Information database. Genetic diversity was assessed using iPBS primers, generating 98 fragments with 88-94% polymorphic bands. Biochemical analysis of fruits showed vitamin C content from 4.64 to 5.61 mg/100 g, vitamin E from 2.26 to 3.16 mg/100 g, vitamin B5 from 3.18 to 4.93 mg/100 g, and quercetin up to 12.5 mg/100 g. Micropropagation stages were optimized with 12% hydrogen peroxide for surface sterilization, achieving up to 73.3% explant viability. Effective hormonal combinations for in vitro culture included WPM with BAP 0.2 mg L[-1] and GA 0.5 mg L[-1], and for propagation, BAP 0.25 mg L[-1], GA 0.5 mg L[-1], and IBA 0.5 mg L[-1]. Mannitol (20 g L[-1]) was used for slow-growth storage, keeping explants viable for 4 months without re-cultivation.}, }
@article {pmid39729996, year = {2025}, author = {Park, J and Cook, S and Lee, D and Choi, J and Yoo, S and Bae, S and Im, HJ and Lee, D and Choi, H}, title = {Generation of super-resolution images from barcode-based spatial transcriptomics by deep image prior.}, journal = {Cell reports methods}, volume = {5}, number = {1}, pages = {100937}, pmid = {39729996}, issn = {2667-2375}, mesh = {*Image Processing, Computer-Assisted/methods ; Algorithms ; *Gene Expression Profiling/methods ; *Transcriptome/genetics ; Humans ; }, abstract = {Spatially resolved transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expression in situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, an algorithm that enables the reconstruction of dense matrices (higher-resolution and non-zero-inflated matrices) from low-resolution ST libraries. SuperST is based on deep image prior, which reconstructs spatial gene expression patterns as image matrices. Compared with previous methods, SuperST generated output images that more closely resembled immunofluorescence images for given gene expression maps. Furthermore, we demonstrated how one can combine images created by SuperST with computer vision algorithms. In this context, we proposed a method for extracting features from the images, which can aid in spatial clustering of genes. By providing a dense matrix for each gene in situ, SuperST can successfully address the resolution and zero-inflation issue.}, }
@article {pmid39729477, year = {2024}, author = {Lee, M and Lee, HY and Kang, JS and Lee, H and Park, KJ and Park, JY and Yang, TJ}, title = {Correction: Authentication of Allium ulleungense, A. microdictyon and A. ochotense based on super-barcoding of plastid genome and 45S nrDNA.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0316742}, pmid = {39729477}, issn = {1932-6203}, abstract = {[This corrects the article DOI: 10.1371/journal.pone.0294457.].}, }
@article {pmid39729273, year = {2025}, author = {Randall, E and Keillor, B and Cooke, DEL}, title = {The Use of eDNA Metabarcoding to Detect and Identify Phytophthora in Water Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2892}, number = {}, pages = {117-138}, pmid = {39729273}, issn = {1940-6029}, mesh = {*Phytophthora/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Water/chemistry ; Water Microbiology ; Metagenomics/methods ; }, abstract = {We describe a protocol to amplify DNA barcodes of known and unknown taxa of Phytophthora and related plant pathogenic oomycetes from a range of environments. The methods focus on sampling pathogen propagules from water using in situ sampling and filtration equipment and buffers that enable efficient storage and DNA extraction for later downstream processing.}, }
@article {pmid39728620, year = {2024}, author = {Husted, AL and Sutton, VR and Presnar, LA and Blackburn, RK and Staton, JL and Borgianini, SA and D'Antonio, EL}, title = {The Multifunctional Catalytic Hemoglobin from Amphitrite ornata: Protocols on Isolation, Taxonomic Identification, Protein Extraction, Purification, and Characterization.}, journal = {Methods and protocols}, volume = {7}, number = {6}, pages = {}, pmid = {39728620}, issn = {2409-9279}, support = {n/a//Pritchards Island State Funding/ ; 17220-15-39011//University of South Carolina, Office of the Vice President for Research/ ; n/a//University of South Carolina, Office of Undergraduate Research/ ; }, abstract = {The multifunctional catalytic hemoglobin from the terebellid polychaete Amphitrite ornata, also named dehaloperoxidase (AoDHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of AoDHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel. Traditional visual taxonomic species identification by the non-specialist, at least for A. ornata or even for other marine worms, is a very difficult and time-consuming task since a large diversity is present and the method is restricted to adult worm specimens. The work herein aimed to describe a method that simplifies the taxonomic identification of A. ornata in particular through the assessment of its mitochondrial cytochrome c oxidase subunit I gene by employing the DNA barcoding technique. Furthermore, whole-worm specimens of A. ornata were used to extract and purify AoDHP followed by an H2O2-dependent peroxidase activity assay evaluation against substrate 2,4,6-trichlorophenol. AoDHP isoenzyme A was also overexpressed as the recombinant protein in Escherichia coli, and its peroxidase activity parameters were compared to AoDHP from the natural source. The activity assay assessment indicated a tight correlation for all Michaelis-Menten parameters evaluated. We conclude that the method described herein exhibits a streamlined approach to identify the polychaete A. ornata, which can be adopted by the non-specialist, and the full procedure is predicted to facilitate the discovery of novel dehaloperoxidases from other marine invertebrates.}, }
@article {pmid39725934, year = {2024}, author = {Feng, W and Zhang, Z and Zhang, J and Nan, P and Song, Z and Zhang, W and Yang, J and Wang, Y}, title = {Comparative plastomic analysis of cultivated Dioscorea polystachya and its close relatives provides insights on the inter- and intraspecific phylogenies and potential wild origins of domestication.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1255}, pmid = {39725934}, issn = {1471-2229}, mesh = {*Dioscorea/genetics/classification/growth &amp; development ; *Phylogeny ; *Genome, Chloroplast ; Domestication ; China ; }, abstract = {BACKGROUND: Dioscorea polystachya and its closely related species are original plants of the tuber crop "yam", which had been intensively use for medicinal and food purposes and widely cultivated in northern China and its surrounding areas with a long history. Many cultivars of these species are often confused with one another because of similar tuber morphology, however, conventional DNA barcoding faces practical limitations restricting the method to effectively identify closely related species. In addition, phylogenetic relationships among various cultivar groups of Chinese yam (D. polystachya) remains unclear. To solve these problems, genomic DNAs of 15 Dioscorea samples were sequenced to assemble and annotate chloroplast genomes, which were used for analyzing their structural characteristics and identifying phylogenetic relationships at the inter- and intraspecific levels.<br><br>RESULTS: The size of chloroplast genomes of the tested samples is about 153&#xa0;kb, and 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes are annotated. Phylogenetic analysis showed that D. polystachya were sister to Dioscorea japonica, and for Huaishan yams, Dioscorea persimilis did not cluster with Dioscorea alata and Dioscorea fordii. Four cultivar groups of Chinese yam were determined, namely Tiegun group, Anping group, Foshou group and Taihang complex group. Among these cultivar groups, Foshou and Taihang complex are clustered with different wild yams, respectively. Amino acid preferences are similar at the inter- and intraspecific levels, while synonymous codon usage reflects distinct patterns in the majority of cultivars of D. polystachya. There are distinct SSR variations among species, as well as four cultivar groups. Collinearity and SNP analyses show that nucleotide hypervariable regions among Dioscorea species are mainly concentrated in trnK-atpA, rps16-trnQ, atpA-atpH, rpoB-psbD, atpH-atpI, trnV-ndhC in the LSC region, and ccsA-ndhF in the SSC region, while intraspecific variation of Chinese yam is enriched in the intergenic spacers of rpoB-psbC, ndhD-ndhF, and trnQ-trnS, as well as the gene ycf1.<br><br>CONCLUSION: Phylogenetic analysis supports that Huaishan yams are not of monophyletic origin and the cultivated Chinese yam has at least two wild origins of domestication, which is consistent with the historical records of these wild yams from Mt. Dabie and Mt. Taihang. The identification efficiency of the newly developed barcodes for cultivar groups based on chloroplast genome SNP screening is significantly better than those of conventional barcodes. This approach to generate viable candidate markers based on the comparison from interspecific and intraspecific hypervariable regions of chloroplast genomes can be applied to conduct phylogenetic relationships of more important crop species and their close relatives, which are difficult to identify, as well as their wild origins of domestication.}, }
@article {pmid39719730, year = {2025}, author = {Bergin, R and Samperton, K and Bronikowski, M and Hoar, E and Rolison, J and Shollenberger, Q and Marks, N and Wellons, M and Scott, S}, title = {Synthesis and characterization of isotopically barcoded nickel, molybdenum, and tungsten taggants for intentional nuclear forensics.}, journal = {Talanta}, volume = {285}, number = {}, pages = {127425}, doi = {10.1016/j.talanta.2024.127425}, pmid = {39719730}, issn = {1873-3573}, abstract = {Intentional nuclear forensics is a concept wherein the deliberate addition of benign and persistent material signatures to nuclear material can be used to reduce the time between the discovery of material outside of regulatory control and determination of its original provenance. One concept within intentional nuclear forensics involves the use of perturbed stable isotopes to generate unique isotope ratio "barcodes" to encode information (e.g., production batch, location, etc.) and track material throughout the nuclear fuel cycle. Synthesis of taggant species of nickel (Ni), molybdenum (Mo), and tungsten (W) was undertaken via a double-spike mechanism, wherein two highly enriched isotopes of interest per elemental taggant were mixed to form an enriched "double-spike" which was subsequently isotopically diluted with bulk material having a natural isotopic composition. Two taggant species perturbing isotopic ratios, alpha (α) and beta (β), for each of Ni, Mo, and W were synthesized. Independent measurements of double spikes and alpha and beta taggant species agreed within uncertainty and are clearly resolvable from natural compositions. High-precision analyses were independently performed by MC-ICP-MS at two U.S. National Laboratories, with consensus values and uncertainties calculated for all samples. Observed isotopic perturbations in the final taggant species measured on the order of hundreds to thousands of permille (‰) with respect to natural for isotope ratios of interest (e.g., [60]Ni/[58]Ni, [100]Mo/[98]Mo, [186] W/[183]W). Discrepancies between modeled and measured isotopic compositions were observed and are largely attributed to imprecise vendor assay values for starting materials. Using measured starting material compositions as inputs for the mixing model improved the level of agreement between predicted and measured α and β taggant isotope ratios. Overall, characterization of all taggant species demonstrates that this "barcode" concept could have viability for use in nuclear forensics. It is expected that for any two-isotope mixing array dozens of isotopic barcodes could be encoded into a material system and subsequently resolved utilizing modern mass spectrometric methods.}, }
@article {pmid39719062, year = {2025}, author = {Long, Y and Mora, A and Li, FZ and Gürsoy, E and Johnston, KE and Arnold, FH}, title = {LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning.}, journal = {ACS synthetic biology}, volume = {14}, number = {1}, pages = {230-238}, doi = {10.1021/acssynbio.4c00625}, pmid = {39719062}, issn = {2161-5063}, mesh = {*Machine Learning ; *Directed Molecular Evolution/methods ; Protein Engineering/methods ; Software ; Nanopore Sequencing/methods ; }, abstract = {Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barcoding strategy with nanopore sequencing to rapidly generate sequence-function data for entire protein-coding genes. LevSeq integrates into existing protein engineering workflows and comes with open-source software for data analysis and visualization. The pipeline facilitates data-driven protein engineering by consolidating sequence-function data to inform directed evolution and provide the requisite data for machine learning-guided protein engineering (MLPE). LevSeq enables quality control of mutagenesis libraries prior to screening, which reduces time and resource costs. Simulation studies demonstrate LevSeq's ability to accurately detect variants under various experimental conditions. Finally, we show LevSeq's utility in engineering protoglobins for new-to-nature chemistry. Widespread adoption of LevSeq and sharing of the data will enhance our understanding of protein sequence-function landscapes and empower data-driven directed evolution.}, }
@article {pmid39718626, year = {2024}, author = {Dhabal, S and Chakrabarty, AK and Banerjee, D and Katiyar, CK and Rai, RK and Dubey, SK}, title = {Internal transcribed spacer (ITS): The powerful DNA barcode and phylogenetic marker for successful authentication of Withania somnifera.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {77}, pmid = {39718626}, issn = {1573-4978}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Withania/genetics/classification ; Genetic Markers ; *DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Understanding the evolutionary history of plants and accurately identifying biologically important species and their families is crucial for the herbal and Ayurvedic industries. The genetic approach by DNA barcoding plays a pivotal role in accurate species identification, authentication and quality control. Due to various therapeutic properties, Withania somnifera has been used worldwide in traditional systems of medicine for centuries including Ayurveda and Unani. The increasing demand for W. somnifera products has led to concerns regarding the authenticity and quality of commercial herbal preparations. However, adulteration become major trouble for users and industry for safety reasons and authentication of the plant with proper DNA marker is a major concern.<br><br>METHODOLOGY: DNA barcoding techniques and Phylogenetic analysis were employed to authenticate W. somnifera plant species using universal genetic markers. The markers were PCR amplified, sequenced and analyzed using BLAST-based and phylogeny-based identification methods.<br><br>RESULTS: The BLAST result shows the percent identity (PI) of ITS1, ITS2, trnK, atpB, rbcL and matK was 100%, 100%, 100%, 97.59%, 100 and 99.20% respectively with the NCBI reference sequence. However, ITS1 and ITS2 show the maximum sequence similarity with W. somnifera of NCBI data. Phylogenetic analysis using NCBI data further supports the role of ITS in the discrimination of W. somnifera from closely related species.<br><br>CONCLUSION: Therefore, the ITS gene may be considered promising a candidate for DNA barcoding for discrimination of W. somnifera from other species, its authentication and quality control.}, }
@article {pmid39717638, year = {2024}, author = {Palandačić, A and Reier, S and Diripasko, OA and Jelić, D and Stroj, A and Wanka, A and Marić, D and Bogutskaya, NG}, title = {Substygophily in Dinaric Karst: A Model Case of Locally Endemic Minnows Phoxinellus (Leuciscinae).}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70648}, pmid = {39717638}, issn = {2045-7758}, abstract = {The Dinaric Karst extends along the Adriatic coast of the Western Balkan Peninsula and is home to a group of "karst minnows" of the genera Delminichthys, Phoxinellus, and Telestes, which have adapted to the highly variable water conditions in the karst by spending up to several months underground, but require surface habitats for spawning, defining them as substygophiles. The three species of the genus Phoxinellus, P. alepidotus, P. pseudalepidotus, and P. dalmaticus, are defined by restricted ranges, making them vulnerable to pollution and extended draughts caused by the climate change. In this study, the phylogeny of Leusciscinae was reconstructed using 15 Phoxinellus and one Delminichthys adspersus, one Pelasgus epiroticus, and one Telestes polylepis complete mitochondrial genomes and the position of the genus Phoxinellus within the subfamily as sister species to the Chondrostoma clade was confirmed. The inter- and intrapopulation structure of the genus Phoxinellus was inferred using molecular (nuclear and mitochondrial data) and morphological analyses. For the molecular analysis, more than 150 historical specimens were analyzed for a short fragment of the cytochrome oxidase I (COI) barcoding region and 15 Phoxinellus specimens were subjected to single nucleotide polymorphism analysis. For morphological analysis, 121 Phoxinellus specimens were analyzed for 51 measurements and 8 counts. All analyses confirmed the clear delimitation of the three Phoxinellus species, but were insufficient to fully resolve the intrapopulation structure within the species. This study also included data from field surveys of Phoxinellus collected over the past 20 years, which showed that abundance is declining and ranges are shrinking. Phoxinellus are also threatened by invasive/introduced species. Based on cave observations/occurrence and morphological analysis, P. dalmaticus was classified as an advanced substygophile and P. alepidotus and P. pseudalepidotus were classified as basic stygophiles.}, }
@article {pmid39716438, year = {2025}, author = {Liu, X and Yang, X and Xiang, S and Lv, Y and Zhang, Z}, title = {Coordination-Defect-Driven Construction of Responsive Pure-MOF Microspheres for Switchable Mode-Dependent Anticounterfeiting Labels.}, journal = {ACS applied materials &amp; interfaces}, volume = {17}, number = {1}, pages = {2063-2071}, doi = {10.1021/acsami.4c19719}, pmid = {39716438}, issn = {1944-8252}, abstract = {Luminescent metal-organic frameworks (MOFs) with exceptional dynamics and diverse active sites possess tremendous potential in information security and anticounterfeiting applications. However, traditional MOF systems are based on broadband spectral signals with spectrum overlap, which easily leads to low-resolution signal identification, compromising the overall security level. Here, we report the coordination-defect-induced amorphous pure-MOF microsphere with switchable whispering-gallery-mode (WGM) signals as a mode-dependent security platform. Amorphous MOF microspheres are prepared by a chlorine coordination-defect-driven growth strategy based on the aperiodic arrangement in coordinate networks. The as-prepared amorphous MOF microspheres with well-defined circular morphology display the typical WGM resonance with dimension-dependent character, permitting the creation of photonic barcodes with substantial encoding capacity. Furthermore, the amorphous MOF microspheres exhibit optical mode switching behavior due to reversible framework shrinkage, which enables the design of covert photonic barcodes as anticounterfeiting labels, finally demonstrating responsive coding property and enhanced information security. The results provide a novel strategy for exploring an MOF-based security platform for information encryption and optical anticounterfeiting.}, }
@article {pmid39714325, year = {2025}, author = {Vaidya, K and Regan, MS and Lin, J and Houle, J and Gupta, A and Stopka, SA and Agar, NYR and Hammond, PT and Boehnke, N}, title = {Pooled Nanoparticle Screening Using a Chemical Barcoding Approach.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {64}, number = {5}, pages = {e202420052}, pmid = {39714325}, issn = {1521-3773}, support = {DMR-2011401//National Science Foundation/ ; P41EB028741/EB/NIBIB NIH HHS/United States ; K99 CA255844/CA/NCI NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; ECCS-2025124//National Nanotechnology coordinated infrastructure/ ; P41 EB028741/EB/NIBIB NIH HHS/United States ; P30-CA14051/CA/NCI NIH HHS/United States ; K99CA255844/CA/NCI NIH HHS/United States ; R00CA255844/CA/NCI NIH HHS/United States ; R00 CA255844/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Nanoparticles/chemistry ; Cell Line, Tumor ; Polylactic Acid-Polyglycolic Acid Copolymer/chemistry ; }, abstract = {We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.}, }
@article {pmid39714184, year = {2025}, author = {Leitner, DR and Zingl, FG and Morano, AA and Zhang, H and Waldor, MK}, title = {The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase.}, journal = {mBio}, volume = {16}, number = {2}, pages = {e0343324}, pmid = {39714184}, issn = {2150-7511}, support = {Zingl-2024HHMI//Life Sciences Research Foundation (LSRF)/ ; R01 AI042347/AI/NIAID NIH HHS/United States ; //Howard Hughes Medical Institute (HHMI)/ ; AI-042347//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI042347/AI/NIAID NIH HHS/United States ; }, mesh = {*Vibrio cholerae/genetics/growth &amp; development/metabolism ; DNA Transposable Elements ; Bacterial Proteins/genetics/metabolism ; Mutation ; Phospholipids/metabolism ; }, abstract = {UNLABELLED: Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote pathogen fitness in stationary phase. We discovered that the maintenance of lipid asymmetry (Mla) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type (WT) and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48 h stationary phase cultures. The mutant defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48 h. However, by 96 h the culturability of the WT and mutant strains were equivalent. By monitoring the abundances of genomically barcoded libraries of WT and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96 h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the defect of ∆mlaE. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for maintaining the culturability of V. cholerae because it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.<br><br>IMPORTANCE: Bacteria regularly encounter conditions with nutrient scarcity, where cell growth and division are minimal. Knowledge of the pathways that enable re-growth following nutrient restriction is limited. Here, using the cholera pathogen, we uncovered a role for the Mla pathway, a system that enables phospholipid re-cycling, in promoting Vibrio cholerae re-expansion from stationary phase cultures. Cells labeled with DNA barcodes or fluorophores were useful to demonstrate that though the abundances of wild-type and Mla mutant cells were similar in stationary phase cultures, they had marked differences in their capacities to regrow on plates. Of note, Mla mutant cells lose cell envelope components including high-energy phospholipids due to OMV shedding. Our findings suggest that the defects in cellular energy homeostasis that emerge in the absence of the Mla pathway underlie its importance in maintaining V. cholerae culturability.}, }
@article {pmid39713585, year = {2024}, author = {Wang, H and Wei, Z and Ren, G}, title = {A new species of Laena Dejean (Coleoptera, Tenebrionidae) from Sichuan Province, China, with an updated key.}, journal = {ZooKeys}, volume = {1221}, number = {}, pages = {165-173}, pmid = {39713585}, issn = {1313-2989}, abstract = {In this study, we describe and illustrate a new species of the genus Laena Dejean, 1821, Laenacostata sp. nov., which was collected in Micangshan Nature Reserve of Sichuan Province, China. Additionally, the COI mitochondrial gene was sequenced to provide additional evidence for this new species' validity. The results of phylogenetic analyses suggest that this new species is sister to L.maowenica Schawaller, 2008. Furthermore, an updated key to Laena species from Sichuan Province is provided.}, }
@article {pmid39713068, year = {2024}, author = {Douglas, HB and Hammond, G and Smith, TW and Mutz, J and Konstantinov, AS}, title = {Palaearctic flea beetle Phyllotretaochripes (Curtis) (Coleoptera, Chrysomelidae, Galerucinae), herbivore of Alliariapetiolata (garlic mustard), new to North America.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e135576}, pmid = {39713068}, issn = {1314-2828}, abstract = {BACKGROUND: The univoltine leaf beetle Phyllotretaochripes (Curtis, 1837b) is native to the Palaearctic Region from Japan to western Europe.This species was previously evaluated as a potential biological control agent against invasive populations of the woodland weed Alliariapetiolata (Bieb.) Cavara &amp; Grande (Brassicaceae) in North America, but rejected because it could harm native and at-risk populations of Brassicaceae.<br><br>NEW INFORMATION: First North American records are presented for Phyllotretaochripes (Curtis, 1837). Specimens were examined from the USA: Illinois, Maryland, Michigan, Ohio and Pennsylvania. Internet photographs of apparent additional individuals from USA: Indiana, Michigan, Minnesota, Ohio, Pennsylvania, Tennessee, Wisconsin and Canada: Ontario were also examined. DNA barcoding analysis showed high genetic variability and possible cryptic species within European populations of P.ochripes. Diagnostic information is presented to distinguish P.ochripes. from other North American Chrysomelidae and a species distribution model to assess its potential spread in North America is presented.Phyllotretaochripes breeds on invasive garlic mustard, Alliariapetiolata (Bieb.) Cavara &amp; Grande (Brassicaceae) and also non-native Rorippaamphibia (L.) Besser and other species of Brassicaceae.A species distribution model and the range of its host plant A.petiolata, indicates the most suitable conditions for this species are in humid areas of eastern North America. However, most of the known records of this species were discovered in areas projected to have low suitability. This is likely a consequence of sampling bias towards western Europe and away from the eastern Asian portion of its native range. The United States of America and Canada are now known to be home to 72 or more species of adventive Chrysomelidae.}, }
@article {pmid39711595, year = {2024}, author = {Harun, A and Song, S and You, X and Liu, H and Wen, X and Fang, Z and Cheng, Z and Chen, C}, title = {Comprehensive mapping of molecular cytogenetic markers in pitaya (Hylocereus undatus) and related species.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1493776}, pmid = {39711595}, issn = {1664-462X}, abstract = {Pitaya (Hylocereus undatus; 2n=22) is an important fruit crop from the Cactaceae family, originally domesticated in Mexico and the USA, and is now widely cultivated for its nutritional benefits. It is characterized by its distinctive triangular-shaped stems and large, showy flowers, thriving in arid and semi-arid environments, particularly in hot, dry climates. However, systematic chromosomal studies, including chromosomal mapping of cytogenetic markers in pitaya, are limited, presenting challenges for its cytogenetic improvement. To address this issue, we designed oligo-barcodes specific to thirty-three chromosome regions based on the pitaya reference genome and applied them to both pitaya and cactus (Selenicerus grandifloras; 2n=22) for oligo-barcodes mapping, karyotyping, and chromosome identification. We utilized FISH technology, employing oligo, rDNA, and tandem repeat probes for chromosomal mapping, identification, and karyotyping of pitaya and related species. We successfully localized oligo-barcodes on eleven pairs of chromosomes in both pitaya and cactus, demonstrating the effectiveness of the synthesized oligo-barcodes. We used two ribosomal DNA (rDNA) probes (45S and 5S) and two tandem repeat probes (GTR11 and STR3) in pitaya (both diploid and tetraploid) and two other Cactaceae species (S. grandifloras and Opuntia humifusa; 2n=40) for chromosomal mapping. The analysis of rDNA distribution and CMA (Chromomycin A3) banding across different chromosomes in pitaya and cacti highlights the concept of conserved rDNA. This study provides fundamental insights into cytogenetic markers and their localization across different chromosomes in pitaya and other Cactaceae species.}, }
@article {pmid39711562, year = {2024}, author = {Enninful, A and Zhang, Z and Klymyshyn, D and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Yang, M and Lu, Y and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R}, title = {Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39711562}, issn = {2693-5015}, support = {U54 AG079759/AG/NIA NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; }, abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.}, }
@article {pmid39704725, year = {2025}, author = {Wang, R and Hastings, WJ and Saliba, JG and Bao, D and Huang, Y and Maity, S and Kamal Ahmad, OM and Hu, L and Wang, S and Fan, J and Ning, B}, title = {Applications of Nanotechnology for Spatial Omics: Biological Structures and Functions at Nanoscale Resolution.}, journal = {ACS nano}, volume = {19}, number = {1}, pages = {73-100}, pmid = {39704725}, issn = {1936-086X}, support = {P20 GM109036/GM/NIGMS NIH HHS/United States ; R21 AI126361/AI/NIAID NIH HHS/United States ; S10 OD032453/OD/NIH HHS/United States ; U24 AG066528/AG/NIA NIH HHS/United States ; }, mesh = {*Nanotechnology/methods ; Humans ; *Metabolomics/methods ; Proteomics/methods ; DNA/chemistry ; Animals ; *Genomics/methods ; *Nanostructures/chemistry ; Epigenomics ; }, abstract = {Spatial omics methods are extensions of traditional histological methods that can illuminate important biomedical mechanisms of physiology and disease by examining the distribution of biomolecules, including nucleic acids, proteins, lipids, and metabolites, at microscale resolution within tissues or individual cells. Since, for some applications, the desired resolution for spatial omics approaches the nanometer scale, classical tools have inherent limitations when applied to spatial omics analyses, and they can measure only a limited number of targets. Nanotechnology applications have been instrumental in overcoming these bottlenecks. When nanometer-level resolution is needed for spatial omics, super resolution microscopy or detection imaging techniques, such as mass spectrometer imaging, are required to generate precise spatial images of target expression. DNA nanostructures are widely used in spatial omics for purposes such as nucleic acid detection, signal amplification, and DNA barcoding for target molecule labeling, underscoring advances in spatial omics. Other properties of nanotechnologies include advanced spatial omics methods, such as microfluidic chips and DNA barcodes. In this review, we describe how nanotechnologies have been applied to the development of spatial transcriptomics, proteomics, metabolomics, epigenomics, and multiomics approaches. We focus on how nanotechnology supports improved resolution and throughput of spatial omics, surpassing traditional techniques. We also summarize future challenges and opportunities for the application of nanotechnology to spatial omics methods.}, }
@article {pmid39704499, year = {2025}, author = {Wäneskog, M and Hoch-Schneider, EE and Garg, S and Kronborg Cantalapiedra, C and Schäfer, E and Krogh Jensen, M and Damgaard Jensen, E}, title = {Accurate phenotype-to-genotype mapping of high-diversity yeast libraries by heat-shock-electroporation (HEEL).}, journal = {mBio}, volume = {16}, number = {2}, pages = {e0319724}, pmid = {39704499}, issn = {2150-7511}, support = {//Wenner-Gren Stiftelserna (Wenner-Gren Foundations)/ ; NNF20SA0035588//Novo Nordisk Fonden (NNF)/ ; NNF210C0069089//Novo Nordisk Fonden (NNF)/ ; NNF20CC0035580//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Saccharomyces cerevisiae/genetics ; *Gene Library ; *Electroporation/methods ; Phenotype ; Genotype ; *Transformation, Genetic ; Heat-Shock Response ; }, abstract = {High-throughput DNA transformation techniques are invaluable when generating high-diversity mutant libraries, a cornerstone of successful protein engineering. However, transformation efficiencies have a direct correlation with the probability of introducing multiple DNA molecules into each cell, although reliable library screenings require cells that contain a single unique genotype. Thus, transformation methods that yield a high multiplicity of transformations are unsuitable for high-diversity library screenings. Here, we describe an innovative yeast library transformation method that is both simple and highly efficient. Our dual heat-shock and electroporation approach (HEEL) creates high-quality DNA libraries by increasing the fraction of mono-transformed yeast cells from 20% to over 70% of all transformed cells, thus allowing for near-perfect phenotype-to-genotype associations. HEEL also allows more than 10[7] yeast cells per reaction to be transformed with a circular plasmid molecule, which corresponds to an almost 100-fold improvement compared with current yeast transformation methods. To further refine our library screening approach, we integrated an automated yeast genotyping workflow with a dual-barcode design that employs both a single nucleotide polymorphism and a high-diversity region. This design allows for robust identification and quantification of unique genotypes within a heterogeneous population using standard Sanger sequencing. Our findings demonstrate that the longstanding trade-off between the size and quality of transformed yeast libraries can be overcome. By employing the HEEL method, large DNA libraries can be transformed into yeast with high-efficiency, while maintaining high library quality, essential for successful mutant screenings. This advancement holds significant promise for the fields of molecular biology and protein engineering.IMPORTANCEWith the recent expansion of artificial intelligence in the field of synthetic biology, there has never been a greater need for high-quality data and reliable measurements of phenotype-to-genotype relationships. However, one major obstacle to creating accurate computer-based models is the current abundance of low-quality phenotypic measurements originating from numerous high-throughput but low-resolution assays. Rather than increasing the quantity of measurements, new studies should aim to generate as accurate measurements as possible. The HEEL methodology presented here aims to address this issue by minimizing the problem of multi-plasmid uptake during high-throughput yeast DNA transformations, which leads to the creation of heterogeneous cellular genotypes. HEEL should enable highly accurate phenotype-to-genotype measurements going forward, which could be used to construct better computer-based models.}, }
@article {pmid39703419, year = {2024}, author = {Chamberlin, JT and Gillen, AE and Quinlan, AR}, title = {Improved characterization of 3' single-cell RNA-seq libraries with paired-end avidity sequencing.}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {4}, pages = {lqae175}, pmid = {39703419}, issn = {2631-9268}, support = {IK2 BX004952/BX/BLRD VA/United States ; S10 OD021644/OD/NIH HHS/United States ; T15 LM007124/LM/NLM NIH HHS/United States ; }, abstract = {Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site or in principle the polyadenylation site. Direct sequencing across this site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the 'barcode' end. Here, we evaluate the capability of 'avidity base chemistry' DNA sequencing from Element Biosciences to sequence through the primer and enable accurate paired-end read alignment and precise quantification of polyadenylation sites. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The additional sequence enables direct and independent assignment of reads to polyadenylation sites, which bypasses the complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and demonstrate necessary adjustments to adapter trimming and sequence alignment regardless of platform, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site measurement but do not rule out the potential for similar performance from other emerging platforms.}, }
@article {pmid39702735, year = {2025}, author = {Fandrey, CI and Jentzsch, M and Konopka, P and Hoch, A and Blumenstock, K and Zackria, A and Maasewerd, S and Lovotti, M and Lapp, DJ and Gohr, FN and Suwara, P and Świeżewski, J and Rossnagel, L and Gobs, F and Cristodaro, M and Muhandes, L and Behrendt, R and Lam, MC and Walgenbach, KJ and Bald, T and Schmidt, FI and Latz, E and Schmid-Burgk, JL}, title = {NIS-Seq enables cell-type-agnostic optical perturbation screening.}, journal = {Nature biotechnology}, volume = {43}, number = {8}, pages = {1337-1347}, pmid = {39702735}, issn = {1546-1696}, mesh = {Humans ; *Single-Cell Analysis/methods ; Animals ; Macrophages/metabolism ; *High-Throughput Nucleotide Sequencing/methods ; *Cell Nucleus/genetics ; Mice ; }, abstract = {Optical pooled screening offers a broader-scale alternative to enrichment-based perturbation screening, using fluorescence microscopy to correlate phenotypes and perturbations across single cells. Previous methods work well in large, transcriptionally active cell lines, because they rely on cytosolic detection of endogenously expressed barcoded transcripts; however, they are limited by reliable cell segmentation, cytosol size, transcriptional activity and cell density. Nuclear In-Situ Sequencing (NIS-Seq) expands this technology by creating bright sequencing signals directly from nuclear genomic DNA to screen nucleated cells at high density and high library complexity. By inserting an inverted phage promoter downstream of the single guide RNA (sgRNA), many RNA copies of the sgRNA can be generated and sequenced independently of cellular transcription. In this study, we benchmarked NIS-Seq across eight cell types from two species and performed four genome-scale optical perturbation screens, identifying key players of inflammation-related cellular pathways. Finally, we performed a small-scale pooled optical screen in primary human macrophages from blood of healthy donors and demonstrated barcode identification in lentivirally transduced human skin tissue.}, }
@article {pmid39701988, year = {2024}, author = {Zhang, J and Ning, Y and Li, J and Deng, Y and Wang, L and Mao, S and Zhao, B}, title = {Comparative chloroplast genome analysis of Ardisia (Myrsinoideae, Primulaceae) in China and implications for phylogenetic relationships and adaptive evolution.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1198}, pmid = {39701988}, issn = {1471-2229}, support = {[2022]-KJ019 and [2021]-KJ014//Science and technology plan project of Guangzhou Construction Group/ ; 32060090//National Natural Science Foundation of China/ ; 2021JJA130119//Natural Science Foundation of Guangxi Province/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; China ; *Ardisia/genetics ; Evolution, Molecular ; Microsatellite Repeats/genetics ; }, abstract = {BACKGROUND: Numerous species of Ardisia are widely used for their medicinal and ornamental values in China. However, accurately identifying Ardisia species at the molecular level remains a challenge due to the morphological similarities among different species, the complexity of interspecific variation, and the limited availability of genetic markers. In this study, we reported 20 chloroplast genomes of Ardisia species from China and combined them with 8 previously published chloroplast genomes to conduct a comprehensive analysis for phylogenetic relationships and adaptive evolution.<br><br>RESULTS: For the 28 Ardisia species analyzed in this study, the size of the chloroplast genomes ranged from 155,088&#xa0;bp to 156,999&#xa0;bp, and all exhibited a typical tetrad structure with conserved gene content and number. Each genome contained 85-88 protein-coding genes, 36-37 tRNA genes, and 8 rRNA genes. Comparative analysis showed that the genomic structures and gene order were relatively conserved with slight variations in the inverted repeat regions (IRs). Simple sequence repeats (SSRs) were predominantly single nucleotide repeats, while repeat sequences were mainly composed of palindromic and forward repeats. Twelve highly variable regions were identified as potential DNA barcodes for species identification and phylogenetic analysis of Ardisia. The phylogenetic tree supported the division of the subgenus Bladhia s.l. into two subgenera: Bladhia s.str. and Odontophylla (Yang) Huang. Further investigation revealed that two protein-coding genes (rbcL and rpoC2) were under positive selection and might be associated with the adaptation of Ardisia species to shaded environments.<br><br>CONCLUSION: Our study analyzed the chloroplast genomes of 20 Ardisia species from China to explore their phylogenetic relationships and adaptive evolution. By combining these results with data from eight previously published chloroplast genomes, the essential characteristics of Ardisia chloroplast genomes were clarified. The research establishes a theoretical basis for the classification, identification, and comprehension of the adaptive evolution of Ardisia species.}, }
@article {pmid39700063, year = {2025}, author = {Munusamy, S and Zheng, H and Jahani, R and Zhou, S and Chen, J and Kong, J and Guan, X}, title = {DNA-Assisted CRISPR-Cas12a Enhanced Fluorescent Assay for Protein Detection in Complicated Matrices.}, journal = {ACS applied bio materials}, volume = {8}, number = {1}, pages = {754-762}, pmid = {39700063}, issn = {2576-6422}, support = {R01 GM147247/GM/NIGMS NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; Humans ; *DNA/chemistry ; *Proteins/analysis ; *Endodeoxyribonucleases/genetics/metabolism ; *CRISPR-Associated Proteins ; Particle Size ; *Fluorescent Dyes/chemistry ; Bacterial Proteins ; }, abstract = {Proteins are important biological macromolecules that perform a wide variety of functions in the cell and human body, and can serve as important biomarkers for early diagnosis and prognosis of human diseases as well as monitoring the effectiveness of disease treatment. Hence, sensitive and accurate detection of proteins in human biospecimens is imperative. However, at present, there is no ideal method available for the detection of proteins in clinical samples, many of which are present at ultralow (less than 1 pM) concentrations and in complicated matrices. Herein, we report an ultrasensitive and selective DNA-assisted CRISPR-Cas12a enhanced fluorescent assay (DACEA) for protein detection with detection limits reaching as low as attomolar concentrations. The high assay sensitivity was accomplished through the combined DNA barcode amplification (by using dual-functionalized AuNPs) and CRISPR analysis, while the high selectivity and high resistance to the matrix effects of our method were accomplished via the formation of protein-antibody sandwich structure and the specific recognition of Cas12a (under the guidance of crRNA) toward the designed target ssDNA. Given its ability to accurately and sensitively detect trace amounts of proteins in complicated matrices, the DACEA protein assay platform pioneered in this work has a potential application in routine protein biomarker testing.}, }
@article {pmid39698230, year = {2024}, author = {Huang, WC and Hibino, Y and Balisco, RA and Liao, TY}, title = {Description of a new uniformly brown estuarine moray eel (Anguilliformes, Muraenidae) from the Central Indo-Pacific Ocean.}, journal = {ZooKeys}, volume = {1220}, number = {}, pages = {15-34}, pmid = {39698230}, issn = {1313-2989}, abstract = {A new estuarine moray eel, Uropterygiushades sp. nov., is described based on 14 specimens from Japan, Taiwan, the Philippines, southern Indonesia, and Fiji. It is a small-bodied, slender, uniformly dark-brown moray separated from congeners within the U.concolor species complex. The new species can be distinguished from congeners by the anteriorly positioned small eyes (5.0-7.2% of head length), absence of branchial pores, and extended inner rows of teeth which reach the posterior end of the jaws. Uropterygiushades sp. nov. represents a rare species of moray eel that inhabits turbid estuarine environments, preferring soft, muddy substrates, and burrowing and hiding among rocks or in fallen mangrove leaves. Additionally, Uropterygiusmactanensis Huang, Balisco, Evacitas &amp; Liao, another species recently separated from the U.concolor species complex, is reported for the first time from Iriomote Island in the Ryukyu Archipelago based on two specimens; this new record expands the geographic range of U.mactanensis from the central Philippines to southern Japan.}, }
@article {pmid39696450, year = {2024}, author = {Wang, YW and Tan, PC and Li, QF and Xu, XW and Zhou, SB}, title = {Adipose tissue protects against skin photodamage through CD151- and AdipoQ- EVs.}, journal = {Cell communication and signaling : CCS}, volume = {22}, number = {1}, pages = {594}, pmid = {39696450}, issn = {1478-811X}, mesh = {Animals ; *Adiponectin/metabolism ; *Skin/metabolism ; *Fibroblasts/metabolism ; Mice ; *Adipose Tissue/metabolism/cytology ; *Extracellular Vesicles/metabolism ; Humans ; Mice, Nude ; Cell Proliferation ; }, abstract = {To clarify the protective effects of subcutaneous adipose tissue (SAT) against photodamage, we utilized nude mouse skin with or without SAT. Skin and fibroblasts were treated with adipose tissue-derived extracellular vesicles (AT-EVs) or extracellular vesicles derived from adipose-derived stem cells (ADSC-EVs) to demonstrate that SAT protects the overlying skin from photodamage primarily through AT-EVs. Surprisingly, AT-EVs stimulated fibroblast proliferation more rapidly than ADSC-EVs did. The yield of AT-EVs from the same volume of AT was 200 times greater than that of ADSC-EVs. To compare the differences between AT-EVs and ADSC-EVs, we used a proximity barcoding assay (PBA) to analyze the surface proteins on individual particles of these two types of EVs. PBA analysis revealed that AT-EVs contain diverse subpopulations, with 83.42% expressing CD151, compared to only 1.98% of ADSC-EVs. Furthermore, AT-EVs are internalized more rapidly by cells than ADSC-EVs, as our study demonstrated that CD151-positive AT-EVs were endocytosed more quickly than their CD151-negative counterparts. Additionally, adiponectin in AT-EVs activated the AMPK pathway and inhibited the NF-κB pathway, enhancing fibroblast protection against photodamage. The significantly higher yield and faster acquisition of AT-EVs compared to ADSC-EVs underscore their potential for broader applications.}, }
@article {pmid39695811, year = {2024}, author = {Jeon, J and Kim, HC and Donnelly, MJ and Choi, KS}, title = {Genetic diversity and Wolbachia infection in the Japanese encephalitis virus vector Culex tritaeniorhynchus in the Republic of Korea.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {518}, pmid = {39695811}, issn = {1756-3305}, mesh = {Animals ; *Culex/virology/microbiology ; *Wolbachia/genetics/isolation &amp; purification/classification ; *Genetic Variation ; *Mosquito Vectors/microbiology/virology ; Republic of Korea/epidemiology ; *Encephalitis Virus, Japanese/genetics/classification/isolation &amp; purification ; Phylogeny ; Encephalitis, Japanese/epidemiology/transmission/virology ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: Culex tritaeniorhynchus, a major vector of Japanese encephalitis virus (JEV), is found across a broad geographical range, including Africa, Asia, Australia and Europe. Understanding the population structure and genetic diversity of pathogen vectors is increasingly seen as important for effective disease control. In China and Japan, two countries in close proximity to the Republic of Korea (ROK), Cx. tritaeniorhynchus has been categorized into two clades based on the DNA barcoding region of mitochondrial cytochrome c oxidase subunit I (COI), suggesting the presence of cryptic species. No comprehensive analysis of the genetic diversity in Cx. tritaeniorhynchus has been conducted in the ROK. To address this gap, we investigated the population structure of Cx. tritaeniorhynchus in the ROK.<br><br>METHODS: In Daegu, mosquito collections were conducted over a 2-year period from 2022 to 2023. For all other regions, Cx. tritaeniorhynchus specimens collected in 2023 were used. The COI barcoding region was analyzed to determine the genetic structure of the populations, supplemented with data from the 28S ribosomal DNA region. Each population was also examined for the eventual presence of Wolbachia infection. Finally, a back trajectory analysis was conducted to assess the possibility of international introduction of Cx. tritaeniorhynchus into the ROK.<br><br>RESULTS: The analysis of the COI region revealed the presence of two distinct clades within Cx. tritaeniorhynchus; these clades were the same as Cx. tritaeniorhynchus continental type (Ct-C) and C. tritaeniorhynchus Japanese type (Ct-J) previously reported. In contrast, the nuclear 28S region showed no significant genetic differentiation between these clades. Wolbachia infection was confirmed in some populations, but there was no evidence of an association with Wolbachia in Ct-C and Ct-J. It was also confirmed that the ROK is currently dominated by the Ct-J clade, with a possible introduction of Ct-C via air currents.<br><br>CONCLUSIONS: Determining the presence of cryptic species is important for preventing vector-borne diseases. The results of this study confirm the existence of two clades of Cx. tritaeniorhynchus in the ROK, with Ct-J being the dominant clade. Our findings enhance current understanding of the genetic diversity within Cx. tritaeniorhynchus and provide valuable insights for the prevention of JEV outbreaks and the effective management of Cx. tritaeniorhynchus populations in East Asia.}, }
@article {pmid39695748, year = {2024}, author = {Aupalee, K and Srisuka, W and Limsopatham, K and Sanit, S and Takaoka, H and Saeung, A}, title = {Reliability of wing morphometrics for species identification of human-biting black flies (Diptera: Simuliidae) in Thailand.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {508}, pmid = {39695748}, issn = {1756-3305}, support = {106-2565//Faculty of Medicine, Chiang Mai University/ ; }, mesh = {Animals ; Thailand ; *Wings, Animal/anatomy &amp; histology ; *Phylogeny ; *Simuliidae/anatomy &amp; histology/classification/genetics ; Female ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Humans ; Reproducibility of Results ; }, abstract = {BACKGROUND: Fast and reliable species identification of black flies is essential for research proposes and effective vector control. Besides traditional identification based on morphology, which is usually supplemented with molecular methods, geometric morphometrics (GM) has emerged as a promising tool for identification. Despite its potential, no specific GM techniques have been established for the identification of black fly species.<br><br>METHODS: Adult female black flies collected using human bait, as well as those reared from pupae, were used in this study. Here, landmark-based GM analysis of wings was assessed for the first time to identify human-biting black fly species in Thailand, comparing this approach with the standard morphological identification method and DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. To explore genetic relationships between species, maximum likelihood (ML) and neighbor-joining (NJ) phylogenetic trees were built. Additionally, three different methods of species delimitation, i.e., assemble species by automatic partitioning (ASAP), generalized mixed yule coalescent (GMYC), and single Poisson tree processes (PTP), were utilized to identify the morphologically defined species. The effectiveness of a COI barcode in identifying black fly species was further examined through the best match (BM) and best close match (BCM) methods.<br><br>RESULTS: Seven black fly species, namely Simulium tenebrosum Takaoka, Srisuka &amp; Saeung, 2018 (complex), S. doipuiense Takaoka &amp; Choochote, 2005 (complex), S. nigrogilvum Summers, 1911, S. nodosum Puri, 1933, S. asakoae Takaoka &amp; Davies, 1995, S. chamlongi Takaoka &amp; Suzuki, 1984, and S. umphangense Takaoka, Srisuka &amp; Saeung, 2017 were morphologically identified. Compared with the standard method, the GM analysis based on wing shape showed high success in separating species, achieving an overall accuracy rate of 88.54%. On the other hand, DNA barcoding surpassed wing GM for species identification with a correct identification rate of 98.57%. Species delimitation analyses confirmed the validity of most nominal species, with an exception for S. tenebrosum complex and S. doipuiense complex, being delimited as a single species. Moreover, the analyses unveiled hidden diversity within S. asakoae, indicating the possible existence of up to four putative species.<br><br>CONCLUSIONS: This study highlights the potential of wing GM as a promising and reliable complementary tool for species identification of human-biting black flies in Thailand.}, }
@article {pmid39695366, year = {2024}, author = {Pere, K and Mburu, K and Muge, EK and Wagacha, JM and Nyaboga, EN}, title = {Molecular identification, genetic diversity, and secondary structure predictions of Physalis species using ITS2 DNA barcoding.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1178}, pmid = {39695366}, issn = {1471-2229}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Physalis/genetics ; *Genetic Variation ; *Phylogeny ; Kenya ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Nucleic Acid Conformation ; }, abstract = {BACKGROUND: The genus Physalis belongs to the Solanaceae family and has different species with important nutritional and medicinal values. Species within this genus have limited morphological differences, a characteristic that hinders accurate identification, safe utilization and genetic conservation of promising genotypes. In addition, to prevent the perceived loss of Physalis diversity due to habitat destruction, species delimitation needs attention. In this study, we used the sequence and structural information of the internal transcribed spacer 2 (ITS2) barcode to efficiently identify and discriminate Physalis species from a collection of 34 Physalis accessions.<br><br>METHODOLOGY: Physalis plant samples were collected from eight Counties in Kenya based on the availability of the germplasm. The voucher specimens were identified using the botanical taxonomy method and were deposited in the University of Nairobi herbarium. A total of 34 Physalis accessions were identified and accessed for diversity based on the ITS2 barcode region. The sequence similarity of the ITS2 genes was analyzed through the Basic Local Alignment Search Tool (BLAST), the nearest Kimura-2-parameter (K2P) genetic distances were calculated and a phylogenetic tree was constructed using the Bayesian inference (BI) method in MrBayes 3.2.7a software. The differences in the ITS2 secondary structure between the species were analyzed.<br><br>RESULTS: The success rate of PCR amplification and sequencing was 75% and 67%, respectively. The analyzed ITS2 sequences displayed significant inter-specific divergences, clear DNA barcoding gaps and high species identification efficiency. Based on the constructed phylogenetic tree, three Physalis species (Physalis peruviana, Physalis purpurea and Physalis cordata) were identified and were clustered in a homogenized distribution. High genetic diversity (0.36923) and genetic distance (0.703) were observed between Physalis peruviana and Physalis cordata. The highest genetic nucleotide diversity (0.26324) and distance (0.46) within species was obtained for Physalis peruviana. The differences in the secondary structures generated from this study discriminated between the Physalis species.<br><br>CONCLUSIONS: Our study demonstrated that ITS2 is a potential DNA barcode for effective identification and discrimination of Physalis species. The results of this study provide insights into the scientific basis of species identification, safe utilization, genetic conservation and future breeding strategies for this important nutritional and medicinal plant species.}, }
@article {pmid39695327, year = {2025}, author = {Schröder, LC and Hüttermann, L and Kliesow Remes, A and Voran, JC and Hille, S and Sommer, W and Lutter, G and Warnecke, G and Frank, D and Schade, D and Müller, OJ}, title = {AAV library screening identifies novel vector for efficient transduction of human aorta.}, journal = {Gene therapy}, volume = {32}, number = {2}, pages = {154-162}, pmid = {39695327}, issn = {1476-5462}, mesh = {*Dependovirus/genetics ; Humans ; *Genetic Vectors/genetics ; *Aorta/metabolism/cytology ; Animals ; *Transduction, Genetic/methods ; Muscle, Smooth, Vascular/metabolism/cytology ; Mice ; Myocytes, Smooth Muscle/metabolism ; Gene Library ; Cells, Cultured ; Capsid Proteins/genetics ; Genetic Therapy/methods ; }, abstract = {Targeted gene delivery to vascular smooth muscle cells (VSMCs) could prevent or improve a variety of diseases affecting the vasculature and particularly the aorta. Thus, we aimed to develop a delivery vector that efficiently targets VSMCs. We selected engineered adeno-associated virus (AAV) capsids from a random AAV capsid library and tested the top enriched motifs in parallel screening through individual barcoding. This approach allowed us to distinguish capsids that only transduce cells based on genomic DNA (gDNA) from those also mediating transgene expression based on transcribed cDNA reads. After three rounds of selection on primary murine VSMCs (mVSMCs), we identified a novel targeting motif (RFTEKPA) that significantly improved transduction and gene expression efficiency over AAV9-wild type (WT) and increased expression in mVSMCs by 70% compared to the previously identified SLRSPPS peptide. Further analysis showed that the novel motif also improved expression in human aortic smooth muscle cells (HAoSMCs) and human aortic tissue ex vivo up to threefold compared to SLRSPPS and approximately 70-fold to AAV9-WT. This high cross-species transduction efficiency makes the novel capsid motif a potential candidate for future clinical application in vascular diseases.}, }
@article {pmid39695009, year = {2024}, author = {Herath, DR and Perera, HACC and Ranasinghe, VK and Amarakoon, AADG and Hettiarachchi, GHCM}, title = {Stomach content analysis of Euthynnus affinis, Auxis thazard and Auxis rochei of the coastal waters of Sri Lanka by DNA barcoding.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {63}, pmid = {39695009}, issn = {1573-4978}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sri Lanka ; *Gastrointestinal Contents ; *Tuna/genetics ; Feeding Behavior/physiology ; Predatory Behavior ; Fishes/genetics/classification ; }, abstract = {BACKGROUND: Analysis of the content of the gut of fish helps in the understanding of their inter- and intra-specific interactions, fish behaviour, condition and energy intake. The stomach contents of the commercially important neritic tuna species of Sri Lanka, kawakawa (Euthynnus affinis), frigate tuna (Auxis thazard) and bullet tuna (Auxis rochei) were analysed to determine their feeding habits and to identify prey species.<br><br>METHODS AND RESULTS: The weighed stomachs of fish were dissected to reveal the types of prey found within. The prey was categorised into prey categories and each prey species was identified morphologically. Prey items which were partially digested were identified using DNA barcoding. The main prey category was small fish, followed by crustaceans and cephalopods. While the highest occurring prey category for E. affinis and A. rochei was fish, crustaceans dominated the A. thazard diet. DNA barcoding identified 11 prey items that were partially digested, which could not be identified to species-level morphologically. Of the prey items identified by DNA barcoding, four species of fish, three species of cephalopod and four species of crustaceans were identified. These prey item identifications confirmed that E. affinis, A. thazard and A. rochei are all nonspecific feeders.<br><br>CONCLUSIONS: This exhibits the value of molecular tools in the identification of species which have lost their distinguishable features due to digestion. Further, it illustrates the predator-prey relationships between these species, aiding in the management of prey and predator populations, ensuring that both populations remain stable, helping in the maintenance of the balance of the ecosystem.}, }
@article {pmid39693934, year = {2025}, author = {Heo, EH and Abrol, R}, title = {Thermodynamic role of receptor phosphorylation barcode in cannabinoid receptor desensitization.}, journal = {Biochemical and biophysical research communications}, volume = {743}, number = {}, pages = {151100}, pmid = {39693934}, issn = {1090-2104}, support = {R16 GM153621/GM/NIGMS NIH HHS/United States ; SC2 GM130480/GM/NIGMS NIH HHS/United States ; }, mesh = {Phosphorylation ; *Thermodynamics ; *Receptor, Cannabinoid, CB2/metabolism/chemistry/genetics ; Humans ; beta-Arrestin 2/metabolism/genetics/chemistry ; Molecular Dynamics Simulation ; Protein Binding ; Signal Transduction ; Models, Molecular ; Protein Conformation ; }, abstract = {The endocannabinoid signaling system is comprised of CB1 and CB2 G protein-coupled receptors (GPCRs). CB2 receptor subtype is predominantly expressed in the immune cells and signals through its transducer proteins (Gi protein and β-arrestin-2). Arrestins are signaling proteins that bind to many GPCRs after receptor phosphorylation to terminate G protein signaling (desensitization) and to initiate specific G protein-independent arrestin-mediated signaling pathways via a "phosphorylation barcode", that captures sequence patterns of phosphorylated Ser/Thr residues in the receptor's intracellular domains and can lead to different signaling effects. The structural basis for how arrestins and G proteins compete with the receptor for biased signaling and how different barcodes lead to different signaling profiles is not well understood as there is a lack of phosphorylated receptor structures in complex with arrestins. In this work, structural models of β-arrestin-2 were built in complex with the phosphorylated and unphosphorylated forms of the CB2 receptor. The complex structures were relaxed in the lipid bilayer environment with molecular dynamics (MD) simulations and analyzed structurally and thermodynamically. The β-arrestin-2 complex with the phosphorylated receptor was more stable than the non-phosphorylated one, highlighting the thermodynamic role of the receptor phosphorylation. It was also more stable than any of the G protein complexes with CB2 suggesting that phosphorylation signals receptor desensitization (end of G protein signaling) and arrest of the receptor by arrestins. These models are beginning to provide the thermodynamic landscape of CB2 signaling, which can help bias signaling towards therapeutically beneficial pathways in drug discovery applications.}, }
@article {pmid39693656, year = {2025}, author = {Eriksen, TE and Brittain, JE and Sandin, L and Friberg, N}, title = {Unveiling cryptic macroinvertebrate sentinels to enhance biomonitoring in tropical rivers: Bridging traditional approaches with DNA barcoding in the Indo-Burma biodiversity hotspot.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178064}, doi = {10.1016/j.scitotenv.2024.178064}, pmid = {39693656}, issn = {1879-1026}, mesh = {*DNA Barcoding, Taxonomic ; Animals ; *Biodiversity ; *Environmental Monitoring/methods ; Rivers ; *Invertebrates/classification ; *Biological Monitoring/methods ; Myanmar ; Ecosystem ; Sentinel Species ; }, abstract = {Human activities present significant threats to tropical freshwater ecosystems, notably in many global biodiversity hotspots, threats that are further increased by inadequate taxonomic knowledge and the lack of appropriate biomonitoring tools. This study integrates globally validated biomonitoring approaches with DNA-based identification methods to create a macroinvertebrate-based tool for diagnosing ecosystem health and assessing the biodiversity of tropical river ecosystems in Myanmar (Indo-Burma bioregion). To evaluate river site degradation, comprehensive data on water and habitat quality, as well as land use information, were collected. Riverine macroinvertebrates were sampled by kick sampling, and subsequent DNA barcoding analysis was used to establish molecular taxonomic units (MTUs) for key bioindicator groups, including Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Odonata (EPTCO) as species-level identification nomenclature was lacking. Tolerance scores for the local fauna were derived along an environmental degradation gradient to enable comparisons with widely adopted global assessment tools relying on macroinvertebrate metrics. In both study areas, the upper parts of the river networks were generally undisturbed by human activities while stressors associated with urban and agricultural land use were evident in the lower parts of the catchments. The highest precision for assessment of river health was found when establishing tolerance scores adjusted to local species composition in each study area separately. Although a family-level-based multimetric approach was significantly related to the main environmental degradation gradient, assessments utilizing cryptic species-level data (MTUs) emerged as the being most precise indicator in both areas. Our study highlights the synergistic benefits of merging traditional biomonitoring with DNA-based methods for species identification for biomonitoring in tropical river ecosystems. To halt biodiversity decline and curb the extent of the escalating nature crisis, such integrated approaches will be highly valuable in understudied and biodiversity-rich aquatic ecosystems.}, }
@article {pmid39688736, year = {2024}, author = {Singha, D and Patidar, A and Pal, S and Tyagi, K and Kumar, V}, title = {Mitochondrial genetic diversity of pest and vector species, Frankliniella schultzei (Thripidae: Thripinae).}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {55}, pmid = {39688736}, issn = {1573-4978}, support = {CRG/2023/000498//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Phylogeny ; *Genetic Variation/genetics ; *Haplotypes/genetics ; India ; *Thysanoptera/genetics/classification ; DNA Barcoding, Taxonomic/methods ; Australia ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Insect Vectors/genetics/classification ; Bayes Theorem ; Gene Flow ; }, abstract = {BACKGROUND: Frankliniella schultzei (Trybom) is a serious pest and a carrier of tospoviruses in major agricultural crops. This species is a historical and unresolved species complex that contains genetically different cryptic species across the globe.<br><br>METHODS AND RESULTS: DNA barcodes were generated from freshly collected specimens of F. schultzei from India and Australia using the sanger sequencing. Seventy-five COI sequences were generated from India and Australia. Moreover, 318 sequences were downloaded (India, Australia, Pakistan, and Africa) from the NCBI GenBank to explore the genetic diversity and phylogeny. The minimum and maximum mean interspecific distance between 393 sequences was found to be 7.97% and 21.50%, respectively. Bayesian and Neighbour joining clustering indicated the presence of five putative species within F. schultzei that had sympatry and allopatry. Moreover, 20 haplotypes and 140 polymorphic sites were identified. The African clade is unique; it does not share haplotypes with any other countries, suggesting it may represent the true F. schultzei. Haplotype network analysis showed shallow gene flow and deep genetic variation between the populations. Signatures of recent population history events were measured using Fu's Fs test and Tajima's D test. Morphometric analysis based on seven characters is also carried out.<br><br>CONCLUSION: Phylogeny and genetic distance revealed the presence of five putative species within F. schultzei. On the contrary, morphology does not unequivocally corroborate the phylogenetic results, as morphometric analysis showed overlap among these clades. To resolve F. schultzei species complex, whole genome-based sequencing data are very much necessitated.}, }
@article {pmid39687742, year = {2024}, author = {Haile, S and Corbett, RD and O'Neill, K and Xu, J and Smailus, DE and Pandoh, PK and Bayega, A and Bala, M and Chuah, E and Coope, RJN and Moore, RA and Mungall, KL and Zhao, Y and Ma, Y and Marra, MA and Jones, SJM and Mungall, AJ}, title = {Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1466338}, pmid = {39687742}, issn = {1664-8021}, abstract = {The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure of transcripts with potential for end-to-end sequencing of full-length RNAs. LR methods that have been described to date include commercial offerings from Oxford Nanopore Technologies (ONT) and Pacific Biosciences. These kits are based on selection of polyadenylated (polyA+) RNAs and/or oligo-dT priming of reverse transcription. Thus, these approaches do not allow comprehensive interrogation of the transcriptome due to their exclusion of non-polyadenylated (polyA-) RNAs. In addition, polyA + specificity also results in 3'-biased measurements of PolyA+ RNAs especially when the RNA input is partially degraded. To address these limitations of current LR protocols, we modified rRNA depletion protocols that have been used in short-read sequencing: one approach representing a ligation-based method and the other a template-switch cDNA synthesis-based method to append ONT-specific adaptor sequences and by removing any deliberate fragmentation/shearing of RNA/cDNA. Here, we present comparisons with poly+ RNA-specific versions of the two approaches including the ONT PCR-cDNA Barcoding kit. The rRNA depletion protocols displayed higher proportions (30%-50%) of intronic content compared to that of the polyA-specific protocols (5%-8%). In addition, the rRNA depletion protocols enabled ∼20-50% higher detection of expressed genes. Other metrics that were favourable to the rRNA depletion protocols include better coverage of long transcripts, and higher accuracy and reproducibility of expression measurements. Overall, these results indicate that the rRNA depletion-based protocols described here allow the comprehensive characterization of polyadenylated and non-polyadenylated RNAs. While the resulting reads are long enough to help decipher transcript structures, future endeavors are warranted to improve the proportion of individual reads representing end-to-end spanning of transcripts.}, }
@article {pmid39684314, year = {2024}, author = {Domingo-Bretón, R and Moroni, F and Toxqui-Rodríguez, S and Belenguer, &#xc1; and Piazzon, MC and Pérez-Sánchez, J and Naya-Català, F}, title = {Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684314}, issn = {1422-0067}, support = {871108//Horizon H2020/ ; PRTR-C17.I1//Ministerio de Ciencia e Innovaci&#xf3;n/ ; THINKINAZUL/2021/024//Generalitat Valenciana/ ; }, mesh = {Animals ; *Microbiota/genetics ; *Fishes/microbiology ; Nanopores ; Feces/microbiology ; Water Microbiology ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Oxford Nanopore Technology (ONT) allows for the rapid profiling of aquaculture microbiomes. However, not all the experimental and downstream methodological possibilities have been benchmarked. Here, we aimed to offer novel insights into the use of different library preparation methods (standard-RAP and native barcoding-LIG), primers (V3-V4, V1-V3, and V1-V9), and basecalling models (fast-FAST, high-HAC, and super-accuracy-SUP) implemented in ONT to elucidate the microbiota associated with the aquatic environment and farmed fish, including faeces, skin, and intestinal mucus. Microbial DNA from water and faeces samples could be amplified regardless of the library-primer strategy, but only with LIG and V1-V3/V1-V9 primers in the case of skin and intestine mucus. Low taxonomic assignment levels were favoured by the use of full-length V1-V9 primers, though in silico hybridisation revealed a lower number of potential matching sequences in the SILVA database, especially evident with the increase in Actinobacteriota in real datasets. SUP execution allowed for a higher median Phred quality (24) than FAST (11) and HAC (17), but its execution time (6-8 h) was higher in comparison to the other models (0.6-7 h). Altogether, we optimised the use of ONT for water- and fish-related microbial analyses, validating, for the first time, the use of the LIG strategy. We consider that LIG-V1-V9-HAC is the optimal time/cost-effective option to amplify the microbial DNA from environmental samples. However, the use of V1-V3 could help to maximise the dataset microbiome diversity, representing an alternative when long amplicon sequences become compromised by microbial DNA quality and/or high host DNA loads interfere with the PCR amplification/sequencing procedures, especially in the case of gut mucus.}, }
@article {pmid39682398, year = {2024}, author = {Zhou, J and Zhang, X and Wang, Y and Liang, H and Yang, Y and Huang, X and Deng, J}, title = {Contamination Survey of Insect Genomic and Transcriptomic Data.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {23}, pages = {}, pmid = {39682398}, issn = {2076-2615}, support = {2022FY100500, KFB23016//the Special Investigation Program for National Science and Technology Basic Resources, the Special Fund for Science and Technology Innovation of Fujian Agriculture and Forestry University/ ; }, abstract = {The rapid advancement of high-throughput sequencing has led to a great increase in sequencing data, resulting in a significant accumulation of contamination, for example, sequences from non-target species may be present in the target species' sequencing data. Insecta, the most diverse group within Arthropoda, still lacks a comprehensive evaluation of contamination prevalence in public databases and an analysis of potential contamination causes. In this study, COI barcodes were used to investigate contamination from insects and mammals in GenBank's genomic and transcriptomic data across four insect orders. Among the 2796 WGS and 1382 TSA assemblies analyzed, contamination was detected in 32 (1.14%) WGS and 152 (11.0%) TSA assemblies. Key findings from this study include the following: (1) TSA data exhibited more severe contamination than WGS data; (2) contamination levels varied significantly among the four orders, with Hemiptera showing 9.22%, Coleoptera 3.48%, Hymenoptera 7.66%, and Diptera 1.89% contamination rates; (3) possible causes of contamination, such as food, parasitism, sample collection, and cross-contamination, were analyzed. Overall, this study proposes a workflow for checking the existence of contamination in WGS and TSA data and some suggestions to mitigate it.}, }
@article {pmid39678441, year = {2024}, author = {Hamdi, I and Benmansour, B and Ahmed, M and Gulsher, M and Bouguerche, C}, title = {A new genus and a new species of microcotylids (Polyopisthocotyla, Platyhelminthes), gill parasite of the pink dentex Dentex gibbosus (Teleostei, Sparidae) off Tunisia and notes on Polyopisthocotyla and Monopisthocotyla from Dentex spp.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {25}, number = {}, pages = {101016}, pmid = {39678441}, issn = {2213-2244}, abstract = {The study of the polyopisthocotylan parasites of marine fishes in the western Mediterranean is carried on using an integrative approach combining morphology and DNA barcodes. Ktarius patrickbrueli n. gen. n. sp (Polyopisthocotyla, Microcotylidae), from the gills of the pink dentex Dentex gibbosus (Teleostei, Sparidae) from the western Mediterranean Sea off Tunisia, is described. Anatomical and morphological features of the new genus are described, and the molecular barcodes for nuclear and mitochondrial markers (28S rRNA and cox1) are generated. The new genus is closely related to Microcotyle by sharing a symmetrical haptor, inverted question mark-shaped ovary and unarmed vagina. However, Ktarius n. gen. can be distinguished from Microcotyle and other Microcotylinae taxa by an unarmed male copulatory organ, formed by a long muscular cirrus, a basal layer of concentric muscles, and an elongated thick-walled ejaculatory bulb. A partial 28S rDNA sequence of K. patrickbrueli n. gen. n. sp. was obtained and found to be distinct from all known microcotylid sequences, with a p-distance of 5-13%. A phylogenetic tree constructed from available microcotylid sequences revealed that K. patrickbrueli n. gen. n. sp. clustered in a strongly supported clade of Microcotylinae, containing species of Omanicotyle, Bivagina, and Microcotyle confirming its belonging to the Microcotylinae subfamily. The cox1 sequences of K. patrickbrueli n. gen. n. sp. were highly divergent from the closely related genus Pauciconfibula and confirmed its distinction. This new genus is the third polyopisthocotylan genus to be described from sparids of Dentex.}, }
@article {pmid39677603, year = {2025}, author = {Twa, GM and Phillips, RA and Robinson, NJ and Day, JJ}, title = {Accurate sample deconvolution of pooled snRNA-seq using sex-dependent gene expression patterns.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39677603}, issn = {2692-8205}, support = {DP1 DA039650/DA/NIDA NIH HHS/United States ; R01 DA053743/DA/NIDA NIH HHS/United States ; R01 DA054714/DA/NIDA NIH HHS/United States ; R01 MH114990/MH/NIMH NIH HHS/United States ; }, abstract = {Single-nucleus RNA sequencing (snRNA-seq) technology offers unprecedented resolution for studying cell type-specific gene expression patterns. However, snRNA-seq poses high costs and technical limitations, often requiring the pooling of independent biological samples and the loss of individual sample-level data. Deconvolution of sample identity using inherent features would enable the incorporation of pooled barcoding and sequencing protocols, thereby increasing data throughput and analytical sample size without requiring increases in experimental sample size and sequencing costs. In this study, we demonstrate a proof of concept that sex-dependent gene expression patterns can be leveraged for the deconvolution of pooled snRNA-seq data. Using previously published snRNA-seq data from the rat ventral tegmental area, we trained a range of machine learning models to classify cell sex using genes differentially expressed in cells from male and female rats. Models that used sex-dependent gene expression predicted cell sex with high accuracy (93-95%) and outperformed simple classification models using only sex chromosome gene expression (88-90%). The generalizability of these models to other brain regions was assessed using an additional published data set from the rat nucleus accumbens. Within this data set, model performance remained highly accurate in cell sex classification (90-92% accuracy) with no additional training. This work provides a model for future snRNA-seq studies to perform sample deconvolution using a two-sex pooled sample sequencing design and benchmarks the performance of various machine learning approaches to deconvolve sample identification from inherent sample features.}, }
@article {pmid39675106, year = {2025}, author = {Mutum, RS and Das, A and Ghosh, SK and Wangkheimayum, VD}, title = {The origins of "Kaunayen" game fowls of Manipur, India: Insights from mitochondrial D-loop sequence analysis.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104667}, pmid = {39675106}, issn = {1525-3171}, mesh = {Animals ; India ; *Chickens/genetics/classification ; *DNA, Mitochondrial/genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Breeding ; *Genetic Variation ; }, abstract = {Notably, poultry animals-particularly chickens-are recognized globally for their valuable contributions to the food, ornamental, and game economies. Further, more robust local and regional breeds can be parental donors for these area-specific consumable breeds' resilient traits. Game birds that are locally significant economically or on a much smaller scale are frequently excluded from the procedure. One such breed is the fighting chicken of Manipur, India, known locally as the Kaunayen breed and listed as the 17th breed at the ICAR, the National Bureau of Animal Genetic Resources, India. When Kaunayen fowl from throughout Manipur are considered, they have anatomical characteristics and common behavioural traits despite the breed's extreme genetic heterogeneity. With this gap in mind, we attempted to use mitochondrial D-loop sequences to characterize Manipur's Kaunayen fowls concerning the global breeds of nearly similar molecular characteristics. We found that Kaunayen fowls share evolutionary traits such as a similar transition/transversion ratio with some Southeast Asian breeds, including a few red jungle fowls. Overall Kaunayen are also more closely related to Southeast Asian birds phylogenetically, after which with a few breeds from East Asian, Bangladesh, North-East India, and the Indian island of Nicobar. The global database including our query has 19 haplotypes, and majority of the Kaunayen fowls share haplotypes with North East Indian fowls; the remaining haplotypes are primarily associated with South East Asia and East Asia. The findings additionally indicated that Kaunayen's and the global breed's D-loop region tended to fixed neutral substitution, contributing to the distinct varieties. Further, migration research demonstrated that Kaunayen fowls originated from a substantial maternal genome influx from Southeast Asia, which may have later made a substantial contribution to East Asian and South Asian breeds. We also display a portion of the D-loop that demonstrates the majority of the substitution diversity across all breeds, and we suggest using sequence stretch to create miniature breed-specific identifying barcodes.}, }
@article {pmid39673434, year = {2024}, author = {Krasilnikova, LA and Tomkins-Tinch, CH and Gayton, AC and Schaffner, SF and Dobbins, ST and Gladden-Young, A and Siddle, KJ and Park, DJ and Sabeti, PC}, title = {Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {12}, pages = {}, pmid = {39673434}, issn = {1367-4811}, support = {U01 AI151812/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; //US National Institutes of Health/ ; U19AI110818//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {*Genome, Viral ; *SARS-CoV-2/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Software ; COVID-19/virology ; Genomics/methods ; }, abstract = {SUMMARY: In viral genomic research and surveillance, inter-sample contamination can affect variant detection, analysis of within-host evolution, outbreak reconstruction, and detection of superinfections and recombination events. While sample barcoding methods exist to track inter-sample contamination, they are not always used and can only detect contamination in the experimental pipeline from the point they are added. The underlying genomic information in a sample, however, carries information about inter-sample contamination occurring at any stage. Here, we present Polyphonia, a tool for detecting inter-sample contamination directly from deep sequencing data without the need for additional controls, using intrahost variant frequencies. We apply Polyphonia to 1102 SARS-CoV-2 samples sequenced at the Broad Institute and already tracked using molecular barcoding for comparison.<br><br>Polyphonia is available as a standalone Docker image and is also included as part of viral-ngs, available in Dockstore. Full documentation, source code, and instructions for use are available at https://github.com/broadinstitute/polyphonia.}, }
@article {pmid39672980, year = {2025}, author = {Garcia-Gonzalez, I and Gambera, S and Rocha, SF and Regano, A and Garcia-Ortega, L and Lytvyn, M and Diago-Domingo, L and Sanchez-Muñoz, MS and Garcia-Cabero, A and Zagorac, I and Luo, W and De Andrés-Laguillo, M and Fernández-Chacón, M and Casquero-Garcia, V and Lunella, FF and Torroja, C and Sánchez-Cabo, F and Benedito, R}, title = {iFlpMosaics enable the multispectral barcoding and high-throughput comparative analysis of mutant and wild-type cells.}, journal = {Nature methods}, volume = {22}, number = {2}, pages = {323-334}, pmid = {39672980}, issn = {1548-7105}, support = {101001814//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 638028//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; HR22-00316//"la Caixa" Foundation (Caixa Foundation)/ ; HR19-00120//"la Caixa" Foundation (Caixa Foundation)/ ; CX-SO-16-1//"la Caixa" Foundation (Caixa Foundation)/ ; CX_E-2015-01//"la Caixa" Foundation (Caixa Foundation)/ ; PRE2018-085283//Ministerio de Econom&#xed;a, Industria y Competitividad, Gobierno de Espa&#xf1;a (Ministerio de Econom&#xed;a, Industria y Competitividad)/ ; }, mesh = {Animals ; Mice ; *Mutation ; *Single-Cell Analysis/methods ; Flow Cytometry/methods ; *Mosaicism ; *DNA Barcoding, Taxonomic/methods ; }, abstract = {To understand gene function, it is necessary to compare cells carrying the mutated target gene with normal cells. In most biomedical studies, the cells being compared are in different mutant and control animals and, therefore, do not experience the same epigenetic changes and tissue microenvironment. The experimental induction of genetic mosaics is essential to determine a gene cell-autonomous function and to model the etiology of diseases caused by somatic mutations. Current technologies used to induce genetic mosaics in mice lack either accuracy, throughput or barcoding diversity. Here we present the iFlpMosaics toolkit comprising a large set of new genetic tools and mouse lines that enable recombinase-dependent ratiometric induction and single-cell clonal tracking of multiple fluorescently labeled wild-type and Cre-mutant cells within the same time window and tissue microenvironment. The labeled cells can be profiled by multispectral imaging or by fluorescence-activated flow cytometry and single-cell RNA sequencing. iFlpMosaics facilitate the induction and analysis of genetic mosaics in any quiescent or progenitor cell, and for any given single or combination of floxed genes, thus enabling a more accurate understanding of how induced genetic mutations affect the biology of single cells during tissue development, homeostasis and disease.}, }
@article {pmid39672483, year = {2025}, author = {Houpt, TA and Houpt, CE and Cassell Erquiaga, CB}, title = {BarTender: A system for recording intakes and body weights in ingestive behavior experiments.}, journal = {Physiology &amp; behavior}, volume = {290}, number = {}, pages = {114783}, doi = {10.1016/j.physbeh.2024.114783}, pmid = {39672483}, issn = {1873-507X}, mesh = {*Body Weight/physiology ; Animals ; *Feeding Behavior/physiology ; *Eating/physiology ; Rats ; *Drinking Behavior/physiology ; }, abstract = {A system is described for the semi-automated collection of fluid bottle, food jar, and rodent body weights. Items are labeled with barcodes, which are scanned by a Macintosh application connected via USB to a scale. Body weights are collected in the animal room by an iPad application connected to a Bluetooth scale. Simple summary statistics are automatically calculated, and data are stored with experiment metadata in a cloud database. Up-to-date graphs of the data are rendered by a web application from any browser, from which data can be downloaded for further analysis. Such a system makes ingestive behavior experiments more accurate, rapid, and higher throughput.}, }
@article {pmid39670108, year = {2024}, author = {Díaz, JA and Ordines, F and Massutí, E and Cárdenas, P}, title = {From caves to seamounts: the hidden diversity of tetractinellid sponges from the Balearic Islands, with the description of eight new species.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16584}, pmid = {39670108}, issn = {2167-8359}, mesh = {Animals ; *Porifera/classification/anatomy &amp; histology ; Spain ; Caves ; Phylogeny ; Biodiversity ; Ecosystem ; DNA Barcoding, Taxonomic ; }, abstract = {The sponge fauna of the Western Mediterranean stands as one of the most studied in the world. Yet sampling new habitats and a poorly studied region like the Balearic Islands highlights once again our limited knowledge of this group of animals. This work focused on demosponges of the order Tetractinellida collected in several research surveys (2016-2021) on a variety of ecosystems of the Balearic Islands, including shallow caves, seamounts and trawl fishing grounds, in a broad depth range (0-725 m). Tetractinellid material from the North Atlantic and more than twenty type specimens were also examined and, for some, re-described in this work. All species were barcoded with the traditional molecular markers COI (Folmer fragment) and 28S (C1-C2 or C1-D2 fragment). A total of 36 species were identified, mostly belonging to the family Geodiidae (15 species), thereby bringing the number of tetractinellids recorded in the Balearic Islands from 15 to 39. Eight species from this study are new: Stelletta mortarium sp. nov., Penares cavernensis sp. nov., Penares isabellae sp. nov., Geodia bibilonae sp. nov., Geodia microsphaera sp. nov. and Geodia matrix sp. nov. from the Balearic Islands; Geodia phlegraeioides sp. nov. and Caminus xavierae sp. nov. from the North East Atlantic. Stelletta dichoclada and Erylus corsicus are reported for the first time since their description in Corsica in 1983. Pachastrella ovisternata is documented for the first time in the Mediterranean Sea. Finally, after comparisons of type material, we propose new synonymies: Geodia anceps as a junior synonym of Geodia geodina, Erylus cantabricus as a junior synonym of Erylus discophorus and Spongosorites maximus as a junior synonym of Characella pachastrelloides.}, }
@article {pmid39664260, year = {2024}, author = {Albaina, A and Garić, R and Yebra, L}, title = {Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa.}, journal = {Journal of plankton research}, volume = {46}, number = {6}, pages = {581-595}, pmid = {39664260}, issn = {0142-7873}, abstract = {Eleven years after the publication of the first work applying deoxyribonucleic acid (DNA) metabarcoding to zooplankton communities, the commonly known "miniCOI" barcode is widely used, becoming the marker of choice. However, several primer combinations co-exist for this barcode and a critical evaluation of their performance is needed. This article reviews the misperformance of miniCOI metabarcoding with marine zooplankton communities, comparing them to microscopy and/or other universal markers. In total, misperformances were reported for 26 zooplankton taxa, including 18 copepods and five tunicates. We report a detection failure with Class Appendicularia and contrasting performances for Oithona similis (from good correspondence to detection failure), two worldwide abundant taxa with a crucial role in the marine pelagic realm. A combination of forward primer mismatches, the presence of long poly-T inserts and a low number of reference sequences would explain the failure to detect appendicularians. However, the contrasting performance with O. similis would correspond to distinct numbers of mismatches in the forward primer in different lineages within this cryptic taxon. This is reinforced by the report of similar patterns with other locally abundant zooplankton taxa. Therefore, we strongly call for the use of miniCOI in combination with alternative methods capable of addressing these limitations.}, }
@article {pmid39663496, year = {2024}, author = {Hu, M and Yang, L and Twarog, N and Ochoada, J and Li, Y and Vrettos, EI and Torres-Hernandez, AX and Martinez, JB and Bhatia, J and Young, BM and Price, J and McGowan, K and Nguyen, TH and Shi, Z and Anyanwu, M and Rimmer, MA and Mercer, S and Rankovic, Z and Shelat, AA and Blair, DJ}, title = {Continuous collective analysis of chemical reactions.}, journal = {Nature}, volume = {636}, number = {8042}, pages = {374-379}, pmid = {39663496}, issn = {1476-4687}, support = {R25 CA023944/CA/NCI NIH HHS/United States ; T32 GM132061/GM/NIGMS NIH HHS/United States ; }, abstract = {The automated synthesis of small organic molecules from modular building blocks has the potential to transform our capacity to create medicines and materials[1-3]. Disruptive acceleration of this molecule-building strategy broadly unlocks its functional potential and requires the integration of many new assembly chemistries. Although recent advances in high-throughput chemistry[4-6] can speed up the development of appropriate synthetic methods, for example, in selecting appropriate chemical reaction conditions from the vast range of potential options, equivalent high-throughput analytical methods are needed. Here we report a streamlined approach for the rapid, quantitative analysis of chemical reactions by mass spectrometry. The intrinsic fragmentation features of chemical building blocks generalize the analyses of chemical reactions, allowing sub-second readouts of reaction outcomes. Central to this advance was identifying that starting material fragmentation patterns function as universal barcodes for downstream product analysis by mass spectrometry. Combining these features with acoustic droplet ejection mass spectrometry[7,8] we could eliminate slow chromatographic steps and continuously evaluate chemical reactions in multiplexed formats. This enabled the assignment of reaction conditions to molecules derived from ultrahigh-throughput chemical synthesis experiments. More generally, these results indicate that fragmentation features inherent to chemical synthesis can empower rapid data-rich experimentation.}, }
@article {pmid39660837, year = {2025}, author = {Lewin, GR}, title = {mSphere of Influence: How the single cell contributes to the collective.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0043124}, pmid = {39660837}, issn = {2379-5042}, support = {DP2 AI184733/AI/NIAID NIH HHS/United States ; R00 DE031018/DE/NIDCR NIH HHS/United States ; }, mesh = {*Single-Cell Analysis ; Humans ; *Bacteria/genetics/classification ; *Microbiota/genetics ; RNA-Seq ; }, abstract = {Gina Lewin works in the field of microbial ecology, with a focus on the human microbiota. In this mSphere of Influence article, she reflects on how two papers describing bacterial single-cell RNA-seq-"Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing" by S. B. Blattman, W. Jiang, P. Oikonomou, and S. Tavazoie (Nat Microbiol 5:1192-1201, 2020, https://doi.org/10.1038/s41564-020-0729-6) and "Microbial single-cell RNA sequencing by split-pool barcoding" by A. Kuchina, L. M. Brettner, L. Paleologu, C. M. Roco, et al. (Science 371:eaba5257, 2021, https://doi.org/10.1126/science.aba5257)-impacted her work by developing a new approach to study how single cells of bacteria contribute to ecosystem-level processes.}, }
@article {pmid39660352, year = {2024}, author = {Yu, T and Ren, Z and Gao, X and Li, G and Han, R}, title = {Generating barcodes for nanopore sequencing data with PRO.}, journal = {Fundamental research}, volume = {4}, number = {4}, pages = {785-794}, pmid = {39660352}, issn = {2667-3258}, abstract = {DNA barcodes, short and unique DNA sequences, play a crucial role in sample identification when processing many samples simultaneously, which helps reduce experimental costs. Nevertheless, the low quality of long-read sequencing makes it difficult to identify barcodes accurately, which poses significant challenges for the design of barcodes for large numbers of samples in a single sequencing run. Here, we present a comprehensive study of the generation of barcodes and develop a tool, PRO, that can be used for selecting optimal barcode sets and demultiplexing. We formulate the barcode design problem as a combinatorial problem and prove that finding the optimal largest barcode set in a given DNA sequence space in which all sequences have the same length is theoretically NP-complete. For practical applications, we developed the novel method PRO by introducing the probability divergence between two DNA sequences to expand the capacity of barcode kits while ensuring demultiplexing accuracy. Specifically, the maximum size of the barcode kits designed by PRO is 2,292, which keeps the length of barcodes the same as that of the official ones used by Oxford Nanopore Technologies (ONT). We validated the performance of PRO on a simulated nanopore dataset with high error rates. The demultiplexing accuracy of PRO reached 98.29% for a barcode kit of size 2,922, 4.31% higher than that of Guppy, the official demultiplexing tool. When the size of the barcode kit generated by PRO is the same as the official size provided by ONT, both tools show superior and comparable demultiplexing accuracy.}, }
@article {pmid39659773, year = {2024}, author = {Xue, XL and Lu, XQ and Du, XC}, title = {The new genus Purpurata (Lepidoptera, Crambidae, Spilomelinae), with descriptions of two new species from China.}, journal = {ZooKeys}, volume = {1219}, number = {}, pages = {175-194}, pmid = {39659773}, issn = {1313-2989}, abstract = {The male genitalia characters of four species, Botysiopasalis Walker, 1859, Pleuroptyaobfuscalis Yamanaka, 1998, Botysplagiatalis Walker, 1859 and Pataniashompen Singh et Ahmad, 2022, placed in the genus Patania Moore, 1888 before the present study, do not conform to the diagnosis of Patania. A new genus, Purpurata gen. nov., is established for these four species, and two new species, Purpuratadirecta sp. nov. and Purpuratalurida sp. nov. are described based on their external morphology and genitalia characters. Purpuratadirecta sp. nov. is designated as the type species of the new genus. Five species of the new genus were clearly separated from Patania species in the Maximum likelihood phylogenetic tree constructed based on COI sequence data. Compared to Patania, the new genus Purpurata exhibits distinctive characters in male genitalia: the uncus is short, broad, and arc-shaped posteriorly; the gnathos is present and setose, or reduced; and the fibula is very small and setose. In addition, Pataniaclava (Xu &amp; Du), syn. nov. is synonymized with Purpurataiopasalis comb. nov. An identification key to species of the new genus is presented based on morphological characters of habitus and genitalia. Images of the habitus and genitalia are provided.}, }
@article {pmid39659496, year = {2024}, author = {Shih, HT and Cai, Y and Niwa, N and Yoshigou, H and Nakahara, Y}, title = {Integrative Taxonomy Reveals Freshwater Shrimp Diversity (Decapoda: Atyidae: Neocaridina) from Kyushu and Southern Honshu of Japan, with a Discussion on Introduced Species.}, journal = {Zoological studies}, volume = {63}, number = {}, pages = {e18}, pmid = {39659496}, issn = {1810-522X}, abstract = {Correct identification of species is crucial for invasion ecology and management, particularly in aquatic systems. In this study, specimens of the freshwater shrimp genus Neocaridina from Kyushu and southern Honshuof Japan were identified by using an integrative approach that combined DNA barcoding of mitochondrial cytochrome oxidase subunit I (COI) and morphological examination. Among the eight species detected, two are native, viz. N. denticulata and N. ikiensis. Four are regarded as non-indigenous, viz. N. davidi, N. koreana, N. palmata, N. aff. palmata, which are believed to have been introduced from other East Asian countries either by the aquarium trade or as live fish bait. The remaining two species are likely cryptic native species, which have either been mistaken for known species, e.g., N. aff. denticulata, or species that have not been discovered before, e.g., N. aff. fukiensis. While the four alien species have spread widely in central Honshu, northern Kyushu and Tsushima Island, their impacts on the native species and the overall ecology remain mostly unexplored. Problems associated with using DNA barcoding for species identification are highlighted for further research.}, }
@article {pmid39657551, year = {2025}, author = {Zhang, D and Zhang, N and Zhao, J and Li, X and Bian, F and Zhang, Y and Ge, Y and Li, Z}, title = {Label-free multiplexed detection based on core-shell photonic barcodes integrated RCA.}, journal = {Biosensors &amp; bioelectronics}, volume = {271}, number = {}, pages = {117037}, doi = {10.1016/j.bios.2024.117037}, pmid = {39657551}, issn = {1873-4235}, mesh = {*Biosensing Techniques/methods/instrumentation ; Humans ; *SARS-CoV-2/isolation &amp; purification/genetics ; *Nucleic Acid Amplification Techniques/instrumentation/methods ; *Limit of Detection ; Influenza A Virus, H1N1 Subtype/isolation &amp; purification/genetics ; COVID-19/diagnosis/virology ; Spike Glycoprotein, Coronavirus/analysis/immunology ; Photons ; Hydrogels/chemistry ; }, abstract = {Multiplexed, rapid, and accurate virus quantification is of great value in biomedical detection. Herein, we proposed a label-free multiplexed virus screening quantitative biosensor based on color core-shell hydrogel photonic crystal (PhC) barcode integrated rolling circle amplification (RCA). The composite hydrogel shell was formed by acrylic acid and polyethylene glycol diacrylate, and the core silica photonic crystal was used as a detector. In addition, by adjusting the internal periodic structure, the PhC microcarrier was able to perform various color barcodes for the detection of different targets. Based on these excellent properties of the nanocomposite barcode, the biosensor not only demonstrated the ability to rapidly and accurately detect SARS-COV-2-N, SARS-COV-2-S, and H1N1 simultaneously in one tube, but also converting the signal of target protein to nucleic acid signal based on DNA decorated antibody complex combine with the blocked primer and RCA strategy. As a result, the platform achieved highly sensitive multiplexed quantitative detection with a detection limit in the range of 0.30 pg/mL. In addition, the platform we developed was validated by clinical sample analysis with acceptable accuracy and high specificity, demonstrating the good potential applicability of the proposed detection method in clinical screening and diagnosis.}, }
@article {pmid39654309, year = {2024}, author = {Frankenburg, R and Oreg, A}, title = {"As long as they remember me, I am alive": Commemoration and memory through stickers.}, journal = {Death studies}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07481187.2024.2435929}, pmid = {39654309}, issn = {1091-7683}, abstract = {This study explores the phenomenon of memorial stickers commemorating victims of the October 7, 2023, massacre and subsequent Israel-Hamas war. Analyzing 600 stickers collected across Israel, we examine how these artifacts shape personal and collective memory of these tragic events. Using content analysis, visual data analysis, and ethnography of texts, we investigate the stickers' distribution, textual content, and visual elements. Three key findings emerged: (1) The widespread distribution of stickers expands commemoration beyond cemeteries, creating a larger community of remembrance; (2) Diverse textual content, from personal traits to universal messages, aims to keep the deceased's values alive in social awareness; (3) Visual elements balance public recognition with private mourning through strategic use of photographs, colors, and barcodes. Drawing on theories of collective memory and continuing bonds, we argue that these stickers symbolically bring the deceased into daily life and public spaces, contributing to the processing of personal and national trauma.}, }
@article {pmid39653555, year = {2024}, author = {Fuchs, KJ and Göransson, M and Kester, MGD and Ettienne, NW and van de Meent, M and de Jong, RCM and Koster, EAS and Halkes, CJM and Scheeren, F and Heemskerk, MHM and van Balen, P and Falkenburg, JHF and Hadrup, SR and Griffioen, M}, title = {DNA barcoded peptide-MHC multimers to measure and monitor minor histocompatibility antigen-specific T cells after allogeneic stem cell transplantation.}, journal = {Journal for immunotherapy of cancer}, volume = {12}, number = {12}, pages = {}, pmid = {39653555}, issn = {2051-1426}, mesh = {Humans ; *Minor Histocompatibility Antigens/immunology/metabolism ; *Transplantation, Homologous ; *Graft vs Host Disease/immunology ; Middle Aged ; Hematopoietic Stem Cell Transplantation/methods ; Male ; Female ; Adult ; Peptides/immunology ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Stem Cell Transplantation/adverse effects ; Aged ; Graft vs Leukemia Effect/immunology ; }, abstract = {Allogeneic stem cell transplantation (alloSCT) provides a curative treatment option for hematological malignancies. After HLA-matched alloSCT, donor-derived T cells recognize minor histocompatibility antigens (MiHAs), which are polymorphic peptides presented by HLA on patient cells. MiHAs are absent on donor cells due to genetic differences between patient and donor. T cells targeting broadly expressed MiHAs induce graft-versus-leukemia (GvL) reactivity as well as graft-versus-host disease (GvHD), while T cells for MiHAs with restricted or preferential expression on hematopoietic or non-hematopoietic cells may skew responses toward GvL or GvHD, respectively. Besides tissue expression, overall strength of GvL and GvHD is also determined by T-cell frequencies against MiHAs.Here, we explored the use of DNA barcode-labeled peptide-MHC multimers to detect and monitor antigen-specific T cells for the recently expanded repertoire of HLA-I-restricted MiHAs. In 16 patients who experienced an immune response after donor lymphocyte infusion, variable T-cell frequencies up to 30.5% of CD8[+] T cells were measured for 49 MiHAs. High T-cell frequencies above 1% were measured in 12 patients for 19 MiHAs, with the majority directed against mismatched MiHAs, typically 6-8 weeks after donor lymphocyte infusion and at the onset of GvHD. The 12 patients included 9 of 10 patients with severe GvHD, 2 of 3 patients with limited GvHD and 1 of 3 patients without GvHD.In conclusion, we demonstrated that barcoded peptide-MHC multimers reliably detect and allow monitoring for MiHA-specific T cells during treatment to investigate the kinetics of immune responses and their impact on development of GvL and GvHD after HLA-matched alloSCT.}, }
@article {pmid39652422, year = {2025}, author = {Ashkin, EL and Tang, YJ and Xu, H and Hung, KL and Belk, JA and Cai, H and Lopez, SS and Dolcen, DN and Hebert, JD and Li, R and Ruiz, PA and Keal, T and Andrejka, L and Chang, HY and Petrov, DA and Dixon, JR and Xu, Z and Winslow, MM}, title = {A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.}, journal = {The Journal of experimental medicine}, volume = {222}, number = {1}, pages = {}, pmid = {39652422}, issn = {1540-9538}, support = {T32 CA009302/CA/NCI NIH HHS/United States ; F99CA284289/CA/NCI NIH HHS/United States ; F99 CA274692/CA/NCI NIH HHS/United States ; 28FT-0019//Tobacco-Related Disease Research Program/ ; //Stanford University/ ; K00 CA245784/CA/NCI NIH HHS/United States ; DGE-2146755//National Science Foundation Graduate Research Fellowship Program/ ; MFE-176568//Canadian Institute of Health Research/ ; R01 CA234349/CA/NCI NIH HHS/United States ; F99 CA284289/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; GT14928/HHMI/Howard Hughes Medical Institute/United States ; R01 CA231253/CA/NCI NIH HHS/United States ; R01-CA231253/NH/NIH HHS/United States ; PF-21-112-01-MM//American Cancer Society/ ; }, mesh = {*Lung Neoplasms/pathology/metabolism/genetics ; Humans ; Animals ; *Cell Cycle Proteins/metabolism/genetics ; Cell Line, Tumor ; Mice ; *Carcinogenesis/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; CRISPR-Cas Systems ; Antigens, Nuclear/metabolism/genetics ; Tumor Suppressor Proteins/metabolism/genetics ; Cohesins ; }, abstract = {The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression.}, }
@article {pmid39649949, year = {2024}, author = {Rocha, LA and Pinheiro, HT and Najeeb, A and Rocha, CR and Shepherd, B}, title = {Chromisabadhah (Teleostei, Pomacentridae), a new species of damselfish from mesophotic coral ecosystems of the Maldives.}, journal = {ZooKeys}, volume = {1219}, number = {}, pages = {165-174}, pmid = {39649949}, issn = {1313-2989}, abstract = {A new species of Chromis (Teleostei, Pomacentridae) is described from four specimens collected between 95 and 110 m depth in mesophotic coral ecosystems in the Maldives, Indian Ocean. Chromisabadhah sp. nov. can be distinguished from all of its congeners by the following combination of characters: dorsal-fin rays XIII, 12-13; anal-fin rays II,11-12; pectoral-fin rays 17-18; tubed lateral-line scales 17; gill rakers 7+17-18 = 24-25; pearly white body with a large black marking covering the anterior two-thirds of the anal fin. The closest DNA barcode sequence (5.1% average uncorrected genetic distance on the mitochondrial COI gene), among those available, is Chromiswoodsi, a similar mesophotic species known from the coastal western Indian Ocean (Somalia to South Africa). The new species is easily distinguished from C.woodsi by having 13 dorsal spines (versus 14 in C.woodsi), the absence of a black band on the base of the tail (present in C.woodsi), and by the genetic difference.}, }
@article {pmid39649948, year = {2024}, author = {Lehr, E and Moravec, J and Wang, Y and Uvizl, M}, title = {A new species of Pristimantis (Amphibia, Anura, Strabomantidae) from a montane forest of the Pui Pui Protected Forest in central Peru.}, journal = {ZooKeys}, volume = {1219}, number = {}, pages = {143-163}, pmid = {39649948}, issn = {1313-2989}, abstract = {Herpetological inventories conducted in the Pui Pui Protected Forest in the central Peruvian Andes between 2012 and 2014 revealed unusually high local anuran richness and endemism. Herein, we describe a new species of Pristimantis discovered in the buffer zone of the protected area between 1550 and 1730 m a.s.l. The description is based on one subadult male (snout-vent length 14.4 mm), one adult female (snout-vent length 26.4 mm), and six juvenile specimens collected in the montane forest between 1550 and 1730 m a.s.l. DNA barcoding placed P.vrazi sp. nov. as the sister taxon to P.rhabdocnemus and in the clade also containing P.lindae, P.sinschi, P.quaquaversus, and one still unnamed Pristimantis species. Pristimantisvrazi sp. nov. differs from all these closely related species by the combination of the following characters: tuberculate dorsum, presence of the tympanum, presence of dentigerous processes on the vomer, absence of vocal slits, a red median horizontal streak across the iris, a narrow black median vertical streak on the lower half of the eye, cream to dark brown dorsal ground coloration, and cream to gray ventral ground coloration.}, }
@article {pmid39649432, year = {2024}, author = {Ollivier, M and Rivers-Moore, J and Pichon, M and Andrieu, E and Carrié, R and Rudelle, R and Sarthou, JP and Ouin, A}, title = {Wild bees (Apoidea, Anthophila) of south-west France: more than 10 years of inventories in mosaic landscapes of "Vallées et Coteaux de Gascogne" (ZA-PYGAR).}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e135157}, pmid = {39649432}, issn = {1314-2828}, abstract = {BACKGROUND: The reported massive decline of arthropods and particularly of pollinators such as wild bees, in terms of abundance and richness, is a threat for crop production and wild plant biodiversity conservation. This decline is mainly explained by a combination of drivers at local- and landscape-scale related to intensive farming practices. Assessing the evolution of wild bee communities in agricultural ecosystems and their response to such practices is needed to address conservation purposes.<br><br>NEW INFORMATION: We provide here data for the 24,329 wild bee specimens held in the collection of DYNAFOR Lab (UMR 1201 INRAE, INP-ENSAT, EI PURPAN), located at INP-ENSAT (Toulouse, France). All bee specimens were collected from the long term socio-ecological research site, ZA-PYGAR, located in south-west France, for more than 10 years (2010 to 2022) within the framework of different research programmes conducted by the DYNAFOR Lab. At least 270 species, representative of the six wild bee families, were identified from this area. The identified specimens are considered reliable as identifications were performed or have been verified by community-recognised experts. In addition, ongoing DNA barcoding performed on certain specimens helped clarify questionable morphological characters and provided cross-validation of species identification.}, }
@article {pmid39648853, year = {2024}, author = {Shi, R and Chen, H and Zhang, W and Leak, RK and Lou, D and Chen, K and Chen, J}, title = {Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {}, number = {}, pages = {271678X241305914}, pmid = {39648853}, issn = {1559-7016}, support = {R15 NS130532/NS/NINDS NIH HHS/United States ; R01 NS124673/NS/NINDS NIH HHS/United States ; R21 NS141002/NS/NINDS NIH HHS/United States ; I01 BX003377/BX/BLRD VA/United States ; I01 BX002495/BX/BLRD VA/United States ; }, abstract = {Single-cell RNA sequencing (scRNA-seq) is a high-throughput transcriptomic approach with the power to identify rare cells, discover new cellular subclusters, and describe novel genes. scRNA-seq can simultaneously reveal dynamic shifts in cellular phenotypes and heterogeneities in cellular subtypes. Since the publication of the first protocol on scRNA-seq in 2009, this evolving technology has continued to improve, through the use of cell-specific barcodes, adoption of droplet-based systems, and development of advanced computational methods. Despite induction of the cellular stress response during the tissue dissociation process, scRNA-seq remains a popular technology, and commercially available scRNA-seq methods have been applied to the brain. Recent advances in spatial transcriptomics now allow the researcher to capture the positional context of transcriptional activity, strengthening our knowledge of cellular organization and cell-cell interactions in spatially intact tissues. A combination of spatial transcriptomic data with proteomic, metabolomic, or chromatin accessibility data is a promising direction for future research. Herein, we provide an overview of the workflow, data analyses methods, and pros and cons of scRNA-seq technology. We also summarize the latest achievements of scRNA-seq in stroke and acute traumatic brain injury, and describe future applications of scRNA-seq and spatial transcriptomics.}, }
@article {pmid39647154, year = {2024}, author = {Liu, YX and Xue, HJ and Liu, GQ}, title = {Two new species of the brachypterous Scirtetellus (Hemiptera: Heteroptera: Miridae) from China.}, journal = {Zootaxa}, volume = {5497}, number = {2}, pages = {244-254}, doi = {10.11646/zootaxa.5497.2.4}, pmid = {39647154}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; *Heteroptera/anatomy &amp; histology/classification ; Female ; *Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {Two new species of the genus Scirtetellus Reuter, 1890 (Heteroptera: Miridae: Orthotylinae: Halticini) are described as new to science from China: Scirtetellus qinghaiensis sp. nov. and Scirtetellus shanxiensis sp. nov. Detailed morphological description, photographs of the dorsal habitus and male parameres, key to species of Scirtetellus from China and species list of Scirtetellus of the world are provided. The 658 bp long fragments of the mitochondrial gene COI (DNA barcode) are provided as a part of the diagnosis of the new species. The type specimens and the DNA sample were deposited in the Institute of Entomology, Nankai University, Tianjin, China.}, }
@article {pmid39647119, year = {2024}, author = {Prieto, C and Pinilla, C and Lorenc-Brudecka, J and Balke, M}, title = {Integrative description of Thaeides ramoni sp. nov. (Lepidoptera: Lycaenidae), a sympatric sibling species of Thaeides theia (Hewitson, 1870) found in the Sierra Nevada de Santa Marta, Colombia.}, journal = {Zootaxa}, volume = {5501}, number = {1}, pages = {181-190}, doi = {10.11646/zootaxa.5501.1.9}, pmid = {39647119}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Colombia ; *Animal Distribution ; *Butterflies/anatomy &amp; histology/classification ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Sympatry ; Phylogeny ; Ecosystem ; }, abstract = {We present evidence from DNA barcodes, wing pattern and distribution to support the hypothesis that an entity flying in sympatry with Thaeides theia in the Sierra Nevada de Santa Marta, is an undescribed biological species named herein as Thaides ramoni Prieto, sp. nov. Adult specimens and genital structures are illustrated for both species along with molecular and morphological diagnostic characters. In addition, we present some considerations about the taxonomy of the species in the Thaeides muela group.}, }
@article {pmid39647095, year = {2024}, author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM and Lisanovskaya, EA}, title = {Morphological description and DNA barcoding of Thalassomya paraskevae sp. nov. (Diptera: Chironomidae: Telmatogetoninae) from coast of the Black Sea.}, journal = {Zootaxa}, volume = {5501}, number = {4}, pages = {524-530}, doi = {10.11646/zootaxa.5501.4.2}, pmid = {39647095}, issn = {1175-5334}, mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; *Chironomidae/anatomy &amp; histology/classification/genetics ; Black Sea ; Female ; *Animal Distribution ; Organ Size ; Body Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Illustrated description of adult male, as well as DNA barcoding, of Thalassomya paraskevae sp. nov. in comparison with close related species T. frauenfeldi Schiner from coast of the Black Sea are provided. Interspecific p-distances using gene COI 5P between T. paraskevae sp. nov. and T. frauenfeldi from Madeira (Portugal) were 8.94%. Divergence between described species and T. frauenfeldi collected near the type locality (Friuli Venezia-Giulia, Italy) using COI 3P were 7.72%. Obtained values corresponds to species level.}, }
@article {pmid39647062, year = {2024}, author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Helmick, EE and Bahder, BW}, title = {A new species of planthopper in the genus Platocerella (Hemiptera: Auchenorrhyncha: Derbidae) from palms in Costa Rica, a key to the genus and an updated molecular phylogeny of available New World Otiocerinae.}, journal = {Zootaxa}, volume = {5512}, number = {2}, pages = {222-232}, doi = {10.11646/zootaxa.5512.2.6}, pmid = {39647062}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/classification/anatomy &amp; histology/genetics ; Costa Rica ; *Phylogeny ; Male ; Female ; Animal Distribution ; Arecaceae/parasitology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Electron Transport Complex IV/genetics ; }, abstract = {The genus Platocerella is a monotypic otiocerine genus (Derbidae: Otiocerinae: Otiocerini) reported from Guyana. A new species of Platocerella associated with palms is herein described from Costa Rica. Molecular data for the barcoding region cytochrome c oxidase subunit I (COI), 18S rRNA gene, and D9-D10 expansion region of the 28S rRNA gene is provided to produce a preliminary phylogenetic tree including the new species and related taxa to place the new species relative to other otiocerine planthoppers.}, }
@article {pmid39647046, year = {2024}, author = {Mukherjee, B and Ray, N and Mukherjee, A and Naskar, A and Banerjee, D}, title = {First report of acifer group of the subgenus Tripodura Townes (Diptera: Chironomidae: Polypedilum) from India, with a new species and updated world checklist.}, journal = {Zootaxa}, volume = {5512}, number = {4}, pages = {531-552}, doi = {10.11646/zootaxa.5512.4.4}, pmid = {39647046}, issn = {1175-5334}, mesh = {Animals ; Male ; India ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development ; *Animal Distribution ; *Checklist ; Phylogeny ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {A new species of the acifer group of the subgenus Tripodura and genus Polypedilum Kieffer is described on the basis of adult male. The acifer species group is recorded firstly from India. The molecular barcoding of the new species is provided. Moreover, molecular phylogeny of all available species of the subgenus Tripodura, along with an Indian key based on adult males of this subgenus have been designed here. Additionally, a world checklist of the subgenus Tripodura has also been furnished in this study.}, }
@article {pmid39647038, year = {2024}, author = {Godfray, HCJ and Achterberg, CV}, title = {Annotated Checklist of the European Dacnusini and the Dapsilarthra genus group of the Alysiini (Hymenoptera: Braconidae, Alysiinae).}, journal = {Zootaxa}, volume = {5513}, number = {1}, pages = {1-73}, doi = {10.11646/zootaxa.5513.1.1}, pmid = {39647038}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; *Wasps/classification/anatomy &amp; histology ; *Checklist ; *Animal Distribution ; Europe ; Hymenoptera/classification/anatomy &amp; histology ; Body Size ; DNA Barcoding, Taxonomic ; }, abstract = {An annotated checklist of the European Dacnusini (426 species) and the Dapsilarthra genus group of the Alysiini (16 species) (Hymenoptera: Braconidae, Alysiinae) is provided. In addition to a species list with synonymy, further details are given of: (i) intrageneric groupings; (ii) a reference to each species' treatment in the unindexed and multipart major revisions of Nixon &amp; Griffith as well as the long keys of Tobias; (iii) a hypothesis about host range for the 60% of species which have been reared, and the evidence upon which it is based; (iv) whether a DNA barcode sequence is available (30% of species); (v) for species published after Griffiths' revision a reference to similar species; (vi) any further relevant notes. One new synonym is established: Chorebus luzulae Griffiths syn. nov. is synonymised with Chorebus aphantus Marshall. Mesocrina Förster is excluded from the Dapsilartha genus group and whether Grandia Goidanich and Lodbrokia Hedqvist are in the Dacnusini is considered uncertain.}, }
@article {pmid39647031, year = {2024}, author = {Nazarov, RA and Nabizadeh, H and Rajabizadeh, M and Melnikov, DA and Volkova, VR and Poyarkov, NA and Rastegar-Pouyani, E}, title = {Taxonomy of Iranian Asaccus (Squamata: Phyllodactylidae) with description of a new species from southern Iran.}, journal = {Zootaxa}, volume = {5514}, number = {2}, pages = {101-128}, doi = {10.11646/zootaxa.5514.2.1}, pmid = {39647031}, issn = {1175-5334}, mesh = {Animals ; Iran ; *Lizards/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Female ; Male ; *Animal Distribution ; *Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {We provide the first diversity assessment of Iranian species of the genus Asaccus based on COI DNA-barcoding. We analyzed 53 samples of Iranian Asaccus representing nine OTU corresponding to 10 currently recognzied nominal species, and evaluated both morphological and genetic data to support the recognition of a new species from Bandar-e Jask, Hormozgan Province, southern Iran-Asaccus authenticus sp. nov. The new species is characterized by medium body size (SVL max 55.5 mm), elongated limbs, and relatively small dorsal tubercles arranged in 12-14 regular rows. Morphologically Asaccus authenticus sp. nov. resembles both Arabian and Iranian representatives of the genus; phylogenetically it forms a highly divergent lineage with sister relationships to all other Iranian congeners. We applied the geometric morphometrics method to compare the position and shape of postmental plates for almost all members of Asaccus and evaluated the importance of this character in species diagnostics in this group. We also critically evaluate the recent phylogenetic data on Asaccus and discuss the most problematic questions on taxonomy of this genus. We also revalidate Asaccus ingae (Eiselt, 1973) as a full species; overall our work raises the total number of species of the genus Asaccus to 20.}, }
@article {pmid39647018, year = {2024}, author = {Bahder, BW and Randretsiferana, SA and Randretsiferana, A and Stroiński, A and Łukasik, P and Bartlett, CR and Pilet, F and Hasinjaka, RH}, title = {A new species of planthopper in the genus Eumyndus (Hemiptera: Cixiidae) from palms in eastern Madagascar and molecular evidence for the synonymy of Eumyndus kraussi and Eumyndus metcalfi.}, journal = {Zootaxa}, volume = {5514}, number = {4}, pages = {338-352}, doi = {10.11646/zootaxa.5514.4.3}, pmid = {39647018}, issn = {1175-5334}, mesh = {Animals ; Madagascar ; *Hemiptera/anatomy &amp; histology/classification/genetics ; Male ; Female ; *Animal Distribution ; Phylogeny ; Organ Size ; Electron Transport Complex IV/genetics ; Arecaceae/parasitology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; RNA, Ribosomal, 18S/genetics ; }, abstract = {A new species of Eumyndus Synave, 1956, a genus endemic to Madagascar, is here described as Eumyndus jeanjacquei sp. nov. The new species was collected from the palm Vonitra fibrosa (C.H.Wright) Becc., 1911. Molecular data are provided for the new species from the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene and support placement of the new species in Eumyndus. A new synonymy is proposed based on examination of type material: E. metcalfi Synave, 1956 equals E. kraussi Synave, 1956, new synonym.}, }
@article {pmid39646982, year = {2024}, author = {Pyrcz, TW and Boyer, P and Petit, JC and Garlacz, R and Garlacz, KSZ and Espeland, M and Willmott, KR}, title = {Bedazzled: a new, striking species of Corades from the outskirts of Quito questions our knowledge of Andean cloud forest butterflies (Lepidoptera, Nymphalidae, Satyrinae).}, journal = {Zootaxa}, volume = {5453}, number = {2}, pages = {255-262}, doi = {10.11646/zootaxa.5453.2.6}, pmid = {39646982}, issn = {1175-5334}, mesh = {Animals ; *Butterflies/anatomy &amp; histology/classification ; Male ; Ecuador ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Forests ; Phylogeny ; }, abstract = {A new butterfly species in the genus Corades, C. yanacocha Pyrcz, Boyer &amp; Petit sp. n., belonging to the diverse, predominantly Andean subtribe Pronophilina (Nymphalidae, Satyrinae), is described from the Yanacocha Reserve situated only a couple of kilometres west of Quito, Ecuador. This is an extremely surprising discovery in a region whose butterfly fauna was considered to be fairly well known, underlying the need to protect remnants of high elevation forests in such overpopulated regions of the Andes. Morphological characters, in particular male genitalia, indicate an affinity of C. yanacocha sp. n. with C. trimaculata from northern Peru. A preliminary molecular study using COI barcodes indicates, however, the widely distributed north Andean C. dymantis as the closest relative.}, }
@article {pmid39646949, year = {2024}, author = {Riccardi, PR and Ang, Y}, title = {New species and new records of Chloropinae from Singapore (Diptera: Chloropidae).}, journal = {Zootaxa}, volume = {5458}, number = {1}, pages = {83-92}, doi = {10.11646/zootaxa.5458.1.4}, pmid = {39646949}, issn = {1175-5334}, mesh = {Animals ; Singapore ; Male ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; Organ Size ; Phylogeny ; Biodiversity ; }, abstract = {Chloropidae biodiversity in the Oriental region is remarkably diverse and yet poorly understood. In this study, we used integrative taxonomy to tackle the species diversity of the subfamily Chloropinae from Singapore. We describe the first Oriental species of Cryptonevra Lioy, C. argenteum Riccardi, sp. nov., a new species of Chloropsina Becker, C. flavipes Riccardi, sp. nov., provide the first record of Eutropha noctilux (Walker) from Singapore and DNA barcodes of Chloropsina minima (Becker), Ensiferella kanmiyai Nartshuk. In addition, we increased the number of Chloropinae records from Singapore from two (Anthracophagella Anderson and Chlorops Meigen) to nine (addition of Cerais van der Wulp, Chloropsina, Cryptonevra, Elliponeura Loew, Ensiferella Andersson, Eutropha Loew, and Thressa Walker) genera and from two to seven described species plus four morphospecies. The species were discovered using NGS barcodes and are part of an ongoing campaign to document the biodiversity of Singapore.}, }
@article {pmid39646947, year = {2024}, author = {Béarez, P and Zavalaga, F and Miranda, J and Mennesson, MI and Campos-León, S and Jiménez-Prado, P}, title = {Aulopus chirichignoae, a new flagfin from the eastern Pacific Ocean (Teleostei, Aulopiformes, Aulopidae).}, journal = {Zootaxa}, volume = {5458}, number = {1}, pages = {108-118}, doi = {10.11646/zootaxa.5458.1.6}, pmid = {39646947}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; Pacific Ocean ; Ecuador ; *Animal Distribution ; *Body Size ; Peru ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {A new species of the Aulopidae is described from the waters of southern Ecuador and northern Peru. Aulopus chirichignoae sp. nov. was previously confused with Aulopus bajacali Parin &amp; Kotlyar, 1984, but it differs from this species by a significantly marked elongation of the dorsal fin rays in males (absent in females), a smaller head, modal differences in dorsal and anal ray counts (15 vs 14 and 11 vs 12, respectively), a higher number of vertebrae (50-51 vs 47-49), and color differences, especially on the dorsal fin. DNA barcoding analysis supported the status of new species, evidencing a 4.2% and 2.8% divergence with Aulopus filamentosus (Bloch, 1792) and A. bajacali, respectively. A sequence of an Aulopus sp., collected in the Tropical Eastern Pacific, matches the new species with only a 0.4% divergence, indicating that Aulopus chirichignoae sp. nov. is distributed at least as far north as the Paramount Seamount at 3°20.35'N, ca. 400 km north of the Galápagos Islands.}, }
@article {pmid39646945, year = {2024}, author = {Fitrian, T and Rahayu, DL and Ismet, MS}, title = {A new species of hermit crab genus Diogenes Dana, 1851 from Papua, Indonesia (Crustacea, Decapoda, Anomura, Diogenidae).}, journal = {Zootaxa}, volume = {5458}, number = {1}, pages = {130-140}, doi = {10.11646/zootaxa.5458.1.8}, pmid = {39646945}, issn = {1175-5334}, mesh = {Animals ; Indonesia ; *Anomura/anatomy &amp; histology/classification/genetics ; Male ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {A new species of hermit crab from the genus Diogenes Dana, 1851 is described on the basis of a specimen from Papua, Indonesia. Diogenes hawisi n. sp. is distinguished from the closest allied species, D. edwardsii (De Haan, 1849) and D. laevicarpus Rahayu, 1996, by the shape and armature of the left cheliped. Morphological differences of these three species are also supported by genetic analysis, through DNA barcoding using the CO1 gene marker.}, }
@article {pmid39646930, year = {2024}, author = {Kaila, L}, title = {A review of Coelopoetinae (Lepidoptera, Gelechioidea, Pterolonchidae), a moth subfamily confined to western North America, with descriptions of seven new species.}, journal = {Zootaxa}, volume = {5458}, number = {3}, pages = {361-384}, doi = {10.11646/zootaxa.5458.3.3}, pmid = {39646930}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification ; *Animal Distribution ; North America ; Phylogeny ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Systematics and taxonomy of the gelechioid subfamily Coelopoetinae are reviewed. Following the current classification, this group is considered to form its own monotypic subfamily in Pterolonchidae with one recognized genus, Coelopoeta, after a convoluted and, in part, arguably conjectural, historical systematic treatment. On morphological basis (appearance, male genitalia) and with support from DNA barcodes, the genus is divided into two discrete units probably meriting recognition as separate genera. The species groups are informally treated as the nominate C. glutinosi species group, and the C. fissurina species group. In the absence of knowledge of females or the biologies of any of the species of the C. fissurina group, species of both groups are here provisionally included in Coelopoeta. In total, 10 species are recognized, seven of which are here described as new: C. glutinosi species group: C. alboflava Kaila, sp. nov., C. aprica Kaila, sp. nov., C. aurora Kaila, sp. nov., C. fulminea Kaila, sp. nov. and C. sariae Kaila, sp. nov.; C. fissurina species group: C. fissurina Kaila, sp. nov. and C. valalbui Kaila, sp. nov. The three previously known species, C. glutinosi Walsingham, 1907, C. maiadella Kaila, 1995 and C. phaceliae Kaila, 1995 are redescribed. All three of these species belong to the glutinosi species group. A lectotype is designated for C. glutinosi Walsingham, 1907. Some southwestern Coelopoeta species are potentially under threat of decline or even extinction due to the apparently increasingly intense and frequent forest fires. This threat is significant as the species with known life histories spend their entire life cycles above ground in low vegetation.}, }
@article {pmid39646926, year = {2024}, author = {Kim, J and Lee, T}, title = {A new species of Janiralata Menzies, 1951 (Isopoda: Asellota, Janiridae) from Korea.}, journal = {Zootaxa}, volume = {5458}, number = {3}, pages = {427-441}, doi = {10.11646/zootaxa.5458.3.7}, pmid = {39646926}, issn = {1175-5334}, mesh = {*Isopoda/classification/anatomy &amp; histology ; Animals ; Male ; Republic of Korea ; *Animal Distribution ; Female ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Phylogeny ; Electron Transport Complex IV/genetics ; }, abstract = {A new isopod species, Janiralata kwangsooi sp. nov., from Dokdo Island located in the East Sea off the Korean Peninsula is described here. This species is distinguished from its congeners by the number of antennular articles, setation of mouthparts and pereopods, length and width ratio of appendages, and shape of male pleopods I and II. To aid species identification, a taxonomic key to species of Janiralata Menzies, 1951 in the Japanese and Korean waters is provided. A partial sequence of mitochondrial cytochrome-c-oxidase (COI) of this new species is also provided for DNA barcoding and compared with those of congeners publicly available in GenBank.}, }
@article {pmid39646853, year = {2024}, author = {Triberti, P and Staude, H and Sharp, I and Lopez-Vaamonde, C}, title = {Exploring the diversity of Gracillariidae (Lepidoptera) in South Africa: host plants, distribution, and DNA barcoding analysis, with the description of nine new species.}, journal = {Zootaxa}, volume = {5529}, number = {1}, pages = {1-51}, doi = {10.11646/zootaxa.5529.1.1}, pmid = {39646853}, issn = {1175-5334}, mesh = {Animals ; South Africa ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Plants ; Biodiversity ; }, abstract = {Despite relatively extensive historical exploration being carried out on Lepidopteran fauna of South Africa, leaf-mining micromoths of the family Gracillariidae remain a source of discovery, with many new species awaiting description. In the present work, 32 gracillariid species from South Africa are treated. For each species, hostplant and distribution information is provided, supplemented by taxonomic and molecular analysis where necessary. Nine species are described here as new to science: Ectropina spirostachydis sp. nov., Leucocercops curatellifoliae sp. nov., Phodoryctis tephrosiella sp. nov., Telamoptilia cordati sp. nov., Phyllonorycter pseudogrewiella sp. nov., Cameraria melhaniella sp. nov., Phyllocnistis magalismontani sp. nov., P. allisonae sp. nov. and P. faureae sp. nov. Sixteen host plant species are reported for the first time for the family Gracillariidae: Searsia pyroides (Anacardiaceae), Parinari curatellifolia (Chrysobalanaceae), Combretum zeyheri, Terminalia sericea (Combretaceae), Euclea divinorum (Ebenaceae), Spirostachys africana (Euphorbiaceae), Peltophorum africanum, Tephrosia rhodesica, Schotia brachypetala (Fabaceae), Cryptocarya transvaalensis (Lauraceae), Melhania acuminata (Malvaceae), Syzygium guineense (Myrtaceae), Ochna pretoriensis (Ochnaceae), Protea rubropilosa, Faurea saligna (Proteaceae), Englerophytum magalismontanum (Sapotaceae). Caloptilia mwamba De Prins, 2015 is recorded for the first time in South Africa.}, }
@article {pmid39646830, year = {2024}, author = {Orr, AGW and Dow, RA and Steinhoff, POM}, title = {Descriptions of larvae of four mainly DNA barcode-matched species of chlorocyphids from south-east Asia (Odonata: Chlorocyphidae) with notes on the generic and species level larval identification of Oriental region members of the family.}, journal = {Zootaxa}, volume = {5486}, number = {3}, pages = {301-337}, doi = {10.11646/zootaxa.5486.3.1}, pmid = {39646830}, issn = {1175-5334}, mesh = {Animals ; *Larva/anatomy &amp; histology/classification/growth &amp; development/genetics ; Female ; Male ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Asia, Southeastern ; *Odonata/anatomy &amp; histology/classification/genetics/growth &amp; development ; Phylogeny ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {The final stadium larvae of the following four species of south-east Asian Chlorocyphidae are described and compared: Aristocypha fenestrella (Rambur), Heliocypha biseriata (Selys), Libellago hyalina (Selys) and Sundacypha petiolata (Selys), including both sexes for the latter two species. Excepting one L. hyalina specimen from Brunei, identified by supposition based on habitat, all specimens were identified by comparing and matching the mitochondrial marker COI with that of known adult specimens from Sarawak, Brunei and several localities throughout tropical Asia. The specimens presented close matches with all adults in this gene. An assessment of the efficacy of this method of identification is provided, noting that in some cases close species cannot be separated by bar-code matching and ultimate determination is partially based on known distributions of adults. Some aspects of the relationships among genera revealed by the genetic analyses are also discussed. In addition, an exuvia of Libellago lineata (Burmeister) from northern Thailand, identified by supposition, is partially described for the purpose of comparison with L. hyalina. For the morphological analysis the unique features of chlorocyphid anatomy are discussed, and some new terminology is introduced. Overall, the morphological analysis revealed numerous clear differences between the four species studied, and comparisons with available literature suggest that some of these may be characteristic of their genera. It is also evident that in some cases clear interspecific differences occur within genera. It is however concluded that a generic level larval key for the Oriental region Chlorocyphidae based on morphology may never be attainable, although local generic or even species level keys addressing the fauna of limited geographic areas may be possible in many places, especially as the larvae of more species come to be known and described in detail.}, }
@article {pmid39646800, year = {2024}, author = {Ahrens, D and Zhao, MZ and Pham, PV and Liu, WG}, title = {Taxonomic updates on Pachyserica Brenske, 1898 and Serica MacLeay, 1819 reveal 38 new species and new challenges of Sericini systematics regarding DNA barcodes and genus-level diagnostic key characters (Coleoptera: Scarabaeidae: Sericinae).}, journal = {Zootaxa}, volume = {5491}, number = {1}, pages = {1-89}, doi = {10.11646/zootaxa.5491.1.1}, pmid = {39646800}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera/classification/anatomy &amp; histology/genetics ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; }, abstract = {Here we present updates on the taxonomy and distribution of the genera Pachyserica Brenske, 1898 and Serica MacLeay, 1819 from East Asia. Thirty eight new species are desribed from China, Myanmar, South Korea, and Vietnam: Pachyserica chenchangchini Ahrens, Zhao, Pham &amp; Liu, new species, P. dieuthuyae Ahrens, Zhao, Pham &amp; Liu, new species, P. hoabinhensis Ahrens, Zhao, Pham &amp; Liu, new species, P. motuo Ahrens, Zhao, Pham &amp; Liu, new species, P. natmatoung Ahrens, Zhao, Pham &amp; Liu, new species, P. sanqingshanensis Ahrens, Zhao, Pham &amp; Liu, new species, P. sunfengyii Ahrens, Zhao, Pham &amp; Liu, new species, P. tayyentu Ahrens, Zhao, Pham &amp; Liu, new species, P. tianxuani Ahrens, Zhao, Pham &amp; Liu, new species, P. wangzizhaoi Ahrens, Zhao, Pham &amp; Liu, new species, P. yaonani Ahrens, Zhao, Pham &amp; Liu, new species, P. yinhengi Ahrens, Zhao, Pham &amp; Liu, new species, P. zhanbaoxiangi Ahrens, Zhao, Pham &amp; Liu, new species, Serica (s. l.) anhua Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) camura Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) fengxue Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) nhiae Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) paracallosericoides Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) taythien Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) wuyishan Ahrens, Zhao, Pham &amp; Liu, new species, S. (s. l.) yuechengling Ahrens, Zhao, Pham &amp; Liu, new species, S. (Serica) assingi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) bomi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) christophreuteri Ahrens, Zhao, Pham &amp; Liu, Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) cuona Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) fansipan Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) gongtonggouensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) guangxiensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) gwangjuensis Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) hongyii Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) jiangda Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) jiulaoci Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) lushui Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) liyitengi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) qizhihaoi Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) xizang Ahrens, Zhao, Pham &amp; Liu, new species, S. (S.) zhamu Ahrens, Zhao, Pham &amp; Liu, new species, and S. (Taiwanoserica) yexiaohani Ahrens, Zhao, Pham &amp; Liu, new species. The lectotype of Pachyserica scalaris Arrow, 1946 is designated and its male genitalia is illustrated. Additional records of 66 other species are provided.}, }
@article {pmid39646795, year = {2024}, author = {Zhang, JY and Sun, XL and Wang, N and Hao, LI and Ma, CX and Zhao, NA and Li, HP and Zhao, M and Yang, ST}, title = {Tardigrades in the alpine region of Northeast China with an integrative description of Crenubiotus liangshuiensis sp. nov.}, journal = {Zootaxa}, volume = {5492}, number = {1}, pages = {96-108}, doi = {10.11646/zootaxa.5492.1.5}, pmid = {39646795}, issn = {1175-5334}, mesh = {Animals ; *Tardigrada/classification/anatomy &amp; histology ; China ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; DNA Barcoding, Taxonomic ; Ecosystem ; RNA, Ribosomal, 18S/genetics ; Female ; Male ; }, abstract = {A new species of tardigrade, Crenubiotus liangshuiensis sp. nov. (Eutardigrada: Parachela: Macrobiotoidea: Adorybiotidae), was identified by combining DNA barcoding and classical morphological analyses (including both light contrast microscopy and scanning electron microscopy) of animals and an egg found in moss Collected in Yichun Liangshui National Nature Reserve. Moreover, nucleotide sequences of the 18S rRNA and COI markers from used to analyse the diversity of the local tardigrade fauna indicated the presence of at least 16 species representing 11 genera.}, }
@article {pmid39646779, year = {2024}, author = {Liang, QR and Shi, L}, title = {Molecular phylogenetic and historical biogeographical relationships of Laudakia (Squamata: Agamidae) and intraspecific differentiation of L. stoliczkana inferred from mitochondrial DNA sequences.}, journal = {Zootaxa}, volume = {5492}, number = {3}, pages = {325-342}, doi = {10.11646/zootaxa.5492.3.2}, pmid = {39646779}, issn = {1175-5334}, mesh = {Animals ; *Lizards/classification/genetics/anatomy &amp; histology ; *Phylogeny ; *DNA, Mitochondrial/genetics ; *Animal Distribution ; Male ; Female ; China ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; DNA Barcoding, Taxonomic ; }, abstract = {The rock lizard genus Laudakia is representative agamid species from the arid zone, and its genus division has not been resolved yet. Laudakia stoliczkana, which occurs in both Xinjiang, China, and the Gobi Altai, Mongolia, is divided into two subspecies, Laudakia stoliczkana stoliczkana and Laudakia stoliczkana altaica, based on morphological differences, but little is known about the molecular genetic differences between the two subspecies. This study reconstructs the phylogenetic tree of Laudakia and analyses molecular differences between two subspecies of L. stoliczkana by DNA barcoding (COI and 16S). Our results show that: (1) Laudakia is monophyletic and the phylogenetic tree is broadly divided into three main branches, namely branch A (L. caucasia and L. stoliczkana), which occurs mainly in Central Asia and the Gobi Altai region to the north, branch B (L. stellio), which occurs in the Middle East, and branch C (L. tuberculata, L. papenfussi, L. himalayana, L. wui, L. stellio), which occurs mainly near the Himalayas; (2) The biogeographic analysis of Laudakia suggests that the genus probably originated at 43.72 Ma (95% confidence interval HPD: 23.53-66.12Ma) and is associated with the uplift of the Tibetan Plateau and the aridification of Central Asias subsequently; (3) Molecular genetic distances and morphological differences support the delimitation of the two subspecies of L. stoliczkana, with divergence between the two subspecies estimated to have occurred at 3.27 Ma (95% confidence interval HPD: 1.58-5.87Ma), in associated with the recent uplift of the Tian Shan Mountains. The results highlight the importance of the uplift of the Central Asian mountains and the Tibetan Plateau for the divergence of Laudakia.}, }
@article {pmid39646691, year = {2024}, author = {Yu, T and Kallies, A and Arita, Y and He, J and Li, H and Yata, N and Li, X}, title = {Two new species of the genus Taikona Arita &amp; Gorbunov, 2001 (Lepidoptera, Sesiidae) from Yunnan, China.}, journal = {Zootaxa}, volume = {5443}, number = {1}, pages = {135-140}, doi = {10.11646/zootaxa.5443.1.8}, pmid = {39646691}, issn = {1175-5334}, mesh = {Animals ; Male ; China ; *Animal Distribution ; *Moths/anatomy &amp; histology/classification ; Female ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Two new species, Taikona gaoligongshana Yu, Arita &amp; Kallies, sp. nov. and Taikona extraordinaria Yu, Kallies &amp; Arita sp. nov. are described from Yunnan Province, China. Illustrations of the holotypes and the male genitalia are provided, along with a key to all currently known species of the genus. DNA barcoding sequences are also provided.}, }
@article {pmid39646654, year = {2024}, author = {David, KJ and Hancock, DL and Salini, S and Ningthoujam, K and Khemrajji, HN and Abhishek, V and Gracy, RG and Sushil, SN}, title = {New species and new records of fruit flies of tribe Acanthonevrini (Diptera: Tephritidae: Phytalmiinae) from India.}, journal = {Zootaxa}, volume = {5506}, number = {3}, pages = {301-321}, doi = {10.11646/zootaxa.5506.3.1}, pmid = {39646654}, issn = {1175-5334}, mesh = {Animals ; India ; Female ; Male ; *Animal Distribution ; *Tephritidae/classification/anatomy &amp; histology ; *Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Phylogeny ; }, abstract = {Two new species of Phytalmiinae belonging to the tribe Acanthonevrini are described from India, namely Ptilona confracta David &amp; Hancock, sp. nov. from Arunachal Pradesh and Tritaeniopteron obscurum David, Salini &amp; Nikhil, sp. nov. from Karnataka. Tritaeniopteron de Meijere is recorded for the first time from India based on the new species T. obscurum; male and female syntypes of T. punctatipleurum (Senior-White) are dissected and illustrated. A female of Erectovena desperata (Hering), both sexes of Felderimyia gombakensis Hancock &amp; Drew and Phorelliosoma hilaratum Hering, recorded for the first time from India are dissected and illustrated. An illustrated key to 23 species of Acanthonevrini belonging to 12 genera from India is included. DNA barcode sequences of Felderimyia fuscipennis Hendel, Ptilona confracta, P. confinis (Walker), Rioxoptilona dunlopi (van der Wulp) and Themara yunnana Zia were obtained and reported.}, }
@article {pmid39646638, year = {2024}, author = {Teslenko, VA and Palatov, DM and Semenchenko, AA}, title = {Overview of the Caucasian Perla Geoffroy, 1762 (Plecoptera: Perlidae) based on morphological and molecular data with description of two new species.}, journal = {Zootaxa}, volume = {5507}, number = {1}, pages = {1-56}, doi = {10.11646/zootaxa.5507.1.1}, pmid = {39646638}, issn = {1175-5334}, mesh = {Male ; Female ; Animals ; *Insecta/anatomy &amp; histology/classification/growth &amp; development/genetics ; Russia ; *Animal Distribution ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; }, abstract = {Six species of Caucasian Perla are reviewed, and diagnostic morphological characteristics of all stages of development (where possible) are described, supplemented, and illustrated in detail with comparative light microscope and scanning electron microscopy images. The DNA barcoding of five species is presented. Two new morphologically and genetically distinct species, Perla schapsugica sp. nov. and Perla palatovi sp. nov., are described for both sexes and all life stages in the North Caucasus, Russia, Krasnodar Kray. Reinstatement of Perla persica Zwick, 1975, as a valid species distinct from P. caucasica Guérin-Méneville, 1843, is proposed. A new record of P. persica is reported for the Greater Caucasus, Russia, North-Ossetia-Alania for the first time. Morphologically, these two latter species can be separated in male adults by the shape of the hemitergal hook on terga X, an additional ventral brush on the penis of P. caucasica, wing length, and color.}, }
@article {pmid39646583, year = {2024}, author = {DU, H and Liu, J and Heller, K and Shah, B and Wang, Q and Huang, J}, title = {Morphology and DNA barcodes of four species of Bradysia hilaris group from China (Diptera, Sciaridae).}, journal = {Zootaxa}, volume = {5493}, number = {2}, pages = {129-140}, doi = {10.11646/zootaxa.5493.2.2}, pmid = {39646583}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; China ; *Diptera/anatomy &amp; histology/classification/genetics ; *Phylogeny ; Male ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {Four morphologically allied species of the Bradysia hilaris group were studied from China. In a DNA metabarcoding based dipteran diversity study in Zhejiang, eastern China, a hyper-abundant sciarid species was discovered. It was further recognized in this study to be new to science, Bradysia tianmuensis Du &amp; Huang sp. nov., as well as a morphologically similar species, Bradysia curvula Du &amp; Huang sp. nov. Both new species were found to be fairly similar morphologically to the holotype of Bradysia noduspina Yang, Zhang &amp; Yang, 1993 from Guizhou in western China. However, the paratype of B. noduspina appeared to be different from the holotype and determined to be new to science, Bradysia chikunae Du &amp; Huang sp. nov. A phylogenetic tree of all the available 31 COI sequences of the Bradysia hilaris group was provided. Molecular work conducted in the current study also supports Bradysia tianmuensis Du &amp; Huang sp. nov. and Bradysia curvula Du &amp; Huang sp. nov. as new to science thus the four species were described or redescribed accompanied by detailed imagery of habitus and other characters useful for determination.}, }
@article {pmid39646580, year = {2024}, author = {Liu, WB and Wang, CY and Tang, YN and Pei, WX and Yan, CC}, title = {DNA barcodes and morphology reveal new species within the Cryptochironomus Kieffer from Oriental China (Diptera: Chironomidae).}, journal = {Zootaxa}, volume = {5493}, number = {2}, pages = {165-174}, doi = {10.11646/zootaxa.5493.2.5}, pmid = {39646580}, issn = {1175-5334}, mesh = {Animals ; *Chironomidae/classification/anatomy &amp; histology/genetics/growth &amp; development ; Male ; China ; *DNA Barcoding, Taxonomic ; Female ; Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The genus Cryptochironomus has a cosmopolitan distribution including over 140 valid described species worldwide. The morphological characteristics and DNA barcode data of Cryptochironomus inflatus Liu, sp. nov. based on specimens collected from Oriental China. DNA barcode analysis including the partial COI sequences of species of genus Cryptochironomus is conducted. An updated key to adult males of the genus is provided.}, }
@article {pmid39646562, year = {2024}, author = {Makarchenko, EA}, title = {Pseudokiefferiella ferringtoni sp. nov. (Diptera: Chironomidae: Diamesinae) from North America.}, journal = {Zootaxa}, volume = {5493}, number = {4}, pages = {446-450}, doi = {10.11646/zootaxa.5493.4.10}, pmid = {39646562}, issn = {1175-5334}, mesh = {Animals ; Male ; *Chironomidae/classification/anatomy &amp; histology/growth &amp; development/genetics ; North America ; Female ; *Animal Distribution ; *Body Size ; Organ Size ; Pupa/anatomy &amp; histology/classification/growth &amp; development ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {In this article I continue to publish the data obtained as a result of the revision of the subfamily Diamesinae, namely of the genus Pseudokiefferiella Zavřel, 1941. As we noted earlier (Makarchenko &amp; Semenchenko 2023), before the start of molecular genetic study this genus was considered as monotypic, that is, with one species of Ps. parva (Edwards) in Holarctic region (Ashe &amp; O'Connor 2009). According to work of Stur and Ekrem (2020), as well as the results of our research and data of GenBank, there are at least 6 species in the genus Pseudokiefferiella that are well separated by DNA barcoding, while adult males poorly differ morphologically. However, species of this genus can be successfully identified by the morphological structures of the pupa, if it is associated with a male imago. As confirmation of this, below is provided a description of Pseudokiefferiella ferringtoni sp. nov. from North America based on the adult male and pupa, in which the originality of a new species is corroborated by the morphological structures of the pupa.}, }
@article {pmid39646561, year = {2024}, author = {Saha, S and Bogorodsky, SV and Baki, MA and Gao, T and McKay, RJ and Alpermann, TJ and Song, NA}, title = {Assessment of the diversity of the family Sillaginidae in the Indian Ocean with emphasis on the taxonomic identity of Sillago sihama.}, journal = {Zootaxa}, volume = {5493}, number = {5}, pages = {451-485}, doi = {10.11646/zootaxa.5493.5.1}, pmid = {39646561}, issn = {1175-5334}, mesh = {Animals ; Indian Ocean ; *Phylogeny ; *Animal Distribution ; Male ; Female ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Biodiversity ; Ecosystem ; }, abstract = {The present study contributes to the taxonomy of the family Sillaginidae, with comments on the distribution of its species in the Indian Ocean and an emphasis on the taxonomy and distribution of Sillago sihama. Thirty described and putative species with Indian Ocean distribution are listed, and a distribution range for each species is provided based on published data and results from the present study. A comprehensive phylogenetic analysis of the barcoding portion of the mitochondrial COI gene is provided together with three approaches for molecular species delimitation, which includes 44 to 47 genetic lineages (depending on the species delimitation approach used) in the family Sillaginidae, 33 of them applying to described species and also 8 putative species, formerly misidentified as S. sihama. Inclusion of specimens from South Africa, Iran, Pakistan, India, Bangladesh and the southern Red Sea (type locality) reveals one genetic lineage representing the true Sillago sihama. Distribution of the species is confined to the Red Sea and the Indian Ocean, and other records under the name S. sihama are based on misidentifications. Several undescribed species identified as S. sihama are distributed in the Indo-West Pacific region and closely resemble S. sihama, but are not identical with this species and can be identified as members of different evolutionary lineages. Two species, S. sihama and S. soringa, reported from Bangladesh, represent the easternmost record of both species. These two species are described in detail, including swimbladder morphology. The study also shows that specimens from India identified as Sillago ingenuua McKay, 1985 are nested within a lineage previously referred to as S. ingenuua A, but are different from the lineage S. ingenuua B, representing a confirmed record of the clade S. ingenuua in the northern Indian Ocean. Comments on misidentifications of S. sihama from the Indian Ocean and western Pacific are provided. Furthermore, we propose that Sillago erythraea should be resurrected from its synonymy with S. sihama. As Sillago suezensis is identical with the former species, it becomes a junior synonym of S. erythraea.}, }
@article {pmid39646546, year = {2024}, author = {Li, D and Xia, L and Wang, H}, title = {DNA barcodes and morphological evidence reveal a new genus of Nygmiini (Lepidoptera: Erebidae: Lymantriinae) from China.}, journal = {Zootaxa}, volume = {5496}, number = {1}, pages = {101-110}, doi = {10.11646/zootaxa.5496.1.5}, pmid = {39646546}, issn = {1175-5334}, mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics/growth &amp; development ; *Animal Distribution ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {A new genus Aurivalva Li &amp; Wang gen. nov. is proposed for Nygmiini to accommodate three species previously placed in Euproctis Hübner: A. yunnanpina (Chao, 1984) comb. nov., A. telephanes (Collenette, 1939) comb. nov. and A. conistica (Collenette, 1936) comb. nov.. The new genus is supported by DNA barcodes and morphological evidence. A key to all currently recognized Aurivalva species in China is provided, with illustrations of the adults, wing venations and genitalia, together with a barcode-based tree.}, }
@article {pmid39646525, year = {2024}, author = {Shah, B and Shao, Y and DU, H and Wang, Y and Huang, J}, title = {Taxonomy and DNA barcoding of the dark-winged fungus gnat genus Zygoneura Meigen (Diptera: Sciaridae) from China, with revision of the type materials.}, journal = {Zootaxa}, volume = {5496}, number = {3}, pages = {377-400}, doi = {10.11646/zootaxa.5496.3.5}, pmid = {39646525}, issn = {1175-5334}, mesh = {Animals ; China ; Male ; *DNA Barcoding, Taxonomic ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Phylogeny ; Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {The genus Zygoneura Meigen is revised thoroughly from China, and 14 species are recognized and illustrated, including four new species: Zygoneura (Allozygoneura) xizangensis Shah &amp; Huang sp. nov., Zygoneura (Pharetratula) minuscula sp. nov., Zygoneura (Pharetratula) motuoensis sp. nov. and Zygoneura (Pharetratula) yangi sp. nov. In addition, Zygoneura (Pharetratula) divergens (Mamaev), Zygoneura (Pharetratula) flavicornis (Mamaev), and Zygoneura (Pharetratula) subdivergens (Mohrig &amp; Mamaev) are reported for the first time from China. The identification of these species is supported by both morphological characteristics and sequence data obtained from cytochrome oxidase subunit one (COI) in the DNA barcode analysis. Furthermore, a checklist of the known Zygoneura species in China is also provided, along with an identification key for males.}, }
@article {pmid39646519, year = {2024}, author = {Almeida, LH and Duarte, T and Bispo, PDC}, title = {Complementary studies of the Perlidae (Insecta: Plecoptera) fauna from the Paranapiacaba Mountains using DNA barcode data.}, journal = {Zootaxa}, volume = {5496}, number = {4}, pages = {500-508}, doi = {10.11646/zootaxa.5496.4.2}, pmid = {39646519}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Brazil ; Female ; Male ; *Animal Distribution ; Phylogeny ; Insecta/classification/anatomy &amp; histology/genetics ; Nymph/anatomy &amp; histology/classification/growth &amp; development/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The Paranapiacaba Mountains are a region of Brazil where the stonefly fauna is relatively well known. Despite this, there are still gaps in knowledge that need to be filled. In this study, through field sampling and molecular analyses, we have updated the taxonomic knowledge of Perlidae species in this region. Our study employed DNA barcoding methods to complement traditional morphological approaches, facilitating the association and description of the nymphs of Anacroneuria itajaimirim Bispo &amp; Froehlich 2004. Additionally, we generated DNA barcode sequences for Anacroneuria iporanga Bispo &amp; Froehlich 2004. Our results contributed to knowledge about Perlidae from the Paranapiacaba Mountains, highlighting the importance of DNA barcode data in the association of immature stages and species delimitations. Although the stoneflies of Paranapiacaba Mountains have been relatively well-studied, our results reveal that we still have deficits in knowledge of the fauna of this region.}, }
@article {pmid39646485, year = {2024}, author = {Gordon, ML and Colville, JF and Engelbrecht, A and Couldridge, VCK}, title = {Ancient Grasshoppers: A revision of the genus Bullacris (Orthoptera: Pneumoridae).}, journal = {Zootaxa}, volume = {5474}, number = {4}, pages = {301-354}, doi = {10.11646/zootaxa.5474.4.1}, pmid = {39646485}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Grasshoppers/anatomy &amp; histology/classification/genetics ; *Phylogeny ; *Animal Distribution ; Body Size ; Organ Size ; South Africa ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The genus Bullacris in the family Pneumoridae was most recently revised by Dirsh in 1965 based on morphological comparisons between species. However, since that time, new information about the genus and the family has come to light, necessitating a revision of the genus. In addition, the species B. boschimana was originally described based on a single female specimen. Here we present and describe the male of the species for the first time. The aim of this study was to update the current species descriptions by including additional specimens and incorporating additional methods for a more comprehensive comparison. Analyses consisted of morphometric measurements from high-quality images of type specimens, existing South African museum specimens, as well as personally collected specimens. Acoustic signals are also presented and compared between species. In addition, phylogenetic analyses were conducted on the barcoding mitochondrial gene COI and two nuclear genes, namely ITS and 18S. Results show that according to morphological, acoustic and genetic data, B. discolor and B. serrata as well as B. intermedia and B. membracioides share notable similarities. Bullacris discolor and B. serrata share similar phenotypic traits, in which B. discolor can either appear uniform in colour or have a speckled variation that is very similar in appearance to B. serrata. Bullacris intermedia and B. membracioides have a 5% mitochondrial DNA pairwise distance, suggesting that they may have not be fully diverged; however, morphological analysis shows that these species are morphologically distinguishable. It is suggested that these species may have undergone spatial separation at one point; however, further investigation is required. Additional sampling across a wider geographic range is essential to clarify the relationships between B. discolor and B. serrata, as well as between B. intermedia and B. membracioides.}, }
@article {pmid39646451, year = {2024}, author = {Jimenez, PJ and Chang, K and Shih, HT and Yasuhara, M}, title = {Confirming the occurrence of two fiddler crabs, Tubuca dussumieri (H. Milne Edwards, 1852) and T. coarctata (H. Milne Edwards, 1852) (Crustacea: Decapoda: Ocypodidae), in Hong Kong by DNA barcoding and morphology.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {177-191}, doi = {10.11646/zootaxa.5476.1.17}, pmid = {39646451}, issn = {1175-5334}, mesh = {Animals ; *Brachyura/classification/anatomy &amp; histology/genetics ; Male ; Female ; Hong Kong ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Body Size ; Ecosystem ; Organ Size ; Phylogeny ; Electron Transport Complex IV/genetics ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The Indo-West Pacific region has a rich fiddler crab fauna. In East Asia, some species of fiddler crabs, such as Tubuca coarctata (H. Milne Edwards, 1852) and T. dussumieri (H. Milne Edwards, 1852), are considered insular, being present in the Philippines, Taiwan, and Ryukyus, but with no consistent record on continental China. Although T. dussumieri has been previously recorded in continental China, these records were considered dubious or misidentified. The nature of the Kuroshio Current and the colder waters of the China Coastal Current, compared to the currents along the eastern coasts of the Philippines and Taiwan, are considered barriers to the entrance of larvae of these species into the region. Nonetheless, using the cytochrome oxidase subunit I (COI) gene and morphological evidence, we present the first record of T. coarctata and show the presence of a T. dussumieri population in Hong Kong SAR, China. We hypothesize that the newly found T. coarctata in Hong Kong may be related to water temperature increases due to anthropogenic climate change, which allows its larvae to survive in this region and develop into adult crabs. Furthermore, our findings corroborate previous records of T. dussumieri in continental China. The restricted distribution of T. dussumieri in China and the smaller size of individuals, however, may indicate suboptimal habitats for arriving larvae. The limited presence of the two crabs on Chinese shores indicates that the intense coastal development in the country, such as in Hong Kong, may destroy suitable habitats and render these species susceptible to local extinction.}, }
@article {pmid39646447, year = {2024}, author = {Ma, L and Wu, Y and Li, XZ}, title = {A new species of the genus Porirualia Huys &amp; Mu, 2021 (Copepoda, Harpacticoida, Parastenheliidae) from the intertidal zone of Qingdao, China, with a key to species of the genus.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {241-252}, doi = {10.11646/zootaxa.5476.1.21}, pmid = {39646447}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; China ; *Animal Distribution ; *Copepoda/classification/anatomy &amp; histology/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Ecosystem ; Phylogeny ; }, abstract = {A new species belonging to the genus Porirualia Huys &amp; Mu, 2021 was identified and described here based on samples collected from No. 1 Bathing Beach, Qingdao, China. The new species differs from Porirualia pyriformis mainly in the following characteristics: P3 and P4 exp-3 with three inner setae (two inner setae in P. pyriformis), ratio of length to maximum width of female P5 3.83 (3.25 in P. pyriformis). The new species differs from Porirualia megarostrum by the characters including rostrum reaching to distal margin of third segment of antennule (reaching to distal margin of fifth segment of antennule in P. megarostrum), ratio of length to maximum width of female P5 3.83 (2.2 in P. megarostrum); male P2 and P3 two-segmented (three-segmented in P. megarostrum); male P5 bearing five elements (six in P. megarostrum). This is the first report of the genus Porirualia from the China Seas. The DNA barcode (COI) sequence of the new species was obtained and submitted to GenBank (PP761118), which is the first submission of COI sequence of the family Parastenheliidae to GenBank.}, }
@article {pmid39646433, year = {2024}, author = {Wong, KJH and Meij, SETV and Chan, BKK}, title = {A new species of coral-dwelling crab (Decapoda: Brachyura: Cryptochiridae: Opecarcinus) from the West Pacific.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {474-504}, doi = {10.11646/zootaxa.5476.1.35}, pmid = {39646433}, issn = {1175-5334}, mesh = {Animals ; *Brachyura/classification/anatomy &amp; histology/genetics ; Female ; Male ; *Animal Distribution ; *Body Size ; *Anthozoa/classification/anatomy &amp; histology ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Taiwan ; Pacific Ocean ; Phylogeny ; }, abstract = {Based on material acquired from Green Island, Taiwan, using a combined approach of traditional morphology-based taxonomy and molecular barcoding, we describe a new species of coral-dwelling crab, Opecarcinus ngankeeae sp. nov., from the scleractinian hosts Pavona decussata and P. varians (family Agariciidae). The DNA sequences of the present species matched with O. sp. SET6, associated with plate-forming Leptoseris and Pavona corals, available on Genbank, provided by Xu et al. (2022). The geographical distribution of O. ngankeeae sp. nov. spans from the Coral Triangle and Taiwan to Japan in West Pacific.}, }
@article {pmid39646432, year = {2024}, author = {Yang, CH and Kumar, AB and Chan, TY}, title = {On the differences between the two widely distributed and closely related rock shrimps Sicyonia japonica Balss, 1914 and S. parajaponica Crosnier, 2003 (Dendrobranchiata, Penaeoidea, Sicyoniidae), with a new record of S. japonica from Taiwan.}, journal = {Zootaxa}, volume = {5476}, number = {1}, pages = {505-513}, doi = {10.11646/zootaxa.5476.1.36}, pmid = {39646432}, issn = {1175-5334}, mesh = {Animals ; Taiwan ; Male ; Female ; *Animal Distribution ; Penaeidae/classification/anatomy &amp; histology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The rock shrimp Sicyonia japonica Balss, 1914 is recorded from Taiwan for the first time. The availability of many fresh specimens of S. japonica and S. parajaponica Crosnier, 2003 from various localities in the Indo-West Pacific allowed a detailed comparison of the morphology, fresh coloration and genetics between these two closely related species. Their major differences are illustrated by line drawings, micro-computed tomography (micro-CT) images and color photographs. DNA barcoding comparison supports the specific status of these two species and reveals that the western Indian Ocean material of S. japonica may represent another cryptic taxon.}, }
@article {pmid39646412, year = {2024}, author = {Radashevsky, VI and Al-Kandari, M and Malyar, VV and Pankova, VV}, title = {A twin of Polydora hoplura (Annelida: Spionidae) from the Arabian (Persian) Gulf, with review of primers used for barcoding of Spionidae.}, journal = {Zootaxa}, volume = {5529}, number = {2}, pages = {245-268}, doi = {10.11646/zootaxa.5529.2.2}, pmid = {39646412}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Polychaeta/classification/genetics/anatomy &amp; histology ; *Phylogeny ; Male ; Indian Ocean ; Female ; Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; }, abstract = {The spionid polychaete Polydora hoplura Claparède, 1868 has been widely recorded boring in shells of abalone, oysters, clams, barnacle tests and sponges in temperate and subtropical waters. Molecular studies have suggested conspecificity of individuals collected worldwide but showed high genetic variability of the species with the highest diversity of haplotypes in the South African population. We have compared the morphology and genetic data of shell-boring worms from Kuwait, which were previously assigned to P. hoplura, with American, Asian and European individuals, including those from the type locality in Italy. The Kuwaiti individuals share key diagnostic morphological characters with P. hoplura but differ in ochre pigment on the anterior chaetigers in life, pattern of pigmentation after fixation in formalin, and pattern of methyl green staining of fixed specimens. They also differ in the dimensions of mature spermatozoa. The analysis of sequence data of five gene fragments (total 3483 bp) showed that the intraspecific diversity of P. hoplura and the variability of Polydora individuals from Kuwait are less than the divergences in all studied genes, except for 28S rDNA, between these two groups. These data, as well as the absence of common cytochrome c oxidase subunit I (COI) and 16S haplotypes, and morphological differences between individuals from Kuwait and P. hoplura, allowed us to conclude that the Kuwaiti population is not conspecific with P. hoplura. This conclusion was confirmed by the results of the species delimitation analysis. In the Bayesian inference analysis of the sequence data individuals from Kuwait formed a well-supported clade sister to P. hoplura. These individuals are described and illustrated here as a new species, Polydora mohammadi sp. nov. Primers used for successful amplification of the mitochondrial COI gene in various species of Spionidae are reviewed and we suggest future studies on Polydora use a combination of two primer pairs (2F-spionid-LCO/1R-spionid-HCO and Dorid_COI.3F/Dorid_COI.1R) to target sequences that include the barcode fragments covered with "Folmer" and "Dorid" primers.}, }
@article {pmid39646401, year = {2024}, author = {Wesener, T}, title = {Five new species and numerous locality records of Spirobolida millipedes from Madagascar (Diplopoda, Spirobolida, Pachybolidae).}, journal = {Zootaxa}, volume = {5529}, number = {3}, pages = {461-486}, doi = {10.11646/zootaxa.5529.3.3}, pmid = {39646401}, issn = {1175-5334}, mesh = {Madagascar ; Animals ; Male ; *Animal Distribution ; Female ; *Arthropods/classification/anatomy &amp; histology ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Ecosystem ; }, abstract = {Based mainly on the results of generalized American biodiversity inventory programmes, several samples of Malagasy Spirobolida millipedes became available to study. Based on this material, five new species of Spirobolida are described from Madagascar: four potential microendemic species, Aphistogoniulus amberivery sp. nov. from the Amberivery forest, A. manombo sp. nov., from the lowland rainforest of Manombo, Spiromimus endemicus sp. nov. from the Montagne des Français, and a species from the littoral forest of Tampolo, tentatively placed in the genus Eucarlia Brölemann, 1913, E. tampolo sp. nov.. A fifth species appears to be more widespread and is a morphologically unusual species of the genus Alluviobolus Wesener, 2009, A. omega sp. nov.. Aphistogoniulus manombo sp. nov. was previously described as a population of A. jeekeli Decker &amp; Wesener, 2011. One of the most enigmatic Malagasy millipede species, Spirobolus olympiacus Karsch, 1881, is redescribed based on topotypic material as Colossobolus olympiacus (Karsch, 1881) new combination. Additional locality data is provided for 14 other Spirobolida species, of which 11 are listed on the IUCN Red List: Aphistogoniulus aridus Wesener, 2009, A. diabolicus Wesener, 2009, A. erythrocephalus (Pocock, 1893), A. hova (de Saussure &amp; Zehntner, 1897), Colossobolus semicyclus Wesener, 2009, Spiromimus albipes Wesener &amp; Enghoff, 2009, S. litoralis Wesener &amp; Enghoff, 2009, S. simplex Wesener &amp; Enghoff, 2009, S. triaureus Wesener &amp; Enghoff, 2009, S. univirgatus deSaussure &amp; Zehntner, 1901, Flagellobolus pauliani Wesener, 2009, Dactylobolus bivirgatus (Karsch, 1881), Madabolus maximus Wesener &amp; Enghoff, 2008 and Hylekobolus rufus Wesener, 2009. Fourteen new genetic barcoding COI sequences are provided for nine species: Hylekobolus rufus, Colossobolus semicyclus, Aphistogoniulus amberivery sp. nov., A. aridus, A. diabolicus, A. erythrocephalus, A. hova, Spiromimus univirgatus and S. scapularis Wesener &amp; Enghoff, 2009.}, }
@article {pmid39646399, year = {2024}, author = {Zuñiga, R and Valerio, AA and Hanson, P and Smith, MA and Hallwachs, W and Janzen, DH}, title = {Cryptic diversity of Leurus wasps (Hymenoptera: Ichneumonidae: Metopiinae), parasitoids of caterpillars in Area de Conservación Guanacaste, Costa Rica.}, journal = {Zootaxa}, volume = {5529}, number = {3}, pages = {511-531}, doi = {10.11646/zootaxa.5529.3.5}, pmid = {39646399}, issn = {1175-5334}, mesh = {Animals ; Costa Rica ; *Wasps/anatomy &amp; histology/classification ; Male ; Female ; *Larva/anatomy &amp; histology/growth &amp; development ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Moths/anatomy &amp; histology/parasitology ; Ecosystem ; }, abstract = {As a consequence of COI barcoding hundreds of reared specimens of what appeared to be Leurus caeruliventris, a parasitoid of leaf-rolling Crambidae (Lepidoptera) from the Area de Conservación Guanacaste, northwestern Costa Rica, and matching them with their host caterpillars and morphological traits, we describe ten new sympatric species and redescribe L. caeruliventris. The new species, authored by Zuñiga &amp; Valerio, are: Leurus billeberhardi, L. henrytownesi, L. hugokonsi, L. iangauldi, L. jesusugaldei, L. marjorietownesae, L. maryjanewestae, L. pammitchellae, L. sondrawardae, and L. wahli. We also provide an illustrated key to the eleven species and an ecological glimpse into the lives of these very similar wasp species.}, }
@article {pmid39646383, year = {2024}, author = {Haÿ, V and Mennesson, MI and Dahruddin, H and Sauri, S and Limmon, G and Wowor, D and Hubert, N and Keith, P and Lord, C}, title = {A new freshwater pipefish species (Syngnathidae: Microphis) from the Sunda shelf islands, Indonesia.}, journal = {Zootaxa}, volume = {5536}, number = {1}, pages = {139-152}, doi = {10.11646/zootaxa.5536.1.5}, pmid = {39646383}, issn = {1175-5334}, mesh = {Animals ; Indonesia ; Male ; Female ; *Animal Distribution ; *Smegmamorpha/genetics/classification/anatomy &amp; histology ; Islands ; Phylogeny ; Organ Size ; Fresh Water ; Body Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {A new species of freshwater pipefish, Microphis arrakisae sp. nov., is described from the West Indonesian Islands (Java, Bali and Lombok). This species is morphologically very close to Microphis retzii (Bleeker, 1856), which is found in the eastern Indonesian Islands (Sulawesi, Ceram, Ambon and Papua). However, it can be distinguished by its in vivo coloration. Furthermore, genetic analysis of the partial COI gene (barcoding) indicates that it represents a distinct genetic lineage in the Indonesian region.}, }
@article {pmid39646344, year = {2024}, author = {Selis, M and Fateryga, AV and Cilia, G}, title = {The genus Euodynerus Dalla Torre in Europe and the Maghreb (Hymenoptera: Vespidae: Eumeninae).}, journal = {Zootaxa}, volume = {5537}, number = {2}, pages = {151-194}, doi = {10.11646/zootaxa.5537.2.1}, pmid = {39646344}, issn = {1175-5334}, mesh = {Animals ; Europe ; *Wasps/anatomy &amp; histology/classification ; Male ; Female ; *Animal Distribution ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Phylogeny ; DNA Barcoding, Taxonomic ; }, abstract = {The genus Euodynerus Dalla Torre, 1904 (= Extraepipona Gusenleitner, 2014, syn. nov.; Euodynerus occultus (Gusenleitner, 2014), comb. nov.) is revised in Europe and the Maghreb, combining morphological data and DNA barcoding. New synonymies are proposed for E. (Pareuodynerus) Blüthgen, 1938 (= E. (Incolepipona) Giordani Soika, 1994, syn. nov.), E. annae (Kostylev, 1937) (= Euodynerus shirazensis Giordani Soika, 1970, syn. nov.), E. caspicus (Morawitz, 1873) (= Euodynerus caspicus armeniacus Gusenleitner, 2016, syn. nov.), E. curictensis Blüthgen, 1940 (= Euodynerus curictensis sardous Borsato, 2006, syn. nov.), E. dantici (Rossi, 1790) (= Euodynerus dantici poggii Giordani Soika, 1986, syn. nov.; = Euodynerus minoricensis Sanza, 2003, syn. nov.), E. quadrifasciatus (Fabricius, 1793) (= Euodynerus quadrifasciatus atripes Giordani Soika, 1976, syn. nov.; = Euodynerus quadrifasciatus rufipes Gusenleitner, 1984, syn. nov.; = Euodynerus quadrifasciatus eburnus Yamane, 1987, syn. nov.), E. rubrosignatus Gusenleitner, 1984, stat. nov. (= Euodynerus notatus cyrenaicus Giordani Soika, 1986, syn. nov.) and E. variegatus (Fabricius, 1793) (= Odynerus crenatus kruegeri von Schulthess, 1928, syn. nov.). Euodynerus quadrifasciatus rubrosignatus Gusenleitner, 1984 is raised to species-level (E. rubrosignatus, stat. nov.), and E. bidentoides (Giordani Soika, 1953), sp. resurr. is removed from synonymy with E. bidentiformis (Giordani Soika, 1942). Euodynerus bidentatus (Lepeletier, 1841) is transferred from the subgenus Pareuodynerus to Euodynerus s. str. A key for the identification of the Euro-Maghrebi species of Euodynerus and reference photos for each species are provided.}, }
@article {pmid39646260, year = {2024}, author = {Makarchenko, EA and Semenchenko, AA and Krasheninnikov, AB and Yanygina, LV and Yavorskaya, NM}, title = {Review of archaic nymphomyiids (Diptera, Nymphomyiidae) of the Russian Far East and bordering territories, with describing of new taxa and DNA barcoding of known species.}, journal = {Zootaxa}, volume = {5448}, number = {2}, pages = {183-211}, doi = {10.11646/zootaxa.5448.2.2}, pmid = {39646260}, issn = {1175-5334}, mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; Female ; *Diptera/classification/anatomy &amp; histology/genetics ; *Animal Distribution ; Russia ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Ecosystem ; }, abstract = {Nymphomyiidae from the Russian Far East and bordering territories are revised, including data on taxonomy, redescriptions, and results of DNA barcoding. Nymphomyia orientalis sp. nov. with two subspecies N orientalis orientalis subsp. nov. and N. orientalis makcha subsp. nov. are described and information on biology, ecology and distribution are presented. Key of Nymphomyia species for adult males and females of the world is provided. Three species delimitation approaches (ASAP, mPTP, GMYC) using the mitochondrial gene cytochrome c oxidase I (COI) confirm validity of described taxa as well as available nymphomyiids in GenBank. Morphologically indistinguishable specimens of N. orientalis sp. nov. from Makcha and Polovinka rivers belongs to separate mOTUs with the lowest distances in the genus 1.99% that is the lower interspecific threshold.}, }
@article {pmid39646227, year = {2024}, author = {Sanz-Veiga, PA and Leivas, FWT and Díaz-Grisales, V and Anzaldo, S and Rosado-Neto, GH and Lampert, S and Maggio, DH and Corrêa, AS and Savaris, M}, title = {Sympatric species of Heilipus Germar (Coleoptera: Curculionidae: Hylobiini) on fruits of Lauraceae: a new species from Brazil and redescription of Heilipus draco (Fabricius, 1801).}, journal = {Zootaxa}, volume = {5463}, number = {1}, pages = {63-83}, doi = {10.11646/zootaxa.5463.1.4}, pmid = {39646227}, issn = {1175-5334}, mesh = {Animals ; Brazil ; *Weevils/anatomy &amp; histology/classification ; Male ; Female ; *Animal Distribution ; *Fruit ; Lauraceae/classification ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Body Size ; Sympatry ; }, abstract = {The genus Heilipus Germar (Curculionidae: Hylobiini) is an American weevil group with 89 described species, of which 28 species are known from Brazil. Here, we describe a new species of Heilipus from Brazil and redescribe H. draco (Fabricius, 1801). Heilipus vividaensis Sanz-Veiga, Savaris &amp; Leivas, sp. nov. and H. draco are similar sympatric species, reared from fruits of Ocotea puberula (Rich.) Nees and Nectandra angustifolia (Schrad.) Nees &amp; Mart. (Lauraceae) in south and southeast Brazil. External morphological and genitalia descriptions, illustrations, distribution records, notes on the host plant, and a barcode DNA sequence are provided for both species.}, }
@article {pmid39646215, year = {2024}, author = {Lee, I and Park, KH}, title = {A new species of Homidia (Collembola: Entomobridae) from Korea, with notes on its DNA data.}, journal = {Zootaxa}, volume = {5463}, number = {2}, pages = {262-272}, doi = {10.11646/zootaxa.5463.2.6}, pmid = {39646215}, issn = {1175-5334}, mesh = {Animals ; Republic of Korea ; *Arthropods/classification/anatomy &amp; histology/genetics ; Male ; Female ; *DNA Barcoding, Taxonomic ; Animal Distribution ; Phylogeny ; Organ Size ; Electron Transport Complex IV/genetics ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {A new species, Homidia pseudokoreana sp. nov., from South Korea described based on morphological data and DNA barcodes. This species is morphologically characterized by the body color pattern with a longitudinal dark stripe on medial area of Th. II to Th. III, coxal macrochaetal formula as 3/4+1,3/4+2, and unguis III with three inner teeth. In this study, DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI) gene were used as DNA barcode to distinguish species. It showed distinct differences in genetic distances between Homidia species. DNA barcoding was a useful tool when identifying morphologically closely related species in Homidia.}, }
@article {pmid39646203, year = {2024}, author = {Bahder, BW and Myrie, W and Helmick, EE and Bartlett, CR}, title = {A new species of planthopper in the genus Patara (Hemiptera: Auchenorrhyncha: Fulgoroidea: Derbidae) from central Jamaica.}, journal = {Zootaxa}, volume = {5463}, number = {3}, pages = {429-440}, doi = {10.11646/zootaxa.5463.3.8}, pmid = {39646203}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/classification/anatomy &amp; histology/genetics ; Male ; Female ; Jamaica ; *Animal Distribution ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {During survey work for planthoppers associated with palms in Jamaica, one new species of Patara was collected at the Castleton Botanic Garden and is here described as Patara euryfrons sp. n. The species is unusual in having a much broader head than is normally found in members of the genus. Supplementary molecular data for the barcoding region (5' half) of the cytochrome c oxidase subunit I (COI), 18S rRNA gene and D9-D10 expansion region of the 28S rRNA gene is provided to support the placement of the novel taxon in Patara.}, }
@article {pmid39646164, year = {2024}, author = {Lukhtanov, VA and Botman, RV and Gagarina, AV}, title = {DNA barcode based phylogeographic analysis of the Aricia anteros (Freyer, 1838) species complex (Lepidoptera: Lycaenidae) with description of a new subspecies from SE Europe.}, journal = {Zootaxa}, volume = {5468}, number = {3}, pages = {505-522}, doi = {10.11646/zootaxa.5468.3.5}, pmid = {39646164}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Phylogeography ; Male ; *Animal Distribution ; Female ; Europe ; Butterflies/classification/genetics/anatomy &amp; histology ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; }, abstract = {The complex of taxa closely related to Aricia anteros includes the species A. anteros sensu stricto, A. crassipuncta, A. bassoni, and A. vandarbani. All of them are sometimes considered as subspecies of a single polytypic species. Representatives of this complex are found in the Balkan Peninsula, Asia Minor, the Levant, the Caucasus, Transcaucasia, and Northern and Western Iran. In addition, an isolated population of A. anteros occurs in the Northern Black Sea region. In this work, based on DNA barcodes of all species and main populations of the complex, we show the existence of seven differentiated mitochondrial lineages: anteros (predominant in the Balkans), crassipuncta (predominant in Asia Minor), bassoni (the Levant), vandarbani (Talysh Mts), varicolor (Zagros Mts), dombaiensis (the Caucasus) and kalmius (Kalmius River basin in the Northern Black Sea region). The taxa of the A. anteros species complex are allopatric, except for A. anteros s.s. and A. crassipuncta, which have a mosaic distribution in eastern Anatolia and Transcaucasia. On the Balkan Peninsula, within the species A. anteros s.s, both the anteros and the crassipuncta mitochondrial haplogroups are found. This pattern is likely a consequence of interspecific hybridization and mitochondrial introgression. Based on mitochondrial DNA, the taxon A. crassipuncta mehmetcik from SE Anatolia is indistinguishable from A. crassipuncta crassipuncta, and the taxon varicolor from Central Iran is closer to the geographically distant European A. anteros than to the Anatolian A. crassipuncta. The geographically isolated and genetically differentiated population from the Kalmius River basin in the Northern Black Sea region is described here as a new subspecies.}, }
@article {pmid39646142, year = {2024}, author = {Wesener, T}, title = {Integrative redescription of Glomeris cingulata C. L. Koch, 1847, an almost forgotten microendemic pill millipede (Diplopoda, Glomerida, Glomeridae).}, journal = {Zootaxa}, volume = {5541}, number = {3}, pages = {326-338}, doi = {10.11646/zootaxa.5541.3.4}, pmid = {39646142}, issn = {1175-5334}, mesh = {Animals ; *Arthropods/classification/anatomy &amp; histology ; Male ; Female ; *Animal Distribution ; *Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Slovenia ; Ecosystem ; }, abstract = {Among the more than 80 species of the common pill millipede genus Glomeris Latreille, 1803, there are several microendemic species that have not been recorded for the last 80-120 years. To discover whether these species are colour morphs of widespread species or true local endemics is important from a conservation point of view as well as for understanding the biogeography and evolution of the group. The author received three specimens that were morphologically identical to C. L. Koch's 175-year-old first description of Glomeris cingulata Koch, 1847 from the Triglav Mountain in Slovenia, close to the border with Italy. No clear specimen-based records are available for G. cingulata and the type specimen is apparently lost. In order to clarify the taxonomy of this microendemic species, an integrative redescription was conducted, including scanning electron microscopy and DNA barcoding. Glomeris cingulata is a distinct species, with genetic distances of 12.6-15.5% compared to the seven syntopic and numerous other widespread Glomeris species. Based on characters of the first description and following other authors, the synonymy of Glomeris cingulata intercedens Latzel, 1884 under Glomeris transalpina Koch, 1836 is confirmed. The dark colour with posterior red bands closely resembles that of some other high-altitude Glomeris species like G. transalpina Koch, 1836, Glomeris aurita Koch, 1847 and Glomeris oropensis Verhoeff, 1936. Glomeris cingulata is genetically close to, but distant enough from the small-bodied and widespread taxa like Glomeris pustulata Latreille, 1804 and Glomeris tetrasticha Brandt, 1833.}, }
@article {pmid39646033, year = {2024}, author = {Krupitsky, AV and Naderi, A and Hagen, WT and Lukhtanov, VA and Nazari, V}, title = {New data on distribution of Phoenicurusia transcaucasicus (Miller, 1923) (Lepidoptera, Lycaenidae) with description of a new subspecies from Iran.}, journal = {Zootaxa}, volume = {5481}, number = {3}, pages = {373-383}, doi = {10.11646/zootaxa.5481.3.6}, pmid = {39646033}, issn = {1175-5334}, mesh = {Animals ; Iran ; Male ; Female ; *Animal Distribution ; *Phylogeny ; Butterflies/anatomy &amp; histology/classification/genetics/growth &amp; development ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Distribution of Phoenicurusia transcaucasicus (Miller, 1923) in Iran and neighbouring territories is clarified based on analysis of DNA barcodes, the male genitalia and wing pattern of adults. Our study revealed the widespread distribution of Ph. transcaucasicus throughout northern, northeastern and central Iran. Based on integrative analysis, a new subspecies, Ph. transcaucasicus flamma ssp. n., is described from the Zagros Mountains, the Central Iranian Range and the Alborz Mountains. Compared to the nominotypical subspecies, the new subspecies differs in well-developed orange pattern both of dorsal and ventral sides of the wings, shape of the valva in the male genitalia and distinct COI haplotypes. Additionally, distinct phylogenetic lineage of Ph. transcaucasicus is reported from Kerman Province. Diagnostic characters of the species of Ph. phoenicurus (Lederer, 1870) group of Iran are illustrated.}, }
@article {pmid39646026, year = {2024}, author = {Baldizzone, G and Huemer, P}, title = {Coleophora elea Baldizzone &amp; Huemer, new species of the Coleophora oriolella Zeller, 1849 species-group (Lepidoptera, Coleophoridae).}, journal = {Zootaxa}, volume = {5481}, number = {4}, pages = {463-470}, doi = {10.11646/zootaxa.5481.4.4}, pmid = {39646026}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Moths/anatomy &amp; histology/classification/genetics ; *Animal Distribution ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; }, abstract = {Coleophora elea Baldizzone &amp; Huemer, sp. nov., is described based on specimens collected from the Peloponnese peninsula (Greece). This species is closely related to C. oriolella Zeller, 1849, but it differs in external appearance and in characters of the male and female genitalia. Additionally, the two species are genetically distinct as evidenced by a p-distance of approximately 4% between their DNA barcodes (cytochrome c-oxidase subunit 1). Adult specimens and the genitalia of both species are illustrated for comparative purposes.}, }
@article {pmid39646024, year = {2024}, author = {Makarchenko, EA and Semenchenko, AA and Palatov, DM}, title = {Morphological description and DNA barcoding of Diamesa achipseensis sp. nov. (Diptera: Chironomidae: Diamesinae) from Southwestern Caucasus.}, journal = {Zootaxa}, volume = {5481}, number = {4}, pages = {477-482}, doi = {10.11646/zootaxa.5481.4.6}, pmid = {39646024}, issn = {1175-5334}, mesh = {Animals ; Male ; *DNA Barcoding, Taxonomic ; *Chironomidae/anatomy &amp; histology/classification/genetics/growth &amp; development ; Female ; Body Size ; Animal Distribution ; Phylogeny ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Illustrated description of adult male, as well as DNA barcoding, of Diamesa achipseensis sp. nov. in comparison with close related species D. caucasica Kownacki et Kownacka from Southwestern Caucasus are provided. Interspecific distances between D. achipseensis sp. nov. and D. caucasica are extremely low (0.64% in average) despite the identified morphological differences. High similarity of these species is new example of genetically indistinguishable of some species of the genus Diamesa Meigen.}, }
@article {pmid39645963, year = {2024}, author = {Gebremeskel, A and Salnitska, M and Solodovnikov, A}, title = {DNA barcode polymorphism within a common widespread rove beetle Quedius molochinus (Coleoptera: Staphylinidae).}, journal = {Zootaxa}, volume = {5519}, number = {4}, pages = {538-548}, doi = {10.11646/zootaxa.5519.4.3}, pmid = {39645963}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera/genetics/classification/anatomy &amp; histology ; *DNA Barcoding, Taxonomic ; Male ; Female ; *Phylogeny ; *Animal Distribution ; Body Size ; Polymorphism, Genetic ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {Phylogenetic assessment of COI barcodes from 22 specimens identified as Q. molochinus based on external morphology and shape of the aedeagus revealed three non-sister clades within this recently revised species, with large molecular distance (6.3-7.8%) among them, suggesting their species status. On the contrary, preliminary study of the aedeagal internal sac (endophallus) of the available males from these clades and from the more numerous additional non-sequenced materials of Q. molochinus did not reveal notable variants. We report this case here because firstly, this goes against some cases observed in other beetles where endophallic characters may be the only morphological traits supporting molecular-based cryptic species, and secondly, these molecular clades are unexpected within a species we thought to be well-known. DNA barcoding, exploration of nuclear DNA markers and an in-depth examination of the fully everted endophallus for a wider sample of freshly collected specimens are required for further study and explanation of the detected molecular polymorphism of Q. molochinus. An illustration of the everted internal sac as a reference and new distributional data for this species are provided.}, }
@article {pmid39645938, year = {2024}, author = {Ballon-Estacio, R and Alvarado, M}, title = {Three new species of parasitoid wasps of the genus Mnioes Townes, 1946 (Ichneumonidae: Banchinae) in a humid forest in Peru.}, journal = {Zootaxa}, volume = {5523}, number = {2}, pages = {269-283}, doi = {10.11646/zootaxa.5523.2.8}, pmid = {39645938}, issn = {1175-5334}, mesh = {Animals ; Peru ; Female ; Male ; *Forests ; *Animal Distribution ; *Wasps/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {Mnioes is a predominantly Neotropical genus of Banchinae (Ichneumonidae), currently including 26 species. Three new species of Mnioes are described, found in a humid montane forest in southern Peru, M. chunka sp. nov, M. chusaq sp. nov. and M. isqun sp. nov, and the male of M. huk Alvarado 2020 is also described. DNA barcoding for all the species treated here is included and provides information to match females with males, especially for M. chunka sp. nov., M. chusaq sp. nov., and M. soqta Alvarado 2020 where females are similar to each other and occur in sympatry. Additionally, an updated key to the Peruvian species is provided.}, }
@article {pmid39645925, year = {2024}, author = {Jiang, ZH and Yan, M and Wang, JX and Hu, SJ}, title = {Review of the genus Pseudodolbina Rothschild, 1894, with the description of a new species from Yunnan, China (Lepidoptera: Sphingidae).}, journal = {Zootaxa}, volume = {5523}, number = {4}, pages = {423-436}, doi = {10.11646/zootaxa.5523.4.2}, pmid = {39645925}, issn = {1175-5334}, mesh = {Animals ; China ; Male ; Female ; *Animal Distribution ; *Phylogeny ; *Moths/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The two species currently included in the genus Pseudodolbina Rothschild, 1894, Pseudodolbina fo (Walker, 1856) and Pseudodolbina aequalis Rothschild &amp; Jordan, 1903, were studied and a new species, Pseudodolbina yunnana sp. nov., was described from Yunnan, China. The diagnostic features and a distribution map of three species are provided, with a phylogenetic analysis based on DNA barcodes.}, }
@article {pmid39645924, year = {2024}, author = {Huemer, P and Özden, &#xd6;}, title = {Scrobipalpa chardonnayi Huemer and Özden, sp. nov.: a new presumably endemic species from Cyprus (Lepidoptera, Gelechiidae).}, journal = {Zootaxa}, volume = {5523}, number = {4}, pages = {437-447}, doi = {10.11646/zootaxa.5523.4.3}, pmid = {39645924}, issn = {1175-5334}, mesh = {Animals ; Cyprus ; Female ; Male ; *Animal Distribution ; *Moths/anatomy &amp; histology/classification ; *Phylogeny ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Ecosystem ; }, abstract = {Scrobipalpa chardonnayi Huemer &amp; Özden, sp. nov. is described from the limestone mountains of northern Cyprus and considered as a possible island endemism. The new species shows closer phylogenetic relationships to S. vasconiella (Rössler, 1877) and some related species, but differs phenotypically and in male and female genitalia, as well as through significant divergences in DNA barcode. Morphologically relevant diagnostic characters are compared and figured. Finally, S. vasconiella is reported from Kyrgyzstan for the first time.}, }
@article {pmid39645904, year = {2024}, author = {Komai, T and Hanai, M}, title = {A new shallow water species of the palaemonid shrimp genus Palaemon Weber, 1795 (Decapoda: Caridea) from Japan.}, journal = {Zootaxa}, volume = {5443}, number = {3}, pages = {417-430}, doi = {10.11646/zootaxa.5443.3.6}, pmid = {39645904}, issn = {1175-5334}, mesh = {Animals ; *Palaemonidae/classification/anatomy &amp; histology/genetics ; Japan ; Male ; Female ; *Animal Distribution ; *Body Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; }, abstract = {During a survey of the shallow water decapod fauna in the Miura Peninsula, Kanagawa Prefecture, central Japan, four specimens of a new palaemonid shrimp, Palaemon parvibrachium n. sp., were collected from sea grass beds of Nanozostera japonica (Ascherson &amp; Graebner) Tomlinson &amp; Posluszny, 2001. The new species appears morphologically similar to P. serrifer (Stimpson, 1860), one of the most common representatives of Palaemon Weber, 1795 in Japanese waters, but the short carpus of the second pereopod and the different live colouration readily differentiate the new species from the latter. A DNA barcode (a partial fragment of the mitochondrial CO1 gene), as well as a partial fragment of the mitochondrial 16S rRNA gene, are provided to genetically characterize the new species.}, }
@article {pmid39645896, year = {2024}, author = {Barrantes, EAB and Echavarria, MAZ and Bartlett, CR and Helmick, EE and Bahder, BW}, title = {A new species of planthopper in the genus Myconus (Hemiptera: Auchenorrhyncha: Fulgoroidea: Achilidae) from the Osa Peninsula in Costa Rica.}, journal = {Zootaxa}, volume = {5443}, number = {4}, pages = {580-590}, doi = {10.11646/zootaxa.5443.4.6}, pmid = {39645896}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/anatomy &amp; histology/classification ; Costa Rica ; Male ; Female ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Phylogeny ; }, abstract = {Recent surveys of palm-associated planthoppers in Costa Rica have revealed many new species, primarily in the families Derbidae and Cixiidae, but also Myconus jacquelinae Bahder &amp; Bartlett, in the Achilidae. Here a new species of Myconus from the the Osa peninsula is described as Myconus florae sp. n. with supplemental molecular data for the barcoding region (5'-half) of the cytochrome c oxidase subunit I (COI) gene, 18S rRNA gene, and histone 3 (H3) gene. A key to all species of Myconus is provided.}, }
@article {pmid39645882, year = {2024}, author = {Samoh, A and Grootaert, P}, title = {New species and records of the genus Hercostomus Loew (Diptera: Dolichopodidae) from Thailand mangroves, with notes on the Hercostomus fauna of Singapore mangroves.}, journal = {Zootaxa}, volume = {5446}, number = {2}, pages = {179-204}, doi = {10.11646/zootaxa.5446.2.2}, pmid = {39645882}, issn = {1175-5334}, mesh = {Animals ; Thailand ; Female ; *Animal Distribution ; *Diptera/classification/anatomy &amp; histology/genetics ; Singapore ; Male ; *Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; Organ Size ; Wetlands ; }, abstract = {The long-legged fly genus Hercostomus Loew, 1857 is reported for the first time from mangrove habitats in Thailand. Two new species, H. obtusus sp. nov. and H. squamatus sp. nov. are described based on external morphology and supported by NGS barcoding. Four described species, namely, H. brevicornis Zhang, Yang &amp; Grootaert, 2008, H. brevidigitalis Zhang, Yang &amp; Grootaert, 2008, H. lanceolatus Zhang, Yang &amp; Grootaert, 2008, and H. plumatus Zhang, Yang &amp; Grootaert, 2008, previously known only from Singapore mangroves, are recorded for the first time from Thailand mangroves. In addition, species distributions are mapped and taxonomic notes are provided.}, }
@article {pmid39645866, year = {2024}, author = {Yagi, S and Goto, K and Sohn, JC}, title = {A new species of Caloptilia (Lepidoptera: Gracillariidae) from Japan and Korea.}, journal = {Zootaxa}, volume = {5446}, number = {3}, pages = {420-432}, doi = {10.11646/zootaxa.5446.3.6}, pmid = {39645866}, issn = {1175-5334}, mesh = {Animals ; Male ; Republic of Korea ; Japan ; *Moths/classification/anatomy &amp; histology/genetics/growth &amp; development ; Female ; *Animal Distribution ; Larva/growth &amp; development/anatomy &amp; histology/classification ; Body Size ; Organ Size ; Phylogeny ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {A new species of Caloptilia, C. rhynchosiae n. sp. is described, based on 16 specimens from Japan and Korea. The species is characterized by the presence of the saccular process in the male genitalia. A fabaceous vine, Rhynchosia tomentosa (L.) Hook. &amp; Arn. is reported as the larval host of C. rhynchosiae n. sp. Larval feeding preference, biology and pupation process are described for the species. The species turned out to be host-specific. Two sets of COI barcodes were generated for C. rhynchosiae n. sp. The genetic distances of COI barcodes between the new species and other congeners in the public databases are compared. The conclusion was made that C. rhynchosiae n. sp. was misidentified as C. soyella in the BOLD and GenBank DNA barcode depositories.}, }
@article {pmid39645854, year = {2024}, author = {Xue, G and Xie, Y and Shen, G and Li, X and Li, M and Guo, Y}, title = {Study on the intraspecific variation of Capila lineata lineata Chou &amp; Gu, 1994, with some taxonomic notes on the related taxa (Hesperiidae, Pyrginae).}, journal = {Zootaxa}, volume = {5446}, number = {4}, pages = {573-580}, doi = {10.11646/zootaxa.5446.4.9}, pmid = {39645854}, issn = {1175-5334}, mesh = {Animals ; Male ; Female ; *Animal Distribution ; Organ Size ; Phylogeny ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {The history with regard to questions on Capila lineata lineata Chou &amp; Gu, 1994, C. lineata magna Devyatkin &amp; Monastyrskii, 1999, C. lineata irregularis Devyatkin &amp; Monastyrskii, 2002 and C. neolineata Fan, Wang &amp; Huang, 2003 was reviewed. The intraspecific variation of C. lineata lineata was explored by DNA barcoding and morphological comparison. The results revealed a remarkable variability in wing patterns and a slight variability in female genitalia, whereas characters of the male genitalia were uniform. C. lineata irregularis syn. n. and C. neolineata syn. n. are treated as junior subjective synonyms of C. lineata lineata because morphological characters of the two taxa fall into the range of individual variation of the latter.}, }
@article {pmid39645812, year = {2024}, author = {Navarro-Rodríguez, CI and Valdez-Mondragón, A}, title = {Violins we see, species we don't… Species delimitation of the spider genus Loxosceles Heineken &amp; Lowe (Araneae: Sicariidae) from North America using morphological and molecular evidence.}, journal = {Zootaxa}, volume = {5428}, number = {4}, pages = {527-548}, doi = {10.11646/zootaxa.5428.4.4}, pmid = {39645812}, issn = {1175-5334}, mesh = {Animals ; *Spiders/anatomy &amp; histology/classification/genetics ; Male ; Female ; North America ; *Phylogeny ; DNA Barcoding, Taxonomic ; Animal Distribution ; Electron Transport Complex IV/genetics ; Organ Size ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {In modern systematics, different sources of evidence are commonly used for the discovery, identification, and delimitation of species, especially when morphology fails to delineate between species or in underestimated species complexes or cryptic species. In this study, morphological data and two DNA barcoding markers-cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2)-were used to delimit species in the spider genus Loxosceles from North America. The molecular species delimitation analyses were carried out using three different methods under the corrected p-distance Neighbor-Joining (NJ) criteria: 1) Assemble Species by Automatic Partitioning (ASAP), 2) General Mixed Yule Coalescent model (GMYC), and 3) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 192 terminals corresponding to 43 putative species of Loxosceles, of which 15 are newly recognized herein, as putative new species, based on morphology and congruence between molecular methods with COI. The average intraspecific genetic distance (p-distance) was <2%, whereas the average interspecific genetic distance was 15.6%. The GMYC and bPTP molecular methods recovered 65-79 and 69 species respectively, overestimating the diversity in comparison with morphology, whereas the ASAP method delimited 60 species. The morphology of primary sexual structures (males palps and female seminal receptacles) was congruent with most of the molecular methods mainly with COI, showing that they are robust characters for identification at the species level. For species delimitation COI was more informative than ITS2. The diversity of Loxosceles species is still underestimated for North America, particularly in Mexico which holds the highest diversity of this genus worldwide.}, }
@article {pmid39645769, year = {2024}, author = {Jia, J and Zhao, X and Skarżyński, D and Wu, R and Cheng, L and An, J}, title = {Morphological description and DNA barcoding of Ceratophysella gracilimucronata sp. nov. (Collembola: Hypogastruridae) from China, with a key to species of the C. armata group of the Sino-Japanese Region.}, journal = {Zootaxa}, volume = {5432}, number = {4}, pages = {555-566}, doi = {10.11646/zootaxa.5432.4.5}, pmid = {39645769}, issn = {1175-5334}, mesh = {Animals ; China ; *DNA Barcoding, Taxonomic ; *Arthropods/anatomy &amp; histology/classification/genetics ; Female ; Male ; Phylogeny ; Animal Distribution ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Body Size ; }, abstract = {A new species, Ceratophysella gracilimucronata sp. nov. from Nan Ling Mountains (Guangdong Province, China), is described. It resembles C. ainu (Yosii, 1972), C. glancei Hammer, 1953 and C. falcifer Cassagnau, 1959 due to the B type chaeotataxy and short and slender mucro. Mitochondrial COI gene sequence of C. gracilimucronata sp. nov. is provided. A key to species of the C. armata group of the Sino-Japanese Region is given.}, }
@article {pmid39645686, year = {2024}, author = {Oh, JI and Lee, JY and Kim, SY and Jeong, JH and Song, YG and Byun, BK}, title = {Discovery of Bucculatrix koreana sp. nov. and newly recorded Bucculatrix duanwuia (Lepidoptera: Bucculatricidae) in Korea.}, journal = {Zootaxa}, volume = {5538}, number = {5}, pages = {485-491}, doi = {10.11646/zootaxa.5538.5.9}, pmid = {39645686}, issn = {1175-5334}, mesh = {Animals ; Republic of Korea ; Male ; Female ; *Moths/anatomy &amp; histology/classification ; *Animal Distribution ; *Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; DNA Barcoding, Taxonomic ; }, abstract = {In this study, we describe a new species, Bucculatrix koreana sp. nov., and report B. duanwuia Liu, 2020, for the first time in Korea. Adults and genitalia of both species are illustrated. Additionally, we provide and discuss DNA barcode sequences for Bucculatrix species known from Korea.}, }
@article {pmid39645681, year = {2024}, author = {Röll, B and Pinto, PV and Lobón-Rovira, J}, title = {A new species of African diurnal dwarf geckos (Gekkonidae: Lygodactylus) from the Lower Guinea rainforest.}, journal = {Zootaxa}, volume = {5538}, number = {6}, pages = {561-574}, doi = {10.11646/zootaxa.5538.6.3}, pmid = {39645681}, issn = {1175-5334}, mesh = {Animals ; *Lizards/classification/anatomy &amp; histology/genetics ; Female ; Male ; *Animal Distribution ; *Phylogeny ; Rainforest ; Body Size ; Ecosystem ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; Guinea ; }, abstract = {The genus Lygodactylus Gray is a species-rich group of small, diurnal geckos distributed in Africa, Madagascar, and South America. The genus is divided into several species groups based on morphological characters, biogeographical affinities and/or phylogenetic investigations. To date, some of these groups still contain candidate species. One of these candidate species, provisionally designed as L. sp. B (a single female from Cameroon), had been placed phylogenetically within the East African Lygodactylus scheffleri-group. Furthermore, it shares typical scale characters with all members of this group. However, L. fischeri Boulenger, eponym and member of the West/Central African L. fischeri-group, also shares these scale characters with the L. scheffleri-group and with L. sp. B. While it could be ruled out that L. sp. B was conspecific with any member of the L. scheffleri-group, it could not be ruled out that L. sp. B represents a female of L. fischeri, as there is no female type material nor a clear description of a female of L. fischeri. Only when a male of this taxon was discovered in Cabinda (Angola) in a case of barcoding, the problem could be solved. We here describe the female L. sp. B from Cameroon and the male from Cabinda as new species Lygodactylus lobeke sp. nov. It is a small nondescript species without any bold color markings, such as dark blotches above the shoulder and on the flanks, which mark the male L. fischeri. The male and the female do not differ in coloration. In captivity, the female showed distinct 'mood dependent' colorations, including a 'pyjamas' coloration. For phylogenetic analysis, only sequences of L. laterimaculatus Pasteur, L. gravis Pasteur and L. lobeke sp. nov. were available. Lygodactylus lobeke sp. nov. was recovered as an independent clade which differs greatly in 16S uncorrected pairwise distance (>10%) from these two congeners. The new species is known from two localities in the Lower Guinea rainforests, with a linear distance of about 850 km. Despite this great distance, both specimens of L. lobeke sp. nov. are genetically surprisingly similar (3.5%). Presumably, the species has a wide distribution within the Lower Guinea region and a continuous gene flow within the population.}, }
@article {pmid39645676, year = {2024}, author = {Wu, J and Liu, X}, title = {Systematics of the green lacewing tribe Ankylopterygini Navás, 1910 (Neuroptera: Chrysopidae: Chrysopinae) from China.}, journal = {Zootaxa}, volume = {5540}, number = {1}, pages = {1-169}, doi = {10.11646/zootaxa.5540.1.1}, pmid = {39645676}, issn = {1175-5334}, mesh = {China ; Animals ; Male ; Female ; *Animal Distribution ; Insecta/anatomy &amp; histology/classification ; Body Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Organ Size ; }, abstract = {A systematic revision of the taxonomy of the green lacewing tribe Ankylopterygini (Neuroptera: Chrysopidae: Chrysopinae) from China is present. Sixty-six species belonging to six genera are recorded and described. Keys to genera, subgenera and species are provided. A total of 201 COI barcodes (partial sequence of cytochrome c oxidase subunit I (COI)) from 49 species of the tribe are provided and used for molecular species delimitation. Nineta Navás, 1912 is treated as a subgenus of Tumeochrysa Needham, 1909. Two new generic synonyms are proposed: Tibetochrysa Yang, 1988, junior synonym of Retipenna Brooks, 1986; Sencera Navás, 1925, junior synonym of Ankylopteryx Brauer, 1864. Sixteen new species are described: Ankylopteryx hainanensis sp. nov., A. montipunctata sp. nov., A. stena sp. nov., Chrysopidia arcta sp. nov., C. macrosterna sp. nov., C. abdominata sp. nov., Tumeochrysa acuta sp. nov., T. breva sp. nov., T. biloba sp. nov., T. minina sp. nov., T. yangi sp. nov., Retipenna interrupta sp. nov., R. triphlebia sp. nov., Semachrysa pura sp. nov., Se. triloba sp. nov. and Signochrysa jianfenglingensis sp. nov. Twelve specific synonyms are proposed: Ankylopteryx yangi Ma, Yang &amp; Liu, 2020, junior synonym of Ankylopteryx octopunctata candida (Fabricius, 1798), Chrysopidia yangi Yang &amp; Lin, 1977, junior synonym of Chrysopidia junbesiana Hölzel, 1973; Chrysopidia fuscata Navás, 1914 and Chrysopidia tjederi Ma, 2022, junior synonyms of Chrysopidia regulata Navás, 1914; Tumeochrysa hui Yang, 1987, junior synonym of Tumeochrysa praeclara Hölzel, 1973; Tumeochrysa nyingchiana Yang, 1987, junior synonym of Tumeochrysa yunica Yang, 1986; Retipenna inordinata, Yang, 1997, junior synonym of Retipenna dasyphlebia (McLachlan, 1894); Retipenna chione (Banks, 1942 [1940]), junior synonym of Retipenna grahami (Banks, 1942 [1940]); Retipenna chaoi Yang &amp; Yang, 1987, Retipenna guangdongana Yang &amp; Yang, 1987 and Retipenna huai Yang &amp; Yang, 1987, junior synonyms of Retipenna burmana Brooks, 1986; and Signochrysa hainanus (Yang &amp; Yang, 1991), junior synonym of Signochrysa ornatissima (Nakahara, 1955). Eight new combinations are proposed: Retipenna phanera (Yang, 1987) comb. nov., R. sinica (Yang, 1988) comb. nov., Tumeochrysa abunda (Yang &amp; Yang, 1989) comb. nov., T. dolichoptera (Navás, 1910) comb. nov., T. grandis (Navás, 1915) comb. nov., T. inpunctata (Reuter, 1894) comb. nov., T. shaanxiensis (Yang &amp; Yang, 1989) comb. nov. and T. vittata (Wesmael, 1841) comb. nov. Ten species are newly recorded from China: Chrysopidia junbesiana Hölzel, 1973, C. nigrata Navás, 1910, C. ciliata (Wesmael, 1841), C. orientalis (Hölzel, 1973), Tumeochrysa inpunctata (Reuter, 1894), T. praeclara Hölzel, 1973, T. magnifica Hölzel, 1973, Retipenna burmana Brooks, 1986, R. variegata Brooks, 1986, and Semachrysa contorta Brooks, 1983. One species is transferred from Ankylopterygini to Chrysopini: Chrysopa yananica (Yang &amp; Yang, 1989) comb. nov.}, }
@article {pmid39645675, year = {2024}, author = {Kasparek, M}, title = {New species, new synonyms, and resurrected taxa: A review of West and Central Palaearctic members of the genus Pseudoanthidium (Apoidea: Megachilidae).}, journal = {Zootaxa}, volume = {5541}, number = {1}, pages = {1-50}, doi = {10.11646/zootaxa.5541.1.1}, pmid = {39645675}, issn = {1175-5334}, mesh = {*Bees/anatomy &amp; histology/classification/genetics ; *Terminology as Topic ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Genes, Insect/genetics ; DNA, Mitochondrial/genetics ; Male ; Female ; Animals ; Animal Distribution ; }, abstract = {Wool carder bees of the genus Pseudoanthidium comprise approximately 60-65 species, which are found in the Palaearctic, Indo-Malayan and Afrotropical realms. Their taxonomic relationships are little understood. Herein, I revised West and Central Palaearctic members of the genus. Four species are described as new, namely P. farsiense sp. nov. from Iran, P. microrubrum sp. nov. from Morocco, P. syriacum sp. nov. from Syria, and P. tajikistanicum sp. nov. from Tajikistan. The largely overlooked species Anthidium fulviventre Friese, 1917, described from Russia, and Anthidium ivanovi Mavromoustakis, 1954, described from Tajikistan, are recognized as members of the Pseudoanthidium genus, as P. fulviventre (Friese, 1917) comb. nov. and P. ivanovi (Mavromoustakis, 1954) stat. resurrect. &amp; comb. nov. Anthidium moricei Friese, 1911, from Jordan, and A. royoi Dusmet, 1915, from Morocco, are resurrected from synonymy with P. melanurum and suggested to be treated as P. moricei (Friese, 1911) stat. resurrect. and P. royoi (Dusmet, 1915) stat. resurrect. &amp; comb. nov. The hitherto unknown males of P. moricei (Friese, 1911) and P. rubellulum Pasteels, 1969 are described based on material from Jordan and Israel, respectively. Royanthidium bicoloripenne Pasteels, 1981 (syn. nov.) from Morocco, is revealed to be a junior synonym of P. octodentatum (Pérez, 1895). Morphological traits, along with DNA sequences of the mitochondrial COI gene ("barcoding gene"), allowed clustering the species in five polytypic and five monotypic species groups. As key character traits of the type species of nominate Pseudoanthidium largely fit the subgeneric characters of the subgenus Royanthidium Pasteels, 1969, Royanthidium is regarded as a junior synonym (syn. nov.) of nominate Pseudoanthidium. The species of the subgenus Exanthidium Pasteels, 1969 form a uniform clade both in terms of morphology and DNA marker. An examination of the non-Palaearctic Pseudoanthidium species is suggested to determine whether Exanthidium deserves subgenus status.}, }
@article {pmid39645672, year = {2024}, author = {Wang, S and Jiang, J and Wei, C}, title = {A review of the cicada genus Mata Distant, 1906 (Hemiptera: Cicadidae) with description of one new species from China.}, journal = {Zootaxa}, volume = {5541}, number = {1}, pages = {73-83}, doi = {10.11646/zootaxa.5541.1.4}, pmid = {39645672}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera/anatomy &amp; histology/classification/genetics ; China ; Male ; Female ; *Phylogeny ; *Animal Distribution ; Body Size ; Organ Size ; Animal Structures/anatomy &amp; histology/growth &amp; development ; }, abstract = {The cicada genus Mata Distant, 1906 was reviewed based on the description of one new species, Mata uncinulata sp. nov., from China. Mata kama (Distant, 1881) and Mata meghalayana Sarkar, Mahapatra, Mohapatra, Nair &amp; Kunte, 2021 are reported for the first time in China. Morphological phylogenetic analysis reveals the relationships among related species of Mata. Partial mitochondrial COI gene (DNA barcoding) of M. uncinulata sp. nov. and M. kama rec. nov. are sequenced and uploaded to GenBank. A key to species of Mata is provided.}, }
@article {pmid39644641, year = {2025}, author = {Leidenberger, S and Wiese, V and Schaumann, F and Pleiss, F and Langen, K and Bourlat, SJ}, title = {Freshwater mollusc community screening - Classical and eDNA monitoring methods to detect rare, indicator and invasive species.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177763}, doi = {10.1016/j.scitotenv.2024.177763}, pmid = {39644641}, issn = {1879-1026}, mesh = {Animals ; *Environmental Monitoring/methods ; Sweden ; *Introduced Species ; *Mollusca/classification ; DNA Barcoding, Taxonomic ; Fresh Water ; Biodiversity ; Ecosystem ; Lakes ; }, abstract = {Freshwater habitats and their quality have always been of utmost importance for human subsistence. Water quality assessment is an important tool, covering biological, chemical and hydromorphological aspects. Bioindicators such as the bivalves can be used as evidence for good water quality, but widespread groups such as species of the family Sphaeriidae Deshayes,1855 (1822) and genus Pisidium/Euglesa/Odhneripidisium also known as 'pea clams' are poorly known and lack taxonomic expertise. The situation is similar for many other benthic macroinvertebrate species used in biomonitoring. In this study, we tested if pea clams can be detected using eDNA metabarcoding methods applied to sediment and plankton samples from 15 lakes and rivers in Sweden. Additionally, we detected benthic macroinvertebrates, so-called indicator species used in freshwater monitoring, as well as rare or red-listed and invasive species. We created a COI reference barcode library of 22 species of Swedish freshwater molluscs, of which one species is new, and five species have less than five records on NCBI and BOLD. From 272 sediment and plankton samples, we detected 497 benthic macroinvertebrate indicator species, 20 mollusc species and 3 invasive species in 15 freshwater environments in Sweden using eDNA metabarcoding. We show that one of the sediment sampling methods (M42) can detect slightly more species in autumn compared to the plankton or sediment kick-net methods, or to collecting samples in spring. A clear advantage is that biological water quality indices formerly calculated using taxa identified to the family level can now be calculated using the species level, giving higher precision. We suggest that future freshwater monitoring efforts can be greatly improved and sped up through large-scale and strategic habitat screening using barcoding and metabarcoding methods to support decision-making and help fulfill the goals of the UN 2030 Agenda.}, }
@article {pmid39642167, year = {2025}, author = {Buri, MC and Shoeb, MR and Bykov, A and Repiscak, P and Baik, H and Dupanovic, A and David, FO and Kovacic, B and Hall-Glenn, F and Dopa, S and Urbanus, J and Sippl, L and Stofner, S and Emminger, D and Cosgrove, J and Schinnerl, D and Poetsch, AR and Lehner, M and Koenig, X and Perié, L and Schumacher, TN and Gotthardt, D and Halbritter, F and Putz, EM}, title = {Natural Killer Cell-Mediated Cytotoxicity Shapes the Clonal Evolution of B-cell Leukemia.}, journal = {Cancer immunology research}, volume = {13}, number = {3}, pages = {430-446}, pmid = {39642167}, issn = {2326-6074}, support = {20-17258//Alex's Lemonade Stand Foundation for Childhood Cancer (ALSF)/ ; 10.55776/P32001//Austrian Science Fund (FWF)/ ; //Fellinger Krebsforschung/ ; TAI 454/FWF_/Austrian Science Fund FWF/Austria ; TAI 732/FWF_/Austrian Science Fund FWF/Austria ; I 4649/FWF_/Austrian Science Fund FWF/Austria ; //Dr. Mildred Scheel Stiftung f&#xfc;r Krebsforschung/ ; 10.55776/TAI454//Austrian Science Fund (FWF)/ ; P 32001/FWF_/Austrian Science Fund FWF/Austria ; P 34832/FWF_/Austrian Science Fund FWF/Austria ; WKP 132/FWF_/Austrian Science Fund FWF/Austria ; P 31563/FWF_/Austrian Science Fund FWF/Austria ; 10.55776/P31563//Austrian Science Fund (FWF)/ ; //St. Anna Kinderkrebsforschung/ ; #25905//&#xd6;sterreichischen Akademie der Wissenschaften (&#xd6;AW)/ ; }, mesh = {*Killer Cells, Natural/immunology/metabolism ; Animals ; Mice ; *Clonal Evolution/immunology ; Humans ; *Cytotoxicity, Immunologic/immunology ; *Leukemia, B-Cell/immunology/pathology/genetics ; Cell Line, Tumor ; Tumor Escape ; Coculture Techniques ; Mice, Inbred C57BL ; }, abstract = {The term cancer immunoediting describes the dual role by which the immune system can suppress and promote tumor growth and is divided into three phases: elimination, equilibrium, and escape. The role of NK cells has mainly been attributed to the elimination phase. Here, we show that NK cells play a role in all three phases of cancer immunoediting. Extended co-culturing of DNA-barcoded mouse BCR/ABLp185+ B-cell acute lymphoblastic leukemia (B-ALL) cells with NK cells allowed for a quantitative measure of NK cell-mediated immunoediting. Although most tumor cell clones were efficiently eliminated by NK cells, a certain fraction of tumor cells harbored an intrinsic primary resistance. Furthermore, DNA barcoding revealed tumor cell clones with secondary resistance, which stochastically acquired resistance to NK cells. NK cell-mediated cytotoxicity put a selective pressure on B-ALL cells, which led to an outgrowth of primary and secondary resistant tumor cell clones, which were characterized by an IFNγ signature. Besides well-known regulators of immune evasion, our analysis of NK cell-resistant tumor cells revealed the upregulation of genes, including lymphocyte antigen 6 complex, locus A (Ly6a), which we found to promote leukemic cell resistance to NK cells. Translation of our findings to the human system showed that high expression of LY6E on tumor cells impaired their physical interaction with NK cells and led to worse prognosis in patients with leukemia. Our results demonstrate that tumor cells are actively edited by NK cells during the equilibrium phase and use different avenues to escape NK cell-mediated eradication.}, }
@article {pmid39641628, year = {2024}, author = {Hossain, A and Cetnar, DP and LaFleur, TL and McLellan, JR and Salis, HM}, title = {Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.}, journal = {ACS synthetic biology}, volume = {13}, number = {12}, pages = {4218-4232}, pmid = {39641628}, issn = {2161-5063}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Algorithms ; Oligonucleotides/genetics ; Software ; Gene Library ; Sequence Analysis, DNA/methods ; }, abstract = {Oligopool synthesis and next-generation sequencing enable the construction and characterization of large libraries of designed genetic parts and systems. As library sizes grow, it becomes computationally challenging to optimally design large numbers of primer binding sites, barcode sequences, and overlap regions to obtain efficient assemblies and precise measurements. We present the Oligopool Calculator, an end-to-end suite of algorithms and data structures that rapidly designs many thousands of oligonucleotides within an oligopool and rapidly analyzes many billions of barcoded sequencing reads. We introduce several novel concepts that greatly increase the design and analysis throughput, including orthogonally symmetric barcode design, adaptive decision trees for primer design, a Scry barcode classifier, and efficient read packing. We demonstrate the Oligopool Calculator's capabilities across computational benchmarks and real-data projects, including the design of over four million highly unique and compact barcodes in 1.2 h, the design of universal primer binding sites for one million 200-mer oligos in 15 min, and the analysis of about 500 million deep sequencing reads per hour, all on an 8-core desktop computer. Overall, the Oligopool Calculator accelerates the creative use of massively parallel experiments by eliminating the computational complexity of their design and analysis.}, }
@article {pmid39641617, year = {2024}, author = {Jiang, H and Qian, C and Deng, Y and Lv, X and Liu, Y and Li, A and Li, X}, title = {Novel Multimode Assay Based on Asymmetrically Competitive CRISPR and Raman Barcode Spectra for Multiple Hepatocellular Carcinoma Biomarkers Detection.}, journal = {Analytical chemistry}, volume = {96}, number = {50}, pages = {20004-20014}, doi = {10.1021/acs.analchem.4c04593}, pmid = {39641617}, issn = {1520-6882}, mesh = {*Spectrum Analysis, Raman/methods ; *Carcinoma, Hepatocellular/diagnosis/genetics ; Humans ; *Liver Neoplasms/diagnosis/genetics ; *Biomarkers, Tumor/genetics ; *MicroRNAs/analysis ; Gold/chemistry ; Metal Nanoparticles/chemistry ; CRISPR-Cas Systems/genetics ; }, abstract = {Commercial pregnancy test strips (PTS) possess the advantages of lower price, higher stability, and better repeatability and have been popularized to integrate with novel sensing strategies to detect other disease biomarkers, which accelerates the commercialization process of those novel sensing strategies. However, the current integration of novel sensing strategies into commercial PTS still faced the problems of insufficient quantification, low sensitivity, and lack of multiple detection capabilities. Hence, we proposed the concept of "visual classification recognition, spectral signal subdivision" for multiple hepatocellular carcinoma biomarkers (miRNA122 and miRNA233) detection with dual signals based on asymmetric competitive CRISPR (acCRISPR) and surface-enhanced Raman spectroscopy coupling with PTS, named the acCRISPR-PTS-SERS assay. In this assay, acCRISPR was used as a nonamplified cascaded signal amplification method to improve the sensitivity of detection. Two AuNPs-based core-shell Raman tags, each corresponding to different miRNA biomarkers, were used to achieve both visual recognition and spectral segmentation to enhance the quantification of PTS detection and the capability for multiple detection. Under the optimal conditions, the LOD for miRNA122 and miRNA223 were 10.36 and 4.65 fM, respectively. The sensitivity was enhanced by nearly 2 orders of magnitude. In the future, simultaneous hand-held detection for fingerprint barcodes of different cancers can be achieved with the assistance of a microfluidic chip and smartphone.}, }
@article {pmid39640376, year = {2024}, author = {Tabares-Medina, J and García-Blandón, K and García-Montoya, GM and Soto-Calderón, ID}, title = {Redefining infections with trypanosomatids in Neotropical primates: Case study of the white-footed tamarin (Oedipomidas leucopus).}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {25}, number = {}, pages = {101021}, pmid = {39640376}, issn = {2213-2244}, abstract = {Trypanosomes are blood parasites capable of infecting nearly any vertebrate. Many Neotropical primates frequently host trypanosomes and are considered potential reservoirs for Trypanosoma cruzi and other human-pathogenic trypanosomatids. However, diagnostic methods originally developed for detecting these trypanosomatids in humans and domestic species must be validated to reliably diagnose infections in non-human primates. Without such validation, taxonomic biases and incorrect assignments of wildlife reservoirs can occur. The white-footed tamarin (Oedipomidas leucopus), a primate endemic to northwestern Colombia, is classified by the World Health Organization as a reservoir of T. cruzi. However, this classification is based on studies with small sample sizes, ambiguous diagnostic methods, and questionable geographic records. In this study, the 18S ribosomal RNA gene was amplified via PCR and sequenced to estimate trypanosome infection rates and identify species in natural populations of O. leucopus across a wide geographic range, as well as in (ex situ) specimens. This molecular approach was also compared with traditional microscopy diagnosis using blood smears. The molecular diagnosis revealed that over 60% of the tested specimens were infected, whereas traditional microscopy resulted in 58% false negatives compared to the molecular method. A Bayesian phylogeny of the 18S gene identified T. minasense as the sole trypanosomatid species present in O. leucopus, with no detections of T. cruzi or other trypanosomatids of concern to human or domestic animal health. This study highlights the risk of overestimating the presence of human-infecting trypanosomes, such as T. cruzi, in tamarins and other vertebrates, and underscores the importance of validating diagnostic methods to accurately assess the zoonotic potential of wild species. Accurate identification of wildlife reservoirs is essential for understanding parasite life cycles and implementing effective management and conservation strategies for primates and other potential reservoirs.}, }
@article {pmid39638898, year = {2024}, author = {Aggarwal, SD and Lokken-Toyli, KL and Weiser, JN}, title = {Pneumococcal pneumonia is driven by increased bacterial turnover due to bacteriocin-mediated intra-strain competition.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1628}, pmid = {39638898}, issn = {2399-3642}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 AI038446/AI/NIAID NIH HHS/United States ; R01 AI50893//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; }, mesh = {*Bacteriocins/metabolism/genetics ; *Streptococcus pneumoniae/genetics/metabolism ; Animals ; Mice ; *Pneumonia, Pneumococcal/microbiology/metabolism ; *Streptolysins/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Lung/microbiology/metabolism/pathology ; Mice, Inbred C57BL ; Female ; Disease Models, Animal ; Quorum Sensing ; }, abstract = {Using chromosomal barcoding, we observed that >97% of the Streptococcus pneumoniae (Spn) population turns over in the lung within 2 days post-inoculation in a murine model. This marked collapse of diversity and bacterial turnover was associated with acute inflammation (severe pneumococcal pneumonia), high bacterial numbers in the lungs, bacteremia, and mortality. Intra-strain competition mediated by the blp locus, which expresses bacteriocins in a quorum-sensing-dependent manner, was required for each of these effects. Bacterial turnover from the activity of Blp-bacteriocins increased the release of the pneumococcal toxin, pneumolysin (Ply), which was sufficient to account for the lung pathology. The ability of Ply to evade complement, rather than its pore-forming activity, prevented opsonophagocytic clearance of Spn enabling its multiplication in the lung, facilitating the inflammatory response and subsequent invasion into the bloodstream. Thus, our study demonstrates how an appreciation for bacterial population dynamics during infection provides new insight into pathogenesis.}, }
@article {pmid39636545, year = {2025}, author = {Dlauchy, D and Kachalkin, A and Glushakova, A and Buda, K and Fehér, C and Péter, G}, title = {Description of Wickerhamia europaea sp. nov. and revisitation of the ascospore number of W. fluorescens.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {6}, pages = {1321-1330}, pmid = {39636545}, issn = {1618-1905}, support = {075-15-2021-1396//Ministry of Science and Higher Education of the Russian Federation/ ; TKP2021-EGA//Ministry of Culture and Innovation of Hungary from the National Research, Development and Innovation Fund/ ; }, abstract = {During the course of two independent studies, six conspecific yeast strains were recovered from flowers, soil, bird faeces and wood of different geographical origins. The six strains share identical DNA sequences in two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2). According to sequence comparisons and phylogenetic analysis, they represent an undescribed Wickerhamia species. The novel species is not only genetically distinct from W. fluorescens, the single species of the genus but can also be distinguished from it by some phenotypic characters. We propose Wickerhamia europaea sp. nov. (holotype: NCAIM Y.01938; isotype: CBS 18675; MycoBank no.: 856571) to accommodate the above noted strains. Under certain fermentation conditions, we detected the production of phenyllactic acid, a potential broad-spectrum antimicrobial compound against food-borne pathogens, by the type strain of the novel species, although in smaller concentrations than in the case of W. fluorescens. Comparing our observations on the formation and properties of the ascospores of Wickerhamia europaea sp. nov. and the ambiguous data on the number of ascospores per ascus of W. fluorescens, we suggest a possible explanation to reconcile the different data regarding the number of ascospores per ascus formed by W. fluorescens.}, }
@article {pmid39633475, year = {2024}, author = {Evasco, KL and Brockway, C and Falkingham, T and Hall, M and Wilson, NG and Potter, A}, title = {First detection of Culex tritaeniorhynchus in Western Australia using molecular diagnostics and morphological identification.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {500}, pmid = {39633475}, issn = {1756-3305}, mesh = {*Culex/virology/classification/genetics ; Animals ; Western Australia ; *Phylogeny ; *Mosquito Vectors/virology/classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Encephalitis Virus, Japanese/genetics/isolation &amp; purification/classification ; Encephalitis, Japanese/virology/transmission/epidemiology ; }, abstract = {BACKGROUND: Culex tritaeniorhynchus has long been considered the primary vector of Japanese encephalitis virus (JEV), but until recently, it was considered exotic to Australia. When the species was detected in the country's Northern Territory (NT) for the first time, the Western Australia (WA) Department of Health was cognisant of the risk it posed to the State because of the shared border and continuous mosquito habitat adjoining the two jurisdictions. The aim of this study was to undertake intensive mosquito surveillance in the Kimberley region to ascertain whether Cx. tritaeniorhynchus was present in WA, define the extent of its distribution and undertake phylogenetic analysis of select specimens to support hypothesized routes of entry into the state.<br><br>METHODS: Carbon dioxide (CO2)-baited encephalitis virus surveillance (EVS) mosquito traps were deployed at various sites throughout the Kimberley region by surveillance officers within the Medical Entomology unit of the Western Australia (WA) Department of Health. Mosquitoes were then morphologically identified, and a subset of four specimens were confirmed as Cx. tritaeniorhynchus by molecular identification using Cytochrome Oxidase I (COI) DNA data and phylogenetic analysis.<br><br>RESULTS: From 31 March 2021 to 30 May 2024, a total of 211 female Cx. tritaeniorhynchus specimens were collected from 21 unique trap sites in the Kimberley's Shire of Wyndham-East Kimberley (SWEK). Four COI DNA barcode regions were amplified and successfully sequenced for analysis. These sequences fell within a clade recognised as Cx. tritaeniorhynchus and specifically all sequences were in a clade with other specimens from the NT and Timor-Leste.<br><br>CONCLUSIONS: This study represents the first detection of Cx. tritaeniorhynchus in WA. Given the widespread nature of trap sites that yielded the species and consecutive seasons over which it was observed, the authors surmise that Cx. tritaeniorhynchus is now established within the northeast Kimberley region. The findings are significant given the detection of the species coincides with the first significant outbreak of JEV activity on mainland Australia involving an estimated 45 human cases of Japanese encephalitis, 80 impacted commercial piggeries and widespread feral pig activity. Although the role that Cx. tritaeniorhynchus&#xa0;may play in JEV transmission into the future is not yet understood, it presents a potential risk to public health in the region.}, }
@article {pmid39632768, year = {2025}, author = {Martínez-Sánchez, A and Szpila, K and Villet, MH and Ståhls, G and Thomas-Cabianca, A and Velásquez, Y and Parrott, JJ and Rojo, S}, title = {Morphology, biology and molecular characterisation of the endemic Canary Islands blowfly Calliphora splendens Macquart, 1838 (Diptera: Calliphoridae).}, journal = {Medical and veterinary entomology}, volume = {39}, number = {2}, pages = {229-251}, doi = {10.1111/mve.12777}, pmid = {39632768}, issn = {1365-2915}, support = {//Universidad de Alicante/ ; //Horizon 2020/ ; //Rhodes University/ ; }, mesh = {Animals ; *Calliphoridae/genetics/anatomy &amp; histology/growth &amp; development/classification/physiology ; Spain ; Larva/anatomy &amp; histology/genetics/growth &amp; development/classification ; Electron Transport Complex IV/genetics ; Pupa/anatomy &amp; histology/genetics/growth &amp; development ; Phylogeny ; Female ; Male ; Insect Proteins/genetics/metabolism ; *Diptera/genetics/anatomy &amp; histology ; }, abstract = {The Canary Islands are an excellent natural laboratory for understanding ecological and evolutionary processes such as biogeographical colonisation. The morphology of the larva, puparium and adult of the endemic Canarian copper fly, Calliphora splendens, is described, illustrated and contrasted with those of the other species of Calliphora that occur in Africa, the Iberian Peninsula and Macaronesia. Partial cytochrome oxidase I sequences show a connection between C. splendens, Calliphora vicina, Calliphora loewi and Calliphora croceipalpis, but more distant relationship with Calliphora vomitoria. Calliphora splendens produced unisexual offspring in captivity. This work confirms the relict character of the Canarian copper fly associated with the endemic laurel forest habitat.}, }
@article {pmid39629927, year = {2025}, author = {Ma, W and Li, J and Qu, X and Sun, S and Zhou, Y and Liu, Y and Wang, P and Sha, Z}, title = {Liquid-Solid Triboelectric Nanogenerator-Based DNA Barcode Detection Biosensor for Species Identification.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {12}, number = {4}, pages = {e2408718}, pmid = {39629927}, issn = {2198-3844}, support = {2022LSL050102//Laoshan Laboratory/ ; No. 42276216//National Natural Science Foundation of China/ ; No. GuiKeAD24010036//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; SDCX-ZG-202400209//Shandong Postdoctoral Science Foundation/ ; }, mesh = {*Biosensing Techniques/methods/instrumentation ; *DNA Barcoding, Taxonomic/methods ; Metal Nanoparticles/chemistry ; Animals ; Gold/chemistry ; *Nanotechnology/methods ; DNA/genetics ; }, abstract = {DNA barcode detection method is widely applied for species identification, which is imperative to evaluate the effect of human economic activities on the biodiversity of ecosystem. However, the wide utilization of existing detection biosensors is limited by bulky and expensive instruments, such as Raman spectroscopy and electrochemical station. Herein, a liquid-solid triboelectric nanogenerator (TENG)-based DNA barcode detection biosensor is proposed, which consists of water flow, fluid channel, and PDMS film attached by specifically designed capture probe. Through sequentially combining capture probe, targeted DNA barcode, and signal probe with Au nanoparticles (NPs), the surface charge density of friction layer of TENG decreases under the effect of AuNPs, verified by the density functional theory (DFT) method. Consequently, the peak value of output current spike signal for targeted DNA is smaller than that for other DNA, which is the working mechanism of the present TENG-based biosensor. Such biosensor successfully recognizes Alvinocaris muricola among different types of Alvinocarididae shrimps, and its low limit detection can reach 1×10[-12] m. The present work provides a paradigm-shift way to develop an inexpensive and accurate technique to detect DNA barcode for species identification, and paves a novel way for the application of liquid-solid TENG.}, }
@article {pmid39628840, year = {2024}, author = {Mukalel, AJ and Hamilton, AG and Billingsley, MM and Li, J and Thatte, AS and Han, X and Safford, HC and Padilla, MS and Papp, T and Parhiz, H and Weissman, D and Mitchell, MJ}, title = {Oxidized mRNA Lipid Nanoparticles for In Situ Chimeric Antigen Receptor Monocyte Engineering.}, journal = {Advanced functional materials}, volume = {34}, number = {27}, pages = {}, pmid = {39628840}, issn = {1616-301X}, support = {DP2 TR002776/TR/NCATS NIH HHS/United States ; }, abstract = {Chimeric antigen receptor (CAR) monocyte and macrophage therapies are promising solid tumor immunotherapies that can overcome the challenges facing conventional CAR T cell therapy. mRNA lipid nanoparticles (mRNA-LNPs) offer a viable platform for in situ engineering of CAR monocytes with transient and tunable CAR expression to reduce off-tumor toxicity and streamline cell manufacturing. However, identifying LNPs with monocyte tropism and intracellular delivery potency is difficult using traditional screening techniques. Here, ionizable lipid design and high-throughput in vivo screening are utilized to identify a new class of oxidized LNPs with innate tropism and mRNA delivery to monocytes. A library of oxidized (oLNPs) and unoxidized LNPs (uLNPs) is synthesized to evaluate mRNA delivery to immune cells. oLNPs demonstrate notable differences in morphology, ionization energy, and pKa, therefore enhancing delivery to human macrophages, but not T cells. Subsequently, in vivo library screening with DNA barcodes identifies an oLNP formulation, C14-O2, with innate tropism to monocytes. In a proof-of-concept study, the C14-O2 LNP is used to engineer functional CD19-CAR monocytes in situ for robust B cell aplasia (45%) in healthy mice. This work highlights the utility of oxidized LNPs as a promising platform for engineering CAR macrophages/monocytes for solid tumor CAR monocyte therapy.}, }
@article {pmid39626340, year = {2025}, author = {Huang, Z and Wu, K and Ju, F and He, R and Tang, Y and Chen, Y and He, X and Zhang, J and Nie, L}, title = {Copper nanocluster based cascade amplified DNA electrochemical detection combining with bio-barcode assay and surface-initiated enzyme polymerization.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {163}, number = {}, pages = {108857}, doi = {10.1016/j.bioelechem.2024.108857}, pmid = {39626340}, issn = {1878-562X}, mesh = {*Copper/chemistry ; *Biosensing Techniques/methods ; *Electrochemical Techniques/methods ; Humans ; Polymerization ; *Metal Nanoparticles/chemistry ; *DNA/analysis ; Limit of Detection ; Graphite/chemistry ; Gold/chemistry ; Stomach Neoplasms/diagnosis/genetics ; Nucleic Acid Amplification Techniques/methods ; }, abstract = {Early cancer diagnosis is paramount for enhancing treatment efficacy, extending patient survival, and improving the quality of life. We developed a highly sensitive electrochemical biosensor for the detection of target DNA (tDNA) associated with gastric cancer. This advancement integrates dual signal amplification strategies: bio-barcode amplification (BCA) and surface-initiated enzyme polymerization (SIEP), with copper nanoclusters (CuNCs) serving as signal labels. Silica nanoparticles (SiO2) were covalently linked with polythymine (poly T) and complementary DNA to create bio-barcode probes. These probes, through hybridization, were immobilized on the reduced graphene oxide and Au nanoparticle (rGO-AuNPs) modified interface and marking the first amplification of the electrical signal. Subsequently, the extended poly T prompted by SIEP bound additional CuNCs through the combination of T-Cu[2+], leading to a second round of signal amplification. The biosensor demonstrated a minimum detection limit of 0.13 fmol/L over a linear response range from 1 fmol/L to 1 nmol/L. It also showcased excellent specificity, repeatability, and stability, making it a promising tool for the sensitive detection of gastric cancer biomarkers.}, }
@article {pmid39623507, year = {2024}, author = {Chen, Y and Shentu, J and Lou, H and Xia, Y and Jiang, Y and Duan, S}, title = {Hematopoietic stem cell heterogeneity and age-related platelet bias: implications for bone marrow transplantation and blood disorders.}, journal = {Stem cell research &amp; therapy}, volume = {15}, number = {1}, pages = {459}, pmid = {39623507}, issn = {1757-6512}, support = {210000-581835//the Qiantang Scholars Fund in Hangzhou City University/ ; 20221JCGY010610//the Natural Science Foundation of Ningbo Municipality, Zhejiang Province/ ; }, mesh = {Animals ; Humans ; Aging ; Blood Platelets/metabolism ; *Bone Marrow Transplantation/methods ; Hematologic Diseases/therapy/pathology ; Hematopoietic Stem Cell Transplantation/methods ; *Hematopoietic Stem Cells/metabolism/cytology ; }, abstract = {Hematopoietic stem cells (HSCs) are critical for maintaining lifelong blood production and immune function, especially in the context of bone marrow transplantation, where their ability to reconstruct multiple blood lineages is essential. However, recent studies have revealed that certain HSCs exhibit a bias toward platelet differentiation, termed platelet-biased HSCs (P-HSCs). This lineage bias, particularly pronounced with aging, can lead to imbalances in post-transplant blood recovery, negatively affecting patient outcomes. Research by Claus Nerlov's team has provided key insights into the heterogeneity of HSCs, focusing on the age-related expansion of P-HSCs. Using advanced techniques such as single-cell RNA sequencing and molecular barcoding, their work highlights the evolutionary conservation of platelet bias in HSCs across species. This work delves into these findings, discussing their clinical implications for bone marrow transplantation, aging-related blood disorders, and potential therapeutic strategies. Moreover, we address limitations in current methodologies and propose future directions for research to optimize HSC-based therapies and improve clinical outcomes in hematological diseases.}, }
@article {pmid39622837, year = {2024}, author = {Kuo, LY and Tang, SK and Huang, YH and Xie, PJ and Chen, CW and Chang, ZX and Hsu, TC and Chang, YH and Chao, YS and Chen, CW and Fawcett, S and Nitta, JH and Sundue, M and Kao, TT and Luu, HT and Mustapeng, AMA and Coritico, FP and Amoroso, VB and Thai, YK}, title = {A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1314}, pmid = {39622837}, issn = {2052-4463}, mesh = {*DNA Barcoding, Taxonomic ; *Ferns/genetics/classification ; *Biodiversity ; *Phylogeny ; DNA, Plant/genetics ; }, abstract = {Ferns belong to species-rich group of land plants, encompassing more than 11,000 extant species, and are crucial for reflecting terrestrial ecosystem changes. However, our understanding of their biodiversity hotspots, particularly in Southeast Asia, remains limited due to scarce genetic data. Despite harboring around one-third of the world's fern species, less than 6% of Southeast Asian ferns have been DNA-sequenced. In this study, we addressed this gap by sequencing 1,496 voucher-referenced and expert-identified fern samples from (sub)tropical Asia, spanning Malaysia, the Philippines, Taiwan, and Vietnam, to retrieve their rbcL and trnL-F sequences. This DNA barcode collection of Asian ferns encompasses 956 species across 152 genera and 34 families, filling major gaps in fern biodiversity understanding and advancing research in systematics, phylogenetics, ecology and conservation. This dataset significantly expands the Fern Tree of Life to over 6,000 species, serving as a pivotal and global reference for worldwide barcoding identification of ferns.}, }
@article {pmid39621694, year = {2024}, author = {Mata-Somarribas, C and Cardoso das Graças, G and de Oliveira R Pereira, L and Côrtes Boité, M and Motta Cantanhêde, L and Braga Filgueira, CP and Fallas, A and Quirós-Rojas, L and Morelli, KA and Ferreira, GEM and Cupolillo, E}, title = {Applying a cytochrome c oxidase I barcode for Leishmania species typing.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0309277}, pmid = {39621694}, issn = {1932-6203}, mesh = {*Electron Transport Complex IV/genetics ; *Leishmania/genetics/enzymology/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Species Specificity ; }, abstract = {Species delimitation has always been a challenge for taxonomists and for Leishmania studies there is no exception. Herein we attempt to display the usefulness of the mitochondrial gene Cytochrome Oxidase I-coI in classical and barcode-based approaches for Leishmania characterization. A total of 228 samples were analyzed, comprising 28 Leishmania related taxa, mainly from cultures of the Oswaldo Cruz Foundation`s Leishmania Collection. Primers were designed for amplification of coI; sequences were analyzed by distance-based indicators and both the Neighbor Joining and NeighborNet as species grouping techniques. Automatic Barcode Gap Discovery was applied to define species delimitation while for the character-based analysis a software for Barcoding with Logic formulas was employed. Final sequences of 486 bp with 238 parsimonious sites were aligned and edited. Robust groups were formed for most of the genus species, distinctive nucleotide positions in the barcode sequence were observed for 11 of them. A good agreement between the techniques applied and the original characterization was observed. Few species were not distinguished by coI: (i) L. (V.) peruviana, L. (V.) lindenbergi, and L. (V.) utingensis; (ii) L. (L.) venezuelensis and (iii) L. colombiensis and L. equatorensis with identical sequences. Some of these taxa have been, at one time or another, classified as controversial and, for most of them, a higher number of isolates should be studied to properly infer their taxonomic status. CoI represents a mitochondrial target that stands out as a taxonomically important asset with multiple advantages over other genes. This paper corresponds to the first report of coI analysis in Leishmania, a potentially advantageous target for the characterization of this parasite.}, }
@article {pmid39619925, year = {2024}, author = {Santanumurti, MB and Nugraha, MAR and Dewi, NR and Awaluddin, M and Tang, PW and Pardede, HI and Solami, LA and Sulmartiwi, L and El-Regal, MAA}, title = {Fish diversity assessment through conventional morphological identification and recent advances in Saudi Arabia: A review.}, journal = {Veterinary world}, volume = {17}, number = {10}, pages = {2267-2285}, pmid = {39619925}, issn = {0972-8988}, abstract = {Fish identification in the Red Sea, particularly in Saudi Arabia, has a long history. Because of the vast fish diversity in Saudi Arabia, proper species identification is required. Indeed, identifying fish species is critical for biodiversity conservation, food and drug safety, and sustainable fishery management. Numerous approaches have been used to identify fish species, including conventional morphological identification, next-generation sequencing (NGS), nanopore sequencing, DNA barcoding, and environmental DNA analysis. In this review, we collected as much scientific information as possible on species identification in Saudi Arabia. Our findings suggest that the identification process has advanced and spread rapidly and broadly, as evidenced by the discovery of new fish species in Saudi Arabia. The advantages and disadvantages of each method were discussed as part of a comprehensive comparison. This study aimed to provide further scientific knowledge to promote the growth of fish diversity worldwide.}, }
@article {pmid39619666, year = {2024}, author = {Réblová, M and Nekvindová, J and Kolařík, M and Jurjević, &#x17d; and Kolář, M and Hubka, V}, title = {Re-evaluation of Ceratostomella and Xylomelasma with introduction of two new species (Sordariomycetes).}, journal = {MycoKeys}, volume = {110}, number = {}, pages = {319-360}, pmid = {39619666}, issn = {1314-4049}, abstract = {In this study, we assessed the phylogenetic relationships among members of Ceratostomella and the morphologically similar genus Xylomelasma, currently classified within the Sordariomycetes. Our phylogenetic analyses, utilising three and five gene markers, revealed that species from these two genera are congeneric, supporting the transfer of Xylomelasma to Ceratostomella. Consequently, we propose two new combinations: C.sordida comb. nov. and C.novae-zelandiae comb. nov. In addition, we identified two cryptic species within the C.sordida species complex, which are described as C.crypta sp. nov. and C.melanospora sp. nov. Traditional micromorphological characters have proven insufficient for differentiating these new species; however, they are clearly distinguishable by molecular data, particularly using the internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) of the nuclear rRNA cistron, and genes encoding the second largest subunit of RNA polymerase II (rpb2), and translation elongation factor 1-α (tef1-α) as primary and secondary barcodes. This study provides new insights into the morphological characteristics of Ceratostomella, identifying the ascogenous system as an important diagnostic trait at the generic level, which distinguishes Ceratostomella from morphologically similar fungi. Ceratostomella is currently recognised with eight species. We also investigated the relationship between Ceratostomella and the closely related Barbatosphaeria. The lack of statistical support in the Maximum likelihood analysis is discussed and the inclusion of Ceratostomella in Barbatosphaeriaceae is not supported. Ceratostomella is accepted as a genus incertae sedis, while Barbatosphaeriaceae remains a monotypic family. The global diversity of Ceratostomella is inferred from metabarcoding data and published field observations. Biogeographic analysis indicates that members of Ceratostomella are widespread, found in soil and decaying wood, as well as in air, dust, roots, shoots, and water across temperate, subtropical and tropical regions in both the Northern and Southern Hemispheres. We are concurrently publishing whole-genome analyses of three ex-type strains of Ceratostomella, i.e. C.crypta, C.melanospora and C.sordida. This effort aims to establish a new standard for high-quality taxonomic studies, which, in accordance with current trends, should incorporate whole-genome sequencing data for future research and application. Our findings underscore the importance of integrating morphological, biogeographic and molecular data for accurate species delineation and highlight the complexity within the genus Ceratostomella.}, }
@article {pmid39619289, year = {2024}, author = {Iqbal, Z and Azad, R and Jin, X and Hassan, MA and Abbas, M and Nasir, MF and Bodlah, I and Ali, M and Szawaryn, K and Nie, RE}, title = {The review of the genus Coccinella (Coleoptera, Coccinellidae) from Pakistan.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e137417}, pmid = {39619289}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Coccinella is reviewed with seven species found in Pakistan: C.luteopicta (Mulsant, 1866), C.marussii Kapur, 1973, C.iranica Dobzhansky, 1926, C.transversalis Fabricius, 1781, C.septempunctata Linnaeus, 1758, C.transversoguttatatransversoguttata Faldermann, 1835 and C.undecimpunctata Linnaeus, 1758. Information on prey, host plants, distribution and an identification key for Coccinella species in Pakistan is provided. Additionally, newly-sequenced partial COI (cytochrome-c-oxidase subunit I) for C.luteopicta and C.marussii were used to determine their phylogenetic positions within the genus Coccinella.<br><br>NEW INFORMATION: This study comprehensively reviews the genus Coccinella in Pakistan and highlights Coccinellaluteopicta as a new country record. Morphological features of adults, including male genital characters and an identification key to known species in Pakistan are presented. Records of prey, host plants and distributions for all identified species are included. The new data (COI-barcode) shows that C.luteopicta (Mulsant, 1866) was recorded first in Pakistan.}, }
@article {pmid39619181, year = {2024}, author = {McCartin, L and Saso, E and Vohsen, SA and Pittoors, N and Demetriades, P and McFadden, CS and Quattrini, AM and Herrera, S}, title = {Nuclear eDNA metabarcoding primers for anthozoan coral biodiversity assessment.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18607}, pmid = {39619181}, issn = {2167-8359}, mesh = {*Anthozoa/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; DNA Primers/genetics ; Gulf of Mexico ; RNA, Ribosomal, 28S/genetics ; Polymerase Chain Reaction/methods ; Coral Reefs ; }, abstract = {The distributions of anthozoan corals are undercharacterized due to their wide bathymetric ranges, occurrences in remote locales, and difficulties of identification from morphology alone. Environmental DNA (eDNA) sequencing promises to be a noninvasive strategy to complement conventional approaches for mapping and monitoring the distribution and biodiversity of coral communities. Primers for eDNA metabarcoding have been designed to amplify nuclear and mitochondrial DNA barcodes in shallow scleractinians and mitochondrial MutS in deep-sea octocorals. However, a comprehensive method for eDNA metabarcoding of all anthozoan corals, including black corals, has not been developed. We leveraged a sequence database of global coral collections, from shallow water to the deep sea, to design new PCR primers for coral eDNA sequencing that target the 28S rRNA gene (28S rDNA). We tested the performance of these primers by amplifying and sequencing eDNA from water samples collected in the Gulf of Mexico near mesophotic and deep-sea corals that were also imaged, sampled, and sequenced. Sequencing libraries produced using the primers were highly enriched in eDNA from octocorals, black corals and scleractinians, with up to 99.9% of the reads originating from these corals. Further, the 28S barcode amplified using the primers distinguished coral genera and species in many cases, like previously developed methods that target eDNA in only octocorals or scleractinians. We recovered amplicon sequencing variants (ASVs) identical to DNA barcodes derived from Sanger sequencing and genome skimming of corals sampled at the same field sites. This new eDNA metabarcoding strategy permits targeted eDNA sequencing of black corals, octocorals, and scleractinians at sites where they co-occur and expands our current toolkit for mapping and monitoring coral communities in shallow coral reefs and the deep sea.}, }
@article {pmid39616387, year = {2024}, author = {Huang, G and Peng, X}, title = {Genus Bithynia: morphological classification to molecular identification.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {496}, pmid = {39616387}, issn = {1756-3305}, support = {82060376//National Natural Science Foundation of China/ ; No.2024GXNSFAA010039//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, mesh = {Animals ; *Snails/parasitology ; Trematode Infections/parasitology/veterinary ; Phylogeny ; Humans ; }, abstract = {Snails of the genus Bithynia, whose primary habitat is slow-flowing ponds and ditches, serve as the first intermediate hosts of liver fluke. Currently, approximately 200 million individuals worldwide are at risk of liver fluke infection, yet questions still persist regarding the taxonomic identification of Bithynia genus, a crucial player in the transmission of this disease. Accurate taxonomic classification of the Bithynia genus could significantly enhance current understanding of the disease's transmission mechanisms. In this article we comprehensively review the extensive research conducted on Bithynia genus, spanning past inquiries up to the latest findings. The primary emphasis is placed on exploring the taxonomic identification of this genus within various technological settings. We then present a consolidated analysis of the morphological taxonomic identification methods, highlighting their strengths and limitations. We also introduce a novel perspective on the future direction of identification and classification efforts for the members of this genus, emphasizing the crucial role Bithynia plays in the epidemiological cycle of liver fluke transmission. We conclude by urging researchers to prioritize the significance of the members of this genus in the epidemiological cycle of liver fluke transmission and in control measures for disease dissemination, within the context of the vector organisms.}, }
@article {pmid39615483, year = {2024}, author = {Michaels, YS and Major, MC and Bonham-Carter, B and Zhang, J and Heydari, T and Edgar, JM and Siu, MM and Greenstreet, L and Vilarrasa-Blasi, R and Kim, S and Castle, EL and Forrow, A and Ibanez-Rios, MI and Zimmerman, C and Chung, Y and Stach, T and Werschler, N and Knapp, DJHF and Vento-Tormo, R and Schiebinger, G and Zandstra, PW}, title = {Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells.}, journal = {Cell systems}, volume = {15}, number = {12}, pages = {1245-1263.e10}, doi = {10.1016/j.cels.2024.11.001}, pmid = {39615483}, issn = {2405-4720}, mesh = {Humans ; *Cell Lineage/genetics ; *Cell Differentiation/genetics ; *T-Lymphocytes/cytology/metabolism ; Myeloid Cells/metabolism ; Mast Cells/metabolism ; Gene Regulatory Networks/genetics ; Hematopoietic Stem Cells/metabolism/cytology ; Hematopoiesis/genetics ; }, abstract = {T cells develop from hematopoietic progenitors in the thymus and protect against pathogens and cancer. However, the emergence of human T cell-competent blood progenitors and their subsequent specification to the T lineage have been challenging to capture in real time. Here, we leveraged a pluripotent stem cell differentiation system to understand the transcriptional dynamics and cell fate restriction events that underlie this critical developmental process. Time-resolved single-cell RNA sequencing revealed that downregulation of the multipotent hematopoietic program, upregulation of >90 lineage-associated transcription factors, and cell-cycle exit all occur within a highly coordinated developmental window. Gene-regulatory network inference uncovered a role for YBX1 in T lineage specification. We mapped the differentiation cell fate hierarchy using transcribed lineage barcoding and discovered that mast and myeloid potential bifurcate from each other early in hematopoiesis, upstream of T lineage restriction. Our systems-level analyses provide a quantitative, time-resolved model of human T cell fate specification. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid39613881, year = {2024}, author = {Ghauri, MSZ and Soomro, S and Novianto, D and Arnuphapprasert, A and Kaewthamasorn, M}, title = {Molecular detection and genetic characterization of hemotropic mycoplasmas in goats and fleas from Thailand.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29702}, pmid = {39613881}, issn = {2045-2322}, mesh = {Animals ; *Goats/microbiology ; Thailand/epidemiology ; *Mycoplasma/genetics/isolation &amp; purification ; *Siphonaptera/microbiology ; Goat Diseases/microbiology/epidemiology ; Mycoplasma Infections/veterinary/epidemiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {Arthropod vectors play a crucial role in the transmission of hemotropic mycoplasmas, small bacteria that infect red blood cells in a wide range of animals and humans globally, leading to intravascular infections. Traditional Giemsa-stained thin blood smears, used for diagnosing hemotropic mycoplasmas through microscopic examination, have low sensitivity and are effective only when bacteremia levels are high. This study aimed to employ molecular methods to detect and genetically characterize hemotropic mycoplasmas in goats as well as investigate the potential role of fleas as vectors. Blood and flea samples were collected concurrently from goats on 16 farms across seven provinces in Thailand from January 2017 to October 2023. The 16 S rRNA, 23 S rRNA, and rnpB genes of hemoplasmas were amplified and sequenced. All fleas were identified morphologically and molecularly through DNA barcoding of the cytochrome oxidase I gene. A total of 78 out of 500 goats (15.6%), three pooled flea samples (3/6, 50%), and one individual flea (1/49, 2.04%) tested positive for hemoplasmas and all fleas were identified as Ctenocephalides orientis. BLASTN searches utilizing the three genetic markers revealed that the hemoplasmas detected in this study showed 97.81-100% similarity to Mycoplasma ovis and Candidatus Mycoplasma haemovis, which have been previously reported in sheep, goats, and humans, suggesting their zoonotic potential. The sequences were grouped into 28 unique nucleotide sequence types (ntSTs) based on minor variations in the 16 S rRNA gene. Hemotropic mycoplasma infection was significantly associated with farm locations and seasonality of sample collection (p < 0.0001), indicating that farm management practices or environmental conditions may play a critical role in the epidemiology of these infections. This study represents the first report of hemotropic mycoplasmas in goats in Thailand, confirms their presence in fleas, and provides valuable insights for farm management, such as guiding the rational use of insecticides and antibiotics.}, }
@article {pmid39610807, year = {2024}, author = {Wang, C and Gan, J and Mi, X}, title = {On two species of Phintella Strand, 1906 from Hainan, China (Araneae, Salticidae).}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e138400}, pmid = {39610807}, issn = {1314-2828}, abstract = {BACKGROUND: In our recent examination of the Phintella specimens collected from Hainan Tropical Rainforest National Park, a new species and the unknown female of P.liae Wang, Mi &amp; Peng, 2023 were recognised, based on the morphological characteristics and molecular evidence.<br><br>NEW INFORMATION: A new species of Phintella Strand, 1906 is described: P.hongkan sp. nov. (&#x2642;&#x2640;) from Hainan, China. The unknown female of P.liae Wang, Mi &amp; Peng, 2023 is also described for the first time. Diagnostic photos of both species are provided.}, }
@article {pmid39609739, year = {2024}, author = {Li, JW and Li, RY and Chen, YM and Wu, YH and Zou, LH and Tang, SL and Zhai, JW}, title = {Comprehensive characterization and phylogenetic analysis of the complete plastomes of two ant-orchids, Caularthron bicornutum and Myrmecophila thomsoniana.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1146}, pmid = {39609739}, issn = {1471-2229}, support = {2023YFD1600504//the National Key Research and Development Program of China/ ; KH230350A//the Construction and Management Program of the Research Center for the Protection and Utilization of Orchids in Motuo County, Xizang Autonomous Region, China/ ; }, mesh = {*Phylogeny ; Animals ; *Orchidaceae/genetics/classification ; Genome, Plastid ; Ants/genetics/classification ; Plastids/genetics ; Symbiosis ; Gryllidae ; }, abstract = {BACKGROUND: Myrmecophytes, characterized by specialized structures like hollow stems that facilitate mutualistic relationships with ants, serve as an important system for studying ant-plant interactions and the adaptation mechanisms. Caularthron and Myrmecophila are exemplary myrmecophytes within Orchidaceae. Previous studies suggested a genetic relationship between these two genera, placing them within Laeliinae (Epidendreae), yet the precise phylogenetic positioning remained uncertain. The absence of available plastome resources has hindered investigations into plastome evolution and phylogeny.<br><br>RESULTS: In this study, we sequenced and assembled the complete plastomes of Caularthron bicornutum and Myrmecophila thomsoniana to elucidate their plastome characteristics and phylogenetic relationships. The determined plastome sizes were 150,557&#xa0;bp for C. bicornutum and 156,905&#xa0;bp for M. thomsoniana, with GC contents of 37.3% and 37.1%, respectively. Notably, M. thomsoniana exhibited a distinctive IR expansion and SSC contraction, with the SSC region measuring only 4532&#xa0;bp and containing five genes (ccsA, ndhD, rpl32, psaC, and trnL-UAG), a unique feature observed for the first time in Epidendreae. Comparative analyses with species from the related genus Epidendrum revealed that C. bicornutum plastome exhibited conserved genome size, GC content, gene content, and gene order. A total of 32 and 33 long sequence repeats, 50 and 40 tandem repeats, and 99 and 109 SSRs were identified in the plastomes of C. bicornutum and M. thomsoniana, respectively. The RSCU analysis demonstrated a consistent pattern in both plastomes, with 29 out of 30 codons with RSCU values greater than 1 featuring A/U at the third codon position. Leucine was the most prevalent amino acid, while Cysteine was the least common. Four potential DNA barcoding regions with Pi values exceeding 0.07, namely ycf1, ccsA-psaC, petN-psbM, and accD-psaI, were identified for subsequent phylogenetic reconstructions within Laeliinae. Phylogenetic analysis underscored the close relationships among Caularthron, Epidendrum, and Myrmecophila.<br><br>CONCLUSIONS: This study represents the first comprehensive analysis of the plastome characteristics of Caularthron bicornutum and Myrmecophila thomsoniana. Through our characterization and phylogenetic analyses, we unveiled the unique IR expansion/SSC contraction and further elucidated their phylogenetic positions. Our research contributes significant data and insights into the dynamic evolution of ant-orchid plastomes and the phylogeny of the Laeliinae.}, }
@article {pmid39608688, year = {2025}, author = {Devan, J and Sandalova, M and Bitterli, P and Herger, N and Mengis, T and Brender, K and Heggli, I and Distler, O and Dudli, S}, title = {Massively parallel flow-cytometry-based screening of hematopoietic lineage cell populations from up to 25 donors simultaneously.}, journal = {Methods (San Diego, Calif.)}, volume = {234}, number = {}, pages = {45-53}, doi = {10.1016/j.ymeth.2024.11.014}, pmid = {39608688}, issn = {1095-9130}, mesh = {Humans ; *Flow Cytometry/methods ; *Immunophenotyping/methods ; *Hematopoietic Stem Cells/cytology/immunology/metabolism ; Cell Lineage ; Leukocyte Common Antigens/genetics ; Single-Cell Analysis/methods ; Antigens, CD ; Receptors, Transferrin/genetics ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {This study aimed to develop a method allowing high-dimensional and technically uniform screening of surface markers on cells of hematopoietic origin. High-dimensional screening of cell phenotypes is primarily the domain of single-cell RNA sequencing (RNAseq), which allows simultaneous analysis of the expression of thousands of genes in several thousands of cells. However, rare cell populations can often substantially impact tissue homeostasis or disease pathogenesis, and dysregulation of rare populations can easily be missed when only a few thousand cells are analyzed. With the presented methodological approach, it is possible to screen hundreds of markers on millions of cells in a technically uniform manner and thus identify and characterize changes in rare populations. We utilize the highly expressed markers CD45 on immune cells and CD71 on erythroid progenitors to create unique fluorescent barcodes on each of the 25 samples. Double-barcoded samples are co-stained with a broad immunophenotyping panel. The panel is designed in such a way that allows the addition of PE-labelled antibody, which was used for screening purposes. Multiplexed samples are divided into hundreds of aliquots and co-stained, each aliquot with a different PE-labelled antibody. Utilizing a broad immunophenotyping panel and machine-learning algorithms, we can predict the co-expression of hundreds of screened markers with a high degree of precision. This technique is suitable for screening immune cells in bone marrow from different locations, blood specimens, or any tissue with a substantial presence of immune cells, such as tumors or inflamed tissue areas in autoimmune conditions. It represents an approach that can significantly improve our ability to recognize dysregulated immune cell populations and, if needed, precisely target subsequent experiments covering lower cell counts such as RNAseq.}, }
@article {pmid39606648, year = {2024}, author = {Alvarez Rojas, CA and Bonacic, C and Salgado, R and Peters, L and Fredes, D and Rubio, AV and Muñoz-Leal, S and Oyarzún-Ruiz, P and Aguirre, AA}, title = {Genetic and biological insights into Hydatigera taeniaeformis in invasive black rats from southern Chile.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1466409}, pmid = {39606648}, issn = {2297-1769}, abstract = {INTRODUCTION: This study investigates the genetic variability of Hydatigera taeniaeformis in black rats (Rattus rattus), a common tapeworm that infects cats and rodents worldwide. Despite its widespread presence and zoonotic potential, little is known about the genetic diversity of this parasite in the Americas.<br><br>METHODS: We conducted DNA barcoding analysis using mitochondrial cox1 gene sequences using samples collected from 171 invasive wild black rats, captured in the temperate rainforest of Southern Chile. We also included two adult parasites isolated from road killed Kodkods (Leopardus guigna), a small felid species native to the Americas.<br><br>RESULTS: Our findings revealed only two haplotypes, suggesting low genetic variability in a parasite that arrived in the Americas with the Spanish colonization.<br><br>DISCUSSION: These haplotypes are more closely related to parasite populations from Peru, Africa, Australia, and Europe, suggesting an origin linked to the Spanish colonization, possibly from North Africa via the Canary Islands. The study also analyzed infection rates, parasite size, and their correlation with host body size, age, and weight, revealing significant patterns. These results provide new insights into the biogeography and genetic diversity of H. taeniaeformis in a new geographical area, enhancing our understanding of its evolutionary history.}, }
@article {pmid39606254, year = {2024}, author = {Ding, M and Cheng, H and Li, X and Li, X and Zhang, M and Cui, D and Yang, Y and Tian, X and Wang, H and Yang, W}, title = {Phytochemistry, quality control and biosynthesis in ginseng research from 2021 to 2023: A state-of-the-art review concerning advances and challenges.}, journal = {Chinese herbal medicines}, volume = {16}, number = {4}, pages = {505-520}, pmid = {39606254}, issn = {2589-3610}, abstract = {Panax L. (Araliaceae) has a long history of medicinal and edible use due to its significant tonifying effects, and ginseng research has been a hot topic in natural products research and food science. In continuation of our recent ginseng review, we highlighted the advances in ginseng research from 2021 to 2023 with 157 citations, which exhibited the increasingly systematic, collaborative, and intelligent characteristics. In this review, we firstly updated the progress in phytochemistry involving the ginsenosides and polysaccharides and summarized the researches on the active components. Then, some specific applications by feat of the multidimensional chromatography, mass spectrometry imaging, DNA barcoding, and metabolomics, were analyzed, which could provide rich information supporting the multi-component characterization, authentication, and quality control of ginseng and the versatile products. Finally, the recent biosynthesis studies concerning ginsenosides were retrospected. Additionally, the current challenges and future trends with respect to ginseng research were discussed.}, }
@article {pmid39605649, year = {2024}, author = {Diamond, B and Chahar, D and Jain, MD and Poos, AM and Durante, M and Ziccheddu, B and Kaddoura, M and Papadimitriou, M and Maclachlan, K and Jelinek, T and Davies, F and Figura, NB and Morgan, G and Mai, E and Weisel, KC and Fenk, R and Raab, MS and Usmani, S and Landgren, O and Locke, FL and Goldschmidt, H and Schatz, JH and Weinhold, N and Maura, F}, title = {Mutagenic impact and evolutionary influence of radiotherapy in hematologic malignancies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605649}, issn = {2692-8205}, support = {K12 CA226330/CA/NCI NIH HHS/United States ; P30 CA240139/CA/NCI NIH HHS/United States ; }, abstract = {Ionizing radiotherapy (RT) is a widely used palliative and curative treatment strategy for malignancies. In solid tumors, RT-induced double strand breaks lead to the accumulation of indels, and their repair by non-homologous end-joining has been linked to the ID8 mutational signature in resistant cells. However, the extent of RT-induced DNA damage in hematologic malignancies and its impact on their evolution and interplay with commonly used chemotherapies has not yet been explored. Here, we interrogated 580 whole genome sequencing (WGS) from patients with large B-cell lymphoma, multiple myeloma, and myeloid neoplasms and identified ID8 only in relapsed disease. Yet, it was detected after exposure to both RT and mutagenic chemotherapy (i.e., platinum). Using WGS of single-cell colonies derived from treated lymphoma cells, we revealed a dose-response relationship between RT and platinum and ID8. Finally, using ID8 as a genomic barcode we demonstrate that a single RT-resistant cell may seed systemic relapse.}, }
@article {pmid39605582, year = {2024}, author = {Meleshko, D and Yang, R and Maharjan, S and Danko, DC and Korobeynikov, A and Hajirasouliha, I}, title = {Blackbird: structural variant detection using synthetic and low-coverage long-reads.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605582}, issn = {2692-8205}, support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: Recent benchmarks of structural variant (SV) detection tools revealed that the majority of human genome structural variations (SVs), especially the medium-range (50-10,000 bp) SVs cannot be resolved with short-read sequencing, but long-read SV callers achieve great results on the same datasets. While improvements have been made, high-coverage long-read sequencing is associated with higher costs and input DNA requirements. To decrease the cost one can lower the sequence coverage, but the current long-read SV callers perform poorly with coverage below 10×. Synthetic long-read (SLR) technologies hold great potential for structural variant (SV) detection, although utilizing their long-range information for events smaller than 50 kbp has been challenging.<br><br>RESULTS: In this work, we propose a hybrid novel integrated alignment- and local-assembly-based algorithm, Blackbird, that uses SLR together with low-coverage long reads to improve SV detection and assembly. Without the need for a computationally expensive whole genome assembly, Blackbird uses a sliding window approach and barcode information encoded in SLR to accurately assemble small segments and use long reads for an improved gap closing and contig assembly. We evaluated Blackbird on simulated and real human genome datasets. Using the HG002 GIAB benchmark set, we demonstrated that in hybrid mode, Blackbird demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5&#xd7; coverage to achieve F1 scores (0.835 and 0.808 for deletions and insertions) similar to PBSV (0.856 and 0.812) and Sniffles2 (0.839 and 0.804) using 10&#xd7; Pacbio Hi-Fi long-read coverage.}, }
@article {pmid39605581, year = {2024}, author = {Enninful, A and Zhang, Z and Klymyshyn, D and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Yang, M and Lu, Y and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R}, title = {Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39605581}, issn = {2692-8205}, support = {U54 AG079759/AG/NIA NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; }, abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.}, }
@article {pmid39605504, year = {2024}, author = {Yan, Y and Cheung, E and Verzier, LH and Appetecchia, F and March, S and Craven, AR and Du, E and Probst, AS and Rinvee, TA and de Vries, LE and Kauffman, J and Bhatia, SN and Nelson, E and Singh, N and Peng, D and Shaw, WR and Catteruccia, F}, title = {Mapping Plasmodium transitions and interactions in the Anopheles female.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.12.623125}, pmid = {39605504}, issn = {2692-8205}, support = {T32 AI049928/AI/NIAID NIH HHS/United States ; }, abstract = {The human malaria parasite, Plasmodium falciparum , relies on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal. How surviving ookinetes interact with midgut cells and form oocysts is unknown, yet these steps are essential to initiate a remarkable, similarly uncharacterized growth process culminating in the production of thousands of infectious sporozoites. Here, using single-cell RNA sequencing of both parasites and mosquito cells across four time points and two metabolic conditions, we unveil key processes shaping developmental transitions and mosquito-parasite interactions occurring in the midgut. In depth functional analyses reveal processes regulating oocyst growth and identify the transcription factor Pf SIP2 as essential for sporozoite infection of human hepatocytes. By combining the analysis of shared mosquito-parasite barcodes with confocal microscopy, we discover that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we unveil tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adhere to the midgut without damaging it. Ultimately, our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.}, }
@article {pmid39605487, year = {2025}, author = {Delamarre, A and Bailey, B and Yavid, J and Koche, R and Mohibullah, N and Whitehouse, I}, title = {Chromatin architecture mapping by multiplex proximity tagging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.12.623258}, pmid = {39605487}, issn = {2692-8205}, abstract = {Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate in 3D space. Using this method - Proximity Copy Paste (PCP) - we mapped the connectivity of individual nucleosomes in Saccharomyces cerevisiae. By analyzing nucleosome positions and spacing on single molecule fibers, we show that chromatin is predominantly organized into regularly spaced nucleosome arrays that can be positioned or delocalized. Basic features of nucleosome arrays are generally explained by gene size and transcription. PCP can also map long-range, multi-way interactions and we provide the first direct evidence supporting a model that metaphase chromosomes are compacted by cohesin loop clustering. Analyzing single-molecule nuclease footprinting data we define distinct chromatin states within a mixed population to show that non-canonical nucleosomes, notably Overlapping-Di-Nucleosomes (OLDN) are a stable feature of chromatin. PCP is a versatile method allowing the detection of the connectivity of individual molecules locally and over large distance to be mapped at high-resolution in a single experiment.}, }
@article {pmid39604449, year = {2024}, author = {Holzmann, M and Nguyen, NL and Angeles, IB and Pawlowski, J}, title = {BFR2: a curated ribosomal reference dataset for benthic foraminifera.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1292}, pmid = {39604449}, issn = {2052-4463}, support = {Exploring abyssal and hadal biodiversity of foraminifera in the North Pacific//Fondation Ernst et Lucie Schmidheiny (Ernst and Lucie Schmidheiny Foundation)/ ; 221959//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_179125//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_159709//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 316030_150817//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic ; RNA, Ribosomal, 18S/genetics ; DNA, Ribosomal/genetics ; }, abstract = {Benthic foraminifera are one of the major groups of marine protists that also occur in freshwater and terrestrial habitats. They are widely used to monitor current and past environmental conditions. Over the last three decades, thousands of DNA sequences have been obtained from benthic foraminiferal isolates. The results of this long-term effort are compiled here in the form of the first curated benthic foraminiferal ribosomal reference dataset (BFR2). The present dataset contains over 5000 sequences of a fragment of the 18S rDNA gene, which is recognized as the DNA barcode of foraminifera. The sequences represent 279 species and 204 genera belonging to 91 families. Thirteen percent of these sequences have not been assigned to any morphologically described group and may represent species new to science. Furthermore, forty-five percent of the sequences have not been previously published. The BFR[2] dataset aims to collect all DNA barcodes of benthic foraminifera and to provide a much-needed reference dataset for the rapidly developing field of molecular foraminiferal studies.}, }
@article {pmid39604411, year = {2024}, author = {Purushothaman, S and Meola, M and Roloff, T and Rooney, AM and Egli, A}, title = {Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29531}, pmid = {39604411}, issn = {2045-2322}, support = {310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 310030_192512//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; Humans ; Bacteria/genetics/isolation &amp; purification/classification ; }, abstract = {During a bacterial infection or colonization, the detection of antimicrobial resistance (AMR) is critical, but slow due to culture-based approaches for clinical and screening samples. Culture-based phenotypic AMR detection and confirmation require up to 72 hours (h) or even weeks for slow-growing bacteria. Direct shotgun metagenomics by long-read sequencing using Oxford Nanopore Technologies (ONT) may reduce the time for bacterial species and AMR gene identification. However, screening swabs for metagenomics is complex due to the range of Gram-negative and -positive bacteria, diverse AMR genes, and host DNA present in the samples. Therefore, DNA extraction is a critical initial step. We aimed to compare the performance of different DNA extraction protocols for ONT applications to reliably identify species and AMR genes using a shotgun long-read metagenomic approach. We included three different sample types: ZymoBIOMICS Microbial Community Standard, an in-house mock community of ESKAPE pathogens including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli (ESKAPE Mock), and anonymized clinical swab samples. We processed all sample types with four different DNA extraction kits utilizing different lysis (enzymatic vs. mechanical) and purification (spin-column vs. magnetic beads) methods. We used kits from Qiagen (QIAamp DNA Mini and QIAamp PowerFecal Pro DNA) and Promega (Maxwell RSC Cultured Cells and Maxwell RSC Buccal Swab DNA). After extraction, samples were subject to the Rapid Barcoding Kit (RBK004) for library preparation followed by sequencing on the GridION with R9.4.1 flow cells. The fast5 files were base called to fastq files using Guppy in High Accuracy (HAC) mode with the inbuilt MinKNOW software. Raw read quality was assessed using NanoPlot and human reads were removed using Minimap2 alignment against the Hg38 genome. Taxonomy identification was performed on the raw reads using Kraken2 and on assembled contigs using Minimap2. The AMR genes were identified using Minimap2 with alignment against the CARD database on both the raw reads and assembled contigs. We identified all bacterial species present in the Zymo Mock Community (8/8) and ESKAPE Mock (6/6) with Qiagen PowerFecal Pro DNA kit (chemical and mechanical lysis) at read and assembly levels. Enzymatic lysis retrieved fewer aligned bases for the Gram-positive species (Staphylococcus aureus and Enterococcus faecium) from the ESKAPE Mock on the assembly level compared to the mechanical lysis. We detected the AMR genes from Gram-negative and -positive species in the ESKAPE Mock with the QIAamp PowerFecal Pro DNA kit on reads level with a maximum median time of 1.9 h of sequencing. Long-read metagenomics with ONT may reduce the turnaround time in screening for AMR genes. Currently, the QIAamp PowerFecal Pro DNA kit (chemical and mechanical lysis) for DNA extraction along with the Rapid Barcoding Kit for the ONT sequencing captured the best taxonomy and AMR identification for our specific use case.}, }
@article {pmid39603810, year = {2025}, author = {Gong, X and Zhang, H and Guo, Y and Yu, S and Tang, M}, title = {Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment.}, journal = {The plant genome}, volume = {18}, number = {1}, pages = {e20534}, pmid = {39603810}, issn = {1940-3372}, support = {SH2023078//Science and Technology Plan Projects of Zhenjiang/ ; JDYY2023009//Medical Education Collaborative Innovation Fund of Jiangsu University/ ; 32002235//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Plant ; *Arthritis, Rheumatoid/drug therapy ; *Chromosomes, Plant/genetics ; Phylogeny ; Humans ; }, abstract = {Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.}, }
@article {pmid39603754, year = {2024}, author = {Maladan, Y and Retnaningrum, E and Daryono, BS and Sarassari, R and Sari, RF and Balqis, SA and Wahid, GA and Safari, D}, title = {A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9-Targeted Sequencing.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {26}, number = {12}, pages = {1045-1054}, doi = {10.1016/j.jmoldx.2024.08.009}, pmid = {39603754}, issn = {1943-7811}, mesh = {*Streptococcus pneumoniae/genetics/classification ; *CRISPR-Cas Systems/genetics ; *Serotyping/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Pneumococcal Infections/microbiology/genetics ; Genome, Bacterial ; }, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) application for targeted sequencing has made a breakthrough in the genomic research era. High diversity in the capsular polysaccharide (cps) locus of Streptococcus pneumoniae has hampered identification of the serotype. This study developed a new serotyping method for S. pneumoniae using CRISPR/Cas9-targeted sequencing with the Oxford Nanopore Technologies platform. A probe was designed at the position of the cps locus using an excision approach on two sides flanking genes between the dexB and aliA genes with approximately 20 kb. A native barcoding method was used for multiplexing. The probe will attach to a specific side followed by attachment of CRISPR/Cas9 to cut the recognition area. The study used de novo assembly to reconstruct sequence reads, which were analyzed using PneumoCRISPR, a new serotyping pipeline for Oxford Nanopore Technologies sequencing data output. Four CRISPR/Cas9 probes have been designed and recognize the cps locus of S. pneumoniae. Serotyping results align precisely with serotyping data from whole-genome sequencing. This serotyping method also allows researchers to use multiple samples in a single run. The new serotyping method based on CRISPR/Cas9-targeted sequencing holds immense promise for serotype identification of S. pneumoniae.}, }
@article {pmid40678274, year = {2024}, author = {Liao, J and Yang, L}, title = {Multimode Sensing by Optical Whispering-gallery-mode Barcodes: A New Route to Expand Dynamic Range for High-resolution Measurement.}, journal = {IEEE transactions on instrumentation and measurement}, volume = {73}, number = {}, pages = {}, pmid = {40678274}, issn = {0018-9456}, support = {R21 EB030845/EB/NIBIB NIH HHS/United States ; }, abstract = {Sensors play a vital role in detecting and quantifying various parameters relevant to the physical and biochemical aspects of the world. In the field of optical sensing, Whispering-Gallery-Mode (WGM) microresonators have emerged as promising candidates, offering the advantages of high sensitivity, high resolution, and small footprint. However, conventional sensing methods, which rely on tracking changes in a single mode, have a limited dynamic range of measurement. In this study, we develop a theoretical framework that offers comprehensive analytical insights for multimode-sensing techniques. We demonstrate an optical WGM barcode technique that enables simultaneous monitoring of the patterns of multiple modes that can provide over-FSR (Free spectral range) tracking with high resolution. By analyzing the Cramer-Rao bound (CRB) for resonance shift estimation, we assess the theoretical limits of measurement resolution and dynamic range, independent of specific sensing system and estimation algorithm. Comparative analysis of the CRBs for single-mode sensing and multimode sensing confirms the improvement in resolution and dynamic range achievable through the barcode technique based on the multimode spectrum. This work lays the foundation for developing a high-resolution sensor with superior sensitivity across a drastically expanded dynamic range.}, }
@article {pmid40028488, year = {2023}, author = {Dhar, R and Devi, A}, title = {Exosomes Barcoding: A smart approach for cancer liquid biopsy.}, journal = {The journal of liquid biopsy}, volume = {2}, number = {}, pages = {100129}, pmid = {40028488}, issn = {2950-1954}, abstract = {Cancer is an unsolved health crisis worldwide. Extracellular vesicles (EVs) address this problem in a new way. In cancer, early detection is highly challenging, exosomes (a subpopulation of EVs, originating from endosomes) overcomes this limitation. In cancer, tumor-derived exosomes (TEXs) play a role as signaling molecules in cancer development and progression. TEXs provide detailed investigation for specific cancer biomarkers research. Exosomes heterogeneity (variation in exosomes size, exosomes origin, and inner molecular diversity) has led to complications in understanding and studying cancer liquid biopsies. Single exosome profiling and exosomes barcoding has helped in supporting and overcoming this limitation and has played a significant role in precision oncology. Exosomes barcoding is a promising interdisciplinary approach for screening cancers more specifically.}, }
@article {pmid39711846, year = {2023}, author = {Adams, SJ and Walker, AK}, title = {Diversity of fungi from marine inundated wood from the Bay of Fundy, Nova Scotia, Canada.}, journal = {Botanica marina}, volume = {66}, number = {4}, pages = {319-329}, pmid = {39711846}, issn = {0006-8055}, abstract = {Marine fungi play an integral role in the decomposition of intertidal organic substrata but remain understudied in cold-water habitats including Atlantic Canada. Marine inundated wood from the intertidal zone was sampled from 30 sites along the Bay of Fundy coastline in Nova Scotia, Canada. Wood types studied included attached and loose intertidal wood, and driftwood. Emergent fungi were cultured and identified using ITS (internal transcribed spacers) rDNA barcoding. Two hundred and twenty cultures representing 86 fungi are reported. Sixty-one fungi were new records for the Bay of Fundy, 41 are first records from the marine environment, and 19 fungi are potentially new to science. Fungi identified included eight obligate marine fungi, with the remaining fungi being facultatively marine. Eight ascomycetes were soft rot fungi; this ecological strategy for decaying woody material in cold-water marine environments is discussed. Historical records and roles of wood type and site on fungal colonization are discussed.}, }
@article {pmid40809480, year = {2023}, author = {Pan, Y and D'Orsogna, MR and Tang, M and Stiehl, T and Chou, T}, title = {Clonal abundance patterns in hematopoiesis: Mathematical modeling and parameter estimation.}, journal = {Frontiers in systems biology}, volume = {3}, number = {}, pages = {893366}, pmid = {40809480}, issn = {2674-0702}, abstract = {Hematopoiesis has been studied via stem cell labeling using barcodes, viral integration sites (VISs), or in situ methods. Subsequent proliferation and differentiation preserve the tag identity, thus defining a clone of mature cells across multiple cell type or lineages. By tracking the population of clones, measured within samples taken at discrete time points, we infer physiological parameters associated with a hybrid stochastic-deterministic mathematical model of hematopoiesis. We analyze clone population data from Koelle et al. (Koelle et al., 2017) and compare the states of clones (mean and variance of their abundances) and the state-space density of clones with the corresponding quantities predicted from our model. Comparing our model to the tagged granulocyte populations, we find parameters (stem cell carrying capacity, stem cell differentiation rates, and the proliferative potential of progenitor cells, and sample sizes) that provide reasonable fits in three out of four animals. Even though some observed features cannot be quantitatively reproduced by our model, our analyses provides insight into how model parameters influence the underlying mechanisms in hematopoiesis. We discuss additional mechanisms not incorporated in our model.}, }
@article {pmid39635013, year = {2022}, author = {Liu, Y and Li, X and Chen, Y and Geng, G and Li, J and Wang, Y and Huang, L}, title = {Imaging-based optical barcoding for relative humidity sensing based on meta-tip.}, journal = {Nanophotonics (Berlin, Germany)}, volume = {11}, number = {1}, pages = {111-118}, pmid = {39635013}, issn = {2192-8614}, abstract = {In a wide range of applications such as healthcare treatment, environmental monitoring, food processing and storage, and semiconductor chip manufacturing, relative humidity (RH) sensing is required. However, traditional fiber-optic humidity sensors face the challenges of miniaturization and indirectly obtaining humidity values. Here, we propose and demonstrate an optical barcode technique by cooperating with RH meta-tip, which can predict the humidity values directly. Such RH meta-tip is composed of fiber-optic sensor based on surface plasmon resonance (SPR) effect and graphene oxide film as humidity sensitizer. While SPR sensor is composed of multimode fiber (MMF) integrated with metallic metasurface. Dynamic time warping (DTW) algorithm is used to obtain the warp path distance (WPD) sequence between the measured reflection spectrum and the spectra of the precalibrated database. The distance sequence is transformed into a pseudo-color barcode, and the humidity value is corresponded to the lowest distance, which can be read by human eyes. The RH measurement depends on the collective changes of the reflection spectrum rather than tracking a single specific resonance peak/dip. This work can open up new doors to the development of a humidity sensor with direct RH recognition by human eyes.}, }
@article {pmid40370414, year = {2016}, author = {Dellinger, TA and Wong, V and Marek, PE}, title = {Makelabels: a Bash script for generating data matrix codes for collection management.}, journal = {Biodiversity data journal}, volume = {4}, number = {}, pages = {e9583}, pmid = {40370414}, issn = {1314-2828}, abstract = {BACKGROUND: Digitization of natural history collections allows easy access and reuse of the invaluable biodiversity data held within a collection by providing access to specimen level data through the Internet. Each digitized specimen in a database requires a unique catalog number to distinguish it from the many other biologically unique specimens within the collection. However, there are few open source barcode generators available, and of these even fewer platforms exist to enable the mass production of barcode labels required by natural history collections. We developed a low-cost, open source solution to generating data matrix barcodes with unique catalog numbers for use in the Virginia Tech Insect Collection.<br><br>NEW INFORMATION: Here we describe the makelabels script, which uses the open source Unix packages libdmtx and ImageMagick to generate unique specimen labels containing both a human-readable catalog number and a machine-readable data matrix barcode. The mass production of labels and use of both types of catalog symbology provides flexibility in specimen management and increased efficiency in digitization and specimen processing workflows.}, }
@article {pmid39603242, year = {2024}, author = {Pahl, V and Lubrano, P and Troßmann, F and Petras, D and Link, H}, title = {Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state.}, journal = {Cell reports methods}, volume = {4}, number = {12}, pages = {100908}, pmid = {39603242}, issn = {2667-2375}, mesh = {*Mass Spectrometry/methods ; Ubiquitin/metabolism/genetics ; CRISPR-Cas Systems/genetics ; Escherichia coli/genetics/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Metabolome ; }, abstract = {Detecting strain-specific barcodes with mass spectrometry can facilitate the screening of genetically engineered bacterial libraries. Here, we introduce intact protein barcoding, a method to measure protein-based library barcodes and metabolites using flow injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin with N-terminal tags of six amino acids. We demonstrate that FI-MS detects intact ubiquitin proteins and identifies the mass of N-terminal barcodes. In the same analysis, we measured relative concentrations of primary metabolites. We constructed six ubiquitin-barcoded CRISPR interference (CRISPRi) strains targeting metabolic enzymes and analyzed their metabolic profiles and ubiquitin barcodes. FI-MS detected barcodes and distinct metabolome changes in CRISPRi-targeted pathways. We demonstrate the scalability of intact protein barcoding by measuring 132 ubiquitin barcodes in microtiter plates. These results show that intact protein barcoding enables fast and simultaneous detection of library barcodes and intracellular metabolites, opening up new possibilities for mass spectrometry-based barcoding.}, }
@article {pmid39602973, year = {2025}, author = {Um, DH and Knowles, DA and Kaiser, GE}, title = {Vector embeddings by sequence similarity and context for improved compression, similarity search, clustering, organization, and manipulation of cDNA libraries.}, journal = {Computational biology and chemistry}, volume = {114}, number = {}, pages = {108251}, doi = {10.1016/j.compbiolchem.2024.108251}, pmid = {39602973}, issn = {1476-928X}, mesh = {*Gene Library ; Cluster Analysis ; Algorithms ; Data Compression ; }, abstract = {This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ[5]). By assigning a unique vector embedding to each short sequence, it is possible to more efficiently cluster and improve upon compression performance for the string representations of cDNA libraries. Furthermore, by studying alternative coordinate vector embeddings trained on the context of codon triplets, we can demonstrate clustering based on amino acid properties. Employing this sequence embedding method to encode barcodes and cDNA sequences, we can improve the time complexity of similarity searches. By pairing vector embeddings with an algorithm that determines the vector proximity in Euclidean space, this approach enables quicker and more flexible sequence searches.}, }
@article {pmid39602792, year = {2024}, author = {Lancioni, GE and Alberti, G and Filippini, C and Singh, NN and O'Reilly, MF and Sigafoos, J and Orlando, I and Desideri, L}, title = {A Technology System to Help People With Intellectual Disability and Blindness Find Room Destinations During Indoor Traveling: Case Series Study.}, journal = {JMIR rehabilitation and assistive technologies}, volume = {11}, number = {}, pages = {e65680}, pmid = {39602792}, issn = {2369-2529}, abstract = {BACKGROUND: People with severe or profound intellectual disability and visual impairment tend to have serious problems in orientation and mobility and need assistance for their indoor traveling. The use of technology solutions may be critically important to help them curb those problems and achieve a level of independence.<br><br>OBJECTIVE: This study aimed to assess a new technology system to help people with severe to profound intellectual disability and blindness find room destinations during indoor traveling.<br><br>METHODS: A total of 7 adults were included in the study. The technology system entailed a barcode reader, a series of barcodes marking the room entrances, a smartphone, and a special app that controlled the presentation of different messages (instructions) for the participants. The messages varied depending on whether the participants were (1) in an area between room entrances, (2) in correspondence with a room entrance to bypass, or (3) in correspondence with a room entrance representing the destination to enter. The intervention with the technology system was implemented according to a nonconcurrent multiple baseline design across participants. Sessions included 7 traveling trials, in each of which the participants were to reach and enter a specific room (1 of the 7 or 9 available) to deliver an object they had carried (transported) during their traveling.<br><br>RESULTS: The participants' mean frequency of traveling trials completed correctly was between zero and 2 per session during the baseline (without the system). Their mean frequency increased to between about 6 and nearly 7 per session during the intervention (with the system).<br><br>CONCLUSIONS: The findings suggest that the new technology system might be a useful support tool for people with severe to profound intellectual disability and blindness.}, }
@article {pmid39599554, year = {2024}, author = {Morelli, M and D'Attoma, G and Saldarelli, P and Minafra, A}, title = {The Evolution of Wisteria Vein Mosaic Virus: A Case Study Approach to Track the Emergence of New Potyvirus Threats.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39599554}, issn = {2076-0817}, mesh = {*Potyvirus/genetics/isolation &amp; purification/classification ; *Phylogeny ; *Plant Diseases/virology ; Genome, Viral/genetics ; Evolution, Molecular ; Brassicaceae/virology ; Genetic Variation/genetics ; }, abstract = {Wisteria vein mosaic virus (WVMV, Potyvirus wisteriae), a virus belonging to the genus Potyvirus, is responsible for Wisteria vein mosaic disease (WMD), a severe disease that affects Wisteria, a genus of garden plants acclaimed worldwide. Although probably originating in the Far East, WVMV infection was first reported in the US, and subsequently in numerous countries. Following the first molecular detection of an Italian isolate, WVMV Bari, its full-length genome was achieved using NGS barcoding technology. A PhyML phylogenetic analysis, supported by clustering algorithm validation, identified a clear separation between two phylogroups. One major clade comprised WVMV strains isolated from Wisteria spp. A second clade grouped three highly divergent strains, at the borderline species threshold, all found in non-wisteria hosts. Relying on a Relative Time Dated Tips (RTDT) molecular clock, the first emergence of WVMV clades has been traced back to around the 17th century. A network inference analysis confirmed the sharp separation between the two host-related phylogroups, also highlighting the presence of potential intermediate variants. Inter-population genetic parameters revealed a very high genetic differentiation in both populations, which was made reliable by statistically significant permutation tests. The migrant number (Nm) and fixation index (FST) evidenced a restricted gene flow and strong population structures. According to the dN/dS ratio and negative neutrality tests, it was derived that purifying selection at the expense of non-silent variants is underway within WVMV populations. Targeting WVMV evolutionary traits, the present effort raised interesting questions about the underestimated potential of this culpably neglected species to spread in economically relevant crops. The main intention of our study is, therefore, to propose an evolution-based analysis approach that serves as a case study to investigate how other potyviruses or newly emerging viruses may spread.}, }
@article {pmid39599494, year = {2024}, author = {Alkathiri, B and Lee, S and Ahn, K and Youn, SY and Yoo, MS and Lee, HS and Cho, YS and Jung, J and Seo, K and Kim, S and Umemiya-Shirafuji, R and Xuan, X and Kwak, D and Shin, S and Lee, SH}, title = {DNA Barcoding Using 18S rRNA Gene Fragments for Identification of Tick-Borne Protists in Ticks in the Republic of Korea.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, pmid = {39599494}, issn = {2076-0817}, support = {//Animal and Plant Quarantine Agency/ ; 2024//Chungbuk National University BK21 program/ ; }, mesh = {Animals ; *RNA, Ribosomal, 18S/genetics ; *DNA Barcoding, Taxonomic/methods ; Republic of Korea/epidemiology ; DNA, Protozoan/genetics ; Ticks/parasitology ; Theileria/genetics/isolation &amp; purification ; Phylogeny ; Ixodes/genetics/parasitology ; }, abstract = {The objective of this study was to evaluate the diversity and prevalence of tick-borne protists in the Republic of Korea via DNA barcoding using 18S rRNA gene fragments and PCR. Between 2021 and 2022, questing ticks were collected using the flagging method, with a total of 13,375 ticks collected and pooled into 1003 samples. Of these, 50 tick pools were selected for DNA barcoding targeting the V4 and V9 regions of 18S rRNA using the MiSeq platform. A taxonomic analysis of the amplicon sequence variants identified three genera of protozoa, namely Hepatozoon canis, Theileria luwenshuni, and Gregarine sp. However, the number and abundance of protists detected were different depending on the primer sets, and T. gondii was not identified in DNA barcoding. Furthermore, conventional PCR confirmed the presence of H. canis, Toxoplasma gondii, T. luwenshuni, and Theileria sp. in the collected ticks. This study identified H. canis and T. gondii in Ixodes nipponensis for the first time. It demonstrated that the results of DNA barcoding using 18S rRNA gene fragments can vary depending on the primer sets and further optimization is required for library construction to identify tick-borne protists in ticks. Despite these limitations, the findings highlight the potential of DNA barcoding using 18S rRNA gene fragments for screening the diversity of tick-borne protists in ticks.}, }
@article {pmid39599378, year = {2024}, author = {De Luca, D and Del Guacchio, E and Cennamo, P and Minutillo, F and Bernardo, L and Caputo, P}, title = {Genetics and Distribution of the Italian Endemic Campanula fragilis Cirillo (Campanulaceae).}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {22}, pages = {}, pmid = {39599378}, issn = {2223-7747}, abstract = {Campanula fragilis Cirillo is a species distributed in central and southern Italy and includes two subspecies with uncertain taxonomic position and distribution. By means of nuclear and chloroplast markers, we attempted at testing the genetic distinctness of the two subspecies, as well as their possible correspondence with geographical or ecological patterns. After a revision of geographic occurrences based on herbarium data, we carried out species distribution modeling to assess the present and future distribution of this species under different ecological variables, also for conservation purposes. Our findings support the recognition of two weakly differentiated taxa, here accepted at subspecific rank, in agreement with the current taxonomic treatment. We found that C. fragilis subsp. cavolinii is monophyletic and limited to mountains and hills of central Italy. On the contrary, C. fragilis subsp. fragilis shows a higher genetic variability and a broader distribution in central and southern Italy, with a wider altitudinal range from coasts to mountain cliffs. We confirmed that both subspecies are narrowly calcicolous and have similar ecological requirements, but C. fragilis subsp. cavolinii occurs in colder habitats. Our results forecast a significant distribution contraction in the long term.}, }
@article {pmid39597591, year = {2024}, author = {Chen, H and Yin, X and Chen, Y and Wang, Y and Li, Q and Ji, N and Zhou, L and Hu, G and Shen, X}, title = {Characterization of a Levanderina fissa Bloom in Aquaculture Ponds and Its Utilization of Dissolved Organic Phosphorus.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597591}, issn = {2076-2607}, support = {SF2303//Lianyungang Key Research and Development Program/ ; }, abstract = {Harmful algal blooms (HABs) pose significant threats to ecosystems and human health worldwide, with their frequency and intensity increasing substantially. The present study reports an algal bloom observed in an aquaculture pond near Haizhou Bay in July 2022. The causative species, identified through morphological observation and DNA barcoding analysis, was the dinoflagellate Levanderina fissa (Levander) Moestrup, Hakanen, Gert Hansen, Daugbjerg &amp; M. Ellegaard, 2014, known for causing extensive HAB events in the coastal waters of China. A sharp decline in phytoplankton species diversity was observed during the transition from the pre-bloom to the bloom phase. Furthermore, the uptake of four types of dissolved organic phosphorus (DOP), including glucose-6-phosphate (G6P), adenosine-5-triphosphate (ATP), sodium tripolyphosphate (TPP), and glyphosate, by isolated L. fissa was investigated in the laboratory. The results showed that G6P, ATP, and TPP supported L. fissa growth as effectively as orthophosphate. Additionally, the elevated concentrations of dissolved inorganic phosphorus in the media of the three treatments indicated the involvement of extracellular hydrolysis. However, alkaline phosphatase was not responsible for the hydrolysis of these three forms of DOP. This study demonstrates that the ability of L. fissa to utilize DOP may confer a competitive advantage within phytoplankton communities, potentially leading to algal blooms in aquaculture ponds.}, }
@article {pmid39596906, year = {2024}, author = {Ismailaj, M and Zangaro, F and Specchia, V and Sangiorgio, F and Marcucci, F and Kiçaj, H and Basset, A and Pinna, M}, title = {Biodiversity Patterns and DNA Barcode Gap Analysis of COI in Coastal Lagoons of Albania.}, journal = {Biology}, volume = {13}, number = {11}, pages = {}, pmid = {39596906}, issn = {2079-7737}, support = {101082327//EU commission/ ; }, abstract = {Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies on morphological species identification methods, but DNA-based taxonomic identification could improve the monitoring and assessment of aquatic ecosystems. This study aims to evaluate the coverage of COI DNA barcodes in the reference libraries for the known aquatic animal species present in the coastal lagoons of Albania. In this study, the six most studied coastal lagoons of Albania were selected. Species data were gathered from the scientific literature and publicly available sites and studies. The collected species lists were taxonomically standardised using global public taxonomic databases like WORMS. The standardised lists were used to analyse the barcode gap of COI based on two public DNA barcode libraries: Barcode of Life Data Systems (BOLD) and NCBI GenBank. The results show that the COI DNA barcode gap in the coastal lagoons of Albania ranges from 7% (Lagoon of Patok) to 33% (Karavasta Lagoon). Fishes and Amphibia represent the groups with the lowest barcode gap (8% each), while Annelida shows the highest (47%). In conclusion, the COI gene marker for DNA-based biodiversity assessments is reliable for the coastal lagoons of Albania.}, }
@article {pmid39596647, year = {2024}, author = {Almerekova, S and Yermagambetova, M and Ivashchenko, A and Abugalieva, S and Turuspekov, Y}, title = {Assessment of Complete Plastid Genome Sequences of Tulipa alberti Regel and Tulipa greigii Regel Species from Kazakhstan.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, pmid = {39596647}, issn = {2073-4425}, support = {AP14870612//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {*Phylogeny ; *Genome, Plastid ; Kazakhstan ; *Tulipa/genetics ; Microsatellite Repeats/genetics ; Plastids/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Tulipa species are economically, culturally, scientifically, and ecologically important. Tulips present taxonomic complexities that cannot be adequately resolved by examining their morphological characteristics alone or by relying on a limited selection of genetic markers.<br><br>METHODS: In the present study, we assessed the complete plastid sequences of Tulipa alberti Regel and Tulipa greigii Regel collected from Kazakhstan. Additionally, 14 previously published plastomes were obtained from GenBank for comparison and phylogenetic analysis.<br><br>RESULTS: The plastid genome sizes of T. alberti and T. greigii were 152,359 bp and 152,242 bp, respectively. In the plastid genomes of T. alberti and T. greigii, 136 genes were annotated, 114 of which were unique. These unique genes comprised eighty protein-coding, thirty transfer RNA, and four ribosomal RNA genes. Additionally, 415 simple sequence repeats were identified, comprising 107 tandem, 40 forward, 49 palindromic, 8 reverse, and 1 complementary repeat. Notably, the region containing ycf1 exhibited high variability and may serve as an informative DNA barcode for this genus.<br><br>CONCLUSION: Phylogenetic analysis showed strong support for the relationships among Tulipa species, indicating the utility of plastid genome data for further taxonomic studies within the genus.}, }
@article {pmid39596617, year = {2024}, author = {Sajjad, S and Islam, M and Muhammad, K and Ghafoor, SU and Ullah, I and Khan, A and Siraj, M and Alrefaei, AF and Shah, JA and Ali, S}, title = {Comprehensive Evaluation of Cryptic Juglans Genotypes: Insight from Molecular Markers and Phylogenetic Analysis.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, pmid = {39596617}, issn = {2073-4425}, mesh = {*Juglans/genetics/classification ; *Phylogeny ; *Genotype ; Genetic Markers/genetics ; DNA Barcoding, Taxonomic/methods ; Pakistan ; }, abstract = {Background/Objectives: The current research work aimed to evaluate the cryptic walnut genotypes of the Hazara region in Pakistan by using DNA barcoding and phylogenetic analysis. Methods: Based on morphological traits such as nut size, nut shape, and the number of leaflets, five genotypes were chosen and samples were collected for the current study. For molecular analysis, gDNA was isolated from the fresh leaves, and the five most effective angiosperm-specific markers, ITS2, rbcLa, rbcLc, rpoC1, and UBE3, were utilized. Based on amplification, sequencing, and identification success rates, ITS2 and UBE3 were recorded as the most efficient markers followed by rbcLa, rbcLc, and rpoC1. Results: During phylogenetic analysis, the query genotype-1 based on ITS2 and genotype-2 based on UBE3 clustered with (KF454101.1-Juglans regia) and (KC870919.1-J. regia) with bootstraps of 56 and 100, respectively. Genotype-3 based on rbcla clustered in a major clade with J. regia L., cultivars (MN397935.1 J. regia 'Vina') and (MN397934.1-J. regia 'Serr'), (MN397933.1 J. regia 'Pedro'), (MN397932.1 J. regia 'Lara'), (MN397931.1 J. regia 'Howard'), and (MN397930.1 J. regia 'Hartley') with bootstrap of 100. Meanwhile, genotype-4 and genotype-5 based on rbclc and rpoC1 clustered with (MN397935.1 J. regia 'Vina') and (MN397934.1 J. regia 'Serr'), across the database sequences. To clarify the taxonomic status of cryptic walnut genotypes, it is necessary to combine diverse DNA barcodes. The results of ITS2 and UBE3, followed by rbcL barcoding markers, are promising taxonomic tools for cryptic walnut genotypes in Pakistan. Conclusions: It has been determined that the genotypes of walnuts in the study area are both J. regia L. and its cultivars and that the accuracy of discrimination regarding the genus Juglans L. is greater than 90%. The reported DNA barcodes are recommended for the correct identification and genetic evaluation of Juglans taxa and its population.}, }
@article {pmid39596209, year = {2024}, author = {Wang, X and Wang, Z and Yang, F and Lin, R and Liu, T}, title = {Assembly, Annotation, and Comparative Analysis of Mitochondrial Genomes in Trichoderma.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596209}, issn = {1422-0067}, support = {XTCX2022NYB12//Collaborative Innovation Center Project of Hainan University/ ; }, mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Trichoderma/genetics ; *Molecular Sequence Annotation ; RNA, Transfer/genetics ; Base Composition/genetics ; Evolution, Molecular ; Introns/genetics ; }, abstract = {Trichoderma is a widely studied ascomycete fungal genus, including more than 400 species. However, genetic information on Trichoderma is limited, with most species reporting only DNA barcodes. Mitochondria possess their own distinct DNA that plays a pivotal role in molecular function and evolution. Here, we report 42 novel mitochondrial genomes (mitogenomes) combined with 18 published mitogenomes of Trichoderma. These circular mitogenomes exhibit sizes of 26,276-94,608 bp, typically comprising 15 core protein-coding genes (PCGs), 2 rRNAs, and 16-30 tRNAs; however, the number of endonucleases and hypothetical proteins encoded in the introns of PCGs increases with genome size enlargement. According to the result of phylogenetic analysis of the whole mitogenome, these strains diverged into six distinct evolutionary branches, supported by the phylogeny based on 2830 single-copy nuclear genes. Comparative analysis revealed that dynamic Trichoderma mitogenomes exhibited variations in genome size, gene number, GC content, tRNA copy, and intron across different branches. We identified three mutation hotspots near the regions encoding nad3, cox2, and nad5 that caused major changes in the mitogenomes. Evolutionary analysis revealed that atp9, cob, nad4L, nad5, and rps3 have been influenced by positive selection during evolution. This study provides a valuable resource for exploring the important roles of the genetic and evolutionary dynamics of Trichoderma mitogenome in the adaptive evolution of biocontrol fungi.}, }
@article {pmid39595947, year = {2024}, author = {Hoffmann, M and Jang, JH and Tallent, SM and Gonzalez-Escalona, N}, title = {Single Laboratory Evaluation of the Q20+ Nanopore Sequencing Kit for Bacterial Outbreak Investigations.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39595947}, issn = {1422-0067}, support = {FDA Foods Program Intramural Funds//United States Food and Drug Administration/ ; FDA Foods Program Intramural Funds//United States Food and Drug Administration/ ; }, mesh = {*Nanopore Sequencing/methods ; *Disease Outbreaks ; Humans ; Polymorphism, Single Nucleotide ; Genome, Bacterial ; Foodborne Diseases/microbiology ; Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification ; Escherichia coli Infections/microbiology/epidemiology/diagnosis ; Sequence Analysis, DNA/methods ; Pilot Projects ; }, abstract = {Leafy greens are a significant source of produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States, with agricultural water often implicated as a potential source. Current FDA outbreak detection protocols are time-consuming and rely on sequencing methods performed in costly equipment. This study evaluated the potential of Oxford Nanopore Technologies (ONT) with Q20+ chemistry as a cost-effective, rapid, and accurate method for identifying and clustering foodborne pathogens. The study focuses on assessing whether ONT Q20+ technology could facilitate near real-time pathogen identification, including SNP differences, serotypes, and antimicrobial resistance genes. This pilot study evaluated different combinations of two DNA extraction methods (Maxwell RSC Cultured Cell DNA kit and Monarch high molecular weight extraction kits) and two ONT library preparation protocols (ligation and the rapid barcoding sequencing kit) using five well-characterized strains representing diverse foodborne pathogens. High-quality, closed bacterial genomes were obtained from all combinations of extraction and sequencing kits. However, variations in assembly length and genome completeness were observed, indicating the need for further optimization. In silico analyses demonstrated that Q20+ nanopore sequencing chemistry accurately identified species, genotype, and virulence factors, with comparable results to Illumina sequencing. Phylogenomic clustering showed that ONT assemblies clustered with reference genomes, though some indels and SNP differences were observed, likely due to sequencing and analysis methodologies rather than inherent genetic variation. Additionally, the study evaluated the impact of a change in the sampling rates from 4 kHz (260 bases pair second) to 5 kHz (400 bases pair second), finding no significant difference in sequencing accuracy. This evaluation workflow offers a framework for evaluating novel technologies for use in surveillance and foodborne outbreak investigations. Overall, the evaluation demonstrated the potential of ONT Q20+ nanopore sequencing chemistry to assist in identifying the correct strain during outbreak investigations. However, further research, validation studies, and optimization efforts are needed to address the observed limitations and fully realize the technology's potential for improving public health outcomes and enabling more efficient responses to foodborne disease threats.}, }
@article {pmid39595309, year = {2024}, author = {Figura, A and Gryzinska, M and Jakubczak, A}, title = {Comparison of Universal mtDNA Primers in Species Identification of Animals in a Sample with Severely Degraded DNA.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {22}, pages = {}, pmid = {39595309}, issn = {2076-2615}, abstract = {Analysis of mitochondrial DNA, specifically the cytochrome b gene (cyt b), has become an essential tool for species identification. In the case of degraded samples, in which DNA is fractionated, universal primers, which are highly effective at amplifying the target region, are necessary. The material analysed in this study was a keychain made of bone, which was secured at a border crossing due to the suspicion that it was made of ivory. Due to processing of the bone and the likelihood of DNA degradation, five pairs of universal primers with different product lengths (from 148 to 990 base pairs) were used for species identification. Fragments of mtDNA from the cyt b and the 12S rRNA and 16S rRNA subunits were analysed. The analysis showed that only one pair of primers (L15601/H15748) enabled identification of the species, which is very common in samples with highly degraded DNA. The material was bone tissue belonging to the species Bos taurus (cattle). Species identification by molecular methods is extremely important in analysis of material when the species cannot be identified on the basis of morphological characteristics.}, }
@article {pmid39591964, year = {2025}, author = {Lu, X and Zhang, Q and Wang, Z and Cheng, X and Yan, H and Cai, S and Zhang, H and Liu, Q}, title = {Development of an inducible DNA barcoding system to understand lineage changes in Arabidopsis regeneration.}, journal = {Developmental cell}, volume = {60}, number = {2}, pages = {305-319.e5}, doi = {10.1016/j.devcel.2024.10.023}, pmid = {39591964}, issn = {1878-1551}, mesh = {*Arabidopsis/genetics/physiology/cytology ; *DNA Barcoding, Taxonomic/methods ; *Cell Lineage/genetics ; *Regeneration/genetics/physiology ; }, abstract = {Plants demonstrate a high degree of developmental plasticity, capable of regenerating entire individuals from detached somatic tissues-a regenerative phenomenon rarely observed in metazoa. Consequently, elucidating the lineage relationship between somatic founder cells and descendant cells in regenerated plant organs has long been a pursuit. In this study, we developed and optimized both DNA barcode- and multi-fluorescence-based cell-lineage tracing toolsets, employing an inducible method to mark individual cells in Arabidopsis donor somatic tissues at the onset of regeneration. Utilizing these complementary methods, we scrutinized cell identities at the single-cell level and presented compelling evidence that all cells in the regenerated Arabidopsis plants, irrespective of their organ types, originated from a single progenitor cell in the donor somatic tissue. Our discovery suggests a single-cell passage directing the transition from multicellular donor tissue to regenerated plants, thereby creating opportunities for cell-cell competition during plant regeneration-a strategy for maximizing survival.}, }
@article {pmid39590688, year = {2024}, author = {Chen, TQ and Yang, C and Xu, XL and Yang, L and He, HQ and Weng, MT and Ying, ZH and Shi, XK and Ding, MG}, title = {Comparative Mitogenomics Provides Valuable Insights for the Phylogeny and New DNA Barcodes of Ganoderma.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {39590688}, issn = {2309-608X}, support = {2023R1106//Science &amp; Technology Department of Fujian Province, the Public Welfare Competitive Research Project/ ; }, abstract = {Ganoderma is the most important genus in the family Ganodermataceae; many species have attracted much attention and widely cultivated because of their medicinal values, but so far, not a sequenced mitogenome derived from dikaryon strains has been explicitly recorded. Herein, four novel mitogenomes of commonly cultivated Ganoderma (G. leucocontextum H4, G. lucidum G6, G. sinense MZ96 and G. tsugae SS) were de novo assembled and given detail functional annotations. Collinearity analysis revealed that the four mitogenomes shared 82.93-92.02% similarity with their corresponding reference mitogenomes at the nucleotide level. A total of 15 core protein-coding genes (PCGs), along with rrnL and rrnS (mtLSU and mtSSU) were chosen as potential candidates for constructing their individual phylogenetic trees. These trees were compared with those derived from the concatenated sequences of 15 core PCGs. And finally, we found that the atp9 and nad4L were the most reliable markers for the phylogenetic analysis of Ganoderma and chosen as standard sequences to generate new DNA barcodes. This finding was further verified by comparing it against almost all available Ganoderma mitogenomes in the NCBI, with Trametes versicolor (Polyporaceae) and Rigidoporus microporus (Meripilaceae) as two outgroups. A total of 52 mitogenomes from three families were highly conserved, with identical gene lengths for atp9 (222 bp) and nad4L (267 bp). These genes were capable of distinguish distinctly different various species, which are grouped into separate clades within the phylogenetic trees. The closest related clades (I and II), including at least 30 samples of the three classical taxonomic species (G. lingzhi, G. sichuanense and G. lucidum), differed in only one SNP. The single base mutation rate increased with the evolutionary divergence of the phylogenetic clades, from two to three SNPs in earlier clades (e.g., clade IV containing G. leucocontextum) to five to six SNPs in later clades (e.g., clade X containing G. sinense). Despite these variations between species, the atp9 and nad4L genes of Ganoderma mitogenomes consistently encoded the same ATP synthase F0 subunit c (73 aa) and NADH dehydrogenase subunit 4L (88 aa). These two genes have been identified as reliable markers of new DNA barcodes, offering valuable insights and contributing significantly to understanding the evolutionary relationships and phylogeny of the Ganoderma genus and even the Ganodermataceae family.}, }
@article {pmid39590509, year = {2024}, author = {Xie, TT and Wang, MQ and Li, Y and Su, CY and Zhang, D and Zhou, QS and Niu, ZQ and Yuan, F and Liu, XW and Ma, KP and Zhu, CD and Hao, JS and Chesters, D}, title = {Blue Vane and Pan Traps Are More Effective for Profiling Multiple Facets of Bee Diversity in Subtropical Forests.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, pmid = {39590509}, issn = {2075-4450}, abstract = {The choice of trap in entomological surveys affects the composition of captured insects, though previous comparative studies have been limited in the types of composition measured, and the effects of environmental context. We assessed the sampling bias of several traps commonly used in pollinator monitoring: blue, yellow, and white pan traps, and blue vane traps, towards different taxonomic and functional groups and their efficiency in measuring taxonomic, phylogenetic, and functional diversity. Analyses were performed in monoculture and mixed forests to understand the environmental context of trap efficiency. We found that blue pan traps generally outperformed other types in bee capture and exhibited a preference for Halictidae bees. Blue pan traps yielded the highest species richness and phylogenetic diversity, while blue vane traps captured the highest functional richness. Bias differences were frequently detected in mixed forests compared with monoculture forests. We also found the combination of blue vane and pan traps consistently correlated highest with a complete survey among two-method combinations. Based on our findings, we recommend a combination of blue vane and pan traps to obtain a more comprehensive bee collection in an efficient manner. Additionally, it is crucial to consider habitat type when designing bee trapping protocols to ensure an accurate representation of bee communities.}, }
@article {pmid39590449, year = {2024}, author = {Schmid-Egger, C and Schmidt, S and Rosa, P and Niehuis, O}, title = {DNA Barcoding of German Cuckoo Wasps (Hymenoptera: Chrysididae) Suggests Cryptic Species in Several Widely Distributed Species.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, pmid = {39590449}, issn = {2075-4450}, support = {NI 1387/1-1, NI 1387/2-1, NI 1387/5-1, NI 1387/6-1/2//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Germany is home to a rich cuckoo wasp fauna (Hymenoptera: Chrysididae) with about 108 species. However, several nomenclatural changes, the lack of identification keys, and the discovery of cryptic species difficult to identify based on external morphology have made the identification of several species a challenge. COI barcoding has been instrumental in the identification of some cuckoo wasp species and could help alleviate some of the above problems, but a reliable large reference database containing the cuckoo wasp barcodes is lacking. We present the COI barcodes of more than 800 specimens of 101 cuckoo wasp species native to Germany to lay the foundation for the barcode-based identification of German species. An analysis of the COI barcode sequences suggested groups that are largely consistent with the current taxonomy of the group. We found a few cases of over- or undersplitting of taxa. In some common species, the high degree of barcode divergence suggests the presence of cryptic species that need to be further assessed by integrative approaches. Our library of cuckoo wasp reference barcodes will enhance researchers' ability to reliably identify species within this fascinating group of insects, in particular for identifying life stages that offer few or no morphological features for species-level identification.}, }
@article {pmid39590434, year = {2024}, author = {Zhu, J and van Achterberg, C and Chen, X and Tang, P}, title = {New Records and New Species of Dacnusini (Hymenoptera: Braconidae, Alysiinae) Based on Morphological and Molecular Evidence.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, pmid = {39590434}, issn = {2075-4450}, support = {2023FY100200//Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 31920103005//Key International Joint Research Program of National Natural Science Foundation of China/ ; 32070467//General Program of National Natural Science Foundation of China/ ; (32200355)//National Natural Science Foundation of China/ ; 226-2024-00095//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Dacnusini is a species-rich tribe in the subfamily Alysiinae, with most species exclusively serving as parasitoids of leaf-mining Diptera (Agromyzidae). The number of genera discovered in China remains limited, which is apparently insufficient considering the global diversity of species and genera within this tribe, particularly given the vast and ecologically diverse landscapes of China. In the present study, three new record genera, Victorovita Tobias, Coloneura Foerster, and Laotris Nixon, were documented for the first time in China. In addition, the species delimitation approach and haplotype network analyses based on the COI sequences, combined with morphological evidence, were employed to delimit species. The findings indicated three new species: Laotris glabella sp. nov., Laotris aethidentata sp. nov., and Victorovita aequalis sp. nov. Additionally, K2P divergences showed no overlap between intra- and interspecific genetic distances in the Laotris and Victorovita species. Detailed descriptions for new species and keys to the species of Laotris and Victorovita are provided in this paper, along with the documentation of two new species records for China: Victorovita caudata (Szépligeti, 1901) and Coloneura stylata Foerster, 1863.}, }
@article {pmid39590432, year = {2024}, author = {Ramos-Lagunes, VH and Laredo-Tiscareño, SV and González-Peña, R and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and de Jesús de Luna-Santillana, E and Hernández-Triana, LM and Velasco-Chino, LE and Laredo-Tiscareño, AG and Garza-Hernández, JA}, title = {Aedes (Georgecraigius) epactius from Zacatecas and Chihuahua Mexico: New Geographical Distribution and Altitude Records.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, pmid = {39590432}, issn = {2075-4450}, support = {740742, 769056, and 842817//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; UACJ-PTC-399 and UACJ-PTC-267//Programa para el Desarrollo Profesional Docente, para el Tipo Superior/ ; No. 419-24-23//CONAHCYT CIENCIA DE FRONTERA 2023/ ; 397-24-01//Proyectos de Investigaci&#xf3;n con Impacto Social (PIISO) UACJ/ ; SV3045//Department for Environment Food and Rural Affairs (DEFRA), Scottish Government and Welsh Government/ ; }, abstract = {Adults and immatures of Aedes epactius were collected in July and December 2022 at sites of high elevation in the states of Chihuahua (2300 masl) and Zacatecas (2182 and 2595 masl), Mexico, respectively. Mosquitoes were identified morphologically and sequenced for a DNA barcode of the cytochrome c oxidase I (COX1). This is the first distributional record of Ae. epactius in Zacatecas and provides evidence of the highest altitude in the Americas, including Mexico. The geographical distribution of Ae. epactius in Mexico was reviewed, and the COX1 analysis, using phylogenetic Bayesian analysis to confirm species identification, was performed.}, }
@article {pmid39589980, year = {2024}, author = {Zhong, L and Chen, H and Cao, S and Hu, S}, title = {Single Nucleotide Recognition and Mutation Site Sequencing Based on a Barcode Assay and Rolling Circle Amplification.}, journal = {Biosensors}, volume = {14}, number = {11}, pages = {}, pmid = {39589980}, issn = {2079-6374}, support = {2021Y9014//innovation of science and Technology, Fujian province/ ; XRCZX2019024//Fujian Medical University's Research Foundation for Talented Scholars/ ; }, mesh = {*Nucleic Acid Amplification Techniques ; *Polymorphism, Single Nucleotide ; *Helicobacter pylori/genetics ; Mutation ; DNA Barcoding, Taxonomic ; Quantum Dots ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Biosensing Techniques ; }, abstract = {Single nucleotide polymorphisms (SNPs) present significant challenges in microbial detection and treatment, further raising the demands on sequencing technologies. In response to these challenges, we have developed a novel barcode-based approach for highly sensitive single nucleotide recognition. This method leverages a dual-head folded complementary template probe in conjunction with DNA ligase to specifically identify the target base. Upon recognition, the system triggers rolling circle amplification (RCA) followed by the self-assembly of CdSe quantum dots onto polystyrene microspheres, enabling a single-particle fluorescence readout. This approach allows for precise base identification at individual loci, which are then analyzed using a bio-barcode array to screen for base changes across multiple sites. This method was applied to sequence a drug-resistant mutation site in Helicobacter pylori (H. pylori), demonstrating excellent accuracy and stability. Offering high precision, high sensitivity, and single nucleotide resolution, this approach shows great promise as a next-generation sequencing method.}, }
@article {pmid39589713, year = {2024}, author = {Guo, P and Deng, Y}, title = {Spatial Omics: Navigating Neuroscience Research into the New Era.}, journal = {Advances in neurobiology}, volume = {41}, number = {}, pages = {133-149}, pmid = {39589713}, issn = {2190-5215}, mesh = {Humans ; *Neurosciences ; *Brain/metabolism ; Proteomics ; Transcriptome ; High-Throughput Nucleotide Sequencing ; Animals ; Genomics ; In Situ Hybridization, Fluorescence ; Neurons/metabolism ; Epigenomics ; }, abstract = {The human brain's complexity is underpinned by billions of neurons and trillions of synapses, necessitating coordinated activities across diverse cell types. Conventional techniques like in situ hybridization and immunohistochemistry, while valuable, face limitations in resolution and comprehensiveness when analyzing neuron types. Advances in spatial omics technologies, especially those integrating transcriptomics and proteomics, have revolutionized our understanding of brain tissue organization. These technologies, such as FISH-based, in situ sequencing-based (ISS), and next-generation sequencing (NGS)-based methods, provide detailed spatial context, overcoming previous limitations. FISH techniques, including smFISH and its variants like seqFISH and MERFISH, offer high-resolution spatial gene expression data. ISS approaches leverage padlock probes and rolling circle amplification to yield spatial transcriptome information. NGS-based methods, such as spatial transcriptomics and spatial-epigenomics, integrate spatial barcodes with single-cell sequencing, enabling comprehensive profiling of gene expression and epigenetic states in tissues. These innovations have propelled insights into neural development and disease, identifying cellular heterogeneity and molecular alterations in conditions like Alzheimer's and major depression. Despite challenges in cost, speed, and data analysis, spatial omics technologies continue to evolve, promising deeper insights into the molecular mechanisms of the brain and neurodegenerative diseases.}, }
@article {pmid39589617, year = {2024}, author = {Argôlo, LA and Ramos, RTC and Bitencourt, JA and Galdino, JH and Sampaio, I and Affonso, PRAM}, title = {Hidden diversity revealed by DNA barcoding of paralichthyidae fish along the caribbean and brazilian coast.}, journal = {Genetica}, volume = {153}, number = {1}, pages = {4}, pmid = {39589617}, issn = {1573-6857}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; code 406489/2023-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Brazil ; *Electron Transport Complex IV/genetics ; *Phylogeny ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Caribbean Region ; Genetic Variation ; Fishes/genetics/classification ; }, abstract = {DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.}, }
@article {pmid39588656, year = {2024}, author = {Jiang, Y and Wang, Y and Luo, W and Luan, X and Zhang, Z and Pan, Y and He, B and Gao, Y and Song, Y}, title = {Detecting telomerase activity at the single-cell level using a CRISPR-Cas12a-based chip.}, journal = {Lab on a chip}, volume = {25}, number = {1}, pages = {49-56}, doi = {10.1039/d4lc00619d}, pmid = {39588656}, issn = {1473-0189}, mesh = {*Telomerase/metabolism ; *CRISPR-Cas Systems ; Humans ; *Single-Cell Analysis/instrumentation ; Lab-On-A-Chip Devices ; Bacterial Proteins ; Endodeoxyribonucleases ; CRISPR-Associated Proteins ; }, abstract = {The intimate association between telomerase activity and cancer has driven the exploration of diverse methodologies for its precise detection. However, detecting telomerase activity at the single-cell level remains a significant challenge. Herein, we present a MOF-DNA barcode-amplified CRISPR-Cas12a strategy integrated with a single-cell microfluidic chip for ultrasensitive detection of telomerase activity. DNA-functionalized UiO-66 nanoparticles act as signal transducers, effectively converting telomerase activity into DNA activation strands, which subsequently trigger the trans-cleavage activity of CRISPR-Cas12a. This amplification-based assay could be integrated with a microfluidic chip to enable highly sensitive detection of telomerase activity at the single-cell level, offering promising advancements in early cancer diagnosis.}, }
@article {pmid39587617, year = {2024}, author = {Landman, F and Jamin, C and de Haan, A and Witteveen, S and Bos, J and van der Heide, HGJ and Schouls, LM and Hendrickx, APA and , }, title = {Genomic surveillance of multidrug-resistant organisms based on long-read sequencing.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {137}, pmid = {39587617}, issn = {1756-994X}, mesh = {*Drug Resistance, Multiple, Bacterial/genetics ; Humans ; *Genome, Bacterial ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/drug effects/classification ; Whole Genome Sequencing/methods ; }, abstract = {BACKGROUND: Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention of MDRO. Molecular characterization based on long-read sequencing has emerged as a promising alternative to short-read sequencing. The aim of this study was to characterize MDRO for surveillance and transmission studies based on long-read sequencing only.<br><br>METHODS: Genomic DNA of 356 MDRO was automatically extracted using the Maxwell-RSC48. The MDRO included 106 Klebsiella pneumoniae isolates, 85 Escherichia coli, 15 Enterobacter cloacae complex, 10 Citrobacter freundii, 34 Pseudomonas aeruginosa, 16 Acinetobacter baumannii, and 69 methicillin-resistant Staphylococcus aureus (MRSA), of which 24 were from an outbreak. MDRO were sequenced using both short-read (Illumina NextSeq 550) and long-read (Nanopore Rapid Barcoding Kit-24-V14, R10.4.1) whole-genome sequencing (WGS). Basecalling was performed for two distinct models using Dorado-0.3.2 duplex mode. Long-read data was assembled using Flye, Canu, Miniasm, Unicycler, Necat, Raven, and Redbean assemblers. Long-read WGS data with&#x2009;>&#x2009;40&#x2009;&#xd7;&#x2009;coverage was used for multi-locus sequence typing (MLST), whole-genome MLST (wgMLST), whole-genome single-nucleotide polymorphisms (wgSNP), in silico multiple locus variable-number of tandem repeat analysis (iMLVA) for MRSA, and identification of resistance genes (ABRicate).<br><br>RESULTS: Comparison of wgMLST profiles based on long-read and short-read WGS data revealed&#x2009;>&#x2009;95% of wgMLST profiles within the species-specific cluster cut-off, except for P. aeruginosa. The wgMLST profiles obtained by long-read and short-read WGS differed only one to nine wgMLST alleles or SNPs for K. pneumoniae, E. coli, E. cloacae complex, C. freundii, A. baumannii complex, and MRSA. For P. aeruginosa, differences were up to 27 wgMLST alleles between long-read and short-read wgMLST and 0-10 SNPs. MLST sequence types and iMLVA types were concordant between long-read and short-read WGS data and conventional MLVA typing. Antimicrobial resistance genes were detected in long-read sequencing data with high sensitivity/specificity (92-100%/99-100%). Long-read sequencing enabled analysis of an MRSA outbreak.<br><br>CONCLUSIONS: We demonstrate that molecular characterization of automatically extracted DNA followed by long-read sequencing is as accurate compared to short-read sequencing and suitable for typing and outbreak analysis as part of genomic surveillance of MDRO. However, the analysis of P. aeruginosa requires further improvement which may be obtained by other basecalling algorithms. The low implementation costs and rapid library preparation for long-read sequencing of MDRO extends its applicability to resource-constrained settings and low-income countries worldwide.}, }
@article {pmid39587359, year = {2024}, author = {Ramani, V}, title = {Split-pool barcoding serves up an epigenomic smorgasbord.}, journal = {Nature genetics}, volume = {56}, number = {12}, pages = {2596-2597}, pmid = {39587359}, issn = {1546-1718}, support = {DP2-HG012442//U.S. Department of Health &amp; Human Services | NIH | NIH Office of the Director (OD)/ ; }, }
@article {pmid39585955, year = {2024}, author = {Osborne, M and Chen, H and Kadhiresan, P and Mahbub, N and Malekjahani, A and Kozlowski, HN and Udugama, B and Nguyen, LNM and Perusini, S and Mubareka, S and Chan, WCW}, title = {QBox: An Automated Portable System for Multiplex Quantum Dot Barcode Diagnostics.}, journal = {ACS nano}, volume = {18}, number = {49}, pages = {33629-33642}, doi = {10.1021/acsnano.4c12306}, pmid = {39585955}, issn = {1936-086X}, mesh = {*Quantum Dots/chemistry ; Humans ; *COVID-19/diagnosis/virology ; *SARS-CoV-2/isolation &amp; purification/genetics ; Point-of-Care Systems ; Automation ; }, abstract = {The COVID-19 pandemic accelerated the development of automated systems for detecting molecular targets for the point-of-care. However, these systems have limited multiplexing capabilities because of the need to alter their hardware to accommodate additional targets and probes. Quantum dot barcodes address this multiplexing obstacle, but their assays have multiple steps that rely on extensive training and laboratory equipment. Here, we built a portable cartridge-and-instrument system that automates the extraction, reverse transcription, amplification, and detection steps of a quantum dot barcode assay. This entire workflow can be completed in 40 minutes. We clinically validated the system with SARS-CoV-2 patient samples (n = 50, 92% sensitivity, 100% specificity). We then demonstrated multiplexing with 4-barcode respiratory and 5-barcode bloodborne pathogen panels. Our portable system opens quantum dot barcodes for broad use in rapid multiplexed detection of infectious pathogens with the potential for detecting cancer and other genetic diseases.}, }
@article {pmid39585918, year = {2024}, author = {Ambu, J and Dufresnes, C}, title = {Genomic and bioacoustic variation in a midwife toad hybrid zone: A role for reinforcement?.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0314477}, pmid = {39585918}, issn = {1932-6203}, mesh = {Animals ; *Anura/genetics/physiology ; *Hybridization, Genetic ; Reproductive Isolation ; Vocalization, Animal/physiology ; Polymorphism, Single Nucleotide ; Genomics/methods ; Gene Flow ; France ; }, abstract = {Hybrid zones, i.e., geographic areas where diverging lineages meet, hybridize and eventually mix their genomes, offer opportunities to understand the mechanisms behind reproductive isolation and speciation. Hybrid zones are particularly well suited to study reinforcement, i.e., the process by which selection against hybridization increases reproductive barriers, which, in anuran amphibians, is typically expressed by increased divergence in advertisement calls-the main cue to assortative mating-in parapatric ranges. Using mitochondrial barcoding (16S sequences), population genomics (thousands of SNPs) and bioacoustic analyses (four call parameters), we examine the hybrid zone between two incipient species of midwife toads (Alytes obstetricans and A. almogavarii) in southern France, with the purposes of locating their transition, measuring genetic introgression, and documenting potential signatures of reinforcement. We map range boundaries in the Eastern Pyrenees and the southwestern foothills of the Massif Central, namely along the Ariège valley and the Montagne Noire area. Similarly to another transition between these species in Spain, we found the hybrid zone to be narrow, involving geographically restricted gene flow (~20 km wide allele frequency clines) and barrier loci (i.e., loci resisting introgression), both suggestive of partial post-zygotic isolation (hybrid incompatibilities). The calls of the species overlap less inside than outside the hybrid zone, due to a reduction of their standing variation rather than a shift towards distinctive variants. While neutral causes cannot be excluded, this pattern follows the general expectations of reinforcement, yet without reproductive character displacement. Our study highlights the potential of amphibian hybrid zones to assess the genetic and behavioral drivers of reproductive isolation in statu nascendi and under various evolutionary contexts.}, }
@article {pmid39582226, year = {2024}, author = {Wu, X and Zhao, Z and Yu, W and Liu, S and Zhou, M and Jiang, N and Du, X and Yang, X and Chen, J and Guo, H and Yang, R}, title = {Single-Cell Multiomics Identifies Glycan Epitope LacNAc as a Potential Cell-Surface Effector Marker of Peripheral T Cells in Bladder Cancer Patients.}, journal = {ACS chemical biology}, volume = {19}, number = {12}, pages = {2535-2547}, pmid = {39582226}, issn = {1554-8937}, mesh = {Humans ; *Urinary Bladder Neoplasms/immunology/pathology ; *Polysaccharides/chemistry ; *T-Lymphocytes/immunology/metabolism ; *Single-Cell Analysis/methods ; Biomarkers, Tumor/immunology/blood/metabolism ; Epitopes/immunology/chemistry ; Receptors, Antigen, T-Cell/immunology/metabolism ; Glycosylation ; Multiomics ; }, abstract = {Cancer is a systemic disease continuously monitored and responded to by the human global immune system. Peripheral blood immune cells, integral to this surveillance, exhibit variable phenotypes during tumor progression. Glycosylation, as one of the most prevalent and significant post-translational modifications of proteins, plays a crucial role in immune system recognition and response. Glycan analysis has become a key method for biomarker discovery. LacNAc, a prominent glycosylation modification, regulates immune cell activity and function. Therefore, we applied our previously developed single-cell glycomic multiomics to analyze peripheral blood in cancer patients. This platform utilizes chemoenzymatic labeling with DNA barcodes for detecting and quantifying LacNAc levels at single-cell resolution without altering the transcriptional status of immune cells. For the first time, we systematically integrated single-cell transcriptome, T cell receptor (TCR) repertoire, and glycan epitope LacNAc analyses in tumor-patient-derived peripheral blood. Our integrated analysis reveals that lower-stage bladder cancer patients showed significantly higher levels of LacNAc in peripheral T cells, and peripheral T cells with high levels of cell-surface LacNAc exhibit higher cytotoxicity and TCR clonal expansion. In summary, we identified LacNAc as a potential cell-surface effector marker for peripheral T cells in bladder cancer patients, which enhances our understanding of peripheral immune cells and offers potential advancements in liquid biopsy.}, }
@article {pmid39582135, year = {2024}, author = {Seo, Y and Fowler, K and Flick, LM and Withers, TA and Savoldo, B and McKinnon, K and Iannone, MA}, title = {Barcoding of viable peripheral blood mononuclear cells with selenium and tellurium isotopes for mass cytometry experiments.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {105}, number = {12}, pages = {899-908}, doi = {10.1002/cyto.a.24907}, pmid = {39582135}, issn = {1552-4930}, support = {//University Cancer Research Fund (UCRF)/ ; //UNC Cancer Center Core Support Grant #P30CA016086/ ; }, mesh = {Humans ; *Tellurium/chemistry ; *Leukocytes, Mononuclear/cytology/drug effects/metabolism ; *Flow Cytometry/methods ; *Selenium/chemistry/pharmacology ; Isotopes ; Staining and Labeling/methods ; Isotope Labeling/methods ; Cell Survival/drug effects ; }, abstract = {Barcoding viable cells combined with pooled sample staining is an effective technique that eliminates batch effects from serial cell staining and facilitates uninterrupted data acquisition. We describe three novel and isotopically pure selenium-containing compounds (SeMals) that are useful cellular labeling tools. The maleimide-functionalized selenophenes ([76]SeMal, [77]SeMal, and [78]SeMal) covalently react with cellular sulfhydryl groups and uniquely label cell samples. The SeMal reagents label viable and paraformaldehyde-fixed peripheral blood mononuclear cells (PBMC), are well resolved by the mass cytometer, and have little spill into adjacent channels. They appear non-toxic to viable cells at working concentrations. We used SeMal reagents in combination with four isotopically pure tellurium maleimide reagents ([124]TeMal, [126]TeMal, [128]TeMal, and [130]TeMal) to label 21 individual PBMC samples with unique combinations of selenium and tellurium isotopes (seven donors with three replicates using a 7 isotope pick 2 combinatorial schema). The individually barcoded samples were pooled, stained with an antibody cocktail as a pool, and acquired on the mass cytometer as a single suspension. The single-cell data were de-barcoded into separate sample-specific files after data acquisition, enabling an uninterrupted instrument run. Each donor sample retained its unique phenotypic profile with excellent replicate reproducibility. Unlike current live cell barcoding methods, this approach does not require antibodies to surface markers, allowing for the labeling of all cells regardless of surface antigen expression. Additionally, since selenium and tellurium isotopes are not currently utilized in CyTOF antibody panels, this method expands barcoding options and frees up commonly used isotopes for more detailed cell profiling.}, }
@article {pmid39581345, year = {2025}, author = {Parmar, DR and Johnston, NP and Wallman, JF and Szpila, K}, title = {Blowfly genomics: current insights, knowledge gaps, and future perspectives.}, journal = {Current opinion in insect science}, volume = {68}, number = {}, pages = {101305}, doi = {10.1016/j.cois.2024.101305}, pmid = {39581345}, issn = {2214-5753}, mesh = {Animals ; *Genome, Insect ; *Genomics ; *Calliphoridae/genetics ; Phylogeny ; }, abstract = {Blowflies (Calliphoridae) form a diverse, species-rich group, yet publicly available genome assemblies are limited to only 16 species, despite recent genomic advances. This knowledge gap extends to mitogenomes and barcode databases, which mainly focus on medically and veterinary-important species. While blowfly phylogenetics has progressed, additional genome sequencing is crucial for various subfamilies, given their diverse life histories. This review presents a quantitative overview of available genetic information for blowflies, highlighting substantial gaps in public databases. DNA barcodes, mitogenomes, and genomes represent only 16.5% (342 species), ∼3% (53 species), and <1% (16 species) of known family diversity, respectively. While 183 genomics-related calliphorid BioProjects are recorded by NCBI, many subfamilies and genera have limited or no genomic representation, impacting studies on identification, systematics, phylogenetics, and evolution. We stress the urgent need for high-quality reference genomes and highlight target species representing all blowfly subfamilies to support a new era of rapid, low-cost genomic research.}, }
@article {pmid39579652, year = {2025}, author = {Bates, SA and Budowle, B and Baker, L and Mittelman, K and Mittelman, D}, title = {A molecular framework for enhancing quality control and sample integrity in forensic genome sequencing.}, journal = {Forensic science international. Genetics}, volume = {75}, number = {}, pages = {103179}, doi = {10.1016/j.fsigen.2024.103179}, pmid = {39579652}, issn = {1878-0326}, mesh = {Humans ; *Quality Control ; *DNA Fingerprinting ; *Forensic Genetics/methods/standards ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Genome, Human ; Oligonucleotides/genetics ; }, abstract = {DNA typing is essential for identifying crime scene evidence and missing and unknown persons. Molecular tags historically have been incorporated into DNA typing reactions to improve result interpretation. Molecular tags like barcodes and unique identifiers are integral to MPS, aiding in sample tracking and error detection. However, these tags do not fully leverage sequence variation to enhance quality control. To address this need, molecular etches, which are synthetic oligonucleotides that serve as an internal molecular information management system, are introduced. Molecular etches encode detailed sample information improving sample workflow history, tracking, contamination detection, and authenticity verification. Validation studies demonstrate the robustness of molecular etches in genomic sequencing, making them a valuable quality tool for forensic DNA analysis.}, }
@article {pmid39578906, year = {2024}, author = {Schack, AK and Garrido-Navas, MC and Galevski, D and Madjarov, G and Krych, L}, title = {SCAN: a nanopore-based, cost effective decision-supporting tool for mass screening of aneuploidies.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {131}, pmid = {39578906}, issn = {1479-7364}, mesh = {Humans ; *Aneuploidy ; Cost-Benefit Analysis ; Infant, Newborn ; Klinefelter Syndrome/genetics/diagnosis ; Genetic Testing/economics/methods ; Nanopore Sequencing/methods ; Neonatal Screening/economics/methods ; Nanopores ; Mass Screening/economics/methods ; Machine Learning ; }, abstract = {In developed countries, Newborn Screening (NBS) programs aim to detect treatable yet clinically silent disorders. The selection of disorders to be included in NBS considers severity, treatment availability, prevalence, and analysis cost. However, numerous genetic disorders remain excluded from routine testing due to high expenses and specialized equipment requirements. Here we present SCAN, a novel, non-invasive, and cost-effective decision-support tool utilizing nanopore sequencing for estimating proportions of chromosomes responsible for the most common aneuploidies. SCAN combines DNA enrichment (amplification), barcoding, nanopore sequencing, and machine learning predictive modeling. In a proof-of-concept study for Klinefelter Syndrome, SCAN achieved 100% sensitivity, specificity, and accuracy, becoming the world's first IVD-certified genetic test utilising nanopore sequencing. Further model training shows promise in expanding this assay to detect other chromosomal aneuploidies included in the protocol.}, }
@article {pmid39577343, year = {2025}, author = {Sanhueza, MI and Montes, CS and Sanhueza, I and Montoya-Gallardo, NI and Escalona, F and Luarte, D and Escribano, R and Torres, S and Godoy, SE and Amigo, JM and Castillo, RDP and Urbina, M}, title = {VIS-NIR hyperspectral imaging and multivariate analysis for direct characterization of pelagic fish species.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {328}, number = {}, pages = {125451}, doi = {10.1016/j.saa.2024.125451}, pmid = {39577343}, issn = {1873-3557}, mesh = {Animals ; *Fishes/classification ; *Spectroscopy, Near-Infrared/methods ; Multivariate Analysis ; *Hyperspectral Imaging/methods ; *Principal Component Analysis ; Discriminant Analysis ; Least-Squares Analysis ; Support Vector Machine ; }, abstract = {The identification of fish species and their physical and chemical characterization play a crucial role in the fishing industry, fish-food research and the management of marine resources. Traditional methods for species identification, such as expert observation, DNA barcoding and meta-barcoding, though effective, require labor-intensive laboratory work. Consequently, there is a pressing need for more objective and efficient methodologies for accurate fish species identification and characterization. This study proposes the use of multivariate analysis and visible-near infrared hyperspectral imaging (HSI) for a rapid characterization of fish, including the evaluation of specific morphological regions of interest (ROIs) in fish images or intrasample spectral variability, species differentiation, and freshness assessment. The study involves three pelagic species: sardine (Strangomera bentincki), silverside (Odontesthes regia) and anchovy (Engraulis ringens). Principal component analysis (PCA), support vector machine regression (SVM-R), partial least squares regression (PLS-R), and partial least squares discriminant analysis (PLS-DA) were applied as multivariate techniques for these purposes. Comparative studies of morphological ROIs revealed significant differences between the spectral characteristics of various fish zones. A decrease in reflectance intensity due to freshness loss was detected, and the prediction of this freshness, quantified as "time after capture," was achievable using SVM-R, with a 9% relative error of prediction. Overall, VIS-NIR HSI, supported by multivariate analysis, enables differentiation between the studied species, highlighting its potential as a robust fish species identification and characterization tool.}, }
@article {pmid39575683, year = {2024}, author = {Siniscalco, AM and Perera, RP and Greenslade, JE and Veeravenkatasubramanian, H and Masters, A and Doll, HM and Raj, B}, title = {Barcoding Notch signaling in the developing brain.}, journal = {Development (Cambridge, England)}, volume = {151}, number = {24}, pages = {}, pmid = {39575683}, issn = {1477-9129}, support = {R00 HD098298/HD/NICHD NIH HHS/United States ; DGE-2236662//National Science Foundation/ ; //University of Pennsylvania/ ; DP2 NS131787/NS/NINDS NIH HHS/United States ; R00HD098298/NH/NIH HHS/United States ; }, mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Brain/metabolism/embryology/growth &amp; development ; *Signal Transduction/genetics ; *Receptors, Notch/metabolism/genetics ; *Zebrafish Proteins/genetics/metabolism ; CRISPR-Cas Systems/genetics ; Neurons/metabolism/cytology ; Gene Expression Regulation, Developmental ; Single-Cell Analysis ; }, abstract = {Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control, while the recorder obtains mutations in ancestral cells where Notch is active. We combine SABER-seq with an expanded juvenile brain atlas to identify cell types derived from Notch-active founders. Our data reveal rare examples where differential Notch activities in ancestral progenitors are detected in terminally differentiated neuronal subtypes. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.}, }
@article {pmid39574722, year = {2024}, author = {Leitner, DR and Zingl, FG and Morano, AA and Zhang, H and Waldor, MK}, title = {The Mla pathway promotes Vibrio cholerae re-expansion from stationary phase.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39574722}, issn = {2692-8205}, support = {R01 AI042347/AI/NIAID NIH HHS/United States ; R37 AI042347/AI/NIAID NIH HHS/United States ; }, abstract = {Bacteria have evolved diverse strategies to ensure survival under nutrient-limited conditions, where rapid energy generation is not achievable. Here, we performed a transposon insertion site sequencing loss-of-function screen to identify Vibrio cholerae genes that promote the pathogen's fitness in stationary phase. We discovered that the Mla (maintenance of lipid asymmetry) pathway, which is crucial for transferring phospholipids from the outer to the inner membrane, is critical for stationary phase fitness. Competition experiments with barcoded and fluorophore labeled wild-type and mlaE mutant V. cholerae revealed that the Mla pathway promotes re-expansion from 48h stationary phase cultures. The mutant's defect in transitioning out of stationary phase into active growth (culturability) was also observed in monocultures at 48h. However, by 96h the culturability of the mutant and wild-type strains were equivalent. By monitoring the abundances of genomically barcoded libraries of wild-type and ∆mlaE strains, we observed that a few barcodes dominated the mutant culture at 96h, suggesting that the similarity of the population sizes at this time was caused by expansion of a subpopulation containing a mutation that suppressed the mlaE mutant's defect. Whole genome sequencing revealed that mlaE suppressors inactivated flagellar biosynthesis. Additional mechanistic studies support the idea that the Mla pathway is critical for the maintenance of V. cholerae's culturability as it promotes energy homeostasis, likely due to its role in regulating outer membrane vesicle shedding. Together our findings provide insights into the cellular processes that control re-expansion from stationary phase and demonstrate a previously undiscovered role for the Mla pathway.}, }
@article {pmid39574588, year = {2024}, author = {Stevenson, ZC and Laufer, E and Estevez, AO and Robinson, K and Phillips, PC}, title = {Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39574588}, issn = {2692-8205}, support = {P40 OD010440/OD/NIH HHS/United States ; R35 GM131838/GM/NIGMS NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; U24 AG056052/AG/NIA NIH HHS/United States ; }, abstract = {A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode experimental evolution animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, yielding the largest animal experimental evolution study to date. The frequency of each barcode was determined at multiple time points via sequencing at deep coverage and then used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.}, }
@article {pmid39572229, year = {2024}, author = {Zhang, X and Huang, Y and Yang, Y and Wang, QE and Li, L}, title = {Advancements in prospective single-cell lineage barcoding and their applications in research.}, journal = {Genome research}, volume = {34}, number = {12}, pages = {2147-2162}, pmid = {39572229}, issn = {1549-5469}, mesh = {*Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Humans ; *DNA Barcoding, Taxonomic/methods ; Animals ; Neoplasms/genetics ; }, abstract = {Single-cell lineage tracing (scLT) has emerged as a powerful tool, providing unparalleled resolution to investigate cellular dynamics, fate determination, and the underlying molecular mechanisms. This review thoroughly examines the latest prospective lineage DNA barcode tracing technologies. It further highlights pivotal studies that leverage single-cell lentiviral integration barcoding technology to unravel the dynamic nature of cell lineages in both developmental biology and cancer research. Additionally, the review navigates through critical considerations for successful experimental design in lineage tracing and addresses challenges inherent in this field, including technical limitations, complexities in data analysis, and the imperative for standardization. It also outlines current gaps in knowledge and suggests future research directions, contributing to the ongoing advancement of scLT studies.}, }
@article {pmid39570496, year = {2024}, author = {Dilrukshi, HAC and Ruklani, NCS and Rubasinghe, SCK}, title = {Cryptogams as bio-indicators for ecosystem monitoring in Sri Lanka: a comprehensive review and recommendations.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1231}, pmid = {39570496}, issn = {1573-2959}, support = {22-101//National Research Council/ ; 22-101//National Research Council/ ; 22-101//National Research Council/ ; }, mesh = {Sri Lanka ; *Environmental Monitoring/methods ; *Ecosystem ; *Fungi ; *Biodiversity ; Lichens ; Climate Change ; Bryophyta ; }, abstract = {Cryptogams, encompassing algae, fungi, lichens, bryophytes, and pteridophytes play essential roles in soil formation, nutrient cycling, and ecological stability. Sri Lanka faces numerous environmental challenges, including habitat loss, climate change, and pollution and there is an urgent need for effective monitoring programs to assess and mitigate these changes. This comprehensive review compiles existing literature on the importance of cryptogams and their responses to various environmental stressors and highlights the specific characteristics that make cryptogams valuable bio-indicators, such as their sensitivity to pollution, climate change, and land-use changes in habitats such as forests, agricultural lands, and urban areas, as well as their ability to accumulate and retain pollutants over time. The diversity of cryptogams is integral to their effectiveness as bio-indicators, providing a comprehensive picture of ecosystem health. Furthermore, recommendations for the development of monitoring programs are provided for different areas in the country. These recommendations include establishing baseline data for cryptogam diversity and abundance and incorporating the integration of modern molecular techniques such as DNA barcoding which are widely used in biodiversity monitoring programs to track the responses of cryptogams to environmental changes. This review seeks to emphasize the importance of cryptogams in ecosystem health assessment raising awareness among policymakers, researchers, and conservationists in Sri Lanka. Through the implementation of effective monitoring programs, we can enhance our understanding of local ecosystem dynamics, improve conservation efforts, and contribute to the sustainable management of Sri Lanka's natural resources in the face of ongoing environmental changes.}, }
@article {pmid39570169, year = {2024}, author = {Oliveira, RCG and Silva, JLN and Silva, ACC and Sousa, PRS and Almeida, MS and Nascimento, MHS and Rodrigues-Filho, LFS and Barros, MC and Fraga, EC}, title = {DNA barcode reveals a new lineage of Astyanax bimaculatus (Linnaeus 1758) in the basins of the Western Northeast Atlantic Region, Brazil.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {96}, number = {4}, pages = {e20240161}, doi = {10.1590/0001-3765202420240161}, pmid = {39570169}, issn = {1678-2690}, mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; *Genetic Variation/genetics ; *Characidae/genetics/classification ; *Haplotypes/genetics ; Phylogeny ; Bayes Theorem ; DNA, Mitochondrial/genetics ; }, abstract = {Astyanax bimaculatus are small characids known as piabas or lambaris that form a complex encompassing 18 species, including cryptic species. The present study aimed to use DNA barcode to analyze populations of A. bimaculatus found in Maranhão hydrographic basins, comparing molecular diversity indices between populations from the other Brazilian basins. The results revealed the formation of 32 haplotypes (h = 0.9289; π = 0.0523). Seven haplogroups were formed with intrapopulation genetic distance ranging from 0 to 2%. The Maranhão populations of the Western Northeast Atlantic Region basins separated from the other analyzed basins, corroborating with the groups generated in BAPS and with the Bayesian Inference tree. The occurrence of exclusive OTUs for the Maranhão populations of the Western Northeast Atlantic Region was confirmed through delimitation models. Thus, the data from this study provide information on the genetic diversity of the A. bimaculatus complex with the detection of a different lineage for the State of Maranhão, contributing to the understanding of the group's systematics.}, }
@article {pmid39568955, year = {2024}, author = {Park, J and Yagi, S and Kobayashi, S and Hirowatari, T}, title = {A new species of the genus Dryadaula Meyrick (Lepidoptera, Dryadaulidae) from Japan, with a redescription of D.epischista (Meyrick, 1936).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {327-342}, pmid = {39568955}, issn = {1313-2989}, abstract = {Dryadaulaepischista (Meyrick, 1936), initially described from a single male specimen in Japan, is herein redescribed based on newly collected specimens from the type locality. Furthermore, we describe Dryadaulaorientalis Park &amp; Yagi, sp. nov., a new species from Japan that closely resembles D.epischista. The adults and genitalia of the two species are illustrated. The genitalia of D.epischista from a specimen collected at the type locality are shown for the first time. DNA barcodes of the two Dryadaula species and the genetic distances of barcode regions among them and other congeners are provided.}, }
@article {pmid39567484, year = {2024}, author = {Zhang, P and Tian, Z and Jin, K and Yang, K and Collyer, W and Rufo, J and Upreti, N and Dong, X and Lee, LP and Huang, TJ}, title = {Automating life science labs at the single-cell level through precise ultrasonic liquid sample ejection: PULSE.}, journal = {Microsystems &amp; nanoengineering}, volume = {10}, number = {1}, pages = {172}, pmid = {39567484}, issn = {2055-7434}, support = {UH3TR002978//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; UH3 TR002978/TR/NCATS NIH HHS/United States ; R01 GM141055/GM/NIGMS NIH HHS/United States ; R44 AG063643/AG/NIA NIH HHS/United States ; R01HD103727//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01GM141055//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R44 HL140800/HL/NHLBI NIH HHS/United States ; R44 OD024963/OD/NIH HHS/United States ; R01 HD103727/HD/NICHD NIH HHS/United States ; }, abstract = {Laboratory automation technologies have revolutionized biomedical research. However, the availability of automation solutions at the single-cell level remains scarce, primarily owing to the inherent challenges of handling cells with such small dimensions in a precise, biocompatible manner. Here, we present a single-cell-level laboratory automation solution that configures various experiments onto standardized, microscale test-tube matrices via our precise ultrasonic liquid sample ejection technology, known as PULSE. PULSE enables the transformation of titer plates into microdroplet arrays by printing nanodrops and single cells acoustically in a programmable, scalable, and biocompatible manner. Unlike pipetting robots, PULSE enables researchers to conduct biological experiments using single cells as anchoring points (e.g., 1 cell vs. 1000 cells per "tube"), achieving higher resolution and potentially more relevant data for modeling and downstream analyses. We demonstrate the ability of PULSE to perform biofabrication, precision gating, and deterministic array barcoding via preallocated droplet-addressable primers. Single cells can be gently printed at a speed range of 5-20 cell⋅s[-1] with an accuracy of 90.5-97.7%, which can then adhere to the substrate and grow for up to 72 h while preserving cell integrity. In the deterministic barcoding experiment, 95.6% barcoding accuracy and 2.7% barcode hopping were observed by comparing the phenotypic data with known genotypic data from two types of single cells. Our PULSE platform allows for precise and dynamic analyses by automating experiments at the single-cell level, offering researchers a powerful tool in biomedical research.}, }
@article {pmid39565827, year = {2024}, author = {Nazari, V and Yen, SH and Hsu, YF and Shapoval, G and Shapoval, N and Todisco, V}, title = {Wiped out by an earthquake? The 'extinct' Taiwanese swallowtail butterfly (Lepidoptera, Papilionidae) was morphologically and genetically distinct.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0310318}, pmid = {39565827}, issn = {1932-6203}, mesh = {Animals ; *Butterflies/genetics ; Taiwan ; *Earthquakes ; DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Male ; }, abstract = {For the first time, we obtained for the first time a COI DNA barcode from museum specimens of the Old World swallowtail butterfly endemic to Taiwan, Papilio machaon ssp. sylvina, that has disappeared since the devastating Jiji earthquake in 1999 that shook Central Taiwan. We demonstrate that this population was not only phenotypically distinct, but also had a unique mitochondrial haplotype among all other Holarctic populations of P. machaon. The life history of P. m. sylvina from rearing experiments carried out in the 1990s is illustrated and discussed.}, }
@article {pmid39563389, year = {2024}, author = {Jumpato, W and Wannasingha, W and Jaroenchaiwattanachote, C and Mintara, R and Wongpakam, K and Adler, PH and Pramual, P}, title = {Diversity and prevalence of Leucocytozoon in black flies (Diptera: Simuliidae) of Thailand.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {475}, pmid = {39563389}, issn = {1756-3305}, support = {6720001/2567//Mahasarakham University/ ; }, mesh = {Animals ; Thailand/epidemiology ; *Simuliidae/parasitology/classification ; *Haemosporida/isolation &amp; purification/classification/genetics ; Prevalence ; Phylogeny ; Cytochromes b/genetics ; Insect Vectors/parasitology/classification ; Female ; Genetic Variation ; Birds/parasitology ; Bird Diseases/parasitology/epidemiology ; Protozoan Infections, Animal/epidemiology/parasitology ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: Leucocytozoonosis, a parasitic disease of birds, is caused by haemosporidian protozoan parasites of the genus Leucocytozoon, which infect diverse avian species, including poultry. These parasites are transmitted by several black fly species, but knowledge of the factors determining the diversity and prevalence in these vectors, which is crucial for fully understanding disease epidemiology, is largely unexplored. In this study, we investigated factors associated with the prevalence and diversity of Leucocytozoon species in black flies from Thailand.<br><br>METHODS: Adults of two black fly taxa (Simulium asakoae Takaoka and Davies complex and S. khelangense Takaoka, Srisuka and Saeung) were collected using sweep nets at nine locations in northern and northeastern regions of Thailand. Specimens were identified morphologically and the results corroborated by DNA barcoding. Molecular methods using specific primers for amplification of the mitochondrial cytochrome b (cyt b) gene of Leucocytozoon were used to detect the parasite in black flies. Species and lineages of Leucocytozoon were determined using the MalAvi database of malaria parasites and related haemosporidians in avian hosts. Regression analysis was used to examine relationships between Leucocytozoon diversity and prevalence, black fly abundance and habitat characteristics.<br><br>RESULTS: A total of 11,718 adult black flies were collected, of which 4367 were members of the S. asakoae complex and 7351 were S. khelangense. For molecular detection of Leucocytozoon, we randomly selected 300 individual female black flies of the S. asakoae complex and 850 females of S. khelangense pooled into groups of five individuals (= 170 pools). A total of 34 of the 300 specimens of the S. asakoae complex and 118 of the 170 pools of S. khelangense were positive for Leucocytozoon. Fifty-four lineages (haplotypes) were identified, all of which belonged to those reported in domestic chickens, Gallus gallus, with one exception that was identified in S. khelangense and found to be closely related to the Leucocytozoon lineages reported in owls; this is the first record of the latter lineage in Asian black flies. Among these haplotypes, nine and 45 were exclusively found in the S. asakoae complex and S. khelangense, respectively. No lineage was shared between these black fly taxa. Analysis of similarity (ANOSIM) revealed significant Leucocytozoon lineage composition between the two black flies. Phylogenetic analysis found that Leucocytozoon lineages in the S. asakoae complex and S. khelangense are largely isolated, agreeing with the ANOSIM result. The overall prevalence of Leucocytozoon in the S. asakoae complex was 11.3% and ranged from 9% to 13% in each collection. Leucocytozoon prevalence in S. khelangense was 21%, varying from 13% to 37% in each collection. The Shannon H' index indicated greater Leucocytozoon diversity in S. khelangense (H'&#x2009;=&#x2009;3.044) than in the S. asakoae complex (H'&#x2009;=&#x2009;1.920). Regression analysis revealed that Leucocytozoon diversity was positively related to black fly abundance and negatively related to maximum air temperature.<br><br>CONCLUSIONS: The results of this study show that the prevalence and diversity of Leucocytozoon lineages in the S. asakoae complex and S. khelangense from Thailand were associated with the abundance of these black flies and with air temperature. The Leucocytozoon lineages identified also showed some degree of black fly taxon specificity, possibly related to different abundance peaks of these vectors. The environmental conditions that favor the development of black flies are possibly a driver of Leucocytozoon prevalence, diversity and vector-parasite co-evolution.}, }
@article {pmid39562752, year = {2025}, author = {Cipurko, D and Ueda, T and Mei, L and Chevrier, N}, title = {Repurposing large-format microarrays for scalable spatial transcriptomics.}, journal = {Nature methods}, volume = {22}, number = {1}, pages = {145-155}, pmid = {39562752}, issn = {1548-7105}, support = {U01 AI160418/AI/NIAID NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; DP2 AI145100/AI/NIAID NIH HHS/United States ; T32 GM007281/GM/NIGMS NIH HHS/United States ; U01-AI160418//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; DP2-AI145100//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30 DK020595/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Mice ; Humans ; *Gene Expression Profiling/methods ; *Oligonucleotide Array Sequence Analysis/methods ; *Transcriptome ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Spatiomolecular analyses are key to study tissue functions and malfunctions. However, we lack profiling tools for spatial transcriptomics that are easy to adopt, low cost and scalable in terms of sample size and number. Here, we describe a method, Array-seq, to repurpose classical oligonucleotide microarrays for spatial transcriptomics profiling. We generate Array-seq slides from microarrays carrying custom-design probes that contain common sequences flanking unique barcodes at known coordinates. Then we perform a simple, two-step reaction that produces mRNA capture probes across all spots on the microarray. We demonstrate that Array-seq yields spatial transcriptomes with high detection sensitivity and localization specificity using histological sections from mouse tissues as test systems. Moreover, we show that the large surface area of Array-seq slides yields spatial transcriptomes (i) at high throughput by profiling multi-organ sections, (ii) in three dimensions by processing serial sections from one sample, and (iii) across whole human organs. Thus, by combining classical DNA microarrays and next-generation sequencing, we have created a simple and flexible platform for spatiomolecular studies of small-to-large specimens at scale.}, }
@article {pmid39562573, year = {2024}, author = {Kunitake, K and Mizuno, T and Hattori, K and Oneyama, C and Kamiya, M and Ota, S and Urano, Y and Kojima, R}, title = {Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis and release regulators.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9777}, pmid = {39562573}, issn = {2041-1723}, support = {24H00868//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJPR17H5//MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO)/ ; CDA-00008/2019-C//Human Frontier Science Program (HFSP)/ ; K05 DA000008/DA/NIDA NIH HHS/United States ; JPMJCR19H1, JPMJCR23B7//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; }, mesh = {*Extracellular Vesicles/metabolism/genetics ; Humans ; *CRISPR-Cas Systems ; *RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Tetraspanin 29/metabolism/genetics ; *Tetraspanin 30/metabolism/genetics ; HEK293 Cells ; Exosomes/metabolism/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; }, abstract = {Small extracellular vesicles (sEVs) are important intercellular information transmitters in various biological contexts, but their release processes remain poorly understood. Herein, we describe a high-throughput assay platform, CRISPR-assisted individually barcoded sEV-based release regulator (CIBER) screening, for identifying key players in sEV release. CIBER screening employs sEVs barcoded with CRISPR-gRNA through the interaction of gRNA and dead Cas9 fused with an sEV marker. Barcode quantification enables the estimation of the sEV amount released from each cell in a massively parallel manner. Barcoding sEVs with different sEV markers in a CRISPR pooled-screening format allows genome-wide exploration of sEV release regulators in a subpopulation-specific manner, successfully identifying previously unknown sEV release regulators and uncovering the exosomal/ectosomal nature of CD63[+]/CD9[+] sEVs, respectively, as well as the synchronization of CD9[+] sEV release with the cell cycle. CIBER should be a valuable tool for detailed studies on the biogenesis, release, and heterogeneity of sEVs.}, }
@article {pmid39559832, year = {2024}, author = {Grasshoff, M and Kalmer, M and Chatain, N and Kricheldorf, K and Maurer, A and Weiskirchen, R and Koschmieder, S and Costa, IG}, title = {SIngle cell level Genotyping Using scRna Data (SIGURD).}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39559832}, issn = {1477-4054}, support = {KO2155/7-1 and 7-2//German Research Foundation/ ; KO 2155/6-1//German Research Foundation/ ; //German Ministry of Education and Science/ ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; Sequence Analysis, RNA/methods ; Genotype ; Genotyping Techniques/methods ; Computational Biology/methods ; Mitochondria/genetics/metabolism ; }, abstract = {MOTIVATION: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3' ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones.<br><br>RESULTS: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.}, }
@article {pmid39559559, year = {2024}, author = {Lu, SC and Lee, YY and Andres, FGM and Moyer, DA and Barry, MA}, title = {FastAd: A versatile toolkit for rapid generation of single adenoviruses or diverse adenoviral vector libraries.}, journal = {Molecular therapy. Methods &amp; clinical development}, volume = {32}, number = {4}, pages = {101356}, pmid = {39559559}, issn = {2329-0501}, abstract = {Adenoviruses (Ads) are potent gene delivery vectors for in vitro and in vivo applications. However, current methods for their construction are time-consuming and inefficient, limiting their rapid production and utility in generating complex genetic libraries. Here, we introduce FastAd, a rapid and easy-to-use technology for inserting recombinant "donor" DNA directly into infectious "receiver" Ads in mammalian cells by the concerted action of two efficient recombinases: Cre and Bxb1. Subsequently, the resulting mixed recombinant Ad population is subjected to negative selections by flippase recombinase to remove viruses that missed the initial recombination. With this approach, recombinant Ad production time is reduced from 2 months to 10 days or less. FastAd can be applied for inserting complex genetic DNA libraries into Ad genomes, as demonstrated by the generation of barcode libraries with over 3 million unique clones from a T25 flask-scale transfection of 3 million cells. Furthermore, we leveraged FastAd to construct an Ad library containing a comprehensive genome-wide CRISPR-Cas9 guide RNA library and demonstrated its effectiveness in uncovering novel virus-host interactions. In summary, FastAd enables the rapid generation of single Ad vectors or complex genetic libraries, facilitating not only novel applications of Ad vectors but also research in foundamental virology.}, }
@article {pmid39557939, year = {2024}, author = {Shah, HK and Fathima, PA and Ajithlal, PM and Kumar, A and Rawani, A and Thakur, MS and Mohanty, SS and Sarma, DK and Pandey, K and Kumar, A and Rahi, M and Saini, P}, title = {Nationwide cross-sectional surveillance of Leishmania donovani in phlebotomine sand flies and its impact on national kala-azar elimination in India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28455}, pmid = {39557939}, issn = {2045-2322}, support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; }, mesh = {Animals ; *Leishmaniasis, Visceral/epidemiology/parasitology/prevention &amp; control/transmission ; *Leishmania donovani/genetics/isolation &amp; purification ; India/epidemiology ; Cross-Sectional Studies ; *Insect Vectors/parasitology ; Psychodidae/parasitology ; Phlebotomus/parasitology ; Humans ; Disease Eradication/methods ; }, abstract = {India is accelerating efforts to eliminate kala-azar by aligning its National Kala-Azar Elimination Program with the World Health Organization's (WHO) roadmap for Neglected Tropical Diseases (NTDs) 2021-2030. Elimination relies on comprehensive vector surveillance and integrated vector management. This study aimed to conduct nationwide entomological surveillance to detect Leishmania donovani in phlebotomine sand flies. A cross-sectional survey was conducted from January 2022 to December 2023 in five different biogeographical zones in India. Mechanical aspirator, light traps were used for sampling. The collected sand flies were identified to species level. Molecular xenomonitoring was conducted using kDNA qPCR, and parasite characterization targeting ITS1 gene sequencing and RFLP. Sand fly species was confirmed by DNA barcode. Molecular xenomonitoring revealed that Phlebotomus argentipes from Bihar, West Bengal, and Kerala exhibited high levels of L. donovani parasitic DNA. In Rajasthan, P. sergenti and P. papatasi and in Himachal Pradesh, P. longiductus, P. major, and P. bruneyi were positive. The high levels of L. donovani parasitic DNA detected in various Phlebotomus species, along with its presence in other sand fly species beyond the established vectors, underscore the urgent need for the National Kala-Azar Elimination Program to prioritize comprehensive and rigorous vector surveillance. Strengthening these efforts is crucial for achieving the program's goal of eliminating the disease.}, }
@article {pmid39555796, year = {2024}, author = {Yang, S and Chen, S and Mo, J and Liu, J and Pan, Q and Song, C}, title = {Application of DNA Barcoding to Identify Medicinal Plants.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {213}, pages = {}, doi = {10.3791/66925}, pmid = {39555796}, issn = {1940-087X}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants, Medicinal/genetics/classification ; *DNA, Plant/genetics ; }, abstract = {Medicinal plants are valuable resources globally and are used worldwide to maintain health and treat disease; however, the presence of adulteration obstructs their development. DNA barcoding, a technique for species identification by standard DNA regions, facilitates prompt and accurate identification of traditional medicinal plants. The process of DNA barcoding entails six basic steps: 1) processing the medicinal plants, 2) extracting high-quality total DNA from the medicinal plants using centrifugal column method, 3) amplifying target DNA region internal transcribed spacer 2 (ITS2) with universal primers of plants and performing Sanger sequencing, 4) splicing and aligning sequence to obtain the target sequence, 5) matching the barcode sequence against the barcode library for identification, 6) aligning sequence, comparing intraspecific and interspecific variation, constructing phylogenetic neighbor-joining tree. As shown in the results, the universal primer can amplify the target region. Basic Local Alignment Search Tool (BLAST) demonstrates the percentage identified was 100%, and the neighbor-joining tree demonstrates that the splicing sequences were clustered with the A. sinensis OR879715.1 clade, and the clade support value is 100. This protocol provides a reference for applying DNA barcoding technology as an effective method to identify medicinal plants and adulterants.}, }
@article {pmid39552916, year = {2024}, author = {Chen, HP and Chan, FT and Shiao, SF and Chiu, MC}, title = {New record of Carnidae (Diptera) from Taiwan and potential challenges in DNA barcode amplification due to pseudogene.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e137532}, pmid = {39552916}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Carnus Nitzsch, 1818 comprises small ectoparasites that feed on the blood of juvenile avians. They are characterised by dealated adults with setose abdominal intersegmental membranes. Carnusorientalis Maa, 1968 was previously recorded in Malaysia and the Ryukyu Islands of Japan, parasitising two owl species: Ketupaketupu (Horsfield, 1821) and Otuselegans (Cassin, 1852). This study confirms the occurrence of C.orientalis in Taiwan and presents a new host record, along with COI barcode sequences. Additionally, the study also elucidates the difficulties posed by blood meal contamination and pseudogene amplification as confounding factors intrinsic to the molecular taxonomic delineation of C.orientalis via universal DNA barcoding primers.<br><br>NEW INFORMATION: The following new information regarding C.orientalis is provided in this study: Carnusorientalis is first recorded in Taiwan, filling the gap in its East Asian distribution. This is also the first record of Carnidae from Taiwan.Otuslettia (Hodgson, 1836) (Aves, Strigidae) is reported as a new host for C.orientalis, identified on a fallen fledgling.Co-amplification of the host's COI is reported in this study using the universal PCR primer set LCO1490/HCO2198. Additionally, the amplification of a COI-like pseudogene using a newly-designed primer set is detected through abnormal translated amino acid sequences and the occurrence of a stop codon.New specific primers for the COI gene of Carnus were designed in this study. The new distribution and ecological data of C.orientalis enhance our understanding of this species. The provision of new COI primers is anticipated to contribute to future studies employing DNA barcoding in bird-parasitic flies.}, }
@article {pmid39552768, year = {2024}, author = {Jiang, YY and Zhao, H and Chen, Y}, title = {A new species of Proaphelinoides Girault (Hymenoptera, Aphelinidae) from China, with a phylogenetic analysis.}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {263-272}, pmid = {39552768}, issn = {1313-2989}, abstract = {A new species of Proaphelinoides Girault, Proaphelinoideshuangi Chen &amp; Jiang, sp. nov., is reported from China. A key to all species of the genus is provided. DNA standard barcode COI and partial nuclear ribosomal 28S-D2 from two individuals of Proaphelinoides were sequenced, and 28S-D2 rDNA was included in a phylogenetic analysis, confirming Proaphelinoides as the sister group to Aphytis.}, }
@article {pmid39552767, year = {2024}, author = {Kits, JH}, title = {Boreolimnus, a new leafhopper genus from northern North America, with a review of Cribrus Oman (Hemiptera, Cicadellidae, Deltocephalinae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {273-290}, pmid = {39552767}, issn = {1313-2989}, abstract = {The poorly known leafhopper species described as Deltocephalus (Laevicephalus) concinnus var. incisurus DeLong, 1926 previously had no accepted generic placement. It is here redescribed and placed in Boreolimnus gen. nov. in the tribe Paralimnini, as Boreolimnusincisurus (DeLong) comb. nov. Cribrusmicmac Hamilton, 1987 is a junior syn. nov. of B.incisurus. Due to historic confusion, the species currently placed in Cribrus Oman, 1949 were also reviewed. Cribrusconcinnus (Sanders &amp; DeLong, 1917) is redescribed, and a lectotype is designated to clarify the application of the name. Deltocephalusplagus Ball &amp; DeLong, 1926 and Laevicephalusshingwauki Beamer &amp; Tuthill, 1934 are recognized as junior syn. nov. of C.concinnus, now the only recognized species in the genus.}, }
@article {pmid39549753, year = {2024}, author = {Pogner, CE and Antunes, C and Apangu, GP and Bruffaerts, N and Celenk, S and Cristofori, A and González Roldán, N and Grinn-Gofroń, A and Lara, B and Lika, M and Magyar, D and Martinez-Bracero, M and Muggia, L and Muyshondt, B and O'Connor, D and Pallavicini, A and Marchã Penha, MA and Pérez-Badia, R and Ribeiro, H and Rodrigues Costa, A and Tischner, Z and Xhetani, M and Ambelas Skjøth, C}, title = {Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177439}, doi = {10.1016/j.scitotenv.2024.177439}, pmid = {39549753}, issn = {1879-1026}, mesh = {Aerosols/analysis ; *Air Microbiology ; Air Pollutants/analysis ; Bacteria/genetics ; Biodiversity ; *DNA/analysis ; *Environmental Monitoring/methods ; Fungi/genetics ; Plants/genetics ; Pollen ; Viruses/genetics ; }, abstract = {Bioaerosol is composed of different particles, originating from organisms, or their fragments with different origin, shape, and size. Sampling, analysing, identification and describing this airborne diversity has been carried out for over 100 years, and more recently the use of molecular genetic tools has been implemented. However, up to now there are no established protocols or standards for detecting airborne diversity of bacteria, fungi, viruses, pollen, and plant particles. In this review we evaluated commonalities of methods used in molecular genetic based studies in the last 23 years, to give an overview of applicable methods as well as knowledge gaps in diversity assessment. Various sampling techniques show different levels of effectiveness in detecting airborne particles based on their DNA. The storage and processing of samples, as well as DNA processing, influences the outcome of sampling campaigns. Moreover, the decisions on barcode selection, method of analysis, reference database as well as negative and positive controls may severely impact the results obtained. To date, the chain of decisions, methodological biases and error propagation have hindered DNA based molecular sequencing from offering a holistic picture of the airborne biodiversity. Reviewing the available studies, revealed a great diversity in used methodology and many publications didn't state all used methods in detail, making comparisons with other studies difficult or impossible. To overcome these limitations and ensure genuine comparability across studies, it is crucial to standardize protocols. Publications need to include all necessary information to enable comparison among different studies and to evaluate how methodological choices can impacts the results. Besides standardization, implementing of automatic tools and combining of different analytical techniques, such as real-time evaluation combined with sampling and molecular genetic analysis, could assist in achieving the goal of accurately assessing the actual airborne biodiversity.}, }
@article {pmid39548171, year = {2024}, author = {Raupach, MJ and Charzinski, N and Villastrigo, A and Gossner, MM and Niedringhaus, R and Schäfer, P and Schmelzle, S and Strauß, G and Hendrich, L}, title = {The discovery of an overseen pygmy backswimmer in Europe (Heteroptera, Nepomorpha, Pleidae).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {28139}, pmid = {39548171}, issn = {2045-2322}, mesh = {Animals ; *Heteroptera/genetics/classification/anatomy &amp; histology ; *Phylogeny ; Europe ; Male ; Genome, Mitochondrial ; DNA Barcoding, Taxonomic ; Female ; }, abstract = {The Pleidae, or pygmy backswimmers, is a family of aquatic bugs (Hemiptera, Heteroptera, Nepomorpha) containing four genera. Here, we describe Plea cryptica sp. nov. and redescribe its sister species, Plea minutissima Leach, 1817. Whereas the morphological distinction of these closely related species is only possible for males, molecular data clearly separate them. As part of our taxonomic study, we provide comprehensive molecular data including more than 200 DNA barcodes from all over Europe, complete nuclear ribosomal DNA, full mitochondrial genome data, and 3D scans for both species. Furthermore, the same molecular markers are also presented for Neoplea striola (Fieber, 1844). We used Maximum Likelihood (ML) analyses to reconstruct the phylogeny of the Pleidae and Notonectoidea based on available mitogenomic data. Our study represents a successful implementation of the proposed concept of taxonomics, using data from high-throughput sequencing technologies for integrative taxonomic studies, and allowing high confidence for both biodiversity and ecological research.}, }
@article {pmid39544525, year = {2024}, author = {López-Blanco, C and Tasevska, O and Kostoski, G and Vicente, E and Epp, LS and García-Alix, A}, title = {Ancient Endemic or Recent Invader? Phylogenetic Position and the Probable Origin of the Ccladoceran Diaphanosoma macedonicum (Diplostraca, Sididae) from the Ancient Lakes in the Balkans.}, journal = {Zoological studies}, volume = {62}, number = {}, pages = {e9}, pmid = {39544525}, issn = {1810-522X}, abstract = {Ancient lakes contain unique and very vulnerable fauna. Determining and understanding the origin of such biodiversity is a key factor in promoting conservation and management actions in some of the most singular ecosystems on the planet. Lake Ohrid in the Balkans is known as a natural laboratory for speciation, containing a high number of endemic species. However, the identity and origin of the planktonic cladoceran Diaphanosoma is uncertain. Representatives of the genus were long considered to have invaded the lake, but recent morphological studies have suggested that they belonged to the endemic taxon in the Balkans, D. macedonicum. Here, phylogenetic methods based on two mitochondrial gene fragments (COI and 16S) were used to identify Diaphanosoma specimens from the ancient Lake Ohrid and Lake Prespa in the Balkans and compare them with other species in Europe, including those living in nearby water bodies. Molecular evidence showed that D. macedonicum was constrained to the ancient lakes Ohrid, Prespa, and Mikri Prespa, which suggests reproductive isolation within the lakes. Phylogenetic analyses supported previous morphological assessments and situated D. macedonicum within the D. mongolianum species group, which contains three sibling species (D. mongolianum, D. lacustris, and D. macedonicum). Nuclear markers are needed to study intraspecific gene flow in these organisms and discard a potential formation of hybrids.}, }
@article {pmid39542856, year = {2024}, author = {Valkiūnas, G and Iezhova, TA and Duc, M and Dunn, JC and Bensch, S}, title = {A new blood parasite of the accentor birds: description, molecular characterization, phylogenetic relationships and distribution.}, journal = {Parasitology}, volume = {151}, number = {10}, pages = {1163-1173}, pmid = {39542856}, issn = {1469-8161}, support = {RG170086//Royal Society/ ; }, mesh = {Animals ; Phylogeny ; *Haemosporida/genetics/classification/isolation &amp; purification ; *Bird Diseases/parasitology/epidemiology ; *Protozoan Infections, Animal/parasitology/epidemiology ; Cytochromes b/genetics ; *Passeriformes/parasitology ; Genome, Mitochondrial ; Europe/epidemiology ; North America/epidemiology ; }, abstract = {Haemoproteus bobricklefsi sp. nov. (Haemosporida, Haemoproteidae) was found in the dunnock Prunella modularis and represents the first blood parasite described in accentor birds of the Prunellidae. The description is based on the morphology of blood stages and includes information about a barcoding segment of the mitochondrial cytochrome b gene (lineage hDUNNO01) and the full mitochondrial genome, which can be used for identification and diagnosis of this infection. The new parasite can be readily distinguished from described species of haemoproteids parasitizing passeriform birds due to markedly variable position of nuclei in advanced and fully grown macrogametocytes. Illustrations of blood stages of the new species are given, and phylogenetic analyses based on partial mitochondrial cytochrome b gene sequences and the full mitochondrial genome identified the closely related lineages. DNA haplotype networks showed that transmission occurs in Europe and North America. This parasite was found in the dunnock in Europe and several species of the Passerellidae in North America. It is probably of Holarctic distribution, with the highest reported prevalence in the UK. The parasite distribution seems to be geographically patchy, with preference for areas of relatively cool climates. Phylogenetic analysis suggests that H. bobricklefsi sp. nov. belongs to the Parahaemoproteus subgenus and is probably transmitted by biting midges belonging to Culicoides (Ceratopogonidae). The available data on molecular occurrence indicate that this pathogen is prone to abortive development, so worth attention in regard of consequences for bird health.}, }
@article {pmid39541669, year = {2024}, author = {Kusuda, K and Yamashita, K and Morishita, E and Ishibashi, N and Shiraishi, Y and Yamaguchi, H}, title = {Comparison of Reading Times of RFID-Tagged and Barcode-Engraved Surgical Instruments.}, journal = {The Journal of surgical research}, volume = {304}, number = {}, pages = {121-125}, doi = {10.1016/j.jss.2024.09.087}, pmid = {39541669}, issn = {1095-8673}, mesh = {*Radio Frequency Identification Device/methods ; Humans ; *Surgical Instruments/economics ; Time Factors ; Electronic Data Processing ; Clinical Competence/statistics &amp; numerical data ; Adult ; Male ; Patient Safety ; Female ; }, abstract = {INTRODUCTION: To improve patient safety and reduce burden on healthcare professionals and institutions, the individual management of surgical instruments is essential. There are two methods for individual item management: radio-frequency identification (RFID) and barcoding. However, there has been no examination of efficiency regarding reading times. Therefore, this study aimed to compare the reading times of RFID-tagged and barcode-engraved surgical instruments and evaluate the influence of operator proficiency.<br><br>METHODS: The participants included 8 individuals and 41 surgical instruments from a varicose vein set. RFID tags and barcodes were attached to the surgical instruments. Five trials were conducted for each, and the reading times were measured.<br><br>RESULTS: The reading times for RFID-tagged surgical instruments in the skilled and unskilled groups were 64.0&#xa0;&#xb1;&#xa0;9.0s and 79.4&#xa0;&#xb1;&#xa0;17.0&#xa0;s, respectively, whereas those for barcode-engraved surgical instruments were 190.4&#xa0;&#xb1;&#xa0;28.1&#xa0;s and 212.3&#xa0;&#xb1;&#xa0;40.3&#xa0;s, respectively. Barcodes took 3.0 and 2.7 times longer to read than RFID-tagged instruments for the skilled and unskilled groups, respectively. Additionally, skilled operators using barcodes required 2.4 times more time than unskilled operators using RFID. Even nonmedical individuals were able to achieve quick and accurate readings with RFID. The estimated labor hours per person were $24,146-$42,322 for RFID and $71,078-$110,898 for barcode scanning for a year (working 8&#xa0;h/d for 250&#xa0;d).<br><br>CONCLUSIONS: RFID-tagged surgical instruments impose a lighter workload and financial burden than barcode-engraved surgical instruments. RFID technology may also improve patient safety due to less dependency on operator proficiency.}, }
@article {pmid39538416, year = {2024}, author = {Hua, J and Wang, K and Chen, Y and Xu, X and Dong, G and Li, Y and Liu, R and Xiong, Y and Ding, J and Zhang, T and Zeng, X and Li, Y and Sun, H and Gu, Y and Liu, S and Ouyang, W and Liu, C}, title = {Molecular characterization of human HSPCs with different cell fates in vivo using single-cell transcriptome analysis and lentiviral barcoding technology.}, journal = {Clinical and translational medicine}, volume = {14}, number = {11}, pages = {e70085}, pmid = {39538416}, issn = {2001-1326}, support = {No.31970816//National Natural Science Foundation of China (NSFC)/ ; No.BGIRSZ20210006//Open fund project of Shenzhen BGI Institute of Life Science/ ; No. KJZD20230923114911023//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; No.SZSM202211033//Sanming Project of Medicine in Shenzen Municipality/ ; }, mesh = {Humans ; *Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; *Hematopoietic Stem Cells/metabolism/cytology ; Cell Differentiation/genetics ; Lentivirus/genetics ; Single-Cell Gene Expression Analysis ; }, abstract = {Hematopoietic stem and progenitor cells (HSPCs) possess the potential to produce all types of blood cells throughout their lives. It is well recognized that HSPCs are heterogeneous, which is of great significance for their clinical applications and the treatment of diseases associated with HSPCs. This study presents a novel technology called Single-Cell transcriptome Analysis and Lentiviral Barcoding (SCALeBa) to investigate the molecular mechanisms underlying the heterogeneity of human HSPCs in vivo. The SCALeBa incorporates a transcribed barcoding library and algorithm to analyze the individual cell fates and their gene expression profiles simultaneously. Our findings using SCALeBa reveal that HSPCs subset with stronger stemness highly expressed MYL6B, ATP2A2, MYO19, MDN1, ING3, and so on. The high expression of COA3, RIF1, RAB14, and GOLGA4 may contribute to the pluripotent-lineage differentiation of HSPCs. Moreover, the roles of the representative genes revealed in this study regarding the stemness of HPSCs were confirmed with biological experiments. HSPCs expressing MRPL23 and RBM4 genes may contribute to differentiation bias into myeloid and lymphoid lineage, respectively. In addition, transcription factor (TF) characteristics of lymphoid and myeloid differentiation bias HSPCs subsets were identified and linked to previously identified genes. Furthermore, the stemness, pluripotency, and differentiation-bias genes identified with SCALeBa were verified in another independent HSPCs dataset. Finally, this study proposes using the SCALeBa-generated tracking trajectory to improve the accuracy of pseudo-time analysis results. In summary, our study provides valuable insights for understanding the heterogeneity of human HSPCs in vivo and introduces a novel technology, SCALeBa, which holds promise for broader applications. KEY POINTS: SCALeBa and its algorithm are developed to study the molecular mechanism underlying human HSPCs identity and function. The human HSPCs expressing MYL6B, MYO19, ATP2A2, MDN1, ING3, and PHF20 may have the capability for high stemness. The human HSPCs expressing COA3, RIF1, RAB14, and GOLGA4 may have the capability for pluripotent-lineage differentiation. The human HSPCs expressing MRPL23 and RBM4 genes may have the capability to differentiate into myeloid and lymphoid lineage respectively in vivo. The legitimacy of the identified genes with SCALeBa was validated using biological experiments and a public human HSPCs dataset. SCALeBa improves the accuracy of differentiation trajectories in monocle2-based pseudo-time analysis.}, }
@article {pmid39538182, year = {2024}, author = {Anwar, A and Wahab, H and Wahab, A and Afshan, NUS and Moussa, IM and Elhindi, KM and Ahmed, M and Malik, A and Singh, MP and Gaidhane, S and Uddin, S}, title = {Molecular and morphoanatomical characterization of Urocystis heteropogonis sp. nov.: a novel smut fungus infecting Heteropogon contortus.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1070}, pmid = {39538182}, issn = {1471-2229}, mesh = {*Phylogeny ; DNA, Fungal/genetics ; Spores, Fungal/genetics ; Pakistan ; Animals ; }, abstract = {BACKGROUND: A new species of smut fungus, Urocystis heteropogonis, was discovered infecting Heteropogon contortus in Shawar Valley, Swat district, Khyber Pakhtunkhwa, Pakistan. The study aimed to characterize this fungus based on its morpho-anatomical and molecular features and clarify its phylogenetic position within the genus Urocystis.<br><br>RESULTS: Urocystis heteropogonis was identified as a novel species, distinct from other Urocystis species. Morphologically, it is characterized by larger spore balls (14-69&#x2009;&#xd7;&#x2009;11-45&#xa0;&#x3bc;m) and central spores that are 14-28&#x2009;&#xd7;&#x2009;11-20&#xa0;&#x3bc;m in size, with each spore containing1-8 central spores. The spore walls measure 0.9-2.5&#xa0;&#x3bc;m in thickness and the species differs in infection patterns compared to other Urocystis species. Phylogenetic analysis based on the ITS and LSU regions of nuclear ribosomal DNA (nrDNA) further confirmed the novelty of the species, placing it within a distinct clade alongside U. agropyri, U. occulta, U. piptatheri, and U. tritici.<br><br>CONCLUSIONS: The discovery of Urocystis heteropogonis adds to the diversity of smut fungi infecting grasses and highlights the need for further research into its ecological and agricultural implications. Future studies should focus on the disease's spread, management, and potential impact on host populations.}, }
@article {pmid39538137, year = {2024}, author = {El-Demerdash, MM and El-Sayed, ASA and Teleb, SS and Sadek, AM and Elsehely, HH}, title = {DNA barcoding, micromorphology and metabolic traits of selected Ficus L. (Moraceae) species from Egypt.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1067}, pmid = {39538137}, issn = {1471-2229}, mesh = {*DNA Barcoding, Taxonomic ; *Ficus/genetics/anatomy &amp; histology/classification ; Egypt ; Phylogeny ; DNA, Plant/genetics ; Plant Leaves/anatomy &amp; histology/genetics/metabolism ; Species Specificity ; }, abstract = {The genus Ficus of the family Moraceae, is one of the largest genera of angiosperms, with diverse pharmaceutical applications and biological activities. The traditional approaches based on the morphological traits have been frequently implemented for taxonomical identification of the different taxa of Ficus, however, encompassing these features are quite laborious, due to the dependence of these phenotypic traits on the environmental conditions. So, authenticating the taxonomical identity of the Ficus taxa with molecular barcoding and metabolic profiling, as relatively stable traits, could be a relevant approach for confirming the traditional phenotypic traits of this genus. Nine species of the genus Ficus namely F. amplissima Sm., F. benjamina L. F. binnendijkii, F. drupacea var. pubescens, F. elastica Roxb., F. microcarpa L., F. religiosa L., F. tinctoria subsp. gibbosa and F. virens var. sublancelata in Egypt, were selected for this study. From the anatomical features, three species of subsection Urostigma, F. religiosa, F. virens var. sublanceolata have cystoliths on the abaxial layer, whereas in F. amplissima it was on the adaxial layer. The UPGMA dendrogram of the studied Ficus taxa has been generated from the 21 anatomical characters, categorized the studied taxa into two clusters (I and II) of average distance ~ 3.5, each cluster has been further divided into subclusters I and II. The sub-cluster I includes F. religiosa, F. virens var. sublanceolata and F. tinctoria subsp. gibbosa were grouped together to subsection Urostigma, while the sub-cluster II of the cluster I includes F. benjamina and F. amplissima. From the DNA barcoding analysis, three clusters I, II and III were emerged, the cluster I includes F. benjamina, F. binnendjikee, and F. amplissima. The cluster II, F. virens var. sublanceolata and F. religiosa that belong to subsection Urostigma, while, the cluster III includes F. elastica and F. drupacea var. pubescens, F. microcarpa that belongs to subsection Conosycea. From the metabolic profiling of Ficus species, the major compounds; H-cycloprop-azulen-7-ol, 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, 2-(9-octadecenyloxy), pentadecanoic acid, phytol, sitosterol and 9,12-octadecadienoic acid were the common among the taxa, with an obvious fluctuation, that could be a chemotaxonomic markers for these species of Ficus. Based on the metabolic profiling, two distinct clusters I and II were evolved, the cluster I involve F. elastica, F. benjamina, F. drupacea var. pubescens, F. amplissima, while, the cluster II had F. tinctoria subsp. gibbosa and F. religiosa. The fluctuation on the metabolites of the tested Ficus species could be a metabolic fingerprint for each species. So, the delamination of the tested plants based on their anatomical traits was typically matched to the separation based on the ITS sequence analysis.}, }
@article {pmid39537812, year = {2024}, author = {Mingeot, D and Chavalle, S and Buhl, PN and Sonet, G and Dubois, B and Hautier, L}, title = {Molecular methods for the detection and identification of parasitoids within larval wheat midges.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27770}, pmid = {39537812}, issn = {2045-2322}, mesh = {Animals ; *Larva/parasitology ; *Triticum/parasitology ; *Diptera/parasitology ; *DNA Barcoding, Taxonomic/methods ; Hymenoptera/genetics ; }, abstract = {Three species of cecidomyiid midges (Diptera: Cecidomyiidae) cause significant yield losses on wheat in Europe: Sitodiplosis mosellana (Géhin), Contarinia tritici (Kirby) and Haplodiplosis marginata (von Roser). Eggs and young larvae may be parasitised by a complex of hymenopteran parasitoids belonging to the Pteromalidae and Platygastridae families which contributes to natural pest control. We have developed molecular tools for detecting and identifying seven parasitoid species previously encountered in Belgium inside individual wheat midge larvae. Barcode DNA sequences from COI, 18S and 28S genes were obtained from the midges and parasitoid species. Each of the three genes allowed all the species to be distinguished although 18S was the only one displaying a barcoding gap, both between parasitoids and midges, and at the species level. Based on the 18S gene, we developed a TaqMan assay to assess parasitism in midge larvae, regardless of the midge and parasitoid species. Next, two group-specific PCR primer pairs were generated, allowing the separate amplification of midge DNA or parasitoid DNA in parasitised individuals and subsequent identification by Sanger sequencing. Finally, species-specific primers were designed to identify six parasitoid species by simple PCR amplification. These tools were successfully applied to assess the parasitism rate of S. mosellana larvae in seven Belgian fields.}, }
@article {pmid39535995, year = {2024}, author = {Shah, SHA and Nisar, M and Ihsan, M and Zahoor, M and Ullah, R and Iqbal, Z and Shah, AB}, title = {Estimation of genetic polymorphism in quince (Cydonia oblonga Mill.) genotypes using morphological traits and molecular (DNA barcoding) characterizations.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0310048}, pmid = {39535995}, issn = {1932-6203}, mesh = {*Rosaceae/genetics ; *Genotype ; *Polymorphism, Genetic ; *DNA Barcoding, Taxonomic/methods ; Fruit/genetics/anatomy &amp; histology ; Pakistan ; Phylogeny ; DNA, Plant/genetics ; }, abstract = {Quince (Cydonia oblonga) is a medicinal plant and a member of family Rosaceae. It is native plant of Asia Minor and Europe. It is used in production of jam and jellies and also as a remedy of several ailments. The present study was conducted to evaluate the genetic polymorphism based on morphological and molecular traits. Different varieties of Quince were collected from different ecological zones of Khyber Pakhtunkhwa Pakistan and a total of 26 different morphological traits were recorded among studied genotypes. Based on qualitative morphological trait study, the variety collected from Tindodag was unique one with highest fruit weight (328.82 g). The lowest fruit weight (68.38 g) was recorded for Talash genotype. The Charbagh and Tindodag genotypes showed highest seed length (10.6 mm) while genotypes of Chitral was recorded as lowest (8.4 mm). Statistically, significant level of variation was noted with coefficient of variance ranged from 2.23% to 30.38%. Based on correlation analysis, fruit length had strongly correlation with fruit weight (r = 0.89**), Average Fruit width was found significant with fruit weight (r = 0.90**). Similarly, the Core Width was found strongly significant with Core Length (r = 0.95**). ANOVA analysis indicated 10 quantitative characters to be highly significant, 2 significant and 1 insignificant. Principal component analysis was also computed for the 13 quantitative traits with Eigen value of 0.48 and a total variance of 97.78%. The first principal component shows total variation of 52.52%. In PC2 the total variation was 80.15%, PC3 94.06% while in PC4 it was 97.78%. The NCBI BLAST results shows that all the genotypes have similar origin except Tindodag genotype, which shows differences in its origin. Accession number for all other genotypes is MN216014.1, while accession number of Tindodag genotype is KF861967.1. Based on this study, it can be concluded that Tindodag genotype is unique out of the studied localities. NCBI BLAST have provided further support for the drawn conclusion.}, }
@article {pmid39534104, year = {2024}, author = {Wang, L and Li, F and Zhao, K and Yang, J and Sun, H and Cui, X and Dong, W and Li, E and Wang, N}, title = {Comparative plastomes sheds light on phylogeny of Weigela.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1487725}, pmid = {39534104}, issn = {1664-462X}, abstract = {Weigela Thunb. is a genus in the family Caprifoliaceae. All species in this genus have high ornamental and medicinal value. However, the genetic divergence between species and the phylogeny within Weigela is still unclear. Therefore, we sequenced and analyzed four plastomes from four different Weigela species to reveal the genetic divergence among species of this genus, and the phylogeny within Weigela. The four plastomes from Weigela ranged from 156,909 bp to 157,739 bp in size, and presented a typical circular quadripartite structure. Each complete plastome contained a pair of inverted repeat regions (23,592~24,957 bp), a larger single-copy (LSC) region (89,922~90,229 bp), and a small single-copy (SSC) region (17,668~20,429 bp). We identified three types of repeats, corresponding to 268 forward repeats, 128 palindromic repeats, and 867 tandem repeats, for a total of 1,263 long repeats. A total of 352 SSRs were identified from the four plastomes, and most of them were concentrated in the LSC region and the noncoding regions. Mononucleotide repeat units were the most frequently detected types of repeats, of which A/T repeat units were the most abundant. Three mutational hotspots (trnH-psbA, trnR-ndhF, and trnN-ndhF) were identified as candidate barcodes for Weigela species. Weigela belongs to Diervilloideae located at an early diverging position in the Caprifoliaceae. Within Weigela, W. japonica and W. floribunda were sister with W. subsessilis and W. florida. This study revealed the plastome structure and variation of four well-known Weigela species, and found three candidate barcodes for further study of four well-known Weigela species. In addition, the phylogenetic location of Weigela within the Caprifoliaceae was identified.}, }
@article {pmid39528918, year = {2024}, author = {Filippov, I and Philip, CS and Schauser, L and Peterson, P}, title = {Comparative transcriptomic analyses of thymocytes using 10x Genomics and Parse scRNA-seq technologies.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1069}, pmid = {39528918}, issn = {1471-2164}, support = {955321//Horizon 2020 Framework Programme/ ; 955321//Horizon 2020 Framework Programme/ ; PRG2011//Eesti Teadusagentuur/ ; }, mesh = {Animals ; *Thymocytes/metabolism/cytology ; *Single-Cell Analysis/methods ; Mice ; *Genomics/methods ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; RNA-Seq/methods ; Single-Cell Gene Expression Analysis ; }, abstract = {BACKGROUND: Single-cell RNA sequencing experiments commonly use 10x Genomics (10x) kits due to their high-throughput capacity and standardized protocols. Recently, Parse Biosciences (Parse) introduced an alternative technology that uses multiple in-situ barcoding rounds within standard 96-well plates. Parse enables the analysis of more cells from multiple samples in a single run without the need for additional reagents or specialized microfluidics equipment. To evaluate the performance of both platforms, we conducted a benchmark study using biological and technical replicates of mouse thymus as a complex immune tissue.<br><br>RESULTS: We found that Parse detected nearly twice the number of genes compared to 10x, with each platform detecting a distinct set of genes. The comparison of multiplexed samples generated from 10x&#xa0;and Parse techniques showed 10x&#xa0;data to have lower technical variability and more precise annotation of biological states in the thymus compared to Parse.<br><br>CONCLUSION: Our results provide a comprehensive comparison of the suitability of both single-cell platforms for immunological studies.}, }
@article {pmid39526042, year = {2024}, author = {Pešić, V and Zawal, A and Ferreira, S and Benitez-Bosco, L and Cruz-Oliveira, A and Girão, D and Padilha, A and Turaccio, P and Rossini, S and Ballini, L and Staffoni, G and Fratini, S and Ciofi, C and Iannucci, A and Ekrem, T and Stur, E}, title = {DNA barcode library of Portuguese water mites, with the descriptions of two new species (Acari, Hydrachnidia).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {119-171}, pmid = {39526042}, issn = {1313-2989}, abstract = {This study presents the first results from the analysis of water mites collected in Portugal as part of the Biodiversity Genomics Europe project. 307 COI DNA barcodes clustered into 75 BINs are provided, with 38 BINs being unique and deposited for the first time in the Barcode of Life Data Systems (BOLD). 65 species have been identified, of which 36 are new to the water mite fauna of Portugal. Two species, Torrenticolasoniae Pešić, sp. nov. and T.elisabethae Pešić, sp. nov. (Torrenticolidae), are described as new to science. 47% of the water mite species currently known from Portugal now have reference barcodes in BOLD. High intraspecific distances were recorded for some species, suggesting the presence of cryptic diversity and species complexes that needs further study. Our results improve the DNA barcode reference database for Portuguese water mites, enhancing species identification accuracy and stimulating future investigation.}, }
@article {pmid39524431, year = {2024}, author = {Kan, J and Nie, L and Mi, Z and Liu, X and Xu, D and Tembrock, LR and Wu, Z and Hong, Z}, title = {Insights into Aquilaria phylogenetics through comparative plastomic resources.}, journal = {Forestry research}, volume = {4}, number = {}, pages = {e030}, pmid = {39524431}, issn = {2767-3812}, abstract = {The plastid is an essential organelle for its role in photosynthesis and energy production and its genomic information is always employed as important evolutionary markers to explore the relationship among species. Agarwood (Aquilaria), prized for its aromatic blend, finds extensive use in various cultures as incense and perfume. Despite its high economic importance, the phylogenetic status among Aquilaria based on plastomes remains ambiguous due to the lack of available plastomic resources. To bridge this knowledge gap, 22 Aquilaria plastomes were newly sequenced, similar variation patterns in this genus were determined, including a shared 16 bp extension of the rps19 gene and seven highly variable regions. The analysis highlighted the highest prevalence of the A/T motif among simple sequence repeats in these plastomes. Further phylogenetic analysis revealed Aquilaria's phylogenetic implications with an expanded dataset. This comprehensive plastomic resource not only enhances our understanding of Aquilaria evolution but also presents potential molecular markers for DNA barcoding.}, }
@article {pmid39524315, year = {2024}, author = {Lamichhane, B and Brockway, C and Evasco, K and Nicholson, J and Neville, PJ and Mackenzie, JS and Smith, D and Imrie, A}, title = {DNA Barcoding for the Identification of Adult Mosquitoes (Diptera: Culicidae) in Western Australia.}, journal = {Ecology and evolution}, volume = {14}, number = {11}, pages = {e70493}, pmid = {39524315}, issn = {2045-7758}, abstract = {Precise mosquito identification is integral to effective arbovirus surveillance. Nonetheless, the conventional morphological approach to identifying mosquito species is laborious, demands expertise and presents challenges when specimens are damaged. DNA barcoding offers a promising alternative, surmounting challenges inherent in morphological identification. To integrate DNA barcoding into arbovirus surveillance effectively, a robust dataset of mosquito barcode sequences is required. This study established a comprehensive repository of Cytochrome Oxidase I (COI) barcodes, encompassing 177 samples representing 45 mosquito species from southern and northern Western Australia (WA), including 16 species which have not been previously barcoded. The average intraspecific and interspecific genetic distances were 1% and 6.8%, respectively. Anopheles annulipes sensu lato had the highest intraspecific distance at 9.1%, signifying a genetically diverse species. While validating the potential of COI barcodes to accurately differentiate mosquito species, we identified that some species pairs have low COI divergence. This includes Aedes clelandi and Ae. hesperonotius, Tripteroides atripes and Tp. punctolaeralis and Ae. turneri and Ae. stricklandi. In addition, we observed ambiguity in identification of the members of Culex sitiens subgroup (Cx. annulirostris, Cx. palpalis and Cx. sitiens) and three members of Cx. pipiens complex (Cx. australicus, Cx. globocoxitus, Cx. quinquefasciatus). In summary, despite presenting challenges in the identification of some mosquito species, the COI barcode accurately identified most of the species and generated a valuable resource that will support the WA arbovirus surveillance program and enhance public health intervention strategies for mosquito-borne disease control.}, }
@article {pmid39535538, year = {2024}, author = {Singh, Y and Farrelly, C and Hathaway, QA and Carlsson, G}, title = {Persistence barcodes: A novel approach to reducing bias in radiological analysis.}, journal = {Oncotarget}, volume = {15}, number = {}, pages = {784-786}, pmid = {39535538}, issn = {1949-2553}, mesh = {Humans ; *Bias ; Diagnostic Imaging/methods/standards ; Image Processing, Computer-Assisted/methods/standards ; Algorithms ; Neural Networks, Computer ; Radiology/methods/standards ; }, abstract = {Persistence barcodes emerge as a promising tool in radiological analysis, offering a novel approach to reduce bias and uncover hidden patterns in medical imaging. By leveraging topological data analysis, this technique provides a robust, multi-scale perspective on image features, potentially overcoming limitations in traditional methods and Graph Neural Networks. While challenges in interpretation and implementation remain, persistence barcodes show significant potential for improving diagnostic accuracy, standardization, and ultimately, patient outcomes in the evolving field of radiology.}, }
@article {pmid39534110, year = {2024}, author = {Oeum, K and Suong, M and Uon, K and Jobert, L and Bellafiore, S and Comte, A and Thomas, E and Kuok, F and Moulin, L}, title = {Comparison of plant microbiota in diseased and healthy rice reveals methylobacteria as health signatures with biocontrol capabilities.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1468192}, pmid = {39534110}, issn = {1664-462X}, abstract = {INTRODUCTION: Rice (Oryza sativa) is a staple food worldwide, but its production is under constant pressure from both abiotic and biotic stresses, resulting in high use of agrochemicals. The plant microbiome harbours microorganisms that can benefit plant health and provide alternatives to the use of agrochemicals. The composition of plant microbiomes depends on many factors (soil composition, age, and health) and is considered a primary driver of future plant health. To identify plant microbiomes that protect against disease, we hypothesised that asymptomatic rice plants in fields under high pathogen pressure (i.e., healthy islands of plants among predominantly diseased plants) might harbour a microbiota that protects them from disease.<br><br>MATERIAL AND METHODS: We sampled healthy and leaf-diseased plants in rice fields with high disease incidence in Cambodia and profiled their microbiota at leaf, root, and rhizosphere levels using 16S V3V4 and 18S V4 amplicon barcoding sequencing.<br><br>RESULTS: Comparison of amplicon sequence variants (ASV) of the microbiota of healthy and diseased samples revealed both disease and healthy signatures (significant enrichment or depletion at ASV/species/genus level) in both fields. The genera Methylobacterium and Methylorubrum were identified health taxa signatures with several species significantly enriched in healthy leaf samples (Methylobacterium indicum, Methylobacterium komagatae, Methylobacterium aerolatum, and Methylorubrum rhodinum). A cultivation approach on rice samples led to the isolation of bacterial strains of these two genera, which were further tested as bioinoculants on rice leaves under controlled conditions, showing for some of them a significant reduction (up to 77%) in symptoms induced by Xanthomonas oryzae pv. oryzae infection.<br><br>DISCUSSION: We validated the hypothesis that healthy plants in fields under high disease occurrence can host specific microbiota with biocontrol capacities. This strategy could help identify new microbes with biocontrol potential for sustainable rice production.}, }
@article {pmid39532481, year = {2025}, author = {Nazar, N and Saxena, A and Sebastian, A and Slater, A and Sundaresan, V and Sgamma, T}, title = {Integrating DNA Barcoding Within an Orthogonal Approach for Herbal Product Authentication: A Narrative Review.}, journal = {Phytochemical analysis : PCA}, volume = {36}, number = {1}, pages = {7-29}, pmid = {39532481}, issn = {1099-1565}, support = {//Daphne Jackson Trust/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants, Medicinal/genetics/chemistry/classification ; *DNA, Plant/genetics ; Quality Control ; }, abstract = {INTRODUCTION: Existing methods for morphological, organoleptic, and chemical authentication may not adequately ensure the accurate identification of plant species or guarantee safety. Herbal raw material authentication remains a major challenge in herbal medicine. Over the past decade, DNA barcoding, combined with an orthogonal approach integrating various testing methods for quality assurance, has emerged as a new trend in plant authentication.<br><br>OBJECTIVE: The review evaluates DNA barcoding and common alternative testing in plant-related sectors to enhance quality assurance and accurate authentication.<br><br>METHOD: Studies were selected based on their relevance to the identification, quality assurance, and safety of herbal products. Inclusion criteria were peer-reviewed articles, systematic reviews, and relevant case studies from the last two decades focused on DNA barcoding, identification methods, and their applications. Exclusion criteria involved studies lacking empirical data, those not peer-reviewed, or those unrelated to the main focus. This ensured the inclusion of high-quality, pertinent sources while excluding less relevant studies.<br><br>RESULTS: An orthogonal approach refers to the use of multiple, independent methods that provide complementary information for more accurate plant identification and quality assurance. This reduces false positives or negatives by confirming results through different techniques, combining DNA barcoding with morphological analysis or chemical profiling. It enhances confidence in results, particularly in cases of potential adulteration or misidentification of plant materials.<br><br>CONCLUSION: This study highlights the persistent challenges in assuring the quality, purity, and safety of plant materials. Additionally, it stresses the importance of incorporating DNA-based authentication alongside traditional methods, to enhance plant material identification.}, }
@article {pmid39532139, year = {2024}, author = {Calderón-Gutiérrez, F and Labonté, JM and Gonzalez, BC and Iliffe, TM and Mejía-Ortíz, LM and Borda, E}, title = {Cryptic diversity patterns of subterranean estuaries.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2034}, pages = {20241483}, pmid = {39532139}, issn = {1471-2954}, support = {//T3: Texas A&amp;M Triads for transformation/ ; //Texas A&amp;M University Galveston/ ; //Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; //CONACYT- Texas A&amp;M University/ ; //Mohamed bin Zayed Species Conservation Fund/ ; //National Science Foundation/ ; //Texas A&amp;M University San Antonio/ ; }, mesh = {*RNA, Ribosomal, 16S/analysis ; *Estuaries ; *Biodiversity ; Animals ; *Electron Transport Complex IV/genetics/analysis ; *DNA Barcoding, Taxonomic ; *Phylogeny ; Mexico ; Sequence Analysis, DNA ; Genetic Variation ; Invertebrates/genetics ; }, abstract = {Subterranean estuaries are coastal ecosystems characterized by vertically stratified groundwater. The biota within these ecosystems is relatively understudied due to the inherent difficulty of accessing such extreme environments. The fauna inhabiting these ecosystems is considered vulnerable to extinction, and the presence of cryptic species has major implications for research and conservation efforts. Most species lack molecular data; however, the evaluation of genetic data for some taxa has revealed that undocumented species are common. This study employs molecular species delimitation methods and DNA barcoding through the analysis of publicly and newly generated sequences, including individuals from type localities and non-crustacean phyla; the latter are typically overlooked in biodiversity assessments of subterranean estuaries. We analysed 376 cytochrome c oxidase subunit I (COI) gene sequences and 154 16S rRNA gene sequences. The COI sequences represented 32% of previously described species and 50% of stygobiont species from the Yucatan Peninsula and Cozumel Island, while sequences of the 16S rRNA represented 14% of described species and 22% of stygobionts. Our results revealed cryptic genetic lineages and taxonomic misidentification of species. As several species from these ecosystems are recognized as endangered, the use of molecular approaches will improve biodiversity estimates and highlight overlooked cryptic lineages in need of evaluation of conservation status.}, }
@article {pmid39529423, year = {2025}, author = {Bustamante, MI and Elfar, K and Carachure, C and Adaskaveg, A and Kabashima, JN and Shogren, C and Eskalen, A and Lynch, SC}, title = {Etiology of Pine Ghost Canker in Southern California Urban Forests.}, journal = {Plant disease}, volume = {109}, number = {5}, pages = {971-982}, doi = {10.1094/PDIS-08-24-1718-SR}, pmid = {39529423}, issn = {0191-2917}, mesh = {*Plant Diseases/microbiology ; California ; *Pinus/microbiology ; *Ascomycota/genetics/pathogenicity/isolation &amp; purification/classification/physiology ; Forests ; Phylogeny ; }, abstract = {Pine ghost canker is a recently described disease affecting multiple pine species in urban forests of Southern California. Symptoms include wedged cankers with irregular margins and cryptic discoloration on cross sections of branches, which can lead to severe dieback and potentially tree death. In this study, we identified and characterized five Neofusicoccum species (N. luteum, N. mediterraneum, N. parvum, N. stellenboschianum, and N. vitifusiforme) as the primary etiological agents of pine ghost canker. These pathogens were consistently isolated from multiple symptomatic pine samples (n = 41) and identified by morphology and phylogenetic analyses using four DNA barcodes (rDNA ITS, tef1, tub2, and rpb2). Pathogenicity was confirmed on healthy branches of 15-year-old Monterey pines, where the five Neofusicoccum species caused vascular lesions that were not significantly different in length. Secondary fungi (Diaporthe, Diplodia, Neopestalotiopsis, and Pestalotiopsis spp.) were also recovered from symptomatic tissues but did not cause vascular lesions in pathogenicity tests. The five Neofusicoccum species showed significant differences in mycelial growth rate at 20, 25, and 30°C. The optimal temperature for mycelial growth of N. luteum and N. parvum was 30°C, whereas for N. mediterraneum, N. stellenboschianum, and N. vitifusiforme, it was 25°C. All five species were able to resume growth at 20°C after showing no growth during a 7-day exposure to 5 and 40°C. This study also constitutes the first report of N. luteum, N. stellenboschianum, and N. vitifusiforme causing pine ghost canker in California. Environmental factors such as warmer temperatures, irrigation, and pest infestations are discussed as drivers of disease expression in pine trees. Management practices are also proposed.}, }
@article {pmid39526732, year = {2024}, author = {Soto-Serrano, A and Li, W and Panah, FM and Hui, Y and Atienza, P and Fomenkov, A and Roberts, RJ and Deptula, P and Krych, L}, title = {Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.}, journal = {Microbial genomics}, volume = {10}, number = {11}, pages = {}, pmid = {39526732}, issn = {2057-5858}, mesh = {*Genome, Bacterial ; *Base Composition ; Nanopores ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing/methods ; }, abstract = {The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used Propionibacterium freudenreichii, a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT's Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies. Our findings demonstrate, for the first time, that the combination of nanopore-only long-native with shorter PCR DNA reads (~3 kb) results in high-quality genome reconstruction, comparable to hybrid data assembly from two sequencing platforms. This endorses ONT as a cost-effective, stand-alone strategy for bacterial genome reconstruction. Additionally, we compared methylated motif detection between PacBio and ONT R10.4.1 data, showing that results comparable to PacBio are achievable using ONT, especially when utilizing the advanced Nanomotif tool.}, }
@article {pmid39523608, year = {2024}, author = {Hosuru, RV and Yang, J and Zhou, Y and Gin, A and Hayal, TB and Hong, SG and Dunbar, CE and Wu, C}, title = {Long-term tracking of haematopoietic clonal dynamics and mutations in non-human primate undergoing transplantation of lentivirally barcoded haematopoietic stem and progenitor cells.}, journal = {British journal of haematology}, volume = {205}, number = {6}, pages = {2487-2497}, pmid = {39523608}, issn = {1365-2141}, support = {/HI/NHLBI NIH HHS/United States ; /HI/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Macaca mulatta ; *Hematopoietic Stem Cells/metabolism/cytology ; *Hematopoietic Stem Cell Transplantation/methods ; *Mutation ; *Lentivirus/genetics ; Genetic Therapy/methods ; Genetic Vectors ; Cell Tracking/methods ; Humans ; Transplantation, Autologous ; }, abstract = {Haematopoietic stem and progenitor cell (HSPC) autologous gene therapies are promising treatment for a variety of blood disorders. Investigation of the long-term HSPC clonal dynamics and other measures of safety and durability following lentiviral-mediated gene therapies in predictive models are crucial for assessing risks and benefits in order to inform decisions regarding wider utilization. We established an autologous lentivirally barcoded HSPC transplantation model in rhesus macaque (RM), a model offering insights into haematopoiesis and gene therapies with direct relevance to human. Healthy young adult RMs underwent total body irradiation, followed by transplantation of autologous HSPCs transduced with a lentiviral vector containing a diverse genetic barcode library, uniquely labelling individual HSPCs and their progeny. With up to 131 months of follow-up, we now report quantitative clonal dynamics, characterizing the number, diversity, stability and lineage bias of hundreds of thousands of HSPC clones tracked in five RMs. We documented long-term stable and multi-lineage output from a highly polyclonal pool of HSPCs. Clonal succession after stable haematopoietic reconstitution was minimal. There was no evidence for accelerated acquisition of acquired somatic mutations following autologous lentivirally transduced HSPC transplantation. Our results provide relevant insights into long-term HSPC behaviours in vivo following transplantation and gene therapies.}, }
@article {pmid39521085, year = {2024}, author = {Bálint, M and Tumusiime, J and Nakintu, J and Baranski, D and Schardt, L and Romahn, J and Dusabe, MC and Tolo, CU and Kagoro, GR and Ssenkuba, F and Junginger, A and Albrecht, C}, title = {Environmental DNA barcoding reveals general biodiversity patterns in the large tropical rift Lake Albert.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177308}, doi = {10.1016/j.scitotenv.2024.177308}, pmid = {39521085}, issn = {1879-1026}, mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic ; *Lakes ; *Environmental Monitoring/methods ; DNA, Environmental/analysis/genetics ; Animals ; }, abstract = {Lake Albert, Africa's seventh-largest lake and a biodiversity hotspot, faces significant environmental challenges, including unregulated anthropogenic pressure and a lack of comprehensive biological studies. To address the scarcity of biodiversity data, we utilized environmental DNA (eDNA) metabarcoding to assess the lake's eukaryotic and metazoan communities. Surface water samples were collected at three distinct locations: close to the southern inflow of the Semliki River, the central part of the lake, and close to the northern inflow of the Victoria Nile and outflow of the Albert Nile. We aimed to study ecological patterns across the lake, focusing on sequence variant richness and community composition, testing for differences among locations and between shoreline and pelagic zones. Consistent with previous morphology-based observations, our results revealed differences in community composition among the three sites, with cyclopoid copepods dominating the communities. Distance from shore was a significant factor influencing community composition, confirming expectations about the effects of nutrient and oxygen availability gradients. However, the lack of comprehensive reference sequence data limited accurate taxonomic assignments. Despite these limitations, our study demonstrates that eDNA metabarcoding is highly useful for assessing biodiversity in underexplored tropical freshwater ecosystems. We advocate for urgent efforts to generate reference sequences from tropical regions to enhance the utility of eDNA for biodiversity monitoring and conservation. Our findings underscore the potential of eDNA in providing insights into ecological patterns of entire communities and emphasize the need for comprehensive studies addressing the full taxonomic spectrum in tropical freshwater ecosystems.}, }
@article {pmid39519959, year = {2024}, author = {Pun, TB and Thapa Magar, R and Koech, R and Owen, KJ and Adorada, DL}, title = {Emerging Trends and Technologies Used for the Identification, Detection, and Characterisation of Plant-Parasitic Nematode Infestation in Crops.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {21}, pages = {}, pmid = {39519959}, issn = {2223-7747}, abstract = {Accurate identification and estimation of the population densities of microscopic, soil-dwelling plant-parasitic nematodes (PPNs) are essential, as PPNs cause significant economic losses in agricultural production systems worldwide. This study presents a comprehensive review of emerging techniques used for the identification of PPNs, including morphological identification, molecular diagnostics such as polymerase chain reaction (PCR), high-throughput sequencing, meta barcoding, remote sensing, hyperspectral analysis, and image processing. Classical morphological methods require a microscope and nematode taxonomist to identify species, which is laborious and time-consuming. Alternatively, quantitative polymerase chain reaction (qPCR) has emerged as a reliable and efficient approach for PPN identification and quantification; however, the cost associated with the reagents, instrumentation, and careful optimisation of reaction conditions can be prohibitive. High-throughput sequencing and meta-barcoding are used to study the biodiversity of all tropical groups of nematodes, not just PPNs, and are useful for describing changes in soil ecology. Convolutional neural network (CNN) methods are necessary to automate the detection and counting of PPNs from microscopic images, including complex cases like tangled nematodes. Remote sensing and hyperspectral methods offer non-invasive approaches to estimate nematode infestations and facilitate early diagnosis of plant stress caused by nematodes and rapid management of PPNs. This review provides a valuable resource for researchers, practitioners, and policymakers involved in nematology and plant protection. It highlights the importance of fast, efficient, and robust identification protocols and decision-support tools in mitigating the impact of PPNs on global agriculture and food security.}, }
@article {pmid39519254, year = {2024}, author = {Tshiabuila, D and Choga, W and San, JE and Maponga, T and Van Zyl, G and Giandhari, J and Pillay, S and Preiser, W and Naidoo, Y and Baxter, C and Martin, DP and de Oliveira, T}, title = {An Oxford Nanopore Technology-Based Hepatitis B Virus Sequencing Protocol Suitable for Genomic Surveillance Within Clinical Diagnostic Settings.}, journal = {International journal of molecular sciences}, volume = {25}, number = {21}, pages = {}, pmid = {39519254}, issn = {1422-0067}, support = {U01 AI151698/AI/NIAID NIH HHS/United States ; }, mesh = {*Hepatitis B virus/genetics ; Humans ; *Genome, Viral ; *Genotype ; Nanopore Sequencing/methods ; Hepatitis B, Chronic/virology/diagnosis/epidemiology ; Phylogeny ; High-Throughput Nucleotide Sequencing/methods ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Genomics/methods ; Nanopores ; Drug Resistance, Viral/genetics ; Hepatitis B/diagnosis/virology/epidemiology ; Genetic Variation ; }, abstract = {Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A-J). Tests to determine HBV genotypes are based on full-genome sequencing or reverse hybridization. In practice, both approaches have limitations. Whereas diagnostic sequencing, generally using the Sanger approach, tends to focus only on the S-gene and yields little or no information on intra-patient HBV genetic diversity, reverse hybridization detects only known genotype-specific mutations. To resolve these limitations, we developed an Oxford Nanopore Technology (ONT)-based HBV diagnostic sequencing protocol suitable for clinical virology that yields both complete genome sequences and extensive intra-patient HBV diversity data. Specifically, the protocol involves tiling-based PCR amplification of HBV sequences, library preparation using the ONT Rapid Barcoding Kit (Oxford nanopore Technologies, Oxford, OX4 4DQ, UK), ONT GridION sequencing, genotyping using genome detective software v1.132/1.133, a recombination analysis using jpHMM (26 October 2011 version) and RDP5.61 software, and drug resistance profiling using Geno2pheno v2.0 software. We prove the utility of our protocol by efficiently generating and characterizing high-quality near full-length HBV genomes from 148 residual diagnostic samples from HBV-infected patients in the Western Cape province of South Africa, providing valuable insights into the genetic diversity and epidemiology of HBV in this region of the world.}, }
@article {pmid39516507, year = {2024}, author = {Rodrigues, BL and de Oliveira, AG and da Silva, LEH and Vasconcelos Dos Santos, T and de Oliveira, LNC and Rêgo, FD and de Andrade, AJ and Maia, GB and de Souza Pinto, I and Andrade Filho, JD and Galati, EAB}, title = {Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27215}, pmid = {39516507}, issn = {2045-2322}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 314260/2023-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2023/03715-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; *Phylogeny ; *Psychodidae/genetics/classification/anatomy &amp; histology ; *Electron Transport Complex IV/genetics ; *Haplotypes ; Brazil ; *Genetic Variation ; }, abstract = {The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.}, }
@article {pmid39514381, year = {2024}, author = {Barone, ML and Wilson, JD and Zapata, L and Soto, EM and Haddad, CR and Grismado, C and Izquierdo, M and Arias, E and Pizarro-Araya, J and Briones, R and Barriga, JE and Peralta, L and Ramírez, MJ}, title = {Genetic barcodes for species identification and phylogenetic estimation in ghost spiders (Araneae: Anyphaenidae: Amaurobioidinae).}, journal = {Invertebrate systematics}, volume = {38}, number = {}, pages = {}, doi = {10.1071/IS24053}, pmid = {39514381}, issn = {1447-2600}, mesh = {*Spiders/genetics/classification ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Electron Transport Complex IV/genetics ; Species Specificity ; Algorithms ; }, abstract = {The identification of spider species presents many challenges, since in most cases the characters used are from genital structures that are only fully developed in the adult stage, hence the identification of immatures is most often not possible. Additionally, these structures usually also present some intra-specific variability, which in some cases makes the identification of closely related species difficult. The genetic barcode technique (DNA barcodes), based on sequencing of the mitochondrial marker cytochrome c oxidase subunit I (COI), has proven a useful, complementary tool to overcome these limitations. In this work, the contribution of DNA barcoding to the taxonomy of the subfamily Amaurobioidinae is explored using the refined single linkage analysis (RESL) algorithm for the delimitation of operational taxonomic units (OTUs), in comparison with the assemble species by automatic partitioning (ASAP) algorithm, and presented in conjunction with an updated molecular phylogenetic analysis of three other markers (28S rRNA, 16S rRNA, Histone H3), in addition to COI . Of a total of 97 included species identified by morphology, 82 species were concordant with the operational taxonomic units obtained from RESL, representing an 85% correspondence between the two methods. Similar results were obtained using the ASAP algorithm. Previous observations of morphological variation within the same species are supported, and this technique provides new information on genetic structure and potentially cryptic species. Most of the discrepancies between DNA barcoding and morphological identification are explained by low geographic sampling or by divergent or geographically structured lineages. After the addition of many specimens with only COI data, the multi-marker phylogenetic analysis is consistent with previous results and the support is improved. The markers COI , closely followed by 28S , are the most phylogenetically informative. We conclude that the barcode DNA technique is a valuable source of data for the delimitation of species of Amaurobioidinae, in conjunction with morphological and geographic data, and it is also useful for the detection of cases that require a more detailed and meticulous study.}, }
@article {pmid39512489, year = {2024}, author = {Rodrigues, IVB and de Souza, PGC and Nunes, RC and Nunes Godeiro, N and Bellini, BC}, title = {A century later: a new species of Mastigoceras Handschin, 1924 (Collembola, Orchesellidae), with morphological and systematic updates on the genus.}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {79-100}, pmid = {39512489}, issn = {1313-2989}, abstract = {Mastigocerascamponoti Handschin, the sole member of its genus and the Mastigocerini tribe, exhibits unusual dorsal chaetotaxy compared to other Orchesellidae. This includes a reduction in dorsal macrochaetotaxy and a secondary covering of fusiform scales intermixed with ciliate microchaetae. Despite three redescriptions, Mastigoceras chaetotaxy remains poorly understood, with no data on tergal sensilla patterns or dorsal macrochaetae homology. Here, the genus is revisited by describing a new Brazilian species a century after the original description of M.camponoti, based on morphological depiction combined with the use of DNA barcoding, Mastigocerashandschini Rodrigues, Souza &amp; Bellini, sp. nov. The two species are differentiated by a few and unusual aspects of the dorsal chaetotaxy, especially scales distribution, and may be considered as pseudocryptic taxa. Our study of tergal sensilla formula, scales morphology, and distribution in Mastigoceras reveals no clear morphological support for placing Mastigocerini within Heteromurinae.}, }
@article {pmid39512488, year = {2024}, author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL}, title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {1-45}, pmid = {39512488}, issn = {1313-2989}, abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis &amp; Kojima, sp. nov., A.bifidus Kojima &amp; Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis &amp; Kojima, sp. nov., A.falcatus Kojima, Lewis &amp; Fujisawa, sp. nov., A.incurvatus Kojima &amp; Lewis, sp. nov., A.japonicus Lewis &amp; Kojima, sp. nov., A.magnus Lewis &amp; Kojima, sp. nov., A.morimotoi Kojima &amp; Lewis, sp. nov., A.nudus Lewis &amp; Kojima, sp. nov., A.spinosus Lewis &amp; Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa &amp; Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto &amp; Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto &amp; Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.}, }
@article {pmid39502327, year = {2024}, author = {Mao, H and Wang, Z and Shan, Y and Cheng, X and Yu, J}, title = {The complete genome sequence of the chloroplast of Bidens aurea.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {9}, number = {11}, pages = {1487-1491}, pmid = {39502327}, issn = {2380-2359}, abstract = {Bidens aurea (Asteraceae), a native of tropical America is now widespread in Asia and the Americas. We explored the B. aurea chloroplast genome and conducted a phylogenetic analysis. The chloroplast genome was circular, consisting of a large single copy (LSC) of 83,909 base pairs (bp), a small single copy (SSC) of 18,407 bp, and two inverted repeat regions (IR) of 24,729 bp each. Phylogenetic analysis showed that the 19 Bidens taxa were divided into five major clades, and B. aurea was most closely related to two species. Our findings offer a high-quality B. aurea chloroplast genome, aiding DNA barcode development and evolutionary history reconstruction.}, }
@article {pmid39501899, year = {2024}, author = {Zhang, T and Dong, B and Wang, H and Zhang, S}, title = {An innovative electrohydrodynamics-driven SERS platform for molecular stratification and treatment monitoring of lung cancer.}, journal = {Journal of materials chemistry. B}, volume = {12}, number = {47}, pages = {12139-12140}, doi = {10.1039/d4tb01434k}, pmid = {39501899}, issn = {2050-7518}, mesh = {Humans ; Extracellular Vesicles/chemistry ; *Gold/chemistry ; *Lung Neoplasms/diagnosis ; Microelectrodes ; *Spectrum Analysis, Raman ; Surface Properties ; }, abstract = {The advancement of molecular diagnostics for lung cancer stratification and monitoring is essential for the strategic planning and prompt modification of treatments, aiming to enhance clinical results. To address this need, we suggest a nanocavity structure designed to sensitively analyze the protein signature on small extracellular vesicles (sEVs). This approach facilitates precise, noninvasive staging and treatment monitoring of lung cancer. The nanocavity is created through molecular recognition, involving the interaction of sEVs with nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and asymmetric, mirrorlike gold microelectrodes. By applying an alternating current to the gold microelectrodes, a nanofluidic shear force was generated, promoting the binding of sEVs and the effective assembly of the nanoboxes. This interaction induced a nanocavity between the nanobox and the gold microelectrode, which significantly amplified the electromagnetic field. This amplification enhanced Raman signals from four SERS barcodes simultaneously, allowing the generation of patient-specific molecular sEV signatures. When tested on a cohort of clinical samples (n = 76) using the nanocavity architecture, these patient-specific sEV molecular signatures accurately identified, stratified, and monitored lung cancer patients' treatment, demonstrating its potential for clinical application.}, }
@article {pmid39497575, year = {2024}, author = {Velázquez-Urrieta, Y and García-Varela, M and Pérez-Ponce de León, G}, title = {Assessing the diversity of freshwater fish trematodes from Laguna Escondida, Los Tuxtlas tropical rainforest, Mexico, using morphology and 28S rDNA sequences as barcodes.}, journal = {Journal of helminthology}, volume = {98}, number = {}, pages = {e67}, doi = {10.1017/S0022149X2400049X}, pmid = {39497575}, issn = {1475-2697}, mesh = {Animals ; *Trematoda/genetics/classification/isolation &amp; purification/anatomy &amp; histology ; Mexico ; *Fishes/parasitology ; *RNA, Ribosomal, 28S/genetics ; *Phylogeny ; *DNA Barcoding, Taxonomic ; *Fresh Water/parasitology ; *DNA, Ribosomal/genetics ; *Rainforest ; Fish Diseases/parasitology ; Biodiversity ; Trematode Infections/parasitology/veterinary ; DNA, Helminth/genetics ; Lakes/parasitology ; }, abstract = {Despite a great effort made for almost 90 years, the diversity of freshwater fish trematodes in Mexico is still far from being fully known. The addition of molecular data to the description of trematode diversity in the last two decades added the potential to establish more robust species limits and a more accurate biodiversity estimation, but also led in some instances to the recognition of cryptic species complexes. Here, we used sequences of the large subunit of the nuclear ribosomal gene (28S rRNA) as barcodes, and morphological data, to assess the diversity of freshwater fish trematodes from a lake within a tropical rainforest. Eighty freshwater fish specimens of eight species were studied, and 120 trematode specimens were collected. Morphologically, specimens were allocated into nine genera; molecular phylogenetic analyses along with sequence divergence data provided evidence for recognising 11 trematode taxa, six adults and five metacercariae; six of them were identified to species level. Geographical distribution and host association patterns are briefly discussed for each trematode taxa.}, }
@article {pmid39497202, year = {2024}, author = {Benallal, KE and Mefissel, M and Dib, Y and Depaquit, J and Kavan, D and Harrat, Z and Dvořák, V and Volf, P and Halada, P}, title = {Phlebotomine sand fly survey, blood meal source identification, and description of Sergentomyia imihra n. sp. in the central Sahara of Algeria.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {449}, pmid = {39497202}, issn = {1756-3305}, mesh = {Animals ; Algeria ; *Psychodidae/classification/physiology/anatomy &amp; histology ; Female ; Humans ; *Insect Vectors/classification/physiology/parasitology/anatomy &amp; histology ; *Feeding Behavior ; Phlebotomus/classification/anatomy &amp; histology/physiology/genetics ; Male ; Leishmaniasis/transmission ; Leishmania/genetics/physiology/classification ; Goats/parasitology ; }, abstract = {BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are important vectors of various pathogens, mainly Leishmania parasites. In the Old World, the most important genus in term of pathogens transmission is the genus Phlebotomus, which includes many proven or suspected vectors of several Leishmania species, while the genus Sergentomyia remains so far unproven as a vector of human pathogens. Algeria is one of the most affected countries by human leishmaniasis.<br><br>METHODS: In the present study, an entomological survey was carried out in two provinces, Gharda&#xef;a and Illizi, located in the north and central Sahara, respectively, where cases of human leishmaniasis are recorded. Our goal was to understand the role of the local sand fly species in the transmission of Leishmania parasites and to analyze their blood meal preferences. Collected sand flies were identified by a combination of morphological and molecular approaches that included DNA-barcoding and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) protein profiling. In addition, female blood meals were analyzed by peptide mass mapping using MALDI-TOF MS.<br><br>RESULTS: In total, 640 sand fly specimens belonging to Phlebotomus and Sergentomyia genera were collected in the two provinces. Sergentomyia antennata and Se.&#xa0;fallax were most abundant species in Gharda&#xef;a, and Ph.&#xa0;papatasi and Ph.&#xa0;alexandri in Illizi. In addition, a new sand fly species was described in Illizi named Sergentomyia (Sergentomyia) imihra n. sp. Blood meal analysis of the engorged females revealed various mammalian hosts, especially goats, but also humans for Phlebotomus papatasi and Ph.&#xa0;alexandri, suggesting that these vector species are opportunistic feeders.<br><br>CONCLUSIONS: Integrative approach that combined morphological analysis, sequencing of DNA markers, and protein profiling enabled the recognition and description of a new Sergentomyia species, raising the number of the Algerian sand fly fauna to 27 species. Further sand fly surveillance in the central Sahara is recommended to identify the thus-far unknown males of Se.&#xa0;imihra n. sp.}, }
@article {pmid39497190, year = {2024}, author = {Qi, J and Li, Z and Zhang, YZ and Li, G and Gao, X and Han, R}, title = {TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {285}, pmid = {39497190}, issn = {1474-760X}, mesh = {*Nanopore Sequencing/methods ; *Software ; DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Nanopores ; }, abstract = {Oxford Nanopore Technologies (ONT) offers ultrahigh-throughput multi-sample sequencing but only provides barcode kits that enable up to 96-sample multiplexing. We present TDFPS-Designer, a new toolkit for nanopore sequencing barcode design, which creates significantly more barcodes: 137 with a length of 20 base pairs, 410 at 24 bp, and 1779 at 30 bp, far surpassing ONT's offerings. It includes GPU-based acceleration for ultra-fast demultiplexing and designs robust barcodes suitable for high-error ONT data. TDFPS-Designer outperforms current methods, improving the demultiplexing recall rate by 20% relative to Guppy, without a reduction in precision.}, }
@article {pmid39497089, year = {2024}, author = {Zhang, J and Zhou, D and Chen, W and Lin, P and Zhao, S and Wang, M and Wang, H and Shi, S and Mehmood, F and Ye, X and Meng, J and Zhuang, W}, title = {Comparison of the chloroplast genomics of nine endangered Habenaria species and phylogenetic analysis.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1046}, pmid = {39497089}, issn = {1471-2229}, mesh = {*Phylogeny ; *Genome, Chloroplast ; *Endangered Species ; *Orchidaceae/genetics/classification ; Genomics ; Microsatellite Repeats/genetics ; Chloroplasts/genetics ; }, abstract = {BACKGROUND: Habenaria, a genus in the family Orchidaceae, are the nearly cosmopolitan orchids, and most species have significant medicinal and ornamental values. Despite the morphological and molecular data that have been studied in recent years, the phylogenetic relationship is still unclear.<br><br>RESULTS: We sequenced, assembled, and annotated the chloroplast (cp) genomes of two species (Habenaria aitchisonii Rchb.f. and Habenaria tibetica Schltr.ex Limpricht) of Habenaria grown on the Qinghai-Tibetan Plateau (QTP), and compared them with seven previously published cp genomes which may aid in the genomic profiling of these species. The two genomes ranged from 155,259-155,269&#xa0;bp in length and both included 132 genes, encoding 86 proteins, 38 tRNAs and 8 rRNAs. In the cp genomes, the tandem repeats (797), SSRs (2195) and diverse loci (3214) were identified. Comparative analyses of codon usage, amino frequency, microsatellite, oligo repeats and transition and transversion substitutions revealed similarities between the species. Moreover, we identified 16 highly polymorphic regions with a nucleotide diversity above 0.02, which may be suitable for robust authentic barcoding and inferring in the phylogeny of Habenaria species. Among the polymorphic regions, positive selection was significantly exerted on several genes, such as cemA, petA, and ycf1. This finding may suggest an important adaptation strategy for the two Habenaria species on the QTP. The phylogenetic relationship revealed that H. aitchisonii and H. tibetica were more closely related to each other than to the other species, and the other seven species were clustered in three groups. In addition, the estimated divergence time suggested that the two species separated from the others approximately 0.39 Mya in the Neogene period. Our findings also suggest that Habenaria can be divided into different sections.<br><br>CONCLUSIONS: The results of this study enriched the genomics resources of Habenaria, and SSR marker may aid in the conservation management of two endangered species.}, }
@article {pmid39494514, year = {2024}, author = {Pradhan, R and Chimene, D and Ko, BS and Goncharov, A and Ozcan, A and McShane, MJ}, title = {Insertable Biomaterial-Based Multianalyte Barcode Sensor toward Continuous Monitoring of Glucose and Oxygen.}, journal = {ACS sensors}, volume = {9}, number = {11}, pages = {6060-6070}, pmid = {39494514}, issn = {2379-3694}, mesh = {*Oxygen/chemistry ; *Biosensing Techniques/methods/instrumentation ; *Hydrogels/chemistry ; *Biocompatible Materials/chemistry ; Animals ; Glucose/analysis ; Polyethylene Glycols/chemistry ; Blood Glucose/analysis ; Humans ; }, abstract = {Chronic diseases, including diabetes, cardiovascular diseases, and microvascular complications, contribute significantly to global morbidity and mortality. Current monitoring tools such as glucometers and continuous glucose monitors only measure one analyte; multiplexing technologies offer a promising approach for monitoring multiple biomarkers, enabling the management of comorbidities and providing more comprehensive disease insights. In this work, we describe a miniaturized optical "barcode" sensor with high biocompatibility for the continuous monitoring of glucose and oxygen. This enzymatic sensor relies on oxygen consumption in proportion to local glucose levels and the phosphorescence reporting of tissue oxygen with a lifetime-based probe. The sensor was specifically designed to operate in a tissue environment with low levels of dissolved oxygen. The barcode sensor consists of a poly(ethylene glycol) diacrylate (PEGDA) hydrogel with four discrete compartments separately filled with glucose- or oxygen-sensing phosphorescent microparticles. We evaluated the response of the barcode hydrogels to fluctuating glucose levels over the physiological range under low oxygen conditions, demonstrating the controlled tuning of dynamic range and sensitivity. Moreover, the barcode sensor exhibited remarkable storage stability over 12 weeks, along with full reversibility and excellent reproducibility (∼6% variability in the phosphorescence lifetime) over nearly 50 devices. Electron beam sterilization had a negligible effect on the glucose response of the barcode sensors. Furthermore, our investigation revealed minimal phosphorescence lifetime changes in oxygen compartments while exhibiting increased lifetime in glucose-responsive compartments when subjected to alternating glucose concentrations (0 and 200 mg/dL), showcasing the sensor's multianalyte sensing capabilities without crosstalk between compartments. Additionally, the evaluation of chronic tissue response to sensors inserted in pigs revealed the appropriate biocompatibility of the barcodes as well as excellent material stability over many months. These findings support further development of similar technologies for introducing optical assays for multiple biomarkers that can provide continuous or on-demand feedback to individuals to manage chronic conditions.}, }
@article {pmid39494108, year = {2024}, author = {Yetchom Fondjo, JA and Nzoko Fiemapong, AR and Tindo, M and Duressa, TF and Ivković, S and Husemann, M}, title = {Taxonomic review of the grasshopper genus Pteropera Karsch, 1891 (Orthoptera, Acrididea, Catantopinae) with description of three new species and a preliminary phylogeny of the Cameroonian species.}, journal = {ZooKeys}, volume = {1216}, number = {}, pages = {219-264}, pmid = {39494108}, issn = {1313-2989}, abstract = {The Afrotropical grasshopper genus Pteropera Karsch, 1891, is reviewed. Some species present in Cameroon are described, Pteroperaaugustini Donskoff, 1981, is recorded for the first time in the country, and three new species are described from Cameroon, Pteroperakennei Yetchom &amp; Husemann, sp. nov., Pteroperamatzkei Yetchom &amp; Husemann, sp. nov. and Pteroperamissoupi Yetchom &amp; Husemann, sp. nov., increasing the number of Pteropera species in Cameroon from eight to 12, and overall to 30 species in Central Africa. An updated key of Pteropera is provided. Photographs with data on the distributions of all known species are given. In addition, a phylogenetic tree was constructed using maximum likelihood and Bayesian inference on the basis of a concatenated dataset of COI, 16S, and 12S markers of available Cameroonian species. The maximum likelihood and Bayesian inference analyses of the concatenated datasets resulted in a well-resolved phylogeny of the group and species of Pteropera were recovered as monophyletic, largely with high support. In all cases, the discrimination of all studied species based on barcode information was congruent with the species limits determined by traditional taxonomy. Our findings show the potential of integrative taxonomy to resolve the relationships among grasshoppers below the family level. Further analyses, including more comprehensive taxon sampling and additional nuclear markers, are needed, and the occurrence of several taxa still needs to be confirmed in African rainforests.}, }
@article {pmid39490742, year = {2025}, author = {Surwase, SS and Zhou, XMM and Luly, KM and Zhu, Q and Anders, RA and Green, JJ and Tzeng, SY and Sunshine, JC}, title = {Highly Multiplexed Immunofluorescence PhenoCycler Panel for Murine Formalin-Fixed Paraffin-Embedded Tissues Yields Insight Into Tumor Microenvironment Immunoengineering.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {105}, number = {1}, pages = {102165}, doi = {10.1016/j.labinv.2024.102165}, pmid = {39490742}, issn = {1530-0307}, support = {R37 CA246699/CA/NCI NIH HHS/United States ; P41 EB028239/EB/NIBIB NIH HHS/United States ; R01 CA228133/CA/NCI NIH HHS/United States ; P30 CA006973/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Tumor Microenvironment/immunology ; Mice ; Paraffin Embedding ; *Fluorescent Antibody Technique/methods ; Formaldehyde ; Mice, Inbred C57BL ; Tissue Fixation ; }, abstract = {Spatial proteomics profiling is an emerging set of technologies that has the potential to elucidate the cell types, interactions, and molecular signatures that make up complex tissue microenvironments, with applications in the study of cancer, immunity, and much more. An emerging technique in the field is CoDetection by indEXing, recently renamed as the PhenoCycler system. This is a highly multiplexed immunofluorescence imaging technology that relies on oligonucleotide-barcoded antibodies and cyclic immunofluorescence to visualize many antibody markers in a single specimen while preserving tissue architecture. Existing PhenoCycler panels are primarily designed for fresh frozen tissues. Formalin-fixed paraffin-embedded blocks offer several advantages in preclinical research, but few antibody clones have been identified in this setting for PhenoCycler imaging. Here, we present a novel PhenoCycler panel of 28 validated antibodies for murine formalin-fixed paraffin-embedded tissues. We describe our workflow for selecting and validating clones, barcoding antibodies, designing our panel, and performing multiplex imaging. We further detail our analysis pipeline for comparing marker expressions, clustering and phenotyping single-cell proteomics data, and quantifying spatial relationships. We then apply our panel and analysis protocol to profile the effects of 3 gene delivery nanoparticle formulations, in combination with systemic anti-PD1, on the murine melanoma tumor immune microenvironment. Intralesional delivery of genes expressing the costimulatory molecule 4-1BBL and the cytokine IL-12 led to a shift toward intratumoral M1 macrophage polarization and promoted closer associations between intratumoral CD8 T cells and macrophages. Delivery of interferon gamma, in addition to 4-1BBL and IL-12, not only further increased markers of antigen presentation on tumor cells and intratumoral antigen-presenting cells but also promoted greater expression of checkpoint marker PD-L1 and closer associations between intratumoral CD8 T cells and PD-L1-expressing tumor cells. These findings help explain the benefits of 4-1BBL and IL-12 delivery while offering additional mechanistic insights into the limitations of interferon gamma therapeutic efficacy.}, }
@article {pmid39484616, year = {2025}, author = {Lu, X and Pritko, DJ and Abravanel, ME and Huggins, JR and Ogunleye, O and Biswas, T and Ashy, KC and Woods, SK and Livingston, MWT and Blenner, MA and Birtwistle, MR}, title = {Genetically-Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39484616}, issn = {2692-8205}, support = {R35 GM141891/GM/NIGMS NIH HHS/United States ; }, abstract = {Genetically-encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), non-destructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are non-destructive, fast, and inexpensive to readout but lack high diversity. We recently proposed theory for how fluorescent protein combinations may generate a high-diversity barcode library with non-destructive, fast and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ~150 barcodes from two-way combinations of 18 fluorescent proteins, 61 of which are tested experimentally. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ~10[5] and more) generated from hundreds of spectrally-resolvable tandem fluorescent protein probes.}, }
@article {pmid39483244, year = {2024}, author = {Dockerill, M and Sabale, PM and Russo, F and Barluenga, S and Winssinger, N}, title = {Translation of Deoxyribonucleic Acid into Synthetic Alpha Helical Peptides for Darwinian Evolution.}, journal = {JACS Au}, volume = {4}, number = {10}, pages = {4013-4022}, pmid = {39483244}, issn = {2691-3704}, abstract = {DNA-encoded libraries connect the phenotypes of synthetic molecules to a DNA barcode; however, most libraries do not tap into the potential of Darwinian evolution. Herein, we report a DNA-templated synthesis (DTS) architecture to make peptides that are stabilized into α-helical conformations via head-to-tail supramolecular cyclization. Using a pilot library targeting MDM2, we show that repeated screening can amplify a binder from the lowest abundance in the library to a ranking that correlates to binding affinity. The study also highlights the need to design libraries such that the chemistry avoids biases from the heterogeneous yield in DTS.}, }
@article {pmid39480818, year = {2024}, author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z}, title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0309707}, pmid = {39480818}, issn = {1932-6203}, mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; }, abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.}, }
@article {pmid39485438, year = {2024}, author = {Pham, NV and Nguyen, QN and Nguyen, TV and Nguyen, TA and Ta, VD}, title = {High quality factor, monodisperse micron-sized random lasers based on porous PLGA spheres.}, journal = {Optics letters}, volume = {49}, number = {21}, pages = {6165-6168}, doi = {10.1364/OL.538543}, pmid = {39485438}, issn = {1539-4794}, abstract = {Miniature random lasers with high quality factor are crucial for applications in barcoding, bioimaging, and on-chip technologies. However, achieving monodisperse and size-tunable biocompatible random lasers has been a significant challenge. In this study, we employed poly(lactic-co-glycolic) acid (PLGA), a biocompatible material approved for medical use, as the base material for random lasers. By integrating a dye-doped PLGA solution with a microfluidic system, we successfully fabricated monodisperse and miniature dye-doped PLGA spheres with tunable sizes ranging from 25 to 52 µm. Upon optical pulse excitation, these spheres exhibited strong random lasing emission at 610-640 nm with a threshold of approximately 22 µJ·mm[-2]. The lasing modes demonstrated a spectral linewidth of 0.2 nm, corresponding to a quality factor of 3100. Fourier transform analysis of the lasing emission revealed fundamental cavity lengths, providing insights into the properties of the random lasers.}, }
@article {pmid39482470, year = {2025}, author = {Dini, A and Barker, H and Piki, E and Sharma, S and Raivola, J and Murumägi, A and Ungureanu, D}, title = {A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery.}, journal = {Nature chemical biology}, volume = {21}, number = {3}, pages = {432-442}, pmid = {39482470}, issn = {1552-4469}, support = {336449//Academy of Finland (Suomen Akatemia)/ ; 333583//Academy of Finland (Suomen Akatemia)/ ; 288475//Academy of Finland (Suomen Akatemia)/ ; 271845//Academy of Finland (Suomen Akatemia)/ ; 349787//Academy of Finland (Suomen Akatemia)/ ; }, mesh = {Humans ; *Single-Cell Analysis/methods ; *Drug Discovery/methods ; *Ovarian Neoplasms/drug therapy/genetics/metabolism/pathology ; Female ; *RNA-Seq/methods ; *Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; TOR Serine-Threonine Kinases/metabolism/antagonists &amp; inhibitors ; Proto-Oncogene Proteins c-akt/metabolism/antagonists &amp; inhibitors ; Phosphatidylinositol 3-Kinases/metabolism ; ErbB Receptors/metabolism ; Single-Cell Gene Expression Analysis ; }, abstract = {The gene-regulatory dynamics governing drug responses in cancer are yet to be fully understood. Here, we report a pipeline capable of producing high-throughput pharmacotranscriptomic profiling through live-cell barcoding using antibody-oligonucleotide conjugates. This pipeline combines drug screening with 96-plex single-cell RNA sequencing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of phosphatidylinositol 3-OH kinase (PI3K), protein kinase B (AKT) and mammalian target of rapamycin (mTOR) inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this was mediated by the upregulation of caveolin 1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of agents targeting PI3K-AKT-mTOR and EGFR for HGSOC with CAV1 and EGFR expression. Using this workflow could enable the personalized testing of patient-derived tumor samples at single-cell resolution.}, }
@article {pmid39480094, year = {2024}, author = {Alexander, LM and Khalid, S and Gallego-Lopez, GM and Astmann, TJ and Oh, J-H and Heggen, M and Huss, P and Fisher, R and Mukherjee, A and Raman, S and Choi, IY and Smith, MN and Rogers, CJ and Epperly, MW and Knoll, LJ and Greenberger, JS and van Pijkeren, J-P}, title = {Development of a Limosilactobacillus reuteri therapeutic delivery platform with reduced colonization potential.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {11}, pages = {e0031224}, pmid = {39480094}, issn = {1098-5336}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; 75N93021C00008/AI/NIAID NIH HHS/United States ; R01 GM135483/GM/NIGMS NIH HHS/United States ; 2021-67015-34316//U.S. Department of Agriculture (USDA)/ ; R01GM135483//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; U01 AI172885/AI/NIAID NIH HHS/United States ; //Louis and Elsa Thomsen Wisconsin Distinguished Graduate Fellowship from the UW-Madison College of Agricultural &amp; Life Sciences/ ; //Dissertation Completion Fellowship from the UW-Madison Graduate School/ ; U01-AI172885//HHS | National Institutes of Health (NIH)/ ; R41 AI157357/AI/NIAID NIH HHS/United States ; //SciMed Graduate Research Scholars Program at UW-Madison/ ; R21 AI146634/AI/NIAID NIH HHS/United States ; 1R41AI157357-01//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; MSN1856150//UW-Madison Food Research Institute/ ; }, mesh = {*Limosilactobacillus reuteri/genetics/physiology ; Animals ; Mice ; Humans ; Bacterial Adhesion ; HT29 Cells ; Adhesins, Bacterial/genetics ; Drug Delivery Systems ; Female ; }, abstract = {Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics in situ via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered Limosilactobacillus reuteri strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in L. reuteri adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the L. reuteri delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant L. reuteri in humans.}, }
@article {pmid39478489, year = {2024}, author = {Jiang, LQ and Drew, BT and Arthan, W and Yu, GY and Wu, H and Zhao, Y and Peng, H and Xiang, CL}, title = {Comparative plastome analysis of Arundinelleae (Poaceae, Panicoideae), with implications for phylogenetic relationships and plastome evolution.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1016}, pmid = {39478489}, issn = {1471-2164}, support = {31110103911//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Poaceae/genetics/classification ; *Evolution, Molecular ; Genome, Plastid ; Base Composition ; }, abstract = {BACKGROUND: Arundinelleae is a small tribe within the Poaceae (grass family) possessing a widespread distribution that includes Asia, the Americas, and Africa. Several species of Arundinelleae are used as natural forage, feed, and raw materials for paper. The tribe is taxonomically cumbersome due to a paucity of clear diagnostic morphological characters. There has been scant genetic and genomic research conducted for this group, and as a result the phylogenetic relationships and species boundaries within Arundinelleae are poorly understood.<br><br>RESULTS: We compared and analyzed 11 plastomes of Arundinelleae, of which seven plastomes were newly sequenced. The plastomes range from 139,629 base pairs (bp) (Garnotia tenella) to 140,943&#xa0;bp (Arundinella barbinodis), with a standard four-part structure. The average GC content was 38.39%, but varied in different regions of the plastome. In all, 110 genes were annotated, comprising 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Furthermore, 539 simple sequence repeats, 519 long repeats, and 10 hyper-variable regions were identified from the 11 plastomes of Arundinelleae. A phylogenetic reconstruction of Panicoideae based on 98 plastomes demonstrated the monophyly of Arundinella and Garnotia, but the circumscription of Arundinelleae remains unresolved.<br><br>CONCLUSION: Complete chloroplast genome sequences can improve phylogenetic resolution relative to single marker approaches, particularly within taxonomically challenging groups. All phylogenetic analyses strongly support the monophyly of Arundinella and Garnotia, respectively, but the monophylly of Arundinelleae was not well supported. The intergeneric phylogenetic relationships within Arundinelleae require clarification, indicating that more data is necessary to resolve generic boundaries and evaluate the monophyly of Arundinelleae. A comprehensive taxonomic revision for the tribe is necessary. In addition, the identified hyper-variable regions could function as molecular markers for clarifying phylogenetic relationships and potentially as barcoding markers for species identification in the future.}, }
@article {pmid39478225, year = {2024}, author = {Lu, Z and Mo, S and Xie, D and Zhai, X and Deng, S and Zhou, K and Wang, K and Kang, X and Zhang, H and Tong, J and Hou, L and Hu, H and Li, X and Zhou, D and Lee, LTO and Liu, L and Zhu, Y and Yu, J and Lan, P and Wang, J and He, Z and He, X and Hu, Z}, title = {Polyclonal-to-monoclonal transition in colorectal precancerous evolution.}, journal = {Nature}, volume = {636}, number = {8041}, pages = {233-240}, pmid = {39478225}, issn = {1476-4687}, mesh = {Animals ; Humans ; Male ; Mice ; Carcinogenesis/genetics/pathology ; *Cell Lineage ; Cell Transformation, Neoplastic/genetics/pathology ; *Clonal Evolution ; *Clone Cells/metabolism ; Colonic Polyps/pathology/genetics ; *Colorectal Neoplasms/genetics/pathology ; Disease Models, Animal ; DNA Barcoding, Taxonomic ; Exome Sequencing ; Genes, APC ; Inflammation/pathology/genetics ; *Precancerous Conditions/genetics/pathology ; *Single-Cell Analysis ; Single-Cell Gene Expression Analysis ; Whole Genome Sequencing ; Intestines/cytology/pathology ; }, abstract = {Unravelling the origin and evolution of precancerous lesions is crucial for effectively preventing malignant transformation, yet our current knowledge remains limited[1-3]. Here we used a base editor-enabled DNA barcoding system[4] to comprehensively map single-cell phylogenies in mouse models of intestinal tumorigenesis induced by inflammation or loss of the Apc gene. Through quantitative analysis of high-resolution phylogenies including 260,922 single cells from normal, inflamed and neoplastic intestinal tissues, we identified tens of independent cell lineages undergoing parallel clonal expansions within each lesion. We also found polyclonal origins of human sporadic colorectal polyps through bulk whole-exome sequencing and single-gland whole-genome sequencing. Genomic and clinical data support a model of polyclonal-to-monoclonal transition, with monoclonal lesions representing a more advanced stage. Single-cell RNA sequencing revealed extensive intercellular interactions in early polyclonal lesions, but there was significant loss of interactions during monoclonal transition. Therefore, our data suggest that colorectal precancer is often founded by many different lineages and highlight their cooperative interactions in the earliest stages of cancer formation. These findings provide insights into opportunities for earlier intervention in colorectal cancer.}, }
@article {pmid39472907, year = {2024}, author = {Nguyen, TT and Nugraheni, YR and Nguyen, HLA and Arnuphapprasert, A and Pengsakul, T and Thong, LQ and Ampol, R and Siriyasatien, P and Kaewthamasorn, M}, title = {Survey of sand fly fauna in six provinces of Southern Vietnam with species identification using DNA barcoding.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {443}, pmid = {39472907}, issn = {1756-3305}, mesh = {Animals ; Vietnam/epidemiology ; *DNA Barcoding, Taxonomic ; *Psychodidae/classification/genetics ; *Phylogeny ; *Biodiversity ; Electron Transport Complex IV/genetics ; Cytochromes b/genetics ; Insect Vectors/classification/genetics ; Female ; Haplotypes ; Genetic Variation ; }, abstract = {BACKGROUND: Sand flies, belonging to the Psychodidae family, represent small, hairy insects that serve as significant vectors in various important medical and veterinary diseases. Despite being recognized by the World Health Organization as an endemic area for leishmaniasis, Southeast Asia lacks comprehensive information on the species composition and biology of sand flies. To address this, the current study aimed to survey sand fly biodiversity.<br><br>METHODS: Sand flies from six provinces in Southern Vietnam were collected using CDC light traps. Sand flies were subsequently identified morphologically and confirmed molecularly using mitochondrial cytochrome oxidase c subunit I (COI) and cytochrome b (cytb) sequences. BLASTN searches were conducted, and the species identity of sand flies was further confirmed through a Barcode of Life Database (BOLD) search utilizing COI sequences. Subsequently, nucleotide sequences were subjected to a panel of analyses including intraspecific variation, phylogenetic relationships and haplotype network. The average densities of collected sand flies (sand flies/trap/night) and species richness were also recorded.<br><br>RESULTS: A total of 753 sand flies were collected. After excluding damaged specimens, six sand fly species, namely Phlebotomus stantoni, Sergentomyia khawi, Se. silvatica, Se. barraudi, Se. bailyi and Grassomyia indica, were identified. All conspecific sand fly sequences, including Ph. stantoni, Se. barraudi, Gr. indica, Se. bailyi, Se. khawi and Se. silvatica, clustered with their reference sequences, corroborating the results of morphology-based identification, BLASTN analysis and BOLD search. For intraspecific variation of sand flies obtained from the current study, COI diversity indices were consistently higher than those of cytb.<br><br>CONCLUSIONS: This study provides the first updates on morphological and molecular characterization of sand flies in Southern Vietnam. This acquired knowledge on sand fly species composition is essential for controlling sand fly-borne diseases in this potentially endemic region.}, }
@article {pmid39470724, year = {2025}, author = {Jiang, J and Ye, X and Kong, Y and Guo, C and Zhang, M and Cao, F and Zhang, Y and Pei, W}, title = {scLTdb: a comprehensive single-cell lineage tracing database.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D1173-D1185}, pmid = {39470724}, issn = {1362-4962}, support = {2022YFA1105700//National Key R&amp;D Program of China/ ; 82270123//National Natural Science Foundation of China/ ; 2024SSYS0034 to W.P.//Key R&amp;D Program of Zhejiang Province/ ; //Westlake Education Foundation/ ; }, mesh = {*Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Animals ; Humans ; Software ; Mice ; Databases, Genetic ; Cell Differentiation/genetics ; }, abstract = {Single-cell lineage tracing (scLT) is a powerful technique that integrates cellular barcoding with single-cell sequencing technologies. This new approach enables the simultaneous measurement of cell fate and molecular profiles at single-cell resolution, uncovering the gene regulatory program of cell fate determination. However, a comprehensive scLT database is not yet available. Here, we present the single-cell lineage tracing database (scLTdb, https://scltdb.com) containing 109 datasets that are manually curated and analyzed through a standard pipeline. The scLTdb provides interactive analysis modules for visualizing and re-analyzing scLT datasets, especially the comprehensive cell fate analysis and lineage relationship analysis. Importantly, scLTdb also allows users to identify fate-related gene signatures. In conclusion, scLTdb provides an interactive interface of scLT data exploration and analysis, and will facilitate the understanding of cell fate decision and lineage commitment in development and diseases.}, }
@article {pmid39468463, year = {2024}, author = {Jiang, C and Liu, F and Qin, J and Hubert, N and Kang, B and Huang, L and Yan, Y}, title = {DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure.}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {132}, pmid = {39468463}, issn = {2730-7182}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Larva/genetics/anatomy &amp; histology ; China ; Ovum ; Electron Transport Complex IV/genetics ; Gene Library ; }, abstract = {Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.}, }
@article {pmid39467896, year = {2024}, author = {Thakur, P and Khanal, S and Tapwal, A and Kumar, D and Verma, R and Chauhan, P and Sharma, N}, title = {Exploring Ganoderma lucidum: morphology, cultivation and market potential.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {11}, pages = {369}, pmid = {39467896}, issn = {1573-0972}, support = {CRG/2021/001815//DST, New Delhi/ ; CRG/2021/001815//DST, New Delhi/ ; CRG/2021/001815//DST, New Delhi/ ; }, mesh = {*Reishi/growth &amp; development/metabolism/genetics ; *Fermentation ; *Wood/microbiology ; *Phylogeny ; Biomass ; DNA Barcoding, Taxonomic ; }, abstract = {Ganoderma lucidum, known as the "mushroom of immortality," is a white rot fungus renowned for its medicinal properties, attributed to its bioactive compounds. Although species with similar morphological traits to G. lucidum are found across the globe, precise identification is made possible through DNA barcoding and molecular phylogenetic analysis. Global cultivation and wild harvesting of G. lucidum are both done in response to the growing market needs. Artificial cultivation is typically performed on sawdust, but other woody substrates and the wood log method are also employed. This cultivation leverages the fungus's ecological role in converting industrial and agricultural solid wastes into biomass, thereby producing functional food and potential pharmaceutical sources. The review consolidates research on various aspects of, including cultivation methods (sawdust, agricultural waste, wood logs, and submerged fermentation), and the current global market conditions.}, }
@article {pmid39467031, year = {2024}, author = {Fahlberg, MD and Forward, S and Assita, ER and Mazzola, M and Kiem, A and Handley, M and Yun, SH and Kwok, SJJ}, title = {Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {105}, number = {11}, pages = {838-848}, doi = {10.1002/cyto.a.24904}, pmid = {39467031}, issn = {1552-4930}, support = {R44-GM139504/NH/NIH HHS/United States ; R43-GM140527/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; F31HL158020-03/NH/NIH HHS/United States ; T32GM132089-01/NH/NIH HHS/United States ; 5T32GM007226-43/NH/NIH HHS/United States ; R44-GM139504/NH/NIH HHS/United States ; R43-GM140527/NH/NIH HHS/United States ; R01-EB033155/NH/NIH HHS/United States ; F31HL158020-03/NH/NIH HHS/United States ; T32GM132089-01/NH/NIH HHS/United States ; 5T32GM007226-43/NH/NIH HHS/United States ; }, mesh = {*Flow Cytometry/methods ; Humans ; *Fluorescent Dyes/chemistry ; Tissue Fixation/methods ; Biomarkers/metabolism ; Cell Line, Tumor ; }, abstract = {The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins (FPs), and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular FPs and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cellular analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.}, }
@article {pmid39466839, year = {2024}, author = {Dlauchy, D and Álvarez-Pérez, S and Tóbiás, A and Péter, G}, title = {Vishniacozyma floricola sp. nov., a flower-related tremellomycetous yeast species from Europe.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.006555}, pmid = {39466839}, issn = {1466-5034}, mesh = {*Phylogeny ; *DNA, Fungal/genetics ; *Flowers/microbiology ; *Sequence Analysis, DNA ; *DNA, Ribosomal Spacer/genetics ; *Basidiomycota/genetics/classification/isolation &amp; purification ; Hungary ; Spain ; Mycological Typing Techniques ; }, abstract = {During the course of two independent studies conducted in Hungary and Spain, four conspecific yeast strains were isolated from flowers of different plant species. DNA sequences of two barcoding regions, the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region (ITS1-5.8S rRNA gene-ITS2), revealed that the four strains represent an undescribed Vishniacozyma (family Bulleribasidiaceae, Basidiomycota) species. In terms of pairwise sequence similarities and according to our phylogenetic analyses of the concatenated DNA sequences of the ITS region and the D1/D2 domain of the LSU rRNA gene, the undescribed species is most closely related to Vishniacozyma melezitolytica, a yeast species of phylloplane origin. The novel species differs from the type strain of V. melezitolytica by 8 substitutions and 3 insertion/deletion (indels) and 11 substitutions and 5 indels along the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. In addition to the DNA sequence divergences, the two species differ in some physiological characters as well. We propose the species Vishniacozyma floricola sp. nov. to accommodate the above-noted strains (holotype, NCAIM Y.02320; isotype, CBS 18939; MycoBank number, 856028).}, }
@article {pmid39466790, year = {2024}, author = {Reyes Hueros, RA and Gier, RA and Shaffer, SM}, title = {Non-genetic differences underlie variability in proliferation among esophageal epithelial clones.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012360}, pmid = {39466790}, issn = {1553-7358}, support = {DP5 OD028144/OD/NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Cell Proliferation/genetics ; *Epithelial Cells/cytology ; *Esophagus/cytology ; Clone Cells/cytology ; Cell Line ; Single-Cell Analysis/methods ; Computational Biology ; }, abstract = {Individual cells grown in culture exhibit remarkable differences in their growth, with some cells capable of forming large clusters, while others are limited or fail to grow at all. While these differences have been observed across cell lines and human samples, the growth dynamics and associated cell states remain poorly understood. In this study, we performed clonal tracing through imaging and cellular barcoding of an in vitro model of esophageal epithelial cells (EPC2-hTERT). We found that about 10% of clones grow exponentially, while the remaining have cells that become non-proliferative leading to a halt in the growth rate. Using mathematical models, we demonstrate two distinct growth behaviors: exponential and logistic. Further, we discovered that the propensity to grow exponentially is largely heritable through four doublings and that the less proliferative clones can become highly proliferative through increasing plating density. Combining barcoding with single-cell RNA-sequencing (scRNA-seq), we identified the cellular states associated with the highly proliferative clones, which include genes in the WNT and PI3K pathways. Finally, we identified an enrichment of cells resembling the highly proliferative cell state in the proliferating healthy human esophageal epithelium.}, }
@article {pmid39465511, year = {2025}, author = {White, OW and Hall, A and Price, BW and Williams, ST and Clark, MD}, title = {A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14036}, pmid = {39465511}, issn = {1755-0998}, mesh = {*Phylogeny ; *Museums ; *Genome, Mitochondrial/genetics ; Animals ; Gastropoda/genetics/classification ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation/methods ; }, abstract = {Low coverage 'genome-skims' are often used to assemble organelle genomes and ribosomal gene sequences for cost-effective phylogenetic and barcoding studies. Natural history collections hold invaluable biological information, yet poor preservation resulting in degraded DNA often hinders polymerase chain reaction-based analyses. However, it is possible to generate libraries and sequence the short fragments typical of degraded DNA to generate genome-skims from museum collections. Here we introduce a snakemake toolkit comprised of three pipelines skim2mito, skim2rrna and gene2phylo, designed to unlock the genomic potential of historical museum specimens using genome skimming. Specifically, skim2mito and skim2rrna perform the batch assembly, annotation and phylogenetic analysis of mitochondrial genomes and nuclear ribosomal genes, respectively, from low-coverage genome skims. The third pipeline gene2phylo takes a set of gene alignments and performs phylogenetic analysis of individual genes, partitioned analysis of concatenated alignments and a phylogenetic analysis based on gene trees. We benchmark our pipelines with simulated data, followed by testing with a novel genome skimming dataset from both recent and historical solariellid gastropod samples. We show that the toolkit can recover mitochondrial and ribosomal genes from poorly preserved museum specimens of the gastropod family Solariellidae, and the phylogenetic analysis is consistent with our current understanding of taxonomic relationships. The generation of bioinformatic pipelines that facilitate processing large quantities of sequence data from the vast repository of specimens held in natural history museum collections will greatly aid species discovery and exploration of biodiversity over time, ultimately aiding conservation efforts in the face of a changing planet.}, }
@article {pmid39463700, year = {2024}, author = {Recuero, E and Etzler, FE and Caterino, MS}, title = {Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries.}, journal = {Current zoology}, volume = {70}, number = {5}, pages = {637-646}, pmid = {39463700}, issn = {1674-5507}, abstract = {We are far from knowing all species living on the planet. Understanding biodiversity is demanding and requires time and expertise. Most groups are understudied given problems of identifying and delimiting species. DNA barcoding emerged to overcome some of the difficulties in identifying species. Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups. Here, we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the southern Appalachian Mountains (USA). We used 3 reference databases and several automated classification methods on a data set including several arthropod groups. Acari, Araneae, Collembola, Coleoptera, Diptera, and Hymenoptera were well represented, showing different performances across methods and databases. Spiders performed the best, with correct identification rates to species and genus levels of ~50% across databases. Springtails performed poorly, no barcodes were identified to species or genus. Other groups showed poor to mediocre performance, from around 3% (mites) to 20% (beetles) correctly identified barcodes to species, but also with some false identifications. In general, BOLD-based identification offered the best identification results but, in all cases except spiders, performance is poor, with less than a fifth of specimens correctly identified to genus or species. Our results indicate that the soil arthropod fauna is still insufficiently documented, with many species unrepresented in DNA barcode libraries. More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNA barcoding as a universally applicable identification method.}, }
@article {pmid39460611, year = {2024}, author = {Burgos, HL and Mandel, MJ}, title = {Generation of Barcode-Tagged Vibrio fischeri Deletion Strains and Barcode Sequencing (BarSeq) for Multiplex Strain Competitions.}, journal = {Current protocols}, volume = {4}, number = {10}, pages = {e70024}, pmid = {39460611}, issn = {2691-1299}, support = {F32 GM140673/GM/NIGMS NIH HHS/United States ; R35 GM148385/GM/NIGMS NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {*Aliivibrio fischeri/genetics ; *DNA Barcoding, Taxonomic/methods ; Gene Deletion ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Gene Library ; }, abstract = {Vibrio fischeri is a model mutualist for studying molecular processes affecting microbial colonization of animal hosts. We present a detailed protocol for a barcode sequencing (BarSeq) approach that combines targeted gene deletion with short-read sequencing technology to enable studies of mixed bacterial populations. This protocol includes wet lab steps to plan and produce the deletions, approaches to scale up mutant generation, protocols to prepare and conduct the strain competition, library preparation for sequencing on an Illumina iSeq 100 instrument, and data analysis with the barseq python package. Aspects of this protocol could be readily adapted for tagging wild-type V. fischeri strains with a neutral barcode for examination of population dynamics or BarSeq analyses in other species. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Production of the erm-bar DNA Basic Protocol 2: Generation of a targeted and barcoded deletion strain of V. fischeri Alternate Protocol: Parallel generation of multiple barcode-tagged V. fischeri deletion strains Basic Protocol 3: Setting up mixed populations of barcode-tagged strains Basic Protocol 4: Performing a competitive growth assay Basic Protocol 5: Amplicon library preparation and equimolar pooling Basic Protocol 6: Sequencing on Illumina iSeq 100 Basic Protocol 7: BarSeq data analysis.}, }
@article {pmid39460509, year = {2024}, author = {Yang, M and Wang, Y and Dai, P and Feng, D and Hughes, AC and Li, H and Zhang, A}, title = {Sympatric diversity pattern driven by the secondary contact of two deeply divergent lineages of the soybean pod borer Leguminivora glycinivorella.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12917}, pmid = {39460509}, issn = {1749-4877}, abstract = {The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important tortricid pest species widely distributed in most parts of China and its adjacent regions. Here, we analyzed the genetic diversity and population differentiation of L. glycinivorella using diverse genetic information including the standard cox1 barcode sequences, mitochondrial genomes (mitogenomes), and single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Based on a comprehensive sampling (including adults or larvae of L. glycinivorella newly collected at 22 of the total 30 localities examined) that covers most of the known distribution range of this pest, analyses of 543 cox1 barcode sequences and 60 mitogenomes revealed that the traditionally recognized and widely distributed L. glycinivorella contains two sympatric and widely distributed genetic lineages (A and B) that were estimated to have diverged ∼1.14 million years ago during the middle Pleistocene. Moreover, low but statistically significant correlations were recognized between genetic differentiation and geographic or environmental distances, indicating the existence of local adaptation to some extent. Based on SNPs, phylogenetic inference, principal component analysis, fixation index, and admixture analysis all confirm the two divergent sympatric lineages. Compared with the stable demographic history of Lineage B, the expansion of Lineage A had possibly made the secondary contact of the two lineages probable, and this process may be driven by the climate fluctuation during the late Pleistocene as revealed by ecological niche modeling.}, }
@article {pmid39459593, year = {2024}, author = {Xia, X}, title = {Phylogeographic Analysis for Understanding Origin, Speciation, and Biogeographic Expansion of Invasive Asian Hornet, Vespa velutina Lepeletier, 1836 (Hymenoptera, Vespidae).}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {10}, pages = {}, pmid = {39459593}, issn = {2075-1729}, support = {RGPIN-2024-05641//Natural Sciences and Engineering Research Council/ ; }, abstract = {The Asian hornet, Vespa velutina, is an invasive species that has not only expanded its range in Asia but has also invaded European countries, and it incurs significant costs on local apiculture. This phylogeographic study aims to trace the evolutionary trajectory of V. velutina and its close relatives; it aims to identify features that characterize an invasive species. The last successful invasion of Vespa velutina into France occurred in late May, 2002, and into South Korea in early October, 2002, which were estimated by fitting a logistic equation to the number of observations over time. The instantaneous rate of increase is 1.3667 for V. velutina in France and 0.2812 in South Korea, which are consistent with the interpretation of little competition in France and strong competition from local hornet species in South Korea. The invasive potential of two sister lineages can be compared by their distribution area when proper statistical adjustments are made to account for differences in sample size. V. velutina has a greater invasive potential than its sister lineage. The ancestor of V. velutina split into two lineages, one found in Indonesia/Malaysia and the other colonizing the Asian continent. The second lineage split into a sedentary clade inhabiting Pakistan and India and an invasive lineage colonizing much of Southeast Asia. This latter lineage gave rise to the subspecies V. v. nigrithorax, which invaded France, South Korea, and Japan. My software PGT version 1.5, which generates geophylogenies and computes geographic areas for individual taxa, is useful for understanding biogeography in general and invasive species in particular. I discussed the conceptual formulation of an index of invasiveness for a comparison between sister lineages.}, }
@article {pmid39458823, year = {2024}, author = {Tahir, S and Hassan, SS and Yang, L and Ma, M and Li, C}, title = {Detection Methods for Pine Wilt Disease: A Comprehensive Review.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {20}, pages = {}, pmid = {39458823}, issn = {2223-7747}, support = {2022ZD0401602//Biological Breeding-Major Projects/ ; }, abstract = {Pine wilt disease (PWD), caused by the nematode Bursaphelenchus xylophilus, is a highly destructive forest disease that necessitates rapid and precise identification for effective management and control. This study evaluates various detection methods for PWD, including morphological diagnosis, molecular techniques, and remote sensing. While traditional methods are economical, they are limited by their inability to detect subtle or early changes and require considerable time and expertise. To overcome these challenges, this study emphasizes advanced molecular approaches such as real-time polymerase chain reaction (RT-PCR), droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) coupled with CRISPR/Cas12a, which offer fast and accurate pathogen detection. Additionally, DNA barcoding and microarrays facilitate species identification, and proteomics can provide insights into infection-specific protein signatures. The study also highlights remote sensing technologies, including satellite imagery and unmanned aerial vehicle (UAV)-based hyperspectral analysis, for their capability to monitor PWD by detecting asymptomatic diseases through changes in the spectral signatures of trees. Future research should focus on combining traditional and innovative techniques, refining visual inspection processes, developing rapid and portable diagnostic tools for field application, and exploring the potential of volatile organic compound analysis and machine learning algorithms for early disease detection. Integrating diverse methods and adopting innovative technologies are crucial to effectively control this lethal forest disease.}, }
@article {pmid39455411, year = {2024}, author = {He, M and Zhu, X and Chen, Z and Wang, C and Mi, L and Shang, Y and Zheng, J and Xiang, C and Song, H and Liu, X}, title = {Epitaxial Growth of Multicolor Lanthanide MOFs by Ultrasound for Photonic Barcodes.}, journal = {ACS applied materials &amp; interfaces}, volume = {16}, number = {44}, pages = {60884-60889}, doi = {10.1021/acsami.4c16625}, pmid = {39455411}, issn = {1944-8252}, abstract = {Epitaxially grown lanthanide metal-organic frameworks (Ln MOFs) exhibit multicolor and characteristic Ln emission with sharp emission bands, which are of great value in the field of information security and anti-counterfeiting. Epitaxial growth of Ln MOFs is generally achieved by solvothermal or hydrothermal methods, which suffer from challenges such as high reaction temperature and long growth time. Here, we report the fast epitaxial growth of multicolor lanthanide MOFs by an ultrasonic method at room temperature. The TbSmSQ shows a core-shell type structure with the Tb ion in the core and Sm in the shell within one crystal and exhibits the characteristic emission lines of Tb and Sm, respectively. The nonporous structure and large distance between lanthanide ions effectively avoid the influence of solvent vapor on the intensity and color of luminescence emission. Its application as photonic barcodes has been studied. This work demonstrates the feasibility of epitaxial growth of multicolor Ln MOFs by the ultrasonic method and its value for anti-counterfeiting and information security applications.}, }
@article {pmid39454580, year = {2024}, author = {Lima, GM and Jame-Chenarboo, Z and Sojitra, M and Sarkar, S and Carpenter, EJ and Yang, CY and Schmidt, E and Lai, J and Atrazhev, A and Yazdan, D and Peng, C and Volker, EA and Ho, R and Monteiro, G and Lai, R and Mahal, LK and Macauley, MS and Derda, R}, title = {The liquid lectin array detects compositional glycocalyx differences using multivalent DNA-encoded lectins on phage.}, journal = {Cell chemical biology}, volume = {31}, number = {11}, pages = {1986-2001.e9}, doi = {10.1016/j.chembiol.2024.09.010}, pmid = {39454580}, issn = {2451-9448}, mesh = {*Glycocalyx/metabolism/chemistry ; *Lectins/chemistry/metabolism ; Humans ; Bacteriophages/chemistry/metabolism ; Animals ; DNA/chemistry/metabolism ; Mice ; Polysaccharides/chemistry/metabolism ; }, abstract = {Selective detection of disease-associated changes in the glycocalyx is an emerging field in modern targeted therapies. Detecting minor glycan changes on the cell surface is a challenge exacerbated by the lack of correspondence between cellular DNA/RNA and glycan structures. We demonstrate that multivalent displays of lectins on DNA-barcoded phages-liquid lectin array (LiLA)-detect subtle differences in density of glycans on cells. LiLA constructs displaying 73 copies of diCBM40 (CBM) lectin per virion (φ-CBM73) exhibit non-linear ON/OFF-like recognition of sialoglycans on the surface of normal and cancer cells. A high-valency φ-CBM290 display, or soluble CBM protein, cannot amplify the subtle differences detected by φ-CBM73. Similarly, multivalent displays of CBM and Siglec-7 detect differences in the glycocalyx between stem-like and non-stem populations in cancer. Multivalent display of lectins offer in situ detection of minor differences in glycocalyx in cells both in vitro and in vivo not feasible to currently available technologies.}, }
@article {pmid39453698, year = {2024}, author = {Rodger, G and Lipworth, S and Barrett, L and Oakley, S and Crook, DW and Eyre, DW and Stoesser, N}, title = {Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates.}, journal = {Microbial genomics}, volume = {10}, number = {10}, pages = {}, pmid = {39453698}, issn = {2057-5858}, mesh = {*Escherichia coli/genetics ; *Nanopore Sequencing/methods ; *DNA, Complementary/genetics ; Polymerase Chain Reaction/methods ; Humans ; Escherichia coli Infections/microbiology ; Sequence Analysis, RNA/methods ; RNA, Bacterial/genetics ; Gene Expression Profiling/methods ; High-Throughput Nucleotide Sequencing/methods ; Transcriptome ; }, abstract = {Whole-transcriptome (long-read) RNA sequencing (Oxford Nanopore Technologies, ONT) holds promise for reference-agnostic analysis of differential gene expression in pathogenic bacteria, including for antimicrobial resistance genes (ARGs). However, direct cDNA ONT sequencing requires large concentrations of polyadenylated mRNA, and amplification protocols may introduce technical bias. Here we evaluated the impact of direct cDNA- and cDNA PCR-based ONT sequencing on transcriptomic analysis of clinical Escherichia coli. Four E. coli bloodstream infection-associated isolates (n=2 biological replicates per isolate) were sequenced using the ONT Direct cDNA Sequencing SQK-DCS109 and PCR-cDNA Barcoding SQK-PCB111.24 kits. Biological and technical replicates were distributed over eight flow cells using 16 barcodes to minimize batch/barcoding bias. Reads were mapped to a transcript reference and transcript abundance was quantified after in silico depletion of low-abundance and rRNA genes. We found there were strong correlations between read counts using both kits and when restricting the analysis to include only ARGs. We highlighted that correlations were weaker for genes with a higher GC content. Read lengths were longer for the direct cDNA kit compared to the PCR-cDNA kit whereas total yield was higher for the PCR-cDNA kit. In this small but methodologically rigorous evaluation of biological and technical replicates of isolates sequenced with the direct cDNA and PCR-cDNA ONT sequencing kits, we demonstrated that PCR-based amplification substantially improves yield with largely unbiased assessment of core gene and ARG expression. However, users of PCR-based kits should be aware of a small risk of technical bias which appears greater for genes with an unusually high (>52%)/low (<44%) GC content.}, }
@article {pmid39452649, year = {2024}, author = {Yang, J and Reyes Loaiciga, C and Yue, HR and Hou, YJ and Li, J and Li, CX and Li, J and Zou, Y and Zhao, S and Zhang, FL and Zhao, XQ}, title = {Genomic Characterization and Establishment of a Genetic Manipulation System for Trichoderma sp. (Harzianum Clade) LZ117.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {10}, pages = {}, pmid = {39452649}, issn = {2309-608X}, support = {No. 2022YFE0108500//the State Key Research and Development Program of China/ ; }, abstract = {Trichoderma species have been reported as masters in producing cellulolytic enzymes for the biodegradation of lignocellulolytic biomass and biocontrol agents against plant pathogens and pests. In our previous study, a novel Trichoderma strain LZ117, which shows potent capability in cellulase production, was isolated. Herein, we conducted multilocus phylogenetic analyses based on DNA barcodes and performed time-scaled phylogenomic analyses using the whole genome sequences of the strain, annotated by integrating transcriptome data. Our results suggest that this strain represents a new species closely related to T. atrobrunneum (Harzianum clade). Genes encoding carbohydrate-active enzymes (CAZymes), transporters, and secondary metabolites were annotated and predicted secretome in Trichoderma sp. LZ117 was also presented. Furthermore, genetic manipulation of this strain was successfully achieved using PEG-mediated protoplast transformation. A putative transporter gene encoding maltose permease (Mal1) was overexpressed, which proved that this transporter does not affect cellulase production. Moreover, overexpressing the native Cre1 homolog in LZ117 demonstrated a more pronounced impact of glucose-caused carbon catabolite repression (CCR), suggesting the importance of Cre1-mediated CCR in cellulase production of Trichoderma sp. LZ117. The results of this study will benefit further exploration of the strain LZ117 and related species for their applications in bioproduction.}, }
@article {pmid39450195, year = {2024}, author = {Lee, HE and Lee, GH and Min, GS}, title = {A new species of Thoracophelia (Annelida, Opheliidae) from the Yellow Sea of South Korea.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e129526}, pmid = {39450195}, issn = {1314-2828}, abstract = {BACKGROUND: Thoracophelia Ehlers, 1897 is a genus of Opheliidae characterised by the body divided into three distinct regions, modified parapodia in chaetiger 10 and a ventral groove restricted to the posterior half of the body. To date, 18 species have been described in the genus. Amongst them, six species have been recorded in northeast Asia.<br><br>NEW INFORMATION: A new species, Thoracopheliafoliformis sp. nov., was discovered in the intertidal zone of the Yellow Sea, South Korea. This is the first Thoracophelia species report from the Yellow Sea. This new species is closely related to T.dillonensis (Hartman, 1938) from California and T.ezoensis Okuda, 1936 from Japan in having pectinate branchiae. However, the new species can be distinguished from the two species by the unique combination of the following characteristics: 15 pairs of wrinkled pectinate branchiae with 12-15 filaments at best development and a foliaceous mid-ventral plate in the pygidium instead of one or two thick ventral cirri. Detailed descriptions and illustrations of T.foliformis sp. nov. are provided. Sequences of the mitochondrial cytochrome c oxidase subunit I (COI), nuclear 18S ribosomal DNA (rDNA) and 28S rDNA of the new species were determined and analysed.}, }
@article {pmid39450043, year = {2024}, author = {Likhitrakarn, N and Golovatch, SI and Srisonchai, R and Jirapatrasilp, P and Sapparojpattana, P and Jeratthitikul, E and Panha, S and Sutcharit, C}, title = {A new species of the pill millipede genus Rhopalomeris Verhoeff, 1906 (Diplopoda, Glomerida, Glomeridae) from Myanmar, and notes on Rhopalomeriscarnifex (Pocock, 1889).}, journal = {ZooKeys}, volume = {1215}, number = {}, pages = {235-257}, pmid = {39450043}, issn = {1313-2989}, abstract = {The taxonomy of the pill millipede genus Rhopalomeris Verhoeff, 1906, which is restricted to Indochina and currently comprises six described species, is refined and updated. An integrative taxonomic approach was employed that combines morphological examination with DNA barcoding using the cytochrome c oxidase subunit I (COI) gene for species identification and delineation. The first objective was to confirm the identity of Rhopalomeriscarnifex (Pocock, 1889), a charismatic species known as the "candy pill millipede" due to its vivid coloration, based on specimens collected near the type locality in Myanmar. The second objective was to describe a new species, Rhopalomerisnigroflava Likhitrakarn, sp. nov., discovered in Linno Gu, Kayin State, Myanmar. This new species is distinguished by its small body size (5.1-9.7 mm long) and yellow body with contrasting brown to blackish markings on certain terga. In addition, the position of the telopod syncoxital lobe relative to the lateral syncoxite horns separates it from other Rhopalomeris species. The interspecific divergence between R.nigroflava Likhitrakarn, sp. nov. and other congeners ranges from 10.85% to 16.13%, based on uncorrected COI p-distances, while the intraspecific divergence was 0%-7.44%. A distribution map of and a revised identification key to all known species of Rhopalomeris are also provided.}, }
@article {pmid39444847, year = {2024}, author = {Mwamula, AO and Kim, YS and Lee, DW}, title = {Morphological and molecular characterization of Paractinolaimus uljinensis n. sp. (Nematoda: Actinolaimidae) from Korea, with an updated compendium of the genus.}, journal = {Journal of nematology}, volume = {56}, number = {1}, pages = {20240040}, pmid = {39444847}, issn = {0022-300X}, abstract = {A new species of the genus Paractinolaimus isolated from the bark of a dead red pine tree was characterized using morphometric data and molecular DNA barcodes. Paractinolaimus uljinensis n. sp. was characterized by its medium sized body 2.50 to 2.98 mm long; lip region truncate, angular and offset by a depression; odontostyle 23.5 to 27.0 μm long; basal shield of pharynx present; vulval opening wide and longitudinal, positioned slightly anteriorly (V = 42.5-47.7); several advulval papillae; female tail long and filiform (324.0-435.0 μm long, c' = 10.1-14.2); a clearly visible copulatory hump; spicules 60.0 to 70.5 μm long; 12 to 15 (mostly 12-14) large contiguous ventromedian supplements, and male tail conoid to broadly rounded. The new species was morphologically compared with P. intermedius, P. sahandi, P. decraemerae, P. acutus, P. macrolaimus, and P. tuberculatus. The phylogenetic relationships among species were reconstructed using 18S- and 28S-rRNA gene sequences. The phylogenies showed well-supported sister relations of Paractinolaimus uljinensis n. sp. with P. sahandi, P. macrolaimus, and P. decraemerae. In addition, the ITS-rRNA gene sequences of Paractinolaimus uljinensis n. sp. were supplied, representing the first characterization of the gene for the genus.}, }
@article {pmid39443484, year = {2024}, author = {Wu, B and Bennett, HM and Ye, X and Sridhar, A and Eidenschenk, C and Everett, C and Nazarova, EV and Chen, HH and Kim, IK and Deangelis, M and Owen, LA and Chen, C and Lau, J and Shi, M and Lund, JM and Xavier-Magalhães, A and Patel, N and Liang, Y and Modrusan, Z and Darmanis, S}, title = {Overloading And unpacKing (OAK) - droplet-based combinatorial indexing for ultra-high throughput single-cell multiomic profiling.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9146}, pmid = {39443484}, issn = {2041-1723}, support = {R01 EY031209/EY/NEI NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Cell Line, Tumor ; Melanoma/genetics/drug therapy/pathology ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; }, abstract = {Multiomic profiling of single cells by sequencing is a powerful technique for investigating cellular diversity. Existing droplet-based microfluidic methods produce many cell-free droplets, underutilizing bead barcodes and reagents. Combinatorial indexing on microplates is more efficient for barcoding but labor-intensive. Here we present Overloading And unpacKing (OAK), which uses a droplet-based barcoding system for initial compartmentalization followed by a second aliquoting round to achieve combinatorial indexing. We demonstrate OAK's versatility with single-cell RNA sequencing as well as paired single-nucleus RNA sequencing and accessible chromatin profiling. We further showcase OAK's performance on complex samples, including differentiated bronchial epithelial cells and primary retinal tissue. Finally, we examine transcriptomic responses of over 400,000 melanoma cells to a RAF inhibitor, belvarafenib, discovering a rare resistant cell population (0.12%). OAK's ultra-high throughput, broad compatibility, high sensitivity, and simplified procedures make it a powerful tool for large-scale molecular analysis, even for rare cells.}, }
@article {pmid39443100, year = {2024}, author = {Oshiro, A and Sumi, T and Imai, H}, title = {[Identification of Fish Species Involved with Ciguatera Food Poisoning in Okinawan Waters by Using PCR-RFLP analysis].}, journal = {Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan}, volume = {65}, number = {4}, pages = {79-83}, doi = {10.3358/shokueishi.65.79}, pmid = {39443100}, issn = {0015-6426}, mesh = {Animals ; *Polymorphism, Restriction Fragment Length ; *Ciguatera Poisoning ; Japan ; *Polymerase Chain Reaction ; *RNA, Ribosomal, 16S/genetics ; *Fishes/genetics ; DNA, Mitochondrial/genetics/analysis ; Phylogeny ; }, abstract = {Ciguatera fish poisoning (CFP), known as a seafood-borne disease, is caused by consumption of fish contaminated with ciguatoxins in tropical and subtropical sea. The ciguatera fishes, Variola louti, Lutjanus monostigma and L. bohar have an absolute majority in the Ryukyu Archipelago, southwestern Japan. We developed the cluster analysis of phylogenetic tree by using mitochondrial (mt) DNA 16S rRNA sequences of V. louti, L. monostigma and L. bohar and differentiate them from morphologically similar species (L. fulviflamma, L. russellii, L. argentimaculatus, Plectropomus leopardus and V. albimarginata) in our previous study. The fish were acquired from the coastal waters of the Ryukyu Archipelago, and a polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) marker of the mtDNA 16S rRNA region was used, employing the restriction enzymes BmgT120 I, Dde I, and SnaB I, to identify the fish species responsible for CFP. These results showed that a PCR-RFLP marker can be obtained more easily than a nucleotide sequence.}, }
@article {pmid39441940, year = {2024}, author = {Smitha Pillai, K and Laxton, O and Li, G and Lin, J and Karginova, O and Nanda, R and Olopade, OI and Tay, S and Moellering, RE}, title = {Single-cell chemoproteomics identifies metastatic activity signatures in breast cancer.}, journal = {Science advances}, volume = {10}, number = {43}, pages = {eadp2622}, pmid = {39441940}, issn = {2375-2548}, support = {R01 GM127527/GM/NIGMS NIH HHS/United States ; R35 GM148231/GM/NIGMS NIH HHS/United States ; T32 GM144290/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Breast Neoplasms/metabolism/pathology/genetics ; *Single-Cell Analysis/methods ; Female ; *Proteomics/methods ; Cell Line, Tumor ; *Neoplasm Metastasis ; }, abstract = {Protein activity state, rather than protein or mRNA abundance, is a biologically regulated and relevant input to many processes in signaling, differentiation, development, and diseases such as cancer. While there are numerous methods to detect and quantify mRNA and protein abundance in biological samples, there are no general approaches to detect and quantify endogenous protein activity with single-cell resolution. Here, we report the development of a chemoproteomic platform, single-cell activity-dependent proximity ligation, which uses automated, microfluidics-based single-cell capture and nanoliter volume manipulations to convert the interactions of family-wide chemical activity probes with native protein targets into multiplexed, amplifiable oligonucleotide barcodes. We demonstrate accurate, reproducible, and multiplexed quantitation of a six-enzyme (Ag-6) panel with known ties to cancer cell aggressiveness directly in single cells. We further identified increased Ag-6 enzyme activity across breast cancer cell lines of increasing metastatic potential, as well as in primary patient-derived tumor cells and organoids from patients with breast cancer.}, }
@article {pmid39438815, year = {2024}, author = {Bastidas-Caldes, C and Hernández-Alomía, F and Almeida, M and Ormaza, M and Boada, J and Graham, J and Calvopiña, M and Castillejo, P}, title = {Molecular identification and antimicrobial resistance patterns of enterobacterales in community urinary tract infections among indigenous women in Ecuador: addressing microbiological misidentification.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {1195}, pmid = {39438815}, issn = {1471-2334}, mesh = {Humans ; *Urinary Tract Infections/microbiology/drug therapy/epidemiology ; Female ; Ecuador/epidemiology ; Cross-Sectional Studies ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Microbial Sensitivity Tests ; Indigenous Peoples ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Enterobacteriaceae/drug effects/genetics/isolation &amp; purification ; Young Adult ; Enterobacteriaceae Infections/microbiology/epidemiology/drug therapy ; Community-Acquired Infections/microbiology ; }, abstract = {BACKGROUND: Antibiotic resistance of Enterobacterales poses a major challenge in the treatment of urinary tract infections (UTIs). In low- and middle-income countries (LMICs), standard microbiological (i.e. urine culture and simple disk diffusion test) methods are considered the "gold standard" for bacterial identification and drug susceptibility testing, while PCR and DNA sequencing are less commonly used. In this study, we aimed to re-identifying Enterobacterales as the primary bacterial agents responsible for urinary tract infections (UTIs) by comparing the sensitivity and specificity of traditional microbiological methods with advanced molecular techniques for the detection of uropathogens in indigenous women from Otavalo, Ecuador.<br><br>METHODS: A facility-based cross-sectional study was conducted from October 2021 to February 2022 among Kichwa-Otavalo women. Pathogens from urine samples were identified using culture and biochemical typing. Morphological identification was doble-checked through PCR and DNA sequencing of 16S, recA, and rpoB molecular barcodes. The isolates were subjected to antimicrobial susceptibility-testing using disk diffusion test.<br><br>RESULTS: This study highlighted a 32% misidentification rate between biochemical and molecular identification. Using traditional methods, E. coli was 26.19% underrepresented meanwhile Klebsiella oxytoca was overrepresented by 92.86%. Furthermore, the genera Pseudomonas, Proteus, and Serratia were confirmed to be E. coli and Klebsiella spp. by molecular method, and one Klebsiella spp. was reidentified as Enterobacter spp. The susceptibility profile showed that 59% of the isolates were multidrug resistant strains and 31% produced extended spectrum beta-lactamases (ESBLs). Co-trimoxazole was the least effective antibiotic with 61% of the isolates resistant. Compared to previous reports, resistance to nitrofurantoin and fosfomycin showed an increase in resistance by 25% and 15%, respectively.<br><br>CONCLUSIONS: Community-acquired UTIs in indigenous women in Otavalo were primarily caused by E. coli and Klebsiella spp. Molecular identification (16S/rpoB/recA) revealed a high rate of misidentification by standard biochemical and microbiological techniques, which could lead to incorrect antibiotic prescriptions. UTI isolates in this population displayed higher levels of resistance to commonly used antibiotics compared with non-indigenous groups. Accurate identification of pathogens causing UTIs and their antibiotic susceptibility in local populations is important for local antibiotic prescribing guidelines.}, }
@article {pmid39434349, year = {2024}, author = {Hamdan, NT}, title = {Molecular identification of Hypomyces chrysospermus mycoparasitic fungus isolated from mushrooms in a local market of Iraq.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {74}, number = {10 (Supple-8)}, pages = {S398-S401}, doi = {10.47391/JPMA-BAGH-16-90}, pmid = {39434349}, issn = {0030-9982}, mesh = {Iraq ; *Phylogeny ; Agaricales/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; }, abstract = {In this study, mycoparasitic fungus was identified by using the rDNA internal transcribed spacer barcode marker, i.e. ITS rDNA gene. Amplicons were sequenced and identified by NCBI - BLAST (Basic local alignment search tool). The BLAST results revealed that NOOR strain matched 100% with accession numbers [MH854754.1]. The phylogenetic tree shows close relationship between NOOR strain and H. chrysospermus [MH854754-1], H. chrysospermus [MZ389105-1], H. chrysospermus [MK605327- 1], H. chrysospermus [MT595227-1], H. [EU816370-1], H. chrysospermus [MG685885-1]. The Iraqi isolate was recorded as NOOR strain in the National Centre for Biotechnology Information for the first time in Iraq.}, }
@article {pmid39434133, year = {2024}, author = {Gąsiorek, P and Sørensen, MV and Lillemark, MR and Leerhøi, F and Tøttrup, AP}, title = {Massive citizen science sampling and integrated taxonomic approach unravel Danish cryptogam-dwelling tardigrade fauna.}, journal = {Frontiers in zoology}, volume = {21}, number = {1}, pages = {27}, pmid = {39434133}, issn = {1742-9994}, abstract = {Tardigrade diversity and distribution are enigmatic in most parts of the globe, and only some European countries can boast of a relatively well-studied water bear fauna. However, even these suffer from the lack of genetic data, which would substantiate faunistic data and make biogeographic comparisons easier. Denmark has never been intensively and systematically researched in this regard, thus a citizen science sampling of cryptogams (mosses, liverworts, and lichens) was launched in spring 2023, aiming at a comprehensive biodiversity survey across this insular country. Nearly 700 samples were selected out of 8.000 sent to NHMD, based on the quality of samples, representativeness of various regions of Denmark, and the type of substrate to allow unravelling of potential ecological associations between tardigrades and cryptogams. Importantly, a large fraction of morphological identifications was backed up by DNA barcode data based on ITS-2 (1001 sequences), and in some cases also on COI (93 sequences) and ITS-1 (22 sequences) molecular markers, which are recognised DNA fragments used in species delimitation. We quadruple the number of known Danish limno-terrestrial tardigrade species (55 spp. reported in this paper vs. 14 spp. reported in literature so far, most of which were contentious due to the insufficient knowledge on tardigrade taxonomy), demonstrating the power of integrative taxonomy. No fewer than nine spp. are new to science. This is the first case where tardigrade fauna of an entire country is examined both from morphological and DNA barcoding data perspective.}, }
@article {pmid39433876, year = {2024}, author = {Simon, JJ and Fowler, DM and Maly, DJ}, title = {Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq.}, journal = {Nature methods}, volume = {21}, number = {11}, pages = {2094-2106}, pmid = {39433876}, issn = {1548-7105}, support = {RM1HG010461//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; RM1 HG010461/HG/NHGRI NIH HHS/United States ; R01 GM086858/GM/NIGMS NIH HHS/United States ; R01GM145011//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM145011/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Proto-Oncogene Proteins B-raf/genetics/metabolism ; Mutation ; Cell Line, Tumor ; Cell Proliferation/drug effects ; }, abstract = {Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein-protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability.}, }
@article {pmid39432187, year = {2024}, author = {Ben Ahmed, R and Gajda, &#x141; and Świątek, P}, title = {Morphological data and DNA barcoding reveal the presence of the alien freshwater leech Helobdella octatestisaca (Hirudinida: Glossiphoniformes) in North Africa (Tunisia).}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {1081}, pmid = {39432187}, issn = {1573-4978}, mesh = {Animals ; *Phylogeny ; *Leeches/genetics/anatomy &amp; histology/classification ; *DNA Barcoding, Taxonomic/methods ; Tunisia ; Fresh Water ; Introduced Species ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: We hereby report the first occurrence of Helobdella octatestisaca in North Africa, specifically in Tunisia, as a likely introduced species from the Neotropical Region. Historically, leeches bearing a prominent chitinous scute on their dorsal surface were commonly diagnosed as H. stagnalis. Most probably, H. octatestisaca had previously been misidentified as H. stagnalis in Tunisia.<br><br>METHODS AND RESULTS: The identification was primarily based on morphological evidence, supplemented by genetic data obtained from COI DNA barcoding. The morphology of the examined specimens was consistent with the original species description, notably characterized by the presence of four pairs of testisacs. To support our findings, we conducted a phylogenetic analysis using the Maximum Likelihood method based on COI alignment constructed with the newly obtained sequence from Tunisian specimens and complete or nearly complete 'Folmer fragment' sequences of congeners sourced from the GenBank database.<br><br>CONCLUSIONS: This study highlights the first identification of H. octatestisaca in North Africa and suggests that previous records of H. stagnalis in Tunisia likely misidentified this species.}, }
@article {pmid39431921, year = {2024}, author = {Sun, F and Liu, J and Su, Z and Wu, D and Qu, S and Wu, Y and Li, L and Li, G}, title = {Encodable DNA Hairpin Probes for Nanopore Multiplexed Target Detection.}, journal = {Analytical chemistry}, volume = {96}, number = {44}, pages = {17612-17619}, doi = {10.1021/acs.analchem.4c03469}, pmid = {39431921}, issn = {1520-6882}, mesh = {*Nanopores ; *DNA Probes/chemistry/genetics ; *Hemolysin Proteins/chemistry/genetics ; MicroRNAs/analysis ; Biosensing Techniques/methods ; Nucleic Acid Conformation ; Inverted Repeat Sequences ; DNA/chemistry/analysis ; }, abstract = {Owing to the co-occurrence of hazardous compounds, it is crucial to build multiple highly discriminative probe libraries for simultaneous determination. Drawing inspiration from nucleic acid barcodes, we developed a probe system that is exclusively based on the nucleic acid secondary structure's hairpin structure, which can be directly read by nanopores. The highly distinguishable hairpin probes were constructed, and a detailed explanation of the possible patterns in their design was provided. These probe-representative events measured through the α-hemolysin (α-HL) nanopores were both distinguished, either through visual observation or comparison of the nanopore parameters. Besides, the potential design pattern for probes with unique telegraphic switching between the two levels was also unveiled. Finally, these probes were utilized to realize simultaneous, ultrasensitive mycotoxin multiple-detection, and their prospective applications for the detection of proteins and microRNAs were presented, indicating their suitability for a wide range of sensing applications.}, }
@article {pmid39424732, year = {2025}, author = {Holmes, AB and Corinaldesi, C and Basso, K}, title = {Single-Cell Transcriptomic Analysis of Normal and Malignant B Cells.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2865}, number = {}, pages = {347-374}, pmid = {39424732}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; Humans ; *Gene Expression Profiling/methods ; *B-Lymphocytes/metabolism/immunology ; *Transcriptome ; Software ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {In the past decade, single-cell (sc) transcriptomics has overcome the limitations of bulk analysis by measuring gene expression in individual cells, not just a population average. This can identify diverse cell types and states within a sample with high resolution, even without prior purification. Various technologies exist, each with its own capture, barcoding, and library preparation methods. This chapter focuses on the analysis of normal and malignant mature B cells using the 10× Genomics 5' sc-gene expression in parallel with B cell immune repertoire profiling. By integrating the gene expression data from similar cells, the complete transcriptome for each population can be reconstructed, while the identification of the expressed immunoglobulin genes allows investigating clonotype evolution and the detection of tumor clones that share the same clonally rearranged B cell receptor sequence. Researchers are guided through both the experimental protocols and data analysis with a comprehensive, step-by-step walkthrough of how to use some of the more popular single-cell software tools.}, }
@article {pmid39422558, year = {2024}, author = {Zhang, SJ and Wu, C and Walt, DR}, title = {A Multiplexed Digital Platform Enables Detection of Attomolar Protein Levels with Minimal Cross-Reactivity.}, journal = {ACS nano}, volume = {18}, number = {43}, pages = {29891-29901}, doi = {10.1021/acsnano.4c10340}, pmid = {39422558}, issn = {1936-086X}, support = {R01 EB032826/EB/NIBIB NIH HHS/United States ; R56 EB032826/EB/NIBIB NIH HHS/United States ; }, mesh = {Humans ; *Enzyme-Linked Immunosorbent Assay ; Cross Reactions ; Antibodies/immunology/chemistry ; }, abstract = {Protein-based biomarkers are essential for disease diagnostics, yet their low abundance in biofluids often presents significant detection challenges for traditional enzyme-linked immunosorbent assay (ELISA) techniques. While various ultrasensitive methods such as digital ELISA have improved sensitivity, multiplex assays still suffer from considerable cross-reactivities that can compromise result accuracies. To address this challenge, we have developed barcoded Molecular On-bead Signal Amplification for Individual Counting (barcoded MOSAIC), a multiplexed digital ELISA technology that markedly reduces cross-reactivity by pairing barcoded detection antibodies with specific bead types. This approach enables the simultaneous detection of eight analytes from less than 9 μL of blood, with sensitivities ranging from midpicomolar to low-attomolar levels and a collective dynamic range exceeding seven logs across multiple analytes within a single multiplex assay. Additionally, barcoded MOSAIC is compatible with standard immunoassay reagents and workflows, utilizing a rapid, automatable flow cytometric readout for quantification, which makes it a highly accessible benchtop platform that is readily adoptable by both research and clinical laboratories, setting the stage for future translation into point-of-care applications.}, }
@article {pmid39421424, year = {2024}, author = {Subbiah, VK and Gomez, CR and Robben, DM and Subramaniam, R and Hearn, AJ}, title = {Characterization of the complete mitochondrial genome of the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18190}, pmid = {39421424}, issn = {2167-8359}, mesh = {*Genome, Mitochondrial/genetics ; Borneo ; Animals ; *Phylogeny ; *Mustelidae/genetics ; Sequence Analysis, DNA ; RNA, Transfer/genetics ; }, abstract = {BACKGROUND: The Mephitidae is a family of skunks and stink-badgers that includes 12 extant species in four genera, namely, Mydaus, Conepatus, Mephitis and Spilogale. Mydaus is the only genus within Mephitidae found outside the American continent, with its distribution limited to the islands of Borneo, Indonesia and Philippines. There are two extant species of Mydaus i.e., javanensis and marchei. Currently, complete mitogenomes are unavailable for either species. Here, we present the characterization of the first complete mitogenome for the Sunda stink-badger (Mydaus javanensis) from the island of Borneo.<br><br>METHODS: Muscle tissue was obtained and the DNA was sequenced using a combination of Illumina Barcode Tagged Sequence (BTSeq) and Sanger sequencing techniques. The genome was annotated with MITOS and manually checked for accuracy. A circular map of the mitogenome was constructed with Proksee. Relative synonymous codon usage (RSCU) and codon frequency were calculated using MEGA-X. The protein coding genes (PCGs) were aligned with reference sequences from GenBank and used for the construction of phylogenetic trees (maximum liklihood (ML) and Bayesian inference (BI)). Additionally, due to the lack of available complete genomes in public databases, we constructed another tree with the cyt b gene.<br><br>RESULTS: The complete circular mitogenome was 16,391 base pairs in length. It comprises the typical 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes, one control region (CR) and an L-strand replication origin (OL). The G+C content was 38.1% with a clear bias towards A and T nucleotides. Of the 13 PGCs, only ND6 was positioned in the reverse direction, along with five other tRNAs. Five PCGs had incomplete stop codons and rely on post-transcriptional polyadenylation (TAA) for termination. Based on the codon count, Leucine was the most common amino acid (589), followed by Threonine (332) and Isoleucine (325). The ML and BI phylogenetic trees, based on concatenated PCGs and the cyt b gene, respectively, correctly clustered the species with other members of the Mephitidae family but were unique enough to set it apart from Conepatus, Mephitis and Spilogale. The results confirm Mydaus as a member of the mephitids and the mitogenome will be useful for evolutionary analysis and conservation of the species.}, }
@article {pmid39418234, year = {2024}, author = {Cherie, N and Berta, DM and Tamir, M and Yiheyis, Z and Angelo, AA and Mekuanint Tarekegn, A and Chane, E and Nigus, M and Teketelew, BB}, title = {Improving laboratory turnaround times in clinical settings: A systematic review of the impact of lean methodology application.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0312033}, pmid = {39418234}, issn = {1932-6203}, mesh = {Humans ; *Laboratories, Clinical ; Efficiency, Organizational ; Laboratories/standards ; Time Factors ; Workflow ; }, abstract = {BACKGROUND: Lean methodology, originally developed in the manufacturing sector, is a process management philosophy focused on maximizing value by eliminating waste. Its application in laboratory settings, particularly concerning laboratory turnaround times (TAT), involves a systematic approach to identifying inefficiencies and optimizing processes to enhance value for end customers.<br><br>METHODS: This systematic review was registered in PROSPERO with identification number (CRD42024552350) and reported based on the 2020 PRISMA checklist. An extensive search strategy was performed using PubMed, Scopus, and Embase databases and gray literatures. Advanced searching was used using Boolean operators (AND &amp; OR). After articles were exported to endnote x8, duplications were removed and articles were selected based on titles, abstracts, and full texts. The illegibility of the articles was independently assessed by the three authors (NC, DMB, and BBT), and the disagreements were settled through scientific consensus. Methodological quality was assessed using JBI critical appraisal checklist.<br><br>DISCUSSION: In this review, electronic databases search yielded 1261 articles, of which 7 met the inclusion criteria. The review demonstrated, implementation of lean principle into the routine laboratory testing had an overall impact 76.1% on reducing laboratory TAT. Transportation, manual data processing, inefficient workflow, and the heavy workload were identified as the main wasteful procedures. To eliminate these non-value-added steps, several intervention techniques were implemented, including the use of a barcoding system, process redesign, workflow optimization, hiring additional staff, and relocating the sample collection room closer to the result distribution center. Lean implementation is crucial in the medical laboratory industry for optimizing processes, reducing TAT, and ultimately enhancing customer satisfaction. As a result, all clinical laboratories should adopt and implement lean principles in their routine testing processes. The medical laboratory industry should also proactively look for and apply lean tools, provide ongoing training, and foster awareness among laboratory staffs.}, }
@article {pmid39417120, year = {2024}, author = {Sadler, JM and Simkin, A and Tchuenkam, VPK and Gyuricza, IG and Fola, AA and Wamae, K and Assefa, A and Niaré, K and Thwai, K and White, SJ and Moss, WJ and Dinglasan, RR and Nsango, S and Tume, CB and Parr, JB and Ali, IM and Bailey, JA and Juliano, JJ}, title = {Application of a new highly multiplexed amplicon sequencing tool to evaluate Plasmodium falciparum antimalarial resistance and relatedness in individual and pooled samples from Dschang, Cameroon.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {39417120}, support = {R01 AI165537/AI/NIAID NIH HHS/United States ; R01 AI177791/AI/NIAID NIH HHS/United States ; U19 AI089680/AI/NIAID NIH HHS/United States ; R01 AI155730/AI/NIAID NIH HHS/United States ; R01 AI156267/AI/NIAID NIH HHS/United States ; K24 AI134990/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Resistance to antimalarial drugs remains a major obstacle to malaria elimination. Multiplexed, targeted amplicon sequencing is being adopted for surveilling resistance and dissecting the genetics of complex malaria infections. Moreover, genotyping of parasites and detection of molecular markers drug resistance in resource-limited regions requires open-source protocols for processing samples, using accessible reagents, and rapid methods for processing numerous samples including pooled sequencing.<br><br>METHODS: P lasmodium f alciparum Streamlined Multiplex Antimalarial Resistance and Relatedness Testing (Pf-SMARRT) is a PCR-based amplicon panel consisting of 15 amplicons targeting antimalarial resistance mutations and 9 amplicons targeting hypervariable regions. This assay uses oligonucleotide primers in two pools and a non-proprietary library and barcoding approach.<br><br>RESULTS: We evaluated Pf-SMARRT using control mocked dried blood spots (DBS) at varying levels of parasitemia and a mixture of 3D7 and Dd2 strains at known frequencies, showing the ability to genotype at low parasite density and recall within-sample allele frequencies. We then piloted Pf-SMARRT to genotype 100 parasite isolates collected from uncomplicated malaria cases at three health facilities in Dschang, Western Cameroon. Antimalarial resistance genotyping showed high levels of sulfadoxine-pyrimethamine resistance mutations, including 31% prevalence of the DHPS A613S mutation. No K13 candidate or validated artemisinin partial resistance mutations were detected, but one low-level non-synonymous change was observed. Pf-SMARRT's hypervariable targets, used to assess complexity of infections and parasite diversity and relatedness, showed similar levels and patterns compared to molecular inversion probe (MIP) sequencing. While there was strong concordance of antimalarial resistance mutations between individual samples and pools, low-frequency variants in the pooled samples were often missed.<br><br>CONCLUSION: Overall, Pf-SMARRT is a robust tool for assessing parasite relatedness and antimalarial drug resistance markers from both individual and pooled samples. Control samples support that accurate genotyping as low as 1 parasite per microliter is routinely possible.}, }
@article {pmid39416120, year = {2024}, author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416120}, issn = {2692-8205}, support = {P30 DK132710/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R01 AI132403/AI/NIAID NIH HHS/United States ; R01 EB031935/EB/NIBIB NIH HHS/United States ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae, Ruminococceae, and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.}, }
@article {pmid39416026, year = {2024}, author = {Sendinc, E and Yu, H and Hwang Fu, YH and Santos, J and Johnson, Z and Kirstein, JR and Niu, J and Chabot, MB and Cantu, VA and Džakula, &#x17d; and Lam, Q and Anmangandla, A and Burcham, TS and Davis, EM and Miles, ZD and Price, AD and Purse, BW and Gregory, RI and Stengel, G}, title = {Mapping multiple RNA modifications simultaneously by proximity barcode sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39416026}, issn = {2692-8205}, support = {R35 CA232115/CA/NCI NIH HHS/United States ; R43 HG012170/HG/NHGRI NIH HHS/United States ; R44 HG012170/HG/NHGRI NIH HHS/United States ; }, abstract = {RNA is subject to a multitude of different chemical modifications that collectively represent the epitranscriptome. Individual RNA modifications including N6-methyladenosine (m[6]A) on mRNA play essential roles in the posttranscriptional control of gene expression. Recent technological advances have enabled the transcriptome-wide mapping of certain RNA modifications, to reveal their broad relevance and characteristic distribution patterns. However, convenient methods that enable the simultaneous mapping of multiple different RNA marks within the same sample are generally lacking. Here we present EpiPlex RNA modification profiling, a bead-based proximity barcoding assay with sequencing readout that expands the scope of molecular recognition-based RNA modification detection to multiple targets, while providing relative quantification and enabling low RNA input. Measuring signal intensity against spike-in controls provides relative quantification, indicative of the RNA mod abundance at each locus. We report on changes in the modification status of HEK293T cells upon treatment with pharmacological inhibitors separately targeting METTL3, the dominant m[6]A writer enzyme, and the EIF4A3 component of the exon junction complex (EJC). The treatments resulted in decreased or increased m[6]A levels, respectively, without effect on inosine levels. Inhibiting the helicase activity of EIF4A3 and EIF4A3 knockdown both cause a significant increase of m[6]A sites near exon junctions, consistent with the previously reported role of EIF4A3 in shaping the m[6]A landscape. Thus, EpiPlex offers a reliable and convenient method for simultaneous mapping of multiple RNA modifications to facilitate epitranscriptome studies.}, }
@article {pmid39415074, year = {2025}, author = {Sojitra, M and Schmidt, EN and Lima, GM and Carpenter, EJ and McCord, KA and Atrazhev, A and Macauley, MS and Derda, R}, title = {Measuring carbohydrate recognition profile of lectins on live cells using liquid glycan array (LiGA).}, journal = {Nature protocols}, volume = {20}, number = {4}, pages = {989-1019}, pmid = {39415074}, issn = {1750-2799}, support = {RGPIN-2016-402511//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; RGPIN-2018-03815//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; CR-29//UAlberta | Canadian Glycomics Network (GlycoNet)/ ; TP-22//UAlberta | Canadian Glycomics Network (GlycoNet)/ ; R01 GM061126/GM/NIGMS NIH HHS/United States ; }, mesh = {*Polysaccharides/metabolism/chemistry/analysis ; *Lectins/metabolism/chemistry ; Humans ; Bacteriophages/genetics ; High-Throughput Nucleotide Sequencing ; *Microarray Analysis/methods ; }, abstract = {Glycans constitute a significant fraction of biomolecular diversity on cellular surfaces across all kingdoms of life. As the structure of glycans is not directly encoded by the organism's DNA, it is impossible to use high-throughput DNA technologies to study the role of cellular glycosylation or to understand how glycocalyx is recognized by glycan-binding proteins (GBPs). To address this gap, we recently described a liquid glycan array (LiGA) platform that allows profiling of glycan-GBP interactions on the surface of live cells in vitro and in vivo using next-generation sequencing. LiGA is a library of DNA-barcoded bacteriophages, where each clonal bacteriophage displays 5-1,500 copies of a glycan and the distinct DNA barcode inside each bacteriophage clone encodes the structure and density of the displayed glycans. Deep sequencing of the glycophages associated with live cells yields a glycan-binding profile of GBPs expressed on the surface of cells. This protocol provides detailed instructions for how to use LiGA to probe cell surface receptors and includes information on the preparation of glycophages, analysis by MALDI-TOF mass spectrometry, the assembly of a LiGA library and its deep sequencing. Using this protocol, we measure glycan-binding profiles of the immunomodulatory sialic acid-binding immunoglobulin-like lectins‑1, -2, -6, -7 and -9 expressed on the surface of different cell types. Compared with existing methods that require complex specialist equipment, this method allows users with basic molecular biology expertise to measure the precise glycan-binding profile of GBPs on the surface of any cell type expressing exogenous GBP within 2-3 d.}, }
@article {pmid39411212, year = {2024}, author = {Sasaki, M and Fukumoto, N and Fukumoto, S}, title = {DNA barcoding of Anoplocephala perfoliata derived from a draft horse (Ban'ei horse) in Hokkaido, Japan.}, journal = {Journal of equine science}, volume = {35}, number = {3}, pages = {43-46}, pmid = {39411212}, issn = {1340-3516}, abstract = {A two-year-old male Japanese draft horse (known as a "Ban'ei horse") excreted eight cestodes. Based on their morphological features, they were identified as Anoplocephala perfoliata. The partial mitochondrial cytochrome c oxidase subunit 1 (COI) sequences of the worms were nearly identical to A. perfoliata isolated from horses in Europe. The results of phylogenetic analyses of COI revealed that our samples and the European isolates formed the same clade, which was separate from Chinese and Australian isolates. Ban'ei horses were developed by crossbreeding draft horses imported from European countries in the 1900s. Our results suggest that A. perfoliata was transported to Hokkaido with horses from Europe. To our knowledge, this is the first report of A. perfoliata infection in a Japanese draft horse.}, }
@article {pmid39410130, year = {2024}, author = {Liu, J and Sun, J and He, R and Xia, J and He, P}, title = {The Situation of Counterfeited and Mislabeled Commercialized Edible Mushrooms in China and the Development of Possible Controls.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39410130}, issn = {2304-8158}, abstract = {Edible mushroom products, encompassing both cultivated and wild varieties, are highly favored by consumers due to their rich nutritional profiles, including significant levels of proteins and amino acids. These mushrooms have extensive applications across the food, pharmaceutical, and cosmetic industries, making the edible mushroom industry a vital component of global poverty alleviation efforts. Taking China as an example, the country produces over 45 million tons of edible mushrooms annually, accounting for 94.01% of the world's total production, thereby establishing itself as the leading global producer of edible mushrooms. However, alongside the rapid expansion of this industry, concerns have emerged regarding counterfeit products and incidents of poisoning resulting from the consumption of toxic wild mushrooms. As follows, to advance the development and integrity of the mushroom production and processing industry: (1) This study presents the situation of counterfeit edible mushrooms and elucidates the factors contributing to the production of fraudulent products from both subjective and non-subjective perspectives. (2) We provide a detailed introduction to 22 varieties of freshly cultivated edible mushrooms and commonly encountered wild edible mushrooms in the Chinese consumer market, proposing the application of DNA barcoding, environmental DNA analysis, and other technologies for the future authentication of counterfeit mushroom products. (3) Concurrently, we present an overview of mushroom poisoning incidents in China from 2010 to 2023, emphasizing the challenges in mitigating the risks associated with wild mushroom consumption and preventing food poisoning, thereby necessitating heightened consumer caution. (4) Finally, we offer four recommendations aimed at ensuring the healthy, stable, and sustainable growth of the edible mushroom industry.}, }
@article {pmid39409790, year = {2024}, author = {Altvater-Hughes, TE and Hodgins, HP and Hodgins, DC and Bauman, CA and Paibomesai, MA and Mallard, BA}, title = {Investigating the IgM and IgG B Cell Receptor Repertoires and Expression of Ultralong Complementarity Determining Region 3 in Colostrum and Blood from Holstein-Friesian Cows at Calving.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409790}, issn = {2076-2615}, support = {RGPIN04638//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {In cattle, colostral maternal immunoglobulins and lymphocytes transfer across the neonate's intestinal epithelium to provide protection against pathogens. This study aimed to compare repertoires of B cell populations in blood and colostrum in cows for the first time, with an emphasis on ultralong complementarity determining region 3 (CDR3, ≥40 amino acids). Blood mononuclear cells (BMCs, n= 7) and colostral cells (n = 7) were isolated from Holstein-Friesian dairy cows. Magnetic-activated cell sorting was used to capture IgM and IgG B cells from BMCs. Colostral cells were harvested by centrifugation. RNA was extracted and cDNA was produced; IgM and IgG transcripts were amplified using polymerase chain reactions. Amplicons were sequenced using the Nanopore Native barcoding kit 24 V14 and MinION with R10.4 flow cells. In colostrum, there was a significantly greater percentage of IgM B cells with ultralong CDR3s (8.09% ± 1.73 standard error of the mean) compared to blood (4.22% ± 0.70, p = 0.05). There was a significantly greater percentage of IgG B cells in colostrum with ultralong CDR3s (12.98% ± 1.98) compared to blood (6.61% ± 1.11, p = 0.05). A higher percentage of IgM and IgG B cells with ultralong CDR3s in colostrum may be indicative of a potential role in protecting the neonate.}, }
@article {pmid39409782, year = {2024}, author = {Dinh-Hung, N and Mwamburi, SM and Dong, HT and Rodkhum, C and Meemetta, W and Linh, NV and Mai, HN and Dhar, AK and Hirono, I and Senapin, S and Chatchaiphan, S}, title = {Unveiling Insights into the Whole Genome Sequencing of Mycobacterium spp. Isolated from Siamese Fighting Fish (Betta splendens).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409782}, issn = {2076-2615}, abstract = {This study aims to genomically elucidate six isolates of rapidly growing non-tuberculous mycobacteria (RGM) derived from Siamese fighting fish (Betta splendens). These isolates had previously undergone phenotypic and biochemical characterization, antibiotic susceptibility testing, and in vivo virulence assessment. Initial DNA barcoding using the 16S rRNA sequence assigned these six isolates to five different species, namely Mycobacterium chelonae (BN1983), M. cosmeticum (BN1984 and N041), M. farcinogenes (SNSK5), M. mucogenicum (BN1956), and M. senegalense (BN1985). However, the identification relied solely on the highest percent identity of the 16S rRNA gene, raising concerns about the taxonomic ambiguity of these species. Comprehensive whole genome sequencing (WGS) and extended genomic comparisons using multilocus sequence typing (MLST), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) led to the reclassification of BN1985 and SNSK5 as M. conceptionense while confirming BN1983 as M. chelonae and BN1984 and N041 as M. cosmeticum. Notably, the analysis of the BN1956 isolate revealed a potential new species that is proposed here as M. mucogenicum subsp. phocaicum sp. nov. Common genes encoding "mycobacterial" virulence proteins, such as PE and PPE family proteins, MCE, and YrbE proteins, were detected in all six isolates. Two species, namely M. chelonae and M. cosmeticum, appear to have horizontally acquired T6SS-II (clpB), catalase (katA), GroEL (groel), and capsule (rmlb) from distantly related environmental bacteria such as Klebsiella sp., Neisseria sp., Clostridium sp., and Streptococcus sp. This study provides the first draft genome sequence of RGM isolates currently circulating in B. splendens and underscores the necessity of WGS for the identification and classification of mycobacterial species.}, }
@article {pmid39409767, year = {2024}, author = {Mezzasalma, M and Odierna, G and Macirella, R and Brunelli, E}, title = {New Insights on Chromosome Diversification in Malagasy Chameleons.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {19}, pages = {}, pmid = {39409767}, issn = {2076-2615}, abstract = {In this work, we performed a preliminary molecular analysis and a comparative cytogenetic study on 5 different species of Malagasy chameleons of the genus Brookesia (B. superciliaris) and Furcifer (F. balteautus, F. petteri, F. major and F. minor). A DNA barcoding analysis was first carried out on the study samples using a fragment of the mitochondrial gene coding for the cytochrome oxidase subunit 1 (COI) in order to assess the taxonomic identity of the available biological material. Subsequently, we performed on the studied individuals a chromosome analysis with standard karyotyping (5% Giemsa solution at pH 7) and sequential C-banding + Giemsa, + CMA3, and + DAPI. The results obtained indicate that the studied species are characterized by a different chromosome number and a variable heterochromatin content and distribution, with or without differentiated sex chromosomes. In particular, B. superciliaris (2n = 36) and F. balteatus (2n = 34) showed a similar karyotype with 6 macro- and 12-11 microchromosome pairs, without differentiated sex chromosomes. In turn, F. petteri, F. major, and F. minor showed a karyotype with a reduced chromosome number (2n = 22-24) and a differentiated sex chromosome system with female heterogamety (ZZ/ZW). Adding our newly generated data to those available from the literature, we highlight that the remarkable chromosomal diversification of the genus Furcifer was likely driven by non-homologous chromosome fusions, including autosome-autosome, Z-autosome, and W-autosome fusions. The results of this process resulted in a progressive reduction in the chromosome number and partially homologous sex chromosomes of different shapes and sizes.}, }
@article {pmid39409561, year = {2024}, author = {Mehmood, F and Li, M and Bertolli, A and Prosser, F and Varotto, C}, title = {Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {19}, pages = {}, pmid = {39409561}, issn = {2223-7747}, support = {CN00000033, CUPD43C22001280006//European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1034 17/06/2022/ ; }, abstract = {Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species' adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products.}, }
@article {pmid39406839, year = {2024}, author = {Shen, Y and Zhou, X and Zhang, Y and Zhang, J and Li, Q and Chen, Q and Liu, Z and Li, Y and Cheng, R and Luo, Y}, title = {Important fish diversity maintenance status of the tributaries in a hotspot fish conservation area in the upper Yangtze River revealed by eDNA metabarcoding.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24128}, pmid = {39406839}, issn = {2045-2322}, support = {No. 32202939//National Natural Science Foundation of China/ ; No. CSTB2022NSCQ-MSX0793//Natural Science Foundation of Chongqing, China/ ; }, mesh = {Animals ; *Rivers ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; China ; DNA, Environmental/genetics/analysis ; Conservation of Natural Resources ; Ecosystem ; Seasons ; }, abstract = {This study employed Environmental DNA (eDNA) barcoding technology to delve into the influence of the tributaries and mainstem on fish diversity and spatiotemporal distribution in a hotspot fish conservation area in the upper Yangtze River. A total of 123 fish species were detected, belonging to 7 orders, 19 families, and 77 genera. The composition of fish species in tributaries is similar to that in mainstem, with higher fish community diversity in tributaries during the spring and summer. Exploration of fish ecotypes revealed significant differences between mainstem and tributaries. The fish community is mainly influenced by key environmental factors such as water temperature, dissolved oxygen, electrical conductivity, and ammonia nitrogen, with a higher impact of these factors on tributaries than on mainstem. In conclusion, while tributaries and mainstem in the Jiangjin section exhibit similarities in fish community composition, there are notable differences in community structure and diversity. Therefore, the protection of not only mainstem but also tributaries and their associated fish habitats is crucial for promoting the overall health and sustainability.}, }
@article {pmid39406030, year = {2025}, author = {Hymus, CM and Cooper, PL and Rye, MS}, title = {Demonstration of potential DNA contamination introduced by laboratory consumables using Fluorescein.}, journal = {Forensic science international. Genetics}, volume = {74}, number = {}, pages = {103157}, doi = {10.1016/j.fsigen.2024.103157}, pmid = {39406030}, issn = {1878-0326}, mesh = {Humans ; *DNA Contamination ; *Fluorescein ; DNA Fingerprinting ; Fluorescent Dyes ; DNA/analysis/genetics ; Polymerase Chain Reaction ; Specimen Handling/instrumentation ; }, abstract = {The development of increasingly efficient DNA extraction and profiling kits has increased the amount of allelic information obtained from trace DNA samples, but also inadvertently, increased the detection of DNA contamination. This study aimed to evaluate the potential of DNA transfer using fluorescein, fluorescent under an alternate light source, in the use of a range of forensically relevant DNA profiling consumables. An evaluation of two pre-lysis methods adopting three different sample tubes, some with deliberate seal damage, showed the PrepFiler™ Automated Forensic DNA Extraction Kit caused leakage and crusting when the rim of the PrepFiler™ LySep column was compromised, but no leakage was observed under the same conditions using the Investigator STAR Lyse&amp;Prep kit. The AutoLys tube showed minimal leakage using the PrepFiler™ chemistry. A DNA extract tube with an external thread, similar to the AutoLys tube, showed no leakage after fridge or freezer storage. However, it highlighted that a centrifugal spin does not guarantee all the DNA will pool at the base of the tube. A comparison of adhesive plate sealing films to 8-well strip caps for sealing 96-well PCR plates showed the adhesive plate sealing films presented a lower risk of DNA transfer, largely due to the adhesion of dispersed liquid on the sticky surface of the film. Overall, this study highlighted a number of variables that may be considered in the development of more refined contamination minimisation protocols in respect to increased sensitivities of DNA profiling.}, }
@article {pmid39405910, year = {2024}, author = {Popović, L and Brankatschk, B and Palladino, G and Rossner, MJ and Wehr, MC}, title = {Polypharmacological profiling across protein target families and cellular pathways using the multiplexed cell-based assay platform safetyProfiler reveals efficacy, potency and side effects of drugs.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {180}, number = {}, pages = {117523}, doi = {10.1016/j.biopha.2024.117523}, pmid = {39405910}, issn = {1950-6007}, mesh = {Humans ; *Polypharmacology ; HEK293 Cells ; Signal Transduction/drug effects ; Receptors, G-Protein-Coupled/metabolism/drug effects ; }, abstract = {Selectivity profiling is key for assessing the pharmacological properties of multi-target drugs. We have developed a cell-based and barcoded assay encompassing ten druggable targets, including G protein-coupled receptors (GPCRs), receptor tyrosine kinases (RTKs), nuclear receptors, a protease as well as their key downstream pathways and profiled 17 drugs in living cells for efficacy, potency, and side effects. Notably, this multiplex assay, termed safetyProfiler assay, enabled the simultaneous assessment of multiple target and pathway activities, shedding light on the polypharmacological profile of compounds. For example, the neuroleptics clozapine, paliperidone, and risperidone potently inhibited primary targets DRD2 and HTR2A as well as cAMP and calcium pathways. However, while paliperidone and risperidone also potently inhibited the secondary target ADRA1A and mitogen-activated protein kinase (MAPK) downstream pathways, clozapine only exhibited mild antagonistic effects on ADRA1A and lacked MAPK inhibition downstream of DRD2 and HTR2A. Furthermore, we present data on the selectivity for bazedoxifene, an estrogen receptor antagonist currently undergoing clinical phase 2 trials for breast cancer, on MAPK signaling. Additionally, precise potency data for LY2452473, an androgen receptor antagonist, that completed a phase 2 clinical trial for prostate cancer, are presented. The non-selective kinase inhibitor staurosporine was observed to potently inactivate the two RTKs EGFR and ERBB4 as well as MAPK signaling, while eliciting stress-related cAMP responses. Our findings underscore the value of comprehensive profiling in elucidating the pharmacological properties of established and novel therapeutics, thereby facilitating the development of novel multi-target drugs with enhanced efficacy and selectivity.}, }
@article {pmid39403482, year = {2024}, author = {Zhou, QR and Ma, YY and Lv, HQ and Lu, ZC and Wang, LS and Liang, JS and Li, JJ}, title = {Chloroplast mini-barcodes combined with high resolution melting analysis to identify herbal medicine Difengpi (Illicium difengpi).}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38700}, pmid = {39403482}, issn = {2405-8440}, abstract = {Difengpi, derived from the air-dried stem bark of Illicium difengpi and enlisted in the Chinese Pharmacopoeia for its therapeutic effect against common ailments, confronts challenges due to dwindling wild resources and intentional substitution with potentially harmful botanical relatives. The imperative need to authenticate this herbal remedy has led to the development of robust methods. Here, we integrated chloroplast mini-barcoding and high resolution melting (HRM) analysis to distinguish Difengpi from the reported adulterants. We assembled the complete chloroplast (cp) genomes of I. difengpi and substituted close relatives I. jiadifengpi and I. majus, and conducted an in-depth comparative analysis to screen divergent regions for exploiting as DNA mini-barcodes. Despite the conservativeness characterizing the whole cp genomes among these Illicium species, we identified some highly variable regions with promising potential as molecular markers for species identification. Subsequently, we designed DNA mini-barcodes and subjected them to HRM analysis to assess their efficacy in species discrimination. Melting profiles unveiled that mini-barcodes designed from four divergence regions trnL-trnF, trnF-ndhJ, ycf1-ndhF and rpl32-trnL exhibited substantial discriminatory power, distinctly differentiated I. difengpi from I. jiadifengpi, I. majus and I. verum. We tested ten commercially available Difengpi products from online stores and local traditional markets using these four mini-barcodes. All ten samples clustered closely with the reference I. difengpi with genotype confidence higher than 93 %, indicating the presence of the claimed species in these samples, sans any reported toxic adulterants. Consequently, we simulated Difengpi mimic samples utilizing I. jiadifengpi, I. majus and I. verum and subjected them to evaluate the practicability of these mini-barcodes. The outcomes confirmed the precision of the four mini-barcodes in accurately discerning the mimic samples. In conclusion, integrating taxon-specific DNA mini-barcodes with HRM analysis is an efficient strategy for the authentication of species identity within commercial herbal products.}, }
@article {pmid39402626, year = {2024}, author = {Liu, Y and Li, N and Qi, J and Xu, G and Zhao, J and Wang, N and Huang, X and Jiang, W and Wei, H and Justet, A and Adams, TS and Homer, R and Amei, A and Rosas, IO and Kaminski, N and Wang, Z and Yan, X}, title = {SDePER: a hybrid machine learning and regression method for cell-type deconvolution of spatial barcoding-based transcriptomic data.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {271}, pmid = {39402626}, issn = {1474-760X}, support = {R21 LM012884/LM/NLM NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 LM014087/LM/NLM NIH HHS/United States ; R21LM012884//Foundation for the National Institutes of Health/ ; DMS1916246//National Science Foundation/ ; R01LM014087//Foundation for the National Institutes of Health/ ; }, mesh = {*Machine Learning ; *Single-Cell Analysis/methods ; *Transcriptome ; Humans ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; Software ; Animals ; Regression Analysis ; RNA-Seq/methods ; }, abstract = {Spatial barcoding-based transcriptomic (ST) data require deconvolution for cellular-level downstream analysis. Here we present SDePER, a hybrid machine learning and regression method to deconvolve ST data using reference single-cell RNA sequencing (scRNA-seq) data. SDePER tackles platform effects between ST and scRNA-seq data, ensuring a linear relationship between them while addressing sparsity and spatial correlations in cell types across capture spots. SDePER estimates cell-type proportions, enabling enhanced resolution tissue mapping by imputing cell-type compositions and gene expressions at unmeasured locations. Applications to simulated data and four real datasets showed SDePER's superior accuracy and robustness over existing methods.}, }
@article {pmid39400321, year = {2025}, author = {Castellanos-Labarcena, J and Steinke, D and Adamowicz, SJ}, title = {Anomalous latitudinal gradients in parasitoid wasp diversity-Hotspots in regions with larger temperature range.}, journal = {The Journal of animal ecology}, volume = {94}, number = {3}, pages = {410-422}, pmid = {39400321}, issn = {1365-2656}, support = {//Arrell Food Institute/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Genome Canada/ ; //Ontario Ministry of Economic Development, Job Creation and Trade/ ; //Canada First Research Excellence Fund/ ; }, mesh = {Animals ; *Wasps/genetics/physiology ; *Biodiversity ; Temperature ; *Genetic Variation ; DNA, Mitochondrial/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones. Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra- and interspecific diversity, and a positive effect of the temperature range. Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients.}, }
@article {pmid39395971, year = {2024}, author = {Li, Z and Ran, Z and Xiao, X and Yan, C and Xu, J and Tang, M and An, M}, title = {Comparative analysis of the whole mitochondrial genomes of four species in sect. Chrysantha (Camellia L.), endemic taxa in China.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {955}, pmid = {39395971}, issn = {1471-2229}, support = {2022&#xff08;072&#xff09;//Guizhou Provincial Basic Research Program (Natural Science)/ ; 32360101//National Natural Science Foundation of China/ ; 31960043//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial ; China ; *Camellia/genetics ; Phylogeny ; RNA Editing ; Genome, Plant ; Base Composition ; }, abstract = {BACKGROUND: The sect. Chrysantha Chang of plants with yellow flowers of Camellia species as the "Queen of the Tea Family", most of these species are narrowly distributed endemics of China and are currently listed Grde-II in National Key Protected Wild Plant of China. They are commercially important plants with horticultural medicinal and scientific research value. However, the study of the sect. Chrysantha species genetics are still in its infancy, to date, the mitochondrial genome in sect. Chrysantha has been still unexplored.<br><br>RESULTS: In this study, we provide a comprehensive assembly and annotation of the mitochondrial genomes for four species within the sect. Chrysantha. The results showed that the mitochondrial genomes were composed of closed-loop DNA molecules with sizes ranging from 850,836&#xa0;bp (C. nitidissima) to 1,098,121&#xa0;bp (C. tianeensis) with GC content of 45.71-45.78% and contained 48-58 genes, including 28-37 protein-coding genes, 17-20 tRNA genes and 2 rRNA genes. We also examined codon usage, sequence repeats, RNA editing and selective pressure in the four species. Then, we performed a comprehensive comparison of their basic structures, GC contents, codon preferences, repetitive sequences, RNA editing sites, Ka/Ks ratios, haplotypes, and RNA editing sites. The results showed that these plants differ little in gene type and number. C. nitidissima has the greatest variety of genes, while C. tianeensis has the greatest loss of genes. The Ka/Ks values of the atp6 gene in all four plants were greater than 1, indicating positive selection. And the codons ending in A and T were highly used. In addition, the RNA editing sites differed greatly in number, type, location, and efficiency. Twelve, six, five, and twelve horizontal gene transfer (HGT) fragments were found in C. tianeensis, Camellia huana, Camellia liberofilamenta, and C. nitidissima, respectively. The phylogenetic tree clusters the four species of sect. Chrysantha plants into one group, and C. huana and C. liberofilamenta have closer affinities.<br><br>CONCLUSIONS: In this study, the mitochondrial genomes of four sect. Chrysantha plants were assembled and annotated, and these results contribute to the development of new genetic markers, DNA barcode databases, genetic improvement and breeding, and provide important references for scientific research, population genetics, and kinship identification of sect. Chrysantha plants.}, }
@article {pmid39387679, year = {2025}, author = {Hebert, PDN and Floyd, R and Jafarpour, S and Prosser, SWJ}, title = {Barcode 100K Specimens: In a Single Nanopore Run.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14028}, pmid = {39387679}, issn = {1755-0998}, support = {OGI-208//Genome Canada/ ; OGI-233//Ontario Genomics/ ; //Canada Foundation for Innovation/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Nanopores ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; }, abstract = {It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow.}, }
@article {pmid39394065, year = {2024}, author = {Kan, S and Su, X and Yang, L and Zhou, H and Qian, M and Zhang, W and Li, C}, title = {From light into shadow: comparative plastomes in Petrocosmea and implications for low light adaptation.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {949}, pmid = {39394065}, issn = {1471-2229}, support = {32200187//National Natural Science Foundation of China/ ; 82173936//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Plastid ; *Phylogeny ; Light ; Plastids/genetics ; Adaptation, Physiological/genetics ; }, abstract = {BACKGROUND: Plastids originated from an ancient endosymbiotic event and evolved into the photosynthetic organelles in plant cells. They absorb light energy and carbon dioxide, converting them into chemical energy and oxygen, which are crucial for plant development and adaptation. However, little is known about the plastid genome to light adaptation. Petrocosmea, a member of the Gesneriaceae family, comprises approximately 70 species with diverse light environment, serve as an ideal subject for studying plastomes adapt to light.<br><br>RESULTS: In this study, we selected ten representative species of Petrocosmea from diverse light environments, assembled their plastid genomes, and conducted a comparative genomic analysis. We found that the plastid genome of Petrocosmea is highly conserved in both structure and gene content. The phylogenetic relationships reconstructed based on the plastid genes were divided into five clades, which is consistent with the results of previous studies. The vast majority of plastid protein-coding genes were under purifying selection, with only the rps8 and rps16 genes identified under positive selection in different light environments. Notably, significant differences of evolutionary rate were observed in NADH dehydrogenase, ATPase ribosome, and RNA polymerase between Clade A and the other clades. Additionally, we identified ycf1 and several intergenic regions (trnH-psbA, trnK-rps16, rpoB-trnC, petA-psbJ, ccsA-trnL, rps16-trnQ, and trnS-trnG) as candidate barcodes for this emerging ornamental horticulture.<br><br>CONCLUSION: We newly assembled ten plastid genomes of Petrocosmea and identified several hypervariable regions, providing genetic resources and candidate markers for this promising emerging ornamental horticulture. Furthermore, our study suggested that rps8 and rps16 were under positive selection and that the evolutionary patterns of NADH dehydrogenase, ATPase ribosome, and RNA polymerase were related to the diversity light environment in Petrocosmea. This revealed an evolutionary scenario for light adaptation of the plastid genome in plants.}, }
@article {pmid39391540, year = {2024}, author = {Selnekovič, D and Kodada, J and Gülperçin, N and Tezcan, S and Ruzzier, E}, title = {Morphological and molecular characterisation of Mordellistenapeloponnesensis Batten, 1980 (Coleoptera, Mordellidae), with first records from Italy and Turkey.}, journal = {ZooKeys}, volume = {1214}, number = {}, pages = {105-117}, pmid = {39391540}, issn = {1313-2989}, abstract = {Mordellistenapeloponnesensis Batten, 1980, previously known from Cyprus and Greece, is reported from Italy and Turkey for the first time. The species is redescribed based on type specimens and additional material from its entire known distributional range. Eighteen DNA barcoding sequences of M.peloponnesensis from Greece, Cyprus, and Italy were generated, and genetic variability across the sampling localities was examined. Three mitochondrial haplotypes were detected within M.peloponnesensis. Specimens from mainland Italy share the same haplotype as those from Rhodes and Cyprus, whereas Sardinian specimens exhibit a distinct haplotype. The third haplotype is represented by one specimen from Cyprus. The DNA barcoding sequences of M.peloponnesensis were compared with those of the morphologically allied M.gemellata Schilsky, 1898, and M.pyrenaea Ermisch, 1966, to reveal the phylogenetic relationships between the species.}, }
@article {pmid39388461, year = {2024}, author = {Martoni, F and Rako, L and Jaroslow, D and Selleck, C and Kant, P and Nancarrow, N and Blacket, MJ}, title = {Diversity and composition of the bacterial communities associated with the Australian spittlebugs Bathyllus albicinctus and Philagra parva (Hemiptera: Aphrophoridae).}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0311938}, pmid = {39388461}, issn = {1932-6203}, mesh = {Animals ; *Hemiptera/microbiology ; Australia ; Xylella/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Microbiota ; Nymph/microbiology ; Plant Diseases/microbiology/parasitology ; Insect Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Spittlebugs and froghoppers (Hemiptera: Cercopoidea) are insects feeding on xylem, which potentially can cause significant economic damage worldwide by transmitting plant pathogenic bacteria such as Xylella fastidiosa. Australia and New Zealand are currently free from X. fastidiosa, but they are home to at least 45 native spittlebug species. Among these, the Australian natives Bathyllus albicinctus (Erichson, 1842) and Philagra parva (Donovan, 1805) are particularly widespread and can be found across southern and eastern Australia, with B. albicinctus also in New Zealand. The potential that both species might be capable of vectoring Xylella fastidiosa poses a substantial biosecurity risk if the bacterium were to invade these regions. In this study, we examined 87 spittlebug nymphs collected across 12 different host plant species, in five locations in Victoria, Australia. Our objective was to explore the factors influencing bacterial communities within and between these widespread spittlebug species, considering geographic location, insect phylogenetics, and host plant associations. We employed COI barcoding to assess insect genetic variation and 16S high throughput sequencing (HTS) metabarcoding to analyse bacterial microbiome diversity across various host plants. Our findings revealed minimal genetic divergence among spittlebug individuals in the same species, highlighting conspecificity despite conspicuous morphological divergences. On the other hand, we recorded significant variation in bacterial communities harboured by Bathyllus albicinctus nymphs feeding on different plants, even when these were collected within close proximity to each other. Therefore, host plant association appeared to shape the bacterial communities of spittlebugs more than insect genetic divergence or geographical location. These diverse bacterial communities could potentially facilitate transmission of plant pathogenic bacteria, underscoring the risk of widespread transmission among numerous plant hosts through insect-plant interactions. This study emphasizes the critical need to understand these complex interactions, particularly in the context of biosecurity.}, }
@article {pmid39386966, year = {2024}, author = {Twyford, AD and Beasley, J and Barnes, I and Allen, H and Azzopardi, F and Bell, D and Blaxter, ML and Broad, G and Campos-Dominguez, L and Choonea, D and Crowley, L and Cuber, P and Cunliffe, M and Dombrowski, A and Douglas, B and Forrest, LL and Gaya, E and Greeves, C and Griffin, C and Harley, J and Hart, ML and Holland, PWH and Hollingsworth, PM and Januszczak, I and Jones, A and Kersey, P and Kilias, E and Lawniczak, MKN and Lewis, OT and Mian, S and Minotto, A and Misra, R and Mulhair, PO and Pereira da Conceicoa, L and Price, BW and Salatino, S and Shaw, F and Sivell, O and Sivess, L and Uhl, R and Woof, K and , }, title = {A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {339}, pmid = {39386966}, issn = {2398-502X}, abstract = {Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.}, }
@article {pmid39386620, year = {2024}, author = {Mays, JC and Mei, S and Kogenaru, M and Quysbertf, HM and Bosco, N and Zhao, X and Bianchi, JJ and Goldberg, A and Kidiyoor, GR and Holt, LJ and Fenyö, D and Davoli, T}, title = {KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386620}, issn = {2692-8205}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 HG012590/HG/NHGRI NIH HHS/United States ; R37 CA240765/CA/NCI NIH HHS/United States ; R01 DK135089/DK/NIDDK NIH HHS/United States ; R37 CA248631/CA/NCI NIH HHS/United States ; }, abstract = {Investigating chromosomal instability and aneuploidy within tumors is essential for understanding tumorigenesis and developing diagnostic and therapeutic strategies. Single-cell DNA sequencing technologies have enabled such analyses, revealing aneuploidies specific to individual cells within the same tumor. However, it has been difficult to scale the throughput of these methods to detect rare aneuploidies while maintaining high sensitivity. To overcome this deficit, we developed KaryoTap, a method combining custom targeted DNA sequencing panels for the Tapestri platform with a computational framework to enable detection of chromosome- and chromosome arm-scale aneuploidy (gains or losses) and copy number neutral loss of heterozygosity in all human chromosomes across thousands of single cells simultaneously. KaryoTap allows detecting gains and losses with an average accuracy of 83% for arm events and 91% for chromosome events. Importantly, together with chromosomal copy number, our system allows us to detect barcodes and gRNAs integrated into the cells' genome, thus enabling pooled CRISPR- or ORF-based functional screens in single cells. As a proof of principle, we performed a small screen to expand the chromosomes that can be targeted by our recently described CRISPR-based KaryoCreate system for engineering aneuploidy in human cells. KaryoTap will prove a powerful and flexible approach for the study of aneuploidy and chromosomal instability in both tumors and normal tissues.}, }
@article {pmid39386543, year = {2024}, author = {Vong, KI and Alvarez, YD and Noel, G and Barton, ST and Chung, C and Howarth, R and Meave, N and Zhang, Q and Jiwani, F and Barrows, C and Patel, A and Wang, JX and Chi, N and Kingsmore, SF and White, MD and Yang, X and Gleeson, JG}, title = {Genomic mosaicism reveals developmental organization of trunk neural crest-derived ganglia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39386543}, issn = {2692-8205}, support = {U01 MH108898/MH/NIMH NIH HHS/United States ; R01 MH124890/MH/NIMH NIH HHS/United States ; P01 HD104436/HD/NICHD NIH HHS/United States ; K99 HD111686/HD/NICHD NIH HHS/United States ; R21 MH134401/MH/NIMH NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; S10 OD021644/OD/NIH HHS/United States ; }, abstract = {The neural crest generates numerous cell types, but conflicting results leave developmental origins unresolved. Here using somatic mosaic variants as cellular barcodes, we infer embryonic clonal dynamics of trunk neural crest, focusing on the sensory and sympathetic ganglia. From three independent adult neurotypical human donors, we identified 1,278 mosaic variants using deep whole-genome sequencing, then profiled allelic fractions in 187 anatomically dissected ganglia. We found a massive rostrocaudal spread of progenitor clones specific to sensory or sympathetic ganglia, which unlike in the brain, showed robust bilateral distributions. Computational modeling suggested neural crest progenitor fate specification preceded delamination from neural tube. Single-cell multiomic analysis suggested both neurons and glia contributed to the rostrocaudal clonal organization. CRISPR barcoding in mice and live imaging in quail embryos confirmed these clonal dynamics across multiple somite levels. Our findings reveal an evolutionarily conserved clonal spread of cells populating peripheral neural ganglia.}, }
@article {pmid39386478, year = {2024}, author = {Vaidya, K and Regan, MS and Lin, J and Houle, J and Stopka, SA and Agar, NYR and Hammond, PT and Boehnke, N}, title = {Pooled nanoparticle screening using a chemical barcoding approach.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.24.614746}, pmid = {39386478}, issn = {2692-8205}, support = {K99 CA255844/CA/NCI NIH HHS/United States ; P41 EB028741/EB/NIBIB NIH HHS/United States ; }, abstract = {We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.}, }
@article {pmid39386005, year = {2024}, author = {Lin, X and Waring, K and Ghezzi, H and Tropini, C and Tyson, J and Ziels, RM}, title = {High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the Nanopore platform.}, journal = {PNAS nexus}, volume = {3}, number = {10}, pages = {pgae411}, pmid = {39386005}, issn = {2752-6542}, abstract = {Small subunit (SSU) ribosomal RNA (rRNA) gene amplicon sequencing is a foundational method in microbial ecology. Currently, short-read platforms are commonly employed for high-throughput applications of SSU rRNA amplicon sequencing, but at the cost of poor taxonomic classification due to limited fragment lengths. The Oxford Nanopore Technologies (ONT) platform can sequence full-length SSU rRNA genes, but its lower raw-read accuracy has so-far limited accurate taxonomic classification and de novo feature generation. Here, we present a sequencing workflow, termed ssUMI, that combines unique molecular identifier (UMI)-based error correction with newer (R10.4+) ONT chemistry and sample barcoding to enable high throughput near full-length SSU rRNA (e.g. 16S rRNA) amplicon sequencing. The ssUMI workflow generated near full-length 16S rRNA consensus sequences with 99.99% mean accuracy using a minimum subread coverage of 3×, surpassing the accuracy of Illumina short reads. The consensus sequences generated with ssUMI were used to produce error-free de novo sequence features with no false positives with two microbial community standards. In contrast, Nanopore raw reads produced erroneous de novo sequence features, indicating that UMI-based error correction is currently necessary for high-accuracy microbial profiling with R10.4+ ONT sequencing chemistries. We showcase the cost-competitive scalability of the ssUMI workflow by sequencing 87 time-series wastewater samples and 27 human gut samples, obtaining quantitative ecological insights that were missed by short-read amplicon sequencing. ssUMI, therefore, enables accurate and low-cost full-length 16S rRNA amplicon sequencing on Nanopore, improving accessibility to high-resolution microbiome science.}, }
@article {pmid39385931, year = {2024}, author = {Da Silva, C and Mannise, N and Seguí, R and Iriarte, A and Bou, N and Bonifacino, JM and Mailhos, A and Anza, L and Chitaro, S and Ocampo, F and Gándaras, R and Arezo, F and Capurro, L and Iturburu, M and Nieto, N and Juan, H and Garrido, J and Platero, R and Gago, J and Lezama, F and Do Carmo, M and Cosse, M}, title = {Exploring biodiversity of Uruguayan vascular plants through DNA barcoding.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1435592}, pmid = {39385931}, issn = {1664-8021}, }
@article {pmid39385841, year = {2024}, author = {Siedlecki, I and Kochanowski, M and Pawłowska, J and Reszotnik, G and Okrasińska, A and Wrzosek, M}, title = {Ant's Nest as a microenvironment: Distinct Mucoromycota (Fungi) community of the red wood ants' (Formica polyctena) mounds.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70333}, pmid = {39385841}, issn = {2045-7758}, abstract = {Many social insect species build nests, which differ from the surrounding environment and are often occupied by specific organismal communities. These organisms may interact mutualistically or parasitically with the nest-builders, or simply co-occur, being able to survive in these microenvironments. In temperate forests, red wood ants (e.g. Formica polyctena) are known to create distinct, highly developed nests, which consist of large, above-ground mounds, built primarily out of plant matter collected from the forest litter. The microorganismal communities of such mounds remain understudied. As representatives of Mucoromycota fungi commonly engage in the decomposition process of the forest litter, they would be expected to occur in the mounds. However, it is still not known whether the Mucoromycota community of these ants' nests differ from the one of the surrounding forest litter. In order to distinguish mound-associated taxa, we characterized Mucoromycota communities of Formica polyctena mounds and the surrounding forest litter. We sampled four sites, twice in a season. Sampled material was plated on agar media and emerging Mucoromycota colonies were identified based on their morphology. Fungal identification was further confirmed using DNA barcoding. In order to compare described communities, PERMANOVA test and non-metric multidimensional scaling ordinations were used. To distinguish taxa associated with the mounds, multilevel pattern analysis was performed. Our results show that the Mucoromycota community of Formica polyctena's mound differs from the community of the surrounding forest litter. While representatives of Entomortierella lignicola and Absidia cylindrospora clade were found to be associated with the mound environment, representatives of Umbelopsis curvata and Podila verticillata-humilis clade were associated with forest litter, and were rarely present in the mounds. Our findings strongly suggest that the red wood ants' nest is a specific microenvironment in the temperate forest floor, which is a preferred microhabitat for the mound-associated Mucoromycota, possibly adapted to live in proximity to ants.}, }
@article {pmid39385531, year = {2025}, author = {Nirchio, M and Oliveira, C and de Bello Cioffi, M and Sassi, FMC and Rizzi, FP and Benavides, SWN and Berrones, AJC and Romero, JFR and Deon, GA and Kuranaka, M and Valdiviezo-Rivera, JS and Carrión Olmedo, JC and Rossi, AR}, title = {Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae).}, journal = {Journal of fish biology}, volume = {106}, number = {2}, pages = {292-304}, doi = {10.1111/jfb.15924}, pmid = {39385531}, issn = {1095-8649}, support = {2020/UTMACH-GPR-155//Universidad T&#xe9;cnica de Machala/ ; DI-CONV-2017-009//Universidad Central del Ecuador/ ; 2020/13433-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/00955-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2023/08116-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; proc. 306054/2006-0//Consejo de Desarrollo Cient&#xed;fico, Human&#xed;stico, Tecnol&#xf3;gico y de las Artes, Universidad de Los Andes Venezuela/ ; 441128/2020-3//Consejo de Desarrollo Cient&#xed;fico, Human&#xed;stico, Tecnol&#xf3;gico y de las Artes, Universidad de Los Andes Venezuela/ ; RP12117A6764463C//Sapienza Universit&#xe0; di Roma/ ; }, mesh = {Animals ; *Catfishes/genetics/anatomy &amp; histology/classification ; Phylogeny ; Ecuador ; Male ; Female ; Karyotype ; Electron Transport Complex IV/genetics ; Cytogenetic Analysis ; Karyotyping ; }, abstract = {Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.}, }
@article {pmid39384703, year = {2024}, author = {Araújo, KS and Alves, JL and Pereira, OL and de Queiroz, MV}, title = {Five new species of endophytic Penicillium from rubber trees in the Brazilian Amazon.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {4}, pages = {3051-3074}, pmid = {39384703}, issn = {1678-4405}, support = {Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {*Hevea/microbiology ; *Penicillium/classification/genetics/isolation &amp; purification ; Brazil ; Phylogeny ; *Endophytes/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; Tubulin/genetics ; RNA Polymerase II/genetics ; Calmodulin/genetics ; }, abstract = {The Amazon rainforest is the world's most diverse ecosystem, full of fauna and flora. Among the trees that make up the forest are the rubber trees of the genus Hevea (H. brasiliensis and H. guianensis), which stand out for the industrial use of latex. It was previously shown that endophytic fungi colonize the leaves, stems, and roots of Hevea spp. In this study, 47 Penicillium spp. and three Talaromyces spp. isolates were analyzed using specific DNA barcodes: internal transcribed spacers region (ITS), β-tubulin (BenA), calmodulin (CaM), and the DNA-dependent RNA polymerase II second largest subunit (RPB2) genes and additionally, for species delimitation, the genealogical concordance phylogenetic species recognition (GCPSR) criteria were applied. The phylogenetic analyses placed the Penicillium isolates into four sections Lanata-Divaricata, Sclerotiora, Citrina, and Fasciculata. The morphological and molecular characteristics resulted in the discovery of five new species (P. heveae sp. nov., P. acrean sp. nov., P. aquiri sp. nov., P. amazonense sp. nov., and P. pseudomellis sp. nov.). The five new species were also compared to closely related species, with observations on morphologically distinguishing features and colony appearances. Bayesian inference and maximum likelihood analysis have supported the placement of P. heveae sp. nov. as a sister group to P. globosum; P. acrean sp. nov. and P. aquiri sp. nov. as sister groups to P. sumatrense; P. amazonense sp. nov. closely related to isolates of P. rolfsii, and P. pseudomellis sp. nov. closely related to P. mellis. The study of endophytic Penicillium species of rubber trees and the description of five new taxa of Penicillium sect. Citrina, Lanata-Divaricata, and Sclerotiora as endophytes add to the fungal biodiversity knowledge in native rubber trees. Reports of fungi in native tropical plants may reveal taxonomic novelties, potential pathogen control agents, and producers of molecular bioactive compounds of medical and agronomic interest.}, }
@article {pmid39384034, year = {2024}, author = {Martínez Del Río, J and Frutos-Beltrán, E and Sebastián-Martín, A and Lasala, F and Yasukawa, K and Delgado, R and Menéndez-Arias, L}, title = {HIV-1 Reverse Transcriptase Error Rates and Transcriptional Thresholds Based on Single-strand Consensus Sequencing of Target RNA Derived From In Vitro-transcription and HIV-infected Cells.}, journal = {Journal of molecular biology}, volume = {436}, number = {22}, pages = {168815}, doi = {10.1016/j.jmb.2024.168815}, pmid = {39384034}, issn = {1089-8638}, mesh = {*HIV Reverse Transcriptase/genetics/metabolism ; Humans ; *HIV-1/genetics ; *RNA, Viral/genetics ; Reverse Transcription/genetics ; High-Throughput Nucleotide Sequencing/methods ; HIV Infections/virology/genetics ; Transcription, Genetic ; }, abstract = {Nucleotide incorporation and lacZ-based forward mutation assays have been widely used to determine the accuracy of reverse transcriptases (RTs) in RNA-dependent DNA polymerization reactions. However, they involve quite complex and laborious procedures, and cannot provide accurate error rates. Recently, NGS-based methods using barcodes opened the possibility of detecting all errors introduced by the RT, although their widespread use is limited by cost, due to the large size of libraries to be sequenced. In this study, we describe a novel and relatively simple NGS assay based on single-strand consensus sequencing that provides robust results with a relatively small number of raw sequences (around 60 Mb). The method has been validated by determining the error rate of HIV-1 (BH10 strain) RT using the HIV-1 protease-coding sequence as target. HIV-1 reverse transcription error rates in standard conditions (37 °C/3 mM Mg[2+]) using an in vitro-transcribed RNA were around 7.3 × 10[-5]. In agreement with previous reports, an 8-fold increase in RT's accuracy was observed after reducing Mg[2+] concentration to 0.5 mM. The fidelity of HIV-1 RT was also higher at 50 °C than at 37 °C (error rate 1.5 × 10[-5]). Interestingly, error rates obtained with HIV-1 RNA from infected cells as template of the reverse transcription at 3 mM Mg[2+] (7.4 × 10[-5]) were similar to those determined with the in vitro-transcribed RNA, and were reduced to 1.8 × 10[-5] in the presence of 0.5 mM Mg[2+]. Values obtained at low magnesium concentrations were modestly higher than the transcription error rates calculated for human cells, thereby suggesting a realistic transcriptional threshold for our NGS-based error rate determinations.}, }
@article {pmid39383837, year = {2024}, author = {Mansfield, KL and González, E and McKay, S and Apaa, T and Kent, AJ and Cropper, P and Berry, N and Hernández-Triana, LM and Johnson, N}, title = {Short Communication: Anaplasma phagocytophilum and Babesia spp. in ixodid ticks infesting red foxes (Vulpes vulpes) in Great Britain.}, journal = {Ticks and tick-borne diseases}, volume = {15}, number = {6}, pages = {102401}, doi = {10.1016/j.ttbdis.2024.102401}, pmid = {39383837}, issn = {1877-9603}, mesh = {Animals ; *Foxes/parasitology ; *Anaplasma phagocytophilum/isolation &amp; purification/genetics ; *Babesia/isolation &amp; purification/genetics ; United Kingdom/epidemiology ; *Tick Infestations/veterinary/epidemiology/parasitology ; *Nymph/microbiology/growth &amp; development ; Female ; Ixodes/microbiology/parasitology ; Ixodidae/microbiology/parasitology ; Male ; Ehrlichiosis/epidemiology/veterinary/microbiology ; Babesiosis/epidemiology/parasitology ; }, abstract = {Red foxes (Vulpes vulpes) are found throughout the United Kingdom (UK), and can reach high population densities in urban areas. They are often infested with ticks which may carry tick-borne pathogens, leading to a risk of transmission to domestic animals and humans. This study investigated the prevalence of tick-borne pathogens in ticks sourced from red fox carcasses across Great Britain between 2018 and 2022. Tick species were identified using morphological keys and molecular barcoding, followed by specific pathogen testing using PCR. In total, 227 ticks were collected from 93 foxes. Pooling (n = 2) was undertaken for unengorged nymphs from the same tick species and fox host, with 203 homogenates tested in total (24 pools and 179 individual ticks). Ixodes hexagonus was the most abundant tick species sampled (73 %), of which 59 % were nymphs and 41 % were females. Less common were Ixodes ricinus (12 %) and Ixodes canisuga (15 %), the majority of which were females (73 % and 91 %, respectively). One Ixodes sp. larva was identified. Babesia DNA was identified in seven individual ticks and once in pooled ticks (n = 2); seven detections were in I. hexagonus and one in I. canisuga, with an overall detection rate of 7 % (95 % CI: 6 - 8 %). Sequence analysis confirmed that all Babesia detections in I. hexagonus were Babesia vulpes, with detection of Babesia Badger Type A in I. canisuga. Screening for Anaplasma phagocytophilum DNA through amplification of the msp2 gene yielded an overall detection rate of 4 % (detected in I. hexagonus only). Louping ill virus was not detected by qRT-PCR in any tick RNA tested. The majority of pathogen detections were in ticks from red foxes in rural areas of the UK, although a small number of Babesia detections were in ticks collected from semi-rural or urban red foxes. Additionally, B. vulpes was detected in GB red fox tissues, suggesting a potential role as a reservoir host. This study confirms the detection of tick-borne pathogens in ticks infesting UK red foxes and highlights the involvement of GB tick species in animal or human disease transmission.}, }
@article {pmid39380764, year = {2023}, author = {Kartiganer, Z and Rojas, G and Riccio, M and Tyree, A and Noronha, K and Wetzel, M and Barnett, J and McGann, J and Garbarino, J and Massucci, D and Chafi, NS and Decker, S and McDaniels, A and Sabina, J and Levchenko, D and Perez, J and Ng, C and Wang, K}, title = {Improved cell-type identification and comprehensive mapping of regulatory features with spatial epigenomics 96-channel microfluidic platform.}, journal = {GEN biotechnology}, volume = {2}, number = {6}, pages = {503-514}, pmid = {39380764}, issn = {2768-1556}, support = {R44 CA287890/CA/NCI NIH HHS/United States ; }, abstract = {Gene expression is subject to epigenetic regulation and is dependent upon cellular context. Spatial omics tools can provide insight into cellular context; however, development has centered on spatial transcriptomics and proteomics. Deterministic barcoding in tissue for spatial omics sequencing (DBiT-seq) was the first spatial epigenomics platform at the cellular level. Here we present a comparison of spatial epigenomic profiling on both 50-channel and 96-channel platforms. The new 96-channel microfluidics chip design greatly improved precision in cell typing and identification of regulatory elements by spatial-ATAC-seq. Spatial mapping reveals complexity of glial cell and neuronal localization within brain structures as well as cis-regulatory elements controlling cellular function. This technology streamlines spatial analysis of the epigenome and contributes a new layer of spatial omics to uncover the context dependent regulatory mechanisms underpinning development, disease, and normal cellular function.}, }
@article {pmid39380274, year = {2024}, author = {Abdulrahman Ismael, K and Abdul-Qadir Ali, L}, title = {Morphological and molecular identification of freshwater eutardigrade Dactylobiotus parthenogeneticus (Bertolani, 1982) in the Greater Zab River of Kurdistan Region - Iraq.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {70}, number = {9}, pages = {86-90}, doi = {10.14715/cmb/2024.70.9.12}, pmid = {39380274}, issn = {1165-158X}, mesh = {Animals ; Iraq ; *Tardigrada/genetics/classification/anatomy &amp; histology ; *Rivers ; *Electron Transport Complex IV/genetics ; *Phylogeny ; DNA Barcoding, Taxonomic/methods ; Fresh Water ; }, abstract = {Dactylobiotus parthenogeneticus is one of the widespread species of tardigrade all over the world. Tardigrades of this species were collected from the Greater Zab River in Erbil City-Iraq by filtering water of the river through a plankton net with a mesh of 45 µm pore. The samples were mounted on a slide with a cover slip and examined under the microscope to determine morphological characteristics and measurements. Based on these characters the species identified to be D. parthenogeneticus. To support this diagnosis, DNA barcoding techniques were applied to do molecular analysis and sequencing on the cytochrome oxidase subunit I (COI) gene. The sequence was subjected to the GenBank database of NCBI and recorded with the accession number PP140905. The result of the sequencing and molecular analysis of the cytochrome oxidase subunit I (COI) gene confirmed to be the same species diagnosed by relying upon morphological characters. This study represents one of the pioneer researches and documents on tardigrades and found D. parthenogeneticus for the first time in the Greater Zab River in Kurdistan, North of Iraq. Tardigrades play a magnificent role in different trophic levels and can be utilized as an indicator of ecosystem health.}, }
@article {pmid39380264, year = {2024}, author = {Khawaja Ghulam, R and Husain, M and Sharaf, MR and Muhammad Tufail,  and Sutanto, KD and Alwaneen, WS and Aldawood, AS}, title = {Mitochondrial DNA sequence-based identification of two subterranean termite species, from Riyadh Province, Kingdom of Saudi Arabia.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {70}, number = {9}, pages = {189-197}, doi = {10.14715/cmb/2024.70.9.26}, pmid = {39380264}, issn = {1165-158X}, mesh = {Animals ; *Isoptera/genetics/classification ; *Phylogeny ; Saudi Arabia ; *DNA, Mitochondrial/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; Base Sequence ; }, abstract = {Termites are economically important wood-destroying and agricultural pests. The termite fauna almost consists of 2900 described species in 286 genera worldwide. In the present study, hundreds of termite samples from 42 different locations in the Riyadh province were collected. These samples were previously used for morphometric identification and reported two subterranean termite species, Coptotermes heimi and Psammotermes hypostoma, in the family Rhinotermitidae. In the present study, these samples were analysed using DNA barcoding with the mitochondrial cytochrome c oxidase subunit 1 gene to confirm the conventional taxonomical identification on a molecular basis. The obtained COI gene sequences of all 42 termite specimens were submitted to GenBank (accession numbers: ON529959-ON529969, OP825131-OP825132, and OP890882-OP890910). Eleven of the 42 samples were thus identified as C. heimi and the remaining 31 samples as P. hypostoma, which were phylogenetically analysed. All the 11 C. heimi sequences were grouped in a single clade, indicating close relatedness. While 31 sequences of P. hypostoma constituted two clades in the phylogenetic tree. Pairwise nucleotide sequence identity and divergence analysis showed that C. heimi sequences showed high nucleotide identities of 87.6-99.5% and less divergence ranging from 0.5% to 13.6%. Similarly, sequences of P. hypostoma also showed high nucleotide identity of 78.6-100% and low divergence among them ranging from 0-10.7%. A further application, significance, and shortcomings of COI-based DNA barcoding have been discussed. DNA barcoding using the COI gene is a reliable tool to distinguish C. heimi and P. hypostoma genotypes.}, }
@article {pmid39380090, year = {2024}, author = {Amstler, S and Streiter, G and Pfurtscheller, C and Forer, L and Di Maio, S and Weissensteiner, H and Paulweber, B and Schönherr, S and Kronenberg, F and Coassin, S}, title = {Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {117}, pmid = {39380090}, issn = {1756-994X}, mesh = {Humans ; *Haplotypes ; *Minisatellite Repeats ; *Lipoprotein(a)/genetics ; *Nanopore Sequencing/methods ; DNA Mutational Analysis/methods ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Repetitive genome regions, such as variable number of tandem repeats (VNTR) or short tandem repeats (STR), are major constituents of the uncharted dark genome and evade conventional sequencing approaches. The protein-coding LPA kringle IV type-2 (KIV-2) VNTR (5.6 kb per unit, 1-40 units per allele) is a medically highly relevant example with a particularly intricate structure, multiple haplotypes, intragenic homologies, and an intra-VNTR STR. It is the primary regulator of plasma lipoprotein(a) [Lp(a)] concentrations, an important cardiovascular risk factor. Lp(a) concentrations vary widely between individuals and ancestries. Multiple variants and functional haplotypes in the LPA gene and especially in the KIV-2 VNTR strongly contribute to this variance.<br><br>METHODS: We evaluated the performance of amplicon-based nanopore sequencing with unique molecular identifiers (UMI-ONT-Seq) for SNP detection, haplotype mapping, VNTR unit consensus sequence generation, and copy number estimation via coverage-corrected haplotypes quantification in the KIV-2 VNTR. We used 15 human samples and low-level mixtures (0.5 to 5%) of KIV-2 plasmids as a validation set. We then applied UMI-ONT-Seq to extract KIV-2 VNTR haplotypes in 48 multi-ancestry 1000 Genome samples and analyzed at scale a poorly characterized STR within the KIV-2 VNTR.<br><br>RESULTS: UMI-ONT-Seq detected KIV-2 SNPs down to 1% variant level with high sensitivity, specificity, and precision (0.977&#x2009;&#xb1;&#x2009;0.018; 1.000&#x2009;&#xb1;&#x2009;0.0005; 0.993&#x2009;&#xb1;&#x2009;0.02) and accurately retrieved the full-length haplotype of each VNTR unit. Human variant levels were highly correlated with next-generation sequencing (R[2]&#x2009;=&#x2009;0.983) without bias across the whole variant level range. Six reads per UMI produced sequences of each KIV-2 unit with Q40 quality. The KIV-2 repeat number determined by coverage-corrected unique haplotype counting was in close agreement with droplet digital PCR (ddPCR), with 70% of the samples falling even within the narrow confidence interval of ddPCR. We then analyzed 62,679 intra-KIV-2 STR sequences and explored KIV-2 SNP haplotype patterns across five ancestries.<br><br>CONCLUSIONS: UMI-ONT-Seq accurately retrieves the SNP haplotype and precisely quantifies the VNTR copy number of each repeat unit of the complex KIV-2 VNTR region across multiple ancestries. This study utilizes the KIV-2 VNTR, presenting a novel and potent tool for comprehensive characterization of medically relevant complex genome regions at scale.}, }
@article {pmid39380014, year = {2024}, author = {Liu, Z and Pei, Y and Chen, T and Yang, Z and Jiang, W and Feng, X and Li, X}, title = {Molecular quantification of fritillariae cirrhosae bulbus and its adulterants.}, journal = {Chinese medicine}, volume = {19}, number = {1}, pages = {138}, pmid = {39380014}, issn = {1749-8546}, support = {7244492//Beijing Natural Science Foundation/ ; 2019YFC1710600//National Key Research and Development Program of China/ ; CI2021A04106//The Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; ZZ15-YQ-033//Fundamental Research Funds for the Central public welfare research institutes of China/ ; ZXKT23004//Fundamental Research Funds for the Central public welfare research institutes of China/ ; CI2024C003YN//The Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; }, abstract = {BACKGROUND: Fritillariae Cirrhosae Bulbus (FCB) is frequently adulterated with its closely related species due to personal or non-man made factors, leading to alterations in the composition of its constituents and compromising the efficacy of its products.<br><br>METHODS: The specific single nucleotide polymorphisms (SNPs) were screened by comparing candidate barcodes of Fritillaria and verified by amplification and sequencing. Herb molecular quantification (Herb-Q) was established by detecting specific SNPs, and the methodological validation was performed. Quantitative standard curves were established for FCB mixed with each adulterated species, and the quantitative validity of this method was verified based on external standard substance. In addition, eight commercial Shedan Chuanbei capsules (SDCBs) randomly selected were detected.<br><br>RESULTS: FCB and its five adulterants can be distinguished based on the ITS 341 site. The methodological investigation of Herb-Q shows optimal accuracy, and repeatability, which exhibited good linearity with an R[2] of 0.9997 (>&#x2009;0.99). An average bias in quantitative validity was 5.973% between the measured and actual values. Four of eight commercial SDCBs were adulterated with F. ussuriensis or F. thunbergia with adulteration levels ranging from 9 to 15% of the total weight.<br><br>CONCLUSION: This study confirmed that Herb-Q can quantitatively detect both the mixed herbs and Chinese patent medicines (CPMs) containing FCB with high reproducibility and accuracy. This method provides technical support for market regulation and helps safeguard patient rights.}, }
@article {pmid39375852, year = {2025}, author = {Morales-Pulido, JM and Galindo-Sánchez, CE and Jiménez-Rosenberg, SPA and Batta-Lona, PG and Herzka, SZ and Arteaga, MC}, title = {A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny.}, journal = {Journal of fish biology}, volume = {106}, number = {2}, pages = {266-275}, doi = {10.1111/jfb.15921}, pmid = {39375852}, issn = {1095-8649}, support = {Fund Project 201441//Consejo Nacional de Ciencia y Tecnolog&#xed;a in Mexico (National Council for Science and Technology - Mexican Ministry of Energy - Hydrocarbon)/ ; 682136//Internal project: Environmental variations effects on mollusks: a genomic and transcriptomic approximation/ ; }, mesh = {Animals ; *Perciformes/genetics/classification/anatomy &amp; histology/growth &amp; development ; Electron Transport Complex IV/genetics ; Larva/anatomy &amp; histology/growth &amp; development/genetics/classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Mitochondrial/genetics ; Gulf of Mexico ; Sequence Analysis, DNA ; }, abstract = {Sparisoma species (parrotfish) comprise an important functional group contributing to coral-reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid-September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species-level identifications of Sparisoma larvae.}, }
@article {pmid39375541, year = {2024}, author = {Biggs, BW and Price, MN and Lai, D and Escobedo, J and Fortanel, Y and Huang, YY and Kim, K and Trotter, VV and Kuehl, JV and Lui, LM and Chakraborty, R and Deutschbauer, AM and Arkin, AP}, title = {High-throughput protein characterization by complementation using DNA barcoded fragment libraries.}, journal = {Molecular systems biology}, volume = {20}, number = {11}, pages = {1207-1229}, pmid = {39375541}, issn = {1744-4292}, support = {S10 OD018174/OD/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; NIH S10 OD018174//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Escherichia coli/genetics/metabolism ; *Gene Library ; *DNA Barcoding, Taxonomic ; Bacillus subtilis/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genetic Complementation Test ; High-Throughput Nucleotide Sequencing ; Escherichia coli Proteins/genetics/metabolism ; }, abstract = {Our ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we used complementation of auxotrophs and DNA barcode sequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains of Escherichia coli to identify genes that complement missing biochemical activity. We recovered 41% of expected hits, with effectiveness ranging per source genome, and observed success even with distant E. coli relatives like Bacillus subtilis and Bacteroides thetaiotaomicron. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein. Among the unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq's utility is demonstrated, with future applications in ecology, health, and engineering.}, }
@article {pmid39375449, year = {2025}, author = {Kudo, T and Meireles, AM and Moncada, R and Chen, Y and Wu, P and Gould, J and Hu, X and Kornfeld, O and Jesudason, R and Foo, C and Höckendorf, B and Corrada Bravo, H and Town, JP and Wei, R and Rios, A and Chandrasekar, V and Heinlein, M and Chuong, AS and Cai, S and Lu, CS and Coelho, P and Mis, M and Celen, C and Kljavin, N and Jiang, J and Richmond, D and Thakore, P and Benito-Gutiérrez, E and Geiger-Schuller, K and Hleap, JS and Kayagaki, N and de Sousa E Melo, F and McGinnis, L and Li, B and Singh, A and Garraway, L and Rozenblatt-Rosen, O and Regev, A and Lubeck, E}, title = {Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView.}, journal = {Nature biotechnology}, volume = {43}, number = {7}, pages = {1091-1100}, pmid = {39375449}, issn = {1546-1696}, mesh = {Animals ; Humans ; Mice ; Induced Pluripotent Stem Cells/cytology/metabolism ; Macrophages/metabolism ; Neurons/metabolism/cytology ; NF-kappa B/metabolism ; Signal Transduction ; *Image Interpretation, Computer-Assisted ; Phenotype ; Sequence Analysis, DNA ; }, abstract = {Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture due to limitations associated with in situ sequencing of perturbation barcodes. Here, we develop PerturbView, an OPS technology that leverages in vitro transcription to amplify barcodes before in situ sequencing, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in induced pluripotent stem cell-derived neurons, primary immune cells and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF-κB signaling. Furthermore, we combine PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in situ screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.}, }
@article {pmid39375448, year = {2025}, author = {Gu, J and Iyer, A and Wesley, B and Taglialatela, A and Leuzzi, G and Hangai, S and Decker, A and Gu, R and Klickstein, N and Shuai, Y and Jankovic, K and Parker-Burns, L and Jin, Y and Zhang, JY and Hong, J and Niu, X and Costa, JA and Pezet, MG and Chou, J and Chen, C' and Paiva, M and Snoeck, HW and Landau, DA and Azizi, E and Chan, EM and Ciccia, A and Gaublomme, JT}, title = {Mapping multimodal phenotypes to perturbations in cells and tissue with CRISPRmap.}, journal = {Nature biotechnology}, volume = {43}, number = {7}, pages = {1101-1115}, pmid = {39375448}, issn = {1546-1696}, support = {R01 CA227450/CA/NCI NIH HHS/United States ; R33 CA267219/CA/NCI NIH HHS/United States ; 1R21HG012639-01A1//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; DP2 CA281605/CA/NCI NIH HHS/United States ; R01 CA197774/CA/NCI NIH HHS/United States ; 5R01CA227450-04//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 1DP2CA281605//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; K08 CA256173/CA/NCI NIH HHS/United States ; 5R01CA197774-04//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; UG3 NS132139/NS/NINDS NIH HHS/United States ; 1R01HG012875-01//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; Lloyd J. Old STAR award//Cancer Research Institute (CRI)/ ; R21 HG012639/HG/NHGRI NIH HHS/United States ; R01 HG012875/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Phenotype ; *CRISPR-Cas Systems/genetics ; Cell Line, Tumor ; Breast Neoplasms/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Induced Pluripotent Stem Cells ; Mice ; }, abstract = {Unlike sequencing-based methods, which require cell lysis, optical pooled genetic screens enable investigation of spatial phenotypes, including cell morphology, protein subcellular localization, cell-cell interactions and tissue organization, in response to targeted CRISPR perturbations. Here we report a multimodal optical pooled CRISPR screening method, which we call CRISPRmap. CRISPRmap combines in situ CRISPR guide-identifying barcode readout with multiplexed immunofluorescence and RNA detection. Barcodes are detected and read out through combinatorial hybridization of DNA oligos, enhancing barcode detection efficiency. CRISPRmap enables in situ barcode readout in cell types and contexts that were elusive to conventional optical pooled screening, including cultured primary cells, embryonic stem cells, induced pluripotent stem cells, derived neurons and in vivo cells in a tissue context. We conducted a screen in a breast cancer cell line of the effects of DNA damage repair gene variants on cellular responses to commonly used cancer therapies, and we show that optical phenotyping pinpoints likely pathogenic patient-derived mutations that were previously classified as variants of unknown clinical significance.}, }
@article {pmid39372282, year = {2024}, author = {Huber, BA and Meng, G}, title = {Old World Micropholcus spiders, with first records of acrocerid parasitoids in Pholcidae (Araneae).}, journal = {ZooKeys}, volume = {1213}, number = {}, pages = {95-182}, pmid = {39372282}, issn = {1313-2989}, abstract = {Micropholcus Deeleman-Reinhold &amp; Prinsen, 1987 is one of only two Pholcidae genera known to occur both in the Old and New Worlds. However, there are major morphological and ecological differences among geographically separate groups of species, and it was mainly molecular data that have resulted in our current view of uniting all these species into a single genus. In the Old World, only four species have previously been described. Here, current knowledge about Old World Micropholcus is reviewed, redescribing three of the four previously known species, and describing twelve new species, originating from Saudi Arabia (M.dhahran Huber, sp. nov., M.harajah Huber, sp. nov., M.alfara Huber, sp. nov., M.abha Huber, sp. nov., M.tanomah Huber, sp. nov., M.bashayer Huber, sp. nov., M.maysaan Huber, sp. nov.), Oman (M.darbat Huber, sp. nov., M.shaat Huber, sp. nov.), Morocco (M.ghar Huber, sp. nov., M.khenifra Huber, Lecigne &amp; Lips, sp. nov.), and the Philippines (M.bukidnon Huber, sp. nov.). We provide an exploratory species delimitation analysis based on CO1 barcodes, extensive SEM data, and first records of Acroceridae (Diptera) larvae in Pholcidae, extracted from book lungs.}, }
@article {pmid39371081, year = {2024}, author = {Ward, DF}, title = {Building a DNA barcode reference collection of Hymenoptera in New Zealand.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e131701}, pmid = {39371081}, issn = {1314-2828}, abstract = {Molecular tools used for the identification of species are heavily reliant on reference DNA sequences and taxonomic annotation. Despite this, there are large gaps in the availability of DNA sequences for many taxonomic groups and for different parts of the globe. Here, a DNA barcode library for the Hymenoptera of New Zealand is presented, based on the COI region for 3,145 sequences assigned to 837 BINs and which represent 231 genera and 236 species. This study provides a DNA barcode for approximately 25% of species and 42% of genera of Hymenoptera in New Zealand. However, when combined with sequences previously deposited in BOLD (a further 170 genera), DNA barcodes are available for 73% of New Zealand Hymenopteran genera. To further increase coverage, future efforts need to focus predominantly on taxa from seven families (Encyrtidae, Pteromalidae s.l., Mymaridae, Eulophidae, Diapriidae, Braconidae and Platygastridae). This database facilitates DNA-based identification of taxa for use in both taxonomic revisions and biodiversity monitoring.}, }
@article {pmid39370741, year = {2025}, author = {Mayo Ilodiri, W and Huyghe, CET and da Costa, LM and Mambo Baba, T and Danadu Mizani, C and Vreven, EJWMN}, title = {Hidden species diversity in the Enteromius Cope, 1867 (Teleostei: Cyprinidae) from the Aruwimi basin (Middle Congo) in the Okapi Wildlife Reserve (Democratic Republic of the Congo).}, journal = {Journal of fish biology}, volume = {106}, number = {2}, pages = {230-255}, doi = {10.1111/jfb.15883}, pmid = {39370741}, issn = {1095-8649}, support = {//DEA scholarship/ ; //Mbisa Congo II/ ; //BICS project/ ; //Royal Museum for Central Africa (RMCA)/ ; //Directorate-General for Development Cooperation and Humanitarian Aid (DGD)/ ; }, mesh = {Animals ; *Cyprinidae/anatomy &amp; histology/classification/genetics ; Democratic Republic of the Congo ; Phylogeny ; *Biodiversity ; Rivers ; Male ; Female ; }, abstract = {Two new African minnow species, Enteromius cerinus sp. nov. and Enteromius ruforum sp. nov., are described for science from the Angadiko River, a left-bank sub-affluent of first order of the Nepoko River, draining the north-eastern part of the Okapi Wildlife Reserve (OWR). Both new species belong to the group of Enteromius for which the last unbranched dorsal-fin ray is flexible and underrated. Within this morphological group, both are most similar to Enteromius kamolondoensis, especially in life colour pattern characteristics. However, Enteromius cerinus sp. nov. differs from E. kamolondoensis by its low number of circumpeduncular scales, 10-11 (vs. 12), low maximum body depth, 22.8%-25.7% standard length (Ls) (vs. 26.1%-30.0%), and long anterior and posterior barbel lengths, 32.6%-35.3% head length (LH) (vs. 23.6%-27.2%) and 41.6%-43.9% LH (vs. 30.3%-34.9%), respectively. Further, E. ruforum sp. nov. is also easily distinguished from E. kamolondoensis by its high maximum body depth, 30.6%-33.3% Ls (vs. 26.1%-30.0%), and small, isometric, eye diameter, 26.2%-28.0% LH (vs. 29.1%-31.9%). A barcoding study (mtDNA, cytochrome oxidase subunit I [COI]) revealed that specimens of both new species form lineages well differentiated from those of other available species. As such, (i) E. cerinus sp. nov. diverges from E. kamolondoensis by a K2P genetic distance (GD) of 10.3% and (ii) E. ruforum sp. nov. by a K2P GD of 11.2%. To the present day, the fish fauna of the left-bank sub-affluents of the Nepoko River, in general, remains poorly known or undocumented. Unfortunately, at the same time, multiple anthropogenic impacts are affecting this fauna, such as (i) the destruction of habitats along the river banks for agriculture and fishing and (ii) the use of illegal fishing practices, such as fishing with plant-based ichthyotoxins during ecopage, which is combined with dam building. As a result of the demographic growth, this ecopage results in overfishing and thus is threatening both new species in particular, but all other co-occurring fish species as well. Both new species, E. cerinus sp. nov. and E. ruforum sp. nov., should thus be considered Vulnerable (VU) according to IUCN criterion D2. It is therefore hoped that their discovery highlights the urgent need for a better protection and further in situ exploration of the reserve's freshwater (fish) biodiversity, in general, and that of those small sub-affluents, in particular.}, }
@article {pmid39369928, year = {2024}, author = {Chomphuphuang, N and Leamyongyai, C and Songsangchote, C and Piraonapicha, K and Pojprasat, N and Piyatrakulchai, P}, title = {Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107424}, doi = {10.1016/j.actatropica.2024.107424}, pmid = {39369928}, issn = {1873-6254}, mesh = {Animals ; Thailand ; *Phylogeny ; *Spiders/classification/genetics ; *Electron Transport Complex IV/genetics ; *Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; Humans ; }, abstract = {The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.}, }
@article {pmid39369756, year = {2025}, author = {Li, H and Shangqing, Z and Yae, Z and Fan, Y and Xinyue, Z and Shirui, L and Tianyi, Z and Dongling, N}, title = {Classification, identification, and DNA barcoding study for common cockroach species (Dictyoptera: Blattaria) from China.}, journal = {Gene}, volume = {933}, number = {}, pages = {148981}, doi = {10.1016/j.gene.2024.148981}, pmid = {39369756}, issn = {1879-0038}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; China ; *Phylogeny ; *Cockroaches/genetics/classification ; DNA, Mitochondrial/genetics ; Periplaneta/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Cockroaches are well-known pests and quarantined organisms worldwide. Due to morphological diversity and a lack of molecular data, their classification and identification are facing challenges. This study performed classification, identification, and DNA barcoding for cockroaches collected from China. Seventy-six samples were morphologically identified as seven species of two superfamilies that included Blattella germanica, Eublaberus posticus and Blaptica dubia belonging to the superfamily Blaberoidea, and Periplaneta americana, Periplaneta lateralis, Periplaneta fuliginosa and Periplaneta australasiae belonging to the superfamily Blattoidea. Based on sequence alignments of nine ribosomal and mitochondrial genes across the order Blattaria retrieved from GenBank, rDNA ITS2-517 bp and mtDNA 16S-327 bp were screened as candidates for molecular identification. Universal primers were designed for PCR amplification, cloning, and sequencing of the 37 representative samples. Sequence alignments and phylogeny analysis showed that both ITS2 and 16S confirmed samples 1-9, 20-24, and 25-29 as B. germanica, P. americana, and P. lateralis, respectively; only 16S (not ITS2) confirmed samples 10-14, 15-19, 30-34, and 35-37 as E. posticus, Blap. dubia, P. fuliginosa, and P. australasiae, respectively, indicating that 16S was a better target than ITS2 for molecular identification of cockroaches. Conservative motif and divergence analysis further revealed that ITS2 sequences vary significantly among different taxa, whereas 16S sequences are relatively conserved. There is an obvious barcoding gap between maximum intraspecific divergence and minimum interspecific divergence (2.57 % vs. 5.62 %) for ITS2, but not for 16S (6.15 % vs. 2.63 %). Therefore, it was confirmed that ITS2 is an ideal DNA barcode for molecular identification of cockroaches at lower category.}, }
@article {pmid39365069, year = {2024}, author = {Biggel, M and Cernela, N and Horlbog, JA and Stephan, R}, title = {Oxford Nanopore's 2024 sequencing technology for Listeria monocytogenes outbreak detection and source attribution: progress and clone-specific challenges.}, journal = {Journal of clinical microbiology}, volume = {62}, number = {11}, pages = {e0108324}, pmid = {39365069}, issn = {1098-660X}, mesh = {*Listeria monocytogenes/genetics/classification/isolation &amp; purification ; *Listeriosis/microbiology/epidemiology/diagnosis ; *Disease Outbreaks ; Humans ; *Whole Genome Sequencing ; Genome, Bacterial/genetics ; Nanopore Sequencing/methods ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Whole genome sequencing is an essential cornerstone of pathogen surveillance and outbreak detection. Established sequencing technologies are currently being challenged by Oxford Nanopore Technologies (ONT), which offers an accessible and cost-effective alternative enabling gap-free assemblies of chromosomes and plasmids. Limited accuracy has hindered its use for investigating pathogen transmission, but recent technology updates have brought significant improvements. To evaluate its readiness for outbreak detection, we selected 78 Listeria monocytogenes isolates from diverse lineages or known epidemiological clusters for sequencing with ONT's V14 Rapid Barcoding Kit and R10.4.1 flow cells. The most accurate of several tested workflows generated assemblies with a median of one error (SNP or indel) per assembly. For 66 isolates, the cgMLST profiles from ONT-only assemblies were identical to those generated from Illumina data. Eight assemblies were of lower quality, with more than 20 erroneous sites each, primarily caused by methylations at the GAAGAC motif (5'-GAAG6mAC-3'/5'-GT4mCTTC-3'). This led to inaccurate clustering, failing to group isolates from a persistence-associated clone that carried the responsible restriction-modification system. Out of 50 methylation motifs detected among the 78 isolates, only the GAAGAC motif was linked to substantially increased error rates. Our study shows that most L. monocytogenes genomes assembled from ONT-only data are suitable for high-resolution genotyping, but further improvements of chemistries or basecallers are required for reliable routine use in outbreak and food safety investigations.}, }
@article {pmid39364681, year = {2024}, author = {Stancheva, R and Cantonati, M and Manoylov, K and Furey, PC and Cahoon, AB and Jones, RC and Gillevet, P and Amsler, CD and Wehr, JD and Salerno, JL and Krueger-Hadfield, SA}, title = {The importance of integrating phycological research, teaching, outreach, and engagement in a changing world.}, journal = {Journal of phycology}, volume = {60}, number = {6}, pages = {1335-1348}, pmid = {39364681}, issn = {1529-8817}, support = {DEB-2141971//National Science Foundation/ ; DEB-2436117//National Science Foundation/ ; }, mesh = {*Research ; Teaching ; }, abstract = {The ecological, evolutionary, economic, and cultural importance of algae necessitates a continued integration of phycological research, education, outreach, and engagement. Here, we comment on several topics discussed during a networking workshop-Algae and the Environment-that brought together phycological researchers from a variety of institutions and career stages. We share some of our perspectives on the state of phycology by examining gaps in teaching and research. We identify action areas where we urge the phycological community to prepare itself to embrace the rapidly changing world. We emphasize the need for more trained taxonomists as well as integration with molecular techniques, which may be expensive and complicated but are important. An essential benefit of these integrative studies is the creation of high-quality algal reference barcoding libraries augmented with morphological, physiological, and ecological data that are important for studies of systematics and crucial for the accuracy of the metabarcoding bioassessment. We highlight different teaching approaches for engaging undergraduate students in algal studies and the importance of algal field courses, forays, and professional phycological societies in supporting the algal training of students, professionals, and citizen scientists.}, }
@article {pmid39364584, year = {2025}, author = {Buchner, D and Sinclair, JS and Ayasse, M and Beermann, AJ and Buse, J and Dziock, F and Enss, J and Frenzel, M and Hörren, T and Li, Y and Monaghan, MT and Morkel, C and Müller, J and Pauls, SU and Richter, R and Scharnweber, T and Sorg, M and Stoll, S and Twietmeyer, S and Weisser, WW and Wiggering, B and Wilmking, M and Zotz, G and Gessner, MO and Haase, P and Leese, F}, title = {Upscaling biodiversity monitoring: Metabarcoding estimates 31,846 insect species from Malaise traps across Germany.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14023}, pmid = {39364584}, issn = {1755-0998}, support = {//Hessisches Landesamt f&#xfc;r Naturschutz, Umwelt und Geologie/ ; 871128//EU Horizon 2020 project eLTER PLUS/ ; //Landes-Offensive zur Entwicklung Wissenschaftlich-&#xf6;konomischer Exzellenz of the German federal State of Hesse/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Germany ; *Biodiversity ; *Insecta/classification/genetics/physiology ; }, abstract = {Mitigating ongoing losses of insects and their key functions (e.g. pollination) requires tracking large-scale and long-term community changes. However, doing so has been hindered by the high diversity of insect species that requires prohibitively high investments of time, funding and taxonomic expertise when addressed with conventional tools. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 € per sample, including supplies, labour and maintenance. We validated the detected species using two publicly available databases (GBOL and GBIF) and the judgement of taxonomic experts. With an average of 1.4 M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single Operational Taxonomic Unit (OTU). We estimated another 21,043 plausible species, which we argue either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany (~35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow (~80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.}, }
@article {pmid39364448, year = {2024}, author = {Zhou, R and Huang, L and Ma, YT}, title = {Smooth post-labial chaetae in Homidia (Collembola, Entomobryidae) and the description of four new species from China with the aid of DNA barcoding.}, journal = {ZooKeys}, volume = {1213}, number = {}, pages = {41-73}, pmid = {39364448}, issn = {1313-2989}, abstract = {Four new species of Homidia are described from the Guangxi Zhuang Autonomous Region, China. Homidialongiantenna sp. nov. is characterised by its long antenna and slightly expanded post-labial chaetae; H.guangxiensis sp. nov. by the presence of smooth chaetae on the post-labium and posterior face of the ventral tube; H.huapingensis sp. nov. by the presence of smooth post-labial chaetae and pointed tenent hairs; and H.oligoseta sp. nov. by the pointed tenent hairs and fewer macrochaetae on Abdomen IV. Additions to the original description of Homidiaacutus Jing &amp; Ma, 2022 are also provided.}, }
@article {pmid39364039, year = {2024}, author = {Zheng, LL and Yu, D and Sun, N and Wang, C and Chen, WJ and Ding, ZF and He, SP and Yang, LD}, title = {DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70352}, pmid = {39364039}, issn = {2045-7758}, abstract = {The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.}, }
@article {pmid39363107, year = {2025}, author = {Kumar, B and Navarro, C and Yung, PYK and Lyu, J and Salazar Mantero, A and Katsori, AM and Schwämmle, H and Martin, M and Elsässer, SJ}, title = {Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.}, journal = {Nature protocols}, volume = {20}, number = {3}, pages = {779-809}, pmid = {39363107}, issn = {1750-2799}, support = {2020-04313//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, mesh = {*Chromatin Immunoprecipitation Sequencing/methods ; *Chromatin/metabolism/genetics ; *Histones/metabolism ; Protein Processing, Post-Translational ; Humans ; *Histone Code ; High-Throughput Nucleotide Sequencing/methods ; *Chromatin Immunoprecipitation/methods ; }, abstract = {ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.}, }
@article {pmid39363072, year = {2025}, author = {Ramírez Rojas, AA and Brinkmann, CK and Schindler, D}, title = {Validation of Golden Gate Assemblies Using Highly Multiplexed Nanopore Amplicon Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2850}, number = {}, pages = {171-196}, pmid = {39363072}, issn = {1940-6029}, mesh = {*Nanopore Sequencing/methods ; *Synthetic Biology/methods ; Cloning, Molecular/methods ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Nanopores ; Workflow ; }, abstract = {Golden Gate cloning has revolutionized synthetic biology. Its concept of modular, highly characterized libraries of parts that can be combined into higher order assemblies allows engineering principles to be applied to biological systems. The basic parts, typically stored in Level 0 plasmids, are sequence validated by the method of choice and can be combined into higher order assemblies on demand. Higher order assemblies are typically transcriptional units, and multiple transcriptional units can be assembled into multi-gene constructs. Higher order Golden Gate assembly based on defined and validated parts usually does not introduce sequence changes. Therefore, simple validation of the assemblies, e.g., by colony polymerase chain reaction (PCR) or restriction digest pattern analysis is sufficient. However, in many experimental setups, researchers do not use defined parts, but rather part libraries, resulting in assemblies of high combinatorial complexity where sequencing again becomes mandatory. Here, we present a detailed protocol for the use of a highly multiplexed dual barcode amplicon sequencing using the Nanopore sequencing platform for in-house sequence validation. The workflow, called DuBA.flow, is a start-to-finish procedure that provides all necessary steps from a single colony to the final easy-to-interpret sequencing report.}, }
@article {pmid39360178, year = {2024}, author = {Fahldieck, M and Rulik, B and Thormann, J and Mengual, X}, title = {A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e127190}, pmid = {39360178}, issn = {1314-2828}, abstract = {Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.}, }
@article {pmid39353738, year = {2024}, author = {Tek, AL and Nagaki, K and Yıldız Akkamış, H and Tanaka, K and Kobayashi, H}, title = {Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor.}, journal = {Life science alliance}, volume = {7}, number = {12}, pages = {}, pmid = {39353738}, issn = {2575-1077}, mesh = {*Glycine max/genetics ; *Centromere/genetics ; *Chromosomes, Plant/genetics ; DNA Barcoding, Taxonomic/methods ; Domestication ; Genome, Plant/genetics ; Histones/genetics/metabolism ; Plant Breeding/methods ; DNA, Plant/genetics ; }, abstract = {Wild soybean Glycine soja is the progenitor of cultivated soybean Glycine max Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research.}, }
@article {pmid39353436, year = {2024}, author = {Bai, Z and Zhang, D and Gao, Y and Tao, B and Zhang, D and Bao, S and Enninful, A and Wang, Y and Li, H and Su, G and Tian, X and Zhang, N and Xiao, Y and Liu, Y and Gerstein, M and Li, M and Xing, Y and Lu, J and Xu, ML and Fan, R}, title = {Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.}, journal = {Cell}, volume = {187}, number = {23}, pages = {6760-6779.e24}, pmid = {39353436}, issn = {1097-4172}, support = {R01 GM138856/GM/NIGMS NIH HHS/United States ; R56 HG012310/HG/NHGRI NIH HHS/United States ; R33 CA246711/CA/NCI NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; U54 CA268083/CA/NCI NIH HHS/United States ; R01 CA256530/CA/NCI NIH HHS/United States ; R35 GM150838/GM/NIGMS NIH HHS/United States ; U54 DK106857/DK/NIDDK NIH HHS/United States ; U01 CA294514/CA/NCI NIH HHS/United States ; R01 HG013185/HG/NHGRI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; U54 AG079759/AG/NIA NIH HHS/United States ; UM1 MH130991/MH/NIMH NIH HHS/United States ; R01 HL173271/HL/NHLBI NIH HHS/United States ; UH3 CA257393/CA/NCI NIH HHS/United States ; U54 AG076043/AG/NIA NIH HHS/United States ; RM1 MH132648/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Paraffin Embedding ; *Formaldehyde/chemistry ; *Tissue Fixation ; MicroRNAs/genetics/metabolism ; RNA/metabolism/genetics ; Transcriptome/genetics ; RNA Splicing/genetics ; Lymphoma/genetics/pathology ; Gene Expression Profiling/methods ; Polyadenylation ; }, abstract = {The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years. Furthermore, genome-wide single-nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Single-cell level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.}, }
@article {pmid39353093, year = {2025}, author = {Meier, R and Lawniczak, MKN and Srivathsan, A}, title = {Illuminating Entomological Dark Matter with DNA Barcodes in an Era of Insect Decline, Deep Learning, and Genomics.}, journal = {Annual review of entomology}, volume = {70}, number = {1}, pages = {185-204}, doi = {10.1146/annurev-ento-040124-014001}, pmid = {39353093}, issn = {1545-4487}, mesh = {*DNA Barcoding, Taxonomic ; Animals ; *Insecta/genetics/classification ; *Deep Learning ; Genomics ; Biodiversity ; Entomology/methods ; }, abstract = {Most insects encountered in the field are initially entomological dark matter in that they cannot be identified to species while alive. This explains the enduring quest for efficient ways to identify collected specimens. Morphological tools came first but are now routinely replaced or complemented with DNA barcodes. Initially too expensive for widespread use, these barcodes have since evolved into powerful tools for specimen identification and sorting, given that the evolution of sequencing approaches has dramatically reduced the cost of barcodes, thus enabling decentralized deployment across the planet. In this article, we review how DNA barcodes have become a key tool for accelerating biodiversity discovery and analyzing insect communities through both megabarcoding and metabarcoding in an era of insect decline. We predict that DNA barcodes will be particularly important for assembling image training sets for deep learning algorithms, global biodiversity genomics, and functional analysis of insect communities.}, }
@article {pmid39355103, year = {2024}, author = {Truong, C and Gabbarini, LA and Moretto, A and Escobar, JM and Smith, ME}, title = {Ectomycorrhizal fungi and the nitrogen economy of Nothofagus in southern Patagonia.}, journal = {Ecology and evolution}, volume = {14}, number = {10}, pages = {e70299}, pmid = {39355103}, issn = {2045-7758}, abstract = {Subantarctic Nothofagus forests are the southernmost forests in the world, with negligible atmospheric nitrogen (N) deposition. Most paradigms about the role of ectomycorrhizal (ECM) fungi in N cycling and plant N uptake at high latitudes have been tested in boreal coniferous forests, while in the southern hemisphere, ECM hosts are primarily angiosperms. Using ITS1 meta-barcoding, we characterized ECM and saprotrophic fungal communities in evergreen and deciduous Nothofagus forests forming monodominant and mixed stands in the archipelago of Tierra del Fuego (Chile and Argentina). We assessed the N economy of Nothofagus by correlating host species with fungal relative abundances, edaphic variables, net N mineralization, microbial biomass N and the activity of eight extracellular soil enzymes activities. The N economy of deciduous N. pumilio forests was strikingly similar to boreal coniferous forests, with the lowest inorganic N availability and net N mineralization, in correlation to higher relative abundances of ECM fungi with enzymatic capacity for organic N mobilization (genus Cortinarius). In contrast, the N economy of evergreen N. betuloides forests was predominantly inorganic and correlated with ECM lineages from the family Clavulinaceae, in acidic soils with poor drainage. Grassy understory vegetation in deciduous N. antarctica forests likely promoted saprotrophic fungi (i.e., genus Mortierella) in correlation with higher activities of carbon-degrading enzymes. Differences between Nothofagus hosts did not persist in mixed forests, illustrating the range of soil fertility of these ECM angiosperms and the underlying effects of soil and climate on Nothofagus distribution and N cycling in southern Patagonia.}, }
@article {pmid39354174, year = {2024}, author = {Ali, M and Dey, R and Das, M and Kumar, V and Chandra, K and Uniyal, VP and Gupta, SK}, title = {Unique among high passes: Insights into the genetic uniqueness among butterflies of Ladakh Trans-Himalaya through DNA barcoding.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {1033}, pmid = {39354174}, issn = {1573-4978}, mesh = {Animals ; *Butterflies/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Bayes Theorem ; Genetic Variation/genetics ; Genetics, Population ; }, abstract = {BACKGROUND: The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a COI barcode reference library of 60 specimens representing 23 species.<br><br>METHODS AND RESULTS: Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species.<br><br>CONCLUSIONS: Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.}, }
@article {pmid39351591, year = {2025}, author = {Bigirimana, A and Kisekelwa, T and da Costa, LM and Huyghe, CET and Banyankimbona, G and Vreven, EJWMN}, title = {Description of a new endemic Enteromius (Teleostei: Cyprinidae) from the upper Malagarazi in Burundi: Lessons for a protected area under implementation.}, journal = {Journal of fish biology}, volume = {106}, number = {2}, pages = {173-200}, doi = {10.1111/jfb.15652}, pmid = {39351591}, issn = {1095-8649}, mesh = {Animals ; *Cyprinidae/anatomy &amp; histology/classification/genetics ; Electron Transport Complex IV/genetics ; Phylogeny ; *Conservation of Natural Resources ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Male ; }, abstract = {Recent collecting efforts in the upper Malagarazi basin (2013-2022) allowed for an integrative study based on qualitative (colour), quantitative (meristic and metric), and barcoding gene [mtDNA, cytochrome c oxidase (COI)] data of specimens similar to Enteromius sp. 'ascutelatus', being a previously identified, potentially, new species. Based on these data, the present study confirms its identification as a new species for science, which is here formally described as Enteromius nzigidaherai sp. nov. This new species belongs to the group of Enteromius species for which the last unbranched ray of the dorsal fin is flexible and devoid of serrations along its posterior edge. This species has a horizontal series of black spots at the midlateral level of the sides. Three congeneric species, known from the Congo basin sensu lato, with two of them also found in the upper Malagarazi basin, are most similar to it. However, E. nzigidaherai sp. nov. is distinguished from the two sympatric upper Malagarazi species, that is, E. quadrilineatus and E. lineomaculatus, at least by two meristics and two morphometrics. It is also distinguished from E. urostigma, known from the upper Congo basin, by two meristics and one, apparently related, morphometric. In addition, a barcoding (mtDNA, COI) study revealed that the specimens of E. nzigidaherai sp. nov. form a well-supported, separate lineage, with a K2P genetic distance of more than 10% with specimens identified as E. quadrilineatus and E. lineomaculatus, both originating from the upper Malagarazi basin and for which tissue samples were available. Finally, the new species was found to be endemic to the upper reaches of two left bank affluents of the upper Malagarazi basin: the Muyovozi and the Kinwa. However, both affluents are threatened by human activities, which seem to have resulted in its local disappearance as recent intensive collecting efforts in the latter affluent have remained unsuccessful. The species should thus be considered Critically Endangered (CR) according to IUCN criteria B1ab(ii,iv)c(i,iii). Therefore, it is hoped that the present description draws renewed attention to the importance of aquatic protection in the region by highlighting the need for the effective establishment of the Malagarazi Nature Reserve and concern for its optimal delimitation to efficiently protect the entire ichthyofauna of the upper Malagarazi, without excluding the fish species confined to its affluent rivers.}, }
@article {pmid39351291, year = {2024}, author = {Mwamula, AO and Lee, SM and Jung, YH and Kim, YS and Lee, DW}, title = {Description and Molecular Characterization of a New Dorylaimid Nematode, Mesodorylaimus pini n. sp. (Nematoda: Dorylaimidae) from Korea.}, journal = {Journal of nematology}, volume = {56}, number = {1}, pages = {20240028}, pmid = {39351291}, issn = {0022-300X}, abstract = {Mesodorylaimus pini n. sp., a new species isolated from the bark and cambium layer of a dead black pine tree is characterized herein using integrative taxonomy, considering both morphological and molecular phylogenetic analyses of the 18S- and 28S-rRNA genes. Mesodorylaimus pini n. sp. is characterized by having a medium-sized body 1.50-1.89 mm long; lip region angular and offset by a depression; a relatively long odontostyle (17.0-19.0 μm); vulval opening a transverse slit, positioned slightly posteriorly; pars refringens vaginae with two elongated drop-shaped to spindle-shaped sclerotizations; an intestine-prerectum junction with a long anteriorly directed conical or tongue-like projection; a relatively long female tail (115-187 μm); spicules 48.0-57.0 μm long; and regularly spaced 7-8 ventromedian supplements. It is closest to M. subtilis, especially in having similar body length and number of ventromedian supplements but can be differentiated from M. subtilis by the longer odontostyle, tongue-like projection, and longer spicules. The phylogenies based on the 18S- and 28S-rRNA sequences showed a well-supported sister relation of M. pini n. sp. with M. subtilis, M. japonicus, M. bastiani, M. pseudobastiani, Calcaridorylaimus castaneae, C. heynsi, and other member species of the group.}, }
@article {pmid39349515, year = {2024}, author = {Zhang, S and Liao, A and Wang, Y and Liu, Q and Ouyang, L and Peng, H and Yuan, L and Zhao, L and Yang, X and Chen, X and He, Y and Li, Z}, title = {Profiling expressing features of surface proteins on single-exosome in first-episode Schizophrenia patients: a preliminary study.}, journal = {Schizophrenia (Heidelberg, Germany)}, volume = {10}, number = {1}, pages = {84}, pmid = {39349515}, issn = {2754-6993}, support = {82101576//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Proximity barcoding assay, a high-throughput method for single-exosome analysis, was employed to profile surface proteins on individual exosomes of SCZ patients. This analysis identified five differentially expressed proteins (DEPs) between SCZ patients and healthy controls (HC) and six DEPs between antipsychotic responders and non-responders. Furthermore, two exosome clusters were found to be associated with SCZ, and certain DEPs were correlated with cognitive functions.}, }
@article {pmid39349404, year = {2025}, author = {Villa, S and Magoga, G and Montagna, M and Pierce, S}, title = {Elevational shifts in reproductive ecology indicate the climate response of a model chasmophyte, Rainer's bellflower (Campanula raineri).}, journal = {Annals of botany}, volume = {135}, number = {1-2}, pages = {181-198}, pmid = {39349404}, issn = {1095-8290}, support = {PSR2019_DIP_014SPIER//Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, Italy/ ; //Department of Agricultural and Environmental Sciences/ ; //Doctoral School of Agriculture, Environment and Bioenergy/ ; }, mesh = {*Campanulaceae/physiology ; Pollination/physiology ; *Altitude ; Reproduction/physiology ; Seeds/physiology ; Animals ; *Climate Change ; Pollen/physiology ; Hymenoptera/physiology ; }, abstract = {BACKGROUND AND AIMS: Elevation gradients provide 'natural experiments' for investigating plant climate change responses, advantageous for the study of protected species and life forms for which transplantation experiments are illegal or unfeasible, such as chasmophytes with perennial rhizomes pervading rock fissures. Elevational climatic differences impact mountain plant reproductive traits (pollen and seed quality, sexual vs. vegetative investment) and pollinator community composition; we investigated the reproductive ecology of a model chasmophyte, Campanula raineri Perp. (Campanulaceae), throughout its current elevational/climatic range to understand where sub-optimal conditions jeopardise survival. We hypothesised that: 1) reproductive fitness measures are positively correlated with elevation, indicative of the relationship between fitness and climate; 2) C. raineri, like other campanulas, is pollinated mainly by Hymenoptera; 3) potential pollinators shift with elevation.<br><br>METHODS: We measured pollen and seed quality, seed production, the relative investment in sexual vs. vegetative structures and vegetative (Grime's CSR) strategies at different elevations. Potential pollinators were assessed by combining molecular and morphological identification.<br><br>KEY RESULTS: Whereas CSR strategies were not linked to elevation, pollen and seed quality were positively correlated, as was seed production per fruit (Hypothesis 1 is supported). The main pollinators of C. raineri were Apidae, Andrenidae, Halictidae (Hymenoptera) and Syrphidae (Diptera), probably complemented by a range of occasional pollinators and visitors (Hypothesis 2 partially supported). Potential pollinator communities showed a taxonomic shift towards Diptera with elevation (particularly Anthomyiidae and Muscidae) and away from Hymenoptera (Hypothesis 3 was supported).<br><br>CONCLUSIONS: Pollinator availability is maintained at all elevations by taxon replacement. However, reduced pollen quality and seed production at lower elevations suggest an impact of climate change on reproduction (especially <1200 m a.s.l., where seed germination was limited). Aside from guiding targeted conservation actions for C. raineri, our results highlight problems that may be common to mountain chasmophytes worldwide.}, }
@article {pmid39348735, year = {2025}, author = {Wang, S and Zhou, Y and Ding, K and Ding, ZQ and Zhang, W and Liu, Y}, title = {High-throughput and multimodal profiling of antigen-specific T cells with a droplet-based cell-cell interaction screening platform.}, journal = {Biosensors &amp; bioelectronics}, volume = {267}, number = {}, pages = {116815}, doi = {10.1016/j.bios.2024.116815}, pmid = {39348735}, issn = {1873-4235}, mesh = {Humans ; *Cell Communication ; *Biosensing Techniques/methods ; *T-Lymphocytes/immunology/cytology ; Antigen-Presenting Cells/immunology ; Single-Cell Analysis/methods ; High-Throughput Screening Assays/methods ; Animals ; Antigens/immunology/chemistry ; Click Chemistry ; }, abstract = {Identifying antigen-specific T cells from tumor-infiltrating lymphocytes is essential for designing effective T cell immunotherapies. Traditional methods can detect antigen-specific T cells but struggle with high-throughput screening and multimodal profiling simultaneously. To address this issue, we developed DropCCI, a new strategy that transfers antigen information to co-incubated T cells for high-throughput, non-contaminated multimodal profiling. In DropCCI, droplets encapsulated DNA barcodes and antigen-loaded antigen-presenting cells (APCs), while click chemistry-modified T cells were injected into these droplets to capture free barcodes and acquire the corresponding antigen information. Following cell-cell interaction, APCs were removed via streptavidin-biotin conjugation, to prevent contamination. The resulting T cells underwent single-cell omics sequencing for comprehensive profiling of their antigen specificity, transcriptome, and genomics accurately. This click-chemistry method allowed detection of antigen-specific T cells without lysing APCs, avoiding cross-cell contamination and enabling low-noise multimodal profiling of primary T cells. With a completion time within 12 h and no requirement for complex equipment, DropCCI provides unbiased single-cell sequencing results that offer a comprehensive understanding of anti-tumor T cell responses. The concept of DropCCI holds great promise not only for advancing the field of T cell immunotherapy but also for its potential application in studying other cell-cell interactions.}, }
@article {pmid39348593, year = {2024}, author = {Ren, J and Zhang, R}, title = {Delimiting species, revealing cryptic diversity in Molytinae (Coleoptera: Curculionidae) weevil through DNA barcoding.}, journal = {Journal of insect science (Online)}, volume = {24}, number = {4}, pages = {}, pmid = {39348593}, issn = {1536-2442}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Weevils/genetics/classification ; *Electron Transport Complex IV/genetics ; Genetic Variation ; Phylogeny ; }, abstract = {The subfamily Molytinae (Coleoptera: Curculionidae), being the second largest group within the family Curculionidae, exhibits a diverse range of hosts and poses a serious threat to agricultural and forestry industries. We used 1,290 cytochrome c oxidase subunit I (COI) barcodes to assess the efficiency of COI barcodes in species differentiation and uncover cryptic species diversity within weevils of Molytinae. The average Kimura 2-parameter distances within species, genus, and subfamily were 2.90%, 11.0%, and 22.26%, respectively, indicating significant genetic differentiation at both levels. Moreover, there exists a considerable degree of overlap between intraspecific (0%-27.50%) and interspecific genetic distances (GDs; 0%-39.30%). The application of Automatic barcode gap discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Poisson Tree Processes (PTP), Bayesian Poisson Tree Processes (bPTP), and jMOTU resulted in the identification of 279, 275, 494, 322, 320, and 279 molecular operational taxonomic units, respectively. The integration of 6 methods successfully delimited species of Molytinae in 86.6% of all examined morphospecies, surpassing a threshold value of 3% GD (73.0%). A total of 28 morphospecies exhibiting significant intraspecific divergences were assigned to multiple MOTUs, respectively, suggesting the presence of cryptic diversity or population divergence. The identification of cryptic species within certain morphological species in this study necessitates further investigation through comprehensive taxonomic practices in the future.}, }
@article {pmid39347602, year = {2024}, author = {Kamata, K and Birkholz, N and Ceelen, M and Fagerlund, RD and Jackson, SA and Fineran, PC}, title = {Repurposing an Endogenous CRISPR-Cas System to Generate and Study Subtle Mutations in Bacteriophages.}, journal = {The CRISPR journal}, volume = {7}, number = {6}, pages = {343-354}, doi = {10.1089/crispr.2024.0047}, pmid = {39347602}, issn = {2573-1602}, mesh = {*CRISPR-Cas Systems ; *Bacteriophages/genetics ; *Gene Editing/methods ; *Mutation ; Genome, Viral ; Plasmids/genetics ; Pectobacterium carotovorum/virology/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Homologous Recombination ; }, abstract = {While bacteriophage applications benefit from effective phage engineering, selecting the desired genotype after subtle modifications remains challenging. Here, we describe a two-phase endogenous CRISPR-Cas-based phage engineering approach that enables selection of small defined edits in Pectobacterium carotovorum phage ZF40. We designed plasmids containing sequences homologous to ZF40 and a mini-CRISPR array. The plasmids allowed genome editing through homologous recombination and counter-selection against non-recombinant phage genomes using an endogenous type I-E CRISPR-Cas system. With this technique, we first deleted target genes and subsequently restored loci with modifications. This two-phase approach circumvented major challenges in subtle phage modifications, including inadequate sequence distinction for CRISPR-Cas counter-selection and the requirement of a protospacer-adjacent motif, limiting sequences that can be modified. Distinct 20-bp barcodes were incorporated through engineering as differential target sites for programmed CRISPR-Cas activity, which allowed quantification of phage variants in mixed populations. This method aids studies and applications that require mixtures of similar phages.}, }
@article {pmid39345550, year = {2024}, author = {Carlos, AJ and Yang, D and Thomas, DM and Huang, S and Harter, KI and Moellering, RE}, title = {Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345550}, issn = {2692-8205}, support = {DP2 GM128199/GM/NIGMS NIH HHS/United States ; R01 GM145852/GM/NIGMS NIH HHS/United States ; T32 CA009594/CA/NCI NIH HHS/United States ; }, abstract = {Integrin family transmembrane receptors mediate dynamic interactions between cells and their extracellular microenvironment. The heterogeneous interaction partners of integrins directly regulate cell adhesion, motility, proliferation, and intracellular signaling. Despite the recognized importance of protein-protein interactions and the formation of signaling hubs around integrins, the ability to detect and quantify these dynamic binding partners with high spatial and temporal resolution remains challenging. Here, we developed an integrin-family-directed quantitative photoproximity protein interaction (PhotoPPI) profiling method to detect and quantify native integrin-centered protein social networks on live cells and tissues without the need for genetic manipulation, antibodies, or non-physiologic cell culture conditions. We drafted quantitative maps of integrin-centered protein social networks, highlighting conserved and unique binding partners between different cell types and cellular microenvironments. Comparison of integrin social networks in cancer cell lines of diverse tissue of origin and disease state identified specific AND-gate binding partners involved cell migration, microenvironmental interactions and proliferation that serve as markers of tumor cell metastatic state. Finally, we identified unique combinations - or barcodes - of integrin-proximal proteins on the surface of pre- and post-metastatic triple negative breast cancer (TNBC) cells whose expression strongly correlate with both positive and negative disease progression and outcomes in TNBC patients. Taken together, these data provide the first family-wide high-resolution maps of native protein interactors on live cells and identify dynamic integrin-centered social networks as potential AND-gate markers of cell identity, microenvironmental context and disease state.}, }
@article {pmid39345539, year = {2024}, author = {Ashkin, EL and Tang, YJ and Xu, H and Hung, KL and Belk, J and Cai, H and Lopez, S and Dolcen, DN and Hebert, JD and Li, R and Ruiz, PA and Keal, T and Andrejka, L and Chang, HY and Petrov, DA and Dixon, JR and Xu, Z and Winslow, MM}, title = {A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.14.613043}, pmid = {39345539}, issn = {2692-8205}, abstract = {UNLABELLED: The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo , and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo . STAG2 inactivation elicits changes in gene expression, chromatin accessibility and 3D genome conformation that impact cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relates STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin mediated mechanisms of lung tumor suppression.<br><br>SUMMARY: STAG2 is a frequently mutated cohesin subunit across several cancers and one of the most important functional suppressors of lung adenocarcinoma. Our findings underscore important roles of STAG2 in suppressing lung tumorigenesis and highlight a STAG2-PAXIP1/PAGR1 tumor-suppressive program that may transcend cancer type.}, }
@article {pmid39345444, year = {2024}, author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD}, title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.17.612743}, pmid = {39345444}, issn = {2692-8205}, support = {T32 CA009302/CA/NCI NIH HHS/United States ; }, abstract = {TP53 , the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq [Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3 - Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.}, }
@article {pmid39345427, year = {2024}, author = {Fang, C and Lindsey, J and Abbott, LF and Aronov, D and Chettih, S}, title = {Barcode activity in a recurrent network model of the hippocampus enables efficient memory binding.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345427}, issn = {2692-8205}, support = {DP2 AG071918/AG/NIA NIH HHS/United States ; K99 NS136846/NS/NINDS NIH HHS/United States ; T32 NS064929/NS/NINDS NIH HHS/United States ; }, abstract = {Forming an episodic memory requires binding together disparate elements that co-occur in a single experience. One model of this process is that neurons representing different components of a memory bind to an "index" - a subset of neurons unique to that memory. Evidence for this model has recently been found in chickadees, which use hippocampal memory to store and recall locations of cached food. Chickadee hippocampus produces sparse, high-dimensional patterns ("barcodes") that uniquely specify each caching event. Unexpectedly, the same neurons that participate in barcodes also exhibit conventional place tuning. It is unknown how barcode activity is generated, and what role it plays in memory formation and retrieval. It is also unclear how a memory index (e.g. barcodes) could function in the same neural population that represents memory content (e.g. place). Here, we design a biologically plausible model that generates barcodes and uses them to bind experiential content. Our model generates barcodes from place inputs through the chaotic dynamics of a recurrent neural network and uses Hebbian plasticity to store barcodes as attractor states. The model matches experimental observations that memory indices (barcodes) and content signals (place tuning) are randomly intermixed in the activity of single neurons. We demonstrate that barcodes reduce memory interference between correlated experiences. We also show that place tuning plays a complementary role to barcodes, enabling flexible, contextually-appropriate memory retrieval. Finally, our model is compatible with previous models of the hippocampus as generating a predictive map. Distinct predictive and indexing functions of the network are achieved via an adjustment of global recurrent gain. Our results suggest how the hippocampus may use barcodes to resolve fundamental tensions between memory specificity (pattern separation) and flexible recall (pattern completion) in general memory systems.}, }
@article {pmid39342262, year = {2024}, author = {Bisaglia, B and Castelli, M and Soresinetti, L and Negri, A and Arnoldi, I and Montarsi, F and Gobbo, F and Defilippo, F and Callegari, E and Di Luca, M and Calzolari, M and Mastrantonio, V and Porretta, D and Ficetola, GF and Sassera, D and Gabrieli, P and Bandi, C and Epis, S}, title = {Barcoding of Italian mosquitoes (BITMO): generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {407}, pmid = {39342262}, issn = {1756-3305}, support = {MUSA - Multilayered Urban Sustainability Action - project, funded by the European Union - NextGenerationEU, under the National Recovery and Resilience Plan (NRRP) Mission 4 Component 2 Investment Line 1.5: Strengthening of research structures and creation of R&amp;D "innovation ecosystems", set up of "territorial leaders in R&amp;D".//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PNRR Project title "National Biodiversity Future Center - NBFC" Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PNRR project PE-13, INF-ACT "One Health Basic and Translational Research Actions addressing Unmet Needs on Emerging Infectious Diseases"//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; MUSA - Multilayered Urban Sustainability Action - project, funded by the European Union - NextGenerationEU, under the National Recovery and Resilience Plan (NRRP) Mission 4 Component 2 Investment Line 1.5: Strengthening of research structures and creation of R&amp;D "innovation ecosystems", set up of "territorial leaders in R&amp;D".//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *RNA, Ribosomal, 16S/genetics ; *Culicidae/genetics/classification ; Italy ; *Introduced Species ; *Mosquito Vectors/genetics/classification ; *Phylogeny ; Gene Library ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: Mosquitoes (Culicidae), as disease vectors, represent a risk for human health worldwide. Repeated introductions of alien mosquito species and the spread of invasive species have been recorded in different countries. Traditionally, identification of mosquitoes relies on morphological observation. However, morphology-based identification is associated with a number of potential disadvantages, such as the high level of specialisation of the operator and its limited applicability to damaged samples. In these cases, species identification is achieved through molecular methods based on DNA amplification. Molecular-based taxonomy has also enabled the development of techniques for the study of environmental DNA (eDNA). Previous studies indicated the 16S mitochondrial ribosomal RNA (rRNA) gene as a promising target for this application; however, 16S rRNA sequences are available for only a limited number of mosquito species. In addition, although primers for the 16S rRNA gene were designed years ago, they are based on limited numbers of mosquito sequences. Thus, the aims of this study were to: (i) design pan-mosquito 16S rRNA gene primers; (ii) using these primers, generate a 16S rRNA gene mosquito reference library (with a focus on mosquitoes present in Italy); and (iii) compare the discriminatory power of the 16S rRNA gene with two widely used molecular markers, cytochrome c oxidase subunit 1 mitochondrial gene (COI) and internal transcribed spacer 2 (ITS2).<br><br>METHODS: A total of six mosquito genera (28 mosquito species) were included in this study: Aedes (n = 16 species), Anopheles (5 species), Coquillettidia (1 species), Culex (3 species), Culiseta (2 species) and Uranotaenia (1 species). DNA was extracted from the whole mosquito body, and more than one specimen for each species was included in the analysis. Sanger sequencing was used to generate DNA sequences that were then analysed through the Barcode of Life Data Systems (BOLD). Phylogenetic analyses were also performed.<br><br>RESULTS: Novel 16S rDNA gene, COI and ITS2 sequences were generated. The 16S rRNA gene was shown to possess sufficient informativeness for the identification of mosquito species, with a discriminatory power equivalent to that of COI.<br><br>CONCLUSIONS: This study contributes to the generation of DNA barcode libraries, focussed on Italian mosquitoes, with a significant increase in the number of 16S rRNA gene sequences. We hope that these novel sequences will provide a resource for studies on the biodiversity, monitoring and metabarcoding of mosquitoes, including eDNA-based approaches.}, }
@article {pmid39339949, year = {2024}, author = {Sartingen, N and Stürmer, V and Kaltenböck, M and Müller, TG and Schnitzler, P and Kreshuk, A and Kräusslich, HG and Merle, U and Mücksch, F and Müller, B and Pape, C and Laketa, V}, title = {Multiplex Microscopy Assay for Assessment of Therapeutic and Serum Antibodies against Emerging Pathogens.}, journal = {Viruses}, volume = {16}, number = {9}, pages = {}, pmid = {39339949}, issn = {1999-4915}, support = {TTU 04.710//German Center for Infection Research/ ; EXC 2067/1- 390729940//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *SARS-CoV-2/immunology ; *COVID-19/diagnosis/immunology/virology ; *Antibodies, Viral/blood/immunology ; *Spike Glycoprotein, Coronavirus/immunology ; HeLa Cells ; Antigens, Viral/immunology ; Microscopy/methods ; Coronavirus Nucleocapsid Proteins/immunology ; Machine Learning ; Phosphoproteins ; }, abstract = {The emergence of novel pathogens, exemplified recently by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlights the need for rapidly deployable and adaptable diagnostic assays to assess their impact on human health and guide public health responses in future pandemics. In this study, we developed an automated multiplex microscopy assay coupled with machine learning-based analysis for antibody detection. To achieve multiplexing and simultaneous detection of multiple viral antigens, we devised a barcoding strategy utilizing a panel of HeLa-based cell lines. Each cell line expressed a distinct viral antigen, along with a fluorescent protein exhibiting a unique subcellular localization pattern for cell classification. Our robust, cell segmentation and classification algorithm, combined with automated image acquisition, ensured compatibility with a high-throughput approach. As a proof of concept, we successfully applied this approach for quantitation of immunoreactivity against different variants of SARS-CoV-2 spike and nucleocapsid proteins in sera of patients or vaccinees, as well as for the study of selective reactivity of monoclonal antibodies. Importantly, our system can be rapidly adapted to accommodate other SARS-CoV-2 variants as well as any antigen of a newly emerging pathogen, thereby representing an important resource in the context of pandemic preparedness.}, }
@article {pmid39339575, year = {2024}, author = {Heo, JH and Yeon, J and Jung, JK and Shin, IS and Sim, SC}, title = {Development of Cost-Effective SNP Markers for Genetic Variation Analysis and Variety Identification in Cultivated Pears (Pyrus spp.).}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {18}, pages = {}, pmid = {39339575}, issn = {2223-7747}, support = {320040052HD060//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET)/ ; }, abstract = {Pear (Pyrus spp.) is a major fruit crop in the Rosaceae family, and extensive efforts have been undertaken to develop elite varieties. With advances in genome sequencing technologies, single-nucleotide polymorphisms (SNPs) are commonly used as DNA markers in crop species. In this study, a large-scale discovery of SNPs was conducted using genotyping by sequencing in a collection of 48 cultivated pear accessions. A total of 256,538 confident SNPs were found on 17 chromosomes, and 288 SNPs were filtered based on polymorphic information content, heterozygosity rate, and genome distribution. This subset of SNPs was used to genotype an additional 144 accessions, consisting of P. pyrifolia (53), P. ussuriensis (27), P. bretschneideri (19), P. communis (26), interspecific hybrids (14), and others (5). The 232 SNPs with reliable polymorphisms revealed genetic variations between and within species in the 192 pear accessions. The Asian species (P. pyrifolia, P. ussuriensis, and P. bretschneideri) and interspecific hybrids were genetically differentiated from the European species (P. communis). Furthermore, the P. pyrifolia population showed higher genetic diversity relative to the other populations. The 232 SNPs and four subsets (192, 96, 48, and 24 SNPs) were assessed for variety identification. The 192 SNP subset identified 173 (90.1%) of 192 accessions, which was comparable to 175 (91.1%) from the 232 SNPs. The other three subsets showed 81.8% (24 SNPs) to 87.5% (96 SNPs) identification rates. The resulting SNPs will be a useful resource to investigate genetic variations and develop an efficient DNA barcoding system for variety identification in cultivated pears.}, }
@article {pmid39338960, year = {2024}, author = {Olszak-Przybyś, H and Korbecka-Glinka, G}, title = {The Diversity of Seed-Borne Fungi Associated with Soybean Grown in Southern Poland.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {39338960}, issn = {2076-0817}, mesh = {*Glycine max/microbiology ; Poland ; *Seeds/microbiology ; *Fungi/isolation &amp; purification/genetics/classification ; Fusarium/isolation &amp; purification/genetics ; Germination ; Biodiversity ; Aspergillus/isolation &amp; purification/genetics ; }, abstract = {Fungi have the potential to colonize soybean seeds in the field, during their maturation in the pods and after harvest, during storage. The aim of this study was to identify fungi inhabiting soybean seeds after storage with varying germination capacity and to evaluate their chemical composition. The research material consisted of twelve soybean seed lots collected from the fields in southern Poland and stored over winter. The germination percentage of these lots ranged between 20.67% and 81.33%. The seeds were subjected to analyses of the main chemical components and mycological analysis. Fungal isolates were subjected to taxonomic identification using microscopic methods and DNA sequencing (using internal transcribed spacer region and secondary barcoding regions). A total number of 355 fungal isolates from 16 genera were identified, with Aspergillus, Alternaria, and Fusarium being the most common. Species were successfully identified in 94% of isolates. Twelve examined seed lots varied significantly in the number of isolated fungal species (from 1 to 17). Moreover, they also differed in the isolated species composition. Highly significant positive correlation was found between the number of Aspergillus psedudoglaucus isolates and the content of free fatty acids. In turn, the number of Fusarium spp. isolates correlated negatively with protein and nitrogen content. Similarly, highly significant negative correlation was found between the number of all fungal isolates and the 1000-seed weight, indicating that smaller seeds are more vulnerable to fungal infection. The results obtained in this study identify species of fungi which may be responsible for lowering quality of the seeds obtained in southern Poland.}, }
@article {pmid39337711, year = {2024}, author = {Noh, S and Kim, WJ and Cha, JM and Choi, G and Yang, S and Song, JH and Moon, BC}, title = {Rapid Diagnostic PCR Assay Method for Species Identification of Mantidis Ootheca (Sangpiaoxiao) Based on Cytochrom C Oxidase I (COI) Barcode Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337711}, issn = {1422-0067}, support = {KSN1823320//Korea Institute of Oriental Medicine/ ; }, mesh = {*Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Animals ; Polymerase Chain Reaction/methods ; Species Specificity ; Mantodea/genetics/classification ; Rapid Diagnostic Tests ; }, abstract = {Mantidis Ootheca (sangpiaoxiao), the egg case of the mantis, is a type of insect-derived traditional medicine widely used in East Asia. However, species identification based on egg morphology is challenging, leading to the distribution of counterfeit and adulterated products. The use of inauthentic ingredients can pose serious health risks to consumers. This study aimed to develop PCR markers that can rapidly and accurately differentiate between authentic and counterfeit Mantidis Ootheca. The mitochondrial cytochrome c oxidase I (COI) region was sequenced in thirteen samples from four mantis species: Tenodera angustipennis, Statilia maculata, Hierodula patellifera, and T. sinensis. Four sets of SCAR primers were designed based on species-specific nucleotide polymorphisms, and a multiplex SCAR assay was developed by combining all sets of the primers. The sequence-characterized amplified region (SCAR) primers successfully produced amplicons for each target species, even with low-DNA templates or templates containing DNA from multiple samples. No amplification was observed for nontarget species. This study presents a novel approach for identifying authentic Mantidis Ootheca species using DNA-based diagnostic marker assays, which enable rapid and precise species identification. The SCAR assays developed in this study will aid in maintaining quality control and promoting the standardization of commercial Mantidis Ootheca products.}, }
@article {pmid39337663, year = {2024}, author = {Sikora, J and Celiński, K}, title = {Exploring Taxonomic and Genetic Relationships in the Pinus mugo Complex Using Genome Skimming Data.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337663}, issn = {1422-0067}, support = {"Diamond Grant" program No. DI2017003147//Ministry of Science and Higher Education of the Republic of Poland./ ; }, mesh = {*Pinus/genetics/classification ; *Phylogeny ; *Genome, Plant ; *Genetic Variation ; DNA Barcoding, Taxonomic/methods ; Haplotypes/genetics ; Genomics/methods ; }, abstract = {Genome skimming is a novel approach that enables obtaining large-scale genomic information based on high-copy DNA fractions from shallow whole-genome sequencing. The simplicity of this method, low analysis costs, and large amounts of generated data have made it widely used in plant research, including species identification, especially in the case of protected or endangered taxa. This task is particularly difficult in the case of closely related taxa. The Pinus mugo complex includes several dozen closely related taxa occurring in the most important mountain ranges in Europe. The taxonomic rank, origin, or distribution of many of these taxa have been debated for years. In this study, we used genome skimming and multilocus DNA barcoding approaches to obtain different sequence data sets and also to determine their genetic diversity and suitability for distinguishing closely related taxa in the Pinus mugo complex. We generated seven different data sets, which were then analyzed using three discrimination methods, i.e., tree based, distance based, and assembling species by automatic partitioning. Genetic diversity among populations and taxa was also investigated using haplotype network analysis and principal coordinate analysis. The proposed data set based on divergence hotspots is even twenty-times more variable than the other analyzed sets and improves the phylogenetic resolution of the Pinus mugo complex. In light of the obtained results, Pinus × rhaetica does not belong to the Pinus mugo complex and should not be identified with either Pinus uliginosa or Pinus rotundata. It seems to represent a fixed hybrid or introgressant between Pinus sylvestris and Pinus mugo. In turn, Pinus mugo and Pinus uncinata apparently played an important role in the origins of Pinus uliginosa and Pinus rotundata.}, }
@article {pmid39336651, year = {2024}, author = {Pramatarova, M and Burckhardt, D and Malenovský, I and Gjonov, I and Schuler, H and Štarhová Serbina, L}, title = {Unravelling the Molecular Identity of Bulgarian Jumping Plant Lice of the Family Aphalaridae (Hemiptera: Psylloidea).}, journal = {Insects}, volume = {15}, number = {9}, pages = {}, pmid = {39336651}, issn = {2075-4450}, support = {80-10-5/2024//Scientific Research Fund of SU "St. Kliment Ohridski", FWF Austrian Science Fund, Province of Bolzano-Bozen/ ; }, abstract = {Psyllids (Hemiptera: Psylloidea) are plant sap-sucking insects whose identification is often difficult for non-experts. Despite the rapid development of DNA barcoding techniques and their widespread use, only a limited number of sequences of psyllids are available in the public databases, and those that are available are often misidentified. Here, we provide 80 sequences of two mitochondrial genes, cytochrome c oxidase I (COI) and cytochrome b (Cytb), for 25 species of Aphalaridae, mainly from Bulgaria. The DNA barcodes for 15 of these species are published for the first time. In cases where standard primers failed to amplify the target gene fragment, we designed new primers that can be used in future studies. The distance-based thresholds for the analysed species were between 0.0015 and 0.3415 for COI and 0.0771 and 0.4721 for Cytb, indicating that the Cytb gene has a higher interspecific divergence, compared to COI, and therefore allows for more accurate species identification. The species delimitation based on DNA barcodes is largely consistent with the differences resulting from morphological and host plant data, demonstrating that the use of DNA barcodes is suitable for successful identification of most aphalarid species studied. The phylogenetic reconstruction based on maximum likelihood and Bayesian inference analyses, while showing similar results at high taxonomic levels to previously published phylogenies, provides additional information on the placement of aphalarids at the species level. The following five species represent new records for Bulgaria: Agonoscena targionii, Aphalara affinis, Colposcenia aliena, Co. bidentata, and Craspedolepta malachitica. Craspedolepta conspersa is reported for the first time from the Czech Republic, while Agonoscena cisti is reported for the first time from Albania.}, }
@article {pmid39336619, year = {2024}, author = {Costa, MM and Corbel, V and Ben Hamouda, R and Almeras, L}, title = {MALDI-TOF MS Profiling and Its Contribution to Mosquito-Borne Diseases: A Systematic Review.}, journal = {Insects}, volume = {15}, number = {9}, pages = {}, pmid = {39336619}, issn = {2075-4450}, support = {Grant no PDH-2-NBC 2-B-2201//Direction G&#xe9;n&#xe9;rale de l'Armement/ ; }, abstract = {Mosquito-borne diseases are responsible for hundreds of thousands of deaths per year. The identification and control of the vectors that transmit pathogens to humans are crucial for disease prevention and management. Currently, morphological classification and molecular analyses via DNA barcoding are the standard methods used for vector identification. However, these approaches have several limitations. In the last decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an innovative technology in biological sciences and is now considered as a relevant tool for the identification of pathogens and arthropods. Beyond species identification, this tool is also valuable for determining various life traits of arthropod vectors. The purpose of the present systematic review was to highlight the contribution of MALDI-TOF MS to the surveillance and control of mosquito-borne diseases. Published articles from January 2003 to August 2024 were retrieved, focusing on different aspects of mosquito life traits that could be determinants in disease transmission and vector management. The screening of the scientific literature resulted in the selection of 54 published articles that assessed MALDI-TOF MS profiling to study various mosquito biological factors, such species identification, life expectancy, gender, trophic preferences, microbiota, and insecticide resistance. Although a large majority of the selected articles focused on species identification, the present review shows that MALDI-TOF MS profiling is promising for rapidly identifying various mosquito life traits, with high-throughput capacity, reliability, and low cost. The strengths and weaknesses of this proteomic tool for vector control and surveillance are discussed.}, }
@article {pmid39336609, year = {2024}, author = {Stonis, JR and Remeikis, A and Diškus, A and Dobrynina, V and Orlovskytė, S}, title = {A Phenomenon: What Are the Minuscule Grey Moths Abundant in the Dry Season in the Tropical Dry Forests of the Pacific Coast of Honduras?.}, journal = {Insects}, volume = {15}, number = {9}, pages = {}, pmid = {39336609}, issn = {2075-4450}, abstract = {Our investigation centered on the tropical dry forests along the Pacific coast of Honduras, aiming to elucidate the presence and abundance of minuscule grey moths during the dry season. Through specimen dissections and the taxonomic identification of the collected material, we have described three new species: Acalyptris podenasi sp. nov., A. palpiformis sp. nov., and A. tortoris sp. nov. Additionally, we documented two species previously known from neighboring countries, A. lascuevella Puplesis &amp; Robinson and A. basicornis Remeikis &amp; Stonis. The females of A. lascuevella were previously unknown and are documented here for the first time. Morphological examinations were complemented by DNA barcoding, particularly highlighting variation in A. lascuevella. The paper's primary significance lies not only in the description of new species but also in uncovering their taxonomic, morphological, and molecular importance. We found that these species are unique and indicative of the previously unstudied dry forests as a distinct ecosystem. Our findings revealed several novel atypical morphological traits within the studied Nepticulidae, including unusually large signum cells in the female genitalia, a dorso-ventrally divided uncus, and asymmetrical valvae in the male genitalia. These discoveries underscore the morphological diversity of Acalyptris Meyrick and their significance in evolutionary biology. Consequently, the paper addresses a previously unknown phenomenon of the occurrence and astonishing abundance of minuscule plant-mining micromoths in dry deciduous forests during the peak of the dry season. We hope that this paper will encourage Lepidoptera taxonomists to explore micromoths in other tropical dry forests, which, while limited in distribution, hold global importance. The paper is extensively illustrated with photographs of Acalyptris adults and their genitalia, along with maps, habitats, and molecular phylogenetic trees.}, }
@article {pmid39335263, year = {2024}, author = {Poonlaphdecha, S and Ribas, A and Chaisiri, K and Morand, S and Chan, AHE and Thaenkham, U}, title = {Genetic Characterization of the Co-Invasive Rodent Parasite Heterakis spumosa (Nematoda, Heterakidae).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {18}, pages = {}, pmid = {39335263}, issn = {2076-2615}, support = {ANR BiodivHealthSEA , ANR-17-CE35-0003-02//Agence nationale de la recherche/ ; }, abstract = {Heterakis spumosa, a parasitic worm infecting rodents, is globally prevalent in black rats, brown rats, and house mice. It is hypothesized to originate from Asia due to its widespread presence in Southeast Asia in various Murinae. Previous molecular studies focused on European, African, and Japanese specimens, but none included samples from the putative native range. Rodents were collected between 2008 and 2015 across various localities in Southeast Asia and Europe, identified by morphology or genetic barcoding. Viscera were examined or preserved for later inspection. DNA was extracted from H. spumosa. PCR amplification targeting the mtCOI gene and ITS1 region was conducted in this study using newly designed primers (based on Heterakis reference sequences). PCR amplicons were subsequently sequenced and analyzed. In this study, the phylogenetic analysis using ITS1 sequences revealed that Heterakis samples from Thai and Laotian rodents belong to the species H. spumosa, exhibiting low genetic variation compared to samples from other regions. Genetic distance calculations using mtCOI sequences confirmed the marked distinction of H. spumosa from other Heterakis species. Our phylogenetic analyses using partial mtCOI and ITS1 sequences have significantly enhanced our comprehension of the genetic diversity and evolutionary history of the nematode H. spumosa.}, }
@article {pmid39334308, year = {2024}, author = {Hartop, E and Lee, L and Srivathsan, A and Jones, M and Peña-Aguilera, P and Ovaskainen, O and Roslin, T and Meier, R}, title = {Resolving biology's dark matter: species richness, spatiotemporal distribution, and community composition of a dark taxon.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {215}, pmid = {39334308}, issn = {1741-7007}, support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; ERC-synergy grant 856506-LIFEPLAN//H2020 European Research Council/ ; ERC-synergy grant 856506-LIFEPLAN//H2020 European Research Council/ ; 336212 and 345110//Academy of Finland/ ; }, mesh = {Animals ; *Diptera/physiology/genetics ; *Biodiversity ; Sweden ; *DNA Barcoding, Taxonomic ; Seasons ; Climate Change ; Animal Distribution ; }, abstract = {BACKGROUND: Zoology's dark matter comprises hyperdiverse, poorly known taxa that are numerically dominant but largely unstudied, even in temperate regions where charismatic taxa are well understood. Dark taxa are everywhere, but high diversity, abundance, and small size have historically stymied their study. We demonstrate how entomological dark matter can be elucidated using high-throughput DNA barcoding ("megabarcoding"). We reveal the high abundance and diversity of scuttle flies (Diptera: Phoridae) in Sweden using 31,800 specimens from 37 sites across four seasonal periods. We investigate the number of scuttle fly species in Sweden and the environmental factors driving community changes across time and space.<br><br>RESULTS: Swedish scuttle fly diversity is much higher than previously known, with 549 putative specie) detected, compared to 374 previously recorded species. Hierarchical Modelling of Species Communities reveals that scuttle fly communities are highly structured by latitude and strongly driven by climatic factors. Large dissimilarities between sites and seasons are driven by turnover rather than nestedness. Climate change is predicted to significantly affect the 47% of species that show significant responses to mean annual temperature. Results were robust regardless of&#xa0;whether haplotype diversity or species-proxies were used&#xa0;as response variables. Additionally, species-level models of common taxa adequately predict overall species richness.<br><br>CONCLUSIONS: Understanding the bulk of the diversity around us is imperative during an era of biodiversity change. We show that dark insect taxa can be efficiently characterised and surveyed with megabarcoding. Undersampling of rare taxa and choice of operational taxonomic units do not alter the main ecological inferences, making it an opportune time to tackle zoology's dark matter.}, }
@article {pmid39333158, year = {2024}, author = {Yuan, L and Chen, X and Zhan, H and Henry, GL and Zador, AM}, title = {Massive multiplexing of spatially resolved single neuron projections with axonal BARseq.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8371}, pmid = {39333158}, issn = {2041-1723}, support = {RF1MH123403//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1 MH123403/MH/NIMH NIH HHS/United States ; U19NS123716//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U19 NS123716/NS/NINDS NIH HHS/United States ; D16PC0008//ODNI | Intelligence Advanced Research Projects Activity (IARPA)/ ; }, mesh = {Animals ; *Axons/metabolism ; *Neurons/cytology ; Mice ; Male ; *Auditory Cortex/cytology/physiology ; Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Mice, Inbred C57BL ; }, abstract = {Neurons in the cortex are heterogeneous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens. Here we present axonal BARseq, a high-throughput approach based on reading out nucleic acid barcodes using in situ RNA sequencing, which enables analysis of even densely labeled neurons. As a proof of principle, we have mapped the long-range projections of >8000 primary auditory cortex neurons from a single male mouse. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains.}, }
@article {pmid39333091, year = {2024}, author = {O'Neill, MJ and Yang, T and Laudeman, J and Calandranis, ME and Harvey, ML and Solus, JF and Roden, DM and Glazer, AM}, title = {ParSE-seq: a calibrated multiplexed assay to facilitate the clinical classification of putative splice-altering variants.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8320}, pmid = {39333091}, issn = {2041-1723}, support = {R35 GM150465/GM/NIGMS NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; F30 HL163923/HL/NHLBI NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; R01 HL164675/HL/NHLBI NIH HHS/United States ; R00 HG010904/HG/NHGRI NIH HHS/United States ; S10 OD025281/OD/NIH HHS/United States ; R01 HL149826/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Induced Pluripotent Stem Cells/metabolism ; *Myocytes, Cardiac/metabolism/cytology ; *RNA Splicing/genetics ; *NAV1.5 Voltage-Gated Sodium Channel/genetics/metabolism ; Arrhythmias, Cardiac/genetics ; RNA Splice Sites/genetics ; CRISPR-Cas Systems/genetics ; Calibration ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; Introns/genetics ; HEK293 Cells ; }, abstract = {Interpreting the clinical significance of putative splice-altering variants outside canonical splice sites remains difficult without time-intensive experimental studies. To address this, we introduce Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed assay to quantify variant effects on RNA splicing. We first apply this technique to study hundreds of variants in the arrhythmia-associated gene SCN5A. Variants are studied in 'minigene' plasmids with molecular barcodes to allow pooled variant effect quantification. We perform experiments in two cell types, including disease-relevant induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). The assay strongly separates known control variants from ClinVar, enabling quantitative calibration of the ParSE-seq assay. Using these evidence strengths and experimental data, we reclassify 29 of 34 variants with conflicting interpretations and 11 of 42 variants of uncertain significance. In addition to intronic variants, we show that many synonymous and missense variants disrupted RNA splicing. Two splice-altering variants in the assay also disrupt splicing and sodium current when introduced into iPSC-CMs by CRISPR-Cas9 editing. ParSE-seq provides high-throughput experimental data for RNA-splicing to support precision medicine efforts and can be readily adopted to study other loss-of-function genotype-phenotype relationships.}, }
@article {pmid39332616, year = {2025}, author = {Lone, S and Narayan, S and Hussain, K and Malik, M and Yadav, SK and Khan, FA and Safa, A and Ahmad, A and Masoodi, KZ}, title = {Investigating the antioxidant and anticancer potential of Daucus spp. extracts against human prostate cancer cell line C4-2, and lung cancer cell line A549.}, journal = {Journal of ethnopharmacology}, volume = {337}, number = {Pt 2}, pages = {118855}, doi = {10.1016/j.jep.2024.118855}, pmid = {39332616}, issn = {1872-7573}, mesh = {Humans ; *Antioxidants/pharmacology/isolation &amp; purification ; *Plant Extracts/pharmacology/chemistry ; Male ; *Daucus carota/chemistry ; *Prostatic Neoplasms/drug therapy ; *Lung Neoplasms/drug therapy ; *Antineoplastic Agents, Phytogenic/pharmacology/isolation &amp; purification ; A549 Cells ; Cell Line, Tumor ; Cell Proliferation/drug effects ; }, abstract = {The study evaluated 297 carrot germplasm lines, focusing on 52 cultivars to explore their therapeutic potential and address challenges related to the accessibility and affordability of nutraceuticals and health promoting foods. The investigation explores the application of DNA barcoding using the ITS region for precise species identification, highlighting genetic diversity among the examined cultivars. Through ITS sequence-based analysis and phylogenetic examination, six diverse Daucus spp. genotypes were differentiated and classified into distinct groups, indicating the presence of vast genetic variation. Evaluation of antioxidant activities using the DPPH radical scavenging assay revealed varying degrees of scavenging ability among genotypes with SKAU-C-15, SKAU-C-17, and SKAU-C-16 exhibiting the highest activity, suggesting their potential for antioxidant-rich products. Thin Layer Chromatography (TLC) bioautography confirmed the presence of bioactive compounds in carrot extracts responsible for their antioxidant properties. In cell culture studies, specific carrot genotype extracts demonstrated potential anti-proliferative and anti-invasive effects on recurrent prostate cancer cell line - C4-2 (SKAU-C-30, SKAU-C-10, and SKAU-C-42) and non-small cell lung cancer cell line - A549 (SKAU-C-18 and SKAU-C-11) cancer cells, as indicated by MTT assay, wound healing assay, and Colony Forming Unit assay. These findings suggest the promising therapeutic potential of carrot genotypes for developing anti-cancer functional foods, nutraceuticals and health supplements.Therefore, the study contributes to the nutrition security, paving the way for advancements in functional foods and health applications, particularly in cancer treatment and prevention.}, }
@article {pmid39331360, year = {2024}, author = {Foote, NE and Foote, GG and Comai, N and Ibarra Caballero, JR and Stewart, JE and Ambrose, AR and Baxter, WL and Davis, TS}, title = {Patterns of occurrence, phenology, and phylogeny of Phloeosinus punctatus LeConte (Coleoptera: Curculionidae, Scolytinae) in giant sequoia.}, journal = {Environmental entomology}, volume = {53}, number = {6}, pages = {1183-1196}, pmid = {39331360}, issn = {1938-2936}, support = {//Save the Redwoods League/ ; //National Park Service/ ; P21AC12281//Colorado Plateau Cooperative Ecosystem Studies Unit, Northern Arizona University/ ; }, mesh = {Animals ; *Phylogeny ; *Weevils/genetics/physiology ; Male ; Female ; Reproduction ; Flight, Animal ; }, abstract = {Here, we describe patterns of reproduction and flight phenology of putative Phloeosinus punctatus in giant sequoia groves and compare morphology and genotypes of beetles from sympatric giant sequoia (Sequoiadendron giganteum) and California incense-cedar (Calocedrus decurrens). Surveys conducted in 2022 revealed that numerous branches fall from giant sequoia crowns (on average ~30 branches/tree), with 20%-50% of trees per site shedding branches, depositing breeding material for beetles on the forest floor that subsequently becomes colonized. When noninfested branches cut from mature giant sequoias were placed at the ground surface, they were colonized by P. punctatus and produced an average of 28 beetles/kg branch. Climbing and examination of sequoia crowns in 2023 showed that 75% of mature trees across 11 groves showed evidence of adult beetle entrance holes in their crowns. In 2021, tests with sticky traps showed that beetles alighted on fallen branches from 20th May to 20th August (peak landing: 2nd July); a logistic model developed from emergence data in 2021 and 2022 predicts the emergence of F1 offspring from branches between 10th July and 1st September (peak emergence: 8th August). Beetles emerging from giant sequoia preferred to settle on giant sequoia, did not reproduce in incense-cedar, and diverged morphologically from beetles emerging from incense-cedar. However, phylogenetic analysis of three genes (28S, CAD, and COI) revealed no clear pattern of sequence divergence, suggesting a single species (P. punctatus) that colonizes both hosts, though cryptic speciation may not be detectable with standard barcoding genes. Ecological and potential management implications are discussed.}, }
@article {pmid39329134, year = {2024}, author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR}, title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18025}, pmid = {39329134}, issn = {2167-8359}, support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; *Insecta/microbiology/genetics ; *RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/isolation &amp; purification/classification ; Polymerase Chain Reaction/methods ; Biodiversity ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.<br><br>METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.<br><br>RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.<br><br>CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.}, }
@article {pmid39329133, year = {2024}, author = {Morris, MRJ and Summers, MM and Kwan, M and Mee, JA and Rogers, SM}, title = {Mislabeled and ambiguous market names in invertebrate and finfish seafood conceal species of conservation concern in Calgary, Alberta, Canada.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18113}, pmid = {39329133}, issn = {2167-8359}, mesh = {Animals ; Alberta ; *Seafood/analysis ; *DNA Barcoding, Taxonomic ; Food Labeling/legislation &amp; jurisprudence ; Invertebrates/classification ; Conservation of Natural Resources ; Fishes/genetics ; Endangered Species ; }, abstract = {BACKGROUND: The mislabeling of seafood, wherein a food product's marketed name does not match its contents, has the potential to mask species of conservation concern. Less discussed is the role of legally ambiguous market names, wherein a single name could be used to sell multiple species. Here we report the first study in Canada to examine mislabeling and ambiguous market names in both invertebrate (e.g., bivalve, cephalopod, shrimp) and finfish products.<br><br>METHODS: A total of 109 invertebrate and 347 finfish products were sampled in Calgary between 2014 and 2020. Market names were documented from the label or equivalent and determined to be precise (the name could apply to only one species) or ambiguous (multiple species could be sold under that name). A region of the cytochrome c oxidase I gene was sequenced and compared to reference sequences from boldsystems.org. Samples were considered mislabeled if the species identified through DNA barcoding did not correspond to the market name, as determined through the Canadian Food Inspection Agency Fish List. Mislabeling was further differentiated between semantic mislabeling, wherein the market name was not found on the Fish List but the barcode identity was in line with what a consumer could reasonably have expected to have purchased; invalid market names, wherein the market name was so unusual that no legitimate inferences as to the product's identity could be made; and product substitution, wherein the DNA barcode identified the product as a species distinct from that associated with the market name. Invalid market names and product substitutions were used to provide conservative estimates of mislabeling. The global conservation status of the DNA-identified invertebrate or finfish was determined through the International Union for the Conservation of Nature Red List. A logistic regression was used to determine the relationship between precision and accuracy in predicting conservation status of the sampled species.<br><br>RESULTS: There was no significant difference in mislabeling occurrence between invertebrates (33.9% total mislabeling occurrence, 20.2% product substitution) and finfish (32.3% total mislabeling occurrence, 21.3% product substitution/invalid market names). Product substitutions sometimes involved species of conservation concern, such as foods marketed as freshwater eel (Anguilla rostrata) that were determined through DNA barcoding to be European eel (Anguilla anguilla), or cuttlefish balls putatively identified as the Endangered threadfin porgy (Evynnis cardinalis). Product substitutions and ambiguous market names were significantly associated with the sale of species of conservation concern, but ambiguity was a more important predictor. Although preventing the mislabeling of seafoods can and must remain a priority in Canada, our work suggests that moving towards precise names for all seafood products will better support sustainable fisheries goals.}, }
@article {pmid39326961, year = {2024}, author = {Khumalo, N and Ledwaba, MB and Labuschagne, K and Voster, I and Oosthuizen, M and Mwale, M and Chaisi, M}, title = {Identification of ticks and tick-borne pathogens of wildlife necropsy cases submitted to the SANBI National Zoological Gardens, South Africa.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {55}, number = {}, pages = {101105}, doi = {10.1016/j.vprsr.2024.101105}, pmid = {39326961}, issn = {2405-9390}, mesh = {Animals ; South Africa/epidemiology ; *Animals, Wild/parasitology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Tick-Borne Diseases/veterinary/parasitology/epidemiology/microbiology ; *RNA, Ribosomal, 16S/analysis ; *Ticks/parasitology/microbiology ; Phylogeny ; Female ; DNA Barcoding, Taxonomic/veterinary ; Animals, Zoo/parasitology ; }, abstract = {Ticks are arachnid blood-feeding parasites, which infest livestock, wildlife, and humans, transmitting medically and veterinary significant pathogens. Their biodiversity and distribution in wild animals remains complex. This study analysed archived tick samples (n = 48) from the South African Biodiversity Institute (SANBI) Wildlife Biobank utilizing morphology and genetic analyses of the 16S rRNA and COI (DNA barcoding) mitochondrial genes to identify ticks collected among 13 vertebratesavian, reptilian, and mammalian host species. The specimens came from nine localities including nature reserves and captive facilities (zoological garden) in South Africa, Namibia, and Botswana. These ticks were also assessed for associated pathogens with the reverse line blot (RLB) hybridization assay. Seven tick genera, Amblyomma, Hyalomma, Haemaphysalis, Ixodes, Rhipicephalus, Rhipicentor, and Otobius were identified, with Amblyomma being the most prevalent (22.9 %) in our sample set. Obtained sequences were 95-100 % similar to published records of tick species collected from wild and domestic animals, as well as those collected from vegetation, from different southern African areas. However, tick specimens (n = 3) identified morphologically as Hyalomma truncatum, Rhipicephalus e. evertsi, and R. simus, were, on a molecularly level, more closely related to their sister taxa (H. glabrum, R. e. mimeticus, and R. gertrudae, respectively) suggesting a need for taxonomic verification. With the RLB hybridization assay, six samples reacted with the Ehrlichia/Anaplasma genus-specific probe, while two reacted with the Theileria/Babesia genus-specific probe. Sequencing of the RLB amplicons targeting the 18S rRNA gene (n = 2) indicated 100 % similarity to Hepatozoon fitzsimonsi, while one was closely related to He. ingwe with 99.39 % similarity. The results show that wildlife harbour different tick species, and pathogen detection identified novel genotypes, indicating wildlife as potential pathogens reservoirs. This study enhances our understanding of tick biodiversity, distribution and highlights wildlife's role in harbouring diverse tick species and novel pathogens.}, }
@article {pmid39326113, year = {2025}, author = {Zhao, R and Niu, Q and Murtaza, G and Zhang, G and Yang, Y}, title = {Integrated identification and detection of hydration state and its evolution using terahertz technology.}, journal = {Talanta}, volume = {281}, number = {}, pages = {126943}, doi = {10.1016/j.talanta.2024.126943}, pmid = {39326113}, issn = {1873-3573}, abstract = {The accurate detection of dehydration processes in hydrated drugs can reveal various intermolecular vibration modes mediated by hydrogen bonds between water molecules and other components, which underpin the further development of pharmaceutical science, food safety and biophysics. Herein, terahertz (THz) technology is utilized to investigate the dehydration state of d(+)-Raffinose pentahydrate (Rf·5H2O), in conjunction with imaging-based point by point scanning data acquisition and barcodes methods, to establish an innovative platform integrated identification, trace detection, and application capabilities. Our study demonstrates that the dehydration process of Rf·5H2O can be dynamically monitored through the evolution of its THz absorption peaks, offering more precise results compared to XRD and Raman spectroscopies. Moreover, the absorbance spectra data collected at each individual pixel is utilized to build visualized THz images, achieving an ultralow minimum content required for detection of 0.032 μg/(50 μm)[2]. Additionally, we introduce a THz spectra-barcode conversion system that not only ensures efficient electronic recordkeeping but also enhances user readability, thereby facilitating the practical applications of THz technology.}, }
@article {pmid39323091, year = {2024}, author = {Zhang, Y and Shen, C and Xia, K}, title = {Multi-Cover Persistence (MCP)-based machine learning for polymer property prediction.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39323091}, issn = {1477-4054}, support = {//Nanyang Technological University SPMS Collaborative Research Award 2022/ ; MOE-T2EP20220-0010//Singapore Ministry of Education Academic Research/ ; }, mesh = {*Polymers/chemistry ; *Machine Learning ; Algorithms ; }, abstract = {Accurate and efficient prediction of polymers properties is crucial for polymer design. Recently, data-driven artificial intelligence (AI) models have demonstrated great promise in polymers property analysis. Even with the great progresses, a pivotal challenge in all the AI-driven models remains to be the effective representation of molecules. Here we introduce Multi-Cover Persistence (MCP)-based molecular representation and featurization for the first time. Our MCP-based polymer descriptors are combined with machine learning models, in particular, Gradient Boosting Tree (GBT) models, for polymers property prediction. Different from all previous molecular representation, polymer molecular structure and interactions are represented as MCP, which utilizes Delaunay slices at different dimensions and Rhomboid tiling to characterize the complicated geometric and topological information within the data. Statistic features from the generated persistent barcodes are used as polymer descriptors, and further combined with GBT model. Our model has been extensively validated on polymer benchmark datasets. It has been found that our models can outperform traditional fingerprint-based models and has similar accuracy with geometric deep learning models. In particular, our model tends to be more effective on large-sized monomer structures, demonstrating the great potential of MCP in characterizing more complicated polymer data. This work underscores the potential of MCP in polymer informatics, presenting a novel perspective on molecular representation and its application in polymer science.}, }
@article {pmid39322294, year = {2024}, author = {Wang, D and He, Z and Yang, C and Lu, D and Sun, Y and Kou, Y and Qian, D and Zhang, H and Liu, Y}, title = {[Genetic polymorphisms of common sandflies in selected areas of Henan Province based on DNA barcoding].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {36}, number = {4}, pages = {352-360}, doi = {10.16250/j.32.1374.2024036}, pmid = {39322294}, issn = {1005-6661}, support = {222102310722//Henan Provincial Science and Technology Research Project/ ; LHGJ20220171//Henan Provincial Medical Science and Technology Research Project/ ; LHGJ20230640//Henan Provincial Medical Science and Technology Research Project/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Polymorphism, Genetic ; China ; *Phylogeny ; *Psychodidae/genetics/classification ; *Electron Transport Complex IV/genetics ; }, abstract = {OBJECTIVE: To characterize the species of common sandflies in Henan Province using DNA barcoding with cytochrome c oxidase subunit I (COI) gene as the molecular marker, and to analyze the genetic polymorphisms of sandflies, so as to provide insights into visceral leishmaniasis prevention and control in Henan Province.<br><br>METHODS: Sandfly specimens were sampled from 13 sandflies surveillance sites from 2021 to 2023 in Anyang City, Zhengzhou, Luoyang and Xuchang cities (Zhengzhou-Luoyang-Xuchang areas) where visceral leishmaniasis cases were reported and in Jiaozuo and Xinxiang cities (Jiaozuo-Xinxiang areas) without visceral leishmaniasis cases reported. Genomic DNA was extracted from a single sandfly, and COI gene was amplified. The amplification product was subjected to bidirectional sequencing. Following sequence assembly, the species of sandflies was characterized through sequence alignment using the BLAST tool. The intra-specific and inter-specific genetic distances of sandflies were estimated among different areas using the software Mega 11, and phylogenetic trees were created. The polymorphisms of nucleotide sequences in the sandflies COI gene were estimated using the software DnaSP. The fixation index (FST) of different geographical isolates of sandflies was calculated using the Arlequin software, and the gene flow value (Nm) was used to measure the gene flow in the sandflies populations. In addition, the population genetic structure of different geographical populations of Phlebotomus chinensis was analyzed using the STRUCTURE software.<br><br>RESULTS: A total of 978 sandflies were collected from 13 sandflies surveillance sites in Zhengzhou-Luoyang-Xuchang areas, Jiaozuo-Xinxiang areas and Anyang City of Henan Province from 2021 to 2023, and 475 sandflies were randomly sampled for subsequent detections. A total of 304 Ph. chinensis, 162 Se. squamirostris and 9 Se. bailyi were identified based on molecular biological detection of the COI gene, and Se. bailyi was reported for the first time in Henan Province. The intraspecific genetic distances of sandflies were 0.000 to 0.040, and the inter-specific genetic distances ranged from 0.133 to 0.161. Phylogenetic analysis revealed that each of the three sandfly species was clustered into a clade. The genetic polymorphisms of Ph. chinensis populations varied among different areas, with the highest haplotype diversity (0.966 &#xb1; 0.007) and the greatest nucleotide diversity (0.011) in Zhengzhou-Luoyang-Xuchang areas, and the lowest haplotype diversity (0.720 &#xb1; 0.091) and nucleotide diversity (0.004) in Anyang City. The dominant haplotype of Ph. chinensis populations was Pch_Hap_2 in Anyang City and Jiaozuo-Xinxiang areas, with moderate genetic differentiation (0.05 < FST < 0.15) and frequent gene exchange (Nm value > 1) between Ph. chinensis populations sampled from Anyang City, and Jiaozuo-Xinxiang areas. Population genetic structure analysis showed that the dominant component of Ph. chinensis populations was K5 in Anyang City and Jiaozuo-Xinxiang areas. No obvious dominant haplotype was observed in Ph. chinensis populations sampled from Zhengzhou-Luoyang-Xuchang areas, which had very high genetic differentiation (FST > 0.25) and little gene exchange (Nm value < 1) with Ph. chinensis populations from Anyang City, and Jiaozuo-Xinxiang areas, with K3 as the dominant component. In addition, there was no significant difference in the genetic polymorphism level among Se. squamirostris populations from the three areas.<br><br>CONCLUSIONS: There are Ph. chinensis, Se. squamirostris and Se. bailyi in Henan Province, and S. bailyi is recorded for the first time in Henan Province by molecular biological assays. There are different levels of genetic differentiation and gene exchange among P. chinensis populations in different areas of Henan Province.}, }
@article {pmid39318677, year = {2024}, author = {Kaila, L and Huemer, P}, title = {Elachistadimicatella sensu auctt.-a complex of neglected species diversity (Lepidoptera, Elachistidae) from European mountain systems.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {179-194}, pmid = {39318677}, issn = {1313-2989}, abstract = {Elachistadimicatella Rebel, 1903, has so far been considered a species in Europe with restricted distribution from Ukraine to western France. The species occurs on mountainous regions. However, the in-depth analysis of a taxonomically uncertain species of Elachista from the Cottian Alps (Italy), especially through DNA barcoding and subsequent morphological studies, led to the realization that individuals previously identified as E.dimicatella from the Cottian Alps and the Pyrenees were misidentified. According to our research, a total of three species can be differentiated: E.dimicatella from Carpathians and its former junior synonym E.niphadophanes Meyrick, 1937, sp. rev., from the Pyrenees, as well as the newly described E.cottiella sp. nov. from southwestern Alps, hitherto incorrectly identified as E.dimicatella. Diagnostic features of the three species are discussed and illustrated. Elachistadimicatella and E.niphadophanes are redescribed.}, }
@article {pmid39318675, year = {2024}, author = {Dettner, K and Kovács, Z and Rewicz, T and Csabai, Z}, title = {Age-dependent variation of aedeagal morphology in Agabusuliginosus and the status of A.lotti (Coleoptera, Dytiscidae).}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {153-177}, pmid = {39318675}, issn = {1313-2989}, abstract = {A doubt has arisen about the taxonomic status of Agabuslotti within the Agabusuliginosus species group due to morphological similarities and lack of molecular data. In this study, a comprehensive morphological and molecular analysis of specimens from Central Europe was conducted, focusing on the Hungarian population. Morphological comparisons of genital structures revealed age-dependent variations, suggesting a gradual transition from A.lotti to A.uliginosus. Molecular analysis of COI sequences further supported this hypothesis, showing minimal genetic differences among most specimens, with only one individual exhibiting distinctiveness. Therefore, A.lotti syn. nov. must be regarded as a junior synonym of A.uliginosus. Our findings also highlight the need for additional multi-marker studies covering a broader geographic range and including both molecular and morphological approaches to elucidate the taxonomic and phylogenetic relationships within this species group. The inclusion of Hungarian samples notably enriched the diversity of haplotypes, emphasizing the importance of expanding sampling efforts in future research.}, }
@article {pmid39318674, year = {2024}, author = {Qian, X and Tang, C and Wang, N and Yang, D}, title = {Syntormon Loew (Diptera, Dolichopodidae) from Inner Mongolia, China, with the description of a new species.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {143-152}, pmid = {39318674}, issn = {1313-2989}, abstract = {Previously, no records of Syntormon Loew, 1857 species were known from Inner Mongolia (China). The genus is reported here from Inner Mongolia for the first time, with the description of a new species, S.sinicum sp. nov., along with two previously described species, S.dukha Hollis, 1964 and S.henanense Yang &amp; Saigusa, 2000. Syntormonsinicum sp. nov. and S.dukha Hollis, 1964 are barcoded for the first time to support the species delimitation. A key to Syntormon species in China is provided.}, }
@article {pmid39318673, year = {2024}, author = {Silva-Segundo, CA and Funes-Rodríguez, R and Anaya-Godínez, E and Gómez-Gutiérrez, J}, title = {Molecular and morphological identification of larvae of Carangidae (Teleostei, Carangiformes) species from southern Gulf of California.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {195-215}, pmid = {39318673}, issn = {1313-2989}, abstract = {The description of diagnostic morphological characters and DNA barcoding of fish larvae from nine species of the carangid family are provided from specimens collected during a weekly zooplankton time-series (2016-2017) at Cabo Pulmo National Park, Gulf of California, Mexico. Five nominal species (Caranxsexfasciatus, C.caballus, Naucratesductor, Selarcrumenophthalmus, and Seleneperuviana) and three morphotypes of Decapterus spp. and one of Caranx spp. were identified and separated based on morphological, meristic, and pigmentary diagnostic characters. All larvae were genetically sequenced for a fragment of the cytochrome c oxidase subunit I mitochondrial gene. Sequences of larval Caranx and Decapterus showed high genetic similarity (> 99%), low intraspecific divergence (< 1%), and an interspecific divergence between 6% and 11%, allowing the discrimination of diagnostic pigmentation patterns of fish larvae among three sibling species from each genus: Caranx (C.caballus, C.caninus, and C.sexfasciatus) and Decapterus (D.macarellus, D.macrosoma, and D.muroadsi). DNA barcoding supported the presence of Caranxcaballus, C.caninus, C.sexfasciatus, Decapterusmacarellus, D.muroadsi, Selarcrumenophthalmus, and Seleneperuviana, and for the first time Naucratesductor and D.macrosoma at the CPNP. Abundance of these nine species (confirmed molecularly) was estimated throughout the 2016-2017 weekly time series. Decapterusmacarellus and Caranxcaninus were the most abundant species. The morphological and molecular taxonomic methods allowed us to infer the species number and abundance of these commercial species at the CPNP to improve conservation in protected areas and fishery management.}, }
@article {pmid39315963, year = {2024}, author = {George, FM and Venkatesan, S and Srinivasan, V and Semalaiyappan, J and Kuttiatt, VS}, title = {DNA barcoding and phylogenetic analysis of the vector Culex gelidus and its global and public health significance.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {49}, number = {2}, pages = {S5-S9}, doi = {10.52707/1081-1710-49.2.S5}, pmid = {39315963}, issn = {1948-7134}, mesh = {Animals ; *Culex/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Phylogeny ; Public Health ; Mosquito Vectors/genetics ; }, }
@article {pmid39315814, year = {2024}, author = {Loes, AN and Tarabi, RAL and Huddleston, J and Touyon, L and Wong, SS and Cheng, SMS and Leung, NHL and Hannon, WW and Bedford, T and Cobey, S and Cowling, BJ and Bloom, JD}, title = {High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains.}, journal = {Journal of virology}, volume = {98}, number = {10}, pages = {e0068924}, pmid = {39315814}, issn = {1098-5514}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; T11-712/19-N//Research Grants Council, University Grants Committee ()/ ; U01AI153700//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01 AI153700/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; R01AI165821//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; Investigator Support//Howard Hughes Medical Institute (HHMI)/ ; R01 AI165821/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Antibodies, Neutralizing/immunology/blood ; *Influenza A Virus, H1N1 Subtype/immunology/genetics ; *Influenza Vaccines/immunology/administration &amp; dosage ; *Antibodies, Viral/blood/immunology ; *Influenza, Human/prevention &amp; control/immunology/virology ; *Neutralization Tests/methods ; *Vaccination ; *Hemagglutinin Glycoproteins, Influenza Virus/immunology/genetics ; Adult ; Female ; }, abstract = {UNLABELLED: The high genetic diversity of influenza viruses means that traditional serological assays have too low throughput to measure serum antibody neutralization titers against all relevant strains. To overcome this challenge, we developed a sequencing-based neutralization assay that simultaneously measures titers against many viral strains using small serum volumes using a workflow similar to traditional neutralization assays. The key innovation is to incorporate unique nucleotide barcodes into the hemagglutinin (HA) genomic segment, and then pool viruses with numerous different barcoded HA variants and quantify the infectivity of all of them simultaneously using next-generation sequencing. With this approach, a single researcher performed the equivalent of 2,880 traditional neutralization assays (80 serum samples against 36 viral strains) in approximately 1 month. We applied the sequencing-based assay to quantify the impact of influenza vaccination on neutralization titers against recent human H1N1 strains for individuals who had or had not also received a vaccine in the previous year. We found that the viral strain specificities of the neutralizing antibodies elicited by vaccination vary among individuals and that vaccination induced a smaller increase in titers for individuals who had also received a vaccine the previous year-although the titers 6 months after vaccination were similar in individuals with and without the previous-year vaccination. We also identified a subset of individuals with low titers to a subclade of recent H1N1 even after vaccination. We provide an experimental protocol (dx.doi.org/10.17504/protocols.io.kqdg3xdmpg25/v1) and computational pipeline (https://github.com/jbloomlab/seqneut-pipeline) for the sequencing-based neutralization assays to facilitate the use of this method by others.<br><br>IMPORTANCE: We describe a new approach that can rapidly measure how the antibodies in human serum inhibit infection by many different influenza strains. This new approach is useful for understanding how viral evolution affects antibody immunity. We apply the approach to study the effect of repeated influenza vaccination.}, }
@article {pmid39314939, year = {2024}, author = {Shao, F and Hu, J and Zhang, P and Akarapipad, P and Park, JS and Lei, H and Hsieh, K and Wang, TH}, title = {Enhanced CRISPR/Cas-Based Immunoassay through Magnetic Proximity Extension and Detection.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.06.24313206}, pmid = {39314939}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-associated systems have recently emerged as a focal point for developing next-generation molecular diagnosis, particularly for nucleic acid detection. However, the detection of proteins is equally critical across diverse applications in biology, medicine, and the food industry, especially for diagnosing and prognosing diseases like cancer, Alzheimer's and cardiovascular conditions. Despite recent efforts to adapt CRISPR/Cas systems for protein detection with immunoassays, these methods typically achieved sensitivity only in the femtomolar to picomolar range, underscoring the need for enhanced detection capabilities. To address this, we developed CRISPR-AMPED, an innovative CRISPR/Cas-based immunoassay enhanced by magnetic proximity extension and detection. This approach combines proximity extension assay (PEA) with magnetic beads that converts protein into DNA barcodes for quantification with effective washing steps to minimize non-specific binding and hybridization, therefore reducing background noise and increasing detection sensitivity. The resulting DNA barcodes are then detected through isothermal nucleic acid amplification testing (NAAT) using recombinase polymerase amplification (RPA) coupled with the CRISPR/Cas12a system, replacing the traditional PCR. This integration eliminates the need for thermocycling and bulky equipment, reduces amplification time, and provides simultaneous target and signal amplification, thereby significantly boosting detection sensitivity. CRISPR-AMPED achieves attomolar level sensitivity, surpassing ELISA by over three orders of magnitude and outperforming existing CRISPR/Cas-based detection systems. Additionally, our smartphone-based detection device demonstrates potential for point-of-care applications, and the digital format extends dynamic range and enhances quantitation precision. We believe CRISPR-AMPED represents a significant advancement in the field of protein detection.}, }
@article {pmid39314390, year = {2024}, author = {Cabrera-Sosa, L and Safarpour, M and Kattenberg, JH and Ramirez, R and Vinetz, J and Rosanas-Urgell, A and Gamboa, D and Delgado-Ratto, C}, title = {Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.09.611954}, pmid = {39314390}, issn = {2692-8205}, abstract = {Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv &amp; 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs &amp; Pf: 28 SNPs) and MS panels (Pv: 16 MS &amp; Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.}, }
@article {pmid39314385, year = {2024}, author = {Baron, CS and Mitchell, O and Avagyan, S and Menard, R and Yang, S and Robertson, AL and Potluri, R and Shendure, J and Madelaine, R and McKenna, A and Zon, LI}, title = {Leukemia-derived apelin selects endothelial niche clones to promote tumorigenesis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.09.612077}, pmid = {39314385}, issn = {2692-8205}, abstract = {Hematopoietic stem cells are regulated by endothelial and mesenchymal stromal cells in the marrow niche1-3. Leukemogenesis was long believed to be solely driven by genetic perturbations in hematopoietic cells but introduction of genetic mutations in the microenvironment demonstrated the ability of niche cells to drive disease progression4-8. The mechanisms by which the stem cell niche induces leukemia remain poorly understood. Here, using cellular barcoding in zebrafish, we found that clones of niche endothelial and stromal cells are significantly expanded in leukemic marrows. The pro-angiogenic peptide apelin secreted by leukemic cells induced sinusoidal endothelial cell clonal selection and transcriptional reprogramming towards an angiogenic state to promote leukemogenesis in vivo. Overexpression of apelin in normal hematopoietic stem cells led to clonal amplification of the niche endothelial cells and promotes clonal dominance of blood cells. Knock-out of apelin in leukemic zebrafish resulted in a significant reduction in disease progression. Our results demonstrate that leukemic cells remodel the clonal and transcriptional landscape of the marrow niche to promote leukemogenesis and provide a potential therapeutic opportunity for anti-apelin treatment.}, }
@article {pmid39310847, year = {2024}, author = {Böning, S and Schneider, F and Huber, AK and Langhoff, D and Lin, H and Kaczorowski, A and Stenzinger, A and Hohenfellner, M and Duensing, S and Duensing, A}, title = {Region of interest localization, tissue storage time, and antibody binding density-a technical note on the GeoMx® Digital Spatial Profiler.}, journal = {Immuno-oncology technology}, volume = {23}, number = {}, pages = {100727}, pmid = {39310847}, issn = {2590-0188}, abstract = {BACKGROUND: Spatial biology is an emerging concept to interrogate tumor heterogeneity. The NanoString GeoMx® Digital Spatial Profiling (DSP) platform has become increasingly available. It combines high-plex analysis of protein or messenger RNA expression using barcoded antibodies or oligonucleotide probes with investigator-driven selection of regions of interest. Cell populations, e.g. immune cells, can be selectively analyzed via segmentation. A key advantage is the use of archived formalin-fixed, paraffin-embedded tissue, however, begging the question whether and to what extent tissue fixation and storage time affect the results.<br><br>MATERIALS AND METHODS: Antibody binding density (ABD), i.e. the number of barcodes/&#x3bc;m[2], is a key quality control measure for DSP spatial proteomics. To assess whether regional differences in tissue fixation have an influence on ABD, we compared 652 regions of interest selected from tumor center and periphery of 49 prostate cancer and 25 renal cell carcinoma (RCC) specimens. Moreover, the effect of tissue storage time on ABD was examined. Finally, we tested whether regional differences have an influence on ABD of segmented CD45+ or CD8+ cells.<br><br>RESULTS: No significant differences in ABD between tumor center and periphery were found in prostate cancer or RCC. However, ABD was significantly higher in recent specimens (&#x2264;5 years) when compared with those that were older (>5&#xa0;years; P&#xa0;= 0.027). There was a trend towards higher ABD in the tumor periphery of RCC specimens after segmentation for immune cells, albeit without reaching statistical significance.<br><br>CONCLUSIONS: The NanoString GeoMx&#xae; DSP platform delivers robust data to interrogate tumor heterogeneity, but tissue storage time should be considered when interpreting the results.}, }
@article {pmid39309168, year = {2024}, author = {Mitchueachart, B and Sutcharit, C and Tongkerd, P and Panha, S}, title = {Morphological and molecular evidence uncovers hidden species diversity in the leatherleaf slug genus Valiguna (Systellommatophora, Veronicellidae) from Thailand.}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {79-107}, pmid = {39309168}, issn = {1313-2989}, abstract = {The poorly studied leatherleaf slug genus Valiguna in Thailand was carefully investigated. Members of this genus are phenotypically similar, making their identification very challenging. This study clarifies the taxonomic status of all Valiguna species in Thailand by combining morphological and anatomical studies with DNA barcoding. Monophyly of all Valiguna species was confirmed by analysis of the mitochondrial COI data and that all Valiguna species have the acropleurocaulis type of penis. Currently, three Valiguna species are recognised: V.siamensis, V.semicerina Mitchueachart &amp; Panha, sp. nov., and V.crispa Mitchueachart &amp; Panha, sp. nov. that are new to science. For distinct characteristics, V.siamensis is characterised by having a cylindrical penis and honeycomb-like glans, V.semicerina sp. nov. has a lanceolate penis with half honeycomb-like glans, and V.crispa sp. nov. has a cylindrical penis with wavy-like glans. In addition, more detailed descriptions of the radula and genitalia of all three species and their distribution are also carefully presented, enhancing the understanding of this leatherleaf slug genus in Thailand.}, }
@article {pmid39309166, year = {2024}, author = {Srisonchai, R and Likhitrakarn, N and Sutcharit, C and Wesener, T}, title = {Integrative taxonomy reveals two new giant pill-millipedes of the genus Zephronia Gray, 1832 from eastern Thailand (Diplopoda, Sphaerotheriida, Zephroniidae).}, journal = {ZooKeys}, volume = {1212}, number = {}, pages = {29-64}, pmid = {39309166}, issn = {1313-2989}, abstract = {A large amount of material of the millipede genus Zephronia Gray, 1832 was collected during 2014-2023 from many parts of eastern Thailand. An integrative study of morphological characters and genetic data (COI gene) revealed two new species: Z.chantaburiensis Srisonchai &amp; Wesener, sp. nov. and Z.macula Srisonchai &amp; Wesener, sp. nov. The two new species clearly differ from other congeners by their unique characteristics, especially in their colour pattern and telopod shape. The interspecific genetic distances of the 658 bp COI gene barcoding fragment between these new species and all other species of giant pill-millipede from Thailand, Laos and Cambodia are 12.01-23.49% for Z.chantaburiensis sp. nov. and 17.93-25.13% for Z.macula sp. nov. While relationships among species remain preliminary, the phylogenetic tree shows that species of Zephronia are interspersed with species of Sphaerobelum Verhoeff, 1924 and Prionobelum Verhoeff, 1924. Phylogenetic analyses place both new species in a clade termed Zephronia s.s., which receives support also from morphological data, showing a unique position of the organ of Tömösváry. Z.macula sp. nov. appears to occur over a broad distribution whereas Z.chantaburiensis sp. nov. was found only at the type locality. Given that all known records are in the eastern part of Thailand, we thus regard both species as endemic. Morphological illustrations based on SEM micrographs and a distribution map are also provided.}, }
@article {pmid39308990, year = {2024}, author = {Nocella, E and Fassio, G and Zuccon, D and Puillandre, N and Modica, MV and Oliverio, M}, title = {From coral reefs into the abyss: the evolution of corallivory in the Coralliophilinae (Neogastropoda, Muricidae).}, journal = {Coral reefs (Online)}, volume = {43}, number = {5}, pages = {1285-1302}, pmid = {39308990}, issn = {1432-0975}, abstract = {UNLABELLED: In this study, we delved into the interaction between corallivorous marine gastropods, the muricid Coralliophilinae Chenu, 1859, and their cnidarian food targets. Coralliophilinae is a subfamily of specialised corallivorous caenogastropods that feed by browsing on octocorals or hexacorals. Only sparse information is available on the phylogenetic relationships and the degree of specificity of the trophic relationships within this corallivorous lineage. To address these gaps, we generated the largest molecular dataset to date, comprising two mitochondrial (cox1 and 16S rDNA) and one nuclear gene (ITS2 rDNA) from 586 specimens collected worldwide. The coral hosts of coralliophilines were identified through an integrative approach, combining literature data with new records, employing morphological and/or molecular markers, and incorporating data from DNA barcoding of the snail stomach content. Our comprehensive approach unveiled the existence of numerous cryptic species in Coralliophilinae, while the phylogeny showed that most of the currently accepted genera are not monophyletic. The molecular dating confirmed the origin of the Coralliophilinae in Middle Eocene, with diversification of most lineages during the Miocene. Our results indicate that the subfamily's ancestor evolved in shallow waters in association with Scleractinia. Through the evolutionary history of Coralliophilinae, multiple host shifts to other cnidarian orders were observed, not correlated with changes in the depth range. The results of diversification analyses within the subfamily further suggest that the association with the host has influenced the evolutionary patterns of Coralliophilinae, but not vice versa.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-024-02537-1.}, }
@article {pmid39306191, year = {2024}, author = {Seyedabadi, M and Gurevich, VV}, title = {Flavors of GPCR signaling bias.}, journal = {Neuropharmacology}, volume = {261}, number = {}, pages = {110167}, doi = {10.1016/j.neuropharm.2024.110167}, pmid = {39306191}, issn = {1873-7064}, mesh = {*Receptors, G-Protein-Coupled/metabolism ; Humans ; *Signal Transduction/physiology/drug effects ; Animals ; Ligands ; GTP-Binding Proteins/metabolism ; }, abstract = {GPCRs are inherently flexible molecules existing in an equilibrium of multiple conformations. Binding of GPCR agonists shifts this equilibrium. Certain agonists can increase the fraction of active-like conformations that predispose the receptor to coupling to a particular signal transducer or a select group of transducers. Such agonists are called biased, in contrast to balanced agonists that facilitate signaling via all transducers the receptor couples to. These biased agonists preferentially channel the signaling of a GPCR to particular G proteins, GRKs, or arrestins. Preferential activation of particular G protein or arrestin subtypes can be beneficial, as it would reduce unwanted on-target side effects, widening the therapeutic window. However, biasing GPCRs has two important limitations: a) complete bias is impossible due to inherent flexibility of GPCRs; b) receptor-independent functions of signal transducer proteins cannot be directly affected by GPCR ligands or differential receptor barcoding by GRK phosphorylation. This article is part of the Special Issue on "Ligand Bias".}, }
@article {pmid39303852, year = {2025}, author = {Yanar, A and Kamanli, SA and Sönmez, S and Hamdi, &#x130; and Özak, AA and Boxshall, GA}, title = {Caligus minimus Otto, 1821 (Copepoda: Caligidae): A commercially important but poorly described parasite of cultured European Sea Bass, Dicentrarchus labrax (Linnaeus, 1758).}, journal = {Parasitology international}, volume = {104}, number = {}, pages = {102964}, doi = {10.1016/j.parint.2024.102964}, pmid = {39303852}, issn = {1873-0329}, mesh = {Animals ; *Bass/parasitology ; *Copepoda/classification/anatomy &amp; histology/ultrastructure/genetics ; *Fish Diseases/parasitology ; Female ; *Aquaculture ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Microscopy, Electron, Scanning/veterinary ; Phylogeny ; }, abstract = {Caligus minimus Otto, 1821 has been known for over two centuries and it is the second oldest of the approximately 275 species of Caligus O. F. Müller, 1985. Despite the numerous records of this species from European waters, it has never been fully described to modern standards. The lack of a comprehensive modern description has resulted in numerous misidentifications, even in recently published reports, and this is especially problematic for a species that is known to have a significant economic impact in aquaculture. This study presents a detailed description of both sexes and documents newly observed features of C. minimus collected from the buccal cavity of farmed European Sea Bass (ESB), Dicentrarchus labrax (Linnaeus, 1758). The morphology of C. minimus was examined using light microscope (LM), scanning electron microscope (SEM), and confocal laser scanning microscope (CLSM), and new details are revealed regarding the structure and ornamentation of the marginal membrane of the cephalothorax, maxilliped, antenna, sternal furca, abdomen, and legs 1, 3, 4, and 6. The ornamentation of the marginal membrane of the cephalothorax is unique and its impact on the functioning of the cephalothoracic sucker requires further investigation. Additionally, partial COI gene region sequences were obtained from four individuals of C. minimus and provided for future references. A phylogenetic analysis was conducted in conjunction with Caligus sequences available in the NCBI GenBank database.}, }
@article {pmid39302606, year = {2025}, author = {Krishnan, S and Ulagesan, S and Moon, JS and Choi, YH and Nam, TJ}, title = {Establishment, characterization, and sensory characteristics (taste and flavor) of an immortalized muscle cell line from the seven-band grouper Epinephelus septemfasciatus: implications for cultured seafood applications.}, journal = {In vitro cellular &amp; developmental biology. Animal}, volume = {61}, number = {1}, pages = {8-23}, pmid = {39302606}, issn = {1543-706X}, support = {201803932//Future Fisheries Food Research Centre' funded by the Korea Institute of Marine Science and Technology (KIMST) promotions, Ministry of Oceans and Fisheries, Republic of Korea/ ; }, mesh = {Animals ; *Seafood ; *Taste ; Cell Differentiation ; Cell Proliferation ; *Satellite Cells, Skeletal Muscle/cytology/metabolism ; Cell Line ; *Bass ; Cell Survival ; }, abstract = {Grouper muscle satellite cells (GMSCs) from the seven-band grouper (Epinephelus septemfasciatus) were isolated, and their growth conditions were optimized (10% fetal bovine serum, 24°C, 10 ng/mL bFGF). The cells were immortalized at passage 14 and designated as grouper immortalized muscle satellite cells (GIMSCs). DNA barcoding confirmed the grouper origin of both GMSC and GIMSC lines. GIMSCs exhibited enhanced proliferation, accelerated differentiation, and robust myotube formation compared to pre-crisis GMSCs. Western blot analysis showed upregulation of key myogenic factors (Pax7, MyoD, MyoG) and structural proteins (Desmin) in GIMSC, indicating the differentiation potential. The immortalized GIMSC line maintained consistent morphology, growth rates, and viability across multiple passages. Biocompatibility studies showed GIMSCs were compatible with bio-inks (sodium alginate, gelatin, κ-carrageenan) at 250 to 10,000 µg/mL, retaining ~ 80% viability at the highest concentration. Taste sensory analysis revealed GMSCs had the highest umami and lowest saltiness and sourness, contrasting with the muscle of the seven-band grouper, which had higher saltiness and sourness. Flavor analysis identified pronounced fishy, hot fat, and ethereal flavors in the cells at higher level than in the muscle. These findings suggest GMSCs and GIMSCs are promising for producing cultured meat with enhanced umami taste and flavors, advancing cellular agriculture and sustainable food production.}, }
@article {pmid39298427, year = {2024}, author = {Saiperaki, JL and Materu, SF and Mkenda, PA and Ligate, EJ and Rumisha, C}, title = {Field and DNA-barcode based surveys reveal evidence of rare endemic fishes in the Rufiji River Basin.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0310387}, pmid = {39298427}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Rivers ; *Fishes/genetics/classification ; Conservation of Natural Resources ; Fisheries ; Biodiversity ; }, abstract = {Endemic fish species have long supported the livelihoods of local communities in the Rufiji River Basin (RRB). However, destructive fishing practices have led to a concerning decline in endemic fish stocks. To assess these changes, this study employed key informant interviews, focus group discussions (FGDs), and fishery surveys to assess the historical and contemporary distribution of endemic fishes within the RRB. DNA barcoding was also used to verify species identities. Out of 37 reported fish species, 33 species (54.55% endemic and 45.45% exotic to RRB) were confirmed through DNA barcoding and morphological characteristics. About 5 species including, Heterobranchus longifilis, Citharinus congicus, Labeo congoro, Mormyrus longirostris, and Labeobarbus leleupanus were rarely found in the field, despite being classified as Least Concern by IUCN. Additionally, five species that were reported to be present in the RRB by experienced fishers were not captured during sampling. This highlights the need for validation of the existence of such species through eDNA metabarcoding. Moreover, due to the rarity of some species in the area, their IUCN assessment should be revisited.}, }
@article {pmid39296989, year = {2024}, author = {Caboňová, M and Vadkertiová, R and Adamčík, S and Bacigálová, K and Slovák, M and Zaib, S and Caboň, M}, title = {Taxonomic reintroduction of Taphrinaviridis (Taphrinales, Ascomycota) associated with Alnusalnobetula as one of five well defined European species colonizing alders.}, journal = {MycoKeys}, volume = {108}, number = {}, pages = {249-267}, pmid = {39296989}, issn = {1314-4049}, abstract = {Phylogenetic analysis of four DNA regions (ITS, LSU, mtSSU and tef1α) supported the existence of five European Taphrina species which colonise Alnus in Europe. In addition to previously well-defined species, T.viridis is, for the first time recognised, by molecular study as a species related to T.sadebeckii. Analysis of publicly available sequences of barcoding regions suggested that T.viridis is only associated with A.alnobetula and no other Taphrina species colonize this host tree. Symptomatic, morphological, and physiological characterisation of T.viridis are provided together with the key for identification of Alnus associated Taphrina species in Europe and North America.}, }
@article {pmid39293535, year = {2024}, author = {Rosenmai, AK and Svingen, T and Evrard, B and Nguyen, KH and Nielsen, C and Axelstad, M and Chalmel, F and Ramhøj, L}, title = {Distinct transcriptional profiles in rat thyroid glands after developmental exposure to three in vitro thyroperoxidase inhibiting chemicals.}, journal = {Genomics}, volume = {116}, number = {5}, pages = {110938}, doi = {10.1016/j.ygeno.2024.110938}, pmid = {39293535}, issn = {1089-8646}, mesh = {Animals ; *Thyroid Gland/metabolism/drug effects ; Rats ; *Iodide Peroxidase/genetics/metabolism ; Male ; *Transcriptome/drug effects ; Amitrole/pharmacology ; Enzyme Inhibitors/pharmacology ; Benzimidazoles/pharmacology ; }, abstract = {Thyroperoxidase (TPO) is central in thyroid hormone (TH) synthesis and inhibition can lead to TH deficiency. Many chemicals can inhibit TPO activity in vitro, but how this may manifest in the developing thyroid gland at the molecular level is unclear. Here, we characterized the thyroid gland transcriptome of male rats developmentally exposed to the in vitro TPO-inhibitors amitrole, 2-mercaptobenzimidazole (MBI), or cyanamide by use of Bulk-RNA-Barcoding (BRB) and sequencing. Amitrole exposure caused TH deficiency and 149 differentially expressed genes in the thyroid gland. The effects indicated an activated and growing thyroid gland. MBI caused intermittent changes to serum TH concentrations in a previous study and this was accompanied by 60 differentially expressed genes in the present study. More than half of these were also affected by amitrole, indicating that they could be early effect biomarkers of developmental TH system disruption due to TPO inhibition. Further work to validate the signature is needed, including assessment of substance independency and applicability domain.}, }
@article {pmid39293082, year = {2024}, author = {Liu, B and Klatt, D and Zhou, Y and Manis, JP and Sauvageau, G and Pellin, D and Brendel, C and Williams, DA}, title = {UM171 enhances fitness and engraftment of gene-modified hematopoietic stem cells from patients with sickle cell disease.}, journal = {Blood advances}, volume = {8}, number = {22}, pages = {5885-5895}, pmid = {39293082}, issn = {2473-9537}, support = {P01 HL158688/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Hematopoietic Stem Cells/metabolism/cytology ; *Anemia, Sickle Cell/therapy ; Animals ; *Hematopoietic Stem Cell Transplantation/methods ; Mice ; Antigens, CD34/metabolism ; Lentivirus/genetics ; Transduction, Genetic ; Genetic Vectors ; Indoles ; Pyrimidines ; }, abstract = {Hematopoietic stem cell (HSC) transplantation with lentiviral vector (LVV)-transduced autologous cells has proven an effective therapeutic strategy for sickle cell disease (SCD). However, ex vivo culture or proliferative stress associated with in vivo reconstitution may amplify any underlying genetic risk of leukemia. We aimed to minimize culture-induced stress and reduce genomic damage during ex vivo culture and enhance stem cell fitness and reconstitution of SCD CD34+ cells transduced with BCL11A shmiR-encoding LVV. UM171, a pyrimidoindole derivative, can expand normal HSCs during in vitro culture and has been shown to be safe and effective using umbilical cord blood. We examined the effect of UM171 during ex vivo LVV transduction of SCD HSCs. Culture of SCD CD34+ HSCs with UM171 during transduction reduced DNA damage and reactive oxygen species, decreased apoptosis, and was associated with increased numbers of immunophenotypically defined long-term HSCs. UM171 increased the engraftment of LVV-transduced human HSCs in immunodeficient mice and barcode tracing revealed increased clonal diversity of engrafting cells. In competitive transplantation assays, analysis of bone marrow showed that cells transduced in the presence of UM171 consistently outcompeted those transduced under control conditions. In summary, exposure of SCD peripheral blood CD34+ cells to UM171 during LVV transduction enhances stem cell fitness. These findings suggest manufacturing of genetically modified HSCs in the presence of UM171 may improve efficacy, safety, and sustainability of gene therapy using ex vivo approaches. BCL11A shmiR-encoding LVV is in clinical trials to treat SCD (NCT03282656), UM171 is in clinical trials to culture umbilical cord blood (NCT02668315).}, }
@article {pmid39290075, year = {2024}, author = {Sato, H and Lain, A and Mizuno, T and Yamashita, S and Hassan, JB and Othman, KB and Itioka, T}, title = {Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest.}, journal = {Molecular ecology}, volume = {33}, number = {21}, pages = {e17529}, doi = {10.1111/mec.17529}, pmid = {39290075}, issn = {1365-294X}, support = {JPMJSA190//Science and Technology Research Partnership for Sustainable Development/ ; 20K06796//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/genetics/classification ; *Rainforest ; Malaysia ; Dipterocarpaceae/microbiology ; DNA Barcoding, Taxonomic ; Host Specificity ; Symbiosis/genetics ; Phylogeny ; Trees/microbiology ; }, abstract = {Ectomycorrhizal (ECM) fungi are important tree symbionts within forests. The biogeography of ECM fungi remains to be investigated because it is challenging to observe and identify species. Because most ECM plant taxa have a Holarctic distribution, it is difficult to evaluate the extent to which host preference restricts the global distribution of ECM fungi. To address this issue, we aimed to assess whether host preference enhances the endemism of ECM fungi that inhabit dipterocarp rainforests. Highly similar sequences of 175 operational taxonomic units (OTUs) for ECM fungi that were obtained from Lambir Hill's National Park, Sarawak, Malaysia, were searched for in a nucleotide sequence database. Using a two-step binomial model, the probability of presence for the query OTUs and the registration rate of barcode sequences in each country were simultaneously estimated. The results revealed that the probability of presence in the respective countries increased with increasing species richness of Dipterocarpaceae and decreasing geographical distance from the study site (i.e. Lambir). Furthermore, most of the ECM fungi were shown to be endemic to Malaysia and neighbouring countries. These findings suggest that not only dispersal limitation but also host preference are responsible for the high endemism of ECM fungi in dipterocarp rainforests. Moreover, host preference likely determines the areas where ECM fungi potentially expand and dispersal limitation creates distance-decay patterns within suitable habitats. Although host preference has received less attention than dispersal limitation, our findings support that host preference has a profound influence on the global distribution of ECM fungi.}, }
@article {pmid39287819, year = {2024}, author = {Pachalil, VT and Gupta, B and Maile, A and Sunish, IP}, title = {Molecular characterization of anopheline species diversity in the Andaman and Nicobar archipelago, with a particular emphasis on Anopheles barbirostris.}, journal = {Parasitology research}, volume = {123}, number = {9}, pages = {325}, pmid = {39287819}, issn = {1432-1955}, mesh = {Animals ; *Anopheles/genetics/classification ; *RNA, Ribosomal, 28S/genetics ; *DNA, Ribosomal Spacer/genetics ; *Electron Transport Complex IV/genetics ; *Phylogeny ; *Genetic Variation ; Biodiversity ; Sequence Analysis, DNA ; Cluster Analysis ; Molecular Sequence Data ; DNA, Ribosomal/genetics ; Islands ; }, abstract = {This study investigates anopheline species diversity in the Andaman and Nicobar Islands, employing morphological and molecular methods, focusing on the D3 domain of 28S rRNA (D3) and second internal spacer (ITS2). Ten Anopheline species were identified morphologically and confirmed with molecular markers. While the D3 region demonstrated low level of inter- and intra-specific genetic distance in all the species, ITS2 revealed clear barcoding gap. Among the ten species, A. barbirostris exhibited significant diversity when compared with the sequences from other countries available in GenBank. Further analyses of additional samples of A. barbirostris were carried out using ITS2 and cytochrome oxidase I (COI) markers. Limited variations among the sequences from the islands were observed, suggesting a prevalent single molecular form. However, when compared with the GenBank sequences, our samples formed a separate cluster closely related to the A3 species. The genetic distance between our samples and the A3 cluster was 0.02 for COI but very high (0.104) for ITS2, suggesting a potentially new molecular form or species in the island region. This warrants a more comprehensive and detailed analysis of A. barbirostris in these islands at both genetic and morphometric levels. Overall, these observations added-up the new knowledge in the understanding of anopheline diversity in the Andaman and Nicobar archipelago and highlight the necessity for continuous molecular investigations to unravel complexities within mosquito population dynamics.}, }
@article {pmid39285627, year = {2024}, author = {Salis, R and Sunde, J and Gubonin, N and Franzén, M and Forsman, A}, title = {Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity.}, journal = {Molecular ecology resources}, volume = {24}, number = {8}, pages = {e14018}, doi = {10.1111/1755-0998.14018}, pmid = {39285627}, issn = {1755-0998}, support = {//Crafoordska Stiftelsen/ ; 2020-03519//Vetenskapsr&#xe5;det/ ; 2018-02846//Svenska Forskningsr&#xe5;det Formas/ ; 2021-02142//Svenska Forskningsr&#xe5;det Formas/ ; }, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/genetics ; *Insecta/genetics/classification/anatomy &amp; histology ; Wasps/genetics/classification/anatomy &amp; histology ; }, abstract = {For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.}, }
@article {pmid39285331, year = {2024}, author = {Zhang, Y and Song, M and Tang, D and Li, X and Xu, N and Li, H and Qu, L and Wang, Y and Yin, C and Zhang, L and Zhang, Z}, title = {Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {867}, pmid = {39285331}, issn = {1471-2229}, support = {2021-I2M-1-032//Yunnan "Xingdian Talent Support Program " young talents special project and CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; Genetic Markers ; Base Composition ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Lasianthus species are widely used in traditional Chinese folk medicine with high medicinal value. However, source materials and herbarium specimens are often misidentified due to morphological characteristics and commonly used DNA barcode fragments are not sufficient for accurately identifying Lasianthus species. To improve the molecular methods for distinguishing among Lasianthus species, we report the complete chloroplast (CP) genomes of Lasianthus attenuatus, Lasianthus henryi, Lasianthus hookeri, Lasianthus sikkimensis, obtained via high-throughput Illumina sequencing.<br><br>RESULTS: These showed CP genomes size of 160164-160246&#xa0;bp and a typical quadripartite structure, including a large single-copy region (86675-86848&#xa0;bp), a small single-copy region (17177-17326&#xa0;bp), and a pair of inverted repeats (28089-28135&#xa0;bp). As a whole, the gene order, GC content and IR/SC boundary structure were remarkably similar among of the four Lasianthus CP genomes, the partial gene length and IR, LSC and SSC regions length are still different. The average GC content of the CP genomes was 36.71-36.75%, and a total of 129 genes were detected, including 83 different protein-coding genes, 8 different rRNA genes and 38 different tRNA genes. Furthermore, we compared our 4 complete CP genomes data with publicly available CP genome data from six other Lasianthus species, and we initially screened eleven highly variable region fragments were initially screened. We then evaluated the identification efficiency of eleven highly variable region fragments and 5 regular barcode fragments. Ultimately, we found that the optimal combination fragment' ITS2&#x2009;+&#x2009;psaI-ycf4' could authenticated the Lasianthus species well. Additionally, the results of genome comparison of Rubiaceae species showed that the coding region is more conservative than the non-coding region, and the ycf1 gene shows the most significant variation. Finally, 49 species of CP genome sequences belonging to 16 genera of the Rubiaceae family were used to construct phylogenetic trees.<br><br>CONCLUSIONS: Our research is the first to analyze the chloroplast genomes of four species of Lasianthus in detail and we ultimately determined that the combination fragment' ITS2&#x2009;+&#x2009;psaI-ycf4' is the optimal barcode combination for identifying the genus of Lasianthus. Meanwhile, we gathered the available CP genome sequences from the Rubiaceae and used them to construct the most comprehensive phylogenetic tree for the Rubiaceae family. These investigations provide an important reference point for further studies in the species identification, genetic diversity, and phylogenetic analyses of Rubiaceae species.}, }
@article {pmid39282932, year = {2024}, author = {Sun, L and Liu, M and Gong, Y and Zhai, K and Lv, F and He, L and Xue, X and Liu, X and Wang, H and Fan, D and You, Y and Fang, M and Sun, L and Xu, J and Zhang, J}, title = {Rapid Antimicrobial Susceptibility Test of Helicobacter pylori to Metronidazole via Single-Cell Raman Spectrometry.}, journal = {Helicobacter}, volume = {29}, number = {5}, pages = {e13136}, doi = {10.1111/hel.13136}, pmid = {39282932}, issn = {1523-5378}, support = {//Financial&#x2009;Special&#x2009;Fund/ ; //Project for software development and expansive application of Chinese Helicobacter pylori antimicrobial resistance dynamic map/ ; //Project for new techniques exploration for bacterial pathogens laboratory detection/ ; //National Natural Science Foundation of China/ ; //Project for collaborative research on analysis of Helicobacter pylori infection and gut flora changes/ ; }, mesh = {*Helicobacter pylori/drug effects ; *Metronidazole/pharmacology ; *Spectrum Analysis, Raman/methods ; *Microbial Sensitivity Tests/methods ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy/diagnosis ; Single-Cell Analysis/methods ; Drug Resistance, Bacterial ; }, abstract = {BACKGROUND: Metronidazole is a first-line antibiotic to treat Helicobacter pylori infections. However, the Clinical Laboratory Standards Institute guidelines recommend against using antimicrobial susceptibility test (AST) to test metronidazole resistance, due to the unreliable predictive power which can result in treatment failure.<br><br>OBJECTIVES: The aim of this study was to establish an 8-h, metabolic-phenotype based AST for H. pylori metronidazole susceptibility using D2O-probed Raman microspectroscopy.<br><br>METHODS: Minimal inhibitory concentration (MIC) measured by conventional AST (E-test) were compared with expedited MIC via metabolic activity (eMIC-MA) for 10 H. pylori isolates. Raman barcodes of cellular-response to stress (RBCS) incorporating protein and carbohydrate Raman bands, were utilized to identify a biomarker to distinguish metronidazole susceptibility.<br><br>RESULTS: Specifically, eMIC-MA produces metronidazole susceptibility results showing 100% agreement with E-test, and determines the bactericidal dosage for both high- and low-level resistant H. pylori strains. In addition, RBCS not just reliably distinguish between metronidazole-susceptible and -resistant strains, but reveal their distinct mechanisms in bacterial responses to metronidazole.<br><br>CONCLUSION: The speed, accuracy, low cost, and rich information content that reveals the mode-of-action of drugs suggest the method's value in guiding metronidazole prescriptions for H. pylori eradication and in rapid screening based on drug-resistance mechanism.}, }
@article {pmid39282286, year = {2024}, author = {Wu, JW and Yang, JM and Chen, CC and Au, G and Wang, S and Chern, GW and Huang, CH}, title = {Calibration of FRET-based biosensors using multiplexed biosensor barcoding.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.09.04.610346}, pmid = {39282286}, issn = {2692-8205}, support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; S10 OD016374/OD/NIH HHS/United States ; S10 OD023548/OD/NIH HHS/United States ; }, abstract = {Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) is widely used in the design of genetically encoded fluorescent biosensors, which are powerful tools for monitoring the dynamics of biochemical activities in live cells. FRET ratio, defined as the ratio between acceptor and donor signals, is often used as a proxy for the actual FRET efficiency, which must be corrected for signal crosstalk using donor-only and acceptor-only samples. However, the FRET ratio is highly sensitive to imaging conditions, making direct comparisons across different experiments and over time challenging. Inspired by a method for multiplexed biosensor imaging using barcoded cells, we reasoned that calibration standards with fixed FRET efficiency can be introduced into a subset of cells for normalization of biosensor signals. Our theoretical analysis indicated that the FRET ratio of high-FRET species relative to non-FRET species slightly decreases at high excitation intensity, suggesting the need for calibration using both high and low FRET standards. To test these predictions, we created FRET donor-acceptor pairs locked in "FRET-ON" and "FRET-OFF" conformations and introduced them into a subset of barcoded cells. Our results confirmed the theoretical predictions and showed that the calibrated FRET ratio is independent of imaging settings. We also provided a strategy for calculating the FRET efficiency. Together, our study presents a simple strategy for calibrated and highly multiplexed imaging of FRET biosensors, facilitating reliable comparisons across experiments and supporting long-term imaging applications.}, }
@article {pmid39281619, year = {2024}, author = {Lee, YJ and Phang, GJ and Chen, CC and Ou, JH and Fan, YH and Huang, YT}, title = {Optimal liquid-based DNA preservation for DNA barcoding of field-collected fungal specimens.}, journal = {Heliyon}, volume = {10}, number = {17}, pages = {e36829}, pmid = {39281619}, issn = {2405-8440}, abstract = {Preserving fungal tissue DNA in the field is essential for molecular ecological research, enabling the study of fungal biodiversity and community dynamics. This study systematically compares two liquid-based preservation solutions, RNAlater and DESS, for their effectiveness in maintaining macrofungi DNA integrity during field collection and storage. The research encompasses both controlled experiments and real-world field collections. In the controlled experiments, two fungal species were preserved in RNAlater and DESS at different temperatures and durations. DNA extraction success rates were high, but DNA quality and quantity metrics exhibited variations across samples. However, both preservation solutions demonstrated their viability for preserving fungal DNA, with no significant differences between them. In the field-collected macrofungi experiment, 160 paired fungal specimens were preserved in RNAlater and DESS, respectively. Including a drying process to facilitate tissue lysis for DNA extraction significantly impacted the outcomes. RNAlater showed a higher success rate and better DNA quality and quantity compared to DESS. Statistical analysis, including paired and independent t-tests, confirmed significant differences in DNA quality and quantity between the two preservation methods for field-collected samples. This study evaluates RNAlater and DESS for preserving macrofungi DNA in field conditions. Both methods are effective, but RNAlater is superior when a drying step is included in DNA extraction. Researchers can choose based on their specific needs without compromising DNA integrity. These findings advance fungal molecular ecology and DNA preservation strategies in ecological and environmental studies.}, }
@article {pmid39279612, year = {2024}, author = {Biswas, A and Cencillo-Abad, P and Chanda, D}, title = {Multispectral Molecular Chiral Barcoding.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {36}, number = {45}, pages = {e2409565}, doi = {10.1002/adma.202409565}, pmid = {39279612}, issn = {1521-4095}, support = {ECCS-1800845//National Science Foundation/ ; }, abstract = {More than half of pharmaceutical drugs in use are chiral, necessitating accurate techniques for their characterization. Enantiomers, molecules with mirrored symmetry, often exhibit similar physical traits but possess distinct chemical and biological implications. This study harnesses the strong light-matter interaction induced by "superchiral" light to perform Surface-Enhanced Infrared Absorption (SEIRA) induced vibrational circular dichroism measurements in the mid-infrared spectral region. Utilizing a nanopatterned pixelated array of achiral plasmonic nanostructures, the system allows unique identification of enantiomers and biomolecules. Tunability of plasmon resonance facilitates spectral variation of the optical chirality over a wide infrared range, enabling development of a unique chiral "barcoding" scheme to distinguish chiral molecules based on their infrared fingerprint. This simple, yet robust sensor presents a low-cost solution for chiral mapping of drugs and biomolecules.}, }
@article {pmid39278523, year = {2024}, author = {Hoxha, I and Trájer, AJ and Dvorak, V and Halada, P and Šupić, J and Obwaller, AG and Poeppl, W and Walochnik, J and Alić, A and Kniha, E}, title = {Phlebotomine sand flies (Diptera: Psychodidae) of Bosnia and Herzegovina: distribution, ecology and environmental preferences.}, journal = {Acta tropica}, volume = {260}, number = {}, pages = {107393}, doi = {10.1016/j.actatropica.2024.107393}, pmid = {39278523}, issn = {1873-6254}, mesh = {Animals ; Bosnia and Herzegovina ; *Psychodidae/classification/physiology/parasitology ; *Insect Vectors/physiology/parasitology/classification/virology ; Female ; Animal Distribution ; Leishmania/genetics ; Male ; Phlebotomus/classification ; Leishmania infantum/genetics/isolation &amp; purification ; Phlebovirus/isolation &amp; purification/genetics ; Ecosystem ; }, abstract = {Sand flies (Diptera: Phlebotominae) are the principal vectors for the protozoan parasites Leishmania spp. and for phleboviruses. The sand fly fauna on the Balkan Peninsula, including Bosnia and Herzegovina (BIH), is diverse and the circulation of Leishmania infantum as well as phleboviruses has been proven. However, recent data on the sand fly fauna in BIH are scarce. In this study, we surveyed understudied regions in central and northeastern BIH to update the sand fly distribution and gain insights into the ecological and environmental factors shaping their appearance. CDC light trapping was conducted in 2022 and 2023 and a combination of morphological and molecular methods (cytochrome oxidase I barcoding) was performed for species identifications. We mapped the currently known distribution, modelled climatic suitability patterns and performed environmental analyses by applying machine learning methods. In addition, we analyzed blood meals by host gene sequencing and MALDI-TOF peptide mass mapping and screened for Leishmania spp. DNA and Phlebovirus RNA. Altogether, 591 sand flies of four species were trapped, predominantly Phlebotomus neglectus (97 %), but also Ph. balcanicus, Ph. mascittii, and Ph. papatasi. Records of seven sand fly species known to be endemic were plotted onto distribution maps based on 101 datapoints, identifying Ph. neglectus as the overall predominant species. The environmental analyses of sand fly species indicated variation in altitudinal, thermal, and precipitation conditions across the sand fly-positive sites. Phlebotomus simici, Phlebotomus tobbi, and Sergentomyia minuta are typically found exclusively in Mediterranean and subtropical climate zones, whereas other species typically inhabit continental regions. The Inverse Distance Weighted (IDW) interpolation of sand fly species numbers and Shannon entropy values suggested the southeastern coastal region of BIH as a primary focus for sand fly occurrence. This finding was corroborated by modeled average climatic suitability patterns for sand flies, depicting four distinct meso-regions for sand fly occurrence. The results of the ensemble method highlight the importance of annual precipitation to distinguish between positive and negative sand fly trapping sites in BIH. In total, 55 blood meals of two sand fly species, Ph. neglectus and Ph. balcanicus, were analyzed and five host species identified. Our comprehensive assessment of ecological and environmental preferences of sand flies in BIH may support further entomological surveys and help to better understand and evaluate potential hot spots of disease transmission in the country.}, }
@article {pmid39276821, year = {2024}, author = {Katoh, TK and Chen, JM and Yang, JH and Zhang, G and Wang, L and Suwito, A and Ak Meleng, P and Toda, MJ and Zhang, YP and Gao, JJ}, title = {Molecular phylogeny and species diversity of the genus Dichaetophora Duda and related taxa (Diptera: Drosophilidae).}, journal = {Molecular phylogenetics and evolution}, volume = {201}, number = {}, pages = {108194}, doi = {10.1016/j.ympev.2024.108194}, pmid = {39276821}, issn = {1095-9513}, mesh = {Animals ; *Phylogeny ; *Drosophilidae/genetics/classification ; *DNA Barcoding, Taxonomic ; Male ; Electron Transport Complex IV/genetics ; Sequence Analysis, DNA ; Bayes Theorem ; }, abstract = {Our intensive surveys of wild drosophilids in East and Southeast Asia discovered a great species diversity (more than 100 putatively new species) of the genus Dichaetophora, which is currently comprised of 67 formally described species assigned into five species groups, i.e., agbo, tenuicauda, acutissima, sinensis and trilobita. In the present study, we delimited species from a huge amount of samples of Dichaetophora and allied taxa (the genus Mulgravea and the subgenus Dudaica of Drosophila) collected from a wide range of the Oriental and east Palearctic regions. We first sorted all specimens into morpho-species, and representative specimen(s) selected from each morpho-species were subjected to barcoding of COI (the cytochrome c oxidase subunit I gene) sequences. The applied ASAP (Assemble Species by Automatic Partitioning) analysis estimated a total of 166 to 168 MOTUs (molecular operational taxonomic units). Integrating this result with morphological evidence from re-examined, detailed structures of male terminalia, we recognized a total of 144 (109 new and 35 known) species in our sample. Out of them, 83 species representing the supraspecific taxa of Dichaetophora, Mulgravea and Dudaica were selected, along with 33 species from major genera and subgenera of Drosophila in the tribe Drosophilini, as in-group and four species from the tribe Colocasiomyini as out-group for phylogenetic reconstruction based on 12 nuclear gene markers. In the trees constructed by the maximum likelihood and Bayesian inference methods, the three focal taxa (i.e., Dichaetophora, Mulgravea and Dudaica) formed a clade provisionally called the "pan-Dichaetophora". Within this large clade, the agbo, tenuicauda, sinensis and trilobita groups of Dichaetophora, Mulgravea and Dudaica were recovered as monophyletic groups, but Dichaetophora and its acutissima group were regarded as paraphyletic. In addition, two clusters were recognized among ungrouped species of Dichaetophora. Thus, the present study has uncovered some issues concerning the taxonomy of the pan-Dichaetophora. Such issues will be addressed elsewhere in the phylogenetic reclassification of the pan-Dichaetophora, along with descriptions/redescriptions of a large number of new/known species delimited in the present study.}, }
@article {pmid39267427, year = {2024}, author = {Nieto-Lugilde, M and Nieto-Lugilde, D and Piatkowski, B and Duffy, AM and Robinson, SC and Aguero, B and Schuette, S and Wilkens, R and Yavitt, J and Shaw, AJ}, title = {Ecological differentiation and sympatry of cryptic species in the Sphagnum magellanicum complex (Bryophyta).}, journal = {American journal of botany}, volume = {111}, number = {9}, pages = {e16401}, doi = {10.1002/ajb2.16401}, pmid = {39267427}, issn = {1537-2197}, mesh = {*Sympatry ; *Sphagnopsida/genetics ; Ecosystem ; Phylogeny ; North America ; DNA Barcoding, Taxonomic ; Climate ; Species Specificity ; }, abstract = {PREMISE: Sphagnum magellanicum (Sphagnaceae, Bryophyta) has been considered to be a single semi-cosmopolitan species, but recent molecular analyses have shown that it comprises a complex of at least seven reciprocally monophyletic groups, that are difficult or impossible to distinguish morphologically.<br><br>METHODS: Newly developed barcode markers and RADseq analyses were used to identify species among 808 samples from 119 sites. Molecular approaches were used to assess the geographic ranges of four North American species, the frequency at which they occur sympatrically, and ecological differentiation among them. Microhabitats were classified with regard to hydrology and shade. Hierarchical modelling of species communities was used to assess climate variation among the species. Climate niches were projected back to 22,000 years BP to assess the likelihood that the North American species had sympatric ranges during the late Pleistocene.<br><br>RESULTS: The species exhibited parallel morphological variation, making them extremely difficult to distinguish phenotypically. Two to three species frequently co-occurred within peatlands. They had broadly overlapping microhabitat and climate niches. Barcode- versus RADseq-based identifications were in conflict for 6% of the samples and always involved S. diabolicum vs. S. magniae.<br><br>CONCLUSIONS: These species co-occur within peatlands at scales that could permit interbreeding, yet they remain largely distinct genetically and phylogenetically. The four cryptic species exhibited distinct geographic and ecological patterns. Conflicting identifications from barcode vs. RADseq analyses for S. diabolicum versus S. magniae could reflect incomplete speciation or hybridization. They comprise a valuable study system for additional work on climate adaptation.}, }
@article {pmid39273486, year = {2024}, author = {Lei, W and Zhou, P and Pei, Z and Liu, Y and Luo, Y and Xiang, X}, title = {Plastome Evolution and Comparative Analyses of a Recently Radiated Genus Vanda (Aeridinae, Orchidaceae).}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273486}, issn = {1422-0067}, mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; *Evolution, Molecular ; Genome, Plastid ; Base Composition ; DNA Barcoding, Taxonomic ; }, abstract = {Vanda R.Br. is an epiphytic orchid genus with significant horticultural and ornamental value. Previous molecular studies expanded Vanda including some members from five other genera. However, the interspecific relationships of this recently radiated genus have remained unclear based on several DNA markers until now. In this study, the complete plastome has been used to infer the phylogenetic relationships of Vanda s.l. The five newly obtained plastomes ranged from 146,340 bp to 149,273 bp in length, with a GC content ranging from 36.5% to 36.7%. The five plastomes contained 74 protein-coding genes (CDSs), 38 tRNAs, and 8 rRNAs, and their ndh genes underwent loss or pseudogenization. Comparative plastome analyses of 13 Vanda species revealed high conservation in terms of genome size, structure, and gene order, except for a large inversion from trnG[GCC] to ycf3 in V. coerulea. Moreover, six CDSs and five non-CDSs were selected as candidate DNA barcodes. Our phylogenetic analyses demonstrated that Vanda s.l. is a monophyletic group with high supporting values based on five different datasets (complete plastome with one IR, 68 CDSs, LSC, five hypervariable non-CDSs, and six hypervariable CDSs), while the phylogenetic relationships among species were fully resolved based on the complete plastome with one IR dataset. Our results confirmed that the complete plastome has a great power in resolving the phylogenetic relationships of recently radiated lineages.}, }
@article {pmid39270602, year = {2024}, author = {González, MA and Ruiz-Arrondo, I and Magallanes, S and Oboňa, J and Ruiz-López, MJ and Figuerola, J}, title = {Molecular and morphological analysis revealed a new Lipoptena species (Diptera: Hippoboscidae) in southern Spain harbouring Coxiella burnetii and bacterial endosymbionts.}, journal = {Veterinary parasitology}, volume = {332}, number = {}, pages = {110300}, doi = {10.1016/j.vetpar.2024.110300}, pmid = {39270602}, issn = {1873-2550}, mesh = {Animals ; Spain/epidemiology ; *Diptera/microbiology ; Female ; Male ; *Coxiella burnetii/genetics/isolation &amp; purification ; *Symbiosis ; Phylogeny ; Wolbachia/genetics/isolation &amp; purification/physiology ; DNA Barcoding, Taxonomic ; }, abstract = {Hippoboscid flies (Diptera: Hippoboscidae) are obligate bloodsucking ectoparasites of animals. In Europe, limited research has been conducted on this family until the recent introduction of the deer ked Lipoptena fortisetosa Maa, 1965. A new species of the genus Lipoptena, Lipoptena andaluciensis sp. nov., was found in southern Spain after extensive sampling with carbon-dioxide baited suction traps. A total of 52 females and 32 males were collected at 29 out of 476 sites examined over eight months in 2023. Lipoptena andaluciensis sp. nov. was characterized morphologically and molecularly. The new Lipoptena species can be differentiated from the closely related L. fortisetosa by size, chaetotaxy of the dorsal and ventral thorax, abdominal plates, and genitalia. Based on DNA-barcoding, our specimens showed the highest similarity with Melophagus ovinus (Linnaeus, 1758) (88.4 %) and with L. fortisetosa (86-88 %). Individual screening of Lipoptena specimens (n = 76) for seven important zoonotic pathogens such as bacteria (Anaplasmataceae family: Bartonella spp., Borrelia spp., Coxiella burnetii and Rickettsia spp.) and protozoans (Babesia spp. and Theileria spp.) by conventional PCR and RT-PCR was performed. DNA of C. burnetii was detected in one specimen, while two other specimens harboured Anaplasmataceae (Wolbachia spp., 100 % homology and another endosymbiont probably related to Arsenophonus sp., 95.3 % homology, respectively), all representing the first records of these bacteria in the Lipoptena spp. from Europe. Carbon dioxide traps probed its effectiveness as a reliable passive method for keds surveillance. Our study highlights the existence of a new Lipoptena species, presumably widely distributed in southern Spain. The role of this species in the transmission cycle of pathogens of medical-veterinary relevance needs to be considered in the area.}, }
@article {pmid39268009, year = {2024}, author = {Lim, C and Minkina, &#x141;}, title = {A new species of genus Acrossus Mulsant, 1842 (Scarabaeidae, Aphodiinae, Aphodiini) from South Korea.}, journal = {ZooKeys}, volume = {1211}, number = {}, pages = {211-230}, pmid = {39268009}, issn = {1313-2989}, abstract = {A new species of the genus Acrossus Mulsant, 1842, Acrossusbaei sp. nov. from South Korea, is described and illustrated on the basis of morphology and mitochondrial COI sequences. The species was compared with four related species; Acrossusatratus (Waterhouse, 1875), A.humerospinosus (Petrovitz, 1958), A.luridus (Fabricius, 1775), and A.superatratus (Nomura &amp; Nakane, 1951). The taxonomic status and diagnostic characters of the new species are discussed. A key to species of the genus Acrossus in the Korean Peninsula is given.}, }
@article {pmid39267125, year = {2024}, author = {Shah, HK and Fathima, PA and Jicksy, J and Saini, P}, title = {Report of a new species of sand fly, Phlebotomus (Anaphlebotomus) ajithii n. sp. (Diptera: Psychodidae), from Western Ghats, India.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {388}, pmid = {39267125}, issn = {1756-3305}, support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; IM-1905//Indian Council of Medical Research- Vector Control Research Centre/ ; }, mesh = {Animals ; India ; *Phlebotomus/genetics/classification ; *Phylogeny ; *Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Female ; Male ; }, abstract = {BACKGROUND: Western Ghats is a biodiversity treasure trove with reports of indigenous leishmaniasis cases. Hence, systematic sand fly surveillance was carried out among the tribal population. The present study reports a novel sand fly species, Phlebotomus (Anaphlebotomus) ajithii n. sp. (Diptera: Psychodidae), discovered in the Western Ghats of India.<br><br>METHODS: A comprehensive sand fly survey was conducted across the Kollam, Thrissur, Idukki, Kasaragod and Malappuram districts of Kerala, India. The survey spanned both indoor and outdoor habitats using standard collection methods over a 3-year, 3-month period. DNA barcoding of samples was performed targeting mitochondrial cytochrome c oxidase subunit I (COI) gene, and the sequence generated was subjected to phylogenetic analysis.<br><br>RESULTS: Phlebotomus (Anaphlebotomus) ajithii, a new sand fly species, is recorded and described in this communication. The morphological relationship of the new species to other members of the subgenus Anaphlebotomus is discussed. Mitochondrial COI barcode followed by phylogenetic analysis confirmed that specimens of Ph. ajithii belong to the same taxonomic group, while a genetic distance of 11.7% from congeners established it as a distinct species.<br><br>CONCLUSIONS: The Western Ghats, known for its rich biodiversity, has lacked systematic entomological surveys focusing on sand flies. This study aims to fill this gap and reports and describes a new species of sand fly.}, }
@article {pmid39266625, year = {2024}, author = {Almeida-Silva, MA and Braga-Ferreira, RS and Targueta, CP and Corvalán, LCJ and Silva-Neto, CM and Franceschinelli, EV and Sobreiro, MB and Nunes, R and Telles, MPC}, title = {Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21358}, pmid = {39266625}, issn = {2045-2322}, support = {#28/2018//MCTIC/CNPq/ ; 435477/2018-8//MCTIC/CNPq/ ; 441114/2023-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 202210267000536//TWRA/FAPEG/ ; }, mesh = {*Genome, Chloroplast/genetics ; *Phylogeny ; *Evolution, Molecular ; }, abstract = {Simarouba, a neotropical genus in the family Simaroubaceae, currently lacks comprehensive genomic data in existing databases. This study aims to fill this gap by providing genomic resources for three Simarouba species, S. amara, S. versicolor, and S. glauca. It also aims to perform comparative molecular evolutionary analyses in relation to other species within the order Sapindales. The analysis of these three Simarouba species revealed the presence of the typical quadripartite structure expected in plastomes. However, some pseudogenization events were identified in the psbC, infA, rpl22, and ycf1 genes. In particular, the CDS of the psbC gene in S. amara was reduced from 1422 bp to 584 bp due to a premature stop codon. Nucleotide diversity data pointed to gene and intergenic regions as promising candidates for species and family discrimination within the group, specifically matK, ycf1, ndhF, rpl32, petA-psbJ, and trnS-trnG. Selection signal analyses showed strong evidence for positive selection on the rpl23 gene. Phylogenetic analyses indicated that S. versicolor and S. glauca have a closer phylogenetic relationship than S. amara. We provide chloroplast genomes of three Simaruba species and use them to elucidate plastome evolution, highlight the presence of pseudogenization, and identify potential DNA barcode regions.}, }
@article {pmid39265309, year = {2024}, author = {Hung, CC and Chang, JS and Liao, CH and Lee, TM}, title = {Exploring the impact of ocean warming and nutrient overload on macroalgal blooms and carbon sequestration in deep-sea sediments of the subtropical western North Pacific.}, journal = {Marine pollution bulletin}, volume = {208}, number = {}, pages = {116918}, doi = {10.1016/j.marpolbul.2024.116918}, pmid = {39265309}, issn = {1879-3363}, mesh = {*Seaweed ; *Carbon Sequestration ; *Geologic Sediments/chemistry ; Pacific Ocean ; Carbon/analysis ; Eutrophication ; Climate Change ; Nutrients/analysis ; Environmental Monitoring ; Nitrogen/analysis ; }, abstract = {The role of macroalgae as blue carbon (BC) under changing climate was investigated in the subtropical western North Pacific. Sea surface temperatures (SSTs) and nutrient influx increased over the past two decades (2001-2021). The proliferation of climate-resilient macroalgae was facilitated. Using Pterocladiella capillacea and Turbinaria ornata, outdoor laboratory experiments and elemental assays underscored the influence of nutrient enrichment on their resilience under ocean warming and low salinity. Macroalgal incorporation into marine sediments, indicated by environmental DNA barcoding, total organic carbon (TOC), and stable isotope analysis. Over time, an increase in δ[13]C and δ[15]N values, particularly at greater depths, suggests a tendency of carbon signature towards macroalgaeand nitrogen pollution or high tropic levels. eDNA analysis revealed selective deposition of these species. The species-dependent nature of macroalgae in deep-sea sediments highlights the role of nutrients on climate-resilient macroalgal blooms as carbon sinks in the western North Pacific.}, }
@article {pmid39262988, year = {2024}, author = {Mousa, WK and Ghemrawi, R and Abu-Izneid, T and Al Ramadan, N and Al Sheebani, F}, title = {The design and development of EcoBiomes: Multi-species synthetic microbial consortia inspired by natural desert microbiome to enhance the resilience of climate-sensitive ecosystems.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e36548}, pmid = {39262988}, issn = {2405-8440}, abstract = {Synthetic microbial communities, which simplify the complexity of natural ecosystems while retaining their key features, are gaining momentum in engineering and biotechnology applications. One potential application is the development of bioinoculants, offering an eco-friendly, sustainable solution to promote plant growth and increase resilience to abiotic stresses amidst climate change. A potential source for stress-tolerant microbes is those associated with desert plants, evolved and shaped by selective pressures to promote host health under harsh environmental conditions. In our research, we aim to design and develop synthetic microbial consortia inspired by the natural microbiota of four desert plants native to the Arabian Peninsula, inferred from our previous work identifying the structure and predicting the function of these microbial communities using high throughput eDNA barcoding. To obtain culturable microbes that are manageable and traceable yet still representative of natural microbial communities, we combined multiple experimental protocols coupled with compatibility and synergy assessments, along with in planta testing. We isolated a total of 75 bacteria and conducted detailed biological evaluations, revealing that an overwhelming majority (84 %) of all isolates produced indole acetic acid (IAA), with 73 % capable of solubilizing phosphate, 60 % producing siderophores, 47 % forming biofilms, and 35 % producing ACC deaminase, all contributing to plant growth and stress tolerance. We constructed four synthetic microbial consortia, named EcoBiomes, consisting of synergistic combinations of multiple species that can co-exist without significant antagonism. Our preliminary data indicate that EcoBiomes enhance the resilience of heterologous host plants under simulated environmental stresses, including drought, heat, and salinity. EcoBiomes offer a unique, sustainable, and eco-friendly solution to mitigate the impact of climate change on sensitive ecosystems, ultimately affecting global food security.}, }
@article {pmid39262866, year = {2024}, author = {Mohtar, JA and Rahman, KHA and Nyanasilan, S and Abdullah, NAH and Mohamad, F}, title = {Discovery of Web-Building Spiders in Gua Kelam, Perlis State Park, Malaysia.}, journal = {Tropical life sciences research}, volume = {35}, number = {1}, pages = {87-106}, pmid = {39262866}, issn = {1985-3718}, abstract = {A cave represents a subterranean ecosystem that harbours a myriad of unique, peculiar, and secluded flora and fauna. These biotas have evolved with a wide range of ecological adaptations that allow them to thrive in harsh environments with limited light. Gua Kelam 1 constitutes part of the Gua Kelam limestone caves system in the Nakawan Range of Perlis State Park, Malaysia. Previous observations indicated that it harbours a plethora of spider species; however, their existence is still elusive as speleobiological studies remain unexplored. Herein, we identified the cavernicolous spiders found in the dark zone areas of Gua Kelam 1 through a complementary approach based on morphology and DNA barcoding. From the morphological analysis, we described three web-building spiders of JTKK2 and JTKK3 groups down to the species-level to belong to Nephilengys malabarensis, and Orsinome vethi except for Pholcus sp. from JTKK4 individuals. The molecular analysis of the cytochrome oxidase-I (COI) genes of JTKK2 and JTKK3 individuals showed that they exhibited a high degree similarity with N. malabarensis (98.3%), and O. vethi (100.0%), respectively except for JTKK4 individuals with only 91.4% homology with P. kuhapimuk. Phylogenetic analysis also generated a congruent tree, in which the identified species are well nested within the family Araneidae, Tetragnathidae, and Pholcidae. By this integral approach, the three spiders were determined as N. malabarensis, O. vethi, and Pholcus sp. These spiders are originally epigean in their habitat but uniquely thrive in Gua Kelam 1.}, }
@article {pmid39258880, year = {2024}, author = {Xhekaj, B and Hoxha, I and Platzgummer, K and Stefanovska, J and Dvořák, V and Milchram, M and Obwaller, AG and Poeppl, W and Muja-Bajraktari, N and Walochnik, J and Trájer, AJ and Sherifi, K and Cvetkovikj, A and Kniha, E}, title = {A cross-sectional study on phlebotomine sand flies in relation to disease transmission in the Republic of Kosovo.}, journal = {Medical and veterinary entomology}, volume = {38}, number = {4}, pages = {573-585}, doi = {10.1111/mve.12758}, pmid = {39258880}, issn = {1365-2915}, support = {886318//Austrian defence research programme FORTE of the Federal Ministry of Finance/ ; RRF-2.3.1-21-2022-00014//National Multidisciplinary Laboratory for Climate Change/ ; //J&#xe1;nos Bolyai Research Scholarship of the Hungarian Academy of Sciences/ ; }, mesh = {Animals ; Kosovo ; *Insect Vectors/physiology/parasitology ; Cross-Sectional Studies ; *Animal Distribution ; *Phlebotomus/classification/physiology/parasitology ; Female ; Psychodidae/physiology/parasitology ; Male ; Dogs ; Leishmania infantum/physiology ; }, abstract = {Sand flies (Diptera: Psychodidae: Phlebotominae) are blood-feeding insects that transmit the protozoan parasites Leishmania spp. and various arboviruses. The Balkan region, including the Republic of Kosovo, harbours a diverse sand fly fauna. Vector species of Leishmania infantum as well as phleboviruses are endemic; however, recent data are scarce. We performed a cross-sectional study to update the current sand fly distribution in Kosovo and assess biological as well as environmental factors associated with sand fly presence. CDC light trapping was conducted at 46 locations in 2022 and 2023, specifically targeting understudied regions in Kosovo. Individual morphological species identification was supported by molecular barcoding. The occurrence data of sand flies was used to create distribution maps and perform environmental analyses, taking elevation, wind speed and climate-related factors into account. In addition, PCR-based blood meal analysis and pathogen screening were conducted. Overall, 303 specimens of six sand fly species were trapped, predominated by Phlebotomus neglectus (97%). Barcodes from eight of nine known endemic sand fly species were obtained. Combining our data with previous surveys, we mapped the currently known sand fly distribution based on more than 4000 specimens at 177 data points, identifying Ph. neglectus and Ph. perfiliewi as the predominant species. Environmental analyses depicted two geographical groups of sand flies in Kosovo, with notable differences between the species. In total, 223 blood meals of five sand fly species were analysed. Of seven identified host species, the predominant blood meal source was observed to be cattle, but the DNA of dogs and humans, among others, was also detected. This study assessed biological as well as ecological factors of sand fly occurrence, which should help better understand and evaluate potential hot spots of disease transmission in Kosovo.}, }
@article {pmid39258547, year = {2024}, author = {Kristen, M and Lander, M and Kilz, LM and Gleue, L and Jörg, M and Bregeon, D and Hamdane, D and Marchand, V and Motorin, Y and Friedland, K and Helm, M}, title = {DORQ-seq: high-throughput quantification of femtomol tRNA pools by combination of cDNA hybridization and Deep sequencing.}, journal = {Nucleic acids research}, volume = {52}, number = {18}, pages = {e89}, pmid = {39258547}, issn = {1362-4962}, support = {TRR-319 TP A05//Deutsche Forschungsgemeinschaft/ ; //ANR PRCI D-Erase/ ; }, mesh = {*RNA, Transfer/genetics/metabolism ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *DNA, Complementary/genetics ; *Nucleic Acid Hybridization/methods ; Alzheimer Disease/genetics ; Sequence Analysis, RNA/methods ; Brain/metabolism ; }, abstract = {Due to its high modification content tRNAs are notoriously hard to quantify by reverse transcription and RNAseq. Bypassing numerous biases resulting from concatenation of enzymatic treatments, we here report a hybrid approach that harnesses the advantages of hybridization-based and deep sequencing-based approaches. The method renders obsolete any RNAseq related workarounds and correction factors that affect accuracy, sensitivity, and turnaround time. Rather than by reverse transcription, quantitative information on the isoacceptor composition of a tRNA pool is transferred to a cDNA mixture in a single step procedure, thereby omitting all enzymatic conversations except for the subsequent barcoding PCR. As a result, a detailed tRNA composition matrix can be obtained from femtomolar amounts of total tRNA. The method is fast, low in cost, and its bioinformatic data workup surprisingly simple. These properties make the approach amenable to high-throughput investigations including clinical samples, as we have demonstrated by application to a collection of variegated biological questions, each answered with novel findings. These include tRNA pool quantification of polysome-bound tRNA, of tRNA modification knockout strains under stress conditions, and of Alzheimer patients' brain tissues.}, }
@article {pmid39256584, year = {2024}, author = {Zhu, J and Pang, K and Hu, B and He, R and Wang, N and Jiang, Z and Ji, P and Zhao, F}, title = {Custom microfluidic chip design enables cost-effective three-dimensional spatiotemporal transcriptomics with a wide field of view.}, journal = {Nature genetics}, volume = {56}, number = {10}, pages = {2259-2270}, pmid = {39256584}, issn = {1546-1718}, support = {32025009//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Mice ; *Transcriptome ; *Gene Expression Profiling/methods ; Microfluidics/methods ; Brain/metabolism ; Single-Cell Analysis/methods ; Cost-Benefit Analysis ; Lab-On-A-Chip Devices ; Organogenesis/genetics ; }, abstract = {Spatial transcriptomic techniques offer unprecedented insights into the molecular organization of complex tissues. However, integrating cost-effectiveness, high throughput, a wide field of view and compatibility with three-dimensional (3D) volumes has been challenging. Here we introduce microfluidics-assisted grid chips for spatial transcriptome sequencing (MAGIC-seq), a new method that combines carbodiimide chemistry, spatial combinatorial indexing and innovative microfluidics design. This technique allows sensitive and reproducible profiling of diverse tissue types, achieving an eightfold increase in throughput, minimal cost and reduced batch effects. MAGIC-seq breaks conventional microfluidics limits by enhancing barcoding efficiency and enables analysis of whole postnatal mouse sections, providing comprehensive cellular structure elucidation at near single-cell resolution, uncovering transcriptional variations and dynamic trajectories of mouse organogenesis. Our 3D transcriptomic atlas of the developing mouse brain, consisting of 93 sections, reveals the molecular and cellular landscape, serving as a valuable resource for neuroscience and developmental biology. Overall, MAGIC-seq is a high-throughput, cost-effective, large field of view and versatile method for spatial transcriptomic studies.}, }
@article {pmid39255672, year = {2024}, author = {Douard, M and Fernandez, S and Garcia-Vazquez, E and Planes, S}, title = {Rapid expansion and ecosystem health risk of invasive biopollutants dispersed by maritime traffic in French Polynesia.}, journal = {Marine pollution bulletin}, volume = {208}, number = {}, pages = {116927}, doi = {10.1016/j.marpolbul.2024.116927}, pmid = {39255672}, issn = {1879-3363}, mesh = {Polynesia ; *Introduced Species ; Animals ; *Ecosystem ; Biofouling ; Ships ; Environmental Monitoring ; }, abstract = {The introduction of biopollutant species challenge ecosystem health and economy in remote islands. Here we checked the advance of invasive fouling species in five French Polynesian islands. Expansion of invasive species (Acantophora spicifera, Bugula neritina, Chthamalus proteus, Dendostrea frons) was detected using individual barcoding (COI for animals, RBLC for algae), and metabarcoding on biofouling (COI and 18S sequences). They were especially abundant in Port Phaeton (Tahiti), Bora Bora and Rangiroa atoll. Chthamalus proteus is a vector of bacterial diseases and may harm native French Polynesian mollusks. Dendostrea frons is a vector of Perkinsus, a parasite to which black pearl oysters, the mainstay of the Polynesian economy, are susceptible. High ecological and epidemiological risks were estimated for C. proteus and D. frons, and ecological risks also for A. spicifera and especially for B. neritina. Strengthening marine biosecurity measures is highly recommended to conserve these unique ecosystems and their associated services.}, }
@article {pmid39254601, year = {2024}, author = {De Rijk, P and Watzeels, T and Küçükali, F and Van Dongen, J and Faura, J and Willems, P and De Deyn, L and Duchateau, L and Grones, C and Eekhout, T and De Pooter, T and Joris, G and Rombauts, S and De Rybel, B and Rademakers, R and Van Breusegem, F and Strazisar, M and Sleegers, K and De Coster, W}, title = {Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {9}, pages = {}, pmid = {39254601}, issn = {1367-4811}, support = {//University of Antwerp/ ; AARG-20-683760/ALZ/Alzheimer's Association/United States ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; *Software ; *Workflow ; Transcriptome/genetics ; Arabidopsis/genetics ; Brain/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; }, abstract = {MOTIVATION: Existing nanopore single-cell data analysis tools showed severe limitations in handling current data sizes.<br><br>RESULTS: We introduce scywalker, an innovative and scalable package developed to comprehensively analyze long-read sequencing data of full-length single-cell or single-nuclei cDNA. We developed novel scalable methods for cell barcode demultiplexing and single-cell isoform calling and quantification and incorporated these in an easily deployable package. Scywalker streamlines the entire analysis process, from sequenced fragments in FASTQ format to demultiplexed pseudobulk isoform counts, into a single command suitable for execution on either server or cluster. Scywalker includes data quality control, cell type identification, and an interactive report. Assessment of datasets from the human brain, Arabidopsis leaves, and previously benchmarked data from mixed cell lines demonstrate excellent correlation with short-read analyses at both the cell-barcoding and gene quantification levels. At the isoform level, we show that scywalker facilitates the direct identification of cell-type-specific expression of novel isoforms.<br><br>Scywalker is available on github.com/derijkp/scywalker under the GNU General Public License (GPL) and at https://zenodo.org/records/13359438/files/scywalker-0.108.0-Linux-x86_64.tar.gz.}, }
@article {pmid39251911, year = {2024}, author = {Chang, JJM and Ip, YCA and Neo, WL and Mowe, MAD and Jaafar, Z and Huang, D}, title = {Primed and ready: nanopore metabarcoding can now recover highly accurate consensus barcodes that are generally indel-free.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {842}, pmid = {39251911}, issn = {1471-2164}, support = {A-0008413-00-00//National Parks Board - Singapore/ ; MSRDP-P18//National Research Foundation Singapore/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Nanopores ; Animals ; *High-Throughput Nucleotide Sequencing/methods ; INDEL Mutation ; Nanopore Sequencing/methods ; Electron Transport Complex IV/genetics ; Zooplankton/genetics/classification ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: DNA metabarcoding applies high-throughput sequencing approaches to generate numerous DNA barcodes from mixed sample pools for mass species identification and community characterisation. To date, however, most metabarcoding studies employ second-generation sequencing platforms like Illumina, which are limited by short read lengths and longer turnaround times. While third-generation platforms such as the MinION (Oxford Nanopore Technologies) can sequence longer reads and even in real-time, application of these platforms for metabarcoding has remained limited possibly due to the relatively high read error rates as well as the paucity of specialised software for processing such reads.<br><br>RESULTS: We show that this is no longer the case by performing nanopore-based, cytochrome c oxidase subunit I (COI) metabarcoding on 34 zooplankton bulk samples, and benchmarking the results against conventional Illumina MiSeq sequencing. Nanopore R10.3 sequencing chemistry and super accurate (SUP) basecalling model reduced raw read error rates to ~&#x2009;4%, and consensus calling with amplicon_sorter (without further error correction) generated metabarcodes that were &#x2264;&#x2009;1% erroneous. Although Illumina recovered a higher number of molecular operational taxonomic units (MOTUs) than nanopore sequencing (589 vs. 471), we found no significant differences in the zooplankton communities inferred between the sequencing platforms. Importantly, 406 of 444 (91.4%) shared MOTUs between Illumina and nanopore were also found to be free of indel errors, and 85% of the zooplankton richness could be recovered after just 12-15&#xa0;h of sequencing.<br><br>CONCLUSION: Our results demonstrate that nanopore sequencing can generate metabarcodes with Illumina-like accuracy, and we are the first study to show that nanopore metabarcodes are almost always indel-free. We also show that nanopore metabarcoding is viable for characterising species-rich communities rapidly, and that the same ecological conclusions can be obtained regardless of the sequencing platform used. Collectively, our study inspires confidence in nanopore sequencing and paves the way for greater utilisation of nanopore technology in various metabarcoding applications.}, }
@article {pmid39250970, year = {2024}, author = {Jakubska-Busse, A and Wysocki, A and Domagała, PJ and Brudzińska-Kosior, A and Sporek, M and Kosior, G}, title = {Expanding the boundaries in the face of global warming: A lesson from genetic and ecological niche studies of Centaurium erythraea in Europe.}, journal = {The Science of the total environment}, volume = {953}, number = {}, pages = {176134}, doi = {10.1016/j.scitotenv.2024.176134}, pmid = {39250970}, issn = {1879-1026}, mesh = {*Global Warming ; Europe ; *Centaurium/genetics ; *Ecosystem ; *Climate Change ; DNA, Chloroplast/genetics ; }, abstract = {Climate change affects plant species, especially those with restricted ecology and distribution. Centaurium erythraea is a flowering plant species in the Gentianaceae family, native to Europe, with its centre of diversity in the Mediterranean and western Asia. Of the 11 infraspecific taxa distinct from C. erythraea, only two are common in Europe: C. erythraea subsp. erythraea (widespread nominal subspecies) and C. erythraea subsp. majus (mainly distributed in the western Mediterranean region). Freshly collected samples of 36 plants from 11 localities across Lower Silesia (Central Europe) were utilised for taxonomic and genetic analysis. The barcode sequences of chloroplast DNA region matK were used for molecular analysis. Data deposited in GenBank was also used. Five haplotypes were identified among the analysed specimens. Species Distribution Modelling (SDM) techniques were applied to predict the current and future (short- and long-term projections) potential distribution of C. erythraea subsp. majus and to identify the most influential climatic factors. Despite the typical Mediterranean distribution, the presence of C. erythraea subsp. majus outside its natural range in SW Poland has been confirmed by morphological and genetic studies. The mean monthly precipitation of the wettest quarter and the mean daily temperatures of the warmest quarter were identified as the key climatic factors. Short-term scenarios suggest that C. erythraea subsp. majus will maintain most of its current suitable habitats and potentially expand into the lowlands of Central Europe. However, long-term projections indicate a potential reduction in its currently suitable areas, especially in the southern parts of its range, with a possible expansion into north-western Europe. The results of these studies provide clear evidence of the impact of ongoing climate change on species range changes. These findings suggest that climate change may create new opportunities for Mediterranean species to spread to new regions, using C. erythraea subsp. majus as an example.}, }
@article {pmid39250184, year = {2024}, author = {Pallen, MJ}, title = {The dynamic history of prokaryotic phyla: discovery, diversity and division.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {9}, pages = {}, pmid = {39250184}, issn = {1466-5034}, mesh = {Archaea/genetics/classification ; *Bacteria/genetics/classification ; Classification/methods ; History, 20th Century ; History, 21st Century ; *Phylogeny ; Prokaryotic Cells/classification ; History, 19th Century ; }, abstract = {Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.}, }
@article {pmid39247893, year = {2024}, author = {Zhu, L and Bau, T}, title = {Species clarification of fairy inkcap ("Coprinellus disseminatus") in China.}, journal = {Mycology}, volume = {15}, number = {3}, pages = {424-470}, pmid = {39247893}, issn = {2150-1203}, abstract = {Coprinellus disseminatus and other morphologically similar species are widely dispersed worldwide and are commonly referred to as "fairy inkcap". Based on the molecular phylogenetic study and morphological observation, a thorough investigation was carried out utilising 74 collections of related species that were gathered from seventeen provinces and five Chinese fungaria between 1998 and 2023 and revealed 11 lineages of "fairy inkcap", nine of which were found in China, and which belonged to the two genera Coprinellus and Tulosesus. In sect. Disseminati, genetic diversities (π), and fixation index (Fst) amongst lineages were computed, and a haplotype-based network was established to ascertain the relationships amongst each clade. A new section of Coprinellus, sect. Aureodisseminati, were discovered. In addition, four new species (C. aureodisseminatus, C. austrodisseminatus, C. parcus, and C. velutipes), a new subspecies of C. disseminatus, a new combination (Tulosesus pseudodisseminatus), the first discovery of epigamous type of C. magnoliae and a new record to China (T. subdisseminatus) were also identified and thoroughly described with accompanying illustrations. Their differences in macro- and micro-features, as well as their character sequence, were discussed.}, }
@article {pmid39247535, year = {2024}, author = {Zhang, A and Liu, W and Qiu, S}, title = {Mitochondrial genetic variations in leukemia: a comprehensive overview.}, journal = {Blood science (Baltimore, Md.)}, volume = {6}, number = {4}, pages = {e00205}, pmid = {39247535}, issn = {2543-6368}, abstract = {Leukemias are a group of heterogeneous hematological malignancies driven by diverse genetic variations, and the advent of genomic sequencing technologies facilitates the investigation of genetic abnormalities in leukemia. However, these sequencing-based studies mainly focus on nuclear DNAs. Increasing evidence indicates that mitochondrial dysfunction is an important mechanism of leukemia pathogenesis, which is closely related to the mitochondrial genome variations. Here, we provide an overview of current research progress concerning mitochondrial genetic variations in leukemia, encompassing gene mutations and copy number variations. We also summarize currently accessible mitochondrial DNA (mtDNA) sequencing methods. Notably, somatic mtDNA mutations may serve as natural genetic barcodes for lineage tracing and longitudinal assessment of clonal dynamics. Collectively, these findings enhance our understanding of leukemia pathogenesis and foster the identification of novel therapeutic targets and interventions.}, }
@article {pmid39247285, year = {2024}, author = {Lee, HT and Liao, CH and Hsu, TH}, title = {DNA metabarcoding unveils the hidden species composition in fish surimi: Implications for the management of unlabeled and mixed seafood products.}, journal = {Heliyon}, volume = {10}, number = {16}, pages = {e36287}, pmid = {39247285}, issn = {2405-8440}, abstract = {Fish surimi products are traditional foods primarily made from fish meat and may contain a complex species composition. In Taiwan, the abundant fishery resources and diverse fish species lead to local catches being widely used as ingredients in fish surimi products. However, due to growing market demand and increasingly scarce resources, some surimi products contain sensitive species, such as sharks, posing potential threats to the ecological environment and biodiversity. In this study, by applying metabarcoding techniques, we analyzed 120 fish surimi product samples from different brands and types throughout the four seasons in Taiwan's market. The main fish species identified included milkfish (Chanos chanos), dolphinfish (Coryphaena hippurus), Pomfret (Taractes rubescens), swordfish (Istiophorus spp.) and cartilaginous. Moreover, at least 37 species of cartilaginous fish, including 26 endangered species, were found. Through comprehensive and accurate species identification of surimi product ingredients, we unveiled the usage of sensitive species in products on the market. This finding is important for the surimi industry's quality control and market supervision. Furthermore, it can promote the sustainable use of Taiwan's fishery resources and protect biodiversity.}, }
@article {pmid39245155, year = {2024}, author = {Telles-de-Deus, J and Guimarães, LO and Rocha, EC and Helfstein, VC and Reginato, SL and Mucci, LF and Bergo, ES and de Camargo-Neves, VLF and Kirchgatter, K}, title = {COI DNA barcoding to differentiate Haemagogus janthinomys and Haemagogus capricornii (Diptera: Culicidae) mosquitoes.}, journal = {Acta tropica}, volume = {259}, number = {}, pages = {107377}, doi = {10.1016/j.actatropica.2024.107377}, pmid = {39245155}, issn = {1873-6254}, mesh = {Animals ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; *Culicidae/classification/genetics ; *Phylogeny ; Male ; Female ; Brazil ; Sequence Analysis, DNA ; }, abstract = {The genus Haemagogus (Diptera: Culicidae) includes species that are important vectors of pathogens such as the yellow fever virus. The accurate identification of these species is essential for the control of zoonoses. Females of Hg. capricornii and Hg. janthinomys are morphologically indistinguishable, which makes the use of alternative identification techniques desirable. This study aimed to obtain sequences of the mitochondrial cytochrome c oxidase I (COI) gene, in the region widely used for DNA barcoding, of Haemagogus specimens from the state of São Paulo, Brazil, to evaluate the effectiveness of these sequences in the molecular identification of the species. A total of 37 female and 2 male mosquitoes were collected in various locations in the state of São Paulo, using methods such as hand-nets, Shannon traps, CDC light traps with CO2 bait and Nasci aspirators. The sequences of a 710 bp fragment of the COI gene were amplified by PCR and sequenced. A phylogenetic tree reconstruction was conducted using the Bayesian approach implemented in MrBayes v3.2.2, providing support values for taxa where genetic clusters may indicate the presence of new or cryptic species. We obtained 39 COI sequences representing three species: Haemagogus capricornii, Haemagogus leucocelaenus, and Haemagogus janthinomys. Bayesian analysis of the sequences produced clades that corroborate the morphological identification of the species. The separation of Hg. capricornii and Hg. janthinomys received 100 % statistical support and the Hg. capricornii was very well supported (91 %). The two sequences from male specimens, morphologically identified as Hg. capricornii, were grouped in the same clade, a sister clade of Hg. janthinomys. It is important to highlight that the Hg. janthinomys were positioned in several subclades, showing a polymorphism of this species within the state, a situation not observed for Hg. capricornii. For the first time, sequences of the mtCOI gene from Hg. capricornii were obtained and related to morphologically identified specimens. COI sequences proved effective in the molecular identification of Haemagogus species. This study contributes to the expansion of the GenBank database, providing the first sequences of Hg. capricornii and new sequences for Hg. janthinomys and Hg. leucocelaenus.}, }
@article {pmid39244012, year = {2024}, author = {van Ingen-Buijs, VA and van Westerhoven, AC and Skiadas, P and Zuijdgeest, XCL and Haridas, S and Daum, C and Duffy, K and Guo, J and Hundley, H and LaButti, K and Lipzen, A and Pangilinan, J and Riley, R and Wang, J and Yan, M and Martin, F and Barry, K and Grigoriev, IV and Groenewald, JZ and Crous, PW and Seidl, MF}, title = {Phyllosticta paracitricarpa is synonymous with the EU quarantine fungus P. citricarpa based on phylogenomic analyses.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {175}, number = {}, pages = {103925}, doi = {10.1016/j.fgb.2024.103925}, pmid = {39244012}, issn = {1096-0937}, mesh = {*Phylogeny ; *Ascomycota/genetics/classification ; *Plant Diseases/microbiology ; Citrus/microbiology ; Genome, Fungal/genetics ; Genetic Variation ; Genomics ; }, abstract = {Phyllosticta citricarpa is an important citrus-pathogen and a quarantine organism in the European Union. Its recently described relative, P. paracitricarpa, is very closely related and not listed as a quarantine organism. P. paracitricarpa is very difficult to distinguish from P. citricarpa, since its morphological features overlap and the barcoding gene sequences that were originally used to delimit them as distinct species have a low number of species-specific polymorphisms that have subsequently been shown to overlap between the two clades. Therefore, we performed extensive genomic analyses to determine whether the genetic variation between P. citricarpa and P. paracitricarpa strains should be considered to represent infraspecific variation within P. citricarpa, or whether it is indicative of distinct species. Using a phylogenomic analysis with 3,000 single copy ortholog genes and whole-genome comparisons, we determined that the variation between P. citricarpa and P. paracitricarpa can be considered as infraspecies variation within P. citricarpa. We also determined the level of variation in mitochondrial assemblies of several Phyllosticta species and concluded there are only minimal differences between the assemblies of P. citricarpa and P. paracitricarpa. Thus, using several orthogonal approaches, we here demonstrate that variation within the nuclear and mitochondrial genomes of other Phyllosticta species is larger than variation between genomes obtained from P. citricarpa and P. paracitricarpa strains. Thus, P. citricarpa and P. paracitricarpa should be considered as conspecific.}, }
@article {pmid39243221, year = {2024}, author = {Athey, KJ and Chapman, EG and Al-Khatri, S and Moktar, AM and Obrycki, JJ}, title = {Molecular identification of predation on the Dubas bug (Hemiptera: Tropiduchidae) in Oman date palms: density-dependent response to prey.}, journal = {Journal of insect science (Online)}, volume = {24}, number = {4}, pages = {}, pmid = {39243221}, issn = {1536-2442}, support = {TRC/SRG/DB/13/005//Research Council of Oman/ ; }, mesh = {Animals ; *Phoeniceae ; *Predatory Behavior ; Oman ; *Food Chain ; *Heteroptera/physiology ; Hemiptera/physiology ; Pest Control, Biological ; Population Density ; Ants/physiology ; Mites/physiology ; Seasons ; }, abstract = {The date palm (Phoenix dactylifera L.) (Arecales: Arecaceae) is the most economically important crop in Oman with an annual production of >360,000 tons of fruit. The Dubas bug (Ommatissus lybicus de Bergevin) (Hemiptera: Tropiduchidae) is one of the major pests of date palms, causing up to a 50% reduction in fruit production. Across the course of 2 seasons, a variety of arthropod predators living in the date palm canopy were investigated for possible biological control of Dubas bugs, given the growing interest in nonchemical insect pest control in integrated pest management. We collected ~6,900 arthropod predators directly from date palm fronds from 60 Omani date palm plantations and tested them for Dubas bug predation using PCR-based molecular gut content analysis. We determined that ≥56 species of arthropod predators feed on the Dubas bug. We found that predatory mites, ants, and the entire predator community combined showed a positive correlation between predation detection frequency and increasing Dubas bug density. Additionally, there was a significant impact of season on gut content positives, with the spring season having a significantly higher percentage of predators testing positive for Dubas bug, suggesting this season could be the most successful time to target conservation biological control programs utilizing a diverse suite of predators.}, }
@article {pmid39242726, year = {2024}, author = {Rossouw, EI and Landschoff, J and Ndhlovu, A and Neef, G and Miya, M and Courtaillac, KL and Brokensha, R and von der Heyden, S}, title = {Detecting kelp-forest associated metazoan biodiversity with eDNA metabarcoding.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {4}, pmid = {39242726}, issn = {2731-4243}, support = {Keystone Grant 542 (1001 Seaforest Species)//Save Our Seas Foundation/ ; Keystone Grant 542 (1001 Seaforest Species)//Save Our Seas Foundation/ ; 105842//National Research Foundation/ ; }, abstract = {Environmental DNA (eDNA) metabarcoding is a promising tool for monitoring marine biodiversity, but remains underutilised in Africa. In this study, we evaluated the ability of aquatic eDNA metabarcoding as a tool for detecting biodiversity associated with a South African kelp forest, an ecosystem that harbours high diversity of species, many of which are endemic, but are also sensitive to changing environmental conditions and anthropogenic pressures. Using fine-scale spatial (1 m and 8 m) and temporal (every four hours for 24 h) sampling of aquatic environmental DNA and targeting two gene regions (mtDNA COI and 12S rRNA), metabarcoding detected 880 OTUs representing 75 families in the broader metazoan community with 44 OTUs representing 24 fish families. We show extensive variability in the eDNA signal across space and time and did not recover significant spatio-temporal structure in OTU richness and community assemblages. Metabarcoding detected a broad range of taxonomic groups, including arthropods, ascidians, cnidarians, echinoderms, ctenophores, molluscs, polychaetes, ichthyofauna and sponges, as well as Placozoa, previously not reported from South Africa. Fewer than 3% of OTUs could be identified to species level using available databases (COI = 19 OTUs, 12S = 11 OTUs). Our study emphasizes that kelp-forest associated biodiversity in South Africa is understudied, but that with careful consideration for sampling design in combination with increased barcoding efforts and the construction of regional databases, eDNA metabarcoding will become a powerful biomonitoring tool of kelp-forest associated biodiversity.}, }
@article {pmid39240088, year = {2024}, author = {Wang, Y and Li, X and Lu, W and Li, F and Yao, L and Liu, Z and Shi, H and Zhang, W and Bai, Y}, title = {Full-length circRNA sequencing method using low-input RNAs and profiling of circRNAs in MPTP-PD mice on a nanopore platform.}, journal = {The Analyst}, volume = {149}, number = {20}, pages = {5118-5130}, doi = {10.1039/d4an00715h}, pmid = {39240088}, issn = {1364-5528}, mesh = {Animals ; *RNA, Circular/genetics ; Mice ; *Mice, Inbred C57BL ; *Parkinson Disease/genetics ; Sequence Analysis, RNA/methods ; Male ; Nanopores ; High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing/methods ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; Gene Expression Profiling/methods ; }, abstract = {Considering the importance of accurate information of full-length (FL) transcripts in functional analysis, researchers prefer to develop new sequencing methods based on third-generation sequencing (TGS) rather than short-read sequencing. Several FL circRNA sequencing strategies have been developed. However, the current methods are inapplicable to low-biomass samples, since a large amount of total RNAs are acquired for circRNA enrichment before library preparation. In this work, we developed an effective method to detect FL circRNAs from a nanogram level (1-100 ng) of total RNAs based on a nanopore platform. Additionally, prior to the library preparation process, we added a series of 24 nt barcodes for each sample to reduce the cost and operating time. Using this method, we profiled circRNA expression in the striatum, hippocampus and cerebral cortex of a Parkinson's disease (PD) mouse model. Over 6% of reads were effective for FL circRNA identification in most datasets. Notably, a reduction in the RNA initial input resulted in a lower correlation between replicates and the detection efficiency for longer circRNA, but the lowest input (1 ng) was able to detect numerous FL circRNAs. Next, we systematically identified over 263 934 circRNAs in PD and healthy mice using the lower-input FL sequencing method, some of which came from 50.52% of PD-associated genes. Moreover, significant changes were observed in the circRNA expression pattern at an isoform level, and high-confidence protein translation evidence was predicted. Overall, we developed an effective method to characterize FL circRNAs from low-input samples and provide a comprehensive insight into the biological function of circRNAs in PD at an isoform level.}, }
@article {pmid39238034, year = {2024}, author = {Srisuka, W and Takaoka, H and Taai, K and Maleewong, W and Aupalee, K and Saeung, A}, title = {Morphological description and genetic analysis of a new black fly species (Diptera: Simuliidae) in the subgenus Asiosimulium from central Thailand.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {379}, pmid = {39238034}, issn = {1756-3305}, support = {N42A670561//National Research Council of Thailand (NRCT): High-Potential Research Team Grant Program/ ; }, mesh = {Animals ; *Simuliidae/genetics/anatomy &amp; histology/classification ; Thailand ; Female ; Male ; *Pupa/anatomy &amp; histology/genetics/classification ; *Phylogeny ; *Larva/anatomy &amp; histology/genetics/classification ; Electron Transport Complex IV/genetics ; Insect Vectors/anatomy &amp; histology/genetics/classification ; }, abstract = {BACKGROUND: Black flies are among the most medically and veterinary important insects, as adult females of certain species are the sole vector of Onchocerca volvulus. Here, a new black fly species belonging to the subgenus Asiosimulium Takaoka &amp; Choochote, 2005, is described and formally named as Simulium (Asiosimulium) kittipati sp. nov.<br><br>METHODS: Pupae and larvae of black flies were collected from available substrates in the stream from central Thailand. Pupae were individually separated in plastic tubes and maintained until adult flies emerged. The emerged adult flies associated with their pupal exuviae and cocoon as well as mature larvae preserved in 85% ethanol were used to describe the new species based on an integrated approach of morphological examination and molecular analysis of the COI gene.<br><br>RESULTS: The new species is characterized in the female by the medium-long sensory vesicle with a medium-sized opening apically, scutum with three faint longitudinal vittae, and the ellipsoidal spermatheca; in the male by the number of upper-eye (large) facets in 20 vertical columns and 21 horizontal rows, hind basitarsus slender, nearly parallel-sided, and median sclerite much wider and upturned apically; in the pupa by the head and thoracic integument densely covered with tiny tubercles, and the pupal gill of arborescent type with 28-30 filaments; and in the larva by the postgenal cleft deep, nearly reaching the posterior margin of the hypostoma, and dark pigmented sheath of the subesophageal ganglion. The DNA barcode successfully differentiated the new species from its congeners with an interspecific genetic divergence of 1.74-18.72%, confirming the morphological identification that the species is a new member of the subgenus Asiosimulium. Phylogenetic analyses also indicated that the new species is genetically closely related to Simulium phurueaense Tangkawanit, Wongpakam &amp; Pramual, 2018, further supporting its morphological classification.<br><br>CONCLUSIONS: This is the ninth species assigned to the subgenus Asiosimulium within the genus Simulium Latreille, 1802. Taxonomic notes and identification keys are given to distinguish this new species from the eight known species members in its same subgenus. Additionally, a distribution map of all species members in this subgenus occurring in Thailand and other countries is provided.}, }
@article {pmid39237449, year = {2024}, author = {Wallace, JG and Griffis, H}, title = {Preparation of Illumina 16s Amplicon Sequencing Libraries with Peptide Nucleic Acids (PNAs) for the Analysis of Maize-Associated Microbiomes.}, journal = {Cold Spring Harbor protocols}, volume = {}, number = {}, pages = {}, doi = {10.1101/pdb.prot108583}, pmid = {39237449}, issn = {1559-6095}, abstract = {One of the most common methods to survey bacterial communities is targeted amplification of the hypervariable regions of the 16s rRNA gene followed by sequencing. This protocol details Illumina library preparation of such amplicons from communities isolated from maize. We include both staggered PCR primers to improve Illumina base calling and peptide nucleic acids (PNAs) to reduce the presence of plant organelles. Primers are designed with Illumina adapter sequences for the addition of sample-specific indexes (barcodes). We also briefly discuss alternative primer sets, including ones that directly discriminate against plant organelles or that amplify different organisms (e.g., fungal internal transcribed spacer [ITS] sequences).}, }
@article {pmid39234150, year = {2024}, author = {Fang, X and Xu, Z and Yao, Y and Fu, Y}, title = {Two new species of Macropelopia (Diptera, Chironomidae) from Oriental China, delineated with morphology and COI sequences.}, journal = {ZooKeys}, volume = {1210}, number = {}, pages = {287-298}, pmid = {39234150}, issn = {1313-2989}, abstract = {Two new species, Macropelopia (Macropelopia) excavata Xu &amp; Fu, sp. nov. and Macropelopia (Macropelopia) quadrimacula Xu &amp; Fu, sp. nov., are described as male adults. A key to identify the males of Macropelopia from China is provided. Furthermore, in order to ascertain the genetic distance between these species and their morphological characteristics, mitochondrial cytochrome c oxidase subunit I gene sequences were uploaded to the National Center for Biotechnology Information. These COI sequences were then utilized to infer the relationships between the species, employing the neighbor-joining method.}, }
@article {pmid39233723, year = {2024}, author = {Saigal, M and Shueh Yi, HN and Rameez, NA and van Manen, S and Van Anh, BT and Arora, VP and Han, KDM and Lee, JQT and Syaddad, A and Tan, CK and Lim, EXY and Wainwright, BJ}, title = {Beneath the surface: DNA barcoding of shark fins in Singapore.}, journal = {Royal Society open science}, volume = {11}, number = {9}, pages = {240532}, pmid = {39233723}, issn = {2054-5703}, abstract = {The global decline of shark populations, largely driven by overfishing to supply the shark fin trade, poses a significant threat to marine ecosystems. Southeast Asia, and particularly Singapore, is a key hub for the transit and trade of shark fins that contribute to the exploitation of these apex predators. Through the use of DNA barcoding techniques, this study aimed to determine what species of shark are involved in the Singapore shark fin trade. Fins were collected from markets, dried goods shops and traditional Chinese medicine halls throughout Singapore. In total, DNA was extracted from 684 fins collected in January 2024 and PCR amplification targeted a fragment of the mitochondrial COI gene for species identification. Results revealed fins from 24 species across 16 genera, with 19 species listed on CITES Appendices II, and 16 listed as threatened on the IUCN Red List (critically endangered = 2, endangered = 4, vulnerable = 10). The top five most frequently identified species were Carcharhinus falciformis, Galeorhinus galeus, Rhizoprionodon oligolinx, Sphyrna lewini and Rhizoprionodon acutus. Of these, four are listed on CITES Appendix II and four are listed as threatened on the IUCN Red List.}, }
@article {pmid39232201, year = {2025}, author = {Chen, F and Li, X and Bai, M and Zhao, Y}, title = {Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING.}, journal = {Nature protocols}, volume = {20}, number = {1}, pages = {220-247}, pmid = {39232201}, issn = {1750-2799}, support = {22125404//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92068118//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Humans ; 5-Methylcytosine/metabolism/analogs &amp; derivatives ; *DNA/genetics ; *Epigenesis, Genetic ; *In Situ Hybridization, Fluorescence/methods ; Nucleic Acid Amplification Techniques/methods ; *Single-Cell Analysis/methods ; }, abstract = {Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING). They all use the similar core principle of DNA-encoded amplification, which transforms different nonsequence molecular features into unique DNA barcodes for in situ rolling circle amplification and FISH analysis. This involves three key reactions in fixed cell samples: target labeling, DNA encoding and rolling circle amplification imaging. Using this protocol, these three imaging strategies achieve in situ counting of low-abundance modifications alone, the pairwise proximity-differentiated visualization of two modifications and the exploration of multiple modifications around one protein (one-to-many proximity), respectively. Low-abundance modifications, including 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil and 5-formyluracil, are clearly visualized in single cells. Various combinatorial patterns of nucleic acid modifications and/or histone modifications are found. The whole protocol takes ~2-4 d to complete, depending on different imaging applications.}, }
@article {pmid39232051, year = {2024}, author = {Kinya, F and Milugo, TK and Mutero, CM and Wondji, CS and Torto, B and Tchouassi, DP}, title = {Insights into malaria vectors-plant interaction in a dryland ecosystem.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20625}, pmid = {39232051}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; 222005/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; RAF-3058 KEN-18/0005//Norwegian Agency for Development Cooperation (Norad)/ ; }, mesh = {Animals ; *Mosquito Vectors/parasitology/genetics ; *Ecosystem ; *Anopheles/parasitology/genetics/metabolism ; Kenya ; *Plasmodium falciparum/genetics/metabolism ; *DNA Barcoding, Taxonomic ; Malaria/transmission/parasitology ; Acacia/metabolism/parasitology/genetics ; Feeding Behavior/physiology ; Ribulose-Bisphosphate Carboxylase/metabolism/genetics ; }, abstract = {Improved understanding of mosquito-plant feeding interactions can reveal insights into the ecological dynamics of pathogen transmission. In wild malaria vectors Anopheles gambiae s.l. and An. funestus group surveyed in selected dryland ecosystems of Kenya, we found a low level of plant feeding (2.8%) using biochemical cold anthrone test but uncovered 14-fold (41%) higher rate via DNA barcoding targeting the chloroplast rbcL gene. Plasmodium falciparum positivity was associated with either reduced or increased total sugar levels and varied by mosquito species. Gut analysis revealed the mosquitoes to frequently feed on acacia plants (~ 89%) (mainly Vachellia tortilis) in the family Fabaceae. Chemical analysis revealed 1-octen-3-ol (29.9%) as the dominant mosquito attractant, and the sugars glucose, sucrose, fructose, talose and inositol enriched in the vegetative parts, of acacia plants. Nutritional analysis of An. longipalpis C with high plant feeding rates detected fewer sugars (glucose, talose, fructose) compared to acacia plants. These results demonstrate (i) the sensitivity of DNA barcoding to detect plant feeding in malaria vectors, (ii) Plasmodium infection status affects energetic reserves of wild anopheline vectors and (iii) nutrient content and olfactory cues likely represent potent correlates of acacia preferred as a host plant by diverse malaria vectors. The results have relevance in the development of odor-bait control strategies including attractive targeted sugar-baits.}, }
@article {pmid39231998, year = {2024}, author = {Ma, YX and Wang, XD}, title = {Directional self-assembly of organic vertically superposed nanowires.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {7706}, pmid = {39231998}, issn = {2041-1723}, support = {52173177//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Organic crystal-based superimposed heterostructures with inherent multichannel characteristics demonstrate superior potential for manipulating excitons/photons at the micro/nanoscale for integrated optoelectronics. However, the precise construction of organic superimposed heterostructures with fixed superimposed sites remains challenging because of the random molecular nucleation process. Here, organic vertically superimposed heterostructures (OSHs) with fixed superimposed positions are constructed via semi-wrapped core/shell heterostructures with partially exposed cores, which provide preferential nucleation sites for further molecular epitaxial growth processes. Furthermore, the relative length ratio from 21.7% to 95.3% between interlayers is accurately adjusted by regulating the exposed area of the semi-wrapped core/shell heterostructures. Significantly, these OSHs with anisotropic optical characteristics demonstrate well regulation of excitation position-dependent waveguide behaviors and can function as photonic barcodes for information encryption. This strategy provides a facile approach for controlling the nucleation sites for the controllable preparation of organic heterostructures and advanced applications for integrated optoelectronics.}, }
@article {pmid39229105, year = {2024}, author = {Williams, MJ and Vázquez-García, I and Tam, G and Wu, M and Varice, N and Havasov, E and Shi, H and Satas, G and Lees, HJ and Lee, JJ and Myers, MA and Zatzman, M and Rusk, N and Ali, E and Shah, RH and Berger, MF and Mohibullah, N and Lakhman, Y and Chi, DS and Abu-Rustum, NR and Aghajanian, C and McPherson, A and Zamarin, D and Loomis, B and Weigelt, B and Friedman, CF and Shah, SP}, title = {Tracking clonal evolution of drug resistance in ovarian cancer patients by exploiting structural variants in cfDNA.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39229105}, issn = {2692-8205}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; U24 CA264028/CA/NCI NIH HHS/United States ; P50 CA247749/CA/NCI NIH HHS/United States ; K99 CA256508/CA/NCI NIH HHS/United States ; R01 CA281928/CA/NCI NIH HHS/United States ; R01 CA269382/CA/NCI NIH HHS/United States ; }, abstract = {Drug resistance is the major cause of therapeutic failure in high-grade serous ovarian cancer (HGSOC). Yet, the mechanisms by which tumors evolve to drug resistant states remains largely unknown. To address this, we aimed to exploit clone-specific genomic structural variations by combining scaled single-cell whole genome sequencing with longitudinally collected cell-free DNA (cfDNA), enabling clonal tracking before, during and after treatment. We developed a cfDNA hybrid capture, deep sequencing approach based on leveraging clone-specific structural variants as endogenous barcodes, with orders of magnitude lower error rates than single nucleotide variants in ctDNA (circulating tumor DNA) detection, demonstrated on 19 patients at baseline. We then applied this to monitor and model clonal evolution over several years in ten HGSOC patients treated with systemic therapy from diagnosis through recurrence. We found drug resistance to be polyclonal in most cases, but frequently dominated by a single high-fitness and expanding clone, reducing clonal diversity in the relapsed disease state in most patients. Drug-resistant clones frequently displayed notable genomic features, including high-level amplifications of oncogenes such as CCNE1, RAB25, NOTCH3, and ERBB2. Using a population genetics Wright-Fisher model, we found evolutionary trajectories of these features were consistent with drug-induced positive selection. In select cases, these alterations impacted selection of secondary lines of therapy with positive patient outcomes. For cases with matched single-cell RNA sequencing data, pre-existing and genomically encoded phenotypic states such as upregulation of EMT and VEGF were linked to drug resistance. Together, our findings indicate that drug resistant states in HGSOC pre-exist at diagnosis and lead to dramatic clonal expansions that alter clonal composition at the time of relapse. We suggest that combining tumor single cell sequencing with cfDNA enables clonal tracking in patients and harbors potential for evolution-informed adaptive treatment decisions.}, }
@article {pmid39228674, year = {2024}, author = {Vanhoye, X and Mouty, P and Mouty, S and Bargues, N and Couprie, N and Fayolle, E and Géromel, V and Taoudi, M and Raymond, L and Taly, JF}, title = {Implementation of long-read sequencing for routine molecular diagnosis of familial mediterranean fever.}, journal = {Practical laboratory medicine}, volume = {41}, number = {}, pages = {e00423}, pmid = {39228674}, issn = {2352-5517}, abstract = {BACKGROUND: Long-read sequencing technology, widely used in research, is proving useful in clinical diagnosis, especially for infectious diseases. Despite recent advances, it hasn't been routinely applied to constitutional human diseases. Long-read sequencing detects intronic variants and phases variants, crucial for identifying recessive diseases.<br><br>METHODS: We integrated long-read sequencing into the clinical diagnostic workflow for the MEFV gene, responsible for familial Mediterranean fever (FMF), using a Nanopore-based workflow. This involved long-range PCR amplification, native barcoding kit library preparation, GridION sequencing, and in-house bioinformatics. We compared this new workflow against our validated method using 39 patient samples and 3 samples from an external quality assessment scheme to ensure compliance with ISO15189 standards.<br><br>RESULTS: Our evaluation demonstrated excellent performance, meeting ISO15189 requirements for reproducibility, repeatability, sensitivity, and specificity. Since October 2022, 150 patient samples were successfully analyzed with no failures. Among these samples, we identified 13 heterozygous carriers of likely pathogenic (LP) or pathogenic (P) variants, 1 patient with a homozygous LP/P variant in MEFV, and 4 patients with compound heterozygous variants.<br><br>CONCLUSION: This study represents the first integration of long-read sequencing for FMF clinical diagnosis, achieving 100&#xa0;% sensitivity and specificity. Our findings highlight its potential to identify pathogenic variants without parental segregation analysis, offering faster, cost-effective, and accurate clinical diagnosis. This successful implementation lays the groundwork for future applications in other constitutional human diseases, advancing precision medicine.}, }
@article {pmid39228134, year = {2024}, author = {Chan, WWR and Chang, JJM and Tan, CZ and Ng, JX and Ng, MH and Jaafar, Z and Huang, D}, title = {Eyeing DNA barcoding for species identification of fish larvae.}, journal = {Journal of fish biology}, volume = {105}, number = {6}, pages = {1784-1799}, pmid = {39228134}, issn = {1095-8649}, support = {A-0008413-00-00//National Parks Board - Singapore/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Fishes/genetics/classification ; *Larva/genetics/classification ; Electron Transport Complex IV/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Eye/anatomy &amp; histology ; }, abstract = {Identification of fish larvae based on morphology is typically limited to higher taxonomic ranks (e.g., family or order), as larvae possess few morphological diagnostic characters for precise discrimination to species. When many samples are presented at any one time, the use of morphology to identify such specimens can be laborious and time-consuming. Using a reverse workflow for specimen sorting and identification leveraging high-throughput DNA sequencing, thousands of fish larvae can be DNA barcoded and sorted into molecular operational taxonomic units (mOTUs) in a single sequencing run with the nanopore sequencing technology (e.g., MinION). This process reduces the time and financial costs of morphology-based sorting and instead deploys experienced taxonomists for species taxonomic work where they are needed most. In this study, a total of 3022 fish larval specimens from plankton tows across four sites in Singapore were collected and sorted based on this workflow. Eye tissue from individual samples was used for DNA extraction and sequencing of cytochrome c oxidase subunit I. We generated a total of 2746 barcodes after quality filtering (90.9% barcoding success), identified 2067 DNA barcodes (75.3% identification success), and delimited 256 mOTUs (146 genera, 52 families). Our analyses identified specific challenges to species assignment, such as the potential misidentification of publicly available sequences used as reference barcodes. We highlighted how the conservative application and comparison of a local sequence database can help resolve identification conflicts. Overall, this proposed approach enables and expedites taxonomic identification of fish larvae, contributing to the enhancement of reference barcode databases and potentially better understanding of fish connectivity.}, }
@article {pmid39227484, year = {2024}, author = {Oliveira Carvalho, C and Pazirgiannidi, M and Ravelomanana, T and Andriambelomanana, F and Schrøder-Nielsen, A and Stuart Ready, J and de Boer, H and Fusari, CE and Mauvisseau, Q}, title = {Multi-method survey rediscovers critically endangered species and strengthens Madagascar's freshwater fish conservation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20427}, pmid = {39227484}, issn = {2045-2322}, mesh = {Animals ; *Endangered Species ; *Conservation of Natural Resources/methods ; Madagascar ; *Fresh Water ; *Biodiversity ; *Fishes/genetics/classification ; DNA, Environmental/genetics/analysis ; Rivers ; Ecosystem ; }, abstract = {Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies.}, }
@article {pmid39226784, year = {2024}, author = {Xia, Z and Yang, Y and Zeng, Y and Sun, Y and Cui, Q and Chen, Z and Liu, J and Zhang, J and He, P}, title = {Temporal succession of micropropagules during accumulation and dissipation of green tide algae: A case study in Rudong coast, Jiangsu Province.}, journal = {Marine environmental research}, volume = {202}, number = {}, pages = {106719}, doi = {10.1016/j.marenvres.2024.106719}, pmid = {39226784}, issn = {1879-0291}, mesh = {China ; *Ulva/metabolism ; *Environmental Monitoring ; *Eutrophication ; Chlorophyta/genetics ; Seawater/chemistry ; Geologic Sediments ; }, abstract = {Over the past 18 years, green tides have persistently occurred in the Yellow Sea. Micropropagules of these algae are key to bloom formation, yet their species composition and succession during dissipation remain underexplored. During the dissipation process of accumulated green tide algae, a large number of micropropagules are released. This study monitored the dissipation of green tide algae at a coastal site, tracking micropropagules in water and sediment using an internal transcribed spacer (ITS) and 5S rDNA primers. Results showed that the dissipation lasted about one month, with significant micropropagule release. Initially, micropropagules matched 5S-II Ulva prolifera, but later species like Ulva torta, Ulva simplex, Ulva flexuosa, and Ulva meridionalis emerged. Ulva meridionalis dominated sediment in July and August, while U. torta was prevalent in water, and U. flexuosa was dominant in other months. Accumulated U. prolifera in the intertidal zone may not contribute to the seeding of the next year's bloom. This study sheds light on the dissipation process and succession patterns of micropropagules in coastal environments.}, }
@article {pmid39224985, year = {2024}, author = {Isma, LM and Golightly, CG and Bracken-Grissom, HD}, title = {Under the Sea: Investigation of Telson Morphology and Cryptic Diversity within Eucopia sculpticauda, a Deep-Sea Lophogastrid from the Gulf of Mexico (Peracarida: Lophogastrida).}, journal = {Integrative and comparative biology}, volume = {64}, number = {4}, pages = {1154-1161}, doi = {10.1093/icb/icae141}, pmid = {39224985}, issn = {1557-7023}, support = {//Gulf of Mexico Research Initiative/ ; }, mesh = {Animals ; Gulf of Mexico ; *Phylogeny ; Gastropoda/genetics/anatomy &amp; histology/classification ; }, abstract = {The field of phylogenetics employs a variety of methods and techniques to study the evolution of life across the planet. Understanding evolutionary relationships is crucial to enriching our understanding of how genes and organisms have evolved throughout time and how they could possibly evolve in the future. Eucopia sculpticauda Faxon, 1893 is a deep-water peracarid in the order Lophogastrida Boas, 1883, which can often be found in high abundances in pelagic trawls. The species can be found along the Mariana Trench, in the Mid-Atlantic Ridge, west Atlantic and east Pacific Oceans, and in the Gulf of Mexico and as deep as 7526 m. Recent collections of E. sculpticauda in the Gulf of Mexico have revealed putative cryptic diversity within the species based on both molecular and morphological evidence. Previous studies have documented two different morphotypes of the telson: the terminal part of the pleon (abdomen) and part of the tail fan. In adults, the morphotypes can be distinguished by lateral constrictions in the telson. This evidence, combined with a previous barcoding study, led to the speculation that telson morphology may be a distinguishing character useful to define cryptic diversity within E. sculpticauda. This study presents additional molecular data from the mitochondrial genes cytochrome c oxidase subunit I, and the large ribosomal subunit (16S), and the nuclear histone 3 gene (H3) to investigate telson morphotypes in relation to evolutionary history within this species. Molecular data identified two strongly supported clades, lending support for potential cryptic diversification within the Gulf of Mexico. Investigations into telson morphology suggest that this character may be informative, but the morphotypes were sometimes ambiguous and additional characters could not be found that discriminate clades. At present, our data suggest early evidence for cryptic diversification within Gulf of Mexico populations, but additional morphological characters and geographic sampling are needed before a new species can be described.}, }
@article {pmid39223179, year = {2024}, author = {Schmidt, LA and Brix, S and Rossel, S and Forster, S and Eichsteller, A}, title = {Unveiling ophiuroid biodiversity across North Atlantic habitats via an integrative perspective.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20405}, pmid = {39223179}, issn = {2045-2322}, support = {MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; MSM75,MerMet17-05; SO276 MerMet17-06//Germany Science Foundation/ ; }, mesh = {*Biodiversity ; Animals ; *DNA Barcoding, Taxonomic ; Atlantic Ocean ; *Ecosystem ; Echinodermata/genetics/classification ; Phylogeny ; Proteomics/methods ; }, abstract = {The depths of the North Atlantic Ocean host a species-rich fauna providing heterogeneous habitats from thermal vent fields to cold-water coral reefs. With the increasing threat of destruction of deep-sea habitats due to human impacts, such as demersal fishing and the beginning of deep-sea mining, an analysis of the diversity and distribution of species is crucial for conservation efforts. Brittle stars occur in high biomasses, contributing to the biodiversity of the seafloor. Specimens were collected during several scientific expeditions to gain a more detailed insight into the brittle star diversity in the North Atlantic Ocean. An integrative approach to identify the species with DNA barcoding (mtCOI) in combination with morphological studies revealed 24 species. Most species have been previously identified in the North Atlantic, but sequences for 13 species are newly added to public repositories. Additionally, the MALDI-TOF-MS proteomic analysis was successfully applied for 197 specimens with known COI barcodes. Results are congruent with other molecular species delimitations demonstrating the functionality of proteomics for the identification of brittle stars. This dataset significantly expands our understanding of the taxonomic and genetic diversity of brittle stars and contributes to publicly available data. It emphasizes the importance of considering habitat heterogeneity for large scale patterns of biodiversity.}, }
@article {pmid39222178, year = {2025}, author = {Shaban, D and Najm, N and Droin, L and Nijnik, A}, title = {Hematopoietic Stem Cell Fates and the Cellular Hierarchy of Mammalian Hematopoiesis: from Transplantation Models to New Insights from in Situ Analyses.}, journal = {Stem cell reviews and reports}, volume = {21}, number = {1}, pages = {28-44}, pmid = {39222178}, issn = {2629-3277}, support = {Canadian Institutes of Health Research/CAPMC/CIHR/Canada ; Leukemia and Lymphoma Society of Canada//Leukemia and Lymphoma Society of Canada/ ; Canada Research Chairs//Canada Research Chairs/ ; Fonds de Recherche du Qu&#xe9;bec - Sant&#xe9;//Fonds de Recherche du Qu&#xe9;bec - Sant&#xe9;/ ; }, mesh = {Animals ; *Hematopoietic Stem Cells/cytology/metabolism ; Humans ; *Hematopoiesis/genetics ; *Hematopoietic Stem Cell Transplantation ; *Cell Lineage ; Cell Differentiation ; Gene Editing ; Mice ; }, abstract = {Hematopoiesis is the process that generates the cells of the blood and immune system from hematopoietic stem and progenitor cells (HSPCs) and represents the system with the most rapid cell turnover in a mammalian organism. HSPC differentiation trajectories, their underlying molecular mechanisms, and their dysfunctions in hematologic disorders are the focal research questions of experimental hematology. While HSPC transplantations in murine models are the traditional tool in this research field, recent advances in genome editing and next generation sequencing resulted in the development of many fundamentally new approaches for the analyses of mammalian hematopoiesis in situ and at single cell resolution. The current review will cover many recent developments in this field in murine models, from the bulk lineage tracing studies of HSPC differentiation to the barcoding of individual HSPCs with Cre-recombinase, Sleeping Beauty transposase, or CRISPR/Cas9 tools, to map hematopoietic cell fates, together with their transcriptional and epigenetic states. We also address studies of the clonal dynamics of human hematopoiesis, from the tracing of HSPC clonal behaviours based on viral integration sites in gene therapy patients to the recent analyses of unperturbed human hematopoiesis based on naturally accrued mutations in either nuclear or mitochondrial genomes. Such studies are revolutionizing our understanding of HSPC biology and hematopoiesis both under homeostatic conditions and in the response to various forms of physiological stress, reveal the mechanisms responsible for the decline of hematopoietic function with age, and in the future may advance the understanding and management of the diverse disorders of hematopoiesis.}, }
@article {pmid39221955, year = {2024}, author = {Fang, J and Salinas, I and San Vicente, S and Zielinski, C and Sade-Feldman, M}, title = {Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {210}, pages = {}, doi = {10.3791/66766}, pmid = {39221955}, issn = {1940-087X}, mesh = {Humans ; *Single-Cell Analysis/methods ; Mice ; Animals ; *Sequence Analysis, RNA/methods ; Neoplasms/genetics ; }, abstract = {Human tumor samples hold a plethora of information about their microenvironment and immune repertoire. Effective dissociation of human tissue samples into viable cell suspensions is a required input for the single-cell RNA sequencing (scRNAseq) pipeline. Unlike bulk RNA sequencing approaches, scRNAseq enables us to infer the transcriptional heterogeneity in tumor specimens at the single-cell level. Incorporating this approach in recent years has led to many discoveries, such as identifying immune and tumor cellular states and programs associated with clinical responses to immunotherapies and other types of treatments. Moreover, single-cell technologies applied to dissociated tissues can be used to identify accessible chromatin regions T and B cell receptor repertoire, and the expression of proteins, using DNA barcoded antibodies (CITEseq). The viability and quality of the dissociated sample are critical variables when using these technologies, as these can dramatically affect the cross-contamination of single cells with ambient RNA, the quality of the data, and interpretation. Moreover, long dissociation protocols can lead to the elimination of sensitive cell populations and the upregulation of a stress response gene signature. To overcome these limitations, we devised a rapid universal dissociation protocol, which has been validated on multiple types of human and murine tumors. The process begins with mechanical and enzymatic dissociation, followed by filtration, red blood lysis, and live dead enrichment, suitable for samples with a low input of cells (e.g., needle core biopsies). This protocol ensures a clean and viable single-cell suspension paramount to the successful generation of Gel Bead-In Emulsions (GEMs), barcoding, and sequencing.}, }
@article {pmid39221281, year = {2024}, author = {Lutz, &#xcd; and Martins, T and Santana, P and Ferreira, C and Miranda, J and Matos, S and Muhala, V and Sampaio, I and Vallinoto, M and Evangelista-Gomes, G}, title = {Marine catfishes (Ariidae-Siluriformes) from the Coastal Amazon: mitochondrial DNA barcode for a recent diversification group?.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17581}, pmid = {39221281}, issn = {2167-8359}, mesh = {Animals ; *Catfishes/genetics/classification ; *DNA Barcoding, Taxonomic ; *DNA, Mitochondrial/genetics ; Phylogeny ; Genetic Variation/genetics ; Brazil ; Electron Transport Complex IV/genetics ; }, abstract = {BACKGROUND: Ariidae species play a significant role as fishing resources in the Amazon region. However, the family's systematic classification is notably challenging, particularly regarding species delimitation within certain genera. This difficulty arises from pronounced morphological similarities among species, posing obstacles to accurate species recognition.<br><br>METHODS: Following morphological identification, mitochondrial markers (COI and Cytb) were employed to assess the diversity of Ariidae species in the Amazon.<br><br>RESULTS: Our sampling efforts yielded 12 species, representing 92% of the coastal Amazon region's diversity. Morphological identification findings were largely corroborated by molecular data, particularly for species within the Sciades and Bagre genera. Nonetheless, despite morphological support, Cathorops agassizii and Cathorops spixii displayed minimal genetic divergence (0.010). Similarly, Notarius quadriscutis and Notarius phrygiatus formed a single clade with no genetic divergence, indicating mitochondrial introgression. For the majority of taxa examined, both COI and Cytb demonstrated efficacy as DNA barcodes, with Cytb exhibiting greater polymorphism and resolution. Consequently, the molecular tools utilized proved highly effective for species discrimination and identification.}, }
@article {pmid39221104, year = {2024}, author = {Mullin, PG and Harris, T and Higgins, R and Dutta, E and Porazinska, DL and Powers, K and Powers, T}, title = {Taxonomy of Tobrilidae species from the Alkaline Lakes of the western Nebraska Sandhills.}, journal = {Journal of nematology}, volume = {56}, number = {1}, pages = {20240025}, pmid = {39221104}, issn = {0022-300X}, abstract = {Six distinct COI mitochondrial Haplotype Groups (HG) are morphologically, ecologically, and genetically characterized from the aquatic nematode family Tobrilidae. Collection locations included the extreme habitats of the Alkaline Lakes in the western Nebraska Sandhills and the contaminated stream, Johnson Creek, bordering the AltEn 2021 catastrophic pesticide release near the village of Mead in eastern Nebraska. Maximum likelihood and genetic distance metrics supported the genetic integrity of the haplotype groups. Discriminant function analysis of COI haplotype group datasets of combined morphological characters and soil chemistry attributes for both male and female Tobrilidae were classified correctly in all but one case. Scanning electron microscopy revealed new details about amphid apertures, male supplements, and spicules. Partial 18S gene phylogeny suggests that the genus Semitobrilus may not be a member of the subfamily Neotobrilinae, and three specimens in the 226 tobrilid dataset provide evidence of incongruence between COI and 18S derived phylogenies. Given the strong signal provided by the environmental chemistry data, tobrilid mitochondrial haplotypes may well have value as environmental indicators.}, }
@article {pmid39220016, year = {2024}, author = {Chen, L and Song, BN and Yang, L and Wang, Y and Wang, YY and Aou, X and He, XJ and Zhou, SD}, title = {Phylogeny, adaptive evolution, and taxonomy of Acronema (Apiaceae): evidence from plastid phylogenomics and morphological data.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1425158}, pmid = {39220016}, issn = {1664-462X}, abstract = {INTRODUCTION: The genus Acronema, belonging to Apiaceae, includes approximately 25 species distributed in the high-altitude Sino-Himalayan region from E Nepal to SW China. This genus is a taxonomically complex genus with often indistinct species boundaries and problematic generic delimitation with Sinocarum and other close genera, largely due to the varied morphological characteristics.<br><br>METHODS: To explore the phylogenetic relationships and clarify the limits of the genus Acronema and its related genera, we reconstructed a reliable phylogenetic framework with high support and resolution based on two molecular datasets (plastome data and ITS sequences) and performed morphological analyses.<br><br>RESULTS: Both phylogenetic analyses robustly supported that Acronema was a non-monophyletic group that fell into two clades: Acronema Clade and East-Asia Clade. We also newly sequenced and assembled sixteen Acronema complete plastomes and performed comprehensively comparative analyses for this genus. The comparative results showed that the plastome structure, gene number, GC content, codon bias patterns were high similarity, but varied in borders of SC/IR and we identified six different types of SC/IR border. The SC/IR boundaries of Acronema chienii were significantly different from the other Acronema members which was consistent with the type VI pattern in the genus Tongoloa. We also identified twelve potential DNA barcode regions (ccsA, matK, ndhF, ndhG, psaI, psbI, rpl32, rps15, ycf1, ycf3, psaI-ycf4 and psbM-trnD) for species identification in Acronema. The molecular evolution of Acronema was relatively conservative that only one gene (petG) was found to be under positive selection (&#x3c9; = 1.02489).<br><br>DISCUSSION: The gene petG is one of the genes involved in the transmission of photosynthetic electron chains during photosynthesis, which plays a crucial role in the process of photosynthesis in plants. This is also a manifestation of the adaptive evolution of plants in high-altitude areas to the environment. In conclusion, our study provides novel insights into the plastome adaptive evolution, phylogeny, and taxonomy of genus Acronema.}, }
@article {pmid39218175, year = {2024}, author = {Hosseini, SA and Elahian, F and Mirzaei, SA}, title = {Innovative genetic scissor strategies and their applications in cancer treatment and prevention: CRISPR modules and challenges.}, journal = {International journal of biological macromolecules}, volume = {279}, number = {Pt 2}, pages = {135239}, doi = {10.1016/j.ijbiomac.2024.135239}, pmid = {39218175}, issn = {1879-0003}, mesh = {*Neoplasms/genetics/therapy/prevention &amp; control ; Humans ; *CRISPR-Cas Systems ; *Gene Editing/methods ; Animals ; Genetic Therapy/methods ; }, abstract = {There are lots of gene editing tools for targeting genome sequences. Some are almost known, and most are a complete mystery and undiscovered. CRISPR/Cas editing tools have brought about a major revolution in medicine. Researchers have shown that CRISPR can modify DNA much more accurately, economically and easily than previous methods. CRISPR has proven itself effective for the deletion, replacement and insertion of DNA fragments into cell types, tissues and organisms. Recently, combining CRISPR/Cas with factors (transcription factors/repressors, exonucleases, endonucleases, transposons, caspase, fluorescent proteins, oxidoreductive enzymes, DNA/RNA polymerases), and elements (aptamers, barcodes, fluorescent probes, Trigger) have provided genome, transcriptome, proteome and epigenome modification. These modules are being investigated for cancer prevention and therapy and this review focuses on such innovative combinations that hopefully will become a clinical reality in the near future.}, }
@article {pmid39208239, year = {2024}, author = {Douch, JK and Vaughan, LJ and Cooper, JA and Holmes, GD and Robinson, R and Stefani, F and Idnurm, A and May, TW}, title = {Taxonomic revision of fleshy species of Hydnellum, Neosarcodon, and Sarcodon (Thelephorales) from Australasia.}, journal = {Mycologia}, volume = {116}, number = {6}, pages = {965-992}, doi = {10.1080/00275514.2024.2363211}, pmid = {39208239}, issn = {1557-2536}, mesh = {*Phylogeny ; *DNA, Fungal/genetics ; *Basidiomycota/classification/genetics/isolation &amp; purification ; *DNA, Ribosomal Spacer/genetics ; Australia ; New Zealand ; Sequence Analysis, DNA ; RNA, Ribosomal, 28S/genetics ; Australasia ; DNA, Ribosomal/genetics ; Forests ; Mycorrhizae/classification/genetics ; }, abstract = {Stipitate Thelephorales are basidiomycetous, mostly hydnoid, ectomycorrhizal fungi. Some species have declined considerably, and some are threat-listed as vulnerable or endangered. These ecological concerns require a well-resolved taxonomy to understand diversity in this group of fungi and facilitate conservation. However, phylogenetic studies have mostly neglected Southern Hemisphere representatives. This study examines the fleshy species of stipitate Thelephorales from native forests in Australia and New Zealand, using morphological analyses and phylogenetic analyses of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode) and D1-D2 domains at the 5' end of nuc 28S rDNA (28S) sequences amplified from DNA isolated from fungarium collections and environmental DNA (eDNA) sequences from the Australian Microbiome initiative. Five new species, Sarcodon austrofibulatus, Hydnellum gatesiae, H. nothofagacearum, H. pseudoioeides, and H. variisporum, are described, Sarcodon carbonarius is transferred to Neosarcodon, and a key is provided for the six named species in the region. Boletopsis and Neosarcodon are reported from Australia for the first time based on detections from eDNA in soil samples taken from native forests. The Australasian species of Hydnellum occupy a highly derived position with the phylogeny of the genus, the members of which are otherwise all from the Northern Hemisphere, suggestive of a long-distance dispersal origin for the Australasian species.}, }
@article {pmid39204610, year = {2024}, author = {Kali, B and Bekkuzhina, S and Tussipkan, D and Manabayeva, S}, title = {A First Approach for the In Vitro Cultivation, Storage, and DNA Barcoding of the Endangered Endemic Species Euonymus koopmannii.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39204610}, issn = {2223-7747}, support = {BR21882180//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Euonymus koopmannii is a rare and protected species in Kazakhstan, valued for its ecological role in soil stabilization and its ornamental properties. This study presents the first use of micropropagation and phylogenetic analysis for the endemic plant E. koopmannii. Seedlings of E. koopmannii proved to be more effective than internodes as primary explants for plant micropropagation of in vitro culture, with a multiplication coefficient of 28.5 from seedlings and 6.1 from internodes. On MSR I medium supplemented with 0.5 mg/L IBA and 0.05 mg/L IAA, a higher success rate of 67% was achieved for root formation of test tube-grown E. koopmannii plants. Using mannitol as an osmotic agent at a concentration of 8 mg/L prolonged the storage time of E. koopmannii under slow growth conditions when compared to CCC and abscisic acid. Phylogenetic relationships and species identification were analyzed using four DNA-barcoding markers, comparing E. koopmannii with species from NCBI. All candidate barcoding markers showed sufficient levels of interspecific genetic variation among Euonymus species. In addition, ITS region and rbcL gene sequences effectively distinguished E. koopmannii from other species. These results provide fundamental information that will be valuable for future biotechnological and molecular studies.}, }
@article {pmid39203564, year = {2024}, author = {Kamberović, J and Gligora Udovič, M and Kulaš, A and Tapolczai, K and Orlić, S and Jusufović, A and Gajić, A and Žutinić, P and Ahmić, A and Kalamujić Stroil, B}, title = {The Diatom Diversity and Ecological Status of a Tufa-Depositing River through eDNA Metabarcoding vs. a Morphological Approach-A Case Study of the Una River (Bosnia and Herzegovina).}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203564}, issn = {2076-2607}, abstract = {Tufa deposits in karst rivers are unique habitats created by mutual interactions between specific environmental and biotope features and inhabited by diatoms as a highly abundant and diverse algal group. This pilot study aimed to investigate the diversity of diatom communities on tufa depositing habitats and assess the Una River's ecological status using a comparative molecular and morphological approach for diatom identification. The 312 base pairs of the rbcL gene were barcoded and analyzed using MiSeq reads and amplicon sequence variants (ASVs) obtained by the DADA2 pipeline. The reference database Diat.barcode v7 was used for taxonomic assignment. The morphological identification of the diatoms was carried out in parallel. In total, the combined dataset revealed 46 taxa identified at genus rank, 125 on the subgenus, and 145 on combined taxonomy rank. The metabarcoding approach mostly leads to a lower number of identified taxa at species rank (58 in molecular vs. 119 in optical inventory), resulting in higher values of beta diversity and heterogeneity in diatom assemblages in samples obtained by morphological approach. Despite the high percentage of taxonomically not assigned diatom ASVs to the species rank, high Shannon diversity index values and a similar number of taxa per locations compared to the morphological approach were obtained. Taxa Achnanthidium minutissimum (Kützing) Czarnecki, Achnanthidium pyrenaicum (Hustedt) H.Kobayasi, Amphora pediculus (Kützing) Grunow, Diatoma vulgaris Bory, Navicula cryptotenella Lange-Bertalot, and Navicula tripunctata (O.F.Müller) Bory were identified at all locations in both inventories. Although limited consistency in the diatom abundances between the two inventory datasets was found, a similar grouping of samples was observed connected to the river's longitudinal gradient. The data obtained using molecular approach in most sites indicated a mostly lower ecological status (good or moderate) compared to the data obtained from the morphological approach (high, good, and moderate). The potential of environmental DNA (eDNA) diatom metabarcoding for water monitoring and diversity studies is undeniable, but to fully realize the benefits of these methods in the future, it is essential to standardize protocols and expand the reference database for species found in specific habitats, such as tufa deposits.}, }
@article {pmid39201691, year = {2024}, author = {Zhao, Y and Kipkoech, A and Li, ZP and Xu, L and Yang, JB}, title = {Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species.}, journal = {International journal of molecular sciences}, volume = {25}, number = {16}, pages = {}, pmid = {39201691}, issn = {1422-0067}, support = {2021FY100204//Obtaining Super Barcodes of Important Wild Plants in Gaoligong Mountain/ ; }, mesh = {*Phylogeny ; *Plants, Medicinal/genetics/classification ; Sequence Analysis, DNA/methods ; Genome, Plastid ; }, abstract = {The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.}, }
@article {pmid39200507, year = {2024}, author = {Zhao, G and Li, L and Shen, X and Zhong, R and Zhong, Q and Lei, H}, title = {DNA Barcoding Unveils Novel Discoveries in Authenticating High-Value Snow Lotus Seed Food Products.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {39200507}, issn = {2304-8158}, support = {2023M731143//China Postdoctoral Science Foundation/ ; 2022YFD1601712//National Key Research and Development Program of China/ ; 2023A1515110822//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {Snow Lotus Seed (SLS), esteemed for its nutritional and market value, faces challenges of authentication due to the absence of appropriate testing standards and methods. This results in frequent adulteration of SLS sourced from Gleditsia sinensis (G. sinensis) with other plant seeds endosperm. Traditional chloroplast DNA barcoding methods are inadequate for species identification due to the absence of chloroplasts in G. sinensis seeds endosperm. In this study, the homology of 11 ITS genes among 6 common Gleditsia species was analyzed. Universal primers suitable for these species were designed and screened. A DNA barcoding method for distinguishing SLS species was developed using Sanger sequencing technology, leveraging existing GenBank and Barcode of Life Data System (BOLD) databases. Optimized sample pretreatment facilitated effective DNA extraction from phytopolysaccharide-rich SLS. Through testing of commercial SLS products, the species origin has been successfully identified. Additionally, a novel instance of food fraud was uncovered, where the Caesalpinia spinosa endosperm was used to counterfeit SLS for the first time. The study established that the developed DNA barcoding method is effective for authenticating SLS species. It is of great significance for combating food fraud related to SLS, ensuring food safety, and promoting the healthy development of the SLS industry.}, }
@article {pmid39199868, year = {2024}, author = {Shang, Z and Chen, K and Han, T and Bu, F and Sun, S and Zhu, N and Man, D and Yang, K and Yuan, S and Fu, H}, title = {Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {16}, pages = {}, pmid = {39199868}, issn = {2076-2615}, support = {32060256//National Natural Science Foundation of China/ ; 32060395//National Natural Science Foundation of China/ ; 2021ZD0006//Major Science and Technology Project of Inner Mongolia Autonomous Region/ ; BR221307//Basic scientific research business expenses of universities directly under Inner Mongolia Autonomous Region/ ; BR221037//Basic scientific research business expenses of universities directly under Inner Mongolia Autonomous Region/ ; }, abstract = {As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.}, }
@article {pmid39196267, year = {2024}, author = {King, AC and Kumar, N and Mellor, KC and Hawkins, PA and McGee, L and Croucher, NJ and Bentley, SD and Lees, JA and Lo, SW}, title = {Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae.}, journal = {Microbial genomics}, volume = {10}, number = {8}, pages = {}, pmid = {39196267}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Streptococcus pneumoniae/genetics/classification ; *Multilocus Sequence Typing/methods ; *Genome, Bacterial ; *Phylogeny ; Cluster Analysis ; Humans ; Genomics/methods ; }, abstract = {Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26 306 Streptococcus pneumoniae genomes to compare four clustering methods: gene-by-gene seven-locus MLST, core genome MLST (cgMLST)-based hierarchical clustering (HierCC) assignments, life identification number (LIN) barcoding and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (adjusted mutual information score=0.950), which was expected given that both methods utilize cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods shows that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI=0.946), showing that k-mer-based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for S. pneumoniae, standardized and stable nomenclature is important as the number of genomes available expands. Furthermore, the research community should transition away from seven-locus MLST, whilst cgMLST, GPSC and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardized within the research.}, }
@article {pmid39195758, year = {2024}, author = {Chiappa, G and Fassio, G and Modica, MV and Oliverio, M}, title = {Potential Ancestral Conoidean Toxins in the Venom Cocktail of the Carnivorous Snail Raphitoma purpurea (Montagu, 1803) (Neogastropoda: Raphitomidae).}, journal = {Toxins}, volume = {16}, number = {8}, pages = {}, pmid = {39195758}, issn = {2072-6651}, support = {B89J21032850001//Sapienza University of Rome/ ; RM12017276B846BB//Sapienza University of Rome/ ; SEED-3840974//Sapienza University of Rome/ ; }, mesh = {Animals ; *Mollusk Venoms/genetics ; *Snails/genetics ; Transcriptome ; Salivary Glands/metabolism ; }, abstract = {Venomous marine gastropods of the superfamily Conoidea possess a rich arsenal of toxins, including neuroactive toxins. Venom adaptations might have played a fundamental role in the radiation of conoideans; nevertheless, there is still no knowledge about the venom of the most diversified family of the group: Raphitomidae Bellardi, 1875. In this study, transcriptomes were produced from the carcase, salivary glands, and proximal and distal venom ducts of the northeastern Atlantic species Raphitoma purpurea (Montagu, 1803). Using a gut barcoding approach, we were also able to report, for the first time, molecular evidence of a vermivorous diet for the genus. Transcriptomic analyses revealed over a hundred putative venom components (PVC), including 69 neurotoxins. Twenty novel toxin families, including some with high levels of expansion, were discovered. No significant difference was observed between the distal and proximal venom duct secretions. Peptides related to cone snail toxins (Cerm06, Pgam02, and turritoxin) and other venom-related proteins (disulfide isomerase and elevenin) were retrieved from the salivary glands. These salivary venom components may constitute ancestral adaptations for venom production in conoideans. Although often neglected, salivary gland secretions are of extreme importance for understanding the evolutionary history of conoidean venom.}, }
@article {pmid39194872, year = {2024}, author = {Tian, WH and Jin, Y and Liao, YC and Faraj, TK and Guo, XY and Maharachchikumbura, SSN}, title = {New and Interesting Pine-Associated Hyphomycetes from China.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {39194872}, issn = {2309-608X}, support = {A1098531023601245//Talent Introduction and Cultivation Project, University of Electronic Science and Tech-nology of China/ ; RSP2024R487//Researchers Supporting Project at King Saud University, Riyadh, Saudi Arabia/ ; }, abstract = {Pine trees play a crucial role in the forests of Sichuan Province, boasting rich species diversity and a lengthy evolutionary history. However, research and investigation on fungi associated with pine trees are insufficient. This study investigated the diversity of hyphomycetes fungi associated with pine trees in Sichuan Province, China. During the survey, we collected five specimens of hyphomycetes from branches and bark of species of Pinus. Five barcodes were selected for study and sequenced, including ITS, SSU, LSU, TEF1, and RPB2. Morphological examination and multi-locus phylogenetic analyses revealed three new species, viz. Catenulostroma pini sp. nov. within Teratosphaeriaceae, Kirschsteiniothelia longisporum sp. nov. within Kirschsteiniotheliaceae, Sporidesmiella sichuanensis sp. nov. within Junewangiaceae, and two known species, Paradictyoarthrinium diffractum and P. hydei within Paradictyoarthriniaceae, which are the new host records from Pinus species. Catenulostroma pini, distinguished from other species in the genus by its unique morphology, has three conidial morphologies: small terminal helicoconidia, scolecoconidia with many septa, and phragmoconidia conidia. Kirschsteiniothelia longisporum has longer spores when compared to the other species in the genus. According to phylogenetic analysis, Sporidesmiella sichuanensis formed an independent clade sister to S. aquatica and S. juncicola, distinguished by differences in conidial size.}, }
@article {pmid39194831, year = {2024}, author = {Wang, C and He, J and Chen, X}, title = {Revision of the Genus Laelius (Hymenoptera, Chrysidoidea, Bethylidae) from China.}, journal = {Insects}, volume = {15}, number = {8}, pages = {}, pmid = {39194831}, issn = {2075-4450}, support = {31920103005//National Natural Science Foundation of China/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; }, abstract = {The genus Laelius from China is revised for the first time and six species are recognized, including one new species as well as three new records. The new species, Laelius longus sp. nov., which is supported by both morphological and molecular analyses, is described and illustrated. Three new records, L. naniwaensis, L. nigrofemoratus, and L. yamatonis, are illustrated. A key to the Chinese species of Laelius is provided.}, }
@article {pmid39194771, year = {2024}, author = {Dimitrov, R and Gouliamova, D and Guéorguiev, B and Smith, M and Groenewald, M and Boekhout, T}, title = {First DNA Barcoding Survey in Bulgaria Unveiled Huge Diversity of Yeasts in Insects.}, journal = {Insects}, volume = {15}, number = {8}, pages = {}, pmid = {39194771}, issn = {2075-4450}, abstract = {In this study, we conducted a comprehensive survey aimed at assessing the diversity of yeast species inhabiting the guts of various insect species collected mainly from two Bulgarian National Parks, namely, Rila, and Pirin. The insect specimens encompass a broad taxonomic spectrum, including representatives from Coleoptera, Orthoptera, Lepidoptera, Hymenoptera, Dermaptera, Isopoda, and Collembola. Yeast strains were identified with DNA barcoding using the ribosomal markers, specifically, the D1/D2 domains of the ribosomal large subunit (LSU) and the internal transcribed spacers regions ITS 1 + 2 (ITS). The analysis unveiled the presence of 89 ascomycetous and 18 basidiomycetous yeast isolates associated with the insect specimens. Furthermore, our study identified 18 hitherto unknown yeast species.}, }
@article {pmid39193858, year = {2024}, author = {Gómez-Zapata, PA and Johnson, MA and Bonacci, T and Aime, MC}, title = {Phylogeny, biogeography, and host range of gall midges (Diptera: Cecidomyiidae) feeding on spores of rust fungi (Basidiomycota: Pucciniales).}, journal = {Journal of insect science (Online)}, volume = {24}, number = {4}, pages = {}, pmid = {39193858}, issn = {1536-2442}, support = {//U.S. National Science Foundation/ ; DEB-1458290//CSBR/ ; DEB-1502887//TCN/ ; //U.S. Department of Agriculture/ ; AP20PPQS//APHIS/ ; 1010662//NIFA Hatch/ ; 2021-07760//NIFA Specialty Crop Research Initiative/ ; }, mesh = {Animals ; *Basidiomycota/physiology/genetics ; *Host Specificity ; *Phylogeny ; *Larva/microbiology/growth &amp; development/physiology ; Diptera/microbiology ; Phylogeography ; Spores, Fungal/physiology ; }, abstract = {Rust fungi (Pucciniales) are plant pathogens that can cause devastating yield losses to economically important crops and threaten native plants with extinction. Rusts are usually controlled with fungicides when rust-resistant plant varieties are unavailable. However, natural enemies may offer an alternative to chemicals by acting as biological controls. The larvae of Mycodiplosis Rübsaamen (49 spp.) feed on the spores of rusts and powdery mildew fungi and have been suggested as a potential biocontrol candidate for disease-causing rusts. However, little is known about the phylogenetic relationships, biogeography, and host range of this genus. We screened 5,665 rust specimens from fungarium specimens and field collections and recovered a total of 363 larvae on 315 rust specimens from 17 countries. Three mitochondrial and 2 nuclear loci were amplified and sequenced for the phylogenetic reconstruction of 129 individuals. We recovered 12 clades, of which 12 and 10 were supported with maximum likelihood and Bayesian inference, respectively. Of the 12 clades, 7 comprised species from multiple continents and climatic regions, and 5 comprised species from a single region. Individuals forming clades were collected from 2 to 18 rust species, suggesting that Mycodiplosis species have a broad host range. In total, Mycodiplosis larvae were identified on 44 different rust species collected from 18 plant families. Future studies should focus on expanding field sampling efforts, including data from additional gene regions, and incorporating morphological data to further elucidate species diversity and distribution patterns.}, }
@article {pmid39193167, year = {2024}, author = {Catanese, G and Vázquez-Luis, M and Giacobbe, S and García-March, JR and Zotou, M and Patricia, P and Papadakis, O and Tena-Medialdea, J and Katsanevakis, S and Grau, A}, title = {Internal transcribed spacer as effective molecular marker for the detection of natural hybridization between the bivalves Pinna nobilis and Pinna rudis.}, journal = {Ecology and evolution}, volume = {14}, number = {8}, pages = {e70227}, pmid = {39193167}, issn = {2045-7758}, abstract = {The Pinna nobilis, a Mediterranean mollusc, has suffered population declines due to a massive mortality event associated with various factors including the parasite Haplosporidium pinnae. Some populations show resilience, possibly due to local environmental conditions. In this study, a molecular multiplex PCR method was developed using species-specific primers targeting Internal Transcribed Spacer (ITS) regions of P. nobilis and P. rudis, allowing accurate species identification and hybrid detection. Samples from Mediterranean areas were analysed, including putative hybrids and individuals from five other bivalve species. DNA was isolated, ITS regions were amplified and sequenced, and phylogenetic analyses confirmed species differentiation and primer specificity. The multiplex-PCR successfully identified P. nobilis, P. rudis, and their hybrids based on distinct amplicon patterns. This study highlights the value of molecular tools in species conservation, especially for monitoring and managing hybridization, supporting effective biodiversity conservation strategies.}, }
@article {pmid39192093, year = {2024}, author = {Baryshev, A and La Fleur, A and Groves, B and Michel, C and Baker, D and Ljubetič, A and Seelig, G}, title = {Massively parallel measurement of protein-protein interactions by sequencing using MP3-seq.}, journal = {Nature chemical biology}, volume = {20}, number = {11}, pages = {1514-1523}, pmid = {39192093}, issn = {1552-4469}, support = {R01GM120379//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 2312398//National Science Foundation (NSF)/ ; N00014-16-1-3189//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; Protein Interaction Mapping/methods ; Two-Hybrid System Techniques ; Protein Binding ; Proteins/metabolism/chemistry/genetics ; Humans ; }, abstract = {Protein-protein interactions (PPIs) regulate many cellular processes and engineered PPIs have cell and gene therapy applications. Here, we introduce massively parallel PPI measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Lastly, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics-based energy terms to predict MP3-seq values. We find that AF-M-based models could be valuable for prescreening interactions but experimentally measuring interactions remains necessary to rank their strengths quantitatively.}, }
@article {pmid39191105, year = {2024}, author = {Song, SF and Zhang, XW and Chen, S and Shu, Y and Yu, YL and Wang, JH}, title = {CRISPR-based dual-aptamer proximity ligation coupled hybridization chain reaction for precise detection of tumor extracellular vesicles and cancer diagnosis.}, journal = {Talanta}, volume = {280}, number = {}, pages = {126780}, doi = {10.1016/j.talanta.2024.126780}, pmid = {39191105}, issn = {1873-3573}, mesh = {Humans ; *Extracellular Vesicles/chemistry ; *Aptamers, Nucleotide/chemistry ; *Neoplasms/diagnosis/genetics ; *Nucleic Acid Hybridization ; Limit of Detection ; CRISPR-Cas Systems/genetics ; Biomarkers, Tumor/blood/genetics ; }, abstract = {Tumor cell-derived extracellular vesicles (TEVs) contain numerous cellular molecules and are considered potential biomarkers for non-invasive liquid biopsy. However, due to the low abundance of TEVs secreted by tumor cells and their phenotypic heterogeneity, there is a lack of sensitive and specific methods to quantify TEVs. Here, we developed a dual-aptamer proximity ligation-coupled hybridization chain reaction (HCR) method for tracing TEVs, exploiting CRISPR to achieve highly sensitive detection. Taking advantage of the high binding affinity of aptamers, the two aptamers (AptEpCAM, AptHER2) exhibited the high selectivity for TEVs recognition. HCR generated long-repeated sequence containing multiple crRNA targetable barcodes, and the signals were further amplified by CRISPR upon recognizing the HCR sequences, thereby enhancing the sensitivity. Under optimal conditions, the developed method demonstrated a favorable linear relationship in the range of 2 × 10[3]-10[7] particles/μL, with a limit of detection (LOD) of 3.3 × 10[2] particles/μL. We directly applied our assay to clinical plasma analysis, achieving 100 % accuracy in cancer diagnosis, thus demonstrating the potential clinical applications of TEVs. Due to its simplicity and rapidity, excellent sensitivity and specificity, this method has broad applications in clinical medicine.}, }
@article {pmid39189753, year = {2024}, author = {DeCurtis, EK and Machado, I and Kuss-Duerkop, SK and Wang, Y and Khare, R}, title = {MALDI-TOF mass spectrometry from nucleic acid: development and evaluation of a novel platform for identification of mycobacteria and detection of genetic markers of resistance.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0163824}, pmid = {39189753}, issn = {2165-0497}, support = {None//National Jewish Health (NJH)/ ; }, mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; *Drug Resistance, Bacterial/genetics ; Genetic Markers ; Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; DNA, Bacterial/genetics ; Mycobacterium tuberculosis/genetics/isolation &amp; purification/classification/drug effects ; Sensitivity and Specificity ; Polymerase Chain Reaction/methods ; }, abstract = {Complete identification methods are critical for evaluating nontuberculous mycobacteria (NTM). Here, we describe a novel diagnostic method for identification of eight NTM, Mycobacterium tuberculosis complex, and three drug resistance markers using PCR/matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) from cultured organisms. With this technology, a multiplex end-point PCR is performed for targets of interest. Detection probes that are extended in the presence of a target are added. The extended probes have greater molecular weight and can be detected by MALDI-TOF MS. An AFB Primary Panel was designed to differentiate Mycobacterium avium; Mycobacterium intracellulare subsp. chimaera; Mycobacterium avium complex (other); Mycobacterium abscessus subsp. abscessus, bolletii, and massiliense; Mycobacterium kansasii, and M. tuberculosis complex. This design should cover 90% (3,483/3,691) of mycobacteria seen onsite. A development set of unblinded isolates (n = 217) was used to develop PCR primers, detection probes, and probe barcodes. It demonstrated 99.1% (215/217) agreement with reference methods. An evaluation set using blinded isolates (n = 320) showed an overall sensitivity of 94.3% (range by target: 90.0-100%). Overall specificity from negative media, non-target mycobacteria, and bacteria was 99.1% (108/109; range by target: 94.4-100%). Three drug resistance markers erm (41), rrl, and rrs demonstrated 100%, 91%, and 100% sensitivity, respectively, and >99% specificity. Limit of detection per target ranged from 2.2 × 10[3] to 9.9 × 10[6] CFU/mL. The AFB Primary Panel allows for mycobacterial speciation, subspeciation, and resistance mutation detection, which is essential for diagnosis, appropriate therapy, identifying outbreaks, and managing treatment-refractory disease. It can perform with high-throughput and high specificity and sensitivity from isolates.IMPORTANCEEven closely related mycobacteria can have unique treatment patterns, but differentiating these organisms is a challenge. Here, we tested an innovative platform that combines two commonly used technologies and creates something new: matrix-assisted, laser-desorption ionization time-of flight mass spectrometry was performed on PCR amplicons instead of on proteins. This created a robust system with the advantages of PCR (high discriminatory power, high throughput, detection of resistance) with the advantages of mass spectrometry (more targets, lower operational cost) in order to identify closely related mycobacterial organisms.}, }
@article {pmid39185194, year = {2024}, author = {Fahlberg, MD and Forward, S and Assita, ER and Mazzola, M and Kiem, A and Handley, M and Yun, SH and Kwok, SJJ}, title = {Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39185194}, issn = {2692-8205}, support = {T32 GM007226/GM/NIGMS NIH HHS/United States ; R43 GM140527/GM/NIGMS NIH HHS/United States ; T32 GM132089/GM/NIGMS NIH HHS/United States ; F31 HL158020/HL/NHLBI NIH HHS/United States ; R44 GM139504/GM/NIGMS NIH HHS/United States ; R01 EB033155/EB/NIBIB NIH HHS/United States ; }, abstract = {The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins, and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular fluorescent proteins and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cell analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.}, }
@article {pmid39185156, year = {2024}, author = {Handler, JS and Li, Z and Dveirin, RK and Fang, W and Goodarzi, H and Fertig, EJ and Kalhor, R}, title = {Identifying a gene signature of metastatic potential by linking pre-metastatic state to ultimate metastatic fate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39185156}, issn = {2692-8205}, support = {P30 EY001765/EY/NEI NIH HHS/United States ; R01 HG012357/HG/NHGRI NIH HHS/United States ; T32 CA009071/CA/NCI NIH HHS/United States ; }, abstract = {Identifying the key molecular pathways that enable metastasis by analyzing the eventual metastatic tumor is challenging because the state of the founder subclone likely changes following metastatic colonization. To address this challenge, we labeled primary mouse pancreatic ductal adenocarcinoma (PDAC) subclones with DNA barcodes to characterize their pre-metastatic state using ATAC-seq and RNA-seq and determine their relative in vivo metastatic potential prospectively. We identified a gene signature separating metastasis-high and metastasis-low subclones orthogonal to the normal-to-PDAC and classical-to-basal axes. The metastasis-high subclones feature activation of IL-1 pathway genes and high NF-κB and Zeb/Snail family activity and the metastasis-low subclones feature activation of neuroendocrine, motility, and Wnt pathway genes and high CDX2 and HOXA13 activity. In a functional screen, we validated novel mediators of PDAC metastasis in the IL-1 pathway, including the NF-κB targets Fos and Il23a, and beyond the IL-1 pathway including Myo1b and Tmem40. We scored human PDAC tumors for our signature of metastatic potential from mouse and found that metastases have higher scores than primary tumors. Moreover, primary tumors with higher scores are associated with worse prognosis. We also found that our metastatic potential signature is enriched in other human carcinomas, suggesting that it is conserved across epithelial malignancies. This work establishes a strategy for linking cancer cell state to future behavior, reveals novel functional regulators of PDAC metastasis, and establishes a method for scoring human carcinomas based on metastatic potential.}, }
@article {pmid39184369, year = {2024}, author = {Yamamoto, T and Tachihara, K and Toda, M}, title = {Examination of sequence variations in partial mitochondrial 12S gene amongst damselfish species as references for DNA barcoding.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e126744}, pmid = {39184369}, issn = {1314-2828}, abstract = {Accurate species identification, based on DNA barcoding, can be achieved when sufficient sequence variations are present amongst species in the sampled marker. In general, the ability to discriminate species decreases with shorter sequences; however, shorter regions have a merit in amplification success by the polymerase chain reaction. In either case, it is important to investigate sequence variations amongst species before barcoding to understand its reliability and limitations. In this study, we investigate how accurately short, but hypervariable portion of the mitochondrial 12S ribosomal RNA (12S) gene (MiFish region with approximately 180 bp) is used to identify each species in diversified pomacentrid fishes compared with the longer region of the same gene (approximately 750 bp). We prepared three datasets with 301 sequences of the MiFish region for 150 species, the same 301 of sequences of the longer 12S region and 476 sequences of the MiFish region for 183 species. Neighbour-joining (NJ) analyses and genetic distance analyses revealed several indistinguishable pairs of species in these DNA regions. Although the number of such pairs was larger in the MiFish region, 83.6% (153 of 183) of species possessed respective unique sequences even in the MiFish region (versus 96.0% [144 of 150 species] in the longer 12S region). A part of indistinguishable pairs of species might have caused by mitochondrial DNA introgressions and taxonomically unresolved problems. Our analysis clarified the effectiveness and limitations of species identification using DNA barcoding for Pomacentridae and the sequences we provided here contribute to the expansion of references for pomacentrid mitochondrial 12S sequences.}, }
@article {pmid39179166, year = {2024}, author = {Thipphet, K and Horpaopan, S and Jaturas, N and Thanchomnang, T and Moophayak, K and Chaiwong, T and Hongsrichan, N and Nakhonkam, W and Phuwanatsarunya, P and Dumidae, A and Bunthong, S and Kaewbungkord, T and Sanit, S and Ruankham, W and Vitta, A and Kurahashi, H and Sukontason, KL and Bunchu, N}, title = {Molecular identification and genetic variation of forensically important fly species (Order: Diptera) in Thailand using DNA barcoding.}, journal = {Acta tropica}, volume = {258}, number = {}, pages = {107366}, doi = {10.1016/j.actatropica.2024.107366}, pmid = {39179166}, issn = {1873-6254}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Thailand ; *Genetic Variation ; *Electron Transport Complex IV/genetics ; *Forensic Entomology ; Diptera/genetics/classification/anatomy &amp; histology ; Calliphoridae/genetics/classification ; Phylogeny ; Sarcophagidae/genetics/classification ; Muscidae/genetics/classification ; }, abstract = {Forensic entomology plays a crucial role in criminal investigations by providing vital insights into minimum postmortem interval (PMImin) and corpse relocation by identifying insect species that colonize in decomposing remains. This study aimed to identify and analyze the genetic variation of forensically significant fly species in Thailand, using DNA barcoding of the mitochondrial cytochrome c oxidase subunit I COI gene. A total of 3,220 fly specimens were collected from 18 provinces across six regions of Thailand from October 2017 to September 2022. These specimens were classified by morphological identification into 21 species among three Dipteran families: Calliphoridae, Muscidae, and Sarcophagidae, with Chrysomya megacephala Diptera: Calliphoridae being the most abundant species. DNA barcoding confirmed the morphological identifications with 100 % accuracy, showing low intraspecific K2P distances0.0 to 1.1 %) and significant interspecific K2P distances 2.5 % to 17.2 %. A Neighbour-Joining (NJ) analysis was conducted to assess the molecular identification capabilities of the barcoding region. This analysis successfully recovered nearly all species as distinct monophyletic groups. The species groupings obtained were generally consistent with both morphological and molecular identifications. These findings underscore the effectiveness of DNA barcoding for precise species identification and contribute to a comprehensive database of forensically important flies in Thailand, thus facilitating improved forensic investigations and biodiversity studies.}, }
@article {pmid39179112, year = {2024}, author = {Wei, PS and Thota, N and John, G and Chang, E and Lee, S and Wang, Y and Ma, Z and Tsai, YH and Mei, KC}, title = {Enhancing RNA-lipid nanoparticle delivery: Organ- and cell-specificity and barcoding strategies.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {375}, number = {}, pages = {366-388}, pmid = {39179112}, issn = {1873-4995}, support = {R35 GM155362/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Nanoparticles/chemistry ; Animals ; *Lipids/chemistry ; RNA/administration &amp; dosage ; Gene Transfer Techniques ; RNA, Small Interfering/administration &amp; dosage ; Organ Specificity ; }, abstract = {Recent advancements in RNA therapeutics highlight the critical need for precision gene delivery systems that target specific organs and cells. Lipid nanoparticles (LNPs) have emerged as key vectors in delivering mRNA and siRNA, offering protection against enzymatic degradation, enabling targeted delivery and cellular uptake, and facilitating RNA cargo release into the cytosol. This review discusses the development and optimization of organ- and cell-specific LNPs, focusing on their design, mechanisms of action, and therapeutic applications. We explore innovations such as DNA/RNA barcoding, which facilitates high-throughput screening and precise adjustments in formulations. We address major challenges, including improving endosomal escape, minimizing off-target effects, and enhancing delivery efficiencies. Notable clinical trials and recent FDA approvals illustrate the practical applications and future potential of LNP-based RNA therapies. Our findings suggest that while considerable progress has been made, continued research is essential to resolve existing limitations and bridge the gap between preclinical and clinical evaluation of the safety and efficacy of RNA therapeutics. This review highlights the dynamic progress in LNP research. It outlines a roadmap for future advancements in RNA-based precision medicine.}, }
@article {pmid39176612, year = {2024}, author = {Svandova, K and Smutny, Z}, title = {What Technologies Based on Unique Patient Identifiers Are Used for Patient Identification in Healthcare?.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1264-1268}, doi = {10.3233/SHTI240642}, pmid = {39176612}, issn = {1879-8365}, mesh = {Humans ; *Patient Identification Systems ; Patient Safety ; Radio Frequency Identification Device ; }, abstract = {Ensuring the correct identification of the patient is key to matching the correct patients with the proper care (e.g. correct administration of medications and treatments), but it is also applied, for example, to monitoring the patient's movement in the hospital environment. This scoping review aims to find out what technologies based on unique patient identifiers are used to identify patients in healthcare facilities to increase patient safety and to identify future research trends. PRISMA-ScR guidelines were used, and the search focused on Web of Science and Scopus citation databases from 2000 to February 2024. Thirty-two papers dealing with patient identification methods from the point of view of person identification were found. The solutions found were built on the technologies (linear or 2D) of barcodes, RFID and NFC tags. None of the patient identification solutions found offer complete accuracy due to the human factor, and each solution targets a different problem context associated with a particular type of health facility. Future research can focus on the combination of multiple technologies, including biometric methods, to improve identification and tools to support decisions about the use of technology in a particular context and health facility (e.g. hospitals, medical nursing homes).}, }
@article {pmid39172488, year = {2024}, author = {Majima, K and Kojima, Y and Minoura, K and Abe, K and Hirose, H and Shimamura, T}, title = {LineageVAE: reconstructing historical cell states and transcriptomes toward unobserved progenitors.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39172488}, issn = {1367-4811}, support = {20H04281//Grants-in-Aid for Scientific Research/ ; }, mesh = {*Single-Cell Analysis/methods ; *Transcriptome/genetics ; Humans ; Cell Lineage ; Sequence Analysis, RNA/methods ; Hematopoiesis/genetics ; Deep Learning ; Animals ; Computational Biology/methods ; Stem Cells/metabolism/cytology ; }, abstract = {MOTIVATION: Single-cell RNA sequencing (scRNA-seq) enables comprehensive characterization of the cell state. However, its destructive nature prohibits measuring gene expression changes during dynamic processes such as embryogenesis or cell state divergence due to injury or disease. Although recent studies integrating scRNA-seq with lineage tracing have provided clonal insights between progenitor and mature cells, challenges remain. Because of their experimental nature, observations are sparse, and cells observed in the early state are not the exact progenitors of cells observed at later time points. To overcome these limitations, we developed LineageVAE, a novel computational methodology that utilizes deep learning based on the property that cells sharing barcodes have identical progenitors.<br><br>RESULTS: LineageVAE is a deep generative model that transforms scRNA-seq observations with identical lineage barcodes into sequential trajectories toward a common progenitor in a latent cell state space. This method enables the reconstruction of unobservable cell state transitions, historical transcriptomes, and regulatory dynamics at a single-cell resolution. Applied to hematopoiesis and reprogrammed fibroblast datasets, LineageVAE demonstrated its ability to restore backward cell state transitions and infer progenitor heterogeneity and transcription factor activity along differentiation trajectories.<br><br>The LineageVAE model was implemented in Python using the PyTorch deep learning library. The code is available on GitHub at https://github.com/LzrRacer/LineageVAE/.}, }
@article {pmid39172294, year = {2024}, author = {Ikeda, S and Inoue, Y and Imada, Y}, title = {Unveiled species diversity of moss-feeding mites (Stigmaeidae: Eustigmaeus): a research on their distribution, habitat, and host plant use in Japan.}, journal = {Experimental &amp; applied acarology}, volume = {93}, number = {4}, pages = {721-741}, pmid = {39172294}, issn = {1572-9702}, support = {2023-5007//Japan Science Society/ ; 18H06077, JP20K15852, JP22H02684//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Japan ; *Mites/physiology/genetics/classification ; *Bryophyta ; *DNA Barcoding, Taxonomic ; *Animal Distribution ; Electron Transport Complex IV/analysis ; Ecosystem ; Biodiversity ; Feeding Behavior ; Host Specificity ; }, abstract = {The genus Eustigmaeus Berlese, 1910 represents the unique phytophagous group within the superfamily Raphignathoidea. Four species within this genus have been known to inhabit mosses and feed on them as larvae, nymphs, and adults. However, the interactions with mosses have remained poorly understood. In order to reveal the diversity and host-plant use of the moss-feeding species, we conducted an extensive field study in Japan. This study revealed an array of moss-feeding species inhabiting various moss species, with 10 morphologically distinctive species newly documented in Japan. Through DNA barcoding based on cytochrome c oxidase subunit I (COI) sequences, these morphospecies were recovered as distinct entities. Notably, the host-plant use of four species was elucidated. Among these, Eustigmaeus sp. 9 exhibited polyphagy, while three species (Eustigmaeus spp. 1-3) demonstrated varying degrees of host specificity, each using moss species from the Hypnales, Philonotis, and Dicranidae, respectively. While a few moss-feeding species were frequently found in the same geographic area, more than one species rarely co-occurred within the same moss colonies. Eustigmaeus offers a unique study system, with its diverse moss-feeding species and indications of specific host plant use. Consequently, the moss-feeding Eustigmaeus serves as a valuable model for exploring the macroevolutionary patterns underlying diversification in moss-feeding arthropods.}, }
@article {pmid39164496, year = {2024}, author = {Cui, X and Dong, X and Hu, M and Zhou, W and Shi, W}, title = {Large field of view and spatial region of interest transcriptomics in fixed tissue.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1020}, pmid = {39164496}, issn = {2399-3642}, support = {41676119//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41476120//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Mice ; *Gene Expression Profiling/methods ; *Transcriptome ; *Tissue Fixation/methods ; Paraffin Embedding ; Brain/metabolism ; Embryo, Mammalian/metabolism ; }, abstract = {Expression profiling in spatially defined regions is crucial for systematically understanding tissue complexity. Here, we report a method of photo-irradiation for in-situ barcoding hybridization and ligation sequencing, named PBHL-seq, which allows targeted expression profiling from the photo-irradiated region of interest in intact fresh frozen and formalin fixation and paraffin embedding (FFPE) tissue samples. PBHL-seq uses photo-caged oligodeoxynucleotides for in situ reverse transcription followed by spatially targeted barcoding of cDNAs to create spatially indexed transcriptomes of photo-illuminated regions. We recover thousands of differentially enriched transcripts from different regions by applying PBHL-seq to OCT-embedded tissue (E14.5 mouse embryo and mouse brain) and FFPE mouse embryo (E15.5). We also apply PBHL-seq to the subcellular microstructures (cytoplasm and nucleus, respectively) and detect thousands of differential expression genes. Thus, PBHL-seq provides an accessible workflow for expression profiles from the region of interest in frozen and FFPE tissue at subcellular resolution with areas expandable to centimeter scale, while preserving the sample intact for downstream analysis to promote the development of transcriptomics.}, }
@article {pmid39161647, year = {2024}, author = {Padilla-Villavicencio, M and Corzo, G and Guillén-Navarro, K and Ibarra-Núñez, G and Arenas, I and Zamudio, F and Diego-García, E}, title = {Cupiennius spiders (Trechaleidae) from southern Mexico: DNA barcoding, venomics, and biological effect.}, journal = {The journal of venomous animals and toxins including tropical diseases}, volume = {30}, number = {}, pages = {e20230098}, pmid = {39161647}, issn = {1678-9199}, abstract = {BACKGROUND: Members of the genus Cupiennius Simon, 1891 are categorized as wandering spiders and are part of the family Trechaleidae. The genomics and proteomics of Cupiennius spiders from North America remain uncharacterized. The present study explores for the first time molecular data from the endemic species Cupiennius chiapanensis Medina, 2006, and also presents new data for Cupiennius salei (Keyserling, 1878), both collected in southern Mexico.<br><br>METHODS: In total, 88 Cupiennius specimens were collected from southern Mexico and morphologically identified. DNA was extracted and the mitochondrial COI fragment was amplified. COI sequences were analyzed, and a phylogenetic tree was inferred for species from the Americas. Genetic diversity was analyzed using haplotype networks and gene distances. Venom was obtained from C. chiapanensis and C. salei by electrostimulation. The venom was separated by HPLC, visualized using SDS-PAGE, and quantified for use in toxicity bioassays in mice and insects.<br><br>RESULTS: Analysis of COI sequences from C. chiapanensis showed 94% identity with C. salei, while C. salei exhibited 94-97% identity with sequences from Central and South American conspecifics. The venom from C. chiapanensis exhibited toxic activity against crickets. Venoms from C. chiapanensis and C. salei caused death in Anastrepha obliqua flies. Analysis of venom fractions from C. salei and C. chiapanensis revealed molecular masses of a similar size as some previously reported toxins and neurotoxic components. We determined the amino acid sequences of ChiaTx1 and ChiaTx2, toxins that are reported here for the first time and which showed toxicity against mice and insects.<br><br>CONCLUSION: Our work is the first to report COI-based DNA barcoding sequences from southern Mexican Cupiennius spiders. Compounds with toxic activity were identified in venom from both species.}, }
@article {pmid39161631, year = {2024}, author = {Liu, F and Hu, ZD and Yurkov, A and Chen, XH and Bao, WJ and Ma, Q and Zhao, WN and Pan, S and Zhao, XM and Liu, JH and Wang, QM and Boekhout, T}, title = {Saccharomycetaceae: delineation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies.}, journal = {Persoonia}, volume = {52}, number = {}, pages = {1-21}, pmid = {39161631}, issn = {0031-5850}, abstract = {A correct classification of fungi, including yeasts, is of prime importance to understand fungal biodiversity and to communicate about this diversity. Fungal genera are mainly defined based on phenotypic characteristics and the results of single or multigene-based phylogenetic analyses. However, because yeasts often have less phenotypic characters, their classification experienced a strong move towards DNA-based data, from short ribosomal sequences to multigene phylogenies and more recently to phylogenomics. Here, we explore the usefulness of various genomics-based parameters to circumscribe fungal genera more correctly taking the yeast domain as an example. Therefore, we compared the results of a phylogenomic analysis, average amino acid identity (AAI) values, the presence of conserved signature indels (CSIs), the percentage of conserved proteins (POCP) and the presence-absence patterns of orthologs (PAPO). These genome-based metrics were used to investigate their usefulness in demarcating 13 hitherto relatively well accepted genera in Saccharomycetaceae, namely Eremothecium, Grigorovia, Kazachstania, Kluyveromyces, Lachancea, Nakaseomyces, Naumovozyma, Saccharomyces, Tetrapisispora, Torulaspora, Vanderwaltozyma, Zygosaccharomyces and Zygotorulaspora. As a result, most of these genera are supported by the genomics-based metrics, but the genera Kazachstania, Nakaseomyces and Tetrapisispora were shown to be genetically highly diverse based on the above listed analyses. Considering the results obtained for the presently recognized genera, a range of 80-92 % POCP values and a range of 60-70 % AAI values might be valuable thresholds to discriminate genera in Saccharomycetaceae. Furthermore, the genus-specific genes identified in the PAPO analysis and the CSIs were found to be useful as synapomorphies to characterize and define genera in Saccharomycetaceae. Our results indicate that the combined monophyly-based phylogenomic analysis together with genomic relatedness indices and synapomorphies provide promising approaches to delineating yeast genera and likely those of filamentous fungi as well. The genera Kazachstania, Nakaseomyces and Tetrapisispora are revised and we propose eight new genera and 41 new combinations. Citation: Liu F, Hu Z-D, Yurkov A, et al. 2024. Saccharomycetaceae: delinaeation of fungal genera based on phylogenomic analyses, genomic relatedness indices and genomics-based synapomorphies. Persoonia 52: 1-21. https://doi.org/10.3767/persoonia.2024.52.01.}, }
@article {pmid39160260, year = {2024}, author = {Gallego, R and Arias, MB and Corral-Lou, A and Díez-Vives, C and Neave, EF and Wang, C and Cárdenas, P and Steffen, K and Taboada, S and Villamor, A and Kenchington, E and Mariani, S and Riesgo, A}, title = {North Atlantic deep-sea benthic biodiversity unveiled through sponge natural sampler DNA.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1015}, pmid = {39160260}, issn = {2399-3642}, support = {NE/T007028/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/T007028/1//RCUK | Natural Environment Research Council (NERC)/ ; 679849//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ID 100010434//"la Caixa" Foundation (Caixa Foundation)/ ; }, mesh = {*Porifera/genetics/classification ; Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; Atlantic Ocean ; DNA, Environmental/analysis ; Ecosystem ; }, abstract = {The deep-sea remains the biggest challenge to biodiversity exploration, and anthropogenic disturbances extend well into this realm, calling for urgent management strategies. One of the most diverse, productive, and vulnerable ecosystems in the deep sea are sponge grounds. Currently, environmental DNA (eDNA) metabarcoding is revolutionising the field of biodiversity monitoring, yet complex deep-sea benthic ecosystems remain challenging to assess even with these novel technologies. Here, we evaluate the effectiveness of whole-community metabarcoding to characterise metazoan diversity in sponge grounds across the North Atlantic by leveraging the natural eDNA sampling properties of deep-sea sponges themselves. We sampled 97 sponge tissues from four species across four North-Atlantic biogeographic regions in the deep sea and screened them using the universal COI barcode region. We recovered unprecedented levels of taxonomic diversity per unit effort, especially across the phyla Chordata, Cnidaria, Echinodermata and Porifera, with at least 406 metazoan species found in our study area. These assemblages identify strong spatial patterns in relation to both latitude and depth, and detect emblematic species currently employed as indicators for these vulnerable habitats. The remarkable performance of this approach in different species of sponges, in different biogeographic regions and across the whole animal kingdom, illustrates the vast potential of natural samplers as high-resolution biomonitoring solutions for highly diverse and vulnerable deep-sea ecosystems.}, }
@article {pmid39160220, year = {2024}, author = {Liu, F and Zhang, X and Yang, Y}, title = {Simulation of CRISPR-Cas9 editing on evolving barcode and accuracy of lineage tracing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19213}, pmid = {39160220}, issn = {2045-2322}, support = {R01 CA251950/CA/NCI NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; *Gene Editing/methods ; *Computer Simulation ; Algorithms ; DNA Barcoding, Taxonomic/methods ; Cell Lineage/genetics ; INDEL Mutation ; Mutation ; }, abstract = {We designed a simulation program that mimics the CRISPR-Cas9 editing on evolving barcode and double strand break repair procedure along with cell divisions. Emerging barcode mutations tend to build upon previously existing mutations, occurring sequentially with each generation. This process results in a unique mutation profile in each cell. We sample the barcodes in leaf cells and reconstruct the lineage, comparing it to the original lineage tree to test algorithm accuracy under different parameter settings. Our computational simulations validate the reasonable assumptions deduced from experimental observations, emphasizing that factors such as sampling size, barcode length, multiple barcodes, indel probabilities, and Cas9 activity are critical for accurate and successful lineage tracing. Among the many factors we found that sampling size and indel probabilities are two major ones that affect lineage tracing accuracy. Large segment deletions in early generations could greatly impact lineage accuracy. These simulation results offer insightful recommendations for enhancing the design and analysis of Cas9-mediated molecular barcodes in actual experiments.}, }
@article {pmid39159937, year = {2024}, author = {Cavalcante, KS and Rodrigues, BL and Posada-López, L and Peniche, T and Saraiva, JF and Galardo, AKR and Galati, EAB}, title = {Description of Trichophoromyia jariensis, a new species of phlebotomine sand fly (Diptera: Psychodidae) from the eastern Amazon.}, journal = {Journal of medical entomology}, volume = {61}, number = {6}, pages = {1382-1390}, doi = {10.1093/jme/tjae095}, pmid = {39159937}, issn = {1938-2928}, mesh = {Animals ; Brazil ; Female ; Male ; *Psychodidae/classification/genetics/anatomy &amp; histology ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; }, abstract = {A new sand fly species, Trichophoromyia jariensis n. sp. Cavalcante, Rodrigues, &amp; Galati, from the state of Amapá, Brazil, is described based on both male and female morphology and cytochrome c oxidase subunit I DNA barcodes. The DNA barcoding analysis clearly associated males and females of this new species.}, }
@article {pmid39158755, year = {2024}, author = {Krivina, E and Sinetova, M and Zadneprovskaya, E and Ivanova, M and Starikov, A and Shibzukhova, K and Lobakova, E and Bukin, Y and Portnov, A and Temraleeva, A}, title = {The genus Coelastrella (Chlorophyceae, Chlorophyta): molecular species delimitation, biotechnological potential, and description of a new species Coelastrella affinis sp. nov., based on an integrative taxonomic approach.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {113}, pmid = {39158755}, issn = {1572-9699}, support = {075-15-2021-1051//Ministry of Science and Higher Education of the Russian Federation/ ; 122042700045-3//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1051//Ministry of Science and Higher Education of the Russian Federation/ ; 122042700045-3//Ministry of Science and Higher Education of the Russian Federation/ ; 122042700045-3//Ministry of Science and Higher Education of the Russian Federation/ ; 122050400128-1//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1051//Ministry of Science and Higher Education of the Russian Federation/ ; 21-74-30003//Russian Science Foundation/ ; 21-74-30003//Russian Science Foundation/ ; }, mesh = {*Phylogeny ; *Chlorophyceae/classification/genetics ; *RNA, Ribosomal, 18S/genetics ; Fatty Acids/analysis ; Biotechnology ; DNA Barcoding, Taxonomic ; DNA, Algal/genetics/chemistry ; Cluster Analysis ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Despite the long research history on the genus Coelastrella, its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship. It the light of it, the taxonomic status of species can reliably be determined using specific DNA region, such as 18S-ITS1-5.8S-ITS2. The V4 and V9 regions of gene 18S rRNA are relatively conservative fragments which are not suitable for species identification. The ITS2 can be used as a "short barcode". Among the advanced machine methods for delimitation species, the most effective algorithm for distinguishing Coelastrella species was the Generalized Mixed Yule Coalescent (GMYC) method. This paper represented for the first time our comprehensive review of the works devoted to the analysis of the biotechnological potential of representatives of the genus Coelastrella and shows that fatty acid composition of the three main chemogroups within the studied genus differs. In the future, this may form the basis for predicting the composition of the fatty acid profile of new strains, which is important while searching for organisms with specified biotechnological properties. In conclusion, an integrative approach was employed to describe Coelastrella affinis sp. nov., a new species of the genus Coelastrella with high biotechnological potential. Also, a new description of C. thermophila var. astaxanthina comb. nov. was proposed.}, }
@article {pmid39157088, year = {2024}, author = {Hanna, VS and Abd El-Ghany, MN and Ibrahim, MIM and Abdel-Rahman, TM and Tallima, H}, title = {Novel Approaches to Mortierella alpina Identification and Arachidonic Acid Production Optimization.}, journal = {ACS omega}, volume = {9}, number = {32}, pages = {34456-34463}, pmid = {39157088}, issn = {2470-1343}, abstract = {Arachidonic acid (ARA) is an integral constituent of cell structures and is instrumental for the nervous, muscular, and immune systems' functions. The sore need for this nutrient may be fulfilled via production based on the fungus Mortierella alpina. The identity of the M. alpina culture obtained from Assiut University, Egypt, was confirmed based on internal transcribed spacer DNA barcoding and elongation enzyme RNA sequencing. Liquid media glucose and peptone as carbon and nitrogen sources, respectively, and diverse micronutritional factors were adjusted for optimal biomass and ARA production. Shake flask cultivation at 25 °C for 7 days produced around 0.570 g of ARA per liter of culture. M. alpina treatment using mutagen 5-fluorouracil and octyl gallate-supplemented glucose-yeast-agar screening plates and shake-flask incubation at 25 °C, then at 20 °C, followed by aging at 10 °C, led to >3 g ARA/liter culture, a yield considered suitable for potential commercial production.}, }
@article {pmid39152642, year = {2024}, author = {Romeijn, L and Bernatavicius, A and Vu, D}, title = {MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences.}, journal = {Molecular ecology resources}, volume = {24}, number = {8}, pages = {e14006}, doi = {10.1111/1755-0998.14006}, pmid = {39152642}, issn = {1755-0998}, mesh = {*Fungi/classification/genetics ; *DNA, Ribosomal Spacer/genetics/chemistry ; DNA Barcoding, Taxonomic/methods ; DNA, Fungal/genetics ; Neural Networks, Computer ; Deep Learning ; Computational Biology/methods ; }, abstract = {Efficient and accurate classification of DNA barcode data is crucial for large-scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi-head output architecture and multi-level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI-BERT and MycoAI-CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI-CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning-based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI.}, }
@article {pmid39150891, year = {2024}, author = {}, title = {Correction to "Patient and specimen identification in a tertiary care pediatric hospital: Barcodes do not scan themselves".}, journal = {Transfusion}, volume = {64}, number = {9}, pages = {1806}, doi = {10.1111/trf.17945}, pmid = {39150891}, issn = {1537-2995}, }
@article {pmid39149389, year = {2024}, author = {Voorhies, M and Joehnk, B and Uehling, J and Walcott, K and Dubin, C and Mead, HL and Homer, CM and Galgiani, JN and Barker, BM and Brem, RB and Sil, A}, title = {Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39149389}, issn = {2692-8205}, support = {R21 AI172185/AI/NIAID NIH HHS/United States ; S10 OD028511/OD/NIH HHS/United States ; T32 AI007641/AI/NIAID NIH HHS/United States ; U19 AI166798/AI/NIAID NIH HHS/United States ; }, abstract = {Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains a bottleneck for exploiting this information, particularly for pathogens that are difficult to manipulate. Here, we establish a method for high-throughput phenotyping of mixed cultures, in which the pattern of naturally occurring single-nucleotide polymorphisms in each isolate is used as intrinsic barcodes which can be read out by sequencing. We demonstrate that our method can correctly deconvolute strain proportions in simulated mixed-strain pools. As an experimental test of our method, we perform whole genome sequencing of 66 natural isolates of the thermally dimorphic pathogenic fungus Coccidioides posadasii and infer the strain compositions for large mixed pools of these strains after competition at 37°C and room temperature. We validate the results of these selection experiments by recapitulating the temperature-specific enrichment results in smaller pools. Additionally, we demonstrate that strain fitness estimated by our method can be used as a quantitative trait for genome-wide association studies. We anticipate that our method will be broadly applicable to natural populations of microbes and allow high-throughput phenotyping to match the rate of genomic data acquisition.}, }
@article {pmid39149311, year = {2024}, author = {Hu, C and Borji, M and Marrero, GJ and Kumar, V and Weir, JA and Kammula, SV and Macosko, EZ and Chen, F}, title = {Scalable imaging-free spatial genomics through computational reconstruction.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39149311}, issn = {2692-8205}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HG010647/HG/NHGRI NIH HHS/United States ; U24 HG011735/HG/NHGRI NIH HHS/United States ; }, abstract = {Tissue organization arises from the coordinated molecular programs of cells. Spatial genomics maps cells and their molecular programs within the spatial context of tissues. However, current methods measure spatial information through imaging or direct registration, which often require specialized equipment and are limited in scale. Here, we developed an imaging-free spatial transcriptomics method that uses molecular diffusion patterns to computationally reconstruct spatial data. To do so, we utilize a simple experimental protocol on two dimensional barcode arrays to establish an interaction network between barcodes via molecular diffusion. Sequencing these interactions generates a high dimensional matrix of interactions between different spatial barcodes. Then, we perform dimensionality reduction to regenerate a two-dimensional manifold, which represents the spatial locations of the barcode arrays. Surprisingly, we found that the UMAP algorithm, with minimal modifications can faithfully successfully reconstruct the arrays. We demonstrated that this method is compatible with capture array based spatial transcriptomics/genomics methods, Slide-seq and Slide-tags, with high fidelity. We systematically explore the fidelity of the reconstruction through comparisons with experimentally derived ground truth data, and demonstrate that reconstruction generates high quality spatial genomics data. We also scaled this technique to reconstruct high-resolution spatial information over areas up to 1.2 centimeters. This computational reconstruction method effectively converts spatial genomics measurements to molecular biology, enabling spatial transcriptomics with high accessibility, and scalability.}, }
@article {pmid39149288, year = {2024}, author = {Eastburn, DJ and White, KS and Jayne, ND and Camiolo, S and Montis, G and Ha, S and Watson, KG and Yeakley, JM and McComb, J and Seligmann, B}, title = {High-throughput gene expression analysis with TempO-LINC sensitively resolves complex brain, lung and kidney heterogeneity at single-cell resolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39149288}, issn = {2692-8205}, support = {R43 GM140771/GM/NIGMS NIH HHS/United States ; R44 GM140771/GM/NIGMS NIH HHS/United States ; }, abstract = {We report the development and performance of a novel genomics platform, TempO-LINC, for conducting high-throughput transcriptomic analysis on single cells and nuclei. TempO-LINC works by adding cell-identifying molecular barcodes onto highly selective and high-sensitivity gene expression probes within fixed cells, without having to first generate cDNA. Using an instrument-free combinatorial-indexing approach, all probes within the same fixed cell receive an identical barcode, enabling the reconstruction of single-cell gene expression profiles across as few as several hundred cells and up to 100,000+ cells per run. The TempO-LINC approach is easily scalable based on the number of barcodes and rounds of barcoding performed; however, for the experiments reported in this study, the assay utilized over 5.3 million unique barcodes. TempO-LINC has a robust protocol for fixing and banking cells and displays high-sensitivity gene detection from multiple diverse sample types. We show that TempO-LINC has an observed multiplet rate of less than 1.1% and a cell capture rate of ~50%. Although the assay can accurately profile the whole transcriptome (19,683 human or 21,400 mouse genes), it can be targeted to measure only actionable/informative genes and molecular pathways of interest - thereby reducing sequencing requirements. In this study, we applied TempO-LINC to profile the transcriptomes of 89,722 cells across multiple sample types, including nuclei from mouse lung, kidney and brain tissues. The data demonstrated the ability to identify and annotate at least 50 unique cell populations and positively correlate expression of cell type-specific molecular markers within them. TempO-LINC is a robust new single-cell technology that is ideal for large-scale applications/studies across thousands of samples with high data quality.}, }
@article {pmid39149271, year = {2024}, author = {Liao, H and Kottapalli, S and Huang, Y and Chaw, M and Gehring, J and Waltner, O and Phung-Rojas, M and Daza, RM and Matsen, FA and Trapnell, C and Shendure, J and Srivatsan, S}, title = {Optics-free reconstruction of 2D images via DNA barcode proximity graphs.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39149271}, issn = {2692-8205}, support = {R01 AI146028/AI/NIAID NIH HHS/United States ; R01 HG010632/HG/NHGRI NIH HHS/United States ; }, abstract = {Spatial genomic technologies include imaging- and sequencing-based methods (1-3). An emerging subcategory of sequencing-based methods relies on a surface coated with coordinate-associated DNA barcodes, which are leveraged to tag endogenous nucleic acids or cells in an overlaid tissue section (4-7). However, the physical registration of DNA barcodes to spatial coordinates is challenging, necessitating either high density printing of coordinate-specific oligonucleotides or in situ sequencing/probing of randomly deposited, oligonucleotide-bearing beads. As a consequence, the surface areas available to sequencing-based spatial genomic methods are constrained by the time, labor, cost, and instrumentation required to either print, synthesize or decode a coordinate-tagged surface. To address this challenge, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free, DNA microscopy (8) inspired method. With SCOPE, the relative positions of randomly deposited beads on a 2D surface are inferred from the ex situ sequencing of chimeric molecules formed from diffusing "sender" and tethered "receiver" oligonucleotides. As a first proof-of-concept, we apply SCOPE to reconstruct an asymmetric "swoosh" shape resembling the Nike logo (16.75 × 9.25 mm). Next, we use a microarray printer to encode a "color" version of the Snellen eye chart for visual acuity (17.18 × 40.97 mm), and apply SCOPE to achieve optics-free reconstruction of individual letters. Although these are early demonstrations of the concept and much work remains to be done, we envision that the optics-free, sequencing-based quantitation of the molecular proximities of DNA barcodes will enable spatial genomics in constant experimental time, across fields of view and at resolutions that are determined by sequencing depth, bead size, and diffusion kinetics, rather than the limitations of optical instruments or microarray printers.}, }
@article {pmid39148054, year = {2024}, author = {Wen, J and Wu, BC and Li, HM and Zhou, W and Song, CF}, title = {Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {778}, pmid = {39148054}, issn = {1471-2229}, support = {32200191//National Natural Science Foundation of China/ ; JSPKLB202214//Foundation of Jiangsu Key Laboratory for the Research and Utilization of Plant Resources/ ; }, mesh = {*Phylogeny ; Evolution, Molecular ; Genome, Plastid ; Apiaceae/genetics ; }, abstract = {BACKGROUND: The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed.<br><br>RESULTS: Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species.<br><br>CONCLUSIONS: Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.}, }
@article {pmid39145191, year = {2024}, author = {Feng, J and Liu, Y and Xie, A and Yang, Y and Lv, F and Wei, J}, title = {Successful development of molecular diagnostic technology combining mini-barcoding and high-resolution melting for traditional Chinese medicine agarwood species based on single-nucleotide polymorphism in the chloroplast genome.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1405168}, pmid = {39145191}, issn = {1664-462X}, abstract = {Agarwood is a valuable traditional medicine and fragrance. The production process is a typical injury-induced defense response. Currently, there are approximately 22 known species in the genus Aquilaria Lam., all of which can produce agarwood, whereas there are only two legal species of traditional Chinese medicinal agarwood, Aquilaria sinensis (Lour.) Spreng. and Aquilaria agallocha (Lour.) Roxb. The Taiwan herbal Pharmacopoeia of China stipulates that the medicinal agarwood species are A. sinensis and its relatives in the same genus. Moreover, there are five species of agarwood available for clinical medicinal use in Japan, including A. agallocha and A. sinensis, which are often confused with each other or used in a mixed way in the trade process. Therefore, accurate identification of traditional Chinese medicinal agarwood species is important to ensure the authenticity of traditional medicines and to guide the safety of clinical medication. In this study, 59 specific single-nucleotide polymorphism loci were screened and obtained from the chloroplast genomes of 12 species of the genus Aquilaria Lam. We established an identification method for traditional Chinese medicinal agarwood using mini-barcoding combined with high-resolution melting (HRM) and designed and validated 10 pairs of primers from the psbM-trnD, psbA, rps16, petN, ndhE-psaC, rps4, atpE, ycf1, rps15-trnN, and matK regions. The amplification products were all less than 200 bp, with a high success rate of amplification. The method was applied to successfully identify traditional Chinese medicinal agarwood species from commercial agarwood samples. Overall, the sensitivity of this method was sufficient to detect 1% of adulterants in medicinal agarwood products, proving that mini-barcoding HRM is a powerful and flexible tool. This method can be used as a fast and effective high-throughput method for authenticity testing of traditional Chinese medicinal agarwood and its raw materials containing agarwood-containing proprietary Chinese medicines and is recommended for industrial applications.}, }
@article {pmid39144078, year = {2024}, author = {Framst, I and Wolking, RM and Schonfeld, J and Ricker, N and Beeler-Marfisi, J and Chalmers, G and Kamath, PL and Maboni, G}, title = {High-throughput rapid amplicon sequencing for multilocus sequence typing of Mycoplasma ovipneumoniae from archived clinical DNA samples.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1443855}, pmid = {39144078}, issn = {2297-1769}, abstract = {INTRODUCTION: Spillover events of Mycoplasma ovipneumoniae have devastating effects on the wild sheep populations. Multilocus sequence typing (MLST) is used to monitor spillover events and the spread of M. ovipneumoniae between the sheep populations. Most studies involving the typing of M. ovipneumoniae have used Sanger sequencing. However, this technology is time-consuming, expensive, and is not well suited to efficient batch sample processing.<br><br>METHODS: Our study aimed to develop and validate an MLST workflow for typing of M. ovipneumoniae using Nanopore Rapid Barcoding sequencing and multiplex polymerase chain reaction (PCR). We compare the workflow with Nanopore Native Barcoding library preparation and Illumina MiSeq amplicon protocols to determine the most accurate and cost-effective method for sequencing multiplex amplicons. A multiplex PCR was optimized for four housekeeping genes of M. ovipneumoniae using archived DNA samples (N = 68) from nasal swabs.<br><br>RESULTS: Sequences recovered from Nanopore Rapid Barcoding correctly identified all MLST types with the shortest total workflow time and lowest cost per sample when compared with Nanopore Native Barcoding and Illumina MiSeq methods.<br><br>DISCUSSION: Our proposed workflow is a convenient and effective method for strain typing of M. ovipneumoniae and can be applied to other bacterial MLST schemes. The workflow is suitable for diagnostic settings, where reduced hands-on time, cost, and multiplexing capabilities are important.}, }
@article {pmid39141231, year = {2024}, author = {Ansari, SA and Uhlenhaut, NH}, title = {An Optimized High-Resolution Mapping Method for Glucocorticoid Receptor-DNA Binding in Mouse Primary Macrophages.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2846}, number = {}, pages = {91-107}, pmid = {39141231}, issn = {1940-6029}, mesh = {Animals ; *Receptors, Glucocorticoid/metabolism/genetics ; Mice ; *Macrophages/metabolism ; *DNA/metabolism/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Chromatin Immunoprecipitation/methods ; Protein Binding ; Binding Sites ; }, abstract = {ChIP-exo is a powerful tool for achieving enhanced sensitivity and single-base-pair resolution of transcription factor (TF) binding, which utilizes a combination of chromatin immunoprecipitation (ChIP) and lambda exonuclease digestion (exo) followed by high-throughput sequencing. ChIP-nexus (chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode, and single ligation) is an updated and simplified version of the original ChIP-exo method, which has reported an efficient adapter ligation through the DNA circularization step. Building upon an established method, we present a protocol for generating NGS (next-generation sequencing) ready and high-quality ChIP-nexus library for glucocorticoid receptor (GR). This method is specifically optimized for bone marrow-derived macrophage (BMDM) cells. The protocol is initiated by the formation of DNA-protein cross-links in intact cells. This is followed by chromatin shearing, chromatin immunoprecipitation, ligation of sequencing adapters, digestion of adapter-ligated DNA using lambda exonuclease, and purification of single-stranded DNA for circularization and library amplification.}, }
@article {pmid39140204, year = {2024}, author = {Davis, HR and Sanford, HT and Das, I and Nashriq, I and Leaché, AD}, title = {Establishing species boundaries in Bornean geckos.}, journal = {Biology letters}, volume = {20}, number = {8}, pages = {20240157}, pmid = {39140204}, issn = {1744-957X}, support = {//Heerensperger Award/ ; //Orians Award for Tropical Studies/ ; //Ministry of Higher Education, Malaysia/ ; //Society of Systematic Biologists/ ; }, mesh = {Animals ; *Lizards/genetics/classification ; *DNA, Mitochondrial/genetics ; Borneo ; Phylogeny ; Gene Flow ; Species Specificity ; Genetic Speciation ; Genetic Variation ; }, abstract = {Species delimitation using mitochondrial DNA (mtDNA) remains an important and accessible approach for discovering and delimiting species. However, delimiting species with a single locus (e.g. DNA barcoding) is biased towards overestimating species diversity. The highly diverse gecko genus Cyrtodactylus is one such group where delimitation using mtDNA remains the paradigm. In this study, we use genomic data to test putative species boundaries established using mtDNA within three recognized species of Cyrtodactylus on the island of Borneo. We predict that multi-locus genomic data will estimate fewer species than mtDNA, which could have important ramifications for the species diversity within the genus. We aim to (i) investigate the correspondence between species delimitations using mtDNA and genomic data, (ii) infer species trees for each target species, and (iii) quantify gene flow and identify migration patterns to assess population connectivity. We find that species diversity is overestimated and that species boundaries differ between mtDNA and nuclear data. This underscores the value of using genomic data to reassess mtDNA-based species delimitations for taxa lacking clear species boundaries. We expect the number of recognized species within Cyrtodactylus to continue increasing, but, when possible, genomic data should be included to inform more accurate species boundaries.}, }
@article {pmid39140100, year = {2024}, author = {Crous, PW and Jurjević, &#x17d; and Balashov, S and De la Peña-Lastra, S and Mateos, A and Pinruan, U and Rigueiro-Rodríguez, A and Osieck, ER and Altés, A and Czachura, P and Esteve-Raventós, F and Gunaseelan, S and Kaliyaperumal, M and Larsson, E and Luangsa-Ard, JJ and Moreno, G and Pancorbo, F and Piątek, M and Sommai, S and Somrithipol, S and Asif, M and Delgado, G and Flakus, A and Illescas, T and Kezo, K and Khamsuntorn, P and Kubátová, A and Labuda, R and Lavoise, C and Lebel, T and Lueangjaroenkit, P and Maciá-Vicente, JG and Paz, A and Saba, M and Shivas, RG and Tan, YP and Wingfield, MJ and Aas, T and Abramczyk, B and Ainsworth, AM and Akulov, A and Alvarado, P and Armada, F and Assyov, B and Avchar, R and Avesani, M and Bezerra, JL and Bhat, JD and Bilański, P and Bily, DS and Boccardo, F and Bozok, F and Campos, JC and Chaimongkol, S and Chellappan, N and Costa, MM and Dalecká, M and Darmostuk, V and Daskalopoulos, V and Dearnaley, J and Dentinger, BTM and De Silva, NI and Dhotre, D and Carlavilla, JR and Doungsa-Ard, C and Dovana, F and Erhard, A and Ferro, LO and Gallegos, SC and Giles, CE and Gore, G and Gorfer, M and Guard, FE and Hanson, S&#xc5; and Haridev, P and Jankowiak, R and Jeffers, SN and Kandemir, H and Karich, A and Kisło, K and Kiss, L and Krisai-Greilhuber, I and Latha, KPD and Lorenzini, M and Lumyong, S and Manimohan, P and Manjón, JL and Maula, F and Mazur, E and Mesquita, NLS and Młynek, K and Mongkolsamrit, S and Morán, P and Murugadoss, R and Nagarajan, M and Nalumpang, S and Noisripoom, W and Nosalj, S and Novaes, QS and Nowak, M and Pawłowska, J and Peiger, M and Pereira, OL and Pinto, A and Plaza, M and Polemis, E and Polhorský, A and Ramos, DO and Raza, M and Rivas-Ferreiro, M and Rodriguez-Flakus, P and Ruszkiewicz-Michalska, M and Sánchez, A and Santos, A and Schüller, A and Scott, PA and Şen, I and Shelke, D and Śliwa, L and Solheim, H and Sonawane, H and Strašiftáková, D and Stryjak-Bogacka, M and Sudsanguan, M and Suwannarach, N and Suz, LM and Syme, K and Taşkın, H and Tennakoon, DS and Tomka, P and Vaghefi, N and Vasan, V and Vauras, J and Wiktorowicz, D and Villarreal, M and Vizzini, A and Wrzosek, M and Yang, X and Yingkunchao, W and Zapparoli, G and Zervakis, GI and Groenewald, JZ}, title = {Fungal Planet description sheets: 1614-1696.}, journal = {Fungal systematics and evolution}, volume = {13}, number = {}, pages = {183-440}, pmid = {39140100}, issn = {2589-3831}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Australia, Baobabopsis sabindy in leaves of Eragrostis spartinoides, Cortinarius magentiguttatus among deep leaf litter, Laurobasidium azarandamiae from uredinium of Puccinia alyxiae on Alyxia buxifolia, Marasmius pseudoelegans on well-rotted twigs and litter in mixed wet sclerophyll and subtropical rainforest. Bolivia, Favolaschia luminosa on twigs of Byttneria hirsuta, Lecanora thorstenii on bark, in savannas with shrubs and trees. Brazil, Asterina costamaiae on leaves of Rourea bahiensis, Purimyces orchidacearum (incl. Purimyces gen. nov.) as root endophyte on Cattleya locatellii. Bulgaria, Monosporascus bulgaricus and Monosporascus europaeus isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. Finland, Inocybe undatolacera on a lawn, near Betula pendula. France, Inocybe querciphila in humus of mixed forest. Germany, Arrhenia oblongispora on bare soil attached to debris of herbaceous plants and grasses. Greece, Tuber aereum under Quercus coccifera and Acer sempervirens. India, Alfoldia lenyadriensis from the gut of a Platynotus sp. beetle, Fulvifomes subramanianii on living Albizzia amara, Inosperma pavithrum on soil, Phylloporia parvateya on living Lonicera sp., Tropicoporus maritimus on living Peltophorum pterocarpum. Indonesia, Elsinoe atypica on leaf of Eucalyptus pellita. Italy, Apiotrichum vineum from grape wine, Cuphopyllus praecox among grass. Madagascar, Pisolithus madagascariensis on soil under Intsia bijuga. Netherlands, Cytosporella calamagrostidis and Periconia calamagrostidicola on old leaves of Calamagrostis arenaria, Hyaloscypha caricicola on leaves of Carex sp., Neoniesslia phragmiticola (incl. Neoniesslia gen. nov.) on leaf sheaths of standing dead culms of Phragmites australis, Neptunomyces juncicola on culms of Juncus maritimus, Zenophaeosphaeria calamagrostidis (incl. Zenophaeosphaeria gen. nov.) on culms of Calamagrostis arenaria. Norway, Hausneria geniculata (incl. Hausneria gen. nov.) from a gallery of Dryocoetes alni on Alnus incana. Pakistan, Agrocybe auriolus on leaf litter of Eucalyptus camaldulensis, Rhodophana rubrodisca in nutrient-rich loamy soil with Morus alba. Poland, Cladosporium nubilum from hypersaline brine, Entomortierella ferrotolerans from soil at mines and postmining sites, Pseudopezicula epiphylla from sooty mould community on Quercus robur, Quixadomyces sanctacrucensis from resin of Pinus sylvestris, Szafranskia beskidensis (incl. Szafranskia gen. nov.) from resin of Abies alba. Portugal, Ascocoryne laurisilvae on degraded wood of Laurus nobilis, Hygrocybe madeirensis in laurel forests, Hygrocybula terracocta (incl. Hygrocybula gen. nov.) on mossy areas of laurel forests planted with Cryptomeria japonica. Republic of Kenya, Penicillium gorferi from a sterile chicken feather embedded in a soil sample. Slovakia, Cerinomyces tatrensis on bark of Pinus mugo, Metapochonia simonovicovae from soil. South Africa, Acremonium agapanthi on culms of Agapanthus praecox, Alfaria elegiae on culms of Elegia ebracteata, Beaucarneamyces stellenboschensis (incl. Beaucarneamyces gen. nov.) on dead leaves of Beaucarnea stricta, Gardeniomyces kirstenboschensis (incl. Gardeniomyces gen. nov.) rotting fruit of Gardenia thunbergia, Knufia dianellae on dead leaves of Dianella caerulea, Lomaantha quercina on twigs of Quercus suber. Melanina restionis on dead leaves of Restio duthieae, Microdochium buffelskloofinum on seeds of Eragrostis cf. racemosa, Thamnochortomyces kirstenboschensis (incl. Thamnochortomyces gen. nov.) on culms of Thamnochortus fraternus, Tubeufia hagahagana on leaves of Hypoxis angustifolia, Wingfieldomyces cypericola on dead leaves of Cyperus papyrus. Spain, Geastrum federeri in soil under Quercus suber and Q. canariensis, Geastrum nadalii in calcareous soil under Juniperus, Quercus, Cupressus, Pinus and Robinia, Hygrocybe garajonayensis in laurel forests, Inocybe cistophila on acidic soil under Cistus ladanifer, Inocybe sabuligena in a mixed Quercus ilex subsp. ballota/Juniperus thurifera open forest, Mycena calongei on mossy bark base of Juniperus oxycedrus, Rhodophana ulmaria on soil in Ulmus minor forest, Tuber arriacaense in soil under Populus pyramidalis, Volvariella latispora on grassy soils in a Quercus ilex ssp. rotundifolia stand. Sweden, Inocybe iota in alpine heath on calcareous soil. Thailand, Craterellus maerimensis and Craterellus sanbuakwaiensis on laterite and sandy soil, Helicocollum samlanense on scale insects, Leptosporella cassiae on dead twigs of Cassia fistula, Oxydothis coperniciae on dead leaf of Copernicia alba, Russula mukdahanensis on soil, Trechispora sangria on soil, Trechispora sanpatongensis on soil. Türkiye, Amanita corylophila in a plantation of Corylus avellana. Ukraine, Pararthrophiala adonis (incl. Pararthrophiala gen. nov.) on dead stems of Adonis vernalis. USA, Cladorrhinum carnegieae from Carnegiea gigantea, Dematipyriformia americana on swab from basement wall, Dothiora americana from outside air, Dwiroopa aeria from bedroom air, Lithohypha cladosporioides from hospital swab, Macroconia verruculosa on twig of Ilex montana, associated with black destroyed ascomycetous fungus and Biatora sp., Periconia floridana from outside air, Phytophthora fagacearum from necrotic leaves and shoots of Fagus grandifolia, Queenslandipenidiella californica on wood in crawlspace. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Jurjević Z, Balashov S, De la Peña-Lastra S, Mateos A, Pinruan U, Rigueiro-Rodríguez A, Osieck ER, Altés A, Czachura P, Esteve-Raventós F, Gunaseelan S, Kaliyaperumal M, Larsson E, Luangsa-ard JJ, Moreno G, Pancorbo F, Piątek M, Sommai S, Somrithipol S, Asif M, Delgado G, Flakus A, Illescas T, Kezo K, Khamsuntorn P, Kubátová A, Labuda R, Lavoise C, Lebel T, Lueangjaroenkit P, Maciá-Vicente JG, Paz A, Saba M, Shivas RG, Tan YP, Wingfield MJ, Aas T, Abramczyk B, Ainsworth AM, Akulov A, Alvarado P, Armada F, Assyov B, Avchar R, Avesani M, Bezerra JL, Bhat JD, Bilański P, Bily DS, Boccardo F, Bozok F, Campos JC, Chaimongkol S, Chellappan N, Costa MM, Dalecká M, Darmostuk V, Daskalopoulos V, Dearnaley J, Dentinger BTM, De Silva NI, Dhotre D, Carlavilla JR, Doungsa-ard C, Dovana F, Erhard A, Ferro LO, Gallegos SC, Giles CE, Gore G, Gorfer M, Guard FE, Hanson S-A, Haridev P, Jankowiak R, Jeffers SN, Kandemir H, Karich A, Kisło K, Kiss L, Krisai-Greilhuber I, Latha KPD, Lorenzini M, Lumyong S, Manimohan P, Manjón JL, Maula F, Mazur E, Mesquita NLS, Młynek K, Mongkolsamrit S, Morán P, Murugadoss R, Nagarajan M, Nalumpang S, Noisripoom W, Nosalj S, Novaes QS, Nowak M, Pawłowska J, Peiger M, Pereira OL, Pinto A, Plaza M, Polemis E, Polhorský A, Ramos DO, Raza M, Rivas-Ferreiro M, Rodriguez-Flakus P, Ruszkiewicz-Michalska M, Sánchez A, Santos A, Schüller A, Scott PA, Şen İ, Shelke D, Śliwa L, Solheim H, Sonawane H, Strašiftáková D, Stryjak-Bogacka M, Sudsanguan M, Suwannarach N, Suz LM, Syme K, Taşkın H, Tennakoon DS, Tomka P, Vaghefi N, Vasan V, Vauras J, Wiktorowicz D, Villarreal M, Vizzini A, Wrzosek M, Yang X, Yingkunchao W, Zapparoli G, Zervakis GI, Groenewald JZ (2024). Fungal Planet description sheets: 1614-1696. Fungal Systematics and Evolution 13: 183-440. doi: 10.3114/fuse.2024.13.11.}, }
@article {pmid39138532, year = {2024}, author = {Makhanthisa, TI and Guarido, MM and Kemp, A and Weyer, J and Rostal, MK and Karesh, WB and Thompson, PN}, title = {Characterization of mosquito host-biting networks of potential Rift Valley fever virus vectors in north-eastern KwaZulu-Natal province, South Africa.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {341}, pmid = {39138532}, issn = {1756-3305}, mesh = {Animals ; South Africa ; *Mosquito Vectors/virology/physiology ; *Rift Valley fever virus/genetics/isolation &amp; purification/physiology ; *Rift Valley Fever/transmission/virology/epidemiology ; *Aedes/virology/physiology/genetics/classification ; Humans ; Feeding Behavior ; Culex/virology/physiology ; Insect Bites and Stings ; Female ; Culicidae/virology/physiology/classification ; }, abstract = {BACKGROUND: Rift Valley fever virus (RVFV) is a zoonotic mosquito-borne virus with serious implications for livestock health, human health, and the economy in Africa, and is suspected to be endemic in north-eastern KwaZulu-Natal (KZN), South Africa. The vectors of RVFV in this area are poorly known, although several species, such as Aedes (Neomelaniconion) mcintoshi, Aedes (Neomelaniconion) circumluteolus, Aedes (Aedimorphus) durbanensis, and Culex (Lasioconops) poicilipes may be involved. The aim of the study was to determine the vertebrate blood meal sources of potential RVFV mosquito vectors in north-eastern KZN and to characterize the host-biting network.<br><br>METHODS: Blood-fed mosquitoes were collected monthly from November 2019 to February 2023 using a backpack aspirator, CO2-baited Centers for Disease Control and Prevention (CDC) miniature light traps and tent traps, in the vicinity of water bodies and livestock farming households. The mosquitoes were morphologically identified. DNA was extracted from individual mosquitoes and used as templates to amplify the vertebrate cytochrome c oxidase I (COI) and cytochrome b (cytb) genes using conventional polymerase chain reaction (PCR). Amplicons were sequenced and queried in GenBank and the Barcode of Life Data systems to identify the vertebrate blood meal sources and confirm mosquito identifications. All mosquitoes were screened for RVFV using real time reverse transcription (RT)-PCR.<br><br>RESULTS: We identified the mammalian (88.8%) and avian (11.3%) blood meal sources from 409 blood-fed mosquitoes. Aedes circumluteolus (n&#x2009;=&#x2009;128) made up the largest proportion of collected mosquitoes. Cattle (n&#x2009;=&#x2009;195) and nyala (n&#x2009;=&#x2009;61) were the most frequent domestic and wild hosts, respectively. Bipartite network analysis showed that the rural network consisted of more host-biting interactions than the reserve network. All mosquitoes tested negative for RVFV.<br><br>CONCLUSIONS: Several mosquito species, including Ae. circumluteolus, and vertebrate host species, including cattle and nyala, could play a central role in RVFV transmission. Future research in this region should focus on these species to better understand RVFV amplification.}, }
@article {pmid39137246, year = {2024}, author = {Gareri, C and Pfeiffer, CT and Jiang, X and Paulo, JA and Gygi, SP and Pham, U and Chundi, A and Wingler, LM and Staus, DP and Stepniewski, TM and Selent, J and Lucero, EY and Grogan, A and Rajagopal, S and Rockman, HA}, title = {Phosphorylation patterns in the AT1R C-terminal tail specify distinct downstream signaling pathways.}, journal = {Science signaling}, volume = {17}, number = {849}, pages = {eadk5736}, pmid = {39137246}, issn = {1937-9145}, support = {T32 HL007101/HL/NHLBI NIH HHS/United States ; P01 HL075443/HL/NHLBI NIH HHS/United States ; R01 HL056687/HL/NHLBI NIH HHS/United States ; R01 GM122798/GM/NIGMS NIH HHS/United States ; R01 GM067945/GM/NIGMS NIH HHS/United States ; R01 GM132129/GM/NIGMS NIH HHS/United States ; }, mesh = {*Receptor, Angiotensin, Type 1/metabolism/chemistry/genetics ; *Signal Transduction ; Phosphorylation ; Humans ; *beta-Arrestins/metabolism/genetics ; HEK293 Cells ; Molecular Dynamics Simulation ; Angiotensin II/metabolism ; }, abstract = {Different ligands stabilize specific conformations of the angiotensin II type 1 receptor (AT1R) that direct distinct signaling cascades mediated by heterotrimeric G proteins or β-arrestin. These different active conformations are thought to engage distinct intracellular transducers because of differential phosphorylation patterns in the receptor C-terminal tail (the "barcode" hypothesis). Here, we identified the AT1R barcodes for the endogenous agonist AngII, which stimulates both G protein activation and β-arrestin recruitment, and for a synthetic biased agonist that only stimulates β-arrestin recruitment. The endogenous and β-arrestin-biased agonists induced two different ensembles of phosphorylation sites along the C-terminal tail. The phosphorylation of eight serine and threonine residues in the proximal and middle portions of the tail was required for full β-arrestin functionality, whereas phosphorylation of the serine and threonine residues in the distal portion of the tail had little influence on β-arrestin function. Similarly, molecular dynamics simulations showed that the proximal and middle clusters of phosphorylated residues were critical for stable β-arrestin-receptor interactions. These findings demonstrate that ligands that stabilize different receptor conformations induce different phosphorylation clusters in the C-terminal tail as barcodes to evoke distinct receptor-transducer engagement, receptor trafficking, and signaling.}, }
@article {pmid39137139, year = {2024}, author = {Jansen van Rensburg, MJ and Berger, DJ and Yassine, I and Shaw, D and Fohrmann, A and Bray, JE and Jolley, KA and Maiden, MCJ and Brueggemann, AB}, title = {Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.}, journal = {Microbial genomics}, volume = {10}, number = {8}, pages = {}, pmid = {39137139}, issn = {2057-5858}, mesh = {*Streptococcus pneumoniae/genetics/classification/isolation &amp; purification ; *Multilocus Sequence Typing/methods ; *Genome, Bacterial ; Humans ; *DNA Barcoding, Taxonomic/methods ; *Pneumococcal Infections/microbiology/epidemiology ; Phylogeny ; Gene Library ; Whole Genome Sequencing/methods ; }, abstract = {Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.}, }
@article {pmid39135884, year = {2024}, author = {Visagie, CM and Yilmaz, N and Allison, JD and Barreto, RW and Boekhout, T and Boers, J and Delgado, MA and Dewing, C and Fitza, KNE and Furtado, ECA and Gaya, E and Hill, R and Hobden, A and Hu, DM and Hülsewig, T and Khonsanit, A and Luangsa-Ard, JJ and Mthembu, A and Pereira, CM and Price, JL and Pringle, A and Qikani, N and Sandoval-Denis, M and Schumacher, RK and Seifert, KA and Slippers, B and Tennakoon, DS and Thanakitpipattana, D and van Vuuren, NI and Groenewald, JZ and Crous, PW}, title = {New and Interesting Fungi. 7.}, journal = {Fungal systematics and evolution}, volume = {13}, number = {}, pages = {441-494}, pmid = {39135884}, issn = {2589-3831}, abstract = {Two new genera, 17 new species, two epitypes, and six interesting new host and / or geographical records are introduced in this study. New genera include: Cadophorella (based on Cadophorella faginea) and Neosatchmopsis (based on Neosatchmopsis ogrovei). New species include: Alternaria halotolerans (from hypersaline sea water, Qatar), Amylostereum stillwellii (from mycangia of Sirex areolatus, USA), Angiopsora anthurii (on leaves of Anthurium andraeanum, Brazil), Anthracocystis zeae-maydis (from pre-stored Zea mays, South Africa), Bisifusarium solicola (from soil, South Africa), Cadophorella faginea (from dead capsule of Fagus sylvatica, Germany), Devriesia mallochii (from house dust, Canada), Fusarium kirstenboschense (from soil, South Africa), Macroconia podocarpi (on ascomata of ascomycete on twigs of Podocarpus falcatus, South Africa), Neosatchmopsis ogrovei (on Eucalyptus leaf litter, Spain), Ophiocordyceps kuchinaraiensis (on Coleoptera larva, Thailand), Penicillium cederbergense (from soil, South Africa), Penicillium pascuigraminis (from pasture mulch, South Africa), Penicillium viridipigmentum (from soil, South Africa), Pleurotheciella acericola (on stem, bark of living tree of Acer sp., Germany), Protocreopsis physciae (on Physcia caesia, Netherlands), and Talaromyces podocarpi (from soil, South Africa). Citation: Visagie CM, Yilmaz N, Allison JD, Barreto RW, Boekhout T, Boers J, Delgado MA, Dewing C, Fitza KNE, Furtado ECA, Gaya E, Hill R, Hobden A, Hu DM, Hülsewig T, Khonsanit A, Kolecka A, Luangsa-ard JJ, Mthembu A, Pereira CM, Price J-L, Pringle A, Qikani N, Sandoval-Denis M, Schumacher RK, Slippers B, Tennakoon DS, Thanakitpipattana D, van Vuuren NI, Groenewald JZ, Crous PW (2024). New and Interesting Fungi. 7. Fungal Systematics and Evolution 13: 441-494. doi: 10.3114/fuse.2024.13.12.}, }
@article {pmid39133743, year = {2024}, author = {Ibalim, S and Toko, PS and Segar, ST and Sagata, K and Koane, B and Miller, SE and Novotny, V and Janda, M}, title = {Phylogenetic structure of moth communities (Geometridae, Lepidoptera) along a complete rainforest elevational gradient in Papua New Guinea.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308698}, pmid = {39133743}, issn = {1932-6203}, mesh = {Animals ; Papua New Guinea ; *Phylogeny ; *Moths/genetics/physiology/classification ; *Rainforest ; *Altitude ; *Biodiversity ; }, abstract = {We use community phylogenetics to elucidate the community assembly mechanisms for Geometridae moths (Lepidoptera) collected along a complete rainforest elevational gradient (200-3700 m a.s.l) on Mount Wilhelm in Papua New Guinea. A constrained phylogeny based on COI barcodes for 604 species was used to analyse 1390 species x elevation occurrences at eight elevational sites separated by 500 m elevation increments. We obtained Nearest Relatedness Index (NRI), Nearest Taxon Index (NTI) and Standardised Effect Size of Faith's Phylogenetic Diversity (SES.PD) and regressed these on temperature, plant species richness and predator abundance as key abiotic and biotic predictors. We also quantified beta diversity in the moth communities between elevations using the Phylogenetic Sorensen index. Overall, geometrid communities exhibited phylogenetic clustering, suggesting environmental filters, particularly at higher elevations at and above 2200 m a.s.l and no evidence of overdispersion. NRI, NTI and SES.PD showed no consistent trends with elevation or the studied biotic and abiotic variables. Change in community structure was driven by turnover of phylogenetic beta-diversity, except for the highest 2700-3200 m elevations, which were characterised by nested subsets of lower elevation communities. Overall, the elevational signal of geometrid phylogeny was weak-moderate. Additional insect community phylogeny studies are needed to understand this pattern.}, }
@article {pmid39129968, year = {2024}, author = {Trollip, C and Carnegie, AJ and Anderson, C and Priest, MJ and Gorrie, B and Daly, A}, title = {Response to the detection of Rugonectria castaneicola and Rugonectria wingfieldii sp. nov. on Quercus in Australia.}, journal = {Fungal systematics and evolution}, volume = {13}, number = {}, pages = {123-130}, pmid = {39129968}, issn = {2589-3831}, abstract = {Here we report on the detection and surveillance response to two Rugonectria species found in Sydney, Australia, in 2015. Both Rugonectria castaneicola and R. wingfieldii sp. nov. were found in association with cankers on Quercus robur (English oak). The fungi were initially found to be localised on amenity trees in northern Sydney, New South Wales, and as they were new detections for Australia, eradication was considered. Ongoing surveillance across the Sydney basin, regional New South Wales, and the Australian Capital Territory, however, indicated that they were already well established. Species identities were confirmed through morphological examination and molecular barcoding, with the subsequent analysis undertaken to classify R. wingfieldii sp. nov. This study provides the first records of Rugonectria found in association with canker on Oak trees in Australia. Citation: Trollip C, Carnegie AJ, Anderson C, Priest MJ, Gorrie B, Daly A (2024). Response to the detection of Rugonectria castaneicola and Rugonectria wingfieldii sp. nov. on Quercus in Australia. Fungal Systematics and Evolution 13: 123-130. doi: 10.3114/fuse.2024.13.06.}, }
@article {pmid39126069, year = {2024}, author = {Zhou, P and Lei, WS and Shi, YK and Liu, YZ and Luo, Y and Li, JH and Xiang, XG}, title = {Plastome Evolution, Phylogenomics, and DNA Barcoding Investigation of Gastrochilus (Aeridinae, Orchidaceae), with a Focus on the Systematic Position of Haraella retrocalla.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39126069}, issn = {1422-0067}, support = {32060056 and 32360063//National Natural Science Foundation of China/ ; }, mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Evolution, Molecular ; Genome, Plastid ; }, abstract = {Gastrochilus is an orchid genus containing about 70 species in tropical and subtropical Asia with high morphological diversity. The phylogenetic relationships among this genus have not been fully resolved, and the plastome evolution has not been investigated either. In this study, five plastomes of Gastrochilus were newly reported, and sixteen plastomes of Gastrochilus were used to conduct comparative and phylogenetic analyses. Our results showed that the Gastrochilus plastomes ranged from 146,183 to 148,666 bp, with a GC content of 36.7-36.9%. There were 120 genes annotated, consisting of 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. No contraction and expansion of IR borders, gene rearrangements, or inversions were detected. Additionally, the repeat sequences and codon usage bias of Gastrochilus plastomes were highly conserved. Twenty hypervariable regions were selected as potential DNA barcodes. The phylogenetic relationships within Gastrochilus were well resolved based on the whole plastome, especially among main clades. Furthermore, both molecular and morphological data strongly supported Haraella retrocalla as a member of Gastrochilus (G. retrocallus).}, }
@article {pmid39125672, year = {2024}, author = {Park, J and Shin, S and Kim, Y and Bu, Y and Choi, HY and Lee, K}, title = {Effect of Torilis japonica Fruit Extract for Endothelium-Independent Vasorelaxation and Blood Pressure Lowering in Rats.}, journal = {International journal of molecular sciences}, volume = {25}, number = {15}, pages = {}, pmid = {39125672}, issn = {1422-0067}, mesh = {Animals ; Rats ; *Vasodilation/drug effects ; *Plant Extracts/pharmacology ; *Blood Pressure/drug effects ; Male ; *Fruit/chemistry ; *Rats, Sprague-Dawley ; *Endothelium, Vascular/drug effects/metabolism ; Antihypertensive Agents/pharmacology ; Vasodilator Agents/pharmacology ; Aorta, Thoracic/drug effects/metabolism ; Rats, Inbred SHR ; Muscle, Smooth, Vascular/drug effects/metabolism ; Hypertension/drug therapy/metabolism/physiopathology ; }, abstract = {Torilis japonica (TJ) fruit, is a herb that is traditionally used for erectile dysfunction (ED). Given the shared mechanisms of ED and hypertension through vascular smooth muscle, we hypothesized that TJ would be effective in vasodilation and blood pressure reduction. This study confirmed the authenticity of TJ samples via DNA barcoding and quantified the main active compound, torilin, using HPLC. TJ was extracted with distilled water (TJW) and 50% ethanol (TJE), yielding torilin contents of 0.35 ± 0.01% and 2.84 ± 0.02%, respectively. Ex vivo tests on thoracic aortic rings from Sprague-Dawley rats showed that TJE (3-300 µg/mL) induced endothelium-independent, concentration-dependent vasodilation, unlike TJW. Torilin caused concentration-dependent relaxation with an EC50 of 210 ± 1.07 µM. TJE's effects were blocked by a voltage-dependent K[+] channel blocker and alleviated contractions induced by CaCl2 and angiotensin II. TJE inhibited vascular contraction induced by phenylephrine or KCl via extracellular CaCl2 and enhanced inhibition with nifedipine, indicating involvement of voltage-dependent and receptor-operated Ca[2+] channels. Oral administration of TJE (1000 mg/kg) significantly reduced blood pressure in spontaneously hypertensive rats. These findings suggest TJ extract's potential for hypertension treatment through vasorelaxant mechanisms, though further research is needed to confirm its efficacy and safety.}, }
@article {pmid39123731, year = {2024}, author = {Luo, Z and Pei, C and Zhang, H and Wang, Y and Zhang, B and Hu, D}, title = {Nutritional Partitioning among Sympatric Ungulates in Eastern Tibet.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {15}, pages = {}, pmid = {39123731}, issn = {2076-2615}, abstract = {Wild ungulates play crucial roles in maintaining the structure and function of local ecosystems. The alpine musk deer (Moschus chrysogaste), white-lipped deer (Przewalskium albirostris), and red serow (Capricornis rubidus) are widely distributed throughout the Nyenchen Tanglha Mountains of Tibet. However, research on the mechanisms underlying their coexistence in the same habitat remains lacking. This study aimed to investigate the mechanisms underlying the coexistence of these species based on their dietary preferences through DNA barcoding using the fecal samples of these animals collected from the study area. These species consume a wide variety of food types. Alpine musk deer, white-lipped deer, and red serow consume plants belonging to 74 families and 114 genera, 62 families and 122 genera, and 63 families and 113 genera, respectively. Furthermore, significant differences were observed in the nutritional ecological niche among these species, primarily manifested in the differentiation of food types and selection of food at the genus level. Owing to differences in social behavior, body size, and habitat selection, these three species further expand their differentiation in resource selection, thereby making more efficient use of environmental resources. Our findings indicate these factors are the primary reasons for the stable coexistence of these species.}, }
@article {pmid39120762, year = {2024}, author = {Morales-Serna, FN and Camacho-Zepeda, S}, title = {Morphology, DNA barcoding and seasonal occurrence of Ergasilus lizae Krøyer, 1863 (Copepoda: Ergasilidae) parasitizing mullets from northwestern Mexico.}, journal = {Systematic parasitology}, volume = {101}, number = {5}, pages = {54}, pmid = {39120762}, issn = {1573-5192}, support = {IN215722//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT, UNAM)/ ; }, mesh = {Animals ; *Copepoda/genetics/anatomy &amp; histology/classification ; Mexico ; *DNA Barcoding, Taxonomic ; *Seasons ; *Species Specificity ; Smegmamorpha/parasitology ; Phylogeny ; Electron Transport Complex IV/genetics ; }, abstract = {Ergasilus lizae Krøyer, 1863 is a parasitic copepod known to infect mullets (Mugilidae) in different parts of the world. It was originally reported from the east coast of North America, but the original description lacks enough detail, making identification with this information difficult. In this study, we provide a redescription of E. lizae found on Mugil curema Valenciennes and M. cephalus Linnaeus, caught in two coastal lagoons of northwestern Mexico during two climatic seasons: warm/rainy and cold/dry. The prevalence of this parasite was higher in the warm season than in the cold season. To facilitate the species identification, new sequences of the barcoding gene (COI mtDNA) of E. lizae were generated and compared against unpublished sequences of E. lizae available in the Barcode of Life Database (BOLD). Our results suggest that the sequences of BOLD possibly belong to a species misidentified as E. lizae.}, }
@article {pmid39119217, year = {2024}, author = {Murcia-Moreno, D and Gálvez, D}, title = {Preliminary checklist of spiders (Araneae) from Coiba National Park, Panama.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e117642}, pmid = {39119217}, issn = {1314-2828}, abstract = {BACKGROUND: Coiba National Park is an offshore region on the Pacific side of Panama, which hosts several endemic species of animals and plants. It was declared a UNESCO World Heritage Site in 2005. Despite the title awarded to the Park, knowledge about basic elements of its biodiversity are still lacking, which are of vital relevance for management and conservation policies. For instance, until now, no study had ever monitored the araneofauna diversity of the Park.<br><br>NEW INFORMATION: Here, we provide the first checklist of spider species in Coiba National Park, including the main island and several surrounding islands. We sampled during several field trips carried out from August 2021 to August 2023. We identified at least 152 species (98 genera and 30 families) and we report three new spiders species for Panama, namely Ctenusnigrolineatus Berland (1913), Chapodagitae Zhang &amp; Maddison (2012) and Sarindanigra Peckham &amp; Peckham (1892). We discuss the implications of our results and recommend future lines of work that include DNA barcoding, monitoring of population and community dynamics, plus linkage of climatic data from the newly-installed meteorological station on the Island.}, }
@article {pmid39118362, year = {2024}, author = {Everts, T and Van Driessche, C and Neyrinck, S and Haegeman, A and Ruttink, T and Jacquemyn, H and Brys, R}, title = {Phenological mismatches mitigate the ecological impact of a biological invader on amphibian communities.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {34}, number = {6}, pages = {e3017}, doi = {10.1002/eap.3017}, pmid = {39118362}, issn = {1051-0761}, support = {1S01822N//Fonds Wetenschappelijk Onderzoek/ ; 1S23822N//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; *Introduced Species ; *Rana catesbeiana/physiology ; Belgium ; DNA, Environmental ; }, abstract = {Horizon scans have emerged as a valuable tool to anticipate the incoming invasive alien species (IAS) by judging species on their potential impacts. However, little research has been conducted on quantifying actual impacts and assessing causes of species-specific vulnerabilities to particular IAS due to persistent methodological challenges. The underlying interspecific mechanisms driving species-specific vulnerabilities therefore remain poorly understood, even though they can substantially improve the accuracy of risk assessments. Given that interspecific interactions underlying ecological impacts of IAS are often shaped by phenological synchrony, we tested the hypothesis that temporal mismatches in breeding phenology between native species and IAS can mitigate their ecological impacts. Focusing on the invasive American bullfrog (Lithobates catesbeianus), we combined an environmental DNA (eDNA) quantitative barcoding and metabarcoding survey in Belgium with a global meta-analysis, and integrated citizen-science data on breeding phenology. We examined whether the presence of native amphibian species was negatively related to the presence or abundance of invasive bullfrogs and whether this relationship was affected by their phenological mismatches. The field study revealed a significant negative effect of increasing bullfrog eDNA concentrations on native amphibian species richness and community structure. These observations were shaped by species-specific vulnerabilities to invasive bullfrogs, with late spring- and summer-breeding species being strongly affected, while winter-breeding species remained unaffected. This trend was confirmed by the global meta-analysis. A significant negative relationship was observed between phenological mismatch and the impact of bullfrogs. Specifically, native amphibian species with breeding phenology differing by 6 weeks or less from invasive bullfrogs were more likely to be absent in the presence of bullfrogs than species whose phenology differed by more than 6 weeks with that of bullfrogs. Taken together, we present a novel method based on the combination of aqueous eDNA quantitative barcoding and metabarcoding to quantify the ecological impacts of biological invaders at the community level. We show that phenological mismatches between native and invasive species can be a strong predictor of invasion impact regardless of ecological or methodological context. Therefore, we advocate for the integration of temporal alignment between native and IAS's phenologies into invasion impact frameworks.}, }
@article {pmid39117628, year = {2024}, author = {Siegel, SV and Trimarsanto, H and Amato, R and Murie, K and Taylor, AR and Sutanto, E and Kleinecke, M and Whitton, G and Watson, JA and Imwong, M and Assefa, A and Rahim, AG and Nguyen, HC and Tran, TH and Green, JA and Koh, GCKW and White, NJ and Day, N and Kwiatkowski, DP and Rayner, JC and Price, RN and Auburn, S}, title = {Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {6757}, pmid = {39117628}, issn = {2041-1723}, support = {R01AI137154//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; 200909/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; R01 AI137154/AI/NIAID NIH HHS/United States ; 206194/Z17/Z//Wellcome Trust (Wellcome)/ ; APP2001083//Department of Health | National Health and Medical Research Council (NHMRC)/ ; INV-043618//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; 204911/WT_/Wellcome Trust/United Kingdom ; OPP1054404//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; 206194/WT_/Wellcome Trust/United Kingdom ; ICRG GR071614MA//Wellcome Trust (Wellcome)/ ; }, mesh = {*Plasmodium vivax/genetics ; *Malaria, Vivax/parasitology/epidemiology ; Humans ; *Recurrence ; Haplotypes/genetics ; Polymorphism, Single Nucleotide ; Genome, Protozoan/genetics ; Genotype ; }, abstract = {Challenges in classifying recurrent Plasmodium vivax infections constrain surveillance of antimalarial efficacy and transmission. Recurrent infections may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or reinfection. Molecular inference of familial relatedness (identity-by-descent or IBD) can help resolve the probable origin of recurrences. As whole genome sequencing of P. vivax remains challenging, targeted genotyping methods are needed for scalability. We describe a P. vivax marker discovery framework to identify and select panels of microhaplotypes (multi-allelic markers within small, amplifiable segments of the genome) that can accurately capture IBD. We evaluate panels of 50-250 microhaplotypes discovered in a global set of 615 P. vivax genomes. A candidate global 100-microhaplotype panel exhibits high marker diversity in the Asia-Pacific, Latin America and horn of Africa (median HE = 0.70-0.81) and identifies 89% of the polyclonal infections detected with genome-wide datasets. Data simulations reveal lower error in estimating pairwise IBD using microhaplotypes relative to traditional biallelic SNP barcodes. The candidate global panel also exhibits high accuracy in predicting geographic origin and captures local infection outbreak and bottlenecking events. Our framework is open-source enabling customised microhaplotype discovery and selection, with potential for porting to other species or data resources.}, }
@article {pmid39114565, year = {2024}, author = {van Achterberg, C and Shaw, MR and Fernandez-Triana, J and Quicke, DLJ}, title = {Resolution of the Aleiodesseriatus (Herrich-Schäffer, 1838)-aggregate in the western Palaearctic (Hymenoptera, Braconidae, Rogadinae), with description of a new species.}, journal = {ZooKeys}, volume = {1208}, number = {}, pages = {241-258}, pmid = {39114565}, issn = {1313-2989}, abstract = {Two European species are recognised and characterised within the traditional Aleiodesseriatus species concept, based initially on DNA barcoding but with supporting, although slight and sometimes unreliable, morphological differences. Aleiodespseudoseriatus sp. nov. is described and a neotype is designated for Rogasseriatus Herrich-Schäffer, 1838. Specimens from the Russian Far East were also DNA barcoded and were found to belong to a new species distinct from the two European taxa. The two European species were found to use different lithosiine hosts.}, }
@article {pmid39113382, year = {2024}, author = {Lu, Y and Su, J and Cheng, S and Hu, Y and Xia, Q}, title = {Molecular identification and genetic diversity of biting midges (Diptera: Ceratopogonidae) in the tropical environment on Hainan Island, China.}, journal = {Journal of vector borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.4103/JVBD.JVBD_100_23}, pmid = {39113382}, issn = {0972-9062}, abstract = {BACKGROUND OBJECTIVES: Biting midges are hematophagous arthropods responsible for zoonotic infectious diseases and have a wide distribution in temperate and tropical latitudes of the world.<br><br>METHODS: The genomic DNA of midge samples was extracted using the Chelex method and the ITS1gene was amplified by PCR to identify the midge species via BLAST. The sequence characteristics and the genetic diversity were analyzed using ClustalOmega, DnaSP, Arlequin, PopART, and TCS software tool. The validity of the ITS1 gene as a DNA barcode marker was evaluated using DAMBE. The phylogenetic relationship was established in the MEGA software. The ABGD web determined the species boundary and the SDT software visualized the pairwise sequence comparisons.<br><br>RESULTS: A total of 39 midge samples possessed the range from 364 to 429 bp of the ITS1 sequences. The midge samples were identified as Culicoides imicola, Culicoides oxystoma, Culicoides peregrinus, Culicoides jacobsoni, Forcipomyia peregrinator, and Culicoides fulvus, respectively. The ITS1 sequences had 288 conserved sites (60.25%), 167 variable sites (34.94%), 141 parsimony-informative sites (29.50%), and 26 singleton sites (5.44%), with a considerable sequence variation with a high haplotype diversity. Populations in Lingao, Haikou, Tunchang were relatively independent, with a low level of gene flow. A separate population of Forcipomyia genus in Danzhou was observed.<br><br>INTERPRETATION CONCLUSION: The biting midges in Hainan, a tropical island, had abundant genetic diversity. Timely surveillance is a crucial control measure for the spread of midge-borne diseases.}, }
@article {pmid39113366, year = {2024}, author = {Madpathi, S and Daravath, SS and Bannoth, RN}, title = {Molecular characterization of Armigeres Subalbatus from Hyderabad region of Telangana state, India.}, journal = {Journal of vector borne diseases}, volume = {}, number = {}, pages = {}, doi = {10.4103/JVBD.JVBD_13_24}, pmid = {39113366}, issn = {0972-9062}, abstract = {BACKGROUND OBJECTIVES: The mosquito Armigeres subalbatus (Coquillett, 1898) is a significant vector for Japanese encephalitis infection, and breeds in high organic polluted water. Understanding mosquito diversity and there abundance in relation to mosquito-borne diseases is an important component for public health managers. Though the conventional methods for systematic position of mosquito species by using morphological characteristics is a classical method, but it requires perfect expertise and well preserved specimen. Conversely, the molecular analysis of mitochondrial cytochrome C oxidase subunit I (COI) serves as a gene-centric DNA barcoding approach and offers a promising alternative method for mosquito species identification.<br><br>METHODS: The study at hand delves into the morphological characteristics of Armigeres subalbatus were compared with COI- gene to ensure a more dependable verification for identification of mosquito species found in Hyderabad region of Telangana.<br><br>RESULTS: The 489 base pair amplicons were acquired and deposited into the NCBI Gene Bank nucleotide database under the accession number MG686500. The maximum likelihood tree infers that, the Hyderabad species was diverged from USA and Japan species but had ancestral relationship with Tamil Nadu, Karnataka, Maharastra, Kerala and Goa species.<br><br>INTERPRETATION CONCLUSION: Mitochondrial gene (COI) based DNA barcoding is the most reliable and potential alternative technique to identify the mosquito species.}, }
@article {pmid39112930, year = {2024}, author = {Liu, X and Luo, J and Chen, H and Li, T and Qu, T and Tang, M and Fu, Z}, title = {Comparative analysis of complete chloroplast genomes of Synotis species (Asteraceae, Senecioneae) for identification and phylogenetic analysis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {769}, pmid = {39112930}, issn = {1471-2164}, support = {31500166//National Natural Science Foundation of China/ ; 32000158//National Natural Science Foundation of China/ ; 2021XJKK0702//National Science &amp; Technology Fundamental Resources Investigation Program of China/ ; 2020CXZYHJZX03//Foundation of Sustainable Development Research Center of Resources and Environment of Western Sichuan, Sichuan Normal University/ ; }, mesh = {*Genome, Chloroplast ; *Phylogeny ; *Asteraceae/genetics/classification ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The Synotis (C. B. Clarke) C. Jeffrey &amp; Y. L. Chen is an ecologically important genus of the tribe Senecioneae, family Asteraceae. Because most species of the genus bear similar morphology, traditional morphological identification methods are very difficult to discriminate them. Therefore, it is essential to develop a reliable and effective identification method for Synotis species. In this study, the complete chloroplast (cp.) genomes of four Synotis species, S. cavaleriei (H.Lév.) C. Jeffrey &amp; Y.L. Chen, S. duclouxii (Dunn) C. Jeffrey &amp; Y.L. Chen, S. nagensium (C.B. Clarke) C. Jeffrey &amp; Y.L. Chen and S. erythropappa (Bureau &amp; Franch.) C. Jeffrey &amp; Y. L. Chen had been sequenced using next-generation sequencing technology and reported here.<br><br>RESULTS: These four cp. genomes exhibited a typical quadripartite structure and contained the large single-copy regions (LSC, 83,288 to 83,399&#xa0;bp), the small single-copy regions (SSC, 18,262 to 18,287&#xa0;bp), and the inverted repeat regions (IR, 24,837 to 24,842&#xa0;bp). Each of the four cp. genomes encoded 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (ycf1 and rps19). The highly variable regions (trnC-GCA-petN, ccsA-psaC, trnE-UUC-rpoB, ycf1, ccsA and petN) may be used as potential molecular barcodes. The complete cp. genomes sequence of Synotis could be used as the potentially effective super-barcode to accurately identify Synotis species. Phylogenetic analysis demonstrated that the four Synotis species were clustered into a monophyletic group, and they were closed to the Senecio, Crassocephalum and Dendrosenecio in tribe Senecioneae.<br><br>CONCLUSIONS: This study will be useful for further species identification, evolution, genetic diversity and phylogenetic studies within this genus Synotis and the tribe Senecioneae.}, }
@article {pmid39109773, year = {2024}, author = {Dos Reis Júnior, MR and Caixeta, HC and Oliveira, C and Melo, MRS}, title = {New report of the rare Sciadonus alphacrucis Melo et al., 2022 (Teleostei, Ophidiiformes, Bythitidae), DNA barcoding, and range extension in the western South Atlantic.}, journal = {Journal of fish biology}, volume = {105}, number = {4}, pages = {1357-1361}, doi = {10.1111/jfb.15896}, pmid = {39109773}, issn = {1095-8649}, support = {CNPq 403380/2022-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 306054/2006-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441128/2020-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CAPES 88887.644858/202100//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; FAPESP 2017/12909-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/134336//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/056195//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; Brazil ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Atlantic Ocean ; Phylogeny ; Animal Distribution ; Female ; Male ; Fishes/genetics/classification ; }, abstract = {Sciadonus alphacrucis Melo, Gomes, Møller &amp; Nielsen, 2022 is a rare deep-sea species, previously known from only two specimens collected off São Paulo State, southeastern Brazil, in the western South Atlantic. Herein, we report a new specimen of S. alphacrucis collected on the continental slope off Santa Catarina State, southern Brazil, thereby extending its known distribution by 420 km. Additionally, we provide the new meristic and morphometric data, the molecular identification using sequences of the cytochrome c oxidase subunit I (COI), an updated distribution map, and a discussion of troglomorphic traits.}, }
@article {pmid39109414, year = {2024}, author = {You, G and Hou, F and Niu, L and Wang, S and Wang, L and Sun, L and Ren, X}, title = {Identification of Euphorbiae pekinensis Radix and its counterfeit and adulterated products based on DNA barcode, UPLC-Q-TOF-MS, UPLC fingerprint, and chemometrics.}, journal = {Biomedical chromatography : BMC}, volume = {38}, number = {10}, pages = {e5978}, doi = {10.1002/bmc.5978}, pmid = {39109414}, issn = {1099-0801}, support = {2021KJ124//Scientific Research Project of Tianjin Educational Committee/ ; }, mesh = {*Drugs, Chinese Herbal/chemistry/analysis ; Chromatography, High Pressure Liquid/methods ; *Drug Contamination ; *Counterfeit Drugs/analysis/chemistry ; *Mass Spectrometry/methods ; *DNA Barcoding, Taxonomic/methods ; Chemometrics/methods ; Tannins/analysis/chemistry ; }, abstract = {Euphorbiae pekinensis Radix (EPR) is a traditional Chinese herb commonly used to treat edema, pleural effusion, and ascites. However, counterfeit and adulterated products often appear in the market because of the homonym phenomenon, similar appearance, and artificial forgery of Chinese herbs. This study comprehensively evaluated the quality of EPR using multiple methods. The DNA barcode technique was used to identify EPR, while the UPLC-Q-TOF-MS technique was utilized to analyze the chemical composition of EPR. A total of 15 tannin and phenolic acid components were identified. Furthermore, UPLC fingerprints of EPR and its common counterfeit products were established, and unsupervised and supervised pattern recognition models were developed using these fingerprints. The backpropagation artificial neural network and counter-propagation artificial neural network models accurately identified counterfeit and adulterated products, with a counterfeit ratio of more than 25%. Finally, the contents of the chemical markers 3,3'-di-O-methyl ellagic acid-4'-O-β-D-glucopyranoside, ellagic acid, 3,3'-di-O-methyl ellagic acid-4'-O-β-d-xylopyranoside, and 3,3'-di-O-methyl ellagic acid were determined to range from 0.05% to 0.11%, 1.95% to 8.52%, 0.27% to 0.86%, and 0.10% to 0.42%, respectively. This proposed strategy offers a general procedure for identifying Chinese herbs and distinguishing between counterfeit and adulterated products.}, }
@article {pmid39109336, year = {2024}, author = {Chen, X and Feng, Y and Qu, T and Chen, H and Liu, X and Pang, L and Chen, M and Fu, Z}, title = {Complete chloroplast genomes of two Ainsliaea species and the phylogenetic analysis in the tribe Pertyeae.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1408114}, pmid = {39109336}, issn = {1664-8021}, abstract = {The genus Ainsliaea DC. is one of the major groups within the tribe Pertyeae (Asteraceae). It comprises several important Chinese medicinal species. However, the phylogenetic position has undergone a long process of exploration. The complete chloroplast (cp) genome sequences data has not been employed in species identification and phylogeny of Ainsliaea. In this study, the complete cp genomes of two Ainsliaea species (A. gracilis and A. henryi) were reported, followed by structural, comparative, and phylogenetic analyses within the tribe Peryteae. Both cp genomes displayed a typical quadripartite circular structure, with the LSC and SSC regions separated by the IR regions. The genomes were 152,959 (A. gracilis) and 152,805 (A. henryi) base pairs (bp) long, with a GC content of 37.6%. They were highly conserved, containing 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes (rps19 and ycf1). Moreover, thirteen highly polymorphic regions (e.g., trnK-UUU, trnG-UCC, trnT-GGU, accD-psaI, and rpl22-rps19) were identified, indicating their potential as DNA barcodes. The phylogenetic analysis confirmed the placement of Ainsliaea in the tribe Pertyeae, revealing close relationships with the genera Myripnois and Pertya. In comparison with Ainsliaea, Myripnois was more closely related to Pertya. This study lays a theoretical foundation for future research on species identification, population genetics, resource conservation, and sustainable utilization within Ainsliaea and Pertyeae.}, }
@article {pmid39108338, year = {2024}, author = {Namayandeh, A and Guerra, S and Islam, N and James, T and Hudson, PL and Ghaderi, E and Yusuf, T and Vasquez, AA and Ram, JL}, title = {New species and a fascinating diversity of Chironomidae (Diptera, Insecta) in and around an overlooked urban vernal pool.}, journal = {ZooKeys}, volume = {1208}, number = {}, pages = {133-163}, pmid = {39108338}, issn = {1313-2989}, abstract = {In this study, the biodiversity of Chironomidae was investigated in Palmer Park Pond A, an urban vernal pond in Detroit, Michigan, USA. This study is developed as part of our ongoing Public Environmental Outreach Program at the Detroit Exploration and Nature Center in Palmer Park. Twenty-one Chironomidae species were discovered in and on the adjacent riparian vegetation of this pond using molecular and morphological methods. Three species Bryophaenocladiuspalmerparcum Namayandeh &amp; Hudson sp. nov., Limnophyesstagnum Namayandeh, Guerra &amp; Ram sp. nov., and Rheocricotopus (s. s.) angustus Namayandeh &amp; Hudson sp. nov. are new to science. Bryophaenocladiuspalmerparcum sp. nov. and L.stagnum sp. nov. are unusual Orthoclads, with B.palmerparcum sp. nov. possessing a setose, short, and wide anal point and L.stagnum sp. nov. lacking lanceolate setae on both sexes. Based on the shape of superior volsella, R.angustus sp. nov., belongs to the effusus group, which was also confirmed by DNA barcoding molecular analysis. In this study, a new faunistic record was also found for the Nearctic as well as four new faunistic records for the state of Michigan. Ephemeral aquatic habitats such as vernal pools are often overlooked or destroyed by urbanization activities, controlling vector species, creating groomed fields, and/or residential development. Therefore, finding these new species demonstrates the biodiversity value of vernal ponds as important habitats, further motivating us to preserve them.}, }
@article {pmid39105821, year = {2024}, author = {Kobayashi, G and Abe, H}, title = {Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {887}, pmid = {39105821}, issn = {1573-4978}, support = {JP22K15174//JSPS KAKENHI/ ; JPMEERF20204R01//Environment Research and Technology Development Fund/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Aquatic Organisms/genetics ; *Phylogeny ; *Invertebrates/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Electron Transport Complex IV/genetics ; High-Throughput Nucleotide Sequencing/methods ; Biodiversity ; Cost-Benefit Analysis ; }, abstract = {BACKGROUND: The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system.<br><br>METHODS AND RESULTS: We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816&#xa0;bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time.<br><br>CONCLUSIONS: We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.}, }
@article {pmid39099456, year = {2024}, author = {Lee, H and Langseth, CM and Salas, SM and Sariyar, S and Metousis, A and Rueda-Alaña, E and Bekiari, C and Lundberg, E and Garcı A-Moreno, F and Grillo, M and Nilsson, M}, title = {Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.}, journal = {Development (Cambridge, England)}, volume = {151}, number = {16}, pages = {}, pmid = {39099456}, issn = {1477-9129}, support = {//Chan Zuckerberg Initiative/ ; //Familjen Erling-Perssons Stiftelse/ ; //Ikerbasque, Basque Foundation for Science/ ; //Ministerio de Ciencia e Innovacion/ ; //Eusko Jaurlaritza/ ; //EASI genomics TNA/ ; //Silicon Valley Community Foundation/ ; //Erling-Perssons Stiftelse/ ; KAW 2018.0172//Knut och Alice Wallenbergs Stiftelse/ ; 2019-01238//Vetenskapsr&#xe5;det/ ; CAN 2021/1726//Cancerfonden/ ; MICNN PGC2018-096173-A-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PIBA 2020\_1\_0057//Eusko Jaurlaritza/ ; PID14596//European Advanced infraStructure for Innovative Genomics/ ; //Stockholms Universitet/ ; }, mesh = {Animals ; *Gene Expression Profiling/methods ; RNA, Messenger/genetics/metabolism ; Transcriptome/genetics ; Humans ; In Situ Hybridization/methods ; Mice ; Developmental Biology/methods ; }, abstract = {Multiplexed spatial profiling of mRNAs has recently gained traction as a tool to explore the cellular diversity and the architecture of tissues. We propose a sensitive, open-source, simple and flexible method for the generation of in situ expression maps of hundreds of genes. We use direct ligation of padlock probes on mRNAs, coupled with rolling circle amplification and hybridization-based in situ combinatorial barcoding, to achieve high detection efficiency, high-throughput and large multiplexing. We validate the method across a number of species and show its use in combination with orthogonal methods such as antibody staining, highlighting its potential value for developmental and tissue biology studies. Finally, we provide an end-to-end computational workflow that covers the steps of probe design, image processing, data extraction, cell segmentation, clustering and annotation of cell types. By enabling easier access to high-throughput spatially resolved transcriptomics, we hope to encourage a diversity of applications and the exploration of a wide range of biological questions.}, }
@article {pmid39095717, year = {2024}, author = {Nazari, V and Lukhtanov, V and Naderi, A and Bruna, CD and Zahiri, R and Cesaroni, D and Sbordoni, V and Todisco, V}, title = {COI Barcodes combined with multilocus data for representative Aporia taxa shed light on speciation in the high altitude Irano-Turanian mountain plateaus (Lepidoptera: Pieridae).}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {105}, pmid = {39095717}, issn = {2730-7182}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Iran ; *Phylogeny ; *Electron Transport Complex IV/genetics ; *Butterflies/genetics/classification ; Genetic Speciation ; Altitude ; Female ; Male ; }, abstract = {Even though the high plateaus of Qinghai-Tibet and Iran share many faunal elements, the historical biogeography of the species present in this area are not very well understood. We present a complete COI barcode library for Aporia Hübner and a first comprehensive phylogeny for the genus including all known species and majority of subspecies using ten available genes (COI-COII, ND1, ND5, Cytb, EF-1a, Wg, 16S, 28S-D2/D3 and 28S-D8). We then focus on A. leucodice (Eversmann, 1843) and related taxa in order to resolve some long-standing taxonomic issues in this species-group. Based on DNA sequence data as well as morphology, we raise Aporia illumina (Grum-Grshimailo 1890) stat. nov. (= pseudoillumina Tshikolovets 2021 syn. nov.) as a distinct species and designate a lectotype; synonymize Aporia leucodice leucodice Eversmann, 1843 (= A. l. morosevitshae Sheljuzhko, 1908 syn. nov.); and describe a new species, Aporia ahura sp. nov., from the Central Alborz Mountains in northern Iran.}, }
@article {pmid39095612, year = {2024}, author = {Underwood, O and Fritzwanker, S and Glenn, J and Blum, NK and Batista-Gondin, A and Drube, J and Hoffmann, C and Briddon, SJ and Schulz, S and Canals, M}, title = {Key phosphorylation sites for robust β-arrestin2 binding at the MOR revisited.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {933}, pmid = {39095612}, issn = {2399-3642}, support = {AMSPR/1013/AMS_/Academy of Medical Sciences/United Kingdom ; BB/T013966/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MRC IMPACT//RCUK | Medical Research Council (MRC)/ ; }, mesh = {Phosphorylation ; *beta-Arrestin 2/metabolism/genetics ; Humans ; *Receptors, Opioid, mu/metabolism/genetics ; HEK293 Cells ; Protein Binding ; Animals ; G-Protein-Coupled Receptor Kinases/metabolism/genetics ; }, abstract = {Desensitisation of the mu-opioid receptor (MOR) is proposed to underlie the initiation of opioid analgesic tolerance and previous work has shown that agonist-induced phosphorylation of the MOR C-tail contributes to this desensitisation. Moreover, phosphorylation is important for β-arrestin recruitment to the receptor, and ligands of different efficacies induce distinct phosphorylation barcodes. The C-tail [370]TREHPSTANT[379] motif harbours Ser/Thr residues important for these regulatory functions. [375]Ser is the primary phosphorylation site of a ligand-dependent, hierarchical, and sequential process, whereby flanking [370]Thr, [376]Thr and [379]Thr get subsequently and rapidly phosphorylated. Here we used GRK KO cells, phosphosite specific antibodies and site-directed mutagenesis to evaluate the contribution of the different GRK subfamilies to ligand-induced phosphorylation barcodes and β-arrestin2 recruitment. We show that both GRK2/3 and GRK5/6 subfamilies promote phosphorylation of [370]Thr and [375]Ser. Importantly, only GRK2/3 induce phosphorylation of [376]Thr and [379]Thr, and we identify these residues as key sites to promote robust β-arrestin recruitment to the MOR. These data provide insight into the mechanisms of MOR regulation and suggest that the cellular complement of GRK subfamilies plays an important role in determining the tissue responses of opioid agonists.}, }
@article {pmid39091743, year = {2024}, author = {Bernadskaya, YY and Kuan, A and Tjärnberg, A and Brandenburg, J and Zheng, P and Wiechecki, K and Kaplan, N and Failla, M and Bikou, M and Madilian, O and Wang, W and Christiaen, L}, title = {Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39091743}, issn = {2692-8205}, support = {R01 HD096770/HD/NICHD NIH HHS/United States ; R01 HL108643/HL/NHLBI NIH HHS/United States ; }, abstract = {During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10(+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process "transcriptome maturation", and identified candidate "mature genes", including the Rho GAP-coding gene Depdc1, which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.}, }
@article {pmid39091496, year = {2024}, author = {Hulen, TM and Friese, C and Kristensen, NP and Granhøj, JS and Borch, TH and Peeters, MJW and Donia, M and Andersen, MH and Hadrup, SR and Svane, IM and Met, &#xd6;}, title = {Corrigendum: Ex vivo modulation of intact tumor fragments with anti-PD-1 and anti-CTLA-4 influences the expansion and specificity of tumor-infiltrating lymphocytes.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1462081}, doi = {10.3389/fimmu.2024.1462081}, pmid = {39091496}, issn = {1664-3224}, abstract = {[This corrects the article DOI: 10.3389/fimmu.2023.1180997.].}, }
@article {pmid39091449, year = {2024}, author = {Hübner, J and Chemyreva, V and Macek, J and Kolyada, V}, title = {A review of the genus Zygota (Hymenoptera, Diapriidae) in Germany with taxonomic notes on this genus and its distinction from Pantoclis.}, journal = {ZooKeys}, volume = {1207}, number = {}, pages = {325-353}, pmid = {39091449}, issn = {1313-2989}, abstract = {This study provides a comprehensive overview of the genus Zygota Förster combining DNA barcoding and current morphology. Nineteen species of Zygota were found throughout Germany, including the newly described species Zygotawalli sp. nov. First species records for Germany are: Zygotabalteata Macek, 1997; Z.comitans Macek, 1997; Z.spinosipes (Kieffer, 1908); Z.sordida Macek, 1997; Z.angularis Macek, 1997 and Z.vigil Nixon, 1957. We also clarify diagnoses for the two related genera, Pantoclis Förster and Zygota to designate the boundaries of the Zygota genus and propose new synonymies: Zygotacaligula Buhl, 1997 is a junior synonym of Z.congener (Zetterstedt, 1840); Z.reticulata Kozlov, 1978 is a junior synonym of Z.ruficornis (Curtis, 1831). Thirteen species of Zygota sensu Nixon (1957) are transferred to the genus Pantoclis with the following new combinations proposed: Zygotabrevinervis (Kieffer, 1908) (= Pantoclisbrevinervis (Kieffer, 1909), comb. nov.); Z.brevipennis (Kieffer, 1908) (= P.brevipennis (Kieffer, 1908), comb. nov.); Z.caecutiens (Kieffer, 1908) (= P.caecutiens (Kieffer, 1908), comb. nov.); Z.cursor (Kieffer, 1908) (= P.cursor (Kieffer, 1908), comb. nov.); Z.fossulata (Thomson, 1858) (=P.fossulata (Thomson, 1858), comb. nov.); Z.fuscata (Thomson, 1858) (= P.fuscata (Thomson, 1858), comb. nov.); Z.hemiptera (Thomson, 1858) (= P.hemiptera (Thomson, 1858), comb. nov.); Z.microtoma (Kieffer, 1909) (= P.microtoma (Kieffer, 1909), comb. nov.); Z.soluta (Kieffer, 1907) (= P.soluta (Kieffer, 1907), comb. nov.); Z.striata (Kieffer, 1909) (= P.striata (Kieffer, 1909), comb. nov.); Z.subaptera (Thomson, 1858) (= P.subaptera (Thomson, 1858), comb. nov.); Z.sulciventris (Kieffer, 1909) (= P.sulciventris (Kieffer, 1909), comb. nov.), and Z.unicolor (Kieffer, 1908) (= P.unicolor (Kieffer, 1908), comb. nov.).}, }
@article {pmid39090851, year = {2024}, author = {Di Nunzio, M and Barrot-Feixat, C and Gangitano, D}, title = {Characterization and evaluation of nine Cannabis sativa chloroplast SNP markers for crop type determination and biogeographical origin on European samples.}, journal = {Forensic science international. Genetics}, volume = {68}, number = {}, pages = {102971}, doi = {10.1016/j.fsigen.2023.102971}, pmid = {39090851}, issn = {1878-0326}, mesh = {*Cannabis/genetics ; Genetic Markers ; *Polymorphism, Single Nucleotide ; *DNA, Chloroplast/genetics ; Mexico ; Polymerase Chain Reaction ; Europe ; Italy ; Chile ; Spain ; }, abstract = {Cannabis sativa can be classified in two main types, according to psychotropic cannabinoid ∆9-tetrahydrocannabinol (∆9-THC) content: the drug-type and the fiber-type. According to the European Monitoring Center for Drugs and Drug Addiction, most of the European Union countries consider the possession of cannabis, for personal use, a minor offense with possibility of incarceration. Despite of the model of legal supply (i.e., Spanish cannabis clubs, Netherlands coffee shops) or medical use (i.e., Italy), cannabis remains the most used and trafficked illicit plant in the European Union. Differentiating cannabis crops or tracing the biogeographical origin is crucial for law enforcement purposes. Chloroplast DNA (cpDNA) markers may assist to determine biogeographic origin and to differentiate hemp from marijuana. This research aims: to identify and to evaluate nine C. sativa cpDNA polymorphic SNP sites to differentiate crop type and to provide information about its biogeographical origin. Five SNaPshot™ assays for nine chloroplast markers were developed and conducted in marijuana samples seized in Chile, the USA-Mexico border and Spain, and hemp samples grown in Spain and in Italy. The SNapShot™ assays were tested on 122 cannabis samples, which included 16 blind samples, and were able to differentiate marijuana crop type from hemp crop type in all samples. Using phylogenetic analysis, genetic differences were observed between marijuana and hemp samples. Moreover, principal component analysis (PCA) supported the relationship among hemp samples, as well as for USA-Mexico border, Spanish, and Chilean marijuana samples. Genetic differences between groups based on the biogeographical origin and their crop type were observed. Increasing the number of genetic markers, including the most recently studied ones, and expanding the sample database will provide more accurate information about crop differentiation and biogeographical origin.}, }
@article {pmid39086104, year = {2024}, author = {Macher, JN and Martínez, A and Çakir, S and Cholley, PE and Christoforou, E and Curini Galletti, M and van Galen, L and García-Cobo, M and Jondelius, U and de Jong, D and Leasi, F and Lemke, M and Rubio Lopez, I and Sánchez, N and Sørensen, MV and Todaro, MA and Renema, W and Fontaneto, D}, title = {Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna.}, journal = {Molecular ecology resources}, volume = {24}, number = {7}, pages = {e13997}, doi = {10.1111/1755-0998.13997}, pmid = {39086104}, issn = {1755-0998}, support = {T0206/37197/2021/kg//Stemmler Foundation/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Netherlands ; Biodiversity ; North Sea ; Invertebrates/genetics/classification ; Bathing Beaches ; Ecosystem ; Metagenomics/methods ; }, abstract = {Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.}, }
@article {pmid39080687, year = {2024}, author = {Modimo, MY and Bernt, MJ and Monsembula Iyaba, RJC and Mbimbi, JJMM and Liyandja, TLD}, title = {Parauchenoglanis stiassnyae (Siluriformes: Auchenoglanididae): A new species of giraffe catfish from Mfimi-Lukenie basin, central Africa, Democratic Republic of Congo.}, journal = {Journal of fish biology}, volume = {105}, number = {4}, pages = {1227-1239}, doi = {10.1111/jfb.15885}, pmid = {39080687}, issn = {1095-8649}, support = {1655227//National Science Foundation Graduate Research Fellowship Program/ ; //Axelrod Research curatorship (MJLS)/ ; }, mesh = {Animals ; *Catfishes/classification ; Democratic Republic of the Congo ; *Rivers ; Male ; Female ; Spine/anatomy &amp; histology ; }, abstract = {A new, distinctively short-bodied giraffe catfish of Parauchenoglanis is described from the Ndzaa River, a small left-bank tributary of the Mfimi-Lukenie basin in the Central basin of the Congo River in the Democratic Republic of the Congo. The new species can be distinguished from all congeners by having 29 or fewer (vs. 33 or more) total vertebrae. It can further be distinguished from all congeners, except Parauchenoglanis zebratus Sithole et al., 2023 and Parauchenoglanis ngamensis (Boulenger 1911), by having 13 or 14 (vs. 16 or more) pre-anal vertebrae. The species is endemic to the Mfimi River basin, where it has been collected mainly in blackwater tributaries.}, }
@article {pmid39080149, year = {2024}, author = {Barman, M and Bhushan, S and Phukan, B and Kumar, AP and Jaiswar, AK and Talukdar, A and Kalita, R and S, S}, title = {Molecular identification and phylogenetic relationship of fishes belonging to the Family Danionidae from Brahmaputra Basin, Assam, Northeast India.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {875}, pmid = {39080149}, issn = {1573-4978}, support = {FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; FISH/30/2017-FISHERY/27(eCFNo.43140)//SCoPIF, Government of Assam/ ; }, mesh = {Animals ; *Phylogeny ; India ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Fishes/genetics/classification ; DNA, Mitochondrial/genetics ; Biodiversity ; }, abstract = {BACKGROUD: The Northeast India, being part of two global biodiversity hotspot namely the Indo-Burma and Eastern Himalayan Hotspots supports a wide variety of rich aquatic biodiversity including fishes. The family Danionidae is a widely diverse group inhabiting the upper colder stretches of river although few are abundant in the lower stretches. The persisting similarity in the morphological appearance and body colouration within the members of this family seeks an integrated method to identify the species correctly.<br><br>METHODS AND RESULTS: In the present study, the mt-DNA barcode was generated for correct identification and confirmation of the species. A total of nine mitochondrial cytochrome c oxidase subunit I gene sequences were generated for each species under the study. The pairwise distance values ranged from 0.09 to 9.11% within species and 9.06-32.71% between species. A neighbour-joining tree was constructed based on the Kimura 2 parameter model. Two major groups were observed where Danioninae formed a sister group to the Chedrinae and Rasborinae.<br><br>CONCLUSION: The present study is a preliminary work to document and identify the species under the family Danionidae from Brahmaputra basin, Assam, using molecular tools and establish the phylogenetic relationship.}, }
@article {pmid39076800, year = {2024}, author = {Yoshimura, H and Hayakawa, T and Kikuchi, DM and Zhumabai Uulu, K and Qi, H and Sugimoto, T and Sharma, K and Kinoshita, K}, title = {Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard.}, journal = {Royal Society open science}, volume = {11}, number = {5}, pages = {240132}, pmid = {39076800}, issn = {2054-5703}, abstract = {Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.}, }
@article {pmid39075103, year = {2024}, author = {Lovell, MS and Polito, MJ and Schuster, JA and Shallow, EE and Janosik, AM and Falterman, BJ and Dance, MA}, title = {Seasonal variability in the feeding ecology of an oceanic predator.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17353}, pmid = {39075103}, issn = {2045-2322}, mesh = {Animals ; *Seasons ; *Predatory Behavior/physiology ; Food Chain ; Feeding Behavior/physiology ; Tuna/physiology ; Carbon Isotopes/analysis ; Diet ; DNA Barcoding, Taxonomic ; Gulf of Mexico ; Nitrogen Isotopes/analysis ; Ecosystem ; }, abstract = {Complementary approaches (stomach contents, DNA barcoding, and stable isotopes) were used to examine seasonal shifts in the feeding ecology of an oceanic predator, yellowfin tuna (Thunnus albacares, n = 577), in the northern Gulf of Mexico. DNA barcoding greatly enhanced dietary resolution and seasonally distinct prey assemblages were observed for both sub-adults and adults. In general, diet was characterized by ommastrephid squids and exocoetids in spring, juvenile fishes (i.e., carangids and scombrids) in summer, migratory coastal fishes during fall, and an increased consumption of planktonic prey (e.g., amphipods) in winter. Seasonal variability in bulk stable isotope values (δ[13]C, δ[15]N, and δ[34]S) was also observed, with low δ[15]N values and high δ[34]S values during late summer/early fall and high δ[15]N values (low δ[34]S) during late winter/early spring. Bayesian stable isotope mixing models corroborated seasonal diet shifts, highlighting the importance of oceanic nekton in spring/summer, coastal nekton during fall, and oceanic plankton during winter. Seasonal shifts in diet appeared to be influenced by prey reproductive cycles, habitat associations, and environmental conditions. Findings highlight the complex food web dynamics supporting an opportunistic oceanic predator and the importance of seasonal cycles in prey availability to predator resource utilization in open-ocean ecosystems.}, }
@article {pmid39071290, year = {2024}, author = {Shibata, D}, title = {Human Brain Ancestral Barcodes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39071290}, issn = {2692-8205}, support = {P01 CA196569/CA/NCI NIH HHS/United States ; R01 CA271237/CA/NCI NIH HHS/United States ; }, abstract = {Dynamic CpG methylation "barcodes" were read from 15,000 to 21,000 single cells from three human male brains. To overcome sparse sequencing coverage, the barcode had ~31,000 rapidly fluctuating X-chromosome CpG sites (fCpGs), with at least 500 covered sites per cell and at least 30 common sites between cell pairs (average of ~48). Barcodes appear to start methylated and record mitotic ages because excitatory neurons and glial cells that emerge later in development were less methylated. Barcodes are different between most cells, with average pairwise differences (PWDs) of ~0.5 between cells. About 10 cell pairs per million were more closely related with PWDs < 0.05. Barcodes appear to record ancestry and reconstruct trees where more related cells had similar phenotypes, albeit some pairs had phenotypic differences. Inhibitory neurons showed more evidence of tangential migration than excitatory neurons, with related cells in different cortical regions. fCpG barcodes become polymorphic during development and can distinguish between thousands of human cells.}, }
@article {pmid39071121, year = {2024}, author = {Pozzobon, APB and Ready, JS and Di Dario, F and Nunes-da-Fonseca, R}, title = {Identification of pre-flexion fish larvae from the western South Atlantic using DNA barcoding and morphological characters.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17791}, pmid = {39071121}, issn = {2167-8359}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Larva/anatomy &amp; histology/genetics/growth &amp; development ; *Fishes/anatomy &amp; histology/genetics ; Brazil ; *Electron Transport Complex IV/genetics ; Phylogeny ; Atlantic Ocean ; Species Specificity ; }, abstract = {Knowledge on species composition is the first step necessary for the proper conservation and management of biological resources and ecologically relevant species. High species diversity and a lack of diagnostic characters for some groups can impose difficulties for taxonomic identification through traditional methodologies, and ichthyoplankton (fish larvae and eggs) are a good example of such a scenario. With more than 35.000 valid species of fishes worldwide and overall similar anatomies in early developmental stages in closely related groups, fish larvae are often hard to be identified at the species or even more encompassing taxonomic levels. To overcome this situation, molecular techniques have been applied, with different markers tested over the years. Cytochrome c oxidase I (COI) is the most commonly used marker and now has the broadest public reference libraries, providing consistent results for species identification in different metazoan studies. Here we sequenced the mitochondrial COI-5P fragment of 89 fish larvae collected in the Campos Basin, coastal southeastern Brazil, and compared these sequences with references deposited in public databases to obtain taxonomic identifications. Most specimens identified are species of the Blenniiformes, with Parablennius and Labrisomus the most frequently identified genera. Parablennius included two species (P. marmoreus and P. pilicornis), while Labrisomus included three species (L. cricota, L. conditus and L. nuchipinnis). Anatomy of these molecularly identified specimens were then analyzed with the intention of finding anatomical characters that might be diagnostically informative amongst the early development stage (pre-flexion) larvae. Ventral pigmentation patterns are proposed as useful markers to identify Labrisomus species. However, additional specimens are needed to confirm if the character holds stability through the geographic distribution of the species.}, }
@article {pmid39070712, year = {2024}, author = {Quek, ZBR and Yip, ZT and Jain, SS and Wong, HXV and Tan, Z and Joseph, AR and Huang, D}, title = {DNA barcodes are ineffective for species identification of Acropora corals from the aquarium trade.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e125914}, pmid = {39070712}, issn = {1314-2828}, abstract = {Species identification of stony corals (Scleractinia), which are regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora, is critical for effective control of harvest quotas, enforcement of trade regulations and species conservation in general. DNA barcoding has the potential to enhance species identification success, depending on the specific taxon concerned and genetic markers used. For Acropora, DNA barcoding, based on the mitochondrial putative control region (mtCR) and the nuclear PaxC intron (PaxC), has been commonly used for species identification and delimitation, but the reliability and robustness of these loci remain contentious. Therefore, we sought to verify the applicability of this approach. In this study, we obtained 127 Acropora colonies from the aquarium trade to test the effectiveness of barcoding mtCR and PaxC for species identification. We were able to recover sequences for both loci in over half of the samples (n = 68), while gene amplification and sequencing of mtCR (n = 125) outperformed PaxC (n = 70). Amongst the 68 samples with both loci recovered, just a single sample could be unambiguously identified to species. Preliminary identities, based on only one gene, were assigned for 40 and 65 samples with mtCR and PaxC, respectively. Further analyses of 110 complete mitochondrial genomes obtained from GenBank showed that, despite the full length of the sequences, only eight species were delimited, of which only three species were correspondingly monophyletic. Therefore, we conclude that the commonly used DNA barcoding markers for Acropora are ineffective for accurate species assignments due to limited variability in both markers and even across the entire mitochondrial genome. Therefore, we propose that barcoding markers should generally not be the only means for identifying corals.}, }
@article {pmid39065533, year = {2024}, author = {Tirrò, G and Conti Taguali, S and Pane, A and Riolo, M and Ezra, D and Cacciola, SO}, title = {Outbreak of Alternaria Black Spot of Pomegranate (Punica granatum L.) in Italy as a Consequence of Unusual Climatic Conditions.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {14}, pages = {}, pmid = {39065533}, issn = {2223-7747}, abstract = {Alternaria black spot of pomegranate (Punica granatum) was reported for the first time in Italy. In spring 2023, an outbreak of this disease was noticed in commercial pomegranate 'Wonderful' orchards of the municipality of Misterbianco (Sicily), following an unusually rainy period. A total of 30 randomly selected Alternaria isolates recovered from typical necrotic spots of leaves and fruits were characterized. Based on the colony morphology on solid agar media (PDA and MEA), isolates were separated into three distinct morphotypes (1, 2, and 3). The first two morphotypes comprised only isolates from fruits, while morphotype 3 comprised only isolates from leaves. Multigene phylogenetic analysis of four DNA regions, including internal transcribed spacer (ITS), translation elongation factor 1-α (EF-1α), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and a SCAR marker (OPA10-2), identified the isolates of morphotypes 1 and 2 as Alternaria alternata and morphotype 3 isolates as A. arborescens. In pathogenicity tests on unwounded leaves and fruit, the isolates of all three morphotypes produced symptoms on the leaves of three pomegranate cultivars, 'Acco', 'Wonderful', and 'Etna'. The symptoms on 'Acco' leaves were the least severe. Conversely, the fruits of 'Acco' were the most susceptible. The isolates of morphotypes 2 and 3 were not pathogenic on the fruits of 'Wonderful' and 'Etna'. This is the first report of Alternaria black spot in Italy and of A. arborescens associated with Alternaria black spot of pomegranate worldwide.}, }
@article {pmid39065505, year = {2024}, author = {Sokoloff, DD and Degtjareva, GV and Valiejo-Roman, CM and Severova, EE and Barinova, S and Chepinoga, VV and Kuzmin, IV and Sennikov, AN and Shmakov, AI and Skaptsov, MV and Smirnov, SV and Remizowa, MV}, title = {Kazakhstan Has an Unexpected Diversity of Medicinal Plants of the Genus Acorus (Acoraceae) and Could Be a Cradle of the Triploid Species A. calamus.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {14}, pages = {}, pmid = {39065505}, issn = {2223-7747}, support = {075-15-2021-1064//Ministry of Science and Higher Education of Russia/ ; FZMW-2023-0008//State Assignment of the Altai State University/ ; BR18574062//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {The Acorus calamus group, or sweet flag, includes important medicinal plants and is classified into three species: A. americanus (diploid), A. verus (tetraploid), and A. calamus (sterile triploid of hybrid origin). Members of the group are famous as components of traditional Indian medicine, and early researchers suggested the origin of the sweet flag in tropical Asia. Subsequent research led to an idea of the origin of the triploid A. calamus in the Amur River basin in temperate Asia, because this was the only region where both diploids and tetraploids were known to co-occur and be capable of sexual reproduction. Contrary to this hypothesis, triploids are currently very rare in the Amur basin. Here, we provide the first evidence that all three species occur in Kazakhstan. The new records extend earlier data on the range of A. verus for c. 1800 km. Along the valley of the Irtysh River in Kazakhstan and the adjacent Omsk Oblast of Russia, A. verus is recorded in the south, A. americanus in the north, and A. calamus is common in between. We propose the Irtysh River valley as another candidate for a cradle of the triploid species A. calamus. It is possible that the range of at least one parent species (A. americanus) has contracted through competition with its triploid derivative species, for which the Irtysh River floods provide a tool for downstream range expansion. We refine our earlier data and show that the two parent species have non-overlapping ranges of variation in a quantitative metric of leaf aerenchyma structure.}, }
@article {pmid39065465, year = {2024}, author = {Metouekel, A and Badrana, F and Kachkoul, R and Chebaibi, M and Akhazzane, M and El Moussaoui, A and Touil, N and El Amri, H and El Fahime, E and El Kazzouli, S and El Brahmi, N}, title = {Genetic Characterization and Chemical Identification of Moroccan Cannabis sativa (L.) Seeds: Extraction, and In Vitro and In Silico Biological Evaluation.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {14}, pages = {}, pmid = {39065465}, issn = {2223-7747}, abstract = {This study investigated the molecular, phytochemical, and biological aspects of ten local Moroccan traditional landrace Cannabis seeds. Genetic polymorphisms were analyzed using DNA barcode determination, revealing two distinct molecular profiles: "Cannabis, species sativa, subspecies indica" and "Cannabis, species sativa, subspecies sativa". Furthermore, a new sequence was identified by sequencing of the THCA synthase coding gene. Chemical profiling via HPLC-ESI-FULL-MS and GC-MS-MS of AMSD1 maceration extracts revealed 13 non-volatile chemicals, including 3 inactive cannabinoids and 3 polyphenols, and 24 intriguing volatile compounds, including 7 previously unreported in Cannabis seed extracts. Moreover, the in vitro/in silico analysis provision of biological activities through their antioxidant power, antimicrobial effect, and cytotoxicity potency, as well as antiviral activity, were realized. These results contribute to a thorough comprehension of Moroccan Cannabis seeds, illuminating their molecular, phytochemical, and biological features. Furthermore, they highlight the seeds as a potential source of nutritious components with antioxidant properties, offering valuable insights for future research.}, }
@article {pmid39062719, year = {2024}, author = {Zheng, HZ and Dai, W and Xu, MH and Lin, YY and Zhu, XL and Long, H and Tong, LL and Xu, XG}, title = {Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses.}, journal = {Genes}, volume = {15}, number = {7}, pages = {}, pmid = {39062719}, issn = {2073-4425}, mesh = {*Genome, Chloroplast ; *Evolution, Molecular ; *Phylogeny ; Chloroplasts/genetics ; Acanthaceae/genetics ; Polymorphism, Genetic ; }, abstract = {Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.}, }
@article {pmid39062644, year = {2024}, author = {Hopkins, L and Yim, K and Rumora, A and Baykus, MF and Martinez, L and Jimenez, L}, title = {Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities.}, journal = {Genes}, volume = {15}, number = {7}, pages = {}, pmid = {39062644}, issn = {2073-4425}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Rhizosphere ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *RNA, Ribosomal, 16S/genetics ; *Quercus/microbiology/genetics ; *Trees/microbiology/genetics ; Soil Microbiology ; Fagus/microbiology/genetics ; Fungi/genetics/classification ; Genotype ; Phylogeny ; Acer/microbiology/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.}, }
@article {pmid39059835, year = {2024}, author = {Pei, Y and Liu, Z and Yu, D and Zhang, X and Sun, W and Chen, X and Feng, X and Li, X}, title = {Molecular quantification of herbs (Herb-Q): a pyrosequencing-based approach and its application in Pinellia ternata.}, journal = {Chinese journal of natural medicines}, volume = {22}, number = {7}, pages = {663-672}, doi = {10.1016/S1875-5364(24)60636-9}, pmid = {39059835}, issn = {1875-5364}, mesh = {*Pinellia/genetics/chemistry ; *DNA Barcoding, Taxonomic/methods ; Polymorphism, Single Nucleotide ; DNA, Plant/genetics ; Sequence Analysis, DNA/methods ; Drugs, Chinese Herbal/chemistry ; Drug Contamination ; Plants, Medicinal/genetics/chemistry/classification ; }, abstract = {Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy. Accurate species quantification remains challenging, as current methods often yield inconsistent results. This study introduces a novel pyrosequencing-based technique, termed herb molecular quantification (Herb-Q), designed to precisely quantify herbal products. We evaluated its effectiveness using Pinellia ternata and five of its adulterants. Initially, we assessed commonly used DNA barcodes with sequences from a public database, identifying two candidate regions, Maturase K (matK) and internal transcribed spacer 2 (ITS2), for screening specific single nucleotide polymorphism (SNP) loci, allowing for species-specific identification. These loci were validated by amplifying and sequencing genomic material from collected samples. Our validation studies showed that Herb-Q demonstrated excellent linearity, accuracy, repeatability, and detection limits. We established quantitative standard curves with high R[2] values (> 0.99) to enable precise species quantification, which were combined with external standards to provide clear and accurate visual quantification results. The average bias in quantifying the tuber of P. ternata was 2.38%, confirming that Herb-Q can accurately identify and quantify herbal product constituents. Moreover, the entire quantification process took less than 4 h. This study presents a novel, rapid method for accurately quantifying species in herbal products and advances the application of DNA barcoding from species identification to quantitative detection.}, }
@article {pmid39057812, year = {2024}, author = {Aytenov, IS and Bozorov, TA and Zhang, D and Samadiy, SA and Muhammadova, DA and Isokulov, MZ and Murodova, SM and Zakirova, OR and Chinikulov, BK and Sherimbetov, AG}, title = {Uncovering the Antifungal Potential of Plant-Associated Cultivable Bacteria from the Aral Sea Region against Phytopathogenic Fungi.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39057812}, issn = {2076-0817}, support = {PZ-20200929166//Ministry of Innovative Development of Uzbekistan/ ; KFL-BRP-007-008//Biological resources programme, Chinese Academy of the Sciences/ ; }, mesh = {*Fungi/isolation &amp; purification/pathogenicity ; *Bacteria/isolation &amp; purification/drug effects/genetics ; *Rhizosphere ; Antifungal Agents/pharmacology ; Antibiosis/physiology ; Plant Diseases/microbiology/prevention &amp; control ; Plants/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {Two freshwater rivers, the Amu Darya and Syr Darya, flow into the Aral Sea, but they began to diminish in the early 1960s, and by the 1980s, the lake had nearly ceased to exist due to excessive water consumption for agriculture and the unsustainable management of water resources from rivers, which transformed the Aral Sea into a hypersaline lake. Despite this, the flora and fauna of the region began to evolve in the high-salinity seabed soil, which has received little attention in studies. In this study, we isolated approximately 1400 bacterial strains from the rhizosphere and phyllosphere of plant species of distinct families. Bacterial isolates were examined for antifungal activities against a range of pathogenic fungi such as Rhizoctonia gossypii, Trichothecium ovalisporum, Fusarium annulatum, F. oxysporum, F. culmorum, F. brachygibbosum, F. tricinctum, F. verticillioides, Alternaria alternata, A. terreus, Aspergillus niger, and As. flavus. Eighty-eight bacterial isolates exhibited varying antagonistic ability against pathogenic fungi. Furthermore, DNA barcoding of isolates using the 16S rRNA gene indicated that most antagonistic bacteria belonged to the Bacillus and Pseudomonas genera. The study also explored the activity of hydrolytic and cell-wall-degrading enzymes produced by antagonistic bacteria. The findings revealed that antagonistic bacteria can be utilized to widely protect seabed plants and plants growing in saline areas against pathogenic fungi, as well as agricultural crops.}, }
@article {pmid39057785, year = {2024}, author = {Zheng, JX and Sun, XH and Wei, X and Wang, G and Yuan, CQ and Weng, XD and Zuo, QQ and Liu, JY and Mu, ZQ and Mao, TC and Ding, YZ and Wang, XM and Wang, X and Wang, ZH}, title = {Species Composition of a Small Mammal Community and Prevalence of Echinococcus spp. in the Alpine Pastoral Area of the Eastern Tibetan Plateau.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39057785}, issn = {2076-0817}, support = {31071944//National Science Foundation of China/ ; 31470488//National Science Foundation of China/ ; 32071529//National Science Foundation of China/ ; }, mesh = {Animals ; Tibet/epidemiology ; *Echinococcosis/epidemiology/veterinary/parasitology ; Prevalence ; *Echinococcus/isolation &amp; purification/genetics ; *Rodentia/parasitology ; Lagomorpha/parasitology ; Mammals/parasitology ; }, abstract = {We aimed to investigate the species composition of a small mammal community and the prevalence of Echinococcus spp. in a typical endemic area of the Tibetan Plateau. One pika and five rodent species were identified based on the morphological characteristics of 1278 small mammal specimens collected during 2014-2019. Detection of Echinococcus DNA in tissue samples from small mammal specimens revealed that Ochotona curzoniae (pika, total prevalence: 6.02%, 26/432), Neodon fuscus (5.91%, 38/643), N. leucurus (2.50%, 3/120), and Alexandromys limnophilus (21.74%, 10/46) were infected by both E. multilocularis and E. shiquicus; Cricetulus longicaudatus (16.67%, 1/6) was infected by E. shiquicus; and no infection was detected in N. irene (0/15). Neodon fuscus and O. curzoniae were the two most abundant small mammal species. There was no significant difference in the prevalence of pika and the overall rodent species assemblage (6.26%, 53/846); however, the larger rodent populations suggested that more attention should be paid to their role in the transmission of echinococcosis in the wildlife reservoir, which has long been underestimated. Moreover, although DNA barcoding provides a more efficient method than traditional morphological methods for identifying large numbers of small mammal samples, commonly used barcodes failed to distinguish the three Neodon species in this study. The close genetic relationships between these species suggest the need to develop more powerful molecular taxonomic tools.}, }
@article {pmid39057752, year = {2024}, author = {Zhang, J and Jiamahate, A and Feng, H and Bozorov, TA and Zhang, D and Guo, J and Yang, H and Zhang, D}, title = {Distribution and Pathogenicity Differentiation of Physiological Races of Verticillium dahliae from Cotton Stems in Western China.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39057752}, issn = {2076-0817}, support = {31700289//National Natural Science Foundation of China/ ; ZDBS-LY-SM009//Key Research Program of Frontier Sciences, Chinese Academy of Sciences/ ; 2021-XBQNXZ-015//the West Light Talents Cultivation Program of the Chinese Academy of Sciences/ ; 2021xjkk0500//Third Xinjiang Scientific Expedition Program/ ; 2022D01A354//the Natural Science Foundation of the Xinjiang Uygur Autonomous Region/ ; }, mesh = {*Gossypium/microbiology ; China ; *Plant Diseases/microbiology ; Virulence/genetics ; *Ascomycota/genetics/pathogenicity/isolation &amp; purification ; Plant Stems/microbiology ; Genetic Variation/genetics ; Phylogeny ; Haplotypes ; Verticillium ; }, abstract = {Verticillium wilt, caused by the pathogenic fungus Verticillium dahliae, has emerged as a severe threat to cotton globally. However, little is known about the genetic diversity of this pathogen in an infected single cotton plant. In this study, we isolated three new V. dahliae strains from the disease stems of Gossypium hirsutum from the cotton field in Western China and assessed their pathogenicity to the cotton cultivar Xinnongmian-1 and its two transgenic lines, as well as two laboratory strains, VD592 and VD991. These three new V. dahliae strains were identified using DNA barcodes of tryptophan synthase (TS), actin (ACT), elongation factor 1-α (EF), and glyceraldehyde-3-phosphate dehydrogenase (GPD). Moreover, the haplotype analysis revealed that the three new races had distinct haplotypes at the TS locus. Furthermore, the results of culture features and genetic diversity of ISSR (inter-simple sequence repeat) revealed that there were separate V. dahliae strains, which were strong defoliating pathotypes belonging to race 2 type, as determined by particular DNA marker recognition. The identified strains demonstrated varied levels of pathogenicity by leaf disc and entire plant inoculation methods. Conservatively, these strains showed some pathogenicity on cotton lines, but were less pathogenic than the reference strains. The findings revealed that several strong defoliating V. dahliae pathotypes coexist on the same cotton plant. It indicats the importance of regular monitoring as an early warning system, as well as the detection and reporting of virulent pathogen strains and their effects on crop response.}, }
@article {pmid39057277, year = {2024}, author = {Lukhtanov, VA and Dantchenko, AV}, title = {Cryptic Taxa Revealed through Combined Analysis of Chromosomes and DNA Barcodes: The Polyommatus ripartii Species Complex in Armenia and NW Iran.}, journal = {Insects}, volume = {15}, number = {7}, pages = {}, pmid = {39057277}, issn = {2075-4450}, support = {24-14-00047//Russian Science Foundation/ ; }, abstract = {The detection of cryptic species in complexes that have undergone recent speciation is often difficult, since many standard nuclear markers have not yet accumulated differences between closely related taxa, and differences in mitochondrial markers can be leveled out due to mitochondrial introgressions. In these cases, the use of derived chromosomal characters such as non-ancestral chromosomal numbers and/or unusual karyotype features may be a solution to the species delimitation problem. However, non-ancestral but similar karyotypes may arise secondarily as a result of homoplastic evolution, and their interpretation as homologies may lead to incorrect taxonomic conclusions. In our study, we show that the combined use of mitochondrial DNA barcodes and karyotypes helps to solve this problem and identifies cryptic species in situations where each of these markers does not work individually. Using this approach, we show that the fauna of Armenia and adjacent Iran includes the following cryptic taxa of the Polyommatus ripartii species complex (haploid chromosome number, n in parentheses): P. ripartii paralcestis (n = 90), P. ripartii kalashiani, subsp. nov (n close to 90), P. emmeli, sp. nov. (n = 77-79), P. keleybaricus, sp. nov. (n = 86), P. demavendi belovi (n = 73-75), P. demavendi antonius, subsp. nov. (n = 71-73), P. admetus anatoliensis (n = 79) and P. eriwanensis (n = 29-34). Polyommatus admetus yeranyani is synonymized with P. admetus anatoliensis.}, }
@article {pmid39057251, year = {2024}, author = {Kocić, K and Mjǿs, AT and Čkrkić, J and Petrović, A and Popović, N and Paulsen, ES and Tomanović, &#x17d;}, title = {Uncovering Norway: Descriptions of Four New Aphidiinae Species (Hymenoptera, Braconidae) with Identification Key and Notes on Phylogenetic Relationships of the Subgenus Fovephedrus Chen.}, journal = {Insects}, volume = {15}, number = {7}, pages = {}, pmid = {39057251}, issn = {2075-4450}, support = {451-03-65/2024-03/200178//Ministry of Science, Technological Development and Innovation of Serbia/ ; F131//Serbian Academy of Sciences and Arts/ ; }, abstract = {With only 33 reported species, Norway ranks among the European countries with the lowest documented diversity of parasitoids from the subfamily Aphidiinae. The "MUST Malaise" project, carried out by Museum Stavanger in Norway, aimed to assess insect abundance and biodiversity and create a reference base for future studies. The preliminary results of our study revealed four species new to science, indicating that the current number of recorded species in Norway is significantly lower than the actual diversity. All species possess unique combinations of morphological characters, distinguishing them from other known Aphidiinae species. Molecular analysis of the barcoding region confirmed that these specimens all belong to the previously undescribed species. In this study, we describe Aphidius norvegicus sp.n., Praon breviantennalis sp.n., Ephedrus gardenforsi sp.n., and Ephedrus borealis sp.n., all collected in Norway. We also provide an identification key and discuss the phylogenetic relationships within the subgenus Fovephedrus Chen, 1986.}, }
@article {pmid39057241, year = {2024}, author = {Liu, J and Xu, H and Wang, Z and Li, P and Yan, Z and Bai, M and Li, J}, title = {Phylogenetics, Molecular Species Delimitation and Geometric Morphometrics of All Reddish-Brown Species in the Genus Neotriplax Lewis, 1887 (Coleoptera: Erotylidae: Tritomini).}, journal = {Insects}, volume = {15}, number = {7}, pages = {}, pmid = {39057241}, issn = {2075-4450}, support = {No. 31750002//National Natural Science Foundation of China/ ; No. 22326507D//Special Project of Technological innovation for Rural Revitalization/ ; No. 2020GDASYL-20200102021//GDAS Special Project of Science and Technology Development/ ; No. C2023204114//Hebei Provincial Natural Science Foundation/ ; }, abstract = {To date, five species of reddish-brown Neotriplax have been described, but their highly similar body color and other phenotypic traits make accurate taxonomy challenging. To clarify species-level taxonomy and validate potential new species, the cytochrome oxidase subunit I (COI) was used for phylogenetic analysis and the geometric morphometrics of elytron, pronotum, and hind wing were employed to distinguish all reddish-brown Neotriplax species. Phylogenetic results using maximum likelihood and Bayesian analyses of COI sequences aligned well with the current taxonomy of the Neotriplax species group. Significant K2P divergences, with no overlap between intra- and interspecific genetic distances, were obtained in Neotriplax species. The automatic barcode gap discovery (ABGD), assemble species by automatic partitioning (ASAP), and generalized mixed Yule coalescent (GMYC) approaches concurred, dividing the similar species into eight molecular operational taxonomic units (MOTUs). Geometric morphometric analysis using pronotum, elytron, hind wing shape and wing vein patterns also validated the classification of all eight species. By integrating these analytical approaches with morphological evidence, we successfully delineated the reddish-brown species of Neotriplax into eight species with three new species: N. qinghaiensis sp. nov., N. maoershanensis sp. nov., and N. guangxiensis sp. nov. Furthermore, we documented the first record of N. lewisii in China. This study underscores the utility of an integrative taxonomy approach in species delimitation within Neotriplax and serves as a reference for the taxonomic revision of other morphologically challenging beetles through integrative taxonomy.}, }
@article {pmid39057230, year = {2024}, author = {Xi, O and Zhang, S and Li, J and Hu, H and Bai, M}, title = {Geometric Morphometrics and Genetic Diversity Analysis of Chalcidoidea (Diglyphus and Pachyneuron) at Various Elevations.}, journal = {Insects}, volume = {15}, number = {7}, pages = {}, pmid = {39057230}, issn = {2075-4450}, support = {No. 31860612//National Key Research and Development Program of China/ ; No. 32070472//National Key Research and Development Program of China/ ; }, abstract = {Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps.}, }
@article {pmid39055168, year = {2024}, author = {Guo, W and Liu, Y and Han, Y and Tang, H and Fan, X and Wang, C and Chen, PR}, title = {Amplifiable protein identification via residue-resolved barcoding and composition code counting.}, journal = {National science review}, volume = {11}, number = {7}, pages = {nwae183}, pmid = {39055168}, issn = {2053-714X}, abstract = {Ultrasensitive protein identification is of paramount importance in basic research and clinical diagnostics but remains extremely challenging. A key bottleneck in preventing single-molecule protein sequencing is that, unlike the revolutionary nucleic acid sequencing methods that rely on the polymerase chain reaction (PCR) to amplify DNA and RNA molecules, protein molecules cannot be directly amplified. Decoding the proteins via amplification of certain fingerprints rather than the intact protein sequence thus represents an appealing alternative choice to address this formidable challenge. Herein, we report a proof-of-concept method that relies on residue-resolved DNA barcoding and composition code counting for amplifiable protein fingerprinting (AmproCode). In AmproCode, selective types of residues on peptides or proteins are chemically labeled with a DNA barcode, which can be amplified and quantified via quantitative PCR. The operation generates a relative ratio as the residue-resolved 'composition code' for each target protein that can be utilized as the fingerprint to determine its identity from the proteome database. We developed a database searching algorithm and applied it to assess the coverage of the whole proteome and secretome via computational simulations, proving the theoretical feasibility of AmproCode. We then designed the residue-specific DNA barcoding and amplification workflow, and identified different synthetic model peptides found in the secretome at as low as the fmol/L level for demonstration. These results build the foundation for an unprecedented amplifiable protein fingerprinting method. We believe that, in the future, AmproCode could ultimately realize single-molecule amplifiable identification of trace complex samples without further purification, and it may open a new avenue in the development of next-generation protein sequencing techniques.}, }
@article {pmid39054884, year = {2024}, author = {Cilia, G and Caringi, V and Zavatta, L and Bortolotti, L}, title = {Pathogen occurrence in different developmental stages of the invasive Vespa velutina nigrithorax (Buysson, 1905).}, journal = {Pest management science}, volume = {80}, number = {11}, pages = {5909-5917}, doi = {10.1002/ps.8325}, pmid = {39054884}, issn = {1526-4998}, support = {2021/2115//Regulation (EU) of the European Parliament and of the Council/ ; }, mesh = {Animals ; *Wasps/virology/physiology/growth &amp; development ; *Introduced Species ; Nosema/physiology ; Bees/virology ; DNA, Mitochondrial/genetics ; Larva/virology/growth &amp; development ; Italy ; RNA Viruses/physiology/genetics ; Pupa/virology/growth &amp; development ; }, abstract = {BACKGROUND: The yellow-legged hornet (Vespa velutina nigrithorax) is a predatory species native to South-East Asia. The hornet is invasive in Europe, spreading to several countries and becoming a pest for Apis mellifera due to its behaviour of preying in front of apiaries. The aim of this study was (i) to investigate the presence of honey bee pathogens within the developmental stages of V. velutina after neutralizing a nest in Bologna province (Emilia-Romagna, Italy) and (ii) to analyze the mitochondrial DNA to determine if the population derived from the population initially introduced in Europe.<br><br>RESULTS: The results indicated that deformed wing virus (82.76%) and Nosema ceranae (67.28%) were the most prevalent pathogens. Deformed wing virus, N. ceranae and sacbrood virus were found in all investigated stages, while chronic bee paralysis virus and Kashmir bee virus were exclusively found in foraging adults. All detected viruses were found to be replicative, highlighting active infection in the hosts. The mtDNA analysis demonstrated that the origin derived from the invasive population arrived in France.<br><br>CONCLUSION: This study underscores the importance of further research to understand the effect of interspecific transmission, especially concerning the potential role of these pathogens as a biocontrol for the invasive V. velutina nigrithorax. &#xa9; 2024 Society of Chemical Industry.}, }
@article {pmid39052818, year = {2024}, author = {Kawaoka, J and Lomvardas, S}, title = {Barcoding distinct neurons.}, journal = {Science (New York, N.Y.)}, volume = {385}, number = {6707}, pages = {370-371}, doi = {10.1126/science.adq5225}, pmid = {39052818}, issn = {1095-9203}, mesh = {Animals ; Humans ; Mice ; *Neurons/cytology/physiology ; *Gene Expression Regulation ; *Cohesins/genetics ; *Cadherins/genetics/metabolism ; }, abstract = {The genomic landscape of a cell surface protein reveals how neuron identity is displayed.}, }
@article {pmid39051761, year = {2024}, author = {Feng, J and Ren, Q and Xie, A and Jiang, Z and Liu, Y}, title = {High-resolution melting analysis to authenticate deer-derived materials in processed products in China using a cytochrome oxidase I mini-barcode.}, journal = {Journal of the science of food and agriculture}, volume = {104}, number = {15}, pages = {9390-9398}, doi = {10.1002/jsfa.13761}, pmid = {39051761}, issn = {1097-0010}, support = {ZDKJ2021034//Hainan Province Science and Technology Special Fund Program/ ; 2022wnkj10//Wanning City Scientific Research Program/ ; }, mesh = {*Deer ; Animals ; China ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic ; *Antlers/chemistry ; Transition Temperature ; Food Contamination/analysis ; DNA/analysis ; Bone and Bones/chemistry ; }, abstract = {BACKGROUND: Deer-derived materials (antler, venison, fetus, penis, bone, tail, and others) are some of the most valuable traditional animal-based medicinal and food materials in China. In production, processing, and trade, the quality of deer products varies. The market is confusing, and counterfeit and shoddy products are common. There is an urgent need to establish an accurate identification method.<br><br>RESULTS: Two pairs of primers suitable for identifying deer-derived medicinal materials were obtained by screening the cytochrome oxidase I (COI) sequences of 18 species from nine genera of the deer family. The two primers were used to identify the species and adulteration of 22 batches of commercially available deer-derived products with a mini-barcode combining high-resolution melting (HRM) technology and methodical investigation. Deer-derived materials (sika and red deer) were correctly identified by species using varying DNA amounts (1 to 500 ng). The two pairs of primers COI-1FR and COI-2FR yielded melting temperatures (Tm) of 80.55 to 81.00&#x2009;&#xb0;C and 82.00 to 82.50&#x2009;&#xb0;C for sika deer, and 81.00 to 82.00&#x2009;&#xb0;C and 81.40 to 82.00&#x2009;&#xb0;C for red deer. Twenty-two batches of commercially available samples were analyzed by HRM analysis and conventional amplification sequencing, and it was found that the species samples had an error rate of species labeling of 31.8%. Four batches of samples were identified as mixed (adulterated) in the HRM analysis.<br><br>CONCLUSION: The combination of DNA mini-barcode with HRM analysis facilitated the accurate identification of species of deer-derived materials, especially the identification of samples in an adulterated mixed state. &#xa9; 2024 Society of Chemical Industry.}, }
@article {pmid39051560, year = {2024}, author = {Odunze, U and Rustogi, N and Devine, P and Miller, L and Pereira, S and Vashist, S and Snijder, HJ and Corkill, D and Sabirsh, A and Douthwaite, J and Bond, N and Desai, A}, title = {RNA encoded peptide barcodes enable efficient in vivo screening of RNA delivery systems.}, journal = {Nucleic acids research}, volume = {52}, number = {16}, pages = {9384-9396}, pmid = {39051560}, issn = {1362-4962}, support = {//AstraZeneca R&amp;D/ ; //AstraZeneca RNA Therapy/ ; }, mesh = {Animals ; *Peptides/chemistry ; Mice ; *Nanoparticles/chemistry ; RNA, Messenger/genetics/metabolism ; Humans ; Lipids/chemistry ; RNA/genetics/chemistry/metabolism ; Genes, Reporter ; Liposomes ; }, abstract = {Lipid nanoparticles (LNPs) have been demonstrated to hold great promise for the clinical advancement of RNA therapeutics. Continued exploration of LNPs for application in new disease areas requires identification and optimization of leads in a high throughput way. Currently available high throughput in vivo screening platforms are well suited to screen for cellular uptake but less so for functional cargo delivery. We report on a platform which measures functional delivery of LNPs using unique peptide 'barcodes'. We describe the design and selection of the peptide barcodes and the evaluation of these for the screening of LNPs. We show that proteomic analysis of peptide barcodes correlates with quantification and efficacy of barcoded reporter proteins both in vitro and in vivo and, that the ranking of selected LNPs using peptide barcodes in a pool correlates with ranking using alternative methods in groups of animals treated with individual LNPs. We show that this system is sensitive, selective, and capable of reducing the size of an in vivo study by screening up to 10 unique formulations in a single pool, thus accelerating the discovery of new technologies for mRNA delivery.}, }
@article {pmid39045589, year = {2024}, author = {Arya, V and Narayana, S and Sinha, T and Kandan, A and Satyanarayana Raju, SV}, title = {A simple PCR-based quick detection of the economically important oriental fruit fly, Bactrocera dorsalis (Hendel) from India.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1399718}, pmid = {39045589}, issn = {1664-462X}, abstract = {The oriental fruit fly, Bactrocera dorsalis (Hendel), is a significant economic and quarantine pest due to its polyphagous nature. The accurate identification of B. dorsalis is challenging at the egg, maggot, and pupal stages, due to lack of distinct morphological characters and its similarity to other fruit flies. Adult identification requires specialized taxonomist. Existing identification methods are laborious, time consuming, and expensive. Rapid and precise identification is crucial for timely management. By analyzing the variations in the mitochondrial cytochrome oxidase-1 gene sequence (Insect barcoding gene), we developed a species-specific primer (SSP), DorFP1/DorRP1, for accurate identification of B. dorsalis. The optimal annealing temperature for the SSP was determined to be 66°C, with no cross-amplification or primer-dimer formation observed. The SSP was validated with B. dorsalis specimens from various locations in northern and eastern India and tested for cross-specificity with six other economically significant fruit fly species in India. The primer specificity was further confirmed by the analysis of critical threshold (Ct) value from a qPCR assay. Sensitivity analysis showed the primer could detect template DNA concentrations as low as 1 pg/µl, though sensitivity decreased at lower concentrations. Sequencing of the SSP-amplified product revealed over >99% similarity with existing B. dorsalis sequences in the NCBI GenBank. The developed SSP reliably identifies B. dorsalis across all developmental stages and sexes. This assay is expected to significantly impact pest identification, phytosanitary measures, and eradication programs for B. dorsalis.}, }
@article {pmid39045014, year = {2024}, author = {Chien, YC and Valencia, CA and Lee, HY and Yoon, GM and Kim, D}, title = {DNA-encoded probe-based assay for profiling plant kinase activities.}, journal = {PNAS nexus}, volume = {3}, number = {7}, pages = {pgae281}, pmid = {39045014}, issn = {2752-6542}, abstract = {Elucidating kinase-substrate relationships is pivotal for deciphering cellular signaling mechanisms, yet it remains challenging due to the complexity of kinase networks. Herein, we report the development of a versatile DNA-based kinase assay platform for high-throughput profiling of plant protein kinase activities and substrate preferences. Our approach employs DNA-linked peptide substrates, facilitating quantitative and specific kinase activity detection through next-generation DNA sequencing. Leveraging DNA barcodes as quantitative readouts, our approach establishes a high-throughput, sensitive, and specific platform for dissecting kinase-substrate networks in plants, representing a powerful tool for elucidating signaling mechanisms in plants.}, }
@article {pmid39044181, year = {2024}, author = {Askari, F and Paksa, A and Shahabi, S and Saeedi, S and Sofizadeh, A and Vahedi, M and Soltani, A}, title = {Population genetic structure and phylogenetic analysis of Anopheles hyrcanus (Diptera: Culicidae) inferred from DNA sequences of nuclear ITS2 and the mitochondrial COI gene in the northern part of Iran.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {724}, pmid = {39044181}, issn = {1471-2334}, support = {30181//Shiraz University of Medical Sciences/ ; }, mesh = {Animals ; Iran ; *Phylogeny ; *Anopheles/genetics/classification ; *Electron Transport Complex IV/genetics ; *Mosquito Vectors/genetics/classification ; Haplotypes ; Genetic Variation ; Genetics, Population ; Sequence Analysis, DNA ; DNA, Ribosomal Spacer/genetics ; }, abstract = {BACKGROUND: The Anopheles hyrcanus group is distributed throughout the Oriental and Palaearctic regions and can transmit diseases such as malaria, Japanese encephalitis virus, and filariasis. This investigation marks the inaugural comprehensive study to undertake a phylogenetic analysis of the constituents of this malaria vector group in the northeastern region of Iran, juxtaposed with documented occurrences from different areas within Iran and worldwide.<br><br>METHODS: Mosquitoes were collected using various methods from nine different locations in Golestan province from April to December 2023. The collected mosquitoes were identified morphologically using valid taxonomic keys. DNA was isolated using the Sambio&#x2122; Kit. COI and ITS2 primers were designed using Oligo7 and GeneRunner. PCR and purification were performed with the Qiagen kit. Subsequently, sequencing was carried out at the Mehr Mam GENE Center using an Applied Biosystems 3730XL sequencer. The nucleotide sequences were then analyzed and aligned with GenBank data using BioEdit. Kimura 2-parameter was Utilized for base substitutions. DNA models were selected based on AIC and BIC criteria. Bayesian and Maximum Likelihood trees were constructed, along with a haplotype network. Molecular diversity statistics computed using DnaSP software.<br><br>RESULTS: In this study, a total of 819 adult mosquitoes were collected. An. hyrcanus was the second most abundant species, predominantly found in Kalaleh and Turkman counties. The sequenced and edited COI and ITS2 sequences were deposited in GenBank under specific accession numbers. Phylogenetic analyses using ML, BI, and NJ methods confirmed a monophyletic lineage for An. hyrcanus with strong support. Molecular analysis of Iranian An. hyrcanus found 11 diverse haplotypes, with the COI gene displaying low diversity. The ITS2 gene revealed two clades - one associating with Iran, Europe, and Asia; the other originating from southwestern Iran. The haplotype network showed two main groups - one from southwest Iran and the other from north Iran. Iran exhibited six distinct haplotypes, while Turkey showcased the highest diversity.<br><br>CONCLUSIONS: An. hyrcanus in southwestern Iran exhibits a distinct haplogroup, suggesting possible subspecies differentiation. Additional studies are required to validate this phenomenon.}, }
@article {pmid39041315, year = {2024}, author = {Titus, BM and Gibbs, HL and Simões, N and Daly, M}, title = {Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.}, journal = {Systematic biology}, volume = {73}, number = {5}, pages = {758-768}, doi = {10.1093/sysbio/syae045}, pmid = {39041315}, issn = {1076-836X}, support = {DEB-1601645//National Science Foundation Doctoral Dissertation Improvement/ ; //Operation Wallacea, American Philosophical Society/ ; //International Society for Reef Studies Graduate Fellowship/ ; //PADI Foundation Grant/ ; //American Museum of Natural History Lerner Gray Funds/ ; CONACyTCB-2012-01-177293//The Ohio State University Presidential Fellowship/ ; //Trautman Fund of The OSU Museum of Biological Diversity/ ; //The Ohio State Universit/ ; DEB-1257796//National Science Foundation/ ; }, mesh = {Animals ; *Genetic Speciation ; Caribbean Region ; *Phylogeny ; Panama ; Gene Flow ; Decapoda/classification/genetics ; }, abstract = {Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.}, }
@article {pmid39041198, year = {2024}, author = {McGee, RS and Kinsler, G and Petrov, D and Tikhonov, M}, title = {Improving the Accuracy of Bulk Fitness Assays by Correcting Barcode Processing Biases.}, journal = {Molecular biology and evolution}, volume = {41}, number = {8}, pages = {}, pmid = {39041198}, issn = {1537-1719}, support = {R35 GM118165/GM/NIGMS NIH HHS/United States ; PHY-2310746//National Science Foundation/ ; R35GM118165/NH/NIH HHS/United States ; }, mesh = {*Genetic Fitness ; *DNA Barcoding, Taxonomic/methods ; High-Throughput Nucleotide Sequencing/methods ; Bias ; }, abstract = {Measuring the fitnesses of genetic variants is a fundamental objective in evolutionary biology. A standard approach for measuring microbial fitnesses in bulk involves labeling a library of genetic variants with unique sequence barcodes, competing the labeled strains in batch culture, and using deep sequencing to track changes in the barcode abundances over time. However, idiosyncratic properties of barcodes can induce nonuniform amplification or uneven sequencing coverage that causes some barcodes to be over- or under-represented in samples. This systematic bias can result in erroneous read count trajectories and misestimates of fitness. Here, we develop a computational method, named REBAR (Removing the Effects of Bias through Analysis of Residuals), for inferring the effects of barcode processing bias by leveraging the structure of systematic deviations in the data. We illustrate this approach by applying it to two independent data sets, and demonstrate that this method estimates and corrects for bias more accurately than standard proxies, such as GC-based corrections. REBAR mitigates bias and improves fitness estimates in high-throughput assays without introducing additional complexity to the experimental protocols, with potential applications in a range of experimental evolution and mutation screening contexts.}, }
@article {pmid39041008, year = {2024}, author = {Allison, PF and Pickich, ET and Barnett, ZC and Garrick, RC}, title = {DNA barcoding is currently unreliable for species identification in most crayfishes.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e70050}, pmid = {39041008}, issn = {2045-7758}, abstract = {DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.}, }
@article {pmid39040809, year = {2024}, author = {Alojayri, G and Al-Quraishy, S and Al-Shaebi, E and Mohammed, OB and Abdel-Gaber, R}, title = {Morphological and genetic identification of the gill monogenean parasite (Diclidophora merlangi) that infects Twobar Seabream Fish (Acanthopagrus bifasciatus) in the Arabian Gulf, Saudi Arabia.}, journal = {Helminthologia}, volume = {61}, number = {2}, pages = {184-193}, pmid = {39040809}, issn = {0440-6605}, abstract = {Ectoparasites, particularly monogeneans, negatively affect fish health and growth. This study identified monogenean parasites in the twobar seabream, Acanthopagrus bifasciatus (Sparidae), inhabited the Arabian Gulf (Saudi Arabia). Following that, forty A. bifasciatus fish samples were visually examined for monogeneans. Parasite species were collected from the gills and then analyzed morphometrically, morphologically, and molecularly using the partial regions of the large subunit of ribosomal RNA (28S rRNA) and mitochondrial cytochrome C oxidase subunit I (COI) genes. Fish species were also identified using a DNA barcoding approach based on the COI gene. The monogenean species of Diclidophora merlangi (Diclidophoridae) were found in 45% of the fish species studied. The generic features of the Diclidophora genus distinguish this species. This species discriminated itself from congeners by having a muscular bulb with 17 grooved and recurved hooks, 218±10 (184-267) post-ovarian testes, and four pairs of pedunculated clamps of relative sizes. Partial 28S rRNA sequencing from monogeneans revealed that they grouped with members of the genus Diclidophora, forming a monophyletic group that supported the morphological descriptions. Molecular identification revealed that D. merlangi has a unique barcode made up of a COI sequence. The host identity was established as A. bifasciatus based on the COI gene sequences. Furthermore, a molecular phylogenetic study was performed to determine the phylogenetic affinity of parasite species and fish hosts. This study on Diclidophora species is considered the first record of this genus in the examined area.}, }
@article {pmid39037657, year = {2024}, author = {Handly-Santana, A and Oren, Y}, title = {Characterizing Rare Dormant and Cycling Lineages Using the Watermelon System.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2811}, number = {}, pages = {165-175}, pmid = {39037657}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; *Cell Lineage/genetics ; Humans ; Cell Proliferation/genetics ; Sequence Analysis, RNA/methods ; RNA, Messenger/genetics ; }, abstract = {Barcode-based lineage tracing approaches enable molecular characterization of clonal cell families. Barcodes that are expressed as mRNA can be used to deconvolve lineage identity from single-cell RNA sequencing transcriptional data. Here we describe the Watermelon system, which facilitates the simultaneous tracing of lineage, transcriptional, and proliferative state at a single cell level.}, }
@article {pmid39032368, year = {2024}, author = {Kwon, YL and Shin, KJ}, title = {Unique molecular identifier-based amplicon sequencing of microhaplotypes for background noise mitigation.}, journal = {Forensic science international. Genetics}, volume = {72}, number = {}, pages = {103096}, doi = {10.1016/j.fsigen.2024.103096}, pmid = {39032368}, issn = {1878-0326}, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *High-Throughput Nucleotide Sequencing ; *Polymerase Chain Reaction ; *Haplotypes ; Sequence Analysis, DNA ; DNA Fingerprinting/methods ; }, abstract = {Microhaplotypes (MHs), comprising two or more single-nucleotide polymorphisms in a short fragment, are promising forensic markers owing to their remarkable polymorphic nature. Several studies have demonstrated the utility of MHs through massively parallel sequencing (MPS). Nevertheless, the background noise level associated with MHs in MPS, which imposes a practical detection limit for the system, remains uninvestigated. Currently, unique molecular identifier (UMI) systems are known to effectively mitigate background noise by tracking original DNA molecules and facilitating PCR and MPS error corrections. Hence, this study aimed to design a UMI-based amplicon sequencing system, designated MH-UMIseq, which can amplify 46 MHs simultaneously and generate MPS libraries in four steps: barcoding PCR, nuclease reaction, boosting PCR, and indexing PCR. The performance of the MH-UMIseq system was evaluated using the Illumina NextSeq 550 and MiniSeq systems with 31 sets for 5 ng, 1 ng, and 200 pg of input DNA. The fgbio toolkit was used in conjunction with STRait Razor 3.0 and Visual Microhap to analyze the UMI data on MHs. The corresponding average not suppressed noise proportion of MH-UMIseq were 0.1 %, 0.3 %, and 0.7 % for 5 ng, 1 ng, and 200 pg of DNA, respectively, which substantially suppressed the background noise for more than 1 ng of DNA. Interestingly, the proportion of not suppressed noise in MH-UMIseq notably decreased as the amount of input DNA increased. The number of UMI families was proportional to the copy number of the template DNA and closely correlated with the system resolution. Therefore, the resolution of MH-UMIseq system is expected to be higher than that of conventional MPS for the deconvolution of mixtures containing more than 1 ng of DNA.}, }
@article {pmid39031987, year = {2024}, author = {Wang, H and Zhan, Q and Ning, M and Guo, H and Wang, Q and Zhao, J and Bao, P and Xing, S and Chen, S and Zuo, S and Xia, X and Li, M and Wang, P and Lu, ZJ}, title = {Depletion-assisted multiplexed cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicles.}, journal = {Clinical and translational medicine}, volume = {14}, number = {7}, pages = {e1760}, pmid = {39031987}, issn = {2001-1326}, support = {32170671//National Natural Science Foundation of China/ ; 82371855//National Natural Science Foundation of China/ ; 82341101//National Natural Science Foundation of China/ ; 81902384//National Natural Science Foundation of China/ ; CFH 2022-2-4075//Capital's Funds for Health Improvement and Research/ ; 2022ZD0117700//National Key Research and Development Plan of China/ ; 2021GQG1020//Tsinghua University Guoqiang Institute/ ; 2022ZLA003//Tsinghua University Initiative Scientific Research Program of Precision Medicine/ ; //Institute of Health and Medicine, Hefei Comprehensive National Science Center/ ; //Bayer Micro-funding/ ; //Bio-Computing Platform of Tsinghua University Branch of China National Center for Protein Sciences/ ; }, mesh = {Humans ; *Extracellular Vesicles/genetics/metabolism ; *Cell-Free Nucleic Acids/blood/analysis/genetics ; *Sequence Analysis, RNA/methods ; }, abstract = {BACKGROUND: Cell-free long RNAs in human plasma and extracellular vesicles (EVs) have shown promise as biomarkers in liquid biopsy, despite their fragmented nature.<br><br>METHODS: To investigate these fragmented cell-free RNAs (cfRNAs), we developed a cost-effective cfRNA sequencing method called DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing). DETECTOR-seq utilised a meticulously tailored set of customised guide RNAs to remove large amounts of unwanted RNAs (i.e., fragmented ribosomal and mitochondrial RNAs) in human plasma. Early barcoding strategy was implemented to reduce costs and minimise plasma requirements.<br><br>RESULTS: Using DETECTOR-seq, we conducted a comprehensive analysis of cell-free transcriptomes in both whole human plasma and EVs. Our analysis revealed discernible distributions of RNA types in plasma and EVs. Plasma exhibited pronounced enrichment in structured circular RNAs, tRNAs, Y RNAs and viral RNAs, while EVs showed enrichment in messenger RNAs (mRNAs) and signal recognition particle RNAs (srpRNAs). Functional pathway analysis highlighted RNA splicing-related ribonucleoproteins (RNPs) and antimicrobial humoral response genes in plasma, while EVs demonstrated enrichment in transcriptional activity, cell migration and antigen receptor-mediated immune signals. Our study indicates the comparable potential of cfRNAs from whole plasma and EVs in distinguishing cancer patients (i.e., colorectal and lung cancer) from healthy donors. And microbial cfRNAs in plasma showed potential in classifying specific cancer types.<br><br>CONCLUSIONS: Our comprehensive analysis of total and EV cfRNAs in paired plasma samples provides valuable insights for determining the need for EV purification in cfRNA-based studies. We envision the cost effectiveness and efficiency of DETECTOR-seq will empower transcriptome-wide investigations in the fields of cfRNAs and liquid biopsy.<br><br>KEYPOINTS: DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing) enabled efficient and specific depletion of sequences derived from fragmented ribosomal and mitochondrial RNAs in plasma. Distinct human and microbial cell-free RNA (cfRNA) signatures in whole Plasma versus extracellular vesicles (EVs) were revealed. Both Plasma and EV cfRNAs were capable of distinguishing cancer patients from normal individuals, while microbial RNAs in Plasma cfRNAs enabled better classification of cancer types than EV cfRNAs.}, }
@article {pmid39031978, year = {2024}, author = {Bañón, R and de Carlos, A and Comesaña, &#xc1;S and Barreiro Vázquez, JD and Baldó, F}, title = {Second world record for Barathronus roulei Nielsen, 2019 (Ophidiiformes, Bythitidae), from the Porcupine Bank (Northeast Atlantic).}, journal = {Journal of fish biology}, volume = {105}, number = {4}, pages = {1348-1353}, doi = {10.1111/jfb.15878}, pmid = {39031978}, issn = {1095-8649}, support = {PORCUDEM-20233FMP001//European Maritime, Fisheries and Aquaculture Fund/ ; }, mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Phylogeny ; Eels/genetics/anatomy &amp; histology ; Atlantic Ocean ; }, abstract = {Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)-DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species.}, }
@article {pmid39031483, year = {2024}, author = {Gil, F and Beroiz, B and Ballesteros, I and Horreo, JL}, title = {Can consumers avoid mislabelling? Genetic species identification provides recommendations for shrimp/prawn products.}, journal = {Journal of the science of food and agriculture}, volume = {104}, number = {15}, pages = {9486-9493}, doi = {10.1002/jsfa.13771}, pmid = {39031483}, issn = {1097-0010}, mesh = {Animals ; *Food Labeling ; *Penaeidae/genetics/classification ; Spain ; Shellfish/analysis/economics ; Humans ; Consumer Behavior ; DNA, Mitochondrial/genetics ; Food Contamination/analysis ; }, abstract = {BACKGROUND: Crustaceans of the superfamily Penaeoidea (e.g., shrimps and prawns) are among the most commercially available aquatic products worldwide. However, there are few studies regarding not only the presence but also the characteristics of mislabelling in these food products. Such information would be helpful for consumers in order to avoid the typical problems associated with mislabelling (e.g., health and economic issues). For this reason, this work considers Penaeoidea mislabelling by comparing different products (frozen, fresh, boiled), and sources (hypermarkets, supermarkets and fishmongers) from Spain (Europe).<br><br>RESULTS: A total of 94 samples from 55 different products were collected, representing 19 different species from 13 genera. Mitochondrial DNA (COI gene) was amplified, revealing mislabelling in almost 30% of supermarket products and almost exclusively found in frozen samples (95% of the total) regardless of its price. In addition, products from the Pacific Ocean seem to be particularly susceptible to mislabelling.<br><br>CONCLUSIONS: All in all, recommendations for the consumer in order to avoid mislabelling of prawns include purchasing them fresh from fishmongers; aquaculture products must not be avoided. This study represents, to our knowledge, the first attempt to provide recommendations to consumers based on DNA analyses in order to avoid mislabelling in food products. Further research is therefore required to provide such recommendations in different food products, particularly those that are processed, packaged and/or frozen. &#xa9; 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry.}, }
@article {pmid39027082, year = {2024}, author = {Changbunjong, T and Weluwanarak, T and Laojun, S and Duvallet, G and Chaiphongpachara, T}, title = {Genetic and morphometric differentiation between two morphs of Haematobosca sanguinolenta (Diptera: Muscidae) from Thailand.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {6}, number = {}, pages = {100186}, pmid = {39027082}, issn = {2667-114X}, abstract = {Haematobosca is a genus of biting fly within the subfamily Stomoxyinae of the family Muscidae. It is currently recognized to include 16 species worldwide. These species, acting as ectoparasites, are considered to have significant importance in the veterinary and medical fields. To address the color polymorphism related to the genus Haematobosca in Thailand, herein, we focused on the normal (legs mainly black) and yellow (legs mainly yellow) morphs of Haematobosca sanguinolenta and examined them for genetic differences using three molecular markers: the cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes from the mitochondrial genome as well as the internal transcribed spacer 2 (ITS2) region from the nuclear ribosomal DNA. In addition, we analyzed wing differences between the two morphs using geometric morphometrics (GM). The genetic divergences between the two morphs showed that cytb gene showed the greatest divergence, for which the average distance was 5.6%. This was followed by the combination of cox1-cytb-ITS2, exhibiting an average divergence of 4.5%, ITS2 with a divergence of 4.1%, and finally cox1, showing the lowest divergence of 3.5%. Phylogenetic analyses distinctly separated the two morphs of H. sanguinolenta; this separation was supported by high bootstrap values (97-100%). These results were further corroborated by three species delimitation methods, i.e. assemble species by automatic partitioning (ASAP), automated barcode gap discovery (ABGD), and Poisson tree processes (PTP), all of which suggested that the two morphs likely represent separate species. In addition, a GM study identified a statistically significant difference in wing shape between the two morphs of H. sanguinolenta (P < 0.05). This combination of genetic and morphometric results strongly supports the existence of two distinct species within H. sanguinolenta in Thailand.}, }
@article {pmid39027045, year = {2024}, author = {Götz, TI and Cong, X and Rauber, S and Angeli, M and Lang, EW and Ramming, A and Schmidkonz, C}, title = {A novel Slide-seq based image processing software to identify gene expression at the single cell level.}, journal = {Journal of pathology informatics}, volume = {15}, number = {}, pages = {100384}, pmid = {39027045}, issn = {2229-5089}, abstract = {Analysis of gene expression at the single-cell level could help predict the effectiveness of therapies in the field of chronic inflammatory diseases such as arthritis. Here, we demonstrate an adopted approach for processing images from the Slide-seq method. Using a puck, which consists of about 50,000 DNA barcode beads, an RNA sequence of a cell is to be read. The pucks are repeatedly brought into contact with liquids and then recorded with a conventional epifluorescence microscope. The image analysis initially consists of stitching the partial images of a sequence recording, registering images from different sequences, and finally reading out the bases. The new method enables the use of an inexpensive epifluorescence microscope instead of a confocal microscope.}, }
@article {pmid39026955, year = {2024}, author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S}, title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11584}, pmid = {39026955}, issn = {2045-7758}, abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.}, }
@article {pmid39026715, year = {2024}, author = {Chamberlin, JT and Gillen, AE and Quinlan, AR}, title = {Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39026715}, issn = {2692-8205}, support = {S10 OD021644/OD/NIH HHS/United States ; T15 LM007124/LM/NLM NIH HHS/United States ; }, abstract = {Prevailing poly(dT)-primed 3' single-cell RNA-seq protocols generate barcoded cDNA fragments containing the reverse transcriptase priming site, which is expected to be the poly(A) tail or a genomic adenine homopolymer. Direct sequencing across this priming site was historically difficult because of DNA sequencing errors induced by the homopolymeric primer at the 'barcode' end. Here, we evaluate the capability of "avidity base chemistry" DNA sequencing from Element Biosciences to sequence through this homopolymer accurately, and the impact of the additional cDNA sequence on read alignment and precise quantification of polyadenylation site usage. We find that the Element Aviti instrument sequences through the thymine homopolymer into the subsequent cDNA sequence without detectable loss of accuracy. The resulting paired-end alignments enable direct and independent assignment of reads to polyadenylation sites, which bypasses complexities and limitations of conventional approaches but does not consistently improve read mapping rates compared to single-end alignment. We also characterize low-level artifacts and arrive at an adjusted adapter trimming and alignment workflow that significantly improves the alignment of sequence data from Element and Illumina, particularly in the context of extended read lengths. Our analyses confirm that Element avidity sequencing is an effective alternative to Illumina sequencing for standard single-cell RNA-seq, particularly for polyadenylation site analyses but do not rule out the potential for similar performance from other emerging platforms.}, }
@article {pmid39024335, year = {2024}, author = {Gul, A and Shah, SHJ and Faris, S and Qazi, J and Qazi, A and Dey, SK}, title = {An analysis of morphological and genetic diversity of mango fruit flies in Pakistan.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0304472}, pmid = {39024335}, issn = {1932-6203}, mesh = {Animals ; *Tephritidae/genetics/classification ; Pakistan ; *Mangifera/parasitology/genetics ; *Genetic Variation ; *DNA Barcoding, Taxonomic ; *Electron Transport Complex IV/genetics ; Phylogeny ; }, abstract = {Fruit flies of genus Bactrocera are important insect pests of commercially cultivated mangos in Pakistan limiting its successful production in the country. Despite the economic risk, the genetic diversity and population dynamics of this pest have remained unexplored. This study aimed to morphologically identify Bactrocera species infesting Mango in major production areas of the country and to confirm the results with insect DNA barcode techniques. Infested mango fruits from the crop of 2022, were collected from 46 locations of 11major production districts of Punjab and Sindh provinces, and first-generation flies were obtained in the laboratory. All 10,653 first generation flies were morphologically identified as two species of Bactrocera; dorsalis and zonata showing geography-based relative abundance in the two provinces; Punjab and Sindh. Morphological identification was confirmed by mitochondrial cytochrome oxidase gene subunit I (mt-COI) based DNA barcoding. Genetic analysis of mtCOI gene region of 61 selected specimens by the presence of two definite clusters and reliable intraspecific distances validated the results of morphological identification. This study by morphological identification of a large number of fruit fly specimens from the fields across Pakistan validated by insect DNA barcode reports two species of Bactrocera infesting mango in the country.}, }
@article {pmid39023176, year = {2024}, author = {Zhang, LJ and Liu, Y and Wang, YL and Xie, LL and Wang, XY and Ma, YS}, title = {Population genetic diversity and structure of Tephritis angustipennis and Campiglossa loewiana (Diptera: Tephritidae) based on COI DNA barcodes in the three-river source region, China.}, journal = {Journal of insect science (Online)}, volume = {24}, number = {4}, pages = {}, pmid = {39023176}, issn = {1536-2442}, support = {2024-SF-101//Qinghai Science and Technology Department/ ; }, mesh = {Animals ; *Tephritidae/genetics ; China ; *Electron Transport Complex IV/genetics ; *Genetic Variation ; *DNA Barcoding, Taxonomic ; Haplotypes ; Phylogeny ; Insect Proteins/genetics ; }, abstract = {Tephritis angustipennis (Diptera: Tephritidae) and Campiglossa loewiana (Diptera: Tephritidae) are phytophagous pests in China. Their damage has significantly impacted the collection and cultivation of germplasm resources of native Asteraceae plants. However, the genetic characteristics and structure of their population are unclear. This study focused on the highly damaging species of T. angustipennis and C. loewiana collected from the three-river source region (TRSR). We amplified the mitochondrial cytochrome C oxidase subunit I (mtCOI) gene sequences of these pests collected from this area and compared them with COI sequences from GenBank. We also analyzed their genetic diversity and structure. In T. angustipennis, 5 haplotypes were identified from 5 geographic locations; the genetic differentiation between France population FRPY (from Nylandia, Uusimaa) and China populations GLJZ (from Dehe Longwa Village, Maqin County), GLDR (from Zhique Village, Dari County), and GLMQ (from Rijin Village, Maqin County) was the strongest. GLJZ exhibited strong genetic differentiation from GLDR and GLMQ, with relatively low gene flow. For C. loewiana, 11 haplotypes were identified from 5 geographic locations; the genetic differentiation between the Chinese population GLMQ-YY (from Yangyu Forest Farm, Maqin County) and Finnish population FDNL (from Nylandia, Uusimaa) was the strongest, with relatively low gene flow, possibly due to geographical barriers in the Qinghai-Tibet plateau. Only 1 haplotype was identified across GLDR, GLMQ, and GLBM. High gene flow between distant locations indicates that human activities or wind dispersal may facilitate the dispersal of fruit flies and across different geographic. Geostatistical analysis suggested a recent population expansion of these 2 species in TRSR. Our findings provide technical references for identifying pests in the TRSR region and theoretical support for managing resistance, monitoring pest occurrences, analyzing environmental adaptability, and formulating biological control strategies for Tephritidae pests on Asteraceae plants.}, }
@article {pmid39020177, year = {2024}, author = {Chen, W and Choi, J and Li, X and Nathans, JF and Martin, B and Yang, W and Hamazaki, N and Qiu, C and Lalanne, JB and Regalado, S and Kim, H and Agarwal, V and Nichols, E and Leith, A and Lee, C and Shendure, J}, title = {Symbolic recording of signalling and cis-regulatory element activity to DNA.}, journal = {Nature}, volume = {632}, number = {8027}, pages = {1073-1081}, pmid = {39020177}, issn = {1476-4687}, support = {R01 HG010632/HG/NHGRI NIH HHS/United States ; UM1 HG011586/HG/NHGRI NIH HHS/United States ; F31 HG011576/HG/NHGRI NIH HHS/United States ; K99 HG012973/HG/NHGRI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; Cell Differentiation/genetics ; *DNA/genetics/metabolism ; Enhancer Elements, Genetic/genetics ; *Gene Editing/methods ; Genomics ; Mouse Embryonic Stem Cells/cytology ; NF-kappa B/metabolism ; Reproducibility of Results ; RNA, Guide, CRISPR-Cas Systems/genetics/metabolism ; *Signal Transduction/genetics ; Time Factors ; Transcription Factors/metabolism ; *Transcription, Genetic/genetics ; Wnt Signaling Pathway/genetics ; Nucleotide Motifs ; Consensus Sequence/genetics ; Developmental Biology ; Proof of Concept Study ; }, abstract = {Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter[1], we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.}, }
@article {pmid39018572, year = {2024}, author = {Khumalo, N and Chaisi, M and Magoro, R and Mwale, M}, title = {An analysis of the gaps in the South African DNA barcoding library of ticks of veterinary and public health importance.}, journal = {Genome}, volume = {67}, number = {11}, pages = {392-402}, doi = {10.1139/gen-2024-0052}, pmid = {39018572}, issn = {1480-3321}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; South Africa ; *Ticks/genetics/classification ; *Biodiversity ; Public Health ; Phylogeny ; }, abstract = {Ticks transmit pathogens of veterinary and public health importance. Understanding their diversity is critical as infestations lead to significant economic losses globally. To date, over 90 species across three families have been identified in South Africa. However, the taxonomy of most species has not been resolved due to morphological identification challenges. DNA barcoding through the Barcode of Life Data Systems (BOLD) is therefore a valuable tool for species verifications for biodiversity assessments. This study conducted an analysis of South African tick COI barcodes on BOLD by verifying species on checklists, literature, and other sequence databases. The compiled list represented 97 species, including indigenous (59), endemics (27), introduced (2), invasives (1), and eight that could not be classified. Analyses indicated that 31 species (32%) from 11 genera have verified COI barcodes. These are distributed across all nine provinces with the Eastern Cape having the highest species diversity, followed by Limpopo, with KwaZulu-Natal having the least diversity. Rhipicephalus, Hyalomma, and Argas species had multiple barcode index numbers, suggesting cryptic diversity or unresolved taxonomy. We identified 21 species of veterinary or zoonotic importance from the Argasidae and Ixodidae families that should be prioritised for barcoding. Coordinating studies and defining barcoding targets is necessary to ensure that tick checklists are updated to support decision-making for the control of vector-borne diseases and alien invasives.}, }
@article {pmid39018344, year = {2024}, author = {Todisco, V and Basu, DN and Prosser, SWJ and Russell, S and Mutanen, M and Zilli, A and Huertas, B and Kunte, K and Vane-Wright, R}, title = {DNA barcodes from over-a-century-old type specimens shed light on the taxonomy of a group of rare butterflies (Lepidoptera: Nymphalidae: Calinaginae).}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0305825}, pmid = {39018344}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics/classification/anatomy &amp; histology ; *Phylogeny ; Wings, Animal/anatomy &amp; histology ; Electron Transport Complex IV/genetics ; }, abstract = {We analyzed COI barcode sequences from 138 over-a-century old specimens of Calinaga including 36 name-bearing type specimens stored at the Natural History Museum London. These new data, combined with previously available RPS5 sequences, divide the Calinaga samples into four well-supported mitochondrial lineages that together with a novel wing-pattern analysis, support the recognition of six species (lhatso, buddha, brahma, aborica, formosana and davidis), with all other names subsumed either as subspecies or synonyms. One new taxon is described, Calinaga aborica naima Vane-Wright, ssp. n.}, }
@article {pmid39018276, year = {2024}, author = {de Almeida, LH and Gonçalves, MC and da Conceição Bispo, P}, title = {An integrative approach to the study of Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) from Brazil: Support for the description of four new species and a basis for future studies.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0305824}, pmid = {39018276}, issn = {1932-6203}, mesh = {Animals ; Brazil ; *Phylogeny ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Bayes Theorem ; Insecta/classification/genetics/anatomy &amp; histology ; Neoptera/genetics/classification/anatomy &amp; histology ; Species Specificity ; Female ; }, abstract = {Kempnyia (Plecoptera: Perlidae) is an endemic genus of Brazilian stoneflies that has 36 valid species and is distributed primarily in the Atlantic Forest and the mountainous areas of Central Brazil, particularly in Goiás and Tocantins states. Despite being the Brazilian genus with the most DNA sequences available on GenBank, integrative studies on the genus began only recently, in 2014. In this context, herein we studied the morphology and molecular data of Kempnyia specimens deposited in the Aquatic Biology Laboratory (UNESP, Assis) and the Entomology Museum of the Federal University of Viçosa (UFVB, Viçosa) collections. For the integrative approach adopted, in addition to studying the specimens morphologically, we used sequences of the COI mitochondrial gene combined with the following species delimitation methods: Automatic Barcode Gap Discovery (ABGD), both primary (ABGDp) and recursive (ABGDr) partitions; Assemble Species by Automatic Partitioning (ASAP); Poisson Tree Processes (PTP) and the Bayesian implementation of the Poisson Tree Processes (bPTP). As a result, we provided 28 new COI sequences of 21 species and support the description of four new species, namely, K. guarani sp. nov., K. tupiniquim sp. nov., K. una sp. nov., and K. zwickii sp. nov., consequently increasing the known diversity of the genus to 40 species. We also discuss the morphological variations observed in other species of the genus and provide several new geographic records. Therefore, our study brings new insights into the values of intra- and interspecific molecular divergence within Kempnyia, serving as a basis for new studies.}, }
@article {pmid39015799, year = {2024}, author = {Xiaoqi, M and Zhang, T and Wang, C}, title = {Description of two species of the orb-weaver spider genus Argiope Audouin, 1826 (Araneae, Araneidae) from Xizang, China.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e125601}, pmid = {39015799}, issn = {1314-2828}, abstract = {BACKGROUND: The spider genus Argiope Audouin, 1826, comprises 88 species worldwide, including 23 species occurring in China. Two Argiope species were collected by the spider survey on Yarlung Zangbo Grand Canyon National Nature Reserve, Xizang, southwest China, conducted in 2023.<br><br>NEW INFORMATION: Two species of the orb-weaver spider genus Argiope from Xizang, China are described, including a new species, A.beibeng Mi &amp; Wang, sp. nov. (&#x2642;&#x2640;) and a known species, A.caesarea Thorell, 1897 (&#x2642;&#x2640;). The unknown male of A.caesarea is described for the first time.}, }
@article {pmid39015529, year = {2024}, author = {Lee, S and Hwang, S and Lee, M and Seung, J and Choi, W and Bai, M}, title = {DNA barcoding reveals a taxonomic fraud: Note on validity of Propomacrusmuramotoae (Coleoptera, Scarabaeidae).}, journal = {ZooKeys}, volume = {1206}, number = {}, pages = {181-190}, pmid = {39015529}, issn = {1313-2989}, abstract = {Until the early 2000s, the genus Propomacrus was known to comprise two species, occurring in the Eastern Mediterranean and Southeast China. The discovery of Propomacrusmuramotoae Fujioka in Tibet and subsequently in Bhutan and Nepal, might play a crucial role in bridging the geographical distribution gap of the Euchirini tribe between the Mediterranean and Central China, offering profound insights into its evolution and biogeography. However, all specimens, including the holotype specimen, were sourced from a single insect vendor, with no further specimens found or catalogued in museum collections thereafter. During our examination of a P.muramotoae specimen from a private collection in South Korea, we found its COI gene sequence to be identical to that of P.bimucronatus (Pallas) from Turkey, a species known for its wide distribution and genetic variability across regional populations. This overlap in genetic identity raised significant doubts, further compounded by our detection of deliberate modifications in essential diagnostic features during morphological examination. All three specimens we examined showed crude modifications, including staining and artificial grinding. Despite our inability to access the P.muramotoae type specimens for direct examination-a challenge we attempted to overcome through various means-it is evident that significant fraudulent tampering has occurred with the P.muramotoae specimens. Therefore, a new synonymy is proposed: Propomacrusbimucronatus Pallas, 1781 = P.muramotoae Fujioka, 2007 (syn. nov.). We also advocate for a straightforward verification of the type specimen through molecular analysis of the COI barcode region and morphological re-examination under a microscope for those who have access to the type specimens.}, }
@article {pmid39014300, year = {2024}, author = {Darabi, A and Sobhani, S and Aghdam, R and Eslahchi, C}, title = {AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {241}, pmid = {39014300}, issn = {1471-2105}, mesh = {*Metagenomics/methods ; *Algorithms ; Nucleotides/genetics ; High-Throughput Nucleotide Sequencing/methods ; Software ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Cluster Analysis ; Contig Mapping/methods ; Metagenome/genetics ; }, abstract = {BACKGROUND: Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial communities have resulted from the study of metagenomics. The assembly of reads into longer contigs, which are then binned into groups of contigs that correspond to different species in the metagenomic sample, is a crucial step in the analysis of metagenomics. It is necessary to organize these contigs into operational taxonomic units (OTUs) for further taxonomic profiling and functional analysis. For binning, which is synonymous with the clustering of OTUs, the tetra-nucleotide frequency (TNF) is typically utilized as a compositional feature for each OTU.<br><br>RESULTS: In this paper, we present AFIT, a new l-mer statistic vector for each contig, and AFITBin, a novel method for metagenomic binning based on AFIT and a matrix factorization method. To evaluate the performance of the AFIT vector, the t-SNE algorithm is used to compare species clustering based on AFIT and TNF information. In addition, the efficacy of AFITBin is demonstrated on both simulated and real datasets in comparison to state-of-the-art binning methods such as MetaBAT 2, MaxBin 2.0, CONCOT, MetaCon, SolidBin, BusyBee Web, and MetaBinner. To further analyze the performance of the purposed AFIT vector, we compare the barcodes of the AFIT vector and the TNF vector.<br><br>CONCLUSION: The results demonstrate that AFITBin shows superior performance in taxonomic identification compared to existing methods, leveraging the AFIT vector for improved results in metagenomic binning. This approach holds promise for advancing the analysis of metagenomic data, providing more reliable insights into microbial community composition and function.<br><br>AVAILABILITY: A python package is available at: https://github.com/SayehSobhani/AFITBin .}, }
@article {pmid39012608, year = {2024}, author = {Albrecht, C and Bashtrykov, P and Jeltsch, A}, title = {Amplicon-Based Bisulfite Conversion-NGS DNA Methylation Analysis Protocol.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2842}, number = {}, pages = {405-418}, pmid = {39012608}, issn = {1940-6029}, mesh = {*DNA Methylation ; *Sulfites/chemistry ; *High-Throughput Nucleotide Sequencing/methods ; *Polymerase Chain Reaction/methods ; Humans ; DNA/genetics ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Epigenesis, Genetic ; Epigenomics/methods ; }, abstract = {DNA methylation is an important epigenetic modification that regulates chromatin structure and the cell-type-specific expression of genes. The association of aberrant DNA methylation with many diseases, as well as the increasing interest in modifying the methylation mark in a directed manner at genomic sites using epigenome editing for research and therapeutic purposes, increases the need for easy and efficient DNA methylation analysis methods. The standard approach to analyze DNA methylation with a single-cytosine resolution is bisulfite conversion of DNA followed by next-generation sequencing (NGS). In this chapter, we describe a robust, powerful, and cost-efficient protocol for the amplification of target regions from bisulfite-converted DNA, followed by a second PCR step to generate libraries for Illumina NGS. In the two consecutive PCR steps, first, barcodes are added to individual amplicons, and in the second PCR, indices and Illumina adapters are added to the samples. Finally, we describe a detailed bioinformatics approach to extract DNA methylation levels of the target regions from the sequencing data. Combining barcodes with indices enables a high level of multiplexing allowing to sequence multiple pooled samples in the same sequencing run. Therefore, this method is a robust, accurate, quantitative, and cheap approach for the readout of DNA methylation patterns at defined genomic regions.}, }
@article {pmid39011841, year = {2024}, author = {Berteloot, OH and Peusens, G and Beliën, T and De Clercq, P and Van Leeuwen, T}, title = {Unveiling the diet of two generalist stink bugs, Halyomorpha halys and Pentatoma rufipes (Hemiptera: Pentatomidae), through metabarcoding of the ITS2 region from gut content.}, journal = {Pest management science}, volume = {80}, number = {11}, pages = {5694-5705}, doi = {10.1002/ps.8287}, pmid = {39011841}, issn = {1526-4998}, support = {LA-traject HBC.2018.2224//VLAIO (Flanders Innovation and Entrepreneurship)/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Heteroptera/physiology ; *Diet ; Gastrointestinal Contents ; Herbivory ; }, abstract = {BACKGROUND: The use of DNA metabarcoding has become an increasingly popular technique to infer feeding relationships in polyphagous herbivores and predators. Understanding host plant preference of native and invasive herbivore insects can be helpful in establishing effective integrated pest management (IPM) strategies. The invasive Halyomorpha halys and native Pentatoma rufipes are piercing-sucking stink bug pests that are known to cause economic damage in commercial fruit orchards.<br><br>RESULTS: In this study, we performed molecular gut content analysis (MGCA) on field-collected specimens of these two herbivorous pentatomids using next-generation amplicon sequencing (NGAS) of the internal transcribed spacer 2 (ITS2) barcode region. Additionally, a laboratory experiment was set up where H.&#x2009;halys was switched from a mixed diet to a monotypic diet, allowing us to determine the detectability of the initial diet in a time series of &#x2264;3&#x2009;days after the diet switch. We detected 68 unique plant species from 54 genera in the diet of two stink bug species, with fewer genera found per sample and a smaller diet breadth for P.&#x2009;rufipes than for H.&#x2009;halys. Both stink bug species generally prefer deciduous trees over gymnosperms and herbaceous plants. Landscape type significantly impacted the observed genera in the diet of both stink bug species, whereas season only had a significant effect on the diet of H.&#x2009;halys.<br><br>CONCLUSION: This study provides further insights into the dietary composition of two polyphagous pentatomid pests and illustrates that metabarcoding can deliver a relevant species-level resolution of host plant preference. &#xa9; 2024 Society of Chemical Industry.}, }
@article {pmid39008212, year = {2024}, author = {Wengrat, APGS and Carvalho, LC and Pietrowski, V and Schoeninger, K and Costa, VA and Johnson, NF}, title = {First Record of Telenomus dilophonotae (Hymenoptera, Scelionidae), Parasitizing Eggs of Erinnyis ello (Lepidoptera, Sphingidae) in Western Paraná, Brazil, with Molecular Characterization and Records of Occurrences.}, journal = {Neotropical entomology}, volume = {53}, number = {5}, pages = {1162-1167}, pmid = {39008212}, issn = {1678-8052}, support = {152666/2022-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2020/16051-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/50334-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/18965-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 65562/2014-0//Instituto Nacional de Ci&#xea;ncia e Tecnologia de Hymenoptera Parasitoides/ ; 2018/02317-5//S&#xe3;o Paulo Advanced Research Center for Biological Control/ ; }, mesh = {Animals ; Brazil ; *Wasps/classification ; *Ovum/parasitology ; Lepidoptera/parasitology ; DNA Barcoding, Taxonomic ; Female ; Manihot/parasitology ; Hymenoptera/classification ; Hevea/parasitology ; }, abstract = {There are few records for Telenomus dilophonotae Cameron, 1913 (Hymenoptera, Scelionidae) from South America. In Brazil, the first occurrence was reported in Bahia in rubber crops, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. - Arg., there parasitizing eggs of Erinnyis ello Linnaeus, 1758 (Lepidoptera, Sphingidae). It was also found parasitizing the same host in cassava, Manihot esculenta Crantz (Euphorbiaceae). This is the first record of occurrence of T. dilophonotae in the state of Paraná, parasitizing eggs of E. ello in areas of cassava production in the western region of Paraná, this being the southernmost record of the species. Here, photographs, the first sequence of DNA barcode of this species of parasitoid wasp, and a distribution map are provided.}, }
@article {pmid39007612, year = {2024}, author = {Bomidi, C and Zeng, XL and Poplaski, V and Coarfa, C and Estes, MK and Blutt, SE}, title = {Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {208}, pages = {}, pmid = {39007612}, issn = {1940-087X}, support = {U19 AI144297/AI/NIAID NIH HHS/United States ; U19 AI116497/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; P01 AI057788/AI/NIAID NIH HHS/United States ; U01 DK103168/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestine, Small/cytology/metabolism ; *Single-Cell Analysis/methods ; *Intestinal Mucosa/cytology/metabolism ; Gene Expression Profiling/methods ; Transcriptome/genetics ; }, abstract = {Single cell transcriptomics has revolutionized our understanding of the cell biology of the human body. State-of-the-art human small intestinal organoid cultures provide ex vivo model systems that bridge the gap between animal models and clinical studies. The application of single cell transcriptomics to human intestinal organoid (HIO) models is revealing previously unrecognized cell biology, biochemistry, and physiology of the GI tract. The advanced single cell transcriptomics platforms use microfluidic partitioning and barcoding to generate cDNA libraries. These barcoded cDNAs can be easily sequenced by next generation sequencing platforms and used by various visualization tools to generate maps. Here, we describe methods to culture and differentiate human small intestinal HIOs in different formats and procedures for isolating viable cells from these formats that are suitable for use in single-cell transcriptional profiling platforms. These protocols and procedures facilitate the use of small intestinal HIOs to obtain an increased understanding of the cellular response of human intestinal epithelium at the transcriptional level in the context of a variety of different environments.}, }
@article {pmid39006907, year = {2024}, author = {Kantelinen, A and Svensson, M and Malíček, J and Vondrák, J and Thor, G and Palice, Z and Svoboda, S and Myllys, L}, title = {A phylogenetic study of Micareamelaeniza and similar-looking species (Pilocarpaceae) unveils hidden diversity and clarifies species boundaries and reproduction modes.}, journal = {MycoKeys}, volume = {106}, number = {}, pages = {327-354}, pmid = {39006907}, issn = {1314-4049}, abstract = {Micarea (Ascomycota, Pilocarpaceae) is a large cosmopolitan genus of crustose lichens. We investigated molecular systematics and taxonomy of the poorly known Micareamelaeniza group focussing on M.melaeniza, M.nigella and M.osloensis. A total of 54 new sequences were generated and using Bayesian and maximum likelihood analysis of two markers (nuITS and mtSSU), we discovered two previously unrecognized phylogenetic lineages, one of which is described here as Micareaeurasiatica Kantelinen &amp; G. Thor, sp. nov., morphologically characterized by pycnidia that are sessile to emergent, cylindrically shaped, with greenish-black K+ olive green, wall pigmentation and containing large mesoconidia up to 6 µm in length. The species is known from Japan and Finland. In addition, we show that the reproduction biology of M.osloensis has been poorly understood and that the species often occurs as an anamorph with stipitate pycnidia. We present a species synopsis and notes on pigments. Our research supports previous results of asexuality being an important reproductive strategy of species growing on dead wood.}, }
@article {pmid39005645, year = {2024}, author = {Wattanasatja, V and Phisutrattanaporn, J and Doenphai, N and Sirinual, S and Kanjanabuch, T}, title = {Peritoneal dialysis-associated peritonitis due to infected umbilicus.}, journal = {Medical mycology case reports}, volume = {45}, number = {}, pages = {100654}, pmid = {39005645}, issn = {2211-7539}, abstract = {We provide the first case report of peritoneal dialysis (PD)-associated peritonitis due to Lasiodiplodia theobromae, a known plant pathogen causing rotting and dieback in post-harvest citrus fruit, in immunocompetent patient with fungal colonization inside the PD catheter lumen. A root cause analysis suspected the patient's umbilical infection as the source of contamination. The fungal infection was established through microscopic examination of the PD catheter lumen and galactomannan testing in both serum and effluent. The species of pathogen was confirmed by DNA barcoding. The patient responded well to timely PD catheter removal and a 2-week course of oral voriconazole. Preventive strategies should prioritize hygiene practices, including umbilical care, to mitigate the risk of contamination and subsequent infections of fungal pathogens.}, }
@article {pmid39000014, year = {2024}, author = {Kartavtsev, YP and Masalkova, NA}, title = {Structure, Evolution, and Mitochondrial Genome Analysis of Mussel Species (Bivalvia, Mytilidae).}, journal = {International journal of molecular sciences}, volume = {25}, number = {13}, pages = {}, pmid = {39000014}, issn = {1422-0067}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Phylogeny ; *Evolution, Molecular ; Mytilidae/genetics/classification ; RNA, Transfer/genetics ; Bivalvia/genetics/classification ; Mytilus/genetics/classification ; }, abstract = {Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species' mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26-27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20-68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae.}, }
@article {pmid38997781, year = {2024}, author = {Jiang, K and Liu, T and Kales, S and Tewhey, R and Kim, D and Park, Y and Jarvis, JN}, title = {A systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes.}, journal = {BMC medical genomics}, volume = {17}, number = {1}, pages = {185}, pmid = {38997781}, issn = {1755-8794}, support = {UL1 TR001412/TR/NCATS NIH HHS/United States ; UL1TR001412/TR/NCATS NIH HHS/United States ; R35 HG011329/HG/NHGRI NIH HHS/United States ; R21-AR071878//National Institutes of Health (USA)/ ; R21 AR071878/AR/NIAMS NIH HHS/United States ; R21 AR076948/NH/NIH HHS/United States ; R01 AR078785/AR/NIAMS NIH HHS/United States ; R21 AR076948/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Haplotypes ; *Arthritis, Juvenile/genetics ; K562 Cells ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: Although genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucleotide polymorphisms (SNPs) on the disease haplotypes that exert the biological effects that confer risk. Until we identify the risk-driving variants, identifying the genes influenced by these variants, and therefore translating genetic information to improved clinical care, will remain an insurmountable task. We used a function-based approach for identifying causal variant candidates and the target genes on JIA risk haplotypes.<br><br>METHODS: We used a massively parallel reporter assay (MPRA) in myeloid K562 cells to query the effects of 5,226 SNPs in non-coding regions on JIA risk haplotypes for their ability to alter gene expression when compared to the common allele. The assay relies on 180&#xa0;bp oligonucleotide reporters ("oligos") in which the allele of interest is flanked by its cognate genomic sequence. Barcodes were added randomly by PCR to each oligo to achieve&#x2009;>&#x2009;20 barcodes per oligo to provide a quantitative read-out of gene expression for each allele. Assays were performed in both unstimulated K562 cells and cells stimulated overnight with interferon gamma (IFNg). As proof of concept, we then used CRISPRi to demonstrate the feasibility of identifying the genes regulated by enhancers harboring expression-altering SNPs.<br><br>RESULTS: We identified 553 expression-altering SNPs in unstimulated K562 cells and an additional 490 in cells stimulated with IFNg. We further filtered the SNPs to identify those plausibly situated within functional chromatin, using open chromatin and H3K27ac ChIPseq peaks in unstimulated cells and open chromatin plus H3K4me1 in stimulated cells. These procedures yielded 42 unique SNPs (total&#x2009;=&#x2009;84) for each set. Using CRISPRi, we demonstrated that enhancers harboring MPRA-screened variants in the TRAF1 and LNPEP/ERAP2 loci regulated multiple genes, suggesting complex influences of disease-driving variants.<br><br>CONCLUSION: Using MPRA and CRISPRi, JIA risk haplotypes can be queried to identify plausible candidates for disease-driving variants. Once these candidate variants are identified, target genes can be identified using CRISPRi informed by the 3D chromatin structures that encompass the risk haplotypes.}, }
@article {pmid38996389, year = {2024}, author = {Baxter, JR and Kotze, A and de Bruyn, M and Matlou, K and Labuschagne, K and Mwale, M}, title = {DNA barcoding of southern African mammal species and construction of a reference library for forensic application.}, journal = {Genome}, volume = {67}, number = {10}, pages = {378-391}, doi = {10.1139/gen-2023-0050}, pmid = {38996389}, issn = {1480-3321}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Mammals/genetics/classification ; Electron Transport Complex IV/genetics ; Phylogeny ; Cytochromes b/genetics ; South Africa ; Species Specificity ; Forensic Genetics/methods ; Gene Library ; Endangered Species ; Conservation of Natural Resources ; }, abstract = {Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.}, }
@article {pmid38993689, year = {2024}, author = {Shim, J and Song, JH}, title = {A taxonomic review of the order Mantodea in Korea based on morphology and DNA barcodes.}, journal = {ZooKeys}, volume = {1206}, number = {}, pages = {1-43}, pmid = {38993689}, issn = {1313-2989}, abstract = {A taxonomic study of Korean Mantodea using morphological and molecular characters (COI) is presented. Eight species [Amantisnawai (Shiraki, 1908), Acromantisjaponica Westwood, 1889, Mantisreligiosasinica Bazyluk, 1960, Statiliamaculata (Thunberg, 1784), Tenoderaangustipennis Saussure, 1869, T.sinensis Saussure, 1871, Hierodulachinensis Werner, 1929, H.patellifera (Audinet-Serville, 1838)] belonging to six genera in three families are recognized. Interspecific genetic divergence of COI using uncorrected p-distance ranged from 6.7% to 22.4%, while intraspecific divergence ranged from 0% to 2.2% among eight Korean Mantodea species. All eight species were each strongly supported as a single lineage using COI on both neighbor-joining and parsimony trees. An illustrated key, redescriptions, habitus photographs, and illustrations of diagnostic characters of the species of Korean Mantodea are provided to facilitate identification.}, }
@article {pmid38989842, year = {2024}, author = {Slusher, EK and Cottrell, T and Gariepy, T and Acebes-Doria, A and Querejeta Coma, M and Toledo, PFS and Schmidt, JM}, title = {A molecular approach to unravel trophic interactions between parasitoids and hyperparasitoids associated with pecan aphids.}, journal = {Journal of insect science (Online)}, volume = {24}, number = {4}, pages = {}, pmid = {38989842}, issn = {1536-2442}, mesh = {Animals ; *Aphids/parasitology/genetics ; *Food Chain ; *Host-Parasite Interactions ; Carya/parasitology ; DNA Barcoding, Taxonomic ; Wasps/physiology/genetics ; }, abstract = {Advances in molecular ecology can overcome many challenges in understanding host-parasitoid interactions. Genetic characterization of the key-players in systems helps to confirm species and identify trophic linkages essential for ecological service delivery by biological control agents; however, relatively few agroecosystems have been explored using this approach. Pecan production consists of a large tree perennial system containing an assortment of seasonal pests and natural enemies. As a first step to characterizing host-parasitoid associations in pecan food webs, we focus on aphid species and their parasitoids. Based on DNA barcoding of field-collected and reared specimens, we confirmed the presence of 3 species of aphid, one family of primary parasitoids, and 5 species of hyperparasitoids. By applying metabarcoding to field-collected aphid mummies, we were able to identify multiple species within each aphid mummy to unravel a complex food web of 3 aphids, 2 primary parasitoids, and upward of 8 hyperparasitoid species. The results of this study demonstrate that multiple hyperparasitoid species attack a single primary parasitoid of pecan aphids, which may have negative consequences for successful aphid biological control. Although further research is needed on a broader spatial scale, our results suggest multiple species exist in this system and may suggest a complex set of interactions between parasitoids, hyperparasitoids, and the 3 aphid species. This was the first time that many of these species have been characterized and demonstrates the application of novel approaches to analyze the aphid-parasitoid food webs in pecans and other tree crop systems.}, }
@article {pmid38989789, year = {2024}, author = {Ansai, E and Nitta, M and Saito, T and Kojima, Y and Waki, T}, title = {The first intermediate host of the invasive frog trematode Glypthelmins quieta in Japan.}, journal = {Diseases of aquatic organisms}, volume = {159}, number = {}, pages = {9-14}, doi = {10.3354/dao03799}, pmid = {38989789}, issn = {0177-5103}, mesh = {Animals ; Japan ; *Trematoda/genetics ; *Snails/parasitology ; Introduced Species ; Host-Parasite Interactions ; RNA, Ribosomal, 28S/genetics ; }, abstract = {Glypthelmins quieta is a frog trematode native to North and Central America. This trematode was recently detected in Japan in the American bullfrog Lithobates catesbeianus, which was introduced from North America to Japan. As the first intermediate host of G. quieta, typically a snail, has not yet been identified in Japan, we conducted a snail survey in eastern Japan to screen for an intermediate host using DNA barcoding based on the nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1. We sampled 3 different snail species, Orientogalba ollula, Physella acuta, and Sinotaia quadrata histrica (157 individuals in total), and only the freshwater snail Physella acuta, which is also believed to have been introduced from North America to Japan, had sporocysts of G. quieta in its hepatopancreas. The introduction of the intermediate and definitive hosts from North America may have facilitated the invasion of G. quieta into Japan.}, }
@article {pmid38988805, year = {2024}, author = {,  and Bragard, C and Baptista, P and Chatzivassiliou, E and Di Serio, F and Gonthier, P and Jaques Miret, JA and Justesen, AF and Magnusson, CS and Milonas, P and Navas-Cortes, JA and Parnell, S and Potting, R and Reignault, PL and Stefani, E and Thulke, HH and Van der Werf, W and Vicent Civera, A and Yuen, J and Zappalà, L and Grégoire, JC and Malumphy, C and Gobbi, A and Golic, D and Kertesz, V and Sfyra, O and MacLeod, A}, title = {Pest categorisation of Monema flavescens.}, journal = {EFSA journal. European Food Safety Authority}, volume = {22}, number = {7}, pages = {e8831}, pmid = {38988805}, issn = {1831-4732}, abstract = {The EFSA Panel on Plant Health performed a pest categorisation of Monema flavescens (Lepidoptera, Limacodidae), following the commodity risk assessment of Acer palmatum plants grafted on A. davidii from China, in which M. flavescens was identified as a pest of possible concern to the European Union. This species can be identified by morphological taxonomic keys and by barcoding. The adults of the overwintering generation emerge from late June to late August. The eggs are laid in groups on the underside of the host-plant leaves, on which the larvae feed throughout their six to eight larval instars. Pupation occurs in ovoid cocoons at the junction between twigs and branches, or on the trunk. Overwintering occurs as fully grown larvae or prepupae in their cocoon. There are one or two generations per year. M. flavescens is polyphagous and feeds on broadleaves; it has been reported on 51 plant species belonging to 24 families. It mainly occurs in Asia (Bhutan, China, the Democratic People's Republic of Korea, Japan, Nepal, the Republic of Korea), Russia (Eastern Siberia) and Taiwan. It is also present in the USA (Massachusetts). The pest's flight capacities are unknown. The main pathway for entry and spread is plants for planting with cocoons attached. This is partially closed by prohibition of some hosts. In several EU member states climatic conditions are conducive for establishment and many host plants are widespread. Introduction of M. flavescens may result in defoliations influencing tree health and forest diversity. The caterpillars also have urticating spines affecting human health. Phytosanitary measures are available to reduce the likelihood of entry, establishment and spread, and there is a definite potential for classical biological control. Recognising that natural enemies prevent M. flavescens being regarded as a pest in Asia, there is uncertainty regarding the magnitude of potential impact in EU depending on the influence of natural enemies. All criteria assessed by EFSA for consideration as a potential quarantine pest are met.}, }
@article {pmid38988182, year = {2025}, author = {Chen, MY and Tu, YC and Shyu, HY and Lin, TA and Juan, CP and Wu, FC}, title = {Using rDNA ITS2 barcoding to identify kratom (Mitragyna speciosa) from the genus Mitragyna and Neolamarckia cadamba.}, journal = {Electrophoresis}, volume = {46}, number = {3-4}, pages = {192-197}, doi = {10.1002/elps.202400003}, pmid = {38988182}, issn = {1522-2683}, mesh = {*Mitragyna/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Plant/genetics ; *DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA ; Polymerase Chain Reaction ; }, abstract = {This study collected 80 samples of suspected kratom plant powder. A polymerase chain reaction sequence analysis was conducted using two sets of DNA barcode primers for plant ribosomal (r)DNA internal transcribed spacers (ITSs), namely, ITS3/ITS4 and ITS-p3/ITS-u4. Among the 80 samples, 40 were analyzed using the ITS3/ITS4 primer pair, and then DNA sequences were subjected to a National Center for Biotechnology Information-Basic Local Alignment Search Tool (NCBI-BLAST) comparison. Results showed that 29 samples had a 100% match (364/364) with Mitragyna speciosa (kratom), and 6 samples had a 99.73% match (363/364) with M. speciosa, whereas 5 samples had disordered and unreadable sequences. The 5 unreadable samples and an additional 40 suspected kratom samples were then analyzed using the ITS-p3/ITS-u4 primer pair, followed by an NCBI-BLAST comparison. Among these, 32 samples had a 100% match (404/404) with M. speciosa, and 11 samples had a 99.75% match (403/404) with M. speciosa. Among the samples with sequences matching M. speciosa, three distinct types were observed (no variance/404, 287M/404, and 287A/404). One sample had a 99.51% match (404/406) with Neolamarckia cadamba, and another sample had a sequencing length of 305 bp, with 25 positions showing mixed base pairs, indicating a mixture of different species. Analysis of the mixed base pair pattern suggested a possible mixture of M. speciosa and N. cadamba. Actually, M. speciosa and N. cadamba have very similar external morphologies. This indicates that the ITS-p3/ITS-u4 primer pair is effective in distinguishing mixtures of M. speciosa and N. cadamba and is thus more suitable than ITS3/ITS4 for identifying and analyzing samples of suspected kratom plant powder.}, }
@article {pmid38987689, year = {2024}, author = {Wu, X and Wang, M and Li, X and Chen, Y and Liao, Z and Zhang, D and Wen, Y and Wang, S}, title = {Identification and characterization of a new species of Taxus - Taxus qinlingensis by multiple taxonomic methods.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {658}, pmid = {38987689}, issn = {1471-2229}, support = {CX2018B435//Hunan Provincial Innovation Foundation for Postgraduate/ ; 31470666//National Natural Science Foundation of China/ ; }, mesh = {*Taxus/genetics/anatomy &amp; histology/classification ; *Phylogeny ; *Plant Leaves/anatomy &amp; histology/genetics ; *DNA Barcoding, Taxonomic ; China ; DNA, Plant/genetics ; Phenotype ; }, abstract = {BACKGROUND: The taxonomy of Taxus Linn. remains controversial due to its continuous phenotypic variation and unstable topology, thus adversely affecting the formulation of scientific conservation strategies for this genus. Recently, a new ecotype, known as Qinling type, is mainly distributed in the Qinling Mountains and belongs to a monophyletic group. Here, we employed multiple methods including leaf phenotype comparison (leaf shapes and microstructure), DNA barcoding identification (ITS + trnL-trnF + rbcL), and niche analysis to ascertain the taxonomic status of the Qinling type.<br><br>RESULTS: Multiple comparisons revealed significant differences in the morphological characters (length, width, and length/width ratio) among the Qinling type and other Taxus species. Leaf anatomical analysis indicated that only the Qinling type and T. cuspidata had no papilla under the midvein or tannins in the epicuticle. Phylogenetic analysis of Taxus indicated that the Qinling type belonged to a monophyletic group. Moreover, the Qinling type had formed a relatively independent niche, it was mainly distributed around the Qinling Mountains, Ta-pa Mountains, and Taihang Mountains, situated at an elevation below 1500&#xa0;m.<br><br>CONCLUSIONS: Four characters, namely leaf curvature, margin taper, papillation on midvein, and edges were put forward as primary indexes for distinguishing Taxus species. The ecotype Qingling type represented an independent evolutionary lineage and formed a unique ecological niche. Therefore, we suggested that the Qingling type should be treated as a novel species and named it Taxus qinlingensis Y. F. Wen &amp; X. T. Wu, sp. nov.}, }
@article {pmid38985195, year = {2024}, author = {Corradini, B and Gianfreda, D and Ferri, G and Ferrari, F and Borciani, I and Santunione, AL and Cecchi, R}, title = {Forensic species identification: practical guide for animal and plant DNA analysis.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2271-2280}, pmid = {38985195}, issn = {1437-1596}, mesh = {Animals ; Humans ; DNA/analysis ; DNA Fingerprinting/methods ; *DNA, Plant/genetics ; *Forensic Genetics/methods ; Microsatellite Repeats ; Species Specificity ; Specimen Handling/methods ; }, abstract = {The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.}, }
@article {pmid38984293, year = {2024}, author = {Ollinger, N and Malachova, A and Sulyok, M and Krska, R and Weghuber, J}, title = {Mycotoxin contamination in moldy slices of bread is mostly limited to the immediate vicinity of the visible infestation.}, journal = {Food chemistry: X}, volume = {23}, number = {}, pages = {101563}, pmid = {38984293}, issn = {2590-1575}, abstract = {Bread is an important staple food that is susceptible to spoilage, making it one of the most wasted foods. To determine the safety of partially moldy bread, five types of bread were inoculated with common mold species. After incubation, the metabolite profile was determined in and under the inoculation spot, as well as at a lateral distance of 3 cm from the moldy spot. The result showed that the metabolites were exclusively concentrated in the inoculation area and directly below the inoculation area. The only exception was citrinin, a mycotoxin produced by Penicillia such as Penicillium citrinum, which was detected in almost all tested bread areas when inoculated with the corresponding strains. The results of our study suggest that the removal of moldy parts may be a solution to reduce food waste if the remaining bread is to be used, for example for insect farming to produce animal feed.}, }
@article {pmid38982951, year = {2024}, author = {Yang, S and Xu, Y and Lin, R and Feng, X and Wang, K and Wang, Z and Cui, K and Chen, S and Wang, Z and Wang, X and Chen, S and Zhang, W and Zhu, C and Gao, Z}, title = {Conformation-Driven Responsive 1D and 2D Lanthanide-Metal-Organic Framework Heterostructures for High-Security Photonic Barcodes.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {20}, number = {44}, pages = {e2402890}, doi = {10.1002/smll.202402890}, pmid = {38982951}, issn = {1613-6829}, support = {22275104//National Natural Science Foundation of China/ ; ZR2021YQ06//Shandong Provincial Natural Science Foundation/ ; tsqn202306255//Taishan Scholar Program of Shandong Province/ ; kq2206026//The Training Program for Excellent Young Innovators of Changsha/ ; }, abstract = {Development of luminescent segmented heterostructures featuring multiple spatial-responsive blocks is important to achieve miniaturized photonic barcodes toward anti-counterfeit applications. Unfortunately, dynamic manipulation of the spatial color at micro/nanoscale still remains a formidable challenge. Here, a straightforward strategy is proposed to construct spatially varied heterostructures through amplifying the conformation-driven response in flexible lanthanide-metal-organic frameworks (Ln-MOFs), where the thermally induced minor conformational changes in organic donors dramatically modulate the photoluminescence of Ln acceptors. Notably, compositionally and structurally distinct heterostructures (1D and 2D) are further constructed through epitaxial growth of multiple responsive MOF blocks benefiting from the isomorphous Ln-MOF structures. The thermally controlled emissive colors with distinguishable spectra carry the fingerprint information of a specific heterostructure, thus allowing for the effective construction of smart photonic barcodes with spatially responsive characteristics. The results will deepen the understanding of the conformation-driven responsive mechanism and also provide guidance to fabricate complex stimuli-responsive hierarchical microstructures for advanced optical recording and high-security labels.}, }
@article {pmid38979326, year = {2024}, author = {Hotinger, JA and Campbell, IW and Hullahalli, K and Osaki, A and Waldor, MK}, title = {Quantification of Salmonella enterica serovar Typhimurium Population Dynamics in Murine Infection Using a Highly Diverse Barcoded Library.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38979326}, issn = {2692-8205}, support = {R01 AI042347/AI/NIAID NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; F31 AI156949/AI/NIAID NIH HHS/United States ; T32 DK007477/DK/NIDDK NIH HHS/United States ; P30 CA006516/CA/NCI NIH HHS/United States ; }, abstract = {Murine models are often used to study the pathogenicity and dissemination of the enteric pathogen Salmonella enterica serovar Typhimurium. Here, we quantified S. Typhimurium population dynamics in mice using the STAMPR analytic pipeline and a highly diverse S. Typhimurium barcoded library containing [~]55,000 unique strains distinguishable by genomic barcodes by enumerating S. Typhimurium founding populations and deciphering routes of spread in mice. We found that a severe bottleneck allowed only one in a million cells from an oral inoculum to establish a niche in the intestine. Furthermore, we observed compartmentalization of pathogen populations throughout the intestine, with few barcodes shared between intestinal segments and feces. This severe bottleneck widened and compartmentalization was reduced after streptomycin treatment, suggesting the microbiota plays a key role in restricting the pathogen's colonization and movement within the intestine. Additionally, there was minimal sharing between the intestine and extraintestinal organ populations, indicating dissemination to extraintestinal sites occurs rapidly, before substantial pathogen expansion in the intestine. Bypassing the intestinal bottleneck by inoculating mice via intravenous or intraperitoneal injection revealed that Salmonella re-enters the intestine after establishing niches in extraintestinal sites by at least two distinct pathways. One pathway results in a diverse intestinal population. The other re-seeding pathway is through the bile, where the pathogen is often clonal, leading to clonal intestinal populations and correlates with gallbladder pathology. Together, these findings deepen our understanding of Salmonella population dynamics.}, }
@article {pmid38979006, year = {2024}, author = {Ren, J and Ren, L and Zhang, R}, title = {Delimiting species, revealing cryptic diversity, and population divergence in Qinghai-Tibet Plateau weevils through DNA barcoding.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11592}, pmid = {38979006}, issn = {2045-7758}, abstract = {The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.}, }
@article {pmid38979002, year = {2024}, author = {Nakagawa, K and Ogino, K and Katoh, TK and Kono, N}, title = {Species identification of livefood flightless fly (Torinido-shoujoubae) through DNA barcoding.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11622}, pmid = {38979002}, issn = {2045-7758}, abstract = {Torinido-shoujoubae, as it is called in Japanese, is a flightless Drosophila sp. that is sold commercially in Japan. This Drosophila sp. is often used as feeds for model organisms such as reptiles and spiders. There is no scientific name provided for the fruit fly that is known as Torinido-shoujoubae, as well as any historical background or data behind this species. There has been a previous study that was conducted through morphological characteristics analysis of the body as well as the male copulatory organ and has been estimated as Drosophila hydei. The objective of this study was to determine the species of this unidentified fly known as Torinido-shoujoubae based on a molecular evidence with a DNA barcoding. Samples were purchased from four separate suppliers to examine whether there are any differences between them. COI regions were amplified using PCR and the sequenced results were aligned against two databases, NCBI and BOLD. Torinido-shoujoubae samples provided from all suppliers were confirmed to be D. hydei.}, }
@article {pmid38973066, year = {2024}, author = {Kumano, S and Tanaka, K and Akahori, R and Yanagiya, A and Nojima, A}, title = {Using peptide barcodes for simultaneous profiling of protein expression from mRNA.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {38}, number = {18}, pages = {e9867}, doi = {10.1002/rcm.9867}, pmid = {38973066}, issn = {1097-0231}, support = {//Hitachi Ltd/ ; //ARCALIS Inc./ ; }, mesh = {*RNA, Messenger/genetics/analysis ; *Green Fluorescent Proteins/genetics/chemistry/metabolism ; *Peptides/chemistry/analysis/genetics/metabolism ; Humans ; Mass Spectrometry/methods ; Gene Expression Profiling/methods ; }, abstract = {RATIONALE: mRNA technology has begun to play a significant role in the areas of therapeutic intervention and vaccine development. However, optimizing the mRNA sequence that influences protein expression levels is a resource-intensive and time-consuming process. This study introduces a new method to accelerate the selection of sequences of mRNA for optimal protein expression.<br><br>METHODS: We designed the mRNA sequences in such a way that a unique peptide barcode, corresponding to each mRNA sequence, is attached to the expressed protein. These barcodes, cleaved off by a protease and simultaneously quantified by mass spectrometry, reflect the protein expression, enabling a parallel analysis. We validated this method using two mRNAs, each with different untranslated regions (UTRs) but encoding enhanced green fluorescence protein (eGFP), and investigated whether the peptide barcodes could analyze the differential eGFP expression levels.<br><br>RESULTS: The fluorescence intensity of eGFP, a marker of its expression level, has shown noticeable changes between the two UTR sequences in mRNA-transfected cells when measured using flow cytometry. This suggests alterations in the expression level of eGFP due to the influence of different UTR sequences. Furthermore, the quantified amount of peptide barcodes that were released from eGFP showed consistent patterns with these changes.<br><br>CONCLUSIONS: The experimental findings suggest that peptide barcodes serve as a valuable tool for assessing protein expression levels. The process of mRNA sequence selection, aimed at maximizing protein expression, can be enhanced by the parallel analysis of peptide barcodes using mass spectrometry.}, }
@article {pmid38972989, year = {2024}, author = {Ng, DYM and Sun, W and Sit, THC and Brackman, CJ and Tse, ACN and Bui, CHT and Tang, AWY and Wong, ANC and Tsang, ATL and Koo, JCT and Cheng, SMS and Peiris, M and Chin, AWH and Poon, LLM}, title = {Genetic diversity of astroviruses detected in wild aquatic birds in Hong Kong.}, journal = {Virology journal}, volume = {21}, number = {1}, pages = {153}, pmid = {38972989}, issn = {1743-422X}, support = {U01 AI151810/AI/NIAID NIH HHS/United States ; U01AI151810//Division of Microbiology and Infectious Diseases/ ; T11-705/21-N//Research Grants Council, University Grants Committee/ ; }, mesh = {Animals ; Hong Kong ; *Phylogeny ; *Genetic Variation ; *Birds/virology ; *Genome, Viral ; *Feces/virology ; *Astroviridae Infections/veterinary/virology ; Animals, Wild/virology ; Bird Diseases/virology ; High-Throughput Nucleotide Sequencing ; Avastrovirus/genetics/classification/isolation &amp; purification ; RNA, Viral/genetics ; Open Reading Frames ; Astroviridae/genetics/isolation &amp; purification/classification ; }, abstract = {Wild waterfowl serve as a reservoir of some astroviruses. Fecal samples from wild waterfowl collected at Hong Kong's Marshes were tested using pan-astrovirus reverse transcription-PCR. Positive samples underwent subsequent host identification using DNA barcoding. Based on deduced partial sequences, noteworthy samples from three astrovirus groups (mammalian, avian and unclassified astroviruses) were further analyzed by next-generation sequencing. One sample of Avastrovirus 4 clade, MP22-196, had a nearly complete genome identified. The results of ORF2 phylogenetic analysis and genetic distance analysis indicate that Avastrovirus 4 is classified as a distinct subclade within Avastrovirus. MP22-196 has typical astrovirus genome characteristics. The unique characteristics and potential differences of this genome, compared to other avian astrovirus sequences, involve the identification of a modified sgRNA sequence situated near the ORF2 start codon, which precedes the ORF1b stop codon. Additionally, the 3' UTR of MP22-196 is shorter than other avian astroviruses. This study expands our understanding of the Avastrovirus 4 clade.}, }
@article {pmid38972540, year = {2024}, author = {Mizuno, T and Tokoro, M and Yagi, T and Wada, E and Yamadori, I and Arai, M}, title = {Infant gastrointestinal canthariasis caused by cigarette beetle (Lasioderma serricorne).}, journal = {Parasitology international}, volume = {103}, number = {}, pages = {102921}, doi = {10.1016/j.parint.2024.102921}, pmid = {38972540}, issn = {1873-0329}, mesh = {Animals ; Male ; *Coleoptera/parasitology ; *Larva/growth &amp; development ; Child, Preschool ; Humans ; Polymerase Chain Reaction ; }, abstract = {Diseases caused by beetle larvae infestation are known as intestinal canthariasis. Canthariasis from the cigarette beetle, Lasioderma serricorne, is quite rare; however, with the accumulation of genetic references, such cases of accidental pseudo-parasitism have been increasingly recognized. Here, we describe a case of asymptomatic gastrointestinal passage of L. serricorne in a 4-year-old male. Larval identification was conducted by PCR-sequencing targeting cytochrome c oxidase subunit 1 using DNA extracted from the larvae. Due to the difficulty of differential identification of beetles using larval morphology, DNA barcoding is essential.}, }
@article {pmid38969342, year = {2024}, author = {Serio, RN and Scheben, A and Lu, B and Gargiulo, DV and Patruno, L and Buckholtz, CL and Chaffee, RJ and Jibilian, MC and Persaud, SG and Staklinski, SJ and Hassett, R and Brault, LM and Ramazzotti, D and Barbieri, CE and Siepel, AC and Nowak, DG}, title = {Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer.}, journal = {Cancer discovery}, volume = {14}, number = {10}, pages = {1990-2009}, pmid = {38969342}, issn = {2159-8290}, support = {T32 CA203702/CA/NCI NIH HHS/United States ; R35-GM127070//National Institutes of Health (NIH)/ ; R35 GM127070/GM/NIGMS NIH HHS/United States ; Research Scholar Grant//American Cancer Society (ACS)/ ; 22790//Cancer Research UK (CRUK)/ ; T32 GM141949/GM/NIGMS NIH HHS/United States ; T32CA203702//National Cancer Institute (NCI)/ ; P30 CA045508/CA/NCI NIH HHS/United States ; 1T32GM141949//National Institutes of Health (NIH)/ ; W81XWH-22-1-0068//Department of Defense Education Activity (DoDEA)/ ; 22790//Fondazione AIRC per la ricerca sul cancro ETS (AIRC)/ ; 5T32GM141949//National Institutes of Health (NIH)/ ; R01-CA272466//National Cancer Institute (NCI)/ ; R01 CA272466/CA/NCI NIH HHS/United States ; Centennial Scholarship//Starr Foundation (TSF)/ ; }, mesh = {Male ; *Prostatic Neoplasms/pathology/genetics ; Animals ; Mice ; Humans ; *Neoplasm Metastasis ; Cell Movement ; Disease Models, Animal ; }, abstract = {The patterns by which primary tumors spread to metastatic sites remain poorly understood. Here, we define patterns of metastatic seeding in prostate cancer using a novel injection-based mouse model-EvoCaP (Evolution in Cancer of the Prostate), featuring aggressive metastatic cancer to bone, liver, lungs, and lymph nodes. To define migration histories between primary and metastatic sites, we used our EvoTraceR pipeline to track distinct tumor clones containing recordable barcodes. We detected widespread intratumoral heterogeneity from the primary tumor in metastatic seeding, with few clonal populations instigating most migration. Metastasis-to-metastasis seeding was uncommon, as most cells remained confined within the tissue. Migration patterns in our model were congruent with human prostate cancer seeding topologies. Our findings support the view of metastatic prostate cancer as a systemic disease driven by waves of aggressive clones expanding their niche, infrequently overcoming constraints that otherwise keep them confined in the primary or metastatic site. Significance: Defining the kinetics of prostate cancer metastasis is critical for developing novel therapeutic strategies. This study uses CRISPR/Cas9-based barcoding technology to accurately define tumor clonal patterns and routes of migration in a novel somatically engineered mouse model (EvoCaP) that recapitulates human prostate cancer using an in-house developed analytical pipeline (EvoTraceR).}, }
@article {pmid38968228, year = {2024}, author = {Chaumeau, V and Piarroux, M and Kulabkeeree, T and Sawasdichai, S and Inta, A and Watthanaworawit, W and Nosten, F and Piarroux, R and Nabet, C}, title = {Identification of Southeast Asian Anopheles mosquito species using MALDI-TOF mass spectrometry.}, journal = {PloS one}, volume = {19}, number = {7}, pages = {e0305167}, pmid = {38968228}, issn = {1932-6203}, mesh = {Animals ; *Anopheles/genetics/classification ; Asia, Southeastern ; DNA Barcoding, Taxonomic/methods ; Malaria/transmission ; Mosquito Vectors/genetics/classification ; Species Specificity ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Thailand ; }, abstract = {Malaria elimination in Southeast Asia remains a challenge, underscoring the importance of accurately identifying malaria mosquitoes to understand transmission dynamics and improve vector control. Traditional methods such as morphological identification require extensive training and cannot distinguish between sibling species, while molecular approaches are costly for extensive screening. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and cost-effective tool for Anopheles species identification, yet its current use is limited to few specialized laboratories. This study aimed to develop and validate an online reference database for MALDI-TOF MS identification of Southeast Asian Anopheles species. The database, constructed using the in-house data analysis pipeline MSI2 (Sorbonne University), comprised 2046 head mass spectra from 209 specimens collected at the Thailand-Myanmar border. Molecular identification via COI and ITS2 DNA barcodes enabled the identification of 20 sensu stricto species and 5 sibling species complexes. The high quality of the mass spectra was demonstrated by a MSI2 median score (min-max) of 61.62 (15.94-77.55) for correct answers, using the best result of four technical replicates of a test panel. Applying an identification threshold of 45, 93.9% (201/214) of the specimens were identified, with 98.5% (198/201) consistency with the molecular taxonomic assignment. In conclusion, MALDI-TOF MS holds promise for malaria mosquito identification and can be scaled up for entomological surveillance in Southeast Asia. The free online sharing of our database on the MSI2 platform (https://msi.happy-dev.fr/) represents an important step towards the broader use of MALDI-TOF MS in malaria vector surveillance.}, }
@article {pmid38966247, year = {2024}, author = {Turanov, SV and Koltsova, MA and Rutenko, OA}, title = {Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11631}, pmid = {38966247}, issn = {2045-7758}, abstract = {Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at the within-species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode.}, }
@article {pmid38965520, year = {2024}, author = {, }, title = {Retraction Note: DNA barcoding detects contamination and substitution in North American herbal products.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {279}, doi = {10.1186/s12916-024-03504-x}, pmid = {38965520}, issn = {1741-7015}, }
@article {pmid38965405, year = {2024}, author = {LeSavage, BL and Zhang, D and Huerta-López, C and Gilchrist, AE and Krajina, BA and Karlsson, K and Smith, AR and Karagyozova, K and Klett, KC and Huang, MS and Long, C and Kaber, G and Madl, CM and Bollyky, PL and Curtis, C and Kuo, CJ and Heilshorn, SC}, title = {Engineered matrices reveal stiffness-mediated chemoresistance in patient-derived pancreatic cancer organoids.}, journal = {Nature materials}, volume = {23}, number = {8}, pages = {1138-1149}, pmid = {38965405}, issn = {1476-4660}, support = {DP1CA238296//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U01 DK127395/DK/NIDDK NIH HHS/United States ; CBET 2033302//National Science Foundation (NSF)/ ; R01 EB027171/EB/NIBIB NIH HHS/United States ; U01CA217851//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; U54CA224081//U.S. Department of Health Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Drug Resistance, Neoplasm ; *Organoids/metabolism/pathology/drug effects ; *Pancreatic Neoplasms/metabolism/pathology/drug therapy/genetics ; *Carcinoma, Pancreatic Ductal/metabolism/pathology/genetics/drug therapy ; *Extracellular Matrix/metabolism ; Hyaluronic Acid/metabolism/chemistry ; Antineoplastic Agents/pharmacology/therapeutic use ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is characterized by its fibrotic and stiff extracellular matrix. However, how the altered cell/extracellular-matrix signalling contributes to the PDAC tumour phenotype has been difficult to dissect. Here we design and engineer matrices that recapitulate the key hallmarks of the PDAC tumour extracellular matrix to address this knowledge gap. We show that patient-derived PDAC organoids from three patients develop resistance to several clinically relevant chemotherapies when cultured within high-stiffness matrices mechanically matched to in vivo tumours. Using genetic barcoding, we find that while matrix-specific clonal selection occurs, cellular heterogeneity is not the main driver of chemoresistance. Instead, matrix-induced chemoresistance occurs within a stiff environment due to the increased expression of drug efflux transporters mediated by CD44 receptor interactions with hyaluronan. Moreover, PDAC chemoresistance is reversible following transfer from high- to low-stiffness matrices, suggesting that targeting the fibrotic extracellular matrix may sensitize chemoresistant tumours. Overall, our findings support the potential of engineered matrices and patient-derived organoids for elucidating extracellular matrix contributions to human disease pathophysiology.}, }
@article {pmid38963889, year = {2024}, author = {Wu, R and Liu, L and Zhang, L and Bogan, AE and Niu, G and Jin, D and Wu, X and Liu, X}, title = {Taxonomic revision of two species in the genus Ptychorhynchus Simpson, 1900 (Bivalvia: Unionidae: Gonideinae), with description of a new species.}, journal = {Invertebrate systematics}, volume = {38}, number = {}, pages = {}, doi = {10.1071/IS24014}, pmid = {38963889}, issn = {1447-2600}, mesh = {Animals ; *Phylogeny ; *Unionidae/genetics/classification/anatomy &amp; histology ; *Species Specificity ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; }, abstract = {Accurate identification and precise classification of freshwater mussel species that are among the most threatened freshwater taxa in the world, play a crucial role in informing conservation and management efforts for these organisms. However, due to the variability in shell morphology, relying solely on shell characteristics for species taxonomy poses significant challenges, thereby impeding effective conservation planning and management. The freshwater mussel genus Ptychorhynchus Simpson, 1900 is one such group in need of study. We integrate molecular phylogeny, shell morphology and soft-body anatomy to examine the classification of Ptychorhynchus denserugata (Haas, 1910) and Ptychorhynchus resupinatus (von Martens, 1902). The COI barcoding data support the clustering of P. denserugata and Nodularia douglasiae within a single clade, and P. denserugata shares the diagnostic feature of the genus Nodularia , i.e. knobs or bumps on the inner mantle surface in the excurrent aperture. Therefore, by integrating molecular data and anatomical characteristics, we confirm that the nominal species P. denserugata syn. nov. is a new synonym for N. douglasiae . The multi-locus (COI + ND1 + 16S rRNA + 18S rRNA + 28S rRNA) phylogeny and mitochondrial phylogenomics support the transfer of P. resupinatus from Ptychorhynchus to the newly elevated genus Cosmopseudodon stat. rev., as Cosmopseudodon resupinatus stat. rev. that is still considered the designated type species. We also describe a new species based on integrative taxonomy, i.e. Cosmopseudodon wenshanensis sp. nov. The comprehensive understanding of the taxonomy and diversity of the revised Cosmopseudodon species, and shell heteromorphism of N. douglasiae (=P. denserugata syn. nov.), will serve as a crucial foundation for further scientific assessment and conservation strategies pertaining to these taxa. ZooBank: urn:lsid:zoobank.org:pub:E48968B1-DF0F-42AD-8F31-B8C95F23CE57.}, }
@article {pmid38962025, year = {2024}, author = {Mamadashvili, G and Brin, A and Chumak, M and Diedus, V and Drössler, L and Förster, B and Georgiev, KB and Ghrejyan, T and Hleb, R and Kalashian, M and Kamburov, I and Karagyan, G and Kevlishvili, J and Khutsishvili, Z and Larrieu, L and Mazmanyan, M and Petrov, PI and Tabunidze, L and Bässler, C and Müller, J}, title = {Drivers of wood-inhabiting fungal diversity in European and Oriental beech forests.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11660}, pmid = {38962025}, issn = {2045-7758}, abstract = {The hyperdiverse wood-inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood-drilling samples in 18 forests from France to Armenia and identified fungi by meta-barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old-growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old-growth forests.}, }
@article {pmid38962021, year = {2024}, author = {Ma, Y and López-Pujol, J and Yan, D and Zhou, Z and Deng, Z and Niu, J}, title = {Complete chloroplast genomes of the hemiparasitic genus Cymbaria: Insights into comparative analysis, development of molecular markers, and phylogenetic relationships.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11677}, pmid = {38962021}, issn = {2045-7758}, abstract = {The hemiparasitic tribe Cymbarieae (Orobanchaceae) plays a crucial role in elucidating the initial stage of the transition from autotrophism to heterotrophism. However, the complete chloroplast genome of the type genus Cymbaria has yet to be reported. In addition, the traditional Mongolian medicine Cymbaria daurica is frequently subjected to adulteration or substitution because of the minor morphological differences with Cymbaria mongolica. In this study, the complete chloroplast genomes of the two Cymbaria species were assembled and annotated, and those of other published 52 Orobanchaceae species were retrieved for comparative analyses. We found that the Cymbaria chloroplast genomes are characterized by pseudogenization or loss of stress-relevant genes (ndh) and a unique rbcL-matK inversion. Unlike the high variability observed in holoparasites, Cymbaria and other hemiparasites exhibit high similarity to autotrophs in genome size, guanine-cytosine (GC) content, and intact genes. Notably, four pairs of specific DNA barcodes were developed and validated to distinguish the medicinal herb from its adulterants. Phylogenetic analyses revealed that the genus Cymbaria and the Schwalbea-Siphonostegia clade are grouped into the tribe Cymbarieae, which forms a sister clade to the remaining Orobanchaceae parasitic lineages. Moreover, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. Our findings provide valuable genetic resources for studying the phylogeny of Orobanchaceae and plant parasitism, and genetic tools to validate the authenticity of the traditional Mongolian medicine "Xinba.".}, }
@article {pmid38959129, year = {2024}, author = {Luo, J and Walsh, E and Faulborn, A and Gao, K and White, J and Zhang, N}, title = {Pinibarreniales, a new order of Sordariomycetes from pine barrens ecosystem.}, journal = {Mycologia}, volume = {116}, number = {5}, pages = {835-847}, doi = {10.1080/00275514.2024.2363084}, pmid = {38959129}, issn = {1557-2536}, support = {DEB 2224067//US National Science Foundation/ ; }, mesh = {*Phylogeny ; *Ecosystem ; *Plant Roots/microbiology ; *Ascomycota/classification/genetics/isolation &amp; purification ; DNA, Fungal/genetics ; New Jersey ; Arabidopsis/microbiology ; Blueberry Plants/microbiology ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Pinus/microbiology ; DNA Barcoding, Taxonomic ; }, abstract = {Pinibarrenia chlamydospora, sp. nov. isolated from the roots of highbush blueberry in the New Jersey Pine Barrens, is described and illustrated. Based on multigene phylogenetic analysis, as well as morphological and ecological characteristics, Pinibarreniales and Pinibarreniaceae are established to accommodate this novel lineage in Sordariomycetidae, Sordariomycetes. Pinibarreniales, Tracyllalales, and Vermiculariopsiellales are proposed to be included in the subclass Sordariomycetidae. Pinibarreniales likely have a wide distribution and forms association with Ericaceae plants that live in acidic and oligotrophic environments because its DNA barcode matches with environmental sequences from other independent ecological studies. The plant-fungal interaction experiment revealed negative impacts on Arabidopsis, indicating its pathogenicity. This uncovered new fungal lineage will contribute to a better understanding of the diversity and systematics of Sordariomycetes.}, }
@article {pmid38958078, year = {2024}, author = {Xu, Z and Chen, L and Lin, X and Lyu, Y and Zhou, M and Chen, H and Zhang, H and Zhang, T and Chen, Y and Suo, Y and Liang, Q and Qin, Z and Wang, Y}, title = {Single Nucleus Total RNA Sequencing of Formalin-Fixed Paraffin-Embedded Gliomas.}, journal = {Small methods}, volume = {8}, number = {10}, pages = {e2301801}, doi = {10.1002/smtd.202301801}, pmid = {38958078}, issn = {2366-9608}, support = {32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; 82200977//National Natural Science Foundation of China/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//"Pioneer" R&amp;D programs of Zhejiang Province/ ; 2024SSYS0022//Key R&amp;D Program of Zhejiang/ ; Y-zai2021/qn-0204//Beijing Xisike Clinical Oncology Research Foundation/ ; Y-zai2021/zd-0207//Beijing Xisike Clinical Oncology Research Foundation/ ; }, mesh = {Humans ; *Glioma/genetics/pathology ; *Paraffin Embedding ; *Formaldehyde/chemistry ; *Brain Neoplasms/genetics/pathology ; *Single-Cell Analysis/methods ; *Sequence Analysis, RNA/methods ; Tissue Fixation ; Cell Nucleus/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Untranslated/genetics ; }, abstract = {Gliomas, the predominant form of brain cancer, comprise diverse malignant subtypes with limited curative therapies available. The insufficient understanding of their molecular diversity and evolutionary processes hinders the advancement of new treatments. Technical complexities associated with formalin-fixed paraffin-embedded (FFPE) clinical samples hinder molecular-level analyses of gliomas. Current single-cell RNA sequencing (scRNA-seq) platforms are inadequate for large-scale clinical applications. In this study, automated snRandom-seq is developed, a high-throughput single-nucleus total RNA sequencing platform optimized for archival FFPE samples. This platform integrates automated single-nucleus isolation and droplet barcoding systems with the random primer-based scRNA-seq chemistry, accommodating a broad spectrum of sample types. The automated snRandom-seq is applied to analyze 116 492 single nuclei from 17 FFPE samples of various glioma subtypes, including rare clinical samples and matched primary-recurrent glioblastomas (GBMs). The study provides comprehensive insights into the molecular characteristics of gliomas at the single-cell level. Abundant non-coding RNAs (ncRNAs) with distinct expression profiles across different glioma clusters and uncovered promising recurrence-related targets and pathways in primary-recurrent GBMs are identified. These findings establish automated snRandom-seq as a robust tool for scRNA-seq of FFPE samples, enabling exploration of molecular diversities and tumor evolution. This platform holds significant implications for large-scale integrative and retrospective clinical research.}, }
@article {pmid38956928, year = {2024}, author = {Doorenweerd, C and San Jose, M and Leblanc, L and Barr, N and Geib, SM and Chung, AYC and Dupuis, JR and Ekayanti, A and Fiegalan, E and Hemachandra, KS and Aftab Hossain, M and Huang, CL and Hsu, YF and Morris, KY and Maryani A Mustapeng, A and Niogret, J and Pham, TH and Thi Nguyen, N and Sirisena, UGAI and Todd, T and Rubinoff, D}, title = {Towards a better future for DNA barcoding: Evaluating monophyly- and distance-based species identification using COI gene fragments of Dacini fruit flies.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13987}, doi = {10.1111/1755-0998.13987}, pmid = {38956928}, issn = {1755-0998}, support = {8130-0565//United States Department of Agriculture/ ; 8130-0665//United States Department of Agriculture/ ; 8130-0893//United States Department of Agriculture/ ; HAW00942-H//United States Department of Agriculture/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/genetics/classification ; }, abstract = {The utility of a universal DNA 'barcode' fragment (658 base pairs of the Cytochrome C Oxidase I [COI] gene) has been established as a useful tool for species identification, and widely criticized as one for understanding the evolutionary history of a group. Large amounts of COI sequence data have been produced that hold promise for rapid species identification, for example, for biosecurity. The fruit fly tribe Dacini holds about a thousand species, of which 80 are pests of economic concern. We generated a COI reference library for 265 species of Dacini containing 5601 sequences that span most of the COI gene using circular consensus sequencing. We compared distance metrics versus monophyly assessments for species identification and although we found a 'soft' barcode gap around 2% pairwise distance, the exceptions to this rule dictate that a monophyly assessment is the only reliable method for species identification. We found that all fragments regularly used for Dacini fruit fly identification >450 base pairs long provide similar resolution. 11.3% of the species in our dataset were non-monophyletic in a COI tree, which is mostly due to species complexes. We conclude with recommendations for the future generation and use of COI libraries. We revise the generic assignment of Dacus transversus stat. rev. Hardy 1982, and Dacus perpusillus stat. rev. Drew 1971 and we establish Dacus maculipterus White 1998 syn. nov. as a junior synonym of Dacus satanas Liang et al. 1993.}, }
@article {pmid38955202, year = {2024}, author = {Nath, A and Gangopadhayya, A and Ghuge, O and Kumar, S and Ramdasi, A and Karlekar, S and Sudeep, AB and Lole, KS}, title = {Determination of Species Identity and Genetic Diversity of Aedes aegypti and Other Medically Important Mosquitoes of India Using DNA Barcoding.}, journal = {The American journal of tropical medicine and hygiene}, volume = {111}, number = {2}, pages = {324-332}, pmid = {38955202}, issn = {1476-1645}, mesh = {Animals ; India ; *Aedes/genetics/classification/virology ; *DNA Barcoding, Taxonomic ; *Genetic Variation ; *Phylogeny ; *Mosquito Vectors/genetics/classification ; Electron Transport Complex IV/genetics ; Culex/genetics/classification/virology ; Anopheles/genetics/classification ; Species Specificity ; }, abstract = {Aedes aegypti-borne viruses (i.e., dengue, chikungunya, and Zika) have become endemic to India, posing a severe threat to public health. Vector control remains the mainstay of disease management due to nonavailability of licensed vaccines/therapeutics. Conventional morpho-taxonomical methods cannot differentiate between closely related sibling species or species complexes, and hence we evaluated two molecular markers, mitochondrial cytochrome c oxidase subunit 1 (Cox1) and nuclear DNA internal transcribed spacer 2 (-2) gene sequences, to characterize seven populations of Ae. aegypti and four medically important mosquito species (Aedes albopictus, Anopheles stephensi, Culex tritaeniorhyncus, and Culex murrelli). DNA extracted from the 11 mosquito populations (two mosquitoes per population) was polymerase chain reaction amplified, sequenced, and analyzed. Molecular characterization was found to be congruent with morphological identification, suggesting no variants or cryptic species exist in Ae. aegypti and the other mosquitoes studied. Phylogenetic analysis with sequences obtained with Cox1 gene of Ae. aegypti and other Aedes and non-Aedes mosquito species showed clustering of sequences from different species representing different clades, distinctly separating one taxon from the other, whereas ITS-2 sequences of Aedes aegypti from across the world clustered tightly. Nucleotide divergence values revealed a low percentage of intraspecies variation and a higher percentage of interspecies variation. The present study authenticates the applicability of Cox1 and ITS-2 in the precise identification of Ae. aegypti mosquitoes against cryptic or sibling species. Cox1 appeared to be a more reliable marker because it showed distinct clustering of mosquito species, and some sequence variations to represent genetic diversity.}, }
@article {pmid38949306, year = {2024}, author = {Higgins, SA and Kara Murdoch, F and Clifton, JM and Brooks, JH and Fillinger, KL and Middleton, JK and Heater, BS}, title = {CRISPR-Cas9-mediated barcode insertion into Bacillus thuringiensis for surrogate tracking.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0000324}, pmid = {38949306}, issn = {2165-0497}, support = {FA8075-14-D-0003-FA807518F1414//DOD | OSD | Defense Technical Information Center (DTIC)/ ; 70RSAT19KPM0000470001//U.S. Department of Homeland Security (DHS)/ ; }, mesh = {*Bacillus thuringiensis/genetics ; *CRISPR-Cas Systems ; *DNA Barcoding, Taxonomic/methods ; Genome, Bacterial/genetics ; Bacillus anthracis/genetics ; Whole Genome Sequencing/methods ; Plasmids/genetics ; Gene Editing/methods ; }, abstract = {UNLABELLED: The use of surrogate organisms can enable researchers to safely conduct research on pathogens and in a broader set of conditions. Being able to differentiate between the surrogates used in the experiments and background contamination as well as between different experiments will further improve research efforts. One effective approach is to introduce unique genetic barcodes into the surrogate genome and track their presence using the quantitative polymerase chain reaction (qPCR). In this report, we utilized the CRISPR-Cas9 methodology, which employs a single plasmid and a transformation step to insert five distinct barcodes into Bacillus thuringiensis, a well-established surrogate for Bacillus anthracis when Risk Group 1 organisms are needed. We subsequently developed qPCR assays for barcode detection and successfully demonstrated the stability of the barcodes within the genome through five cycles of sporulation and germination. Additionally, we conducted whole-genome sequencing on these modified strains and analyzed 187 potential Cas9 off-target sites. We found no correlation between the mutations observed in the engineered strains and the predicted off-target sites, suggesting this genome engineering strategy did not directly result in off-target mutations in the genome. This simple approach has the potential to streamline the creation of barcoded B. thuringiensis strains for use in future studies on surrogate genomes.<br><br>IMPORTANCE: The use of Bacillus anthracis as a biothreat agent poses significant challenges for public health and national security. Bacillus anthracis surrogates, like Bacillus thuringiensis, are invaluable tools for safely understanding Bacillus anthracis properties without the safety concerns that would arise from using a virulent strain of Bacillus anthracis. We report a simple method for barcode insertion into Bacillus thuringiensis using the CRISPR-Cas9 methodology and subsequent tracking by quantitative polymerase chain reaction (qPCR). Moreover, whole-genome sequencing data and CRISPR-Cas9 off-target analyses in Bacillus thuringiensis suggest that this gene-editing method did not directly cause unwanted mutations in the genome. This study should assist in the facile development of barcoded Bacillus thuringiensis surrogate strains, among other biotechnological applications in Bacillus species.}, }
@article {pmid38949302, year = {2024}, author = {Kramara, J and Kim, M-J and Ollinger, TL and Ristow, LC and Wakade, RS and Zarnowski, R and Wellington, M and Andes, DR and Mitchell, AG and Krysan, DJ}, title = {Systematic analysis of the Candida albicans kinome reveals environmentally contingent protein kinase-mediated regulation of filamentation and biofilm formation in vitro and in vivo.}, journal = {mBio}, volume = {15}, number = {8}, pages = {e0124924}, pmid = {38949302}, issn = {2150-7511}, support = {R01 AI133409/AI/NIAID NIH HHS/United States ; R21AI157341//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI133409//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI177254/AI/NIAID NIH HHS/United States ; R21 AI157341/AI/NIAID NIH HHS/United States ; }, mesh = {*Candida albicans/genetics/enzymology/pathogenicity/physiology ; *Biofilms/growth &amp; development ; *Protein Kinases/genetics/metabolism ; Virulence ; Animals ; Fungal Proteins/genetics/metabolism ; Candidiasis/microbiology ; Gene Expression Regulation, Fungal ; Mice ; Hyphae/growth &amp; development/genetics ; }, abstract = {Protein kinases are critical regulatory proteins in both prokaryotes and eukaryotes. Accordingly, protein kinases represent a common drug target for a wide range of human diseases. Therefore, understanding protein kinase function in human pathogens such as the fungus Candida albicans is likely to extend our knowledge of its pathobiology and identify new potential therapies. To facilitate the study of C. albicans protein kinases, we constructed a library of 99 non-essential protein kinase homozygous deletion mutants marked with barcodes in the widely used SN genetic background. Here, we describe the construction of this library and the characterization of the competitive fitness of the protein kinase mutants under 11 different growth and stress conditions. We also screened the library for protein kinase mutants with altered filamentation and biofilm formation, two critical virulence traits of C. albicans. An extensive network of protein kinases governs these virulence traits in a manner highly dependent on the specific environmental conditions. Studies on specific protein kinases revealed that (i) the cell wall integrity MAPK pathway plays a condition-dependent role in filament initiation and elongation; (ii) the hyper-osmolar glycerol MAPK pathway is required for both filamentation and biofilm formation, particularly in the setting of in vivo catheter infection; and (iii) Sok1 is dispensable for filamentation in hypoxic environments at the basal level of a biofilm but is required for filamentation in normoxia. In addition to providing a new genetic resource for the community, these observations emphasize the environmentally contingent function of C. albicans protein kinases.IMPORTANCECandida albicans is one of the most common causes of fungal disease in humans for which new therapies are needed. Protein kinases are key regulatory proteins and are increasingly targeted by drugs for the treatment of a wide range of diseases. Understanding protein kinase function in C. albicans pathogenesis may facilitate the development of new antifungal drugs. Here, we describe a new library of 99 protein kinase deletion mutants to facilitate the study of protein kinases. Furthermore, we show that the function of protein kinases in two virulence-related processes, filamentation and biofilm formation, is dependent on the specific environmental conditions.}, }
@article {pmid38948916, year = {2024}, author = {Dreyling, L and Boch, S and Lumbsch, HT and Schmitt, I}, title = {Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces.}, journal = {MycoKeys}, volume = {106}, number = {}, pages = {153-172}, pmid = {38948916}, issn = {1314-4049}, abstract = {Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.}, }
@article {pmid38948467, year = {2024}, author = {Shen, L and Zhang, M and Qiu, Y and Yang, L and Lu, Y and Li, H and Zhang, L and Tang, F and Wang, F and Zhu, C and Bao, H and Ding, Y}, title = {DNA barcoding combined with high-resolution melting analysis to discriminate rhubarb species and its traditional Chinese patent medicines.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1371890}, pmid = {38948467}, issn = {1663-9812}, abstract = {Introduction: Rhubarb is a frequently used and beneficial traditional Chinese medicine. Wild resources of these plants are constantly being depleted, meaning that rhubarb products have been subjected to an unparalleled level of adulteration. Consequentially, reliable technology is urgently required to verify the authenticity of rhubarb raw materials and commercial botanical drugs. Methods: In this study, the barcode-DNA high-resolution melting (Bar-HRM) method was applied to characterize 63 rhubarb samples (five Polygonaceae species: Rheum tanguticum, Rh. palmatum, Rh. officinale, Rumex japonicus and Ru. sp.) and distinguish the rhubarb contents of 24 traditional Chinese patent medicine (TCPM) samples. Three markers, namely ITS2, rbcL and psbA-trnH, were tested to assess the candidate DNA barcodes for their effectiveness in distinguishing rhubarb from its adulterants. A segment from ITS2 was selected as the most suitable mini-barcode to identify the botanical drug rhubarb in TCPMs. Then, rhubarbs and TCPM samples were subjected to HRM analysis based on the ITS2 barcode. Results: Among the tested barcoding loci, ITS2 displayed abundant sites of variation and was effective in identifying Polygonaceae species and their botanical origins. HRM analysis based on the ITS2 mini-barcode region successfully distinguished the authenticity of five Polygonaceae species and eight batches of TCPMs. Of the 18 TCPM samples, 66.7 % (12 samples) were identified as containing Rh. tanguticum or Rh. officinale. However, 33.3 % were shown to consist of adulterants. Conclusions: These results demonstrated that DNA barcoding combined with HRM is a specific, suitable and powerful approach for identifying rhubarb species and TCPMs, which is crucial to guaranteeing the security of medicinal plants being traded internationally.}, }
@article {pmid38947432, year = {2024}, author = {Frigerio, J and Campone, L and Giustra, MD and Buzzelli, M and Piccoli, F and Galimberti, A and Cannavacciuolo, C and Ouled Larbi, M and Colombo, M and Ciocca, G and Labra, M}, title = {Convergent technologies to tackle challenges of modern food authentication.}, journal = {Heliyon}, volume = {10}, number = {11}, pages = {e32297}, pmid = {38947432}, issn = {2405-8440}, abstract = {The authentication process involves all the supply chain stakeholders, and it is also adopted to verify food quality and safety. Food authentication tools are an essential part of traceability systems as they provide information on the credibility of origin, species/variety identity, geographical provenance, production entity. Moreover, these systems are useful to evaluate the effect of transformation processes, conservation strategies and the reliability of packaging and distribution flows on food quality and safety. In this manuscript, we identified the innovative characteristics of food authentication systems to respond to market challenges, such as the simplification, the high sensitivity, and the non-destructive ability during authentication procedures. We also discussed the potential of the current identification systems based on molecular markers (chemical, biochemical, genetic) and the effectiveness of new technologies with reference to the miniaturized systems offered by nanotechnologies, and computer vision systems linked to artificial intelligence processes. This overview emphasizes the importance of convergent technologies in food authentication, to support molecular markers with the technological innovation offered by emerging technologies derived from biotechnologies and informatics. The potential of these strategies was evaluated on real examples of high-value food products. Technological innovation can therefore strengthen the system of molecular markers to meet the current market needs; however, food production processes are in profound evolution. The food 3D-printing and the introduction of new raw materials open new challenges for food authentication and this will require both an update of the current regulatory framework, as well as the development and adoption of new analytical systems.}, }
@article {pmid38946964, year = {2024}, author = {Rossouw, L and Ngcobo, N and Clouse, K and Nattey, C and Technau, KG and Maskew, M}, title = {Augmenting maternal clinical cohort data with administrative laboratory dataset linkages: a validation study.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {38946964}, support = {R01 HD103466/HD/NICHD NIH HHS/United States ; U01 AI069924/AI/NIAID NIH HHS/United States ; U01 HD080441/HD/NICHD NIH HHS/United States ; }, abstract = {BACKGROUND: The use of big data and large language models in healthcare can play a key role in improving patient treatment and healthcare management, especially when applied to large-scale administrative data. A major challenge to achieving this is ensuring that patient confidentiality and personal information is protected. One way to overcome this is by augmenting clinical data with administrative laboratory dataset linkages in order to avoid the use of demographic information.<br><br>METHODS: We explored an alternative method to examine patient files from a large administrative dataset in South Africa (the National Health Laboratory Services, or NHLS), by linking external data to the NHLS database using specimen barcodes associated with laboratory tests. This offers us with a deterministic way of performing data linkages without accessing demographic information. In this paper, we quantify the performance metrics of this approach.<br><br>RESULTS: The linkage of the large NHLS data to external hospital data using specimen barcodes achieved a 95% success. Out of the 1200 records in the validation sample, 87% were exact matches and 9% were matches with typographic correction. The remaining 5% were either complete mismatches or were due to duplicates in the administrative data.<br><br>CONCLUSIONS: The high success rate indicates the reliability of using barcodes for linking data without demographic identifiers. Specimen barcodes are an effective tool for deterministic linking in health data, and may provide a method of creating large, linked data sets without compromising patient confidentiality.}, }
@article {pmid38943817, year = {2024}, author = {Piersanti, S and Rebora, M and Turchetti, B and Salerno, G and Ruscetta, M and Zucconi, L and D'Alò, F and Buzzini, P and Sannino, C}, title = {Microplastics in the diet of Hermetia illucens: Implications for development and midgut bacterial and fungal microbiota.}, journal = {Waste management (New York, N.Y.)}, volume = {186}, number = {}, pages = {259-270}, doi = {10.1016/j.wasman.2024.06.021}, pmid = {38943817}, issn = {1879-2456}, mesh = {Animals ; *Larva/microbiology ; *Diptera/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics ; Polyvinyl Chloride ; Fungi/metabolism ; Bacteria/classification/metabolism ; Diet ; Mycobiome ; }, abstract = {In a world with a population exceeding 8 billion people and continuing to grow, pollution from food and plastic waste is causing long-term issues in ecosystems. Potential solutions may be found by exploiting insect-based bioconversion. In this context, we investigated the impact of polyvinyl chloride microparticles (PVC-MPs) on the development of Hermetia illucens (black soldier fly; BSF) and its midgut bacterial and fungal microbiota. The impact of PVC-MPs was evaluated feeding BSF larvae with a PVC-MPs-supplemented diet. The larvae exposed to different PVC-MPs concentrations (2.5%, 5%, 10% and 20% w/w) developed into adults with no significant increase in pupal mortality. Faster development and smaller pupae were observed when 20% PVC-MPs was provided. The BSF larvae ingest PVC-MPs, resulting in a reduction in MPs size. Larvae exposed to PVC-MPs did not exhibit differences in gut morphology. Regarding the impact of PVC-MPs on the structure of both bacterial and fungal communities, the overall alpha- and beta-diversity did not exhibit significant changes. However, the presence of PVC-MPs significantly affected the relative abundances of Enterobacteriaceae and Paenibacillaceae among the bacteria and of Dipodascaceae and Plectospharellaceae among the fungi (including yeast and filamentous life forms), suggesting that PVC-MP contamination has a taxa-dependent impact. These results indicate that BSF larvae can tolerate PVC-MPs in their diet, supporting the potential use of these insects in organic waste management, even in the presence of high levels of PVC-MP contamination.}, }
@article {pmid38943640, year = {2024}, author = {Xiao, S and Yadav, S and Jayant, K}, title = {Probing multiplexed basal dendritic computations using two-photon 3D holographic uncaging.}, journal = {Cell reports}, volume = {43}, number = {7}, pages = {114413}, doi = {10.1016/j.celrep.2024.114413}, pmid = {38943640}, issn = {2211-1247}, support = {R21 EB029740/EB/NIBIB NIH HHS/United States ; }, mesh = {*Dendrites/metabolism/physiology ; Animals ; *Holography/methods ; Pyramidal Cells/metabolism/physiology ; Synapses/metabolism/physiology ; Action Potentials/physiology ; Receptors, N-Methyl-D-Aspartate/metabolism ; Photons ; Mice ; Male ; }, abstract = {Basal dendrites of layer 5 cortical pyramidal neurons exhibit Na[+] and N-methyl-D-aspartate receptor (NMDAR) regenerative spikes and are uniquely poised to influence somatic output. Nevertheless, due to technical limitations, how multibranch basal dendritic integration shapes and enables multiplexed barcoding of synaptic streams remains poorly mapped. Here, we combine 3D two-photon holographic transmitter uncaging, whole-cell dynamic clamp, and biophysical modeling to reveal how synchronously activated synapses (distributed and clustered) across multiple basal dendritic branches are multiplexed under quiescent and in vivo-like conditions. While dendritic regenerative Na[+] spikes promote millisecond somatic spike precision, distributed synaptic inputs and NMDAR spikes regulate gain. These concomitantly occurring dendritic nonlinearities enable multiplexed information transfer amid an ongoing noisy background, including under back-propagating voltage resets, by barcoding the axo-somatic spike structure. Our results unveil a multibranch dendritic integration framework in which dendritic nonlinearities are critical for multiplexing different spatial-temporal synaptic input patterns, enabling optimal feature binding.}, }
@article {pmid38943021, year = {2024}, author = {Farzad, N and Enninful, A and Bao, S and Zhang, D and Deng, Y and Fan, R}, title = {Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue.}, journal = {Nature protocols}, volume = {19}, number = {11}, pages = {3389-3425}, pmid = {38943021}, issn = {1750-2799}, support = {U54 AG076043/AG/NIA NIH HHS/United States ; U54 AG079759/AG/NIA NIH HHS/United States ; UG3 CA257393/CA/NCI NIH HHS/United States ; UG3 CA257393/CA/NCI NIH HHS/United States ; R01 CA245313/CA/NCI NIH HHS/United States ; RF1 MH128876/MH/NIMH NIH HHS/United States ; U54 CA274509/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Transposases/genetics/metabolism ; Mice ; *Epigenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Epigenomics/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; Epigenesis, Genetic ; }, abstract = {Spatial epigenetic mapping of tissues enables the study of gene regulation programs and cellular functions with the dependency on their local tissue environment. Here we outline a complete procedure for two spatial epigenomic profiling methods: spatially resolved genome-wide profiling of histone modifications using in situ cleavage under targets and tagmentation (CUT&amp;Tag) chemistry (spatial-CUT&amp;Tag) and transposase-accessible chromatin sequencing (spatial-ATAC-sequencing) for chromatin accessibility. Both assays utilize in-tissue Tn5 transposition to recognize genomic DNA loci followed by microfluidic deterministic barcoding to incorporate spatial address codes. Furthermore, these two methods do not necessitate prior knowledge of the transcription or epigenetic markers for a given tissue or cell type but permit genome-wide unbiased profiling pixel-by-pixel at the 10 μm pixel size level and single-base resolution. To support the widespread adaptation of these methods, details are provided in five general steps: (1) sample preparation; (2) Tn5 transposition in spatial-ATAC-sequencing or antibody-controlled pA-Tn5 tagmentation in CUT&amp;Tag; (3) library preparation; (4) next-generation sequencing; and (5) data analysis using our customed pipelines available at: https://github.com/dyxmvp/Spatial_ATAC-seq and https://github.com/dyxmvp/spatial-CUT-Tag . The whole procedure can be completed on four samples in 2-3 days. Familiarity with basic molecular biology and bioinformatics skills with access to a high-performance computing environment are required. A rudimentary understanding of pathology and specimen sectioning, as well as deterministic barcoding in tissue-specific skills (e.g., design of a multiparameter barcode panel and creation of microfluidic devices), are also advantageous. In this protocol, we mainly focus on spatial profiling of tissue region-specific epigenetic landscapes in mouse embryos and mouse brains using spatial-ATAC-sequencing and spatial-CUT&amp;Tag, but these methods can be used for other species with no need for species-specific probe design.}, }
@article {pmid38940749, year = {2024}, author = {Nolan, DJ and DaRoza, J and Brody, R and Ganta, K and Luzuriaga, K and Huston, C and Rosenthal, S and Lamers, SL and Rose, R}, title = {Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1 gp160 Single Genome Amplicons.}, journal = {AIDS research and human retroviruses}, volume = {40}, number = {11}, pages = {659-669}, pmid = {38940749}, issn = {1931-8405}, support = {R43 FD008039/FD/FDA HHS/United States ; UL1 TR001453/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods/standards ; *HIV-1/genetics/classification ; *Sequence Analysis, DNA/methods ; HIV Envelope Protein gp160/genetics ; HIV Infections/virology ; Consensus Sequence ; Genome, Viral ; }, abstract = {Our goal was to assess the accuracy of next generation sequencing (NGS) compared with Sanger. We performed single genome amplification (SGA) of HIV-1 gp160 on extracted tissue DNA from two HIV+ individuals. Amplicons (n = 30) were sequenced with Sanger or reamplified with barcoded primers and pooled before sequencing using Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PB). For each amplicon, a consensus sequence for NGS reads was obtained by (1) mapping reads to the Sanger sequence when available ("reference-based") or (2) mapping reads to a "pseudo-reference" sequence, i.e., a consensus sequence of a subset of NGS reads ("reference-free"). PB reads were clustered based on genetic similarity. A Sanger consensus sequence was obtained for 23/30 amplicons, for which all NGS consensus sequences were identical (n = 9) or nearly identical (n = 14) compared with Sanger. For the nine mismatches between Sanger/NGS, the nucleotide in the NGS sequence matched all other sequences from that patient. Of the 7/30 amplicons without a Sanger sequence, NGS sequences had ≥35 ambiguous calls in five amplicons and 0 ambiguities in two amplicons. Analysis of the electropherograms showed failure of a single sequencing primer for the latter two amplicons (consistent with a single template) and overlapping peaks for the other five (consistent with multiple templates). Clustering results closely followed the Sanger/NGS consensus results, where amplicons derived from a single template also had a single cluster and vice versa (with one exception, which could be the result of barcode misidentification). Representative sequences from the clusters contained 2-13 differences compared with Sanger/NGS. In summary, we show that both ONT and PB can produce amplicon consensus sequences with similar or higher accuracy compared with Sanger and, importantly, without the need for a known reference sequence. Clustering could be useful in some circumstances to predict or confirm the presence of multiple starting templates.}, }
@article {pmid38935254, year = {2025}, author = {Saathoff, S and Goodman, CL and Haas, E and Mettelmann, I and Stanley, D}, title = {A cell line derived from the black soldier fly, Hermetia illucens (Diptera: Stratiomyidae).}, journal = {In vitro cellular &amp; developmental biology. Animal}, volume = {61}, number = {5}, pages = {506-510}, pmid = {38935254}, issn = {1543-706X}, support = {5070-22000-038-000-D//Agricultural Research Service/ ; }, mesh = {Animals ; *Diptera/cytology ; Cell Line ; Larva/cytology ; Fatty Acids/metabolism ; }, abstract = {Insect cell lines are effective tools used in industry and academia. For example, they are used in screening potential insecticides, in making certain proteins for biomedical applications, and in basic research into insect biology. So far, there are no cell lines derived from the black soldier fly, Hermetia illucens (BSF). This may become an issue because BSFs are employed in a range of industrial and household processes. BSFs are used in producing biodiesel, in developing cosmetics and skin creams, and in the production of some medicines and animal feeds. BSF larvae process waste streams from a variety of sources into food for some animals and are also used in household composting. Our BSF cell line, designated BCIRL-HiE0122021-SGS, was developed from eggs using the medium CLG#2 (50% L-15 + 50% EX-CELL 420, with 9% FBS and antibiotics), with many other media being tested. This cell line consists of attached cells with a variety of morphologies and its identity was authenticated using CO1 barcoding. A growth curve was generated and the resulting doubling time was 118 h. We quantified the fatty acid methyl esters (FAMES) and recorded the expected range of saturated, monounsaturated, and polyunsaturated FAMEs, with only trace levels of lauric acid being noted. The BSF cell line is available free of charge by request.}, }
@article {pmid38933488, year = {2024}, author = {Kurata, S and Mano, S and Nakahama, N and Hirota, SK and Suyama, Y and Ito, M}, title = {Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e117014}, pmid = {38933488}, issn = {1314-2828}, abstract = {Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.}, }
@article {pmid38927697, year = {2024}, author = {Kim, JE and Kim, KM and Kim, YS and Chung, GY and Che, SH and Na, CS}, title = {Chloroplast Genomes of Vitis flexuosa and Vitis amurensis: Molecular Structure, Phylogenetic, and Comparative Analyses for Wild Plant Conservation.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927697}, issn = {2073-4425}, support = {2021400B10-2425-CA02//Korea Forestry Promotion Institute/ ; }, mesh = {*Vitis/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; Evolution, Molecular ; Genetic Variation ; Republic of Korea ; Chloroplasts/genetics ; Genome, Plant ; }, abstract = {The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges.}, }
@article {pmid38927627, year = {2024}, author = {Li, H and Miao, X and Wang, R and Liao, Y and Wen, Y and Zhang, R and Lin, L}, title = {Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927627}, issn = {2073-4425}, support = {IRASCC01-02-02&amp;02-02//Chinese Arctic and Antarctic Administration, Ministry of Natural Resources of the People's Republic of China/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Antarctic Regions ; *Electron Transport Complex IV/genetics ; Phylogeny ; Oceans and Seas ; }, abstract = {The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses.}, }
@article {pmid38927625, year = {2024}, author = {Karbarz, M and Szlachcikowska, D and Zapał, A and Leśko, A}, title = {Unlocking the Genetic Identity of Endangered Paphiopedilum Orchids: A DNA Barcoding Approach.}, journal = {Genes}, volume = {15}, number = {6}, pages = {}, pmid = {38927625}, issn = {2073-4425}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Orchidaceae/genetics/classification ; *Endangered Species ; Phylogeny ; DNA, Plant/genetics ; }, abstract = {Orchids of the genus Paphiopedilum, also called slippers, are among the most valued representatives of the Orchidaceae family due to their aesthetic qualities. Due to overexploitation, deforestation, and illegal trade in these plants, especially in the vegetative phase, Paphiopedilum requires special protection. This genus is listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Their precise identification is of great importance for the preservation of genetic resources and biodiversity of the orchid family (Orchidaceae). Therefore, the main objective of the study was to investigate the usefulness of the DNA barcoding technique for the identification of endangered orchids of the genus Paphiopedilum and to determine the effectiveness of five loci: matK, rbcL, ITS2, atpF-atpH and trnH-psbA as potential molecular markers for species of this genus. Among single locus barcodes, matK was the most effective at identifying species (64%). Furthermore, matK, ITS2, matK + rbcL, and matK + trnH-psbA barcodes can be successfully used as a complementary tool to identify Paphiopedilum orchids while supporting morphological data provided by taxonomists.}, }
@article {pmid38927245, year = {2024}, author = {Sutula, M and Kakanay, A and Tussipkan, D and Dzhumanov, S and Manabayeva, S}, title = {Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers.}, journal = {Biology}, volume = {13}, number = {6}, pages = {}, pmid = {38927245}, issn = {2079-7737}, support = {BR18574125//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; OR11465422//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.}, }
@article {pmid38926630, year = {2024}, author = {Liu, H}, title = {Bacterial barcoding facilitates plant microbiome studies.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {8}, pages = {459}, pmid = {38926630}, issn = {1740-1534}, mesh = {*Microbiota/genetics ; *Plants/microbiology ; *DNA Barcoding, Taxonomic/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; }, }
@article {pmid38926392, year = {2024}, author = {Li, S and Xv, Y and Sun, Y and Shen, Z and Hao, R and Yan, J and Liu, M and Liu, Z and Jing, T and Li, X and Zhang, X}, title = {Macrophage-derived CD36 + exosome subpopulations as novel biomarkers of Candida albicans infection.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14723}, pmid = {38926392}, issn = {2045-2322}, mesh = {*Exosomes/metabolism ; *Candida albicans ; *Biomarkers/metabolism ; *Macrophages/metabolism/microbiology/immunology ; *CD36 Antigens/metabolism ; *Candidiasis/diagnosis/microbiology/metabolism/immunology ; Humans ; Animals ; Mice ; }, abstract = {Invasive candidiasis (IC) is a notable healthcare-associated fungal infection, characterized by high morbidity, mortality, and substantial treatment costs. Candida albicans emerges as a principal pathogen in this context. Recent academic advancements have shed light on the critical role of exosomes in key biological processes, such as immune responses and antigen presentation. This burgeoning body of research underscores the potential of exosomes in the realm of medical diagnostics and therapeutics, particularly in relation to fungal infections like IC. The exploration of exosomal functions in the pathophysiology of IC not only enhances our understanding of the disease but also opens new avenues for innovative therapeutic interventions. In this investigation, we focus on exosomes (Exos) secreted by macrophages, both uninfected and those infected with C. albicans. Our objective is to extract and analyze these exosomes, delving into the nuances of their protein compositions and subgroups. To achieve this, we employ an innovative technique known as Proximity Barcoding Assay (PBA). This methodology is pivotal in our quest to identify novel biological targets, which could significantly enhance the diagnostic and therapeutic approaches for C. albicans infection. The comparative analysis of exosomal contents from these two distinct cellular states promises to yield insightful data, potentially leading to breakthroughs in understanding and treating this invasive fungal infection. In our study, we analyzed differentially expressed proteins in exosomes from macrophages and C. albicans -infected macrophages, focusing on proteins such as ACE2, CD36, CAV1, LAMP2, CD27, and MPO. We also examined exosome subpopulations, finding a dominant expression of MPO in the most prevalent subgroup, and a distinct expression of CD36 in cluster14. These findings are crucial for understanding the host response to C. albicans and may inform targeted diagnostic and therapeutic approaches. Our study leads us to infer that MPO and CD36 proteins may play roles in the immune escape mechanisms of C. albicans. Additionally, the CD36 exosome subpopulations, identified through our analysis, could serve as potential biomarkers and therapeutic targets for C. albicans infection. This insight opens new avenues for understanding the infection's pathology and developing targeted treatments.}, }
@article {pmid38925122, year = {2024}, author = {Zhang, Z and Melzer, ME and Arun, KM and Sun, H and Eriksson, CJ and Fabian, I and Shaashua, S and Kiani, K and Oren, Y and Goyal, Y}, title = {Synthetic DNA barcodes identify singlets in scRNA-seq datasets and evaluate doublet algorithms.}, journal = {Cell genomics}, volume = {4}, number = {7}, pages = {100592}, pmid = {38925122}, issn = {2666-979X}, mesh = {*Algorithms ; *Single-Cell Analysis/methods ; *DNA Barcoding, Taxonomic/methods ; Humans ; Machine Learning ; Sequence Analysis, RNA/methods ; Animals ; Single-Cell Gene Expression Analysis ; }, abstract = {Single-cell RNA sequencing (scRNA-seq) datasets contain true single cells, or singlets, in addition to cells that coalesce during the protocol, or doublets. Identifying singlets with high fidelity in scRNA-seq is necessary to avoid false negative and false positive discoveries. Although several methodologies have been proposed, they are typically tested on highly heterogeneous datasets and lack a priori knowledge of true singlets. Here, we leveraged datasets with synthetically introduced DNA barcodes for a hitherto unexplored application: to extract ground-truth singlets. We demonstrated the feasibility of our framework, "singletCode," to evaluate existing doublet detection methods across a range of contexts. We also leveraged our ground-truth singlets to train a proof-of-concept machine learning classifier, which outperformed other doublet detection algorithms. Our integrative framework can identify ground-truth singlets and enable robust doublet detection in non-barcoded datasets.}, }
@article {pmid38922410, year = {2024}, author = {Sakae, K and Kawai, S and Kitagami, Y and Matsuo, N and Selosse, MA and Tanikawa, T and Matsuda, Y}, title = {Effects of fungicide treatments on mycorrhizal communities and carbon acquisition in the mixotrophic Pyrola japonica (Ericaceae).}, journal = {Mycorrhiza}, volume = {34}, number = {4}, pages = {293-302}, pmid = {38922410}, issn = {1432-1890}, support = {2023-4099//Japan Science Society/ ; 25304026//Japan Society for the Promotion of Science/ ; }, mesh = {*Mycorrhizae/physiology/drug effects ; *Fungicides, Industrial/pharmacology ; *Carbon/metabolism ; Japan ; *Pyrola/microbiology/metabolism ; Plant Roots/microbiology ; Benomyl/pharmacology ; Soil Microbiology ; Plant Leaves/microbiology ; }, abstract = {Pyrola japonica, a member of the family Ericaceae, is a mixotroph that grows on forest floors and obtains carbon (C) from both its photosynthesis and its mycorrhizal fungi. Its mycorrhizal community is dominated by Russulaceae. However, the mechanism of its C acquisition and its flexibility are not well understood. Our aim was to assess the impact of disturbance of the mycorrhizal fungal communities on C acquisition by P. japonica. We repeatedly applied a fungicide (Benomyl) to soils around P. japonica plants in a broad-leaved forest of central Japan, in order to disturb fungal associates near roots. After fungicide treatment, P. japonica roots were collected and subjected to barcoding by next-generation sequencing, focusing on the ITS2 region. The rate of mycorrhizal formation and α-diversity did not significantly change upon fungicide treatments. Irrespective of the treatments, Russulaceae represented more than 80% of the taxa. Leaves and seeds of the plants were analysed for [13]C stable isotope ratios that reflect fungal C gain. Leaf and seed δ[13]C values with the fungicide treatment were significantly lower than those with the other treatments. Thus the fungicide did not affect mycorrhizal communities in the roots, but disturbed mycorrhizal fungal pathways via extraradical hyphae, and resulted in a more photosynthetic behaviour of P. japonica for leaves and seeds.}, }
@article {pmid38921121, year = {2024}, author = {Ganbaatar, B and Li, Q and Xi, O and Cao, H and Zhu, C}, title = {One Step beyond Species Description: Unveiling a Fine-Scale Diversity within the Genus Dzhanokmenia Kostjukov (Hymenoptera: Eulophidae).}, journal = {Insects}, volume = {15}, number = {6}, pages = {}, pmid = {38921121}, issn = {2075-4450}, support = {32330013//the National Natural Science Foundation of China/ ; 2008DP173354//the Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences/ ; }, abstract = {Although Chalcidoidea is one of the megadiverse superfamilies in Hymenoptera, numerous species are still being discovered and described. However, the difficulties in delimiting intra- and interspecific variation hinder this process. In this study, DNA barcoding methods using the COI gene were employed to investigate the morphological variation within Dzhanokmenia Kostjukov, 1977. The nuclear locus, 28S D2, was used to infer a phylogeny to gain an understanding of the relationship of Dzhanokmenia with other potentially close genera. Through a preliminary DNA barcode library established here, including eight species, we calibrated the intraspecific variation in certain diagnostic characters for the new species described here, D. brevifunis Ganbaatar &amp; Cao sp. nov. Maximum likelihood results show that Dzhanokmenia is clustered with the genera associated with Tetrastichus, such as Chaenotetrastichus Graham, 1987, Baryscapus Förster, 1856, Tetrastichus Haliday, 1844, and Oomyzus Rondani, 1870 involved in this study. Our results indicate that the species diversity of Dzhanokmenia is understudied and tentatively confirm that Dzhanokmenia has a potential close relationship with Baryscapus. Along with the DNA barcode library, the referenced phylogeny datasets improve the understanding of the systematic position of Dzhanokmenia within the subfamily Tetrastichinae and the definition of this genus in terms of morphology, thereby facilitating species delimitation, discovery, and description within Dzhanokmenia.}, }
@article {pmid38920364, year = {2024}, author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E}, title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {7}, pages = {e0080024}, pmid = {38920364}, issn = {1098-5336}, support = {DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; DE-SC0020172//U.S. Department of Energy (DOE)/ ; DE-SC0023126//U.S. Department of Energy (DOE)/ ; }, mesh = {*RNA, Ribosomal, 18S/genetics ; *Computational Biology/methods ; *Eukaryota/genetics/classification ; *DNA Primers/genetics ; *Soil Microbiology ; Biodiversity ; Temperature ; Soil/parasitology/chemistry ; Polymerase Chain Reaction ; }, abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.}, }
@article {pmid38919770, year = {2024}, author = {Vogel, J and Sauren, J and Peters, RS}, title = {New evidence on the identity of the European Helorus species (Hymenoptera, Proctotrupoidea, Heloridae).}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e122523}, pmid = {38919770}, issn = {1314-2828}, abstract = {BACKGROUND: Species of Helorus Latreille 1802 are rarely collected endoparasitoids of Chrysopidae larvae (Neuroptera). Previous work on the limits between the European species of this species-poor genus, based on morphology only, has left some uncertainties. Here, we approach these cases and revisit previous taxonomic decisions using freshly collected and museum material.<br><br>NEW INFORMATION: We generated the first large-scale Heloridae DNA barcode dataset, combined these with morphological data in an integrative taxonomic approach, and added information from studying all relevant type material. We found five species, Helorusanomalipes (Panzer, 1798), H.coruscus Haliday, 1857 stat. rev., H.nigripes F&#xf6;rster, 1856, H.ruficornis F&#xf6;rster, 1856, and H.striolatus Cameron, 1906, for which we provide an updated identification key. DNA barcode data are added to publicly available DNA barcode reference databases, for all species, except H.nigripes.}, }
@article {pmid38918858, year = {2024}, author = {Cardoso, SF and Guesser, JVC and Rodrigues, AAF and Brazil, RP and Rona, LDP and Pitaluga, AN}, title = {Leishmania infantum detection in Nyssomyia neivai and dogs in Southern Brazil.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {269}, pmid = {38918858}, issn = {1756-3305}, support = {16/2014//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; Dogs ; *Leishmania infantum/genetics/isolation &amp; purification ; Brazil/epidemiology ; *Psychodidae/parasitology/classification ; *Dog Diseases/parasitology/epidemiology ; *Leishmaniasis, Visceral/veterinary/epidemiology/parasitology/transmission ; Female ; *Insect Vectors/parasitology ; Polymerase Chain Reaction ; Male ; }, abstract = {BACKGROUND: The sand fly Nyssomyia neivai is one of the most abundant species in Southern Brazil. It is frequently found in areas that are foci of visceral leishmaniasis in the state of Santa Catarina, caused by Leishmania infantum. In this region, the main vector of L. infantum, Lutzomyia longipalpis, has not been detected. In the absence of L. longipalpis, this study aimed to identify the sand fly fauna and diagnose any potential Leishmania spp. infection in sand flies and in dogs in a region of Southern Brazil that experienced a recent canine visceral leishmaniasis outbreak.<br><br>METHODS: This report includes a survey of the sand fly fauna at the Zoonosis Control Center of the Municipality of Tubar&#xe3;o (Santa Catarina, Brazil). Molecular tests were conducted to investigate Leishmania spp. natural infection in sand flies using polymerase chain reaction (PCR). In positive females, in addition to morphological identification, molecular analysis through DNA barcoding was performed to determine the sand fly species. Additionally, the dogs were tested for the presence of Leishmania spp. using a non-invasive technique for the collection of biological material, to be assessed by PCR.<br><br>RESULTS: A total of 3419 sand flies, belonging to five genera, were collected. Nyssomyia neivai was the most abundant species (85.8%), followed by Migonemyia migonei (13.3%), Pintomyia fischeri (0.8%), Evandromyia edwardsi (<&#x2009;0.1%), and species of the genus Brumptomyia. (0.1%). Out of the 509 non-engorged females analyzed by PCR, two (0.4%) carried L. infantum DNA. The naturally infected females were identified as Ny. neivai, in both morphological and molecular analysis. In addition, two out of 47 conjunctival swabs from dogs tested positive for L. infantum, yielding an infection rate of 4.2%.<br><br>CONCLUSIONS: These results confirm the presence of Ny. neivai naturally infected with L. infantum in an area where dogs were also infected by the parasite, suggesting its potential role as a vector in Southern Brazil.}, }
@article {pmid38918509, year = {2024}, author = {Bauer, N and Oberist, C and Poth, M and Stingele, J and Popp, O and Ausländer, S}, title = {Genomic barcoding for clonal diversity monitoring and control in cell-based complex antibody production.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14587}, pmid = {38918509}, issn = {2045-2322}, mesh = {CHO Cells ; *Cricetulus ; Animals ; *DNA Barcoding, Taxonomic/methods ; *Clone Cells ; Genomics/methods ; Antibodies, Monoclonal/genetics ; }, abstract = {Engineered mammalian cells are key for biotechnology by enabling broad applications ranging from in vitro model systems to therapeutic biofactories. Engineered cell lines exist as a population containing sub-lineages of cell clones that exhibit substantial genetic and phenotypic heterogeneity. There is still a limited understanding of the source of this inter-clonal heterogeneity as well as its implications for biotechnological applications. Here, we developed a genomic barcoding strategy for a targeted integration (TI)-based CHO antibody producer cell line development process. This technology provided novel insights about clone diversity during stable cell line selection on pool level, enabled an imaging-independent monoclonality assessment after single cell cloning, and eventually improved hit-picking of antibody producer clones by monitoring of cellular lineages during the cell line development (CLD) process. Specifically, we observed that CHO producer pools generated by TI of two plasmids at a single genomic site displayed a low diversity (< 0.1% RMCE efficiency), which further depends on the expressed molecules, and underwent rapid population skewing towards dominant clones during routine cultivation. Clonal cell lines from one individual TI event demonstrated a significantly lower variance regarding production-relevant and phenotypic parameters as compared to cell lines from distinct TI events. This implies that the observed cellular diversity lies within pre-existing cell-intrinsic factors and that the majority of clonal variation did not develop during the CLD process, especially during single cell cloning. Using cellular barcodes as a proxy for cellular diversity, we improved our CLD screening workflow and enriched diversity of production-relevant parameters substantially. This work, by enabling clonal diversity monitoring and control, paves the way for an economically valuable and data-driven CLD process.}, }
@article {pmid38918059, year = {2024}, author = {Belford, SG}, title = {Combining Morphological Characteristics and DNA Barcoding Techniques Confirm Sea Urchins of the Genus Echinometra (Echinodermata: Echinoidea) in Marine Habitat Located at Extreme Regions of the Caribbean Sea.}, journal = {Integrative and comparative biology}, volume = {64}, number = {4}, pages = {1078-1086}, doi = {10.1093/icb/icae083}, pmid = {38918059}, issn = {1557-7023}, support = {//University of Tennessee/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Sea Urchins/genetics/anatomy &amp; histology ; Caribbean Region ; *Electron Transport Complex IV/genetics ; Phylogeny ; Ecosystem ; Trinidad and Tobago ; }, abstract = {Echinometra spp. are pantropical echinoids found in benthic marine habitat throughout the Caribbean, Atlantic, and Indo-West Pacific oceanic regions. Currently, morphology and molecular data are sparse for echinoids observed along the northeastern coast of Toco, Trinidad, where they are relatively common. Additionally, accurate species identity for Echinometra spp. remains dynamic at both northernmost and southernmost parts of the Caribbean Sea. Although distribution of sea urchins in the genus Echinometra have extensively been studied throughout the Atlantic and Indo-West Pacific, information on its range of distribution at the edge of the Caribbean Sea is lacking. In this study, the mitochondrial Cytochrome c Oxidase subunit I (mt COI) gene was amplified using polymerase chain reaction, then sequenced. Based on successfully obtained gene sequences for 581 base pairs, the echinoid species Echinometra lucunter and Echinometra viridis were identified for black and red color morphotypes from Trinidad (n = 23) and Key Largo, Florida (n = 6), respectively. Furthermore, these specimens were genetically identical to species identified in other studies for Puerto Rico, Panamá, Honduras, and Belize. Although morphological variations, such as spine and test color occur throughout Echinometra spp., molecular identification using the barcoding technique confirmed E. lucunter color morphs for the first time in Trinidad. Since the status of E. lucunter populations, specifically at the most northern and southern regions of the Caribbean Sea is dynamic, further studies using gene markers are essential in determining species distribution, in light of current trends in climate change.}, }
@article {pmid38915710, year = {2024}, author = {Trende, R and Darling, TL and Gan, T and Wang, D and Boon, ACM}, title = {Barcoded SARS-CoV-2 viruses define the impact of time and route of transmission on the transmission bottleneck in a Syrian hamster model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38915710}, issn = {2692-8205}, support = {75N93021C00016/AI/NIAID NIH HHS/United States ; R01 AI169022/AI/NIAID NIH HHS/United States ; U01 AI070374/AI/NIAID NIH HHS/United States ; U01 AI151810/AI/NIAID NIH HHS/United States ; }, abstract = {The transmission bottleneck, defined as the number of viruses that transmit from one host to infect another, is an important determinant of the rate of virus evolution and the level of immunity required to protect against virus transmission. Despite its importance, SARS-CoV-2's transmission bottleneck remains poorly characterized, in part due to a lack of quantitative measurement tools. To address this, we adapted a SARS-CoV-2 reverse genetics system to generate a pool of >200 isogenic SARS-CoV-2 viruses harboring specific 6-nucleotide barcodes inserted in ORF10, a non-translated ORF. We directly inoculated donor Syrian hamsters intranasally with this barcoded virus pool and exposed a paired naïve contact hamster to each donor. Following exposure, the nasal turbinates, trachea, and lungs were collected, viral titers were measured, and the number of barcodes in each tissue were enumerated to quantify the transmission bottleneck. The duration and route (airborne, direct contact, and fomite) of exposure were varied to assess their impact on the transmission bottleneck. In airborne-exposed hamsters, the transmission bottleneck increased with longer exposure durations. We found that direct contact exposure produced the largest transmission bottleneck (average 27 BCs), followed by airborne exposure (average 16 BCs) then fomite exposure (average 8 BCs). Interestingly, we detected unique BCs in both the upper and lower respiratory tract of contact animals from all routes of exposure, suggesting that SARS-CoV-2 can directly infect hamster lungs. Altogether, these findings highlight the utility of barcoded viruses as tools to rigorously study virus transmission. In the future, barcoded SARS-CoV-2 will strengthen studies of immune factors that influence virus transmission.}, }
@article {pmid38912975, year = {2024}, author = {Zahn, FE and Jiang, H and Lee, YI and Gebauer, G}, title = {Mode of carbon gain and fungal associations of Neuwiedia malipoensis within the evolutionarily early-diverging orchid subfamily Apostasioideae.}, journal = {Annals of botany}, volume = {134}, number = {3}, pages = {511-520}, pmid = {38912975}, issn = {1095-8290}, mesh = {*Orchidaceae/microbiology/growth &amp; development/physiology ; *Mycorrhizae/physiology ; *Carbon/metabolism ; Symbiosis ; Biological Evolution ; Seedlings/microbiology/growth &amp; development ; Phylogeny ; }, abstract = {BACKGROUND AND AIMS: The earliest-diverging orchid lineage, Apostasioideae, consists only of two genera: Apostasia and Neuwiedia. Previous reports of Apostasia nipponica indicated a symbiotic association with an ectomycorrhiza-forming Ceratobasidiaceae clade and partial utilization of fungal carbon during the adult stage. However, the trophic strategy of Neuwiedia throughout its development remains unidentified. To further improve our understanding of mycoheterotrophy in the Apostasioideae, this study focused on Neuwiedia malipoensis examining both the mycorrhizal association and the physiological ecology of this orchid species across various development stages.<br><br>METHODS: We identified the major mycorrhizal fungi of N. malipoensis protocorm, leafy seedling and adult stages using molecular barcoding. To reveal nutritional resources utilized by N. malipoensis, we compared stable isotope natural abundances (&#x3b4;13C, &#x3b4;15N, &#x3b4;2H, &#x3b4;18O) of different developmental stages with those of autotrophic reference plants.<br><br>KEY RESULTS: Protocorms exhibited an association with saprotrophic Ceratobasidiaceae rather than ectomycorrhiza-forming Ceratobasidiaceae and the 13C signature was characteristic of their fully mycoheterotrophic nutrition. Seedlings and adults were predominantly associated with saprotrophic fungi belonging to the Tulasnellaceae. While 13C and 2H stable isotope data revealed partial mycoheterotrophy of seedlings, it is unclear to what extent the fungal carbon supply is reduced in adult N. malipoensis. However, the 15N enrichment of mature N. malipoensis suggests partially mycoheterotrophic nutrition. Our data indicated a transition in mycorrhizal partners during ontogenetic development with decreasing dependency of N. malipoensis on fungal nitrogen and carbon.<br><br>CONCLUSIONS: The divergence in mycorrhizal partners between N. malipoensis and A. nipponica indicates different resource acquisition strategies and allows various habitat options in the earliest-diverging orchid lineage, Apostasioideae. While A. nipponica relies on the heterotrophic carbon gain from its ectomycorrhizal fungal partner and thus on forest habitats, N. malipoensis rather relies on own photosynthetic carbon gain as an adult, allowing it to establish in habitats as widely distributed as those where Rhizoctonia fungi occur.}, }
@article {pmid38911824, year = {2024}, author = {Nassiri, I and Kwok, AJ and Bhandari, A and Bull, KR and Garner, LC and Klenerman, P and Webber, C and Parkkinen, L and Lee, AW and Wu, Y and Fairfax, B and Knight, JC and Buck, D and Piazza, P}, title = {Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae085}, pmid = {38911824}, issn = {2635-0041}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {MOTIVATION: Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps.<br><br>RESULTS: We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells.<br><br>EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).}, }
@article {pmid38909361, year = {2024}, author = {Fei, L and Zhang, K and Hautaniemi, S and Sahu, B}, title = {Protocol to identify defined reprogramming factor expression using a factor-indexing single-nuclei multiome sequencing approach.}, journal = {STAR protocols}, volume = {5}, number = {3}, pages = {103148}, pmid = {38909361}, issn = {2666-1667}, mesh = {Humans ; *Cellular Reprogramming/genetics ; *Transcription Factors/genetics/metabolism ; Fibroblasts/metabolism/cytology ; Cell Nucleus/genetics/metabolism ; }, abstract = {Ectopic expression of lineage-specific transcription factors (TFs) of another cell type can induce cell fate reprogramming. However, the heterogeneity of reprogramming cells has been a challenge for data interpretation and model evaluation. Here, we present a protocol to characterize cells expressing defined factors during direct cell reprogramming using a factor-indexing approach based on single-nuclei multiome sequencing (FI-snMultiome-seq). We describe the steps for barcoding TFs, converting human fibroblasts to pancreatic ductal-like cells using defined TFs, and preparing library for FI-snMultiome-seq analysis. For complete details on the use and execution of this protocol, please refer to Fei et al.[1].}, }
@article {pmid38907922, year = {2024}, author = {Bell, CM}, title = {Single-Cell Sequencing of 3' RNA Transcripts.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2822}, number = {}, pages = {227-243}, pmid = {38907922}, issn = {1940-6029}, mesh = {*Single-Cell Analysis/methods ; Humans ; *3' Untranslated Regions ; *RNA, Messenger/genetics ; *Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; Animals ; High-Throughput Nucleotide Sequencing/methods ; Poly A/genetics ; Transcriptome/genetics ; }, abstract = {Single-cell RNA sequencing (scRNA-seq) enables the measurement of RNA expressed from individual cells within a tissue or population. RNA expression profiles may be used to draw conclusions about cellular states, cell subtypes within the population, responses to perturbations, and cellular behavior in the context of disease. Here we describe a method for scRNA-seq via single-cell encapsulation and capture of the polyadenosine tails at the 3' end of mRNA transcripts combined with cell and molecular barcoding, allowing for the sequencing of 3' untranslated regions in order to identify expressed genes from a cell.}, }
@article {pmid38907921, year = {2024}, author = {Orzolek, LD}, title = {Sequencing: 10X Genomics 3' HT Assay for Gene Expression.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2822}, number = {}, pages = {207-226}, pmid = {38907921}, issn = {1940-6029}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics/methods ; *Gene Library ; *Single-Cell Analysis/methods ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; DNA, Complementary/genetics ; }, abstract = {Single-cell RNA sequencing supports the isolation of individual cells and barcoding of cDNA, specific to each cell of origin. Subsequent sequencing of the generated library yields both the gene expression sequences and the cellular barcode, allowing distinction of gene expression patterns across individual cells. The 10X Genomics 3' HT assay uses a droplet-based method to isolate individual cells within oil emulsions, combined with a gel bead coated in uniquely barcoded primers, specific to each bead. The high-throughput, HT, assay is similar to its predecessor (3' v3.1) in reaction chemistry but utilizes (a) higher numbers of cellular barcodes, (b) a new, proprietary chip designed to target up to 60,000 cells per lane, and (c) captures up to 16 samples per run. The 3' HT assay supports whole cells and nuclei as input, with an approximate 60% capture rate. Here we describe the methods for sample quality control (QC) assays, loading and operation of the Chromium X instrument for cell capture, and cDNA synthesis and library preparation for downstream Illumina sequencing.}, }
@article {pmid38906909, year = {2024}, author = {Wang, T and Li, X and Tang, C and Cao, Z and He, H and Ma, X and Li, Y and De, K}, title = {Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14357}, pmid = {38906909}, issn = {2045-2322}, support = {LHZX-2022-01//The Chinese Academy of Sciences - People's Government of Qinghai Province on Sanjiangyuan National Park/ ; 2021-SF-A4//The major science and technology projects of Qinghai Province/ ; }, mesh = {*Phylogeny ; *Genome, Chloroplast ; *Pedicularis/genetics/classification ; *Microsatellite Repeats/genetics ; RNA, Transfer/genetics ; }, abstract = {The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and Pedicularis kansuensis (GenBank accession number: OQ587613) were sequenced, assembled, and annotated. Their chloroplast (cp) genome lengths were 146,452 bp, and 146,852 bp, respectively; 120 and 116 genes were identified, comprising 75 and 72 protein-coding genes (PCGs), 37 and 36 transfer RNA (tRNA) genes, and 8 and 8 ribosomal RNA (rRNA) genes, for P. chinensis and P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences were mainly composed of mononucleotide repeats (A/T motif) and dinucleotide repeats (AT/TA motif). Comparative genomics identified several variant genes (rpl22, rps19, rpl12, ycf1, trnH, psbA, and ndhH) and variant regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, and rpl32-trnL) with a high Pi, indicating the potential to serve as deoxyribo nucleic acid (DNA) barcodes for Pedicularis species identification. The results show that the cp genomes of P. chinensis and P. kansuensis were the same as those of other plants in Pedicularis, with different degrees of AT preference for codons. Large differences in the number of SSRs and the expansion of the inverted repeat (IR) region showed strong variability and interspecific differentiation between these two species and other species represented in the genus Pedicularis. A phylogenetic analysis showed that P. kansuensis had the closest relationship with P. oliveriana, and P. chinensis had the closest relationship with P. aschistorhyncha. These results will facilitate the study of the phylogenetic classification and interspecific evolution of Pedicularis plants.}, }
@article {pmid38903959, year = {2024}, author = {Ferreira, S and Corley, MFV and Nunes, J and Rosete, J and Vasconcelos, S and Mata, VA and Veríssimo, J and Silva, TL and Sousa, P and Andrade, R and Grosso-Silva, JM and Pinho, CJ and Chaves, C and Martins, FM and Pinto, J and Puppo, P and Muñoz-Mérida, A and Archer, J and Pauperio, J and Beja, P}, title = {The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e117169}, pmid = {38903959}, issn = {1314-2828}, abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Dataset - DS-IBILP08 contains records of 2350 specimens of moths (Lepidoptera species that do not belong to the superfamily Papilionoidea). All specimens have been morphologically identified to species or subspecies level and represent 1158 species in total. The species of this dataset correspond to about 42% of mainland Portuguese Lepidoptera species. All specimens were collected in mainland Portugal between 2001 and 2022. All DNA extracts and over 96% of the specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.<br><br>NEW INFORMATION: The authors enabled "The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese moths" in order to release the majority of data of DNA barcodes of Portuguese moths within the InBIO Barcoding Initiative. This dataset increases the knowledge on the DNA barcodes of 1158 species from Portugal belonging to 51 families. There is an increase in DNA barcodes of 205% in Portuguese specimens publicly available. The dataset includes 61 new Barcode Index Numbers. All specimens have their DNA barcodes publicly accessible through BOLD online database and the distribution data can be accessed through the Global Biodiversity Information Facility (GBIF).}, }
@article {pmid38901752, year = {2024}, author = {Negi, N and Ramkrishna,  and Meena, RK and Bhandari, MS and Pandey, S}, title = {Discovery of Botryosphaeria eucalypti sp. nov. from blighted Eucalyptus leaves in India.}, journal = {Microbial pathogenesis}, volume = {193}, number = {}, pages = {106756}, doi = {10.1016/j.micpath.2024.106756}, pmid = {38901752}, issn = {1096-1208}, mesh = {*Eucalyptus/microbiology ; *Plant Diseases/microbiology ; *Ascomycota/genetics/isolation &amp; purification/classification ; *Plant Leaves/microbiology ; India ; *Phylogeny ; *DNA, Fungal/genetics ; *Tubulin/genetics ; *Sequence Analysis, DNA ; Peptide Elongation Factor 1/genetics ; Spores, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; }, abstract = {Eucalyptus spp. are undoubtedly one of the most favored plantation trees globally. Accurately identifying Eucalyptus pathogens is therefore crucial for timely disease prevention and control. Recently, symptoms of a leaf blight disease were observed on Eucalyptus trees in plantations at Jhajjar and Karnal in the state of Haryana, northern India. Asexual morphs resembling the features of the Botryosphaeriaceae were consistently isolated from the symptomatic leaves. Morphological features coupled with DNA sequence analysis confirmed a novel species, which is described and illustrated here as Botryosphaeria eucalypti sp. nov. Conidia of the new taxon are longer and wider than those of its phylogenetic neighbors. A distinct phylogenetic position for the new taxon was established through combined analysis of the internal transcribed spacer (ITS), partial translation elongation factor-1α (tef1) and partial β-tubulin (tub2) regions. Recombination analysis provided additional support for the new species hypothesis. The pathogenicity of the novel species was proved on Eucalyptus leaves, and Koch's postulates were fulfilled. The discovery of new Botryosphaeria species is important because it will help in understanding the species diversity, host range, possible threats and disease control in the long run.}, }
@article {pmid38900825, year = {2024}, author = {Rewicz, A and Monzalvo, R and Myśliwy, M and Tończyk, G and Desiderato, A and Ruchisansakun, S and Rewicz, T}, title = {Pollination biology of Impatiens capensis Meerb. in non-native range.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0302283}, pmid = {38900825}, issn = {1932-6203}, mesh = {*Pollination/physiology ; Animals ; *Impatiens/physiology/genetics ; *Introduced Species ; Diptera/physiology/anatomy &amp; histology ; Poland ; DNA Barcoding, Taxonomic ; Hymenoptera/physiology ; }, abstract = {Pollination biology in the widespread species Impatiens capensis Meerb. has only been studied in America, specifically in zones of the U.S.A. and Canada. In this study, we investigated the pollination biology of I. capensis using an integrative identification approach using morphological and molecular tools in four populations of Northwest Poland. We also determined and compared the functional characteristics of the pollinators of the introduced species from the study sites and the native ones reported, for the latter collecting information from bibliographic sources. Visitors were identified using standard morphological keys, including identifying and classifying insect mouthparts. Molecular identification was carried out using mitochondrial DNA's cytochrome oxidase subunit I (COI). We morphologically identified 20 species of visitors constituted by 17 pollinators and three nectar robbers. DNA barcoding of 59 individuals proved the identification of 18 species (also 18 BINs). The frequency of pollinator species was primarily made up of representatives of both Hymenoptera (75%) and Diptera (21%). The morphological traits, such as the chewing and sucking mouthparts, small and big body height, and robber and pollinator behavior explained mainly the native and introduced visitors' arrangements that allow pollination success. However, to understand the process comprehensively, further investigation of other causalities in pollination success and understanding the diversity of pollinators in outer native ranges are necessary.}, }
@article {pmid38900631, year = {2024}, author = {Li, H and Humphreys, BD}, title = {Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing.}, journal = {STAR protocols}, volume = {5}, number = {3}, pages = {103049}, pmid = {38900631}, issn = {2666-1667}, support = {R01 DK103740/DK/NIDDK NIH HHS/United States ; U54 DK137332/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Kidney/metabolism ; *High-Throughput Nucleotide Sequencing/methods ; Gene Expression Profiling/methods ; Chromatin Immunoprecipitation Sequencing/methods ; Sequence Analysis, RNA/methods ; Transposases/genetics/metabolism ; Single-Cell Analysis/methods ; Gene Library ; Chromatin/genetics/metabolism ; }, abstract = {Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys with SHARE-seq. We describe steps for processing fixed nuclei for SHARE-seq split-pool barcoding and library preparation. We also detail how to determine the optimal working concentration of Tn5 transposase for transposition and tagmentation. This protocol allows researchers to generate large-scale single-cell multiomics data at low reagent cost. For complete details on the use and execution of this protocol, please refer to Li et al.[1].}, }
@article {pmid38899721, year = {2024}, author = {Veltman, MA and Anthoons, B and Schrøder-Nielsen, A and Gravendeel, B and de Boer, HJ}, title = {Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids.}, journal = {Molecular ecology resources}, volume = {24}, number = {6}, pages = {e13986}, doi = {10.1111/1755-0998.13986}, pmid = {38899721}, issn = {1755-0998}, support = {765000//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; }, mesh = {*Orchidaceae/genetics/classification ; *Phylogeny ; Genetic Markers/genetics ; Sequence Analysis, DNA/methods ; Asia ; Mediterranean Region ; Genome, Plant/genetics ; }, abstract = {Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.}, }
@article {pmid38899428, year = {2025}, author = {Laifi-Necibi, N and Amor, N and Merella, P and Mohammed, OB and Medini, L}, title = {DNA barcoding reveals cryptic species in the sea slater Ligia italica (Crustacea, Isopoda) from Tunisia.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {35}, number = {1-2}, pages = {1-11}, doi = {10.1080/24701394.2024.2363350}, pmid = {38899428}, issn = {2470-1408}, mesh = {Animals ; *Isopoda/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Tunisia ; Phylogeny ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Mediterranean Sea ; }, abstract = {Barcoding studies have provided significant insights into phylogenetic relationships among species belonging to the genus Ligia (Crustacea, Isopoda). Herein the diversity of the Italian sea slater Ligia italica from Tunisia is studied for the first time. Samples were collected from 18 localities in Tunisia, and the analysis included previously published sequences from Italy and Greece available in GenBank. Bayesian and Maximum Likelihood phylogenetic analyses were carried out using a fragment of the mitochondrial COI gene. Putative cryptic species were explored using the 'barcode gap' approach in the software ASAP. A genetic landscape shape analysis was carried out using the program Alleles in Space. The analyses revealed highly divergent and well-supported clades of L. italica dispersed across Tunisia (Clades A1 and A2), Greece (Clade B) and Italy (Clades C1 and C2). High genetic dissimilarity among clades suggested that L. italica constitute a cryptic species complex. Divergence among different L. italica lineages (Clades A, B and C) occurred around 7-4.5 Ma. The detected high genetic distances among clades did not result from atypical mitochondrial DNAs or intracellular infection by Wolbachia bacteria. The complex history of the Mediterranean Sea appears to have played a significant role in shaping the phylogeographic pattern of Ligia italica. Additional morphological and molecular studies are needed to confirm the existence of cryptic species in Ligia italica in Mediterranean.}, }
@article {pmid38898172, year = {2024}, author = {Liu, Y and Sundah, NR and Ho, NRY and Shen, WX and Xu, Y and Natalia, A and Yu, Z and Seet, JE and Chan, CW and Loh, TP and Lim, BY and Shao, H}, title = {Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells.}, journal = {Nature biomedical engineering}, volume = {8}, number = {7}, pages = {909-923}, pmid = {38898172}, issn = {2157-846X}, support = {MOH-000564; MOH-000541; MOH-000206//MOH | National Medical Research Council (NMRC)/ ; NRF-CRP29-2022-0001//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; DTC-RGC-09//National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)/ ; T2EP20121-0040//Ministry of Education - Singapore (MOE)/ ; }, mesh = {Humans ; *Breast Neoplasms/genetics/metabolism/pathology ; *DNA Barcoding, Taxonomic/methods ; Protein Interaction Mapping/methods ; Cell Line, Tumor ; DNA/chemistry/metabolism/genetics ; Female ; }, abstract = {Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.}, }
@article {pmid38898081, year = {2024}, author = {Goudarzi, MH and Robinson, SD and Cardoso, FC and Mitchell, ML and Cook, LG and King, GF and Walker, AA}, title = {Phylogeny, envenomation syndrome, and membrane permeabilising venom produced by Australia's electric caterpillar Comana monomorpha.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {14172}, pmid = {38898081}, issn = {2045-2322}, support = {DP200102867//Australian Research Council/ ; CE200100012//Australian Research Council/ ; DP200102867//Australian Research Council/ ; APP2017461//National Health and Medical Research Council/ ; }, mesh = {Animals ; Australia ; *Phylogeny ; Larva ; Proteomics/methods ; Arthropod Venoms/genetics/metabolism ; Moths/genetics ; Cell Membrane Permeability ; Humans ; Bites and Stings ; Proteome ; }, abstract = {Zygaenoidea is a superfamily of lepidopterans containing many venomous species, including the Limacodidae (nettle caterpillars) and Megalopygidae (asp caterpillars). Venom proteomes have been recently documented for several species from each of these families, but further data are required to understand the evolution of venom in Zygaenoidea. In this study, we examined the 'electric' caterpillar from North-Eastern Australia, a limacodid caterpillar densely covered in venomous spines. We used DNA barcoding to identify this caterpillar as the larva of the moth Comana monomorpha (Turner, 1904). We report the clinical symptoms of C. monomorpha envenomation, which include acute pain, and erythema and oedema lasting for more than a week. Combining transcriptomics of venom spines with proteomics of venom harvested from the spine tips revealed a venom markedly different in composition from previously examined limacodid venoms that are rich in peptides. In contrast, the venom of C. monomorpha is rich in aerolysin-like proteins similar to those found in venoms of asp caterpillars (Megalopygidae). Consistent with this composition, the venom potently permeabilises sensory neurons and human neuroblastoma cells. This study highlights the diversity of venom composition in Limacodidae.}, }
@article {pmid38896378, year = {2025}, author = {Akhter, G and Ahmed, I and Ahmad, SM}, title = {Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.}, journal = {Biochemical genetics}, volume = {63}, number = {4}, pages = {3095-3116}, pmid = {38896378}, issn = {1573-4927}, mesh = {Animals ; *Cyprinidae/genetics/classification ; *Cytochromes b/genetics ; Phylogeny ; *Electron Transport Complex IV/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.}, }
@article {pmid38895703, year = {2023}, author = {Hou, LW and Giraldo, A and Groenewald, JZ and Rämä, T and Summerbell, RC and Huang, GZ and Cai, L and Crous, PW}, title = {Redisposition of acremonium-like fungi in Hypocreales.}, journal = {Studies in mycology}, volume = {105}, number = {}, pages = {23-203}, pmid = {38895703}, issn = {0166-0616}, abstract = {Acremonium is acknowledged as a highly ubiquitous genus including saprobic, parasitic, or endophytic fungi that inhabit a variety of environments. Species of this genus are extensively exploited in industrial, commercial, pharmaceutical, and biocontrol applications, and proved to be a rich source of novel and bioactive secondary metabolites. Acremonium has been recognised as a taxonomically difficult group of ascomycetes, due to the reduced and high plasticity of morphological characters, wide ecological distribution and substrate range. Recent advances in molecular phylogenies, revealed that Acremonium is highly polyphyletic and members of Acremonium s. lat. belong to at least three distinct orders of Sordariomycetes, of which numerous orders, families and genera with acremonium-like morphs remain undefined. To infer the phylogenetic relationships and establish a natural classification for acremonium-like taxa, systematic analyses were conducted based on a large number of cultures with a global distribution and varied substrates. A total of 633 cultures with acremonium-like morphology, including 261 ex-type cultures from 89 countries and a variety of substrates including soil, plants, fungi, humans, insects, air, and water were examined. An overview phylogenetic tree based on three loci (ITS, LSU, rpb2) was generated to delimit the orders and families. Separate trees based on a combined analysis of four loci (ITS, LSU, rpb2, tef-1α) were used to delimit species at generic and family levels. Combined with the morphological features, host associations and ecological analyses, acremonium-like species evaluated in the present study are currently assigned to 63 genera, and 14 families in Cephalothecales, Glomerellales and Hypocreales, mainly in the families Bionectriaceae, Plectosphaerellaceae and Sarocladiaceae and five new hypocrealean families, namely Chrysonectriaceae, Neoacremoniaceae, Nothoacremoniaceae, Pseudoniessliaceae and Valsonectriaceae. Among them, 17 new genera and 63 new combinations are proposed, with descriptions of 65 new species. Furthermore, one epitype and one neotype are designated to stabilise the taxonomy and use of older names. Results of this study demonstrated that most species of Acremonium s. lat. grouped in genera of Bionectriaceae, including the type A. alternatum. A phylogenetic backbone tree is provided for Bionectriaceae, in which 183 species are recognised and 39 well-supported genera are resolved, including 10 new genera. Additionally, rpb2 and tef-1α are proposed as potential DNA barcodes for the identification of taxa in Bionectriaceae. Taxonomic novelties: New families: Chrysonectriaceae L.W. Hou, L. Cai &amp; Crous, Neoacremoniaceae L.W. Hou, L. Cai &amp; Crous, Nothoacremoniaceae L.W. Hou, L. Cai &amp; Crous, Pseudoniessliaceae L.W. Hou, L. Cai &amp; Crous, Valsonectriaceae L.W. Hou, L. Cai &amp; Crous. New genera: Bionectriaceae: Alloacremonium L.W. Hou, L. Cai &amp; Crous, Gossypinidium L.W. Hou, L. Cai &amp; Crous, Monohydropisphaera L.W. Hou, L. Cai &amp; Crous, Musananaesporium L.W. Hou, L. Cai &amp; Crous, Paragliomastix L.W. Hou, L. Cai &amp; Crous, Proliferophialis L.W. Hou, L. Cai &amp; Crous, Proxiovicillium L.W. Hou, L. Cai &amp; Crous, Ramosiphorum L.W. Hou, L. Cai &amp; Crous, Verruciconidia L.W. Hou, L. Cai &amp; Crous, Waltergamsia L.W. Hou, L. Cai &amp; Crous; Clavicipitaceae: Subuliphorum L.W. Hou, L. Cai &amp; Crous; Neoacremoniaceae: Neoacremonium L.W. Hou, L. Cai &amp; Crous; Nothoacremoniaceae: Nothoacremonium L.W. Hou, L. Cai &amp; Crous; Plectosphaerellaceae: Allomusicillium L.W. Hou, L. Cai &amp; Crous, Parafuscohypha L.W. Hou, L. Cai &amp; Crous; Pseudoniessliaceae: Pseudoniesslia L.W. Hou, L. Cai &amp; Crous; Sarocladiaceae: Polyphialocladium L.W. Hou, L. Cai &amp; Crous. New species: Bionectriaceae: Alloacremonium ferrugineum L.W. Hou, L. Cai &amp; Crous, Al. humicola L.W. Hou, L. Cai &amp; Crous, Acremonium aerium L.W. Hou, L. Cai &amp; Crous, A. brunneisporum L.W. Hou, L. Cai &amp; Crous, A. chlamydosporium L.W. Hou, L. Cai &amp; Crous, A. ellipsoideum L.W. Hou, Rämä, L. Cai &amp; Crous, A. gamsianum L.W. Hou, L. Cai &amp; Crous, A. longiphialidicum L.W. Hou, L. Cai &amp; Crous, A. multiramosum L.W. Hou, Rämä, L. Cai &amp; Crous, A. mycoparasiticum L.W. Hou, L. Cai &amp; Crous, A. stroudii K. Fletcher, F.C. Küpper &amp; P. van West, A. subulatum L.W. Hou, L. Cai &amp; Crous, A. synnematoferum L.W. Hou, Rämä, L. Cai &amp; Crous, Bulbithecium ammophilae L.W. Hou, L. Cai &amp; Crous, B. ellipsoideum L.W. Hou, L. Cai &amp; Crous, B. truncatum L.W. Hou, L. Cai &amp; Crous, Emericellopsis brunneiguttula L.W. Hou, L. Cai &amp; Crous, Gliomastix musae L.W. Hou, L. Cai &amp; Crous, Gossypinidium sporodochiale L.W. Hou, L. Cai &amp; Crous, Hapsidospora stercoraria L.W. Hou, L. Cai &amp; Crous, H. variabilis L.W. Hou, L. Cai &amp; Crous, Mycocitrus odorus L.W. Hou, L. Cai &amp; Crous, Nectriopsis ellipsoidea L.W. Hou, L. Cai &amp; Crous, Paracylindrocarpon aurantiacum L.W. Hou, L. Cai &amp; Crous, Pn. foliicola Lechat &amp; J. Fourn., Paragliomastix rosea L.W. Hou, L. Cai &amp; Crous, Proliferophialis apiculata L.W. Hou, L. Cai &amp; Crous, Protocreopsis finnmarkica L.W. Hou, L. Cai, Rämä &amp; Crous, Proxiovicillium lepidopterorum L.W. Hou, L. Cai &amp; Crous, Ramosiphorum echinoporiae L.W. Hou, L. Cai &amp; Crous, R. polyporicola L.W. Hou, L. Cai &amp; Crous, R. thailandicum L.W. Hou, L. Cai &amp; Crous, Verruciconidia erythroxyli L.W. Hou, L. Cai &amp; Crous, Ve. infuscata L.W. Hou, L. Cai &amp; Crous, Ve. quercina L.W. Hou, L. Cai &amp; Crous, Ve. siccicapita L.W. Hou, L. Cai &amp; Crous, Ve. unguis L.W. Hou, L. Cai &amp; Crous, Waltergamsia alkalina L.W. Hou, L. Cai &amp; Crous, W. catenata L.W. Hou, L. Cai &amp; Crous, W. moroccensis L.W. Hou, L. Cai &amp; Crous, W. obpyriformis L.W. Hou, L. Cai &amp; Crous; Chrysonectriaceae: Chrysonectria crystallifera L.W. Hou, L. Cai &amp; Crous; Nectriaceae: Xenoacremonium allantoideum L.W. Hou, L. Cai &amp; Crous; Neoacremoniaceae: Neoacremonium distortum L.W. Hou, L. Cai &amp; Crous, N. flavum L.W. Hou, L. Cai &amp; Crous; Nothoacremoniaceae: Nothoacremonium subcylindricum L.W. Hou, L. Cai &amp; Crous, No. vesiculophorum L.W. Hou, L. Cai &amp; Crous; Myrotheciomycetaceae: Trichothecium hongkongense L.W. Hou, L. Cai &amp; Crous; Plectosphaerellaceae: Brunneomyces polyphialidus L.W. Hou, L. Cai &amp; Crous, Parafuscohypha proliferata L.W. Hou, L. Cai &amp; Crous; Sarocladiaceae: Chlamydocillium acaciae L.W. Hou, L. Cai &amp; Crous, C. antarcticum L.W. Hou, L. Cai &amp; Crous, C. guttulatum L.W. Hou, L. Cai &amp; Crous, C. lolii L.W. Hou, L. Cai &amp; Crous, C. soli L.W. Hou, L. Cai &amp; Crous, C. terrestre L.W. Hou, L. Cai &amp; Crous, Parasarocladium chondroidum L.W. Hou, L. Cai &amp; Crous,Polyphialocladium fusisporum L.W. Hou, L. Cai &amp; Crous, Sarocladium agarici L.W. Hou, L. Cai &amp; Crous, S. citri L.W. Hou, L. Cai &amp; Crous, S. ferrugineum L.W. Hou, L. Cai &amp; Crous, S. fuscum L.W. Hou, L. Cai &amp; Crous,S. theobromae L.W. Hou, L. Cai &amp; Crous; Valsonectriaceae: Valsonectria crystalligena L.W. Hou, L. Cai &amp; Crous, V. hilaris L.W. Hou, L. Cai &amp; Crous. New combinations: Bionectriaceae: Acremonium purpurascens (Sukapure &amp; Thirum.) L.W. Hou, L. Cai &amp; Crous, Bulbithecium arxii (Malloch) L.W. Hou, L. Cai &amp; Crous, Bu. borodinense (Tad. Ito et al.) L.W. Hou, L. Cai &amp; Crous, Bu. pinkertoniae (W. Gams) L.W. Hou, L. Cai &amp; Crous, Bu. spinosum (Negroni) L.W. Hou, L. Cai &amp; Crous, Emericellopsis exuviara (Sigler et al.) L.W. Hou, L. Cai &amp; Crous, E. fimetaria (Pers.) L.W. Hou, L. Cai &amp; Crous, E. fuci (Summerb. et al.) L.W. Hou, L. Cai &amp; Crous, E. moniliformis (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, E. salmonea (W. Gams &amp; Lodha) L.W. Hou, L. Cai &amp; Crous, E. tubakii (Gams) L.W. Hou, L. Cai &amp; Crous, Fusariella arenula (Berk. &amp; Broome) L.W. Hou, L. Cai &amp; Crous, Hapsidospora chrysogena (Thirum. &amp; Sukapure) L.W. Hou, L. Cai &amp; Crous, H. flava (W. Gams) L.W. Hou, L. Cai &amp; Crous, H. globosa (Malloch &amp; Cain) L.W. Hou, L. Cai &amp; Crous, H. inversa (Malloch &amp; Cain) L.W. Hou, L. Cai &amp; Crous, Hydropisphaera aurantiaca (C.A. Jørg.) L.W. Hou, L. Cai &amp; Crous, Lasionectria atrorubra (Lechat &amp; J. Fourn.) L.W. Hou, L. Cai &amp; Crous, L. bisepta (W. Gams) L.W. Hou, L. Cai &amp; Crous, L. castaneicola (Lechat &amp; Gardiennet) L.W. Hou, L. Cai &amp; Crous, L. cerealis (P. Karst.) L.W. Hou, L. Cai &amp; Crous, L. olida (W. Gams) L.W. Hou, L. Cai &amp; Crous, Lasionectriopsis dentifera (Samuels) L.W. Hou, L. Cai &amp; Crous, Lasionectriella arenuloides (Samuels) L.W. Hou, L. Cai &amp; Crous, La. marigotensis (Lechat &amp; J. Fourn.) L.W. Hou, L. Cai &amp; Crous, Monohydropisphaera fusigera (Berk. &amp; Broome) L.W. Hou, L. Cai &amp; Crous, Musananaesporium tectonae (R.F. Castañeda) L.W. Hou, L. Cai &amp; Crous, Mycocitrus zonatus (Sawada) L.W. Hou, L. Cai &amp; Crous, Nectriopsis microspora (Jaap) L.W. Hou, L. Cai &amp; Crous, Ovicillium asperulatum (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, O. variecolor (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, Paracylindrocarpon multiloculatum (Samuels) L.W. Hou, L. Cai &amp; Crous, Pn. multiseptatum (Samuels)L.W. Hou, L. Cai &amp; Crous, Paragliomastix chiangraiensis (J.F. Li et al.) L.W. Hou, L. Cai &amp; Crous, Px. luzulae (Fuckel) L.W. Hou, L. Cai &amp; Crous, Px. znieffensis (Lechat &amp; J. Fourn.) L.W. Hou, L. Cai &amp; Crous, Protocreopsis rutila (W. Gams) L.W. Hou, L. Cai &amp; Crous, Proxiovicillium blochii (Matr.)L.W. Hou, L. Cai &amp; Crous, Stanjemonium dichromosporum (Gams &amp; Sivasith.) L.W. Hou, L. Cai &amp; Crous, Verruciconidia persicina (Nicot) L.W. Hou, L. Cai &amp; Crous, Ve. verruculosa (W. Gams &amp; Veenb.-Rijks) L.W. Hou, L. Cai &amp; Crous, Waltergamsia citrina (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. dimorphospora (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. epimycota (Samuels) L.W. Hou, L. Cai &amp; Crous, W. fusidioides (Nicot) L.W. Hou, L. Cai &amp; Crous, W. hennebertii (W. Gams) L.W. Hou, L. Cai &amp; Crous, W. parva (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. pilosa (A. Giraldo et al.) L.W. Hou, L. Cai &amp; Crous, W. zeylanica (Petch) L.W. Hou, L. Cai &amp; Crous; Cephalothecaceae: Phialemonium thermophilum (W. Gams &amp; J. Lacey) L.W. Hou, L. Cai &amp; Crous; Clavicipitaceae: Subuliphorum camptosporum (W. Gams) L.W. Hou, L. Cai &amp; Crous; Coniochaetaceae: Coniochaeta psammospora (W. Gams) L.W. Hou, L. Cai &amp; Crous; Nothoacremoniaceae: Nothoacremonium exiguum (W. Gams) L.W. Hou, L. Cai &amp; Crous; Neoacremoniaceae: Neoacremonium minutisporum (Sukapure &amp; Thirum.) L.W. Hou, L. Cai &amp; Crous; Ne. taiwanense (K.L. Pang et al.) L.W. Hou, L. Cai &amp; Crous; Ne. vitellinum (W. Gams) L.W. Hou, L. Cai &amp; Crous; Plectosphaerellaceae: Allomusicillium domschii (W. Gams) L.W. Hou, L. Cai &amp; Crous, Brunneomyces pseudozeylanicus (W. Gams) L.W. Hou, L. Cai &amp; Crous; Pseudoniessliaceae: Pseudoniesslia minutispora (W. Gams et al.) L.W. Hou, L. Cai &amp; Crous; Sarocladiaceae: Chlamydocillium curvulum (W. Gams) L.W. Hou, L. Cai &amp; Crous, Parasarocladium funiculosum (Sukapure &amp; Thirum.) L.W. Hou, L. Cai &amp; Crous; Valsonectriaceae: Valsonectria inflata (C.H. Dickinson) L.W. Hou, L. Cai &amp; Crous, V. roseola (G. Sm.) L.W. Hou, L. Cai &amp; Crous. Epitype (basionym): Sphaeria violacea J.C. Schmidt ex Fr. Neotype (basionym): Mastigocladium blochii Matr. Citation: Hou LW, Giraldo A, Groenewald JZ, Rämä T, Summerbell RC, Zang P, Cai L, Crous PW (2023). Redisposition of acremonium-like fungi in Hypocreales. Studies in Mycology 105: 23-203. doi: 10.3114/sim.2023.105.02.}, }
@article {pmid38895212, year = {2024}, author = {Totty, M and Hicks, SC and Guo, B}, title = {SpotSweeper: spatially-aware quality control for spatial transcriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38895212}, issn = {2692-8205}, support = {F32 MH135620/MH/NIMH NIH HHS/United States ; R01 MH126393/MH/NIMH NIH HHS/United States ; }, abstract = {Quality control (QC) is a crucial step to ensure the reliability and accuracy of the data obtained from RNA sequencing experiments, including spatially-resolved transcriptomics (SRT). Existing QC approaches for SRT that have been adopted from single-nucleus RNA sequencing (snRNA-seq) methods are confounded by spatial biology and are inappropriate for SRT data. In addition, no methods currently exist for identifying histological tissue artifacts unique to SRT. Here, we introduce SpotSweeper, spatially-aware QC methods for identifying local outliers and regional artifacts in SRT. SpotSweeper evaluates the quality of individual spots relative to their local neighborhood, thus minimizing bias due to biological heterogeneity, and uses multiscale methods to detect regional artifacts. Using SpotSweeper on publicly available data, we identified a consistent set of Visium barcodes/spots as systematically low quality and demonstrate that SpotSweeper accurately identifies two distinct types of regional artifacts, resulting in improved downstream clustering and marker gene detection for spatial domains.}, }
@article {pmid38895104, year = {2024}, author = {Nath, S and VanSlambrouck, JT and Yao, JW and Gullapalli, A and Razi, F and Lu, Y}, title = {DNA barcoding of terrestrial invasive plant species in Southwest Michigan.}, journal = {Plant direct}, volume = {8}, number = {6}, pages = {e615}, pmid = {38895104}, issn = {2475-4455}, abstract = {Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA-based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH-psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR-and-sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH-psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH-psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual-barcode approaches (e.g., ITS + trnH-psbA) might be the efficient and cost-effective method in DNA-based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species.}, }
@article {pmid38891833, year = {2024}, author = {Weber, B and Ritter, A and Han, J and Schaible, I and Sturm, R and Relja, B and Huber-Lang, M and Hildebrand, F and Pallas, C and Widera, M and Henrich, D and Marzi, I and Leppik, L}, title = {Development of a Sampling and Storage Protocol of Extracellular Vesicles (EVs)-Establishment of the First EV Biobank for Polytraumatized Patients.}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38891833}, issn = {1422-0067}, support = {465409392//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Biological Specimen Banks ; *Multiple Trauma/metabolism/blood ; Specimen Handling/methods ; Chromatography, Gel/methods ; Male ; Ultracentrifugation/methods ; MicroRNAs/blood/genetics ; Adult ; Female ; }, abstract = {In the last few years, several studies have emphasized the existence of injury-specific EV "barcodes" that could have significant importance for the precise diagnosis of different organ injuries in polytrauma patients. To expand the research potential of the NTF (network trauma research) biobank of polytraumatized patients, the NTF research group decided to further establish a biobank for EVs. However, until now, the protocols for the isolation, characterization, and storage of EVs for biobank purposes have not been conceptualized. Plasma and serum samples from healthy volunteers (n = 10) were used. Three EV isolation methods of high relevance for the work with patients' samples (ultracentrifugation, size exclusion chromatography, and immune magnetic bead-based isolation) were compared. EVs were quantified using nanoparticle tracking analysis, EV proteins, and miRNAs. The effects of different isolation solutions; the long storage of samples (up to 3 years); and the sensibility of EVs to serial freezing-thawing cycles and different storage conditions (RT, 4/-20/-80 °C, dry ice) were evaluated. The SEC isolation method was considered the most suitable for EV biobanking. We did not find any difference in the quantity of EVs between serum and plasma-EVs. The importance of particle-free PBS as an isolation solution was confirmed. Plasma that has been frozen for a long time can also be used as a source of EVs. Serial freezing-thawing cycles were found to affect the mean size of EVs but not their amount. The storage of EV samples for 5 days on dry ice significantly reduced the EV protein concentration.}, }
@article {pmid38887455, year = {2024}, author = {Wang, J and Kan, J and Wang, J and Yan, X and Li, Y and Soe, T and Tembrock, LR and Xing, G and Li, S and Wu, Z and Jia, M}, title = {The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1404071}, pmid = {38887455}, issn = {1664-462X}, abstract = {BACKGROUNDS: Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated.<br><br>METHODS: We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes.<br><br>RESULTS: The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved.<br><br>CONCLUSION: This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.}, }
@article {pmid38886529, year = {2024}, author = {Gaisser, KD and Skloss, SN and Brettner, LM and Paleologu, L and Roco, CM and Rosenberg, AB and Hirano, M and DePaolo, RW and Seelig, G and Kuchina, A}, title = {High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding.}, journal = {Nature protocols}, volume = {19}, number = {10}, pages = {3048-3084}, pmid = {38886529}, issn = {1750-2799}, support = {DE-SC0023091//U.S. Department of Energy (DOE)/ ; R21 DE032890/DE/NIDCR NIH HHS/United States ; R35GM150994//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R21DE032890//U.S. Department of Health &amp; Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R35 GM150994/GM/NIGMS NIH HHS/United States ; }, mesh = {*Single-Cell Analysis/methods ; *High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/classification ; Gene Expression Profiling/methods ; DNA Barcoding, Taxonomic/methods ; Transcriptome/genetics ; Gene Library ; }, abstract = {Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. The standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.}, }
@article {pmid38886157, year = {2025}, author = {Guarneri, I and Bozzo, M and Perez Criado, N and Serafini, E and Manfè, G and Tagliapietra, D and Fiorin, R and Scapin, L and Povero, P and Bellitto, D and Ferrando, S and Amaroli, A and Castellano, L and Pestarino, M and Schubert, M and Candiani, S}, title = {Amphioxus (Branchiostoma lanceolatum) in the North Adriatic Sea: ecological observations and spawning behavior.}, journal = {Integrative zoology}, volume = {20}, number = {2}, pages = {331-343}, pmid = {38886157}, issn = {1749-4877}, support = {FRA2023//Universit&#xe0; di Genova/ ; //CNRS/ ; ANR-21-CE34-0006-02//ANR/ ; }, mesh = {Animals ; *Lancelets/physiology/genetics ; Reproduction/physiology ; *Ecosystem ; *Sexual Behavior, Animal/physiology ; Seasons ; Mediterranean Sea ; Female ; }, abstract = {The European amphioxus (Branchiostoma lanceolatum) is a member of the chordate subphylum Cephalochordata, and, as such, a key model organism for providing insights into the origin and evolution of vertebrates. Despite its significance and global distribution, detailed characterizations of natural populations of cephalochordates are still very limited. This study investigates the abundance, habitat, and spawning behavior of amphioxus in the North Adriatic Sea. Across 32 sampled sites, adult amphioxus were consistently present, reaching densities exceeding 300 individuals m[-] [2]. DNA barcoding confirmed the species as B. lanceolatum, and environmental analyses revealed an amphioxus preference for slightly gravelly sand with low silt content and a correlation between amphioxus density and the presence of specific macroinvertebrate taxa. Remarkably, the amphioxus population was breeding in early spring and possibly late fall, in contrast to the typical late spring/early summer spawning season described for other populations of European amphioxus. Amphioxus adults kept in captivity maintained the spawning seasonality of their place of origin, suggesting the possibility of extending the overall spawning season of European amphioxus in laboratory settings by exploiting populations from diverse geographic origins. This study thus expands our understanding of B. lanceolatum ecology and reproduction in the Mediterranean Sea, emphasizing the role of the North Adriatic Sea as a substantial reservoir.}, }
@article {pmid38885824, year = {2024}, author = {Oliveira, HFM and Freire-Jr, GB and Silva, DC and Mata, VA and Abra, FD and Camargo, NF and Araujo Goebel, LG and Longo, GR and Silva, JM and Colli, GR and Domingos, FMCB}, title = {Barcoding Brazilian mammals to monitor biological diversity and threats: Trends, perspectives, and knowledge gaps.}, journal = {Environmental research}, volume = {258}, number = {}, pages = {119374}, doi = {10.1016/j.envres.2024.119374}, pmid = {38885824}, issn = {1096-0953}, mesh = {Animals ; Brazil ; *Mammals/genetics/classification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; Conservation of Natural Resources ; Environmental Monitoring/methods ; }, abstract = {DNA barcoding and environmental DNA (eDNA) represent significant advances for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the world's largest and most biologically diverse countries. However, many knowledge gaps still exist for describing, identifying, and monitoring of mammalian biodiversity using molecular methods. We aimed to unravel the patterns of the presence of Brazilian mammal species on molecular databases to improve our understanding of how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to mammalian conservation. We foundt many gaps in molecular databases, with many taxa being poorly represented, particularly from Amazonia, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that species description year was the most important factor determining the probability of a species to being sequenced. Primates are the group with the highest number of species considered a priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.}, }
@article {pmid38884656, year = {2024}, author = {Xing, RR and Bai, WM and Hu, D and Deng, TT and Zhang, JK and Chen, Y}, title = {Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {376}, pmid = {38884656}, issn = {1432-0614}, support = {2022YFF1101000//Key Technologies Research and Development Program/ ; 2023YFF1104700//Key Technologies Research and Development Program/ ; }, mesh = {*Mushroom Poisoning/diagnosis ; *Amanita/genetics ; *DNA Barcoding, Taxonomic ; *Phylogeny ; *DNA, Fungal/genetics ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA ; Humans ; }, abstract = {Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning. KEY POINTS: • Development of a DNA mini-barcoding method for Amanita species identification without fresh samples. • The ITS-a primer set was optimized for robust universality in Amanita samples. • The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases.}, }
@article {pmid38884110, year = {2024}, author = {Rathgeber, AC and Ludwig, LS and Penter, L}, title = {Single-cell genomics-based immune and disease monitoring in blood malignancies.}, journal = {Clinical hematology international}, volume = {6}, number = {2}, pages = {62-84}, pmid = {38884110}, issn = {2590-0048}, support = {UM1 HG012076/HG/NHGRI NIH HHS/United States ; }, abstract = {Achieving long-term disease control using therapeutic immunomodulation is a long-standing concept with a strong tradition in blood malignancies. Besides allogeneic hematopoietic stem cell transplantation that continues to provide potentially curative treatment for otherwise challenging diagnoses, recent years have seen impressive progress in immunotherapies for leukemias and lymphomas with immune checkpoint blockade, bispecific monoclonal antibodies, and CAR T cell therapies. Despite their success, non-response, relapse, and immune toxicities remain frequent, thus prioritizing the elucidation of the underlying mechanisms and identifying predictive biomarkers. The increasing availability of single-cell genomic tools now provides a system's immunology view to resolve the molecular and cellular mechanisms of immunotherapies at unprecedented resolution. Here, we review recent studies that leverage these technological advancements for tracking immune responses, the emergence of immune resistance, and toxicities. As single-cell immune monitoring tools evolve and become more accessible, we expect their wide adoption for routine clinical applications to catalyze more precise therapeutic steering of personal immune responses.}, }
@article {pmid38884003, year = {2024}, author = {Chieochanthanakij, R and Wattanasatja, V and Passorn, P and Wannigama, DL and Kanjanabuch, T}, title = {Caregiver skin infection causing peritoneal dialysis-associated peritonitis.}, journal = {Medical mycology case reports}, volume = {44}, number = {}, pages = {100653}, pmid = {38884003}, issn = {2211-7539}, abstract = {We present the first case report of peritoneal dialysis (PD)-associated peritonitis due to Gibellulopsis nigrescens, with the same pathogen detected in her caregiver's tinea capitis. This confirms that touch contamination from the caregiver's infection was the primary source of this rare organism. The species of pathogen causing peritonitis and her caregiver's scalp lesions were identified by DNA barcoding. The patient responded well to timely PD catheter removal and a 2-week course of systemic amphotericin B deoxycholate. Preventive strategies should prioritize hygiene practices, including maintaining adequate personal hygiene and practicing thorough hand washing, to mitigate the risk of touch contamination and subsequent infection with fungal pathogens.}, }
@article {pmid38883207, year = {2024}, author = {Valsecchi, E and Gabbiadini, A}, title = {An Observatory to monitor range extension of the Mediterranean monk seal based on its eDNA traces: collecting data and delivering results in the "Open Science" era.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e120201}, pmid = {38883207}, issn = {1314-2828}, abstract = {The monk seal is the most endangered pinniped in the world and the only one found in the Mediterranean, where its distribution and abundance have suffered a drastic decline in the last few decades. Data on its status are scattered due to both its rarity and evasiveness and records are biased towards occasional, mostly coastal encounters. Nowadays, molecular techniques allow us to detect and quantify minute amounts of DNA traces released into the environment (eDNA) by any organism. A species-specific molecular assay is now available for detecting the recent presence of the monk seal in the water column through the analysis of sea-water samples collected from the sea surface. The project "Spot the Monk" uses this non-invasive detection tool to monitor monk seal occurrence in Mediterranean waters by means of eDNA analysis. The simplicity in the acquisition of samples together with the need to collect samples in multiple points simultaneously made the project well suited to the involvement of the general public. Up to today, about 350 samples have been collected and analysed in the central-western Mediterranean by researchers and a multifarious range of citizen scientists - from recreational sailing organisations, both amateur and competitive sportsmen, to fishermen. This work announces the launch of an open-source Observatory (https://www.spot-the-monk-observatory.com/) where the project outcomes are publicly accessible as soon as they are produced. Embracing the principles of Open Science, we believe that such an approach can contribute to filling the knowledge gap about the distribution of this charismatic species in our seas, providing, at the same time, a proof of concept on how data collected by a variety of actors can be returned to the scientific and non-scientific communities in an innovative format for immediate consultation.}, }
@article {pmid38883206, year = {2024}, author = {Jaume-Schinkel, S and Müller, B and Avila-Calero, S and Kukowka, S and Rduch, V and Mengual, X}, title = {Preserving morphology while extracting DNA: a non-destructive field-to-museum protocol for slide-mounted specimens.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e119448}, pmid = {38883206}, issn = {1314-2828}, abstract = {Our study aimed to develop an optimised laboratory protocol ensuring the preservation of morphological structures and extraction of high-quality DNA sequences from Psychodidae (Insecta, Diptera) specimens. With 310 analysed specimens, we investigated the impact of distinct laboratory treatments by employing two shaking categories (constant and interrupted) with five different incubation periods (16, 12, 8, 4 and 2 hours) during the DNA extraction process. Notably, 80.65% of the specimens exhibited morphological changes during DNA extraction. Our results indicated no statistical difference between constant and interrupted shaking for the total of morphological structures lost. However, within each shaking category, the loss of structures was influenced significantly by the incubation period. Prolonged incubation correlated with increased structural losses, whereas shorter incubation periods caused minor alterations in structures lost. In addition, our results showed a significant difference between constant and interrupted shaking treatments for DNA concentration. Likewise, the incubation period showed differences within each shaking category. Successful COI sequencing was achieved in 89.6% of specimens, with negligible differences in DNA fragment lengths across treatments. Our findings underscore the importance of an optimised protocol and its potential in systematic research involving nematoceran dipteran specimens by balancing morphological integrity and DNA extraction efficiency.}, }
@article {pmid38882565, year = {2024}, author = {Li, SL and Liu, P and Peng, XJ}, title = {Three new species of jumping spiders (Araneae, Salticidae) from Hunan, China.}, journal = {ZooKeys}, volume = {1204}, number = {}, pages = {301-312}, pmid = {38882565}, issn = {1313-2989}, abstract = {Three new species of the genera Thiania C. L. Koch, 1846 and Yaginumaella Prószyński, 1979 are described and named as T.bamian sp. nov. (♂♀), T.flacata sp. nov. (♀) and Y.curvata sp. nov. (♂♀), from Hunan Province, China. Detailed descriptions, photos of somatic features and copulatory organs, as well as a distribution map are provided. Nucleotide data for the barcoding gene, cytochrome c oxidase subunit I (COI) of T.bamian sp. nov. (♂♀) and Y.curvata sp. nov. (♀) are provided.}, }
@article {pmid38879694, year = {2024}, author = {Siddika, MA and Ahmed, KA and Alam, MS and Bushra, J and Begum, RA}, title = {Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {13820}, pmid = {38879694}, issn = {2045-2322}, support = {NST Fellowship for Masters Thesis Research//Ministry of Science and Technology, Government of the People's Republic of Bangladesh/ ; Post Doctoral Research Fund//CSIRO, Australia/ ; 2022-23/23//University Grants Commission of Bangladesh/ ; }, mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Phylogeny ; *Perciformes/genetics/classification ; Codon Usage ; Gene Order ; }, abstract = {The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.}, }
@article {pmid38877523, year = {2024}, author = {De Silva, S and Cagliero, C and Gostel, MR and Johnson, G and Anderson, JL}, title = {Versatile DNA extraction from diverse plant taxa using ionic liquids and magnetic ionic liquids: a methodological breakthrough for enhanced sample utility.}, journal = {Plant methods}, volume = {20}, number = {1}, pages = {91}, pmid = {38877523}, issn = {1746-4811}, support = {CHE-2203891//U.S. National Science Foundation/ ; }, abstract = {BACKGROUND: There is a growing demand for fast and reliable plant biomolecular analyses. DNA extraction is the major bottleneck in plant nucleic acid-based applications especially due to the complexity of tissues in different plant species. Conventional methods for plant cell lysis and DNA extraction typically require extensive sample preparation processes and large quantities of sample and chemicals, elevated temperatures, and multiple sample transfer steps which pose challenges for high throughput applications.<br><br>RESULTS: In a prior investigation, an ionic liquid (IL)-based modified vortex-assisted matrix solid phase dispersion approach was developed using the model plant, Arabidopsis thaliana (L.) Heynh. Building upon this foundational study, the present study established a simple, rapid and efficient protocol for DNA extraction from milligram fragments of plant tissue representing a diverse range of taxa from the plant Tree of Life including 13 dicots and 4 monocots. Notably, the approach was successful in extracting DNA from a century old herbarium sample. The isolated DNA was of sufficient quality and quantity for sensitive molecular analyses such as qPCR. Two plant DNA barcoding markers, the plastid rbcL and nuclear ribosomal internal transcribed spacer (nrITS) regions were selected for DNA amplification and Sanger sequencing was conducted on PCR products of a representative dicot and monocot species. Successful qPCR amplification of the extracted DNA up to 3 weeks demonstrated that the DNA extracted using this approach remains stable at room temperature for an extended time period prior to downstream analysis.<br><br>CONCLUSIONS: The method presented here is a rapid and simple approach enabling cell lysis and DNA extraction from 1.5&#xa0;mg of plant tissue across a broad range of plant taxa. Additional purification prior to DNA amplification is not required due to the compatibility of the extraction solvents with qPCR. The method has tremendous potential for applications in plant biology that require DNA, including barcoding methods for agriculture, conservation, ecology, evolution, and forensics.}, }
@article {pmid38876979, year = {2024}, author = {Sullivan, DK and Pachter, L}, title = {Flexible parsing, interpretation, and editing of technical sequences with splitcode.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {6}, pages = {}, pmid = {38876979}, issn = {1367-4811}, support = {T32 GM008042/GM/NIGMS NIH HHS/United States ; UM1 HG012077/HG/NHGRI NIH HHS/United States ; U19MH114830/NH/NIH HHS/United States ; }, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Software ; Sequence Analysis, DNA/methods ; Gene Library ; }, abstract = {MOTIVATION: Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed.<br><br>RESULTS: We present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays.<br><br>The splitcode program is available at http://github.com/pachterlab/splitcode.}, }
@article {pmid38874640, year = {2024}, author = {Bhendarkar, M and Rodriguez-Ezpeleta, N}, title = {Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {7}, pages = {617}, pmid = {38874640}, issn = {1573-2959}, mesh = {*Fisheries ; *Biodiversity ; *Conservation of Natural Resources/methods ; Animals ; *Environmental Monitoring/methods ; *DNA, Environmental/analysis ; *Tropical Climate ; Ecosystem ; Fishes/genetics ; }, abstract = {Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.}, }
@article {pmid38873813, year = {2024}, author = {McNamara, LE and Boyn, JN and Anferov, SW and Filatov, AS and Maloney, MW and Mazziotti, DA and Schaller, RD and Anderson, JS}, title = {Variable Peripheral Ligand Donation Tunes Electronic Structure and NIR II Emission in Tetrathiafulvalene Tetrathiolate Diradicaloids.}, journal = {Journal of the American Chemical Society}, volume = {146}, number = {25}, pages = {17285-17295}, doi = {10.1021/jacs.4c04032}, pmid = {38873813}, issn = {1520-5126}, abstract = {Near-infrared (NIR) lumiphores are promising candidates for numerous imaging, communication, and sensing applications, but they typically require large, conjugated scaffolds to achieve emission in this low-energy region. Due to the extended conjugation and synthetic complexity required, it is extremely difficult to tune the photophysical properties of these systems for desired applications. Here, we report facile tuning of deep NIR-emitting diradicaloid complexes through simple modification of peripheral ligands. These new lumiphores are rare examples of air-, acid-, and water-stable emissive diradicaloids. We apply a simple Hammett parameter-based strategy to tune the electron donation of the capping ligand across a series of commercially available triarylphosphines. This minor peripheral modification significantly alters the electronic structure, and consequently, the electrochemical, photophysical, and magnetic properties of the tetrathiafulvalene tetrathiolate (TTFtt)-based lumiphores. The resultant ∼100 nm absorption and emission range spans common laser lines and the desirable telecom region (ca. 1260-1550 nm). Furthermore, these lumiphores are sensitive to local dielectrics, distinguishing them as promising candidates for ratiometric imaging and/or barcoding in the deep NIR region.}, }
@article {pmid38869148, year = {2024}, author = {Yang, C and Zhang, Z and Huang, Y and Xie, X and Liao, H and Xiao, J and Veldsman, WP and Yin, K and Fang, X and Zhang, L}, title = {LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38869148}, issn = {2047-217X}, support = {518000//BGI-Shenzhen, Shenzhen/ ; //Hong Kong Research Grant Council Early Career Scheme/ ; 22201419//HKBU/ ; C2004-23Y//Young Collaborative Research/ ; 11221026//Health and Medical Research Fund/ ; RC-SGT2/19-20/SCI/007//HKBU Start-up Grant Tier 2/ ; IRCMS/19-20/D02//HKBU IRCMS/ ; 2021A1515012226//Guangdong Basic and Applied Basic Research Foundation/ ; SGDX20190919142801722//Science Technology and Innovation Committee of Shenzhen Municipality, China/ ; }, mesh = {Humans ; *Genome, Human ; *Metagenome ; *Software ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; }, abstract = {BACKGROUND: Linked-read sequencing technologies generate high-base quality short reads that contain extrapolative information on long-range DNA connectedness. These advantages of linked-read technologies are well known and have been demonstrated in many human genomic and metagenomic studies. However, existing linked-read analysis pipelines (e.g., Long Ranger) were primarily developed to process sequencing data from the human genome and are not suited for analyzing metagenomic sequencing data. Moreover, linked-read analysis pipelines are typically limited to 1 specific sequencing platform.<br><br>FINDINGS: To address these limitations, we present the Linked-Read ToolKit (LRTK), a unified and versatile toolkit for platform agnostic processing of linked-read sequencing data from both human genome and metagenome. LRTK provides functions to perform linked-read simulation, barcode sequencing error correction, barcode-aware read alignment and metagenome assembly, reconstruction of long DNA fragments, taxonomic classification and quantification, and barcode-assisted genomic variant calling and phasing. LRTK has the ability to process multiple samples automatically and provides users with the option to generate reproducible reports during processing of raw sequencing data and at multiple checkpoints throughout downstream analysis. We applied LRTK on linked reads from simulation, mock community, and real datasets for both human genome and metagenome. We showcased LRTK's ability to generate comparative performance results from preceding benchmark studies and to report these results in publication-ready HTML document plots.<br><br>CONCLUSIONS: LRTK provides comprehensive and flexible modules along with an easy-to-use Python-based workflow for processing linked-read sequencing datasets, thereby filling the current gap in the field caused by platform-centric genome-specific linked-read data analysis tools.}, }
@article {pmid38865431, year = {2024}, author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S}, title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38865431}, issn = {1758-0463}, support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; }, mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; }, abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.}, }
@article {pmid38864889, year = {2024}, author = {Yu, KY and Lam, YH and Ng, SW and Cheung, YT and Tseung, JS and Tong, HF and Ching, CK and Chong, YK}, title = {Plant-origin rotenone poisoning - a rare cause of metabolic acidosis with hyperlactatemia diagnosed with DNA barcoding of gastric contents.}, journal = {Clinical toxicology (Philadelphia, Pa.)}, volume = {62}, number = {6}, pages = {407-408}, doi = {10.1080/15563650.2024.2350597}, pmid = {38864889}, issn = {1556-9519}, mesh = {Humans ; *Acidosis/chemically induced ; *Rotenone/toxicity ; *Hyperlactatemia/chemically induced ; *Gastrointestinal Contents/chemistry ; Male ; Adult ; }, }
@article {pmid38863065, year = {2024}, author = {Van Caenegem, W and Haelewaters, D}, title = {New insights into the DNA extraction and PCR amplification of minute ascomycetes in the genus Laboulbenia (Pezizomycotina, Laboulbeniales).}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {14}, pmid = {38863065}, issn = {2210-6340}, support = {DEB-2127290//Directorate for Biological Sciences/ ; Senior Postdoctoral Fellowship 1206024N//Research Foundation Flanders/ ; }, abstract = {Molecular studies of fungi within the order Laboulbeniales (Ascomycota, Pezizomycotina) have been hampered for years because of their minute size, inability to grow in axenic culture, and lack of reliable and cost-efficient DNA extraction protocols. In particular, the genus Laboulbenia is notorious for low success with DNA extraction and polymerase chain reaction (PCR) amplification. This is attributed to the presence of melanin, a molecule known to inhibit PCR, in the cells. We evaluated the efficacy of a standard single cell-based DNA extraction protocol by halving the recommended amount of reagents to reduce the cost per extraction and adding bovine serum albumin (BSA) during the multiple displacement amplification step to reverse the effect of melanin. A total of 196 extractions were made, 111 of which were successful. We found that halving the reagents used in the single cell-based extraction kit did not significantly affect the probability of successful DNA extraction. Using the halved protocol reduces cost and resource consumption. Moreover, there was no significant difference in the probability of successfully extracting DNA based on whether BSA was added or not, suggesting that the amount of melanin present in cells of the thallus has no major inhibitory effect on PCR. We generated 277 sequences from five loci, but amplification of the internal transcribed spacer region, the mitochondrial small subunit rDNA, and protein-coding genes remains challenging. The probability of successfully extracting DNA from Laboulbeniales was also impacted by specimen storage methods, with material preserved in > 95% ethanol yielding higher success rates compared to material stored in 70% ethanol and dried material. We emphasize the importance of proper preservation of material and propose the design of Laboulbeniales-specific primers to overcome the problems of primer mismatches and contaminants. Our new insights apply not only to the genus Laboulbenia; Laboulbeniales generally are understudied, and the vast majority of species remain unsequenced. New and approachable molecular developments will benefit the study of Laboulbeniales, helping to elucidate the true diversity and evolutionary relationships of these peculiar microfungi.}, }
@article {pmid38861479, year = {2024}, author = {Hamilton, AG and Swingle, KL and Thatte, AS and Mukalel, AJ and Safford, HC and Billingsley, MM and El-Mayta, RD and Han, X and Nachod, BE and Joseph, RA and Metzloff, AE and Mitchell, MJ}, title = {High-Throughput In Vivo Screening Identifies Differential Influences on mRNA Lipid Nanoparticle Immune Cell Delivery by Administration Route.}, journal = {ACS nano}, volume = {18}, number = {25}, pages = {16151-16165}, doi = {10.1021/acsnano.4c01171}, pmid = {38861479}, issn = {1936-086X}, support = {DP2 TR002776/TR/NCATS NIH HHS/United States ; F31 CA260922/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Nanoparticles/chemistry ; *RNA, Messenger/genetics ; Mice ; *Lipids/chemistry ; *Mice, Inbred C57BL ; High-Throughput Screening Assays ; Female ; Injections, Intramuscular ; Dendritic Cells/immunology/metabolism ; Injections, Intravenous ; Immunotherapy ; Liposomes ; }, abstract = {Immune modulation through the intracellular delivery of nucleoside-modified mRNA to immune cells is an attractive approach for in vivo immunoengineering, with applications in infectious disease, cancer immunotherapy, and beyond. Lipid nanoparticles (LNPs) have come to the fore as a promising nucleic acid delivery platform, but LNP design criteria remain poorly defined, making the rate-limiting step for LNP discovery the screening process. In this study, we employed high-throughput in vivo LNP screening based on molecular barcoding to investigate the influence of LNP composition on immune tropism with applications in vaccines and systemic immunotherapies. Screening a large LNP library under both intramuscular (i.m.) and intravenous (i.v.) injection, we observed differential influences on LNP uptake by immune populations across the two administration routes, gleaning insight into LNP design criteria for in vivo immunoengineering. In validation studies, the lead LNP formulation for i.m. administration demonstrated substantial mRNA translation in the spleen and draining lymph nodes with a more favorable biodistribution profile than LNPs formulated with the clinical standard ionizable lipid DLin-MC3-DMA (MC3). The lead LNP formulations for i.v. administration displayed potent immune transfection in the spleen and peripheral blood, with one lead LNP demonstrating substantial transfection of splenic dendritic cells and another inducing substantial transfection of circulating monocytes. Altogether, the immunotropic LNPs identified by high-throughput in vivo screening demonstrated significant promise for both locally- and systemically-delivered mRNA and confirmed the value of the LNP design criteria gleaned from our screening process, which could potentially inform future endeavors in mRNA vaccine and immunotherapy applications.}, }
@article {pmid38859300, year = {2024}, author = {Xu, B and Ji, Y and Xu, C and Zhang, B and Liu, K and Li, J}, title = {Simple modulation of Lissajous MEMS laser beam scanning with reconfigurable structured light patterns for 3D imaging.}, journal = {Optics express}, volume = {32}, number = {8}, pages = {13249-13265}, doi = {10.1364/OE.518283}, pmid = {38859300}, issn = {1094-4087}, abstract = {Structured light 3D imaging systems commonly employ panel-based projectors or 1-axis MEMS mirrors with beam expander lens to project multi-frame barcodes or dot clouds, addressing challenges posed by objects with multi-scale feature sizes. However, these methods often result in large system volumes due to the required projection multi-lens modules, high hardware costs, or limited light pattern generation capabilities that hindering measurement precision enhancement. This paper introduces an innovative approach to reconfigurable spatial light pattern projection using a single bi-axial MEMS mirror with Lissajous scanning. In contrast to the pixel-by-pixel pre-defined image patterns encoding of conventional 2D laser beam scanning, the proposed method simply aligns the MEMS bi-axial resonance frequencies with laser pulse modulation, enabling the projection of diverse structured light patterns such as stripes, lines, dot matrices, and random dot clouds, which can adapt to different 3D imaging algorithms demands. It eliminates the need for multi-frame encoding and streamlines data caching, simplifies digital logic hardware. A prototype 3D imaging system was developed to demonstrate the mathematical model for laser modulation and the technical feasibility based on the proposed principle. Beyond its lens-free essence, the system supports focal-free optics and a compact projection form factor, which accommodates to a broad range of projection distances and field-of-views based on object's location. 3D depth map of polynomial surface and blocks objects are extracted through single-frame pattern projection with a relative high accuracy. The presented modulation theory for diverse structured light pattern generation opens avenues for versatile and compact 3D imaging applications of LiDAR and robotic 3D vision.}, }
@article {pmid38853940, year = {2024}, author = {Willimann, M and Tiyaboonchai, A and Adachi, K and Li, B and Waldburger, L and Nakai, H and Grompe, M and Thöny, B}, title = {AAV Capsid Screening for Translational Pig Research Using a Mouse Xenograft Liver Model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38853940}, issn = {2692-8205}, support = {U01 DK123608/DK/NIDDK NIH HHS/United States ; }, abstract = {In gene therapy, delivery vectors are a key component for successful gene delivery and safety, based on which adeno-associated viruses (AAVs) gained popularity in particular for the liver, but also for other organs. Traditionally, rodents have been used as animal models to develop and optimize treatments, but species and organ specific tropism of AAV desire large animal models more closely related to humans for preclinical in-depth studies. Relevant AAV variants with the potential for clinical translation in liver gene therapy were previously evolved in vivo in a xenogeneic mouse model transplanted with human hepatocytes. Here, we selected and evaluated efficient AAV capsids using chimeric mice with a >90% xenografted pig hepatocytes. The pig is a valuable preclinical model for therapy studies due to its anatomic and immunological similarities to humans. Using a DNA-barcoded recombinant AAV library containing 47 different capsids and subsequent Illumina sequencing of barcodes in the AAV vector genome DNA and transcripts in the porcine hepatocytes, we found the AAVLK03 and AAVrh20 capsid to be the most efficient delivery vectors regarding transgene expression in porcine hepatocytes. In attempting to validate these findings with primary porcine hepatocytes, we observed capsid-specific differences in cell entry and transgene expression efficiency where the AAV2, AAVAnc80, and AAVDJ capsids showed superior efficiency to AAVLK03 and AAVrh20. This work highlights intricacies of in vitro testing with primary hepatocytes and the requirements for suitable pre-clinical animal models but suggests the chimeric mouse to be a valuable model to predict AAV capsids to transduce porcine hepatocytes efficiently.}, }
@article {pmid38853931, year = {2024}, author = {Choudhury, S and Sivankutty, I and Jung, Y and Huang, A and Araten, S and Kenny, C and An, Z and Doan, R and Foijer, F and Matsu, E and Rosen, I and Marciano, J and Jain, A and Sun, L and Hilal, N and Lee, E and Walsh, C and Chen, M}, title = {Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {38853931}, issn = {2693-5015}, support = {R56 AG079857/AG/NIA NIH HHS/United States ; P50 HD105351/HD/NICHD NIH HHS/United States ; DP2 AG072437/AG/NIA NIH HHS/United States ; S10 OD016453/OD/NIH HHS/United States ; UG3 NS132144/NS/NINDS NIH HHS/United States ; R01 HL152063/HL/NHLBI NIH HHS/United States ; R01 AG070921/AG/NIA NIH HHS/United States ; }, abstract = {Understanding the mechanisms of polyploidization in cardiomyocytes is crucial for advancing strategies to stimulate myocardial regeneration. Although endoreplication has long been considered the primary source of polyploid human cardiomyocytes, recent animal work suggests the potential for cardiomyocyte fusion. Moreover, the effects of polyploidization on the genomic-transcriptomic repertoire of human cardiomyocytes have not been studied previously. We applied single-nuclei whole genome sequencing, single nuclei RNA sequencing, and multiome ATAC + gene expression (from the same nuclei) techniques to nuclei isolated from 11 healthy hearts. Utilizing post-zygotic non-inherited somatic mutations occurring during development as "endogenous barcodes," to reconstruct lineage relationships of polyploid cardiomyocytes. Of 482 cardiomyocytes from multiple healthy donor hearts 75.7% can be sorted into several developmental clades marked by one or more somatic single-nucleotide variants (SNVs). At least ~10% of tetraploid cardiomyocytes contain cells from distinct clades, indicating fusion of lineally distinct cells, whereas 60% of higher-ploidy cardiomyocytes contain fused cells from distinct clades. Combined snRNA-seq and snATAC-seq revealed transcriptome and chromatin landscapes of polyploid cardiomyocytes distinct from diploid cardiomyocytes, and show some higher-ploidy cardiomyocytes with transcriptional signatures suggesting fusion between cardiomyocytes and endothelial and fibroblast cells. These observations provide the first evidence for cell and nuclear fusion of human cardiomyocytes, raising the possibility that cell fusion may contribute to developing or maintaining polyploid cardiomyocytes in the human heart.}, }
@article {pmid38853372, year = {2024}, author = {Landers, E and Claridge, B and Kuhn, W and Seymour, V and Peek, H and Fluet, S and Ramgren, J and Phelps, J and Paulk, B and Cordner, L and Blaschke, J}, title = {Using DNA barcoding to identify high-priority taxa (Hymenoptera: Ichneumonidae) from Great Smoky Mountains National Park.}, journal = {Environmental entomology}, volume = {53}, number = {4}, pages = {730-739}, doi = {10.1093/ee/nvae058}, pmid = {38853372}, issn = {1938-2936}, mesh = {Biodiversity ; *DNA Barcoding, Taxonomic/standards ; *Hymenoptera/anatomy &amp; histology/classification/genetics ; *Parks, Recreational ; Species Specificity ; Animals ; }, abstract = {The All Taxa Biodiversity Inventory (ATBI) in Great Smoky Mountains National Park (GSMNP) seeks to document every species of living thing in the park. The ATBI is decades in progress, yet some taxa remain virtually untouched by taxonomists. Such "high priority" taxa include the hyper-diverse parasitoid wasp family Ichneumonidae. Despite the positive and multifaceted effects ichneumonids have on their environment, only a small percentage of those collected in the park have been identified as species, mostly to their complex morphology and overwhelming diversity. Recently, DNA barcoding has transformed biodiversity inventories, streamlining the process to be more rapid and efficient. To test the effectiveness of barcoding 20 + year-old specimens of Ichneumonidae and catalog new records for GSMNP, COI was amplified from 95 ichneumonid morphospecies collected from Andrew's Bald, NC. Species identifications were confirmed morphologically. Eighty-one ichneumonids generated sequence data, representing 16 subfamilies and 44 genera. The subfamily Oxytorinae is newly recorded from GSMNP, along with 10 newly recorded genera and 23 newly recorded species across Ichneumonidae. These results contribute significantly to the ATBI by adding new park records for a high-priority taxon and demonstrate the effectiveness of applying DNA barcoding to samples in long-term storage or those lacking immediate taxonomic expertise.}, }
@article {pmid38853364, year = {2024}, author = {Byrne, GW and McGregor, CGA}, title = {Anti-pig antibodies in swine veterinarian serum: Implications for clinical xenotransplantation.}, journal = {Xenotransplantation}, volume = {31}, number = {3}, pages = {e12865}, doi = {10.1111/xen.12865}, pmid = {38853364}, issn = {1399-3089}, support = {//Experimental Surgical Services/ ; }, mesh = {Animals ; *Transplantation, Heterologous/methods ; Humans ; Swine ; *Graft Rejection/immunology ; HEK293 Cells ; Veterinarians ; Polysaccharides/immunology ; Animals, Genetically Modified ; Antibodies, Heterophile/immunology/blood ; Heterografts/immunology ; Immunoglobulin M/immunology/blood ; }, abstract = {Recent clinical xenotransplantation and human decedent studies demonstrate that clinical hyperacute rejection of genetically engineered porcine organs can be reliably avoided but that antibody mediated rejection (AMR) continues to limit graft survival. We previously identified porcine glycans and proteins which are immunogenic after cardiac xenotransplantation in non-human primates, but the clinical immune response to antigens present in glycan depleted triple knockout (TKO) donor pigs is poorly understood. In this study we use fluorescence barcoded human embryonic kidney cells (HEK) and HEK cell lines expressing porcine glycans (Gal and SDa) or proteins (tetraspanin-29 [CD9], membrane cofactor protein [CD46], protectin, membrane attack complex inhibition factor [CD59], endothelial cell protein C receptor, and Annexin A2) to screen antibody reactivity in human serum from 160 swine veterinarians, a serum source with potential occupational immune challenge from porcine tissues and pathogens. High levels of anti-Gal IgM were present in all samples and lower levels of anti-SDa IgM were present in 41% of samples. IgM binding to porcine proteins, primarily CD9 and CD46, previously identified as immunogenic in pig to non-human primate cardiac xenograft recipients, was detected in 28 of the 160 swine veterinarian samples. These results suggest that barcoded HEK cell lines expressing porcine protein antigens can be useful for screening human patient serum. A comprehensive analysis of sera from clinical xenotransplant recipients to define a panel of commonly immunogenic porcine antigens will likely be necessary to establish an array of porcine non-Gal antigens for effective monitoring of patient immune responses and allow earlier therapies to reverse AMR.}, }
@article {pmid38852495, year = {2024}, author = {Hii, KS and Abdul Manaff, AHN and Gu, H and Lim, PT and Leaw, CP}, title = {A comparative analysis of real-time quantitative PCR and metabarcoding methods for eDNA-based detection of the toxic dinophyte Alexandrium tamiyavanichii (Dinophyceae).}, journal = {Marine environmental research}, volume = {199}, number = {}, pages = {106593}, doi = {10.1016/j.marenvres.2024.106593}, pmid = {38852495}, issn = {1879-0291}, mesh = {*Dinoflagellida/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *DNA Barcoding, Taxonomic/methods ; *Environmental Monitoring/methods ; DNA, Environmental ; China ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The marine dinophyte Alexandrium tamiyavanichii is a toxigenic species that produces a group of neurotoxins that is responsible for paralytic shellfish poisoning in humans. Early detection of the species is essential for efficient monitoring. Harmful microalgal monitoring systems have evolved over the years with the advent of environmental DNA (eDNA)-based species detection techniques. In this study, eDNA samples were collected from a large-scale sampling covering the southern South China Sea. The sensitivity and specificity of metabarcoding of the V4 and V9 18S ribosomal DNA barcodes by high-throughput sequencing (HTS) were compared to the species-specific real-time qPCR targeting the A. tamiyavanichii ITS2 region. Environmental samples were screened for A. tamiyavanichii by qPCR (n = 43) and analyzed with metabarcoding (n = 30). Our results revealed a high occupancy profile across samples for both methods; 88% by qPCR, and 80-83% by HTS. When comparing the consistency between the two approaches, only two samples out of 30 were discordant. The V4 and V9 molecular units detected in each sample were positively correlated with the qPCR ITS2 gene copies (V4, rs = 0.67, p < 0.0001; V9, rs = 0.65, p < 0.0001), indicating that metabarcoding could be used as a useful tool for early detection of the species. Our results also revealed that the estimation of A. tamiyavanichii cell abundances based on the HTS read abundances was comparable to that of the qPCR quantification. For long-term monitoring, metabarcoding could serve as a cost-effective screening of detecting not only single HAB species but also simultaneously detecting a multitude of potentially harmful species, which is valuable in informing the subsequent implementation of species-specific monitoring strategies.}, }
@article {pmid38851103, year = {2024}, author = {Liu, Q and Dai, J and Chen, J and Liu, Z and Lin, Y and Qiu, G and Gao, X and Zhang, R and Zhu, S}, title = {Comparative analysis the chloroplast genomes of Celastrus (Celastraceae) species: Provide insights into molecular evolution, species identification and phylogenetic relationships.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {131}, number = {}, pages = {155770}, doi = {10.1016/j.phymed.2024.155770}, pmid = {38851103}, issn = {1618-095X}, mesh = {*Celastrus/genetics/classification ; *Genome, Chloroplast ; *Phylogeny ; *Evolution, Molecular ; Base Composition ; Plants, Medicinal/genetics/classification ; China ; Introns ; }, abstract = {BACKGROUND: The genus Celastrus is an important medicinal plant resource. The similarity of morphology and the lack of complete chloroplast genome analysis have significantly impeded the exploration of species identification, molecular evolution and phylogeny of Celastrus.<br><br>PURPOSE: In order to resolve the phylogenic controversy of Celastrus species, the chloroplast genome comparative analysis was performed to provide genetic evidence.<br><br>METHODS: In this study, we collected and sequenced ten chloroplast genomes of Celastrus species from China and downloaded three chloroplast genomes from the databases. The chloroplast genomes were compared and analyzed to explore their characteristics and evolution. Furthermore, the phylogenetic relationships of Celastrus species were inferred based on the whole chloroplast genomes and protein-coding genes.<br><br>RESULTS: All the 13 Celastrus species chloroplast genomes showed a typical quadripartite structure with genome sizes ranging from 155,113 to 157,366&#x2009;bp. The intron loss of the rps16 gene occurred in all the 13 Celastrus species. The GC content, gene sequence, repeat types and codon bias pattern were highly conserved. Ten highly variation regions were identified, which can be used as potential DNA markers in molecular identification of Celastrus species. Eight genes, including accD, atp4, ndhB, rpoC1, rbcL, rpl2, rpl20 and ycf1, were detected to experience positive selection. Phylogenetic analysis showed that Celastrus was a monophyletic group and Tripterygium was the closest sister-group. Noteworthy, C. gemmatus Loes. and C. orbiculatus Thunb. can be discriminated using the chloroplast genome as a super barcode. The comparative and phylogenetic analysis results proposed that C. tonkinensis Pitard. was the synonym of C. hindsii Benth.<br><br>CONCLUSION: The comparative analysis of the Celastrus chloroplast genomes can provide comprehensive genetic evidence for molecular evolution, species identification and phylogenetic relationships.}, }
@article {pmid38849559, year = {2024}, author = {Gowri, G and Sheng, K and Yin, P}, title = {Scalable design of orthogonal DNA barcode libraries.}, journal = {Nature computational science}, volume = {4}, number = {6}, pages = {423-428}, pmid = {38849559}, issn = {2662-8457}, support = {R01GM124401//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01HG012926//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DP1GM133052//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DP1 GM133052/GM/NIGMS NIH HHS/United States ; R01 GM124401/GM/NIGMS NIH HHS/United States ; R01 HG012926/HG/NHGRI NIH HHS/United States ; RF1MH128861//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; RF1 MH128861/MH/NIMH NIH HHS/United States ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Gene Library ; Algorithms ; DNA/genetics/chemistry ; }, abstract = {Orthogonal DNA barcode library design is an essential task in bioengineering. Here we present seqwalk, an efficient method for designing barcode libraries that satisfy a sequence symmetry minimization (SSM) heuristic for orthogonality, with theoretical guarantees of maximal or near-maximal library size under certain design constraints. Seqwalk encodes SSM constraints in a de Bruijn graph representation of sequence space, enabling the application of recent advances in discrete mathematics[1] to the problem of orthogonal sequence design. We demonstrate the scalability of seqwalk by designing a library of >10[6] SSM-satisfying barcode sequences in less than 20 s on a standard laptop.}, }
@article {pmid38844664, year = {2024}, author = {Hugel, T}, title = {New dimensions for fluorescence-based barcoding in complex mixtures.}, journal = {Nature nanotechnology}, volume = {19}, number = {8}, pages = {1081-1082}, pmid = {38844664}, issn = {1748-3395}, support = {390951807//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, }
@article {pmid38844553, year = {2024}, author = {Liao, H and Choi, J and Shendure, J}, title = {Molecular recording using DNA Typewriter.}, journal = {Nature protocols}, volume = {19}, number = {10}, pages = {2833-2862}, pmid = {38844553}, issn = {1750-2799}, support = {UM1 HG011586/HG/NHGRI NIH HHS/United States ; K99 HG012973/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *DNA/genetics ; *Gene Editing/methods ; HEK293 Cells ; RNA, Guide, CRISPR-Cas Systems/genetics ; CRISPR-Cas Systems ; }, abstract = {Recording molecular information to genomic DNA is a powerful means of investigating topics ranging from multicellular development to cancer evolution. With molecular recording based on genome editing, events such as cell divisions and signaling pathway activity drive specific alterations in a cell's DNA, marking the genome with information about a cell's history that can be read out after the fact. Although genome editing has been used for molecular recording, capturing the temporal relationships among recorded events in mammalian cells remains challenging. The DNA Typewriter system overcomes this limitation by leveraging prime editing to facilitate sequential insertions to an engineered genomic region. DNA Typewriter includes three distinct components: DNA Tape as the 'substrate' to which edits accrue in an ordered manner, the prime editor enzyme, and prime editing guide RNAs, which program insertional edits to DNA Tape. In this protocol, we describe general design considerations for DNA Typewriter, step-by-step instructions on how to perform recording experiments by using DNA Typewriter in HEK293T cells, and example scripts for analyzing DNA Typewriter data (https://doi.org/10.6084/m9.figshare.22728758). This protocol covers two main applications of DNA Typewriter: recording sequential transfection events with programmed barcode insertions by using prime editing and recording lineage information during the expansion of a single cell to many. Compared with other methods that are compatible with mammalian cells, DNA Typewriter enables the recording of temporal information with higher recording capacities and can be completed within 4-6 weeks with basic expertise in molecular cloning, mammalian cell culturing and DNA sequencing data analysis.}, }
@article {pmid38843225, year = {2024}, author = {Zavadska, D and Henry, N and Auladell, A and Berney, C and Richter, DJ}, title = {Diverse patterns of correspondence between protist metabarcodes and protist metagenome-assembled genomes.}, journal = {PloS one}, volume = {19}, number = {6}, pages = {e0303697}, pmid = {38843225}, issn = {1932-6203}, mesh = {*Metagenome ; *DNA Barcoding, Taxonomic/methods ; Eukaryota/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Metagenomics/methods ; }, abstract = {Two common approaches to study the composition of environmental protist communities are metabarcoding and metagenomics. Raw metabarcoding data are usually processed into Operational Taxonomic Units (OTUs) or amplicon sequence variants (ASVs) through clustering or denoising approaches, respectively. Analogous approaches are used to assemble metagenomic reads into metagenome-assembled genomes (MAGs). Understanding the correspondence between the data produced by these two approaches can help to integrate information between the datasets and to explain how metabarcoding OTUs and MAGs are related with the underlying biological entities they are hypothesised to represent. MAGs do not contain the commonly used barcoding loci, therefore sequence homology approaches cannot be used to match OTUs and MAGs. We made an attempt to match V9 metabarcoding OTUs from the 18S rRNA gene (V9 OTUs) and MAGs from the Tara Oceans expedition based on the correspondence of their relative abundances across the same set of samples. We evaluated several metrics for detecting correspondence between features in these two datasets and developed controls to filter artefacts of data structure and processing. After selecting the best-performing metrics, ranking the V9 OTU/MAG matches by their proportionality/correlation coefficients and applying a set of selection criteria, we identified candidate matches between V9 OTUs and MAGs. In some cases, V9 OTUs and MAGs could be matched with a one-to-one correspondence, implying that they likely represent the same underlying biological entity. More generally, matches we observed could be classified into 4 scenarios: one V9 OTU matches many MAGs; many V9 OTUs match many MAGs; many V9 OTUs match one MAG; one V9 OTU matches one MAG. Notably, we found some instances in which different OTU-MAG matches from the same taxonomic group were not classified in the same scenario, with all four scenarios possible even within the same taxonomic group, illustrating that factors beyond taxonomic lineage influence the relationship between OTUs and MAGs. Overall, each scenario produces a different interpretation of V9 OTUs, MAGs and how they compare in terms of the genomic and ecological diversity they represent.}, }
@article {pmid38841282, year = {2024}, author = {Wei, M and Tian, Y and Zang, E and Tsambaa, B and Liu, J and Shi, L and Borjigidai, A}, title = {Species identification of biological ingredients in herbal product, Gurigumu-7, based on DNA barcoding and shotgun metagenomics.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1358136}, pmid = {38841282}, issn = {1664-462X}, abstract = {Accurate identification the species composition in mixtures poses a significant challenge, especially in processed mixtures comprising multiple species, such as those found in food and pharmaceuticals. Therefore, we have attempted to utilize shotgun metabarcoding technology to tackle this issue. In this study, the method was initially established using two mock samples of the Mongolian compound preparation Gurigumu-7 (G-7), which was then applied to three pharmaceutical products and 12 hospital-made preparations. A total of 119.72 Gb of raw data sets were obtained through shotgun metagenomic sequencing. By combining ITS2, matK, and rbcL, all the labeled bio-ingredients specified in the G-7 prescription can be detected, although some species may not be detectable in all samples. The prevalent substitution of Akebia quinata can be found in all the pharmaceutical and hospital samples, except for YN02 and YN12. The toxic alternative to Akebia quinata, Aristolochia manshuriensis, was exclusively identified in the YN02 sample. To further confirm this result, we validated it in YN02 using HPLC and real-time PCR with TaqMan probes. The results showed that aristolochic acid A (AAA) was detected in YN02 using HPLC, and the ITS2 sequence of Aristolochia manshuriensis has been validated in YN02 through qPCR and the use of a TaqMan probe. This study confirms that shotgun metabarcoding can effectively identify the biological components in Mongolian medicine compound preparation G-7. It also demonstrates the method's potential to be utilized as a general identification technique for mixtures containing a variety of plants.}, }
@article {pmid38841135, year = {2024}, author = {Recuero, E and Caterino, MS}, title = {Molecular diversity of Diplura in southern High Appalachian leaf litter.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e125162}, pmid = {38841135}, issn = {1314-2828}, abstract = {The fauna of Diplura, the two-pronged bristletails (Hexapoda), of the southern Appalachians has received little focused systematic attention. Existing literature suggests the fauna to comprise around a dozen species. Based on a broader DNA barcode-based survey of high elevation litter arthropods in the region, we suggest the fauna to be much richer, with automated species delimitation methods hypothesising as many as 35 species, most highly restricted to single or closely proximate localities. Such a result should not be very surprising for such small, flightless arthropods, although it remains to be seen if other markers or morphology support such high diversity. The region still remains sparsely sampled for these more cryptic elements of the arthropod fauna and much larger numbers of species undoubtedly remain to be discovered.}, }
@article {pmid38838190, year = {2024}, author = {Shirali, H and Hübner, J and Both, R and Raupach, M and Reischl, M and Schmidt, S and Pylatiuk, C}, title = {Image-based recognition of parasitoid wasps using advanced neural networks.}, journal = {Invertebrate systematics}, volume = {38}, number = {}, pages = {}, doi = {10.1071/IS24011}, pmid = {38838190}, issn = {1447-2600}, mesh = {Animals ; *Wasps/genetics/anatomy &amp; histology ; *Neural Networks, Computer ; DNA Barcoding, Taxonomic ; Image Processing, Computer-Assisted/methods ; Female ; Classification/methods ; Species Specificity ; Male ; }, abstract = {Hymenoptera has some of the highest diversity and number of individuals among insects. Many of these species potentially play key roles as food sources, pest controllers and pollinators. However, little is known about the diversity and biology and ~80% of the species have not yet been described. Classical taxonomy based on morphology is a rather slow process but DNA barcoding has already brought considerable progress in identification. Innovative methods such as image-based identification and automation can further speed up the process. We present a proof of concept for image data recognition of a parasitic wasp family, the Diapriidae (Hymenoptera), obtained as part of the GBOL III project. These tiny (1.2-4.5mm) wasps were photographed and identified using DNA barcoding to provide a solid ground truth for training a neural network. Taxonomic identification was used down to the genus level. Subsequently, three different neural network architectures were trained, evaluated and optimised. As a result, 11 different genera of diaprids and one mixed group of 'other Hymenoptera' can be classified with an average accuracy of 96%. Additionally, the sex of the specimen can be classified automatically with an accuracy of >97%.}, }
@article {pmid38837405, year = {2024}, author = {Kutsokon, Y and Bielikova, O and Pekárik, L and Roman, A and Shcherbatiuk, M and Čiamporová-Zaťovičová, Z and Čiampor, F}, title = {The expansion of invasive species to the East: new sites of the bullheads (genus Ameiurus Rafinesque 1820) in Ukraine with morphological and genetic identification.}, journal = {Journal of fish biology}, volume = {105}, number = {3}, pages = {708-720}, doi = {10.1111/jfb.15778}, pmid = {38837405}, issn = {1095-8649}, support = {09I03-03-V01-00004//European Union NextGeneration EU/ ; 09I03-03-V01-00075//European Union NextGeneration EU/ ; }, mesh = {Ukraine ; Animals ; *Introduced Species ; *Electron Transport Complex IV/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Cyprinidae/genetics/anatomy &amp; histology/classification ; Animal Distribution ; }, abstract = {This study confirms the extended distribution of two invasive species of the genus Ameiurus in Ukraine. Specifically, A. melas is recorded for the first time in the Southern Buh basin and A. nebulosus has expanded further eastward within the Dnipro basin. Material collected in 2019 and 2022 was identified by morphological features and confirmed by molecular genetic analysis. The most reliable morphological characters for distinguishing these two species include anal-fin membrane pigmentation (light or black), gill raker count (fewer or more than 16), and serrations on the pectoral-fin spine (well-developed along the full length or small, absent near the tip). The analysis of the cytochrome oxidase subunit I barcoding marker identified all samples from the Dnipro Basin (Tnia and Velykyi Luh localities) as A. nebulosus, while all specimens from the Vinnytsia region within the Southern Buh basin (Sotskoho and Vyshenske lakes) were attributed to A. melas. The maximum-likelihood analysis revealed clearly separated clades with high bootstrap support (>75%), strongly supporting the presence of the two separate species. This study suggests the potential for further eastward expansion of both species within Ukraine: A. nebulosus in the northern direction and A. melas in the southern direction.}, }
@article {pmid38834513, year = {2024}, author = {Latif, H and Pazra, DF and Basri, C and Wibawan, IWT and Rahayu, P}, title = {Whole genome sequencing analysis on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.}, journal = {Journal of veterinary science}, volume = {25}, number = {3}, pages = {e44}, pmid = {38834513}, issn = {1976-555X}, support = {102/E5/PG.02.00.PL/2023/MECRT/Kementerian Pendidikan, Kebudayaan, Riset, dan Teknologi/Indonesia ; }, mesh = {Animals ; *Escherichia coli/genetics/drug effects/isolation &amp; purification ; Swine ; Indonesia/epidemiology ; *Swine Diseases/microbiology/epidemiology ; *Escherichia coli Infections/veterinary/microbiology/epidemiology ; *Whole Genome Sequencing/veterinary ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {IMPORTANCE: The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics.<br><br>OBJECTIVE: This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.<br><br>METHODS: Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder.<br><br>RESULTS: Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%.<br><br>CONCLUSIONS AND RELEVANCE: The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.}, }
@article {pmid38832046, year = {2024}, author = {Samreen, KB and Manzoor, F}, title = {Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17420}, pmid = {38832046}, issn = {2167-8359}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Pakistan ; *Biodiversity ; *Arthropods/genetics/classification ; Gardens ; }, abstract = {Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.}, }
@article {pmid38827149, year = {2024}, author = {Atavliyeva, S and Auganova, D and Tarlykov, P}, title = {Genetic diversity, evolution and drug resistance of Mycobacterium tuberculosis lineage 2.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1384791}, pmid = {38827149}, issn = {1664-302X}, abstract = {Mycobacterium tuberculosis causes a chronic infectious disease called tuberculosis. Phylogenetic lineage 2 (L2) of M. tuberculosis, also known as the East Asian lineage, is associated with high virulence, increased transmissibility, and the spread of multidrug-resistant strains. This review article examines the genomic characteristics of the M. tuberculosis genome and M. tuberculosis lineage 2, such as the unique insertion sequence and spoligotype patterns, as well as MIRU-VNTR typing, and SNP-based barcoding. The review describes the geographical distribution of lineage 2 and its history of origin. In addition, the article discusses recent studies on drug resistance and compensatory mechanisms of M. tuberculosis lineage 2 and its impact on the pathogen's transmissibility and virulence. This review article discusses the importance of establishing a unified classification for lineage 2 to ensure consistency in terminology and criteria across different studies and settings.}, }
@article {pmid38826425, year = {2024}, author = {Ali, M and Dey, R and Das, M and Kumar, V and Chandra, K and Uniyal, VP and Gupta, SK}, title = {Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {38826425}, issn = {2693-5015}, abstract = {The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.}, }
@article {pmid38826396, year = {2024}, author = {Papadimitriou, M and Ahn, S and Diamond, B and Lee, H and McIntyre, J and Truger, M and Durante, M and Ziccheddu, B and Landgren, O and Rasche, L and Bahlis, NJ and Neri, P and Maura, F}, title = {Timing antigenic escape in multiple myeloma treated with T-cell redirecting immunotherapies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38826396}, issn = {2692-8205}, support = {P30 CA240139/CA/NCI NIH HHS/United States ; }, abstract = {Recent data highlight genomic events driving antigen escape as a recurring cause of chimeric antigen receptor T-cell (CAR-T) and bispecific T-cell engager (TCE) resistance in multiple myeloma (MM). Yet, it remains unclear if these events, leading to clonal dominance at progression, result from acquisition under treatment selection or selection of pre-existing undetectable clones. This differentiation gains importance as these immunotherapies progress to earlier lines of treatment, prompting the need for innovative diagnostic testing to detect these events early on. By reconstructing phylogenetic trees and exploring chemotherapy mutational signatures as temporal barcodes in 11 relapsed refractory MM patients with available whole genome sequencing data before and after CART/TCE treatment, we demonstrated that somatic antigen escape mechanisms for BCMA- and GPRC5D-targeting therapies are acquired post-diagnosis, likely during CART/TCE treatment. Longitudinal tracking of these mutations using digital PCR in 4 patients consistently showed that genomic events promoting antigen escape were not detectable during the initial months of therapy but began to emerge nearly 1 year post therapy initiation. This finding reduces the necessity for a diagnostic panel to identify these events before CART/TCE. Instead, it underscores the importance of surveillance and identifying patients at higher risk of acquiring these events.}, }
@article {pmid38826163, year = {2024}, author = {Onyango, B and Copeland, R and Mbogholi, J and Wamalwa, M and Kibet, C and Tonnang, HEZ and Senagi, K}, title = {WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes.}, journal = {Ecology and evolution}, volume = {14}, number = {6}, pages = {e11457}, pmid = {38826163}, issn = {2045-7758}, abstract = {The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.}, }
@article {pmid38821971, year = {2024}, author = {Zhang, Z and Xiao, J and Wang, H and Yang, C and Huang, Y and Yue, Z and Chen, Y and Han, L and Yin, K and Lyu, A and Fang, X and Zhang, L}, title = {Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4631}, pmid = {38821971}, issn = {2041-1723}, mesh = {Humans ; *Metagenome/genetics ; *Algorithms ; *Genome, Microbial ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Deep Learning ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; }, abstract = {Although long-read sequencing enables the generation of complete genomes for unculturable microbes, its high cost limits the widespread adoption of long-read sequencing in large-scale metagenomic studies. An alternative method is to assemble short-reads with long-range connectivity, which can be a cost-effective way to generate high-quality microbial genomes. Here, we develop Pangaea, a bioinformatic approach designed to enhance metagenome assembly using short-reads with long-range connectivity. Pangaea leverages connectivity derived from physical barcodes of linked-reads or virtual barcodes by aligning short-reads to long-reads. Pangaea utilizes a deep learning-based read binning algorithm to assemble co-barcoded reads exhibiting similar sequence contexts and abundances, thereby improving the assembly of high- and medium-abundance microbial genomes. Pangaea also leverages a multi-thresholding algorithm strategy to refine assembly for low-abundance microbes. We benchmark Pangaea on linked-reads and a combination of short- and long-reads from simulation data, mock communities and human gut metagenomes. Pangaea achieves significantly higher contig continuity as well as more near-complete metagenome-assembled genomes (NCMAGs) than the existing assemblers. Pangaea also generates three complete and circular NCMAGs on the human gut microbiomes.}, }
@article {pmid38820740, year = {2024}, author = {An, HE and Mun, MH and Malik, A and Kim, CB}, title = {Development of a two-layer machine learning model for the forensic application of legal and illegal poppy classification based on sequence data.}, journal = {Forensic science international. Genetics}, volume = {71}, number = {}, pages = {103061}, doi = {10.1016/j.fsigen.2024.103061}, pmid = {38820740}, issn = {1878-0326}, mesh = {*Machine Learning ; *Papaver/genetics ; *DNA, Plant/genetics ; Genetic Markers ; *DNA Barcoding, Taxonomic ; Sequence Analysis, DNA ; Forensic Genetics/methods ; }, abstract = {Poppies are beneficial plants with a variety of applications, including medicinal, edible, ornamental, and industrial purposes. Some Papaver species are forensically significant plants because they contain opium, a narcotic substance. Internationally trafficked species of illegal poppies are being identified by DNA barcoding employing multiple markers in response to their forensic value. However, effective markers for precise species identification of legal and illegal poppies are still under discussion, with research on illegal poppies focusing on Papaver somniferum L., and species identification studies of Papaver bracteatum and Papaver setigerum DC. still lacking. As a result, in order to evaluate the performance of genetic markers and classify their DNA sequences in the genus Papaver, this study developed the first machine learning-based two-layer model, in which the first layer classifies legal and illegal poppies from the given sequence and the second layer identifies species of illegal poppies using their sequences. We constructed the dataset and investigated biological features from four markers, internal transcribed spacer 1 (ITS1), internal transcribed spacer 2 (ITS2), transfer RNA Leucine (trnL), transfer RNA Leucine - transfer RNA Phenylalanine intergenic spacer (trnL-trnF intergenic spacer) and their combination, using four machine learning algorithms, K-nearest neighbor (KNN), Naïve Bayes (NB), extreme gradient boost (XGBoost) and Random Forest (RF). According to our findings, for Layer 1 to classify legal and illegal poppies, KNN-based models using combined ITS region achieved the greatest performance of accuracy 0.846 and 0.889 using training and test sets, respectively. Additionally, for Layer 2 to identify illegal poppy species, KNN-based models using combined ITS region achieved the best performance of 0.833 and 1.000 for using training and test sets, respectively. To validate the model, the combined ITS region, which includes ITS 1 and 2 sequences, from blind poppy samples were used as a case study, with the Layer 1 correctly classifying legal and illegal poppies with over 0.830 accuracy. Layer 2 correctly identified P. setigerum DC., however, only one of the three P. somniferum L. species was accurately identified. Nevertheless, our research shows that machine learning can be used to classify and identify legal and illegal poppy species using DNA barcodes which can then be used as an efficient and effective forensic tool for improved law enforcement and a safer society.}, }
@article {pmid38820192, year = {2024}, author = {Smiley, AT and Babilonia-Díaz, NS and Hughes, AJ and Lemmex, ACD and Anderson, MJM and Tompkins, KJ and Gordon, WR}, title = {HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-Tags.}, journal = {ACS synthetic biology}, volume = {13}, number = {6}, pages = {1669-1678}, doi = {10.1021/acssynbio.4c00188}, pmid = {38820192}, issn = {2161-5063}, support = {R35 GM119483/GM/NIGMS NIH HHS/United States ; T32 GM132029/GM/NIGMS NIH HHS/United States ; T32 AR007612/AR/NIAMS NIH HHS/United States ; }, mesh = {*Software ; *DNA, Single-Stranded/metabolism/chemistry/genetics ; Proteins/metabolism/chemistry/genetics ; }, abstract = {HUH-tags have emerged as versatile fusion partners that mediate sequence specific protein-ssDNA bioconjugation through a simple and efficient reaction. Here we present HUHgle, a python-based interactive tool for the visualization, design, and optimization of substrates for HUH-tag mediated covalent labeling of proteins of interest with ssDNA substrates of interest. HUHgle streamlines design processes by integrating an intuitive plotting interface with a search function capable of predicting and displaying protein-ssDNA bioconjugate formation efficiency and specificity in proposed HUH-tag/ssDNA sequence combinations. Validation demonstrates that HUHgle accurately predicts product formation of HUH-tag mediated bioconjugation for single- and orthogonal-labeling reactions. In order to maximize the accessibility and utility of HUHgle, we have implemented it as a user-friendly Google Colab notebook which facilitates broad use of this tool, regardless of coding expertise.}, }
@article {pmid38818076, year = {2024}, author = {Shi, W and Zhang, J and Huang, S and Fan, Q and Cao, J and Zeng, J and Wu, L and Yang, C}, title = {Next-Generation Sequencing-Based Spatial Transcriptomics: A Perspective from Barcoding Chemistry.}, journal = {JACS Au}, volume = {4}, number = {5}, pages = {1723-1743}, pmid = {38818076}, issn = {2691-3704}, abstract = {Gene expression profiling of tissue cells with spatial context is in high demand to reveal cell types, locations, and intercellular or molecular interactions for physiological and pathological studies. With rapid advances in barcoding chemistry and sequencing chemistry, spatially resolved transcriptome (SRT) techniques have emerged to quantify spatial gene expression in tissue samples by correlating transcripts with their spatial locations using diverse strategies. These techniques provide both physical tissue structure and molecular characteristics and are poised to revolutionize many fields, such as developmental biology, neuroscience, oncology, and histopathology. In this context, this Perspective focuses on next-generation sequencing-based SRT methods, particularly highlighting spatial barcoding chemistry. It delves into optically manipulated spatial indexing methods and DNA array-barcoded spatial indexing methods by exploring current advances, challenges, and future development directions in this nascent field.}, }
@article {pmid38817114, year = {2024}, author = {Borbee, EM and Puspa, IA and Gelis, ERE and Setiawan, F and Maduppa, H and Humphries, AT and Lane, CE}, title = {Surface currents shape protist community structure across the Indo-Pacific.}, journal = {Journal of phycology}, volume = {60}, number = {4}, pages = {816-833}, doi = {10.1111/jpy.13465}, pmid = {38817114}, issn = {1529-8817}, support = {1541510//Division of Environmental Biology/ ; AID-497-A-16-00004//United States Agency for International Development/ ; }, mesh = {Indonesia ; Pacific Ocean ; *Biodiversity ; Eukaryota/genetics/classification/physiology ; }, abstract = {Biogeographic structure in marine protist communities is shaped by a combination of dispersal potential and environmental selection. High-throughput sequencing and global sampling efforts have helped better resolve the composition and functions of these communities in the world's oceans using both molecular and visual methods. However, molecular barcoding data are critically lacking across the Indo-Pacific, a region widely considered the epicenter of marine biodiversity. To fill this gap, we characterized protist communities in four sampling regions across Indonesia that represent the latitudinal, longitudinal, and human population gradients of the region: Lombok, Wakatobi, Misool, and Waigeo. We show high spatial structuring in marine protist communities across Indonesia, and biotic factors appear to play little role in driving this observed structure. Our results appear to be driven by abiotic factors linked to surface current patterns across the Indo-Pacific as a result of: (1) a choke point in circulation at the Indonesian Throughflow leading to low diatom diversity in Lombok, Wakatobi, and Misool; (2) an increase in nutrient availability at the edge of the Halmahera Eddy in Waigeo, leading to an increase in diatom diversity; and/or (3) seasonal variations in protist communities in line with shifts in velocity of the Indonesian Throughflow. Overall, our results highlight the importance of abiotic factors in shaping protist communities on broad geographic scales over biotic, top-down pressures, such as grazing from higher trophic levels.}, }
@article {pmid38816489, year = {2024}, author = {Nagakubo, Y and Hirotsu, Y and Yoshino, M and Amemiya, K and Saito, R and Kakizaki, Y and Tsutsui, T and Miyashita, Y and Goto, T and Omata, M}, title = {Comparison of diagnostic performance between Oncomine Dx target test and AmoyDx panel for detecting actionable mutations in lung cancer.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12480}, pmid = {38816489}, issn = {2045-2322}, support = {JP18K16292//Japan Society for the Promotion of Science/ ; 21K08894//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Lung Neoplasms/genetics/diagnosis ; *Mutation ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; ErbB Receptors/genetics ; Middle Aged ; Proto-Oncogene Proteins c-ret/genetics ; Biomarkers, Tumor/genetics ; Aged ; Proto-Oncogene Proteins c-met/genetics ; Protein-Tyrosine Kinases/genetics ; Proto-Oncogene Proteins/genetics ; Multiplex Polymerase Chain Reaction/methods ; }, abstract = {Companion diagnostic (CDx) tests play important roles in identifying oncogenic driver genes and tailoring effective molecularly targeted therapies for lung cancer patients. In Japan, the Oncomine Dx target test (ODxTT) and the AmoyDx pan lung cancer PCR panel (AmoyDx) are prominent CDx tests and only one of these tests is covered by the domestic insurance system. However, these CDx tests cover different target regions and apply different technologies (ODxTT is amplicon-based next-generation sequencing and AmoyDx is multiplex PCR-based assay), which may lead to missing of actionable mutations affecting patient prognosis. Here, we performed a direct comparison analysis of 1059 genetic alterations of eight driver genes from 131 samples and evaluated the concordance between two CDx tests for detecting actionable variants and fusions. When excluding the eight uncovered variants (ODxTT: two variants, AmoyDx: six variants), the overall percent agreement was 97.6% (1026/1051) with 89.0% of overall positive percent agreement (89/100) and 98.5% of overall negative percent agreement (937/951). Of the 25 discordant genetic alterations, two were undetected despite being covered in the AmoyDx (one EGFR variant and one ROS1 fusion). Furthermore, there were potential false positives in the ODxTT (nine MET exon 14 skippings) and in the AmoyDx (five variants, six ROS1 and three RET fusions). These potential false positives in the AmoyDx likely due to non-specific amplification, which was validated by the unique molecular barcoding sequencing. The ODxTT missed two uncovered EGFR rare variants, which was visually confirmed in the raw sequencing data. Our study provides insights into real-world performance of CDx tests for lung cancer and ensures reliability to advance precision medicine.}, }
@article {pmid38814962, year = {2024}, author = {Niu, M and Liu, Y and Xue, L and Cai, B and Zhao, Q and Wei, J}, title = {Improving DNA barcoding library of armored scale insects (Hemiptera: Diaspididae) in China.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0301499}, pmid = {38814962}, issn = {1932-6203}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; China ; *Hemiptera/genetics/classification ; *Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Gene Library ; Bayes Theorem ; }, abstract = {DNA barcoding is used to identify cryptic species, survey environmental samples, and estimate phyletic and genetic diversity. Armored scale insects are phytophagous insects and are the most species-rich taxa in the Coccoidea superfamily. This study developed a DNA barcode library for armored scale insect species collected from southern China during 2021-2022. We sequenced a total of 239 specimens, recognized as 50 morphological species, representing two subfamilies and 21 genera. Sequencing analysis revealed that the average G + C content of the cytochrome oxidase subunit I (COI) gene sequence was very low (~18.06%) and that the average interspecific divergence was 10.07% while intraspecific divergence was 3.20%. The intraspecific divergence value was inflated by the high intraspecific divergence in ten taxa, which may indicate novel species overlooked by current taxonomic treatments. All the Automated Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Taxon DNA analysis and Bayesian Poisson Tree Process methods yielded largely consistent results, indicating a robust and credible species delimitation. Based on these results, an intergeneric distance threshold of ≤ 5% was deemed appropriate for the differentiation of armored scale insect species in China. This study establishes a comprehensive barcode library for the identification of armored scale insects, future research, and application.}, }
@article {pmid38813184, year = {2024}, author = {Wachananawat, B and Kong, BL and Shaw, PC and Bongcheewin, B and Sangvirotjanapat, S and Prombutara, P and Pornputtapong, N and Sukrong, S}, title = {Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma comosa and C. latifolia.}, journal = {Heliyon}, volume = {10}, number = {10}, pages = {e31248}, pmid = {38813184}, issn = {2405-8440}, abstract = {Members of the Curcuma genus, a crop in the Zingiberaceae, are widely utilized rhizomatous herbs globally. There are two distinct species, C. comosa Roxb. and C. latifolia Roscoe, referred to the same vernacular name "Wan Chak Motluk" in Thai. C. comosa holds economic importance and is extensively used as a Thai traditional medicine due to its phytoestrogenic properties. However, its morphology closely resembles that of C. latifolia, which contains zederone, a compound known for its hepatotoxic effects. They are often confused, which may affect the quality, efficacy and safety of the derived herbal materials. Thus, DNA markers were developed for discriminating C. comosa from C. latifolia. This study focused on analyzing core DNA barcode regions, including rbcL, matK, psbA-trnH spacer and ITS2, of the authentic C. comosa and C. latifolia species. As a result, no variable nucleotides in core DNA barcode regions were observed. The complete chloroplast (cp) genome was introduced to differentiate between the two species. The comparison revealed that the cp genomes of C. comosa and C. latifolia were 162,272 and 162,289 bp, respectively, with a total of 133 identified genes. The phylogenetic analysis revealed that C. comosa and C. latifolia exhibited a very close relationship with other Curcuma species. The cp genome of C. comosa and C. latifolia were identified for the first time, providing valuable insights for species identification and evolutionary research within the Zingiberaceae family.}, }
@article {pmid38811654, year = {2024}, author = {Sundebo Meldgaard, T and Viborg, N and Suarez Hernandez, S and Vazquez Albacete, D and Tamhane, T and Reker Hadrup, S}, title = {Validation of novel conditional ligands and large-scale detection of antigen-specific T cells for H-2D[d] and H-2K[d].}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {12292}, pmid = {38811654}, issn = {2045-2322}, mesh = {Animals ; Ligands ; Mice ; *CD8-Positive T-Lymphocytes/immunology/metabolism ; *Peptides/immunology/chemistry ; Mice, Inbred C57BL ; H-2 Antigens/immunology/metabolism/genetics ; Mice, Inbred BALB C ; }, abstract = {The UV-mediated peptide exchange has enabled the generation of multiple different MHC multimer specificities in parallel, surpassing tedious individual refolding of MHC molecules with peptide ligands. Murine models are acknowledged as an effective tool for preclinical research to advance our understanding of immunological mechanisms, with the potential translatability of key learnings from mouse models to the clinic. The common inbred mouse strain BALB/c is frequently used in immunological research. However, for the BALB/c histocompatibility (H)-2 alleles availability of conditional ligand has been limited. To overcome this challenge, we design and experimentally validate conditional ligands restricted to murine MHC class I alleles H2D[d] and H2K[d]. In addition, we demonstrate the ability of the three H2[d] molecules and two additional C57BL/6 H2[b] molecules folded in-house with conditional ligands to generate fluorescently labeled peptide-H2 tetramers that allow staining of antigen-specific CD8+ T cells in splenocyte samples. Finally, we generate large peptide-H-2 multimer libraries with a DNA-barcode labeling system for high-throughput interrogation of CD8+ T cell specificity in murine splenocyte samples. Consequently, the described techniques will contribute to our understanding of the antigen-specific CD8+ T cell repertoire in murine preclinical models of various diseases.}, }
@article {pmid38811354, year = {2024}, author = {Kar, C and Raghavan, R and Ummath, A and Puthiyaalikom, N and Idreesbabu, KK and Sureshkumar, S}, title = {Resolving fusilier puzzles: The identity of Squamosicaesio marri and Pterocaesio flavifasciata, and a new record of Flavicaesio suevica from the Western Indian Ocean.}, journal = {Journal of fish biology}, volume = {105}, number = {3}, pages = {993-997}, doi = {10.1111/jfb.15808}, pmid = {38811354}, issn = {1095-8649}, support = {200510341520//University Grants Commission/ ; CRG/2020/004498//Department of Science and Technology/ ; }, mesh = {Indian Ocean ; Animals ; *Phylogeny ; Electron Transport Complex IV/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {A phylogenetic analysis incorporating mitochondrial cox1 gene sequences of members of the family Caesionidae revealed the conspecificity of Pterocaesio flavifasciata and Squamosicaesio marri, which was also supported by the absence of any clear morphological diagnostic characters and meristic counts to separate the two species. Additionally, we provide the first record of the Suez fusilier, Flavicaesio suevica, from outside the Red Sea, based on specimens collected from the Laccadive archipelago, Western Indian Ocean. Together, these results show that the taxonomy, diversity, and distribution of members of the family Caesionidae continue to be poorly known, necessitating a comprehensive range-wide study.}, }
@article {pmid38809447, year = {2024}, author = {Laojun, S and Chaiphongpachara, T}, title = {Island mosquitoes of Thailand: an update on species diversity and DNA barcoding.}, journal = {Parasitology research}, volume = {123}, number = {5}, pages = {224}, pmid = {38809447}, issn = {1432-1955}, mesh = {Animals ; Thailand ; *DNA Barcoding, Taxonomic ; *Culicidae/classification/genetics ; Islands ; Biodiversity ; Mosquito Vectors/genetics/classification ; Genetic Variation ; Phylogeny ; Electron Transport Complex IV/genetics ; }, abstract = {Mosquitoes (Diptera: Culicidae) are among the most medically significant insects, with several species acting as vectors for human pathogens. Although there are frequent reports of mosquito-borne diseases in the border island areas of Thailand, comprehensive data on the diversity and DNA barcoding of these mosquito species remain limited. This study investigated mosquito diversity in two main archipelagos in Thailand-the Trat archipelago (comprising Chang Island and Kood Island) and the Ranong archipelago (comprising Chang Island and Phayam Island)-and generated DNA barcode data from the mosquitoes found there. The survey across these islands discovered a total of 41 species, highlighting the presence of several species known to be vectors for human diseases. Thirty-seven mosquito species from the island areas were documented to provide reference DNA barcode sequences for mosquitoes in Thailand's island regions. Two species, Aedes fumidus and Finlaya flavipennis, have been added as new COI sequence records in the database. DNA barcoding was highly effective in classifying almost all species by identifying barcoding gaps, except for Anopheles baimaii and Anopheles dirus, which could not be distinguished. Additionally, the study noted that geographical variations might influence certain mosquito species, such as Anopheles barbirostris A3 and Mansonia dives, causing them to be split into two distinct subgroups. The findings of this study are crucial, as they aid in classifying mosquito species using molecular techniques and expand our knowledge of disease vectors in these biodiverse regions.}, }
@article {pmid38808126, year = {2024}, author = {Vogel, J and Peters, RS and Selfa, J and Ferrer-Suay, M}, title = {Characterising the north-western European species of Phaenoglyphis Förster, 1869 (Hymenoptera: Figitidae: Charipinae) with novel insights from DNA barcode data.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e120950}, pmid = {38808126}, issn = {1314-2828}, abstract = {BACKGROUND: The taxonomy of the hymenopteran parasitoid subfamily Charipinae (Hymenoptera: Cynipoidea: Figitidae) has, until recently, been in a state of chaos. While this situation has improved significantly in recent years, most of the efforts were focused on morphological data of typically old specimens. Here, we present the first integrative approach to describe the diversity of the genus Phaenoglyphis Förster, 1869 from north-western Europe.<br><br>NEW INFORMATION: For seven (of a total of 17) species, we provide DNA barcode data. Phaenoglyphisbelizini Pujade-Villar, 2018 and Phaenoglyphisevenhuisi Pujade-Villar &amp; Paretas-Mart&#xed;nez, 2006 are recorded for the first time from Germany. All DNA barcodes and specimen data were added to the publicly available GBOL and BOLD reference database. The presence of a 6 bp long deletion in the CO1 barcode region that is characteristic to the genus and unique amongst Figitidae supports the monophyly of Phaenoglyphis.}, }
@article {pmid38805929, year = {2024}, author = {Sharma, R and Nath, PC and Lodh, BK and Mukherjee, J and Mahata, N and Gopikrishna, K and Tiwari, ON and Bhunia, B}, title = {Rapid and sensitive approaches for detecting food fraud: A review on prospects and challenges.}, journal = {Food chemistry}, volume = {454}, number = {}, pages = {139817}, doi = {10.1016/j.foodchem.2024.139817}, pmid = {38805929}, issn = {1873-7072}, mesh = {*Food Contamination/analysis ; Fraud/prevention &amp; control ; Food Analysis/methods ; Food Safety ; Mass Spectrometry ; }, abstract = {Precise and reliable analytical techniques are required to guarantee food quality in light of the expanding concerns regarding food safety and quality. Because traditional procedures are expensive and time-consuming, quick food control techniques are required to ensure product quality. Various analytical techniques are used to identify and detect food fraud, including spectroscopy, chromatography, DNA barcoding, and inotrope ratio mass spectrometry (IRMS). Due to its quick findings, simplicity of use, high throughput, affordability, and non-destructive evaluations of numerous food matrices, NI spectroscopy and hyperspectral imaging are financially preferred in the food business. The applicability of this technology has increased with the development of chemometric techniques and near-infrared spectroscopy-based instruments. The current research also discusses the use of several multivariate analytical techniques in identifying food fraud, such as principal component analysis, partial least squares, cluster analysis, multivariate curve resolutions, and artificial intelligence.}, }
@article {pmid38803273, year = {2024}, author = {Wang, Y and Yang, Y and Liu, Y and Liu, C and Xu, M and Fang, M and Mu, X}, title = {CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38803273}, issn = {1758-0463}, support = {2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; 2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; }, mesh = {Animals ; *Fishes/genetics/classification ; *RNA, Ribosomal, 18S/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Phylogeny ; Databases, Nucleic Acid ; }, abstract = {Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.}, }
@article {pmid38798722, year = {2024}, author = {Li, ZZ and Xu, Z and Wu, S and Yuan, LX and Zou, CY and Liu, Y and Lin, JY and Liang, SC}, title = {Molecular analyses display the increasing diversity of Podostemaceae in China.}, journal = {Plant diversity}, volume = {46}, number = {3}, pages = {421-424}, pmid = {38798722}, issn = {2468-2659}, abstract = {•Four newly recorded species of Podostemaceae from southern China were identified by molecular and morphological evidence.•17 plastomes of Podostemaceae were newly sequenced and two novel polymorphic barcodes (ccsA and ndhA) detected.•Our findings reveal greater species richness (15 species from five genera) of Podostemaceae in China and supply molecular resources for research on taxonomy and phylogenomics of this enigmatic aquatic family.}, }
@article {pmid38797438, year = {2024}, author = {Meadow, ME and Broas, S and Hoare, M and Alimohammadi, F and Welle, KA and Swovick, K and Hryhorenko, JR and Martinez, JC and Biashad, SA and Seluanov, A and Gorbunova, V and Buchwalter, A and Ghaemmaghami, S}, title = {Proteome Birthdating Reveals Age-Selectivity of Protein Ubiquitination.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {23}, number = {7}, pages = {100791}, pmid = {38797438}, issn = {1535-9484}, support = {R37 AG046320/AG/NIA NIH HHS/United States ; S10 OD025242/OD/NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; R01 AG027237/AG/NIA NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; R35 GM119502/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Ubiquitination ; *Proteome/metabolism ; *Proteasome Endopeptidase Complex/metabolism ; *Ubiquitinated Proteins/metabolism ; Proteomics/methods ; Proteolysis ; Ubiquitin/metabolism ; }, abstract = {Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To investigate the age-selectivity of cellular pathways, we developed a methodology termed "proteome birthdating" that barcodes proteins based on their time of synthesis. We demonstrate that this approach provides accurate measurements of protein turnover kinetics from a single biological sample encoding multiple labeling time-points. As a first application of the birthdated proteome, we investigated the age distribution of the human ubiquitinome. Our results indicate that the vast majority of ubiquitinated proteins in a cell consist of newly synthesized proteins and that these young proteins constitute the bulk of the degradative flux through the proteasome. Rapidly ubiquitinated nascent proteins are enriched in cytosolic subunits of large protein complexes. Conversely, proteins destined for the secretory pathway and vesicular transport have older ubiquitinated populations. Our data also identify a smaller subset of older ubiquitinated cellular proteins that do not appear to be targeted to the proteasome for rapid degradation. Together, our data provide an age census of the human ubiquitinome and establish proteome birthdating as a robust methodology for investigating the protein age-selectivity of diverse cellular pathways.}, }
@article {pmid38794403, year = {2024}, author = {Almerekova, S and Yermagambetova, M and Osmonali, B and Vesselova, P and Abugalieva, S and Turuspekov, Y}, title = {Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {10}, pages = {}, pmid = {38794403}, issn = {2223-7747}, support = {AP14869593//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.}, }
@article {pmid38792756, year = {2024}, author = {Abdillah, A and Kodio, A and Ranque, S}, title = {Malian Children's Core Gut Mycobiome.}, journal = {Microorganisms}, volume = {12}, number = {5}, pages = {}, pmid = {38792756}, issn = {2076-2607}, support = {M&#xe9;diterran&#xe9;e Infection 10-IAHU-03//M&#xe9;diterran&#xe9;e Infection Foundation/ ; }, abstract = {Because data on the fungal gut community structure of African children are scarce, we aimed to describe it by reanalysing rRNA ITS1 and ITS2 metabarcoding data from a study designed to assess the influence of microbiota in malaria susceptibility in Malian children from the Dogon country. More specifically, we aimed to establish the core gut mycobiome and compare the gut fungal community structure of breastfed children, aged 0-2 years, with other age groups. Briefly, DNA was extracted from 296 children's stool samples. Both rRNA ITS1 and ITS2 genomic barcodes were amplified and subjected to Illumina MiSeq sequencing. The ITS2 barcode generated 1,975,320 reads and 532 operational taxonomic units (OTUs), while the ITS1 barcode generated 647,816 reads and 532 OTUs. The alpha diversity was significantly higher by using the ITS1 compared to the ITS2 barcode (p < 0.05); but, regardless of the ITS barcode, we found no significant difference between breastfed children, aged 0-2 years, compared to the other age groups. The core gut mycobiome of the Malian children included Saccharomyces cerevisiae, Candida albicans, Pichia kudriavzevii, Malassezia restricta, Candida tropicalis and Aspergillus section Aspergillus, which were present in at least 50% of the 296 children. Further studies in other African countries are warranted to reach a global view of African children's core gut mycobiome.}, }
@article {pmid38791964, year = {2024}, author = {Zhu, Y and Koleilat, MKI and Roszik, J and Kwong, MK and Wang, Z and Maru, DM and Kopetz, S and Kwong, LN}, title = {A Gold Standard-Derived Modular Barcoding Approach to Cancer Transcriptomics.}, journal = {Cancers}, volume = {16}, number = {10}, pages = {}, pmid = {38791964}, issn = {2072-6694}, support = {1R01CA251608-01, 1R01HG011356-01/NH/NIH HHS/United States ; 1R01CA251608-01 and 1R01HG011356-01/NH/NIH HHS/United States ; }, abstract = {A challenge with studying cancer transcriptomes is in distilling the wealth of information down into manageable portions of information. In this resource, we develop an approach that creates and assembles cancer type-specific gene expression modules into flexible barcodes, allowing for adaptation to a wide variety of uses. Specifically, we propose that modules derived organically from high-quality gold standards such as The Cancer Genome Atlas (TCGA) can accurately capture and describe functionally related genes that are relevant to specific cancer types. We show that such modules can: (1) uncover novel gene relationships and nominate new functional memberships, (2) improve and speed up analysis of smaller or lower-resolution datasets, (3) re-create and expand known cancer subtyping schemes, (4) act as a "decoder" to bridge seemingly disparate established gene signatures, and (5) efficiently apply single-cell RNA sequencing information to other datasets. Moreover, such modules can be used in conjunction with native spreadsheet program commands to create a powerful and rapid approach to hypothesis generation and testing that is readily accessible to non-bioinformaticians. Finally, we provide tools for users to create and interpret their own modules. Overall, the flexible modular nature of the proposed barcoding provides a user-friendly approach to rapidly decoding transcriptome-wide data for research or, potentially, clinical uses.}, }
@article {pmid38791511, year = {2024}, author = {Wu, Y and Jensen, N and Rossner, MJ and Wehr, MC}, title = {Exploiting Cell-Based Assays to Accelerate Drug Development for G Protein-Coupled Receptors.}, journal = {International journal of molecular sciences}, volume = {25}, number = {10}, pages = {}, pmid = {38791511}, issn = {1422-0067}, mesh = {*Receptors, G-Protein-Coupled/metabolism ; Humans ; Signal Transduction/drug effects ; Drug Development/methods ; Drug Discovery/methods ; Animals ; Bioluminescence Resonance Energy Transfer Techniques/methods ; Biological Assay/methods ; }, abstract = {G protein-coupled receptors (GPCRs) are relevant targets for health and disease as they regulate various aspects of metabolism, proliferation, differentiation, and immune pathways. They are implicated in several disease areas, including cancer, diabetes, cardiovascular diseases, and mental disorders. It is worth noting that about a third of all marketed drugs target GPCRs, making them prime pharmacological targets for drug discovery. Numerous functional assays have been developed to assess GPCR activity and GPCR signaling in living cells. Here, we review the current literature of genetically encoded cell-based assays to measure GPCR activation and downstream signaling at different hierarchical levels of signaling, from the receptor to transcription, via transducers, effectors, and second messengers. Singleplex assay formats provide one data point per experimental condition. Typical examples are bioluminescence resonance energy transfer (BRET) assays and protease cleavage assays (e.g., Tango or split TEV). By contrast, multiplex assay formats allow for the parallel measurement of multiple receptors and pathways and typically use molecular barcodes as transcriptional reporters in barcoded assays. This enables the efficient identification of desired on-target and on-pathway effects as well as detrimental off-target and off-pathway effects. Multiplex assays are anticipated to accelerate drug discovery for GPCRs as they provide a comprehensive and broad identification of compound effects.}, }
@article {pmid38790191, year = {2024}, author = {Ciborowski, K and Szczecińska, M and Maździarz, M and Sawicki, J and Paukszto, &#x141;}, title = {Decoding Evolution of Rubioideae: Plastomes Reveal Sweet Secrets of Codon Usage, Diagnostides, and Superbarcoding.}, journal = {Genes}, volume = {15}, number = {5}, pages = {}, pmid = {38790191}, issn = {2073-4425}, support = {N304 364438//National Science Center/ ; }, mesh = {*Codon Usage ; *Phylogeny ; *Genome, Chloroplast/genetics ; *Evolution, Molecular ; *Rubiaceae/genetics ; Codon/genetics ; DNA Barcoding, Taxonomic/methods ; }, abstract = {Galium genus belongs to the Rubiaceae family, which consists of approximately 14,000 species. In comparison to its well-known relatives, the plastomes of the Galium genus have not been explored so far. The plastomes of this genus have a typical, quadripartite structure, but differ in gene content, since the infA gene is missing in Galium palustre and Galium trfidum. An evaluation of the effectiveness of using entire chloroplast genome sequences as superbarcodes for accurate plant species identification revealed the high potential of this method for molecular delimitation within the genus and tribe. The trnE-UUC-psbD region showed the biggest number of diagnostides (diagnostic nucleotides) which might be new potential barcodes, not only in Galium, but also in other closely related genera. Relative synonymous codon usage (RSCU) appeared to be connected with the phylogeny of the Rubiaceae family, showing that during evolution, plants started preferring specific codons over others.}, }
@article {pmid38789603, year = {2024}, author = {Scholtz, L and Eckert, JG and Graf, RT and Kunst, A and Wegner, KD and Bigall, NC and Resch-Genger, U}, title = {Correlating semiconductor nanoparticle architecture and applicability for the controlled encoding of luminescent polymer microparticles.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11904}, pmid = {38789603}, issn = {2045-2322}, abstract = {Luminophore stained micro- and nanobeads made from organic polymers like polystyrene (PS) are broadly used in the life and material sciences as luminescent reporters, for bead-based assays, sensor arrays, printable barcodes, security inks, and the calibration of fluorescence microscopes and flow cytometers. Initially mostly prepared with organic dyes, meanwhile luminescent core/shell nanoparticles (NPs) like spherical semiconductor quantum dots (QDs) are increasingly employed for bead encoding. This is related to their narrower emission spectra, tuneability of emission color, broad wavelength excitability, and better photostability. However, correlations between particle architecture, morphology, and photoluminescence (PL) of the luminescent nanocrystals used for encoding and the optical properties of the NP-stained beads have been rarely explored. This encouraged us to perform a screening study on the incorporation of different types of luminescent core/shell semiconductor nanocrystals into polymer microparticles (PMPs) by a radical-induced polymerization reaction. Nanocrystals explored include CdSe/CdS QDs of varying CdS shell thickness, a CdSe/ZnS core/shell QD, CdSe/CdS quantum rods (QRs), and CdSe/CdS nanoplatelets (NPLs). Thereby, we focused on the applicability of these NPs for the polymerization synthesis approach used and quantified the preservation of the initial NP luminescence. The spectroscopic characterization of the resulting PMPs revealed the successful staining of the PMPs with luminescent CdSe/CdS QDs and CdSe/CdS NPLs. In contrast, usage of CdSe/CdS QRs and CdSe QDs with a ZnS shell did not yield luminescent PMPs. The results of this study provide new insights into structure-property relationships between NP stained PMPs and the initial luminescent NPs applied for staining and underline the importance of such studies for the performance optimization of NP-stained beads.}, }
@article {pmid38787488, year = {2024}, author = {Kumari, A and Sidhu, MC}, title = {Morphological and molecular characterization of two species of genus Ageratum.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {668}, pmid = {38787488}, issn = {1573-4978}, mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *Ageratum/genetics ; DNA, Plant/genetics ; Plant Leaves/genetics ; Sequence Analysis, DNA/methods ; India ; }, abstract = {BACKGROUND: The species of genus Ageratum (family Asteraceae) are distributed in various parts of the world. Ageratum conyzoides and A. houstonianum are the most commonly occurring species in India. These species are quite similar in their morphology thus creating a challenge in identification during the field survey and taxonomic validation. The accurate identification of the species is highly significant especially when those are of medicinal interest. To overcome the barriers in morphological based identification, DNA barcoding has been employed during the present investigation.<br><br>METHODS AND RESULTS: Morphological and DNA barcodes matK and ITS genes, were employed to differentiate between Ageratum conyzoides and A. houstonianum. The obtained matK and ITS gene sequences were submitted to GenBank and BOLD system to obtain accession numbers. The DNA sequences were aligned with database sequences using BLAST and phylogenetic trees were constructed through neighbor-joining algorithm in MEGA 11 software. The distinguish features of A. conyzoides include ovate to elliptic-oblong leaves with a cuneate base and inflorescence heads forming domed to flat-topped clusters. However, A. houstonianum has triangular to ovate leaves with a cordate to truncate base, cymose clusters in the inflorescence and stipulate glandular involucre bracts. The matK gene has shown the highest identity percentages (100%) for A. houstonianum and 99.87% for A. conyzoides. The phylogenetic tree analysis has demonstrated a close association of A. conyzoides and A. houstonianum with their respective species, supported by bootstrap values in the matK and ITS trees.<br><br>CONCLUSION: This study revealed that morphological and molecular data can be successfully utilized in the identification of A. conyzoides and A. houstonianum. The matK and ITS barcodes provide promising results in the identification of Ageratum species, with their phylogeny supporting classification within the family asteraceae.}, }
@article {pmid38786915, year = {2024}, author = {Jiang, ZH and Wang, JX and Xu, ZB and Kitching, IJ and Huang, CL and Hu, SJ and Xiao, YL}, title = {Revision of the Genus Rhagastis Rothschild &amp; Jordan, 1903 (Lepidoptera: Sphingidae) from China, Based on Morphological and Phylogenetic Analyses.}, journal = {Insects}, volume = {15}, number = {5}, pages = {}, pmid = {38786915}, issn = {2075-4450}, support = {2019FY101800//National Science &amp; Technology Fundamental Resources Investigation Program of China (Grant No. 2019FY101800)/ ; 202305AF150037//Academician (Expert) Working Station (202305AF150037), Yunnan Provincial Department of Science/ ; }, abstract = {Here, the taxonomy of the genus Rhagastis Rothschild &amp; Jordan, 1903 (Lepidoptera, Sphingidae, Macroglossinae, Macroglossini) from China is revised based on differences in wing morphology, male and female genitalia, and the phylogenetic relationship of the DNA barcodes. Subspecies of Rhagastis albomarginatus (Rothschild, 1894) and R. castor (Walker, 1856) are treated as "good" species, namely Rhagastis dichroae Mell, 1922 stat. nov.; R. everetti Rothschild &amp; Jordan, 1903 stat. nov.; R. aurifera (Butler, 1875) stat. rev.; R. chinensis Mell, 1922 stat. nov.; R. formosana Clark, 1925 stat. nov.; and R. jordani Oberthür, 1904 stat. rev. The distribution maps, biological notes, and ecological records of the genus Rhagastis Rothschild &amp; Jordan, 1903 from China are given, and a species inventory of genus Rhagastis in the world is also included.}, }
@article {pmid38785505, year = {2024}, author = {Matoute, A and Maestri, S and Saout, M and Laghoe, L and Simon, S and Blanquart, H and Hernandez Martinez, MA and Pierre Demar, M}, title = {Meat-Borne-Parasite: A Nanopore-Based Meta-Barcoding Work-Flow for Parasitic Microbiodiversity Assessment in the Wild Fauna of French Guiana.}, journal = {Current issues in molecular biology}, volume = {46}, number = {5}, pages = {3810-3821}, pmid = {38785505}, issn = {1467-3045}, support = {PARALIM project (Synergie n&#xb0; GY0012553)//European funding (ERDF/FEDER)/ ; CEBA: ANR-10-LABEX-25-01//Investissement d'Avenir 358 grants of the the Agence Nationale de la Recherche/ ; }, abstract = {French Guiana, located in the Guiana Shield, is a natural reservoir for many zoonotic pathogens that are of considerable medical or veterinary importance. Until now, there has been limited data available on the description of parasites circulating in this area, especially on protozoan belonging to the phylum Apicomplexa; conversely, the neighbouring countries describe a high parasitic prevalence in animals and humans. Epidemiological surveillance is necessary, as new potentially virulent strains may emerge from these forest ecosystems, such as Amazonian toxoplasmosis. However, there is no standard tool for detecting protozoa in wildlife. In this study, we developed Meat-Borne-Parasite, a high-throughput meta-barcoding workflow for detecting Apicomplexa based on the Oxford Nanopore Technologies sequencing platform using the 18S gene of 14 Apicomplexa positive samples collected in French Guiana. Sequencing reads were then analysed with MetONTIIME pipeline. Thanks to a scoring rule, we were able to classify 10 samples out of 14 as Apicomplexa positive and reveal the presence of co-carriages. The same samples were also sequenced with the Illumina platform for validation purposes. For samples identified as Apicomplexa positive by both platforms, a strong positive correlation at up to the genus level was reported. Overall, the presented workflow represents a reliable method for Apicomplexa detection, which may pave the way for more comprehensive biomonitoring of zoonotic pathogens.}, }
@article {pmid38784157, year = {2024}, author = {Pina, S and Pauperio, J and Barros, F and Chaves, C and Martins, FM and Pinto, J and Veríssimo, J and Mata, VA and Beja, P and Ferreira, S}, title = {The InBIO Barcoding Initiative Database: DNA barcodes of Orthoptera from Portugal.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e118010}, pmid = {38784157}, issn = {1314-2828}, abstract = {BACKGROUND: The InBIO Barcoding Initiative (IBI) Orthoptera dataset contains records of 420 specimens covering all the eleven Orthoptera families occurring in Portugal. Specimens were collected in continental Portugal from 2005 to 2021 and were morphologically identified to species level by taxonomists. A total of 119 species were identified corresponding to about 77% of all the orthopteran species known from continental Portugal.<br><br>NEW INFORMATION: DNA barcodes of 54 taxa were made public for the first time at the Barcode of Life Data System (BOLD). Furthermore, the submitted sequences were found to cluster in 129 BINs (Barcode Index Numbers), 35 of which were new additions to the Barcode of Life Data System (BOLD). All specimens have their DNA barcodes publicly accessible through BOLD online database. Stenobothruslineatus is recorded for the first time for continental Portugal. This dataset greatly increases the knowledge on the DNA barcodes and distribution of Orthoptera from Portugal. All DNA extractions and most specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources.}, }
@article {pmid38781750, year = {2024}, author = {Bouchali, R and Mandon, C and Danty-Berger, E and Géloën, A and Marjolet, L and Youenou, B and Pozzi, ACM and Vareilles, S and Galia, W and Kouyi, GL and Toussaint, JY and Cournoyer, B}, title = {Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns.}, journal = {International journal of hygiene and environmental health}, volume = {260}, number = {}, pages = {114391}, doi = {10.1016/j.ijheh.2024.114391}, pmid = {38781750}, issn = {1618-131X}, mesh = {*Rain ; Humans ; *Microbiota ; *Water Microbiology ; *Cities ; *Bacteria/isolation &amp; purification/classification/genetics ; *Environmental Monitoring/methods ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.}, }
@article {pmid38781285, year = {2024}, author = {Govorov, V and Shcherbakov, E and Janšta, P and Černá Bolfiková, B}, title = {First assessment of the biodiversity of praying mantises (Insecta: Mantodea) in Cameroon with DNA barcoding.}, journal = {PloS one}, volume = {19}, number = {5}, pages = {e0304163}, pmid = {38781285}, issn = {1932-6203}, mesh = {Cameroon ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *Mantodea/genetics/classification ; *Phylogeny ; }, abstract = {Praying mantises are the apex insect predators in many ecosystems, nevertheless they receive relatively less recognition in biodiversity reviews. We report a first survey of diversity of praying mantises in Cameroon, which is situated in the Congo Basin region, one of the richest biodiversity hotspots. Combination of light trapping with manual collecting resulted in 495 specimens representing 62 species. A total of eight species are novel for the country, at least five species are likely undescribed. DNA barcodes of 72 specimens representing every collected species were obtained, curated, and submitted to NCBI database. For eight species, barcodes are published for the first time. A maximum likelihood phylogenetic tree was created using all available barcodes of Mantodea of Central African subregion. The results obtained during this study stress the importance of combining traditional and molecular approaches during biodiversity assessments of often neglected taxa, the latter aiding in uncovering new species, resolving unknown morphological divergencies and assigning conspecifics.}, }
@article {pmid38778277, year = {2024}, author = {Fu, N and Xu, Y and Jin, L and Xiao, TW and Song, F and Yan, HF and Chen, YS and Ge, XJ}, title = {Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {445}, pmid = {38778277}, issn = {1471-2229}, support = {No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No. XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {*Acer/genetics ; *Phylogeny ; *DNA Barcoding, Taxonomic/methods ; *DNA, Ribosomal/genetics ; *DNA, Plant/genetics ; Plastids/genetics ; Species Specificity ; Cell Nucleus/genetics ; }, abstract = {BACKGROUND: Acer is a taxonomically intractable and speciose genus that contains over 150 species. It is challenging to distinguish Acer species only by morphological method due to their abundant variations. Plastome and nuclear ribosomal DNA (nrDNA) sequences are recommended as powerful next-generation DNA barcodes for species discrimination. However, their efficacies were still poorly studied. The current study will evaluate the application of plastome and nrDNA in species identification and perform phylogenetic analyses for Acer.<br><br>RESULT: Based on a collection of 83 individuals representing 55 species (c. 55% of Chinese species) from 13 sections, our barcoding analyses demonstrated that plastomes exhibited the highest (90.47%) species discriminatory power among all plastid DNA markers, such as the standard plastid barcodes matK&#x2009;+&#x2009;rbcL&#x2009;+&#x2009;trnH-psbA (61.90%) and ycf1 (76.19%). And the nrDNA (80.95%) revealed higher species resolution than ITS (71.43%). Acer plastomes show abundant interspecific variations, however, species identification failure may be due to the incomplete lineage sorting (ILS) and chloroplast capture resulting from hybridization. We found that the usage of nrDNA contributed to identifying those species that were unidentified by plastomes, implying its capability to some extent to mitigate the impact of hybridization and ILS on species discrimination. However, combining plastome and nrDNA is not recommended given the cytonuclear conflict caused by potential hybridization. Our phylogenetic analysis covering 19 sections&#xa0;(95% sections of Acer) and 128 species (over 80% species of this genus) revealed pervasive inter- and intra-section cytonuclear discordances, hinting that hybridization has played an important role in the evolution of Acer.<br><br>CONCLUSION: Plastomes and nrDNA can significantly improve the species resolution in Acer. Our phylogenetic analysis uncovered the scope and depth of cytonuclear conflict in Acer, providing important insights into its evolution.}, }
@article {pmid38776430, year = {2024}, author = {Wang, N and Mcneer, NA and Eton, E and Fass, J and Kentsis, A}, title = {Proteomic Barcoding Platform for Macromolecular Screening and Delivery.}, journal = {Journal of proteome research}, volume = {23}, number = {6}, pages = {2067-2077}, pmid = {38776430}, issn = {1535-3907}, support = {R01 CA204396/CA/NCI NIH HHS/United States ; U54 CA243124/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R21 CA235285/CA/NCI NIH HHS/United States ; //Commonwealth Foundation for Cancer Research the Center for Experimental Therapeutics/ ; R01 CA214812/CA/NCI NIH HHS/United States ; /DDCF/Doris Duke Charitable Foundation/United States ; //Starr Cancer Consortium/ ; }, mesh = {Humans ; *Proteomics/methods ; *Cell-Penetrating Peptides/chemistry ; Algorithms ; Mass Spectrometry/methods ; Peptide Library ; High-Throughput Screening Assays/methods ; Macromolecular Substances/chemistry/analysis ; }, abstract = {Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.}, }
@article {pmid38775954, year = {2024}, author = {Liu, Y and Chen, J and Lin, C and Ke, R}, title = {Multiplexed in situ RNA imaging by combFISH.}, journal = {Analytical and bioanalytical chemistry}, volume = {416}, number = {16}, pages = {3765-3774}, pmid = {38775954}, issn = {1618-2650}, support = {2021Y4001//Natural Science Foundation of Fujian Province/ ; 2022J06022//Natural Science Foundation of Fujian Province/ ; ZQN-1123//Fundamental Research Funds for the Central Universities/ ; 3502Z20234012//Xiamen Municipal Bureau of Science and Technology/ ; }, mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA/analysis ; Humans ; Animals ; Fluorescent Dyes/chemistry ; Gene Expression Profiling/methods ; }, abstract = {Multiplexed in situ RNA imaging offers new opportunities for gene expression profiling by providing high-throughput spatial information. In this work, we present a cyclic combinatorial fluorescent in situ hybridization (combFISH) assay to achieve multiplexed detection of RNA in cell cultures and tissues. Specifically, multiplexing is achieved through cyclic interrogation of barcode sequences on the rolling circle amplicons generated from the padlock probe assay by using sets of combinatorial detection probes. Theoretically, combFISH can detect 64 genes in three hybridization cycles by combinatorial barcoding using 12 fluorescently labeled detection probes. Our method eliminates sequencing-by-ligation (SBL) chemistry in the in situ sequencing protocol and directly uses RNA as targets for ligation, making it more straightforward. We showed that our method works in fresh-frozen and formalin-fixed paraffin-embedded tissue sections. With its straightforward protocols, we expect our method to be adopted by the scientific community and extended to clinical settings.}, }
@article {pmid38775145, year = {2024}, author = {Graham, K and Cantu, C and Houston, R}, title = {Sequence variation of commercially available kratom products at universal DNA barcode regions.}, journal = {Journal of forensic sciences}, volume = {69}, number = {4}, pages = {1421-1428}, doi = {10.1111/1556-4029.15547}, pmid = {38775145}, issn = {1556-4029}, mesh = {*Mitragyna/genetics/chemistry ; *DNA Barcoding, Taxonomic ; *DNA, Plant/genetics ; Humans ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Polymorphism, Genetic ; Genetic Variation ; DNA, Chloroplast/genetics ; }, abstract = {Mitragyna speciosa, commonly known as kratom, is a narcotic plant that is used for its unique mood-enhancing and pain-relieving effects. It is marketed throughout the United States as a 'legal high' and has gained popularity as an alternative to opioids. However, kratom's increasing involvement in accidental overdoses, especially among polydrug users, has prompted warnings from the Drug Enforcement Agency (DEA) and the Food and Drug Administration (FDA). Despite these warnings, kratom remains legal federally, although it is banned in six states. This legal disparity complicates monitoring and enforcement efforts in states where kratom is illegal. Common forensic techniques using morphology or chemical analysis are beneficial in some instances but are not useful in source attribution because most seized kratom is powdered and the alkaloid content of samples can vary within products, making sourcing unreliable. This study focused on developing a DNA barcoding method to access sequence variation in commercial kratom products. It evaluated the utility of one nuclear barcode region (ITS) and three chloroplast barcode regions (matK, rbcL, and trnH-psbA) in assessing sequence variation across commercially available kratom products. Novel polymorphisms were discovered, and the ITS region showed the greatest variation between samples. Among the 15 kratom products tested, only two haplotypes were identified across the four barcoding regions. The findings highlight the potential of DNA barcoding as a forensic tool in the traceability and enforcement against illegal kratom distribution. Nonetheless, the limited haplotypic diversity points to a need for further development and expansion of the M. speciosa DNA sequence database.}, }
@article {pmid38774420, year = {2024}, author = {Parker, TB and Meiklejohn, KA and Dahlem, GA and Eagle, RC and Heersink, MJ}, title = {Ophthalmomyiasis Case Caused by Two Blow Fly (Diptera: Calliphoridae) Species in North America.}, journal = {TheScientificWorldJournal}, volume = {2024}, number = {}, pages = {2209301}, pmid = {38774420}, issn = {1537-744X}, mesh = {Animals ; *Calliphoridae/genetics ; Male ; Humans ; *Larva ; Myiasis/parasitology/diagnosis ; North America ; Phylogeny ; Diptera/parasitology ; Genome, Mitochondrial ; }, abstract = {Ophthalmomyiasis is the result of fly larvae feeding on the tissues of the eye. Commonly associated with poor hygiene and open wounds, this condition is rare and often stigmatized. Treatment can be straightforward, and full recovery is common. Identifying the species responsible for ophthalmomyiasis is important for the medical, forensic, and entomological communities. Here, we present a case of ophthalmomyiasis where 30-40 blow fly (Diptera: Calliphoridae) larvae were removed from the eye of a human male. A representative subsample of five larvae was used for taxonomic identification via two approaches (a) DNA analysis, via sequencing of the complete mitochondrial genome (mtGenome) and comparison of the mtGenome and mitochondrial COI barcode region to GenBank, and (b) morphology, examination of the posterior spiracles using microscopy, and comparison to published larval descriptions of blow flies. Two species of blow flies were identified from the DNA analysis: Lucilia coeruleiviridis and Phormia regina. Morphological examination could only confirm L. coeruleiviridis as being present. To our knowledge, finding two blow fly species causing ophthalmomyiasis in a single individual has not been previously reported in the scientific literature. Neither P. regina nor L. coeruleiviridis prefers living tissue for larva development, but since they fill similar ecological niches, perhaps this was a show of competition rather than a normal feeding habit. Knowing these blow fly species can resort to this behavior, and that it can affect human populations, is valuable to the education of patients and providers.}, }
@article {pmid38774237, year = {2024}, author = {Hoang, CV and Tu, TQ and Lo, TTM and Chu, MH}, title = {Dataset on intergenic spacer regions of chloroplast genome and potential DNA barcode of Hoya varticillata var varticillata in Vietnam.}, journal = {Data in brief}, volume = {54}, number = {}, pages = {110471}, pmid = {38774237}, issn = {2352-3409}, abstract = {Hoya verticillata var verticillata, an epiphytic plant, is both an ornamental and a valuable medicinal plant. However, H. verticillata has a similar morphology to other species belonging to the Hoya genus, so it is challenging to distinguish the H. verticillata var verticillata, plant accurately. Alternatively, if H. verticillata var verticillata, is deformed or powdered, it is more challenging to identify. This dataset includes information on H. verticillata var verticillata, samples collected from the natural environment and four chloroplast DNA markers to support H. verticillata var verticillata, species identification. Phylogenetic analysis based on sequences of intergenic spacer regions (trnK-rps16, rps16-trnQ, psbI-atpA, and ndhC-trnV) shows that H. verticilata var verticillata, is very closely related and distributed in the same group as Hoya carnosa with a Bootstrap coefficient of 99-100 %. Four intergenic spacer region sequences, trnK-rps16, rps16-trnQ, psbI-atpA, and ndhC-trnV from the chloroplast genome are potential DNA barcoding candidates to distinguish H. verticilata var verticillata, from different species in the Hoya genus.}, }
@article {pmid38773773, year = {2024}, author = {Yoon, CJ and Nam, CH and Kim, T and Lee, JS and Kim, R and Yi, K and Koh, JY and Kim, J and Won, H and Oh, JW and Griffith, OL and Griffith, M and Sung, J and Kim, TY and Cho, D and Choi, JS and Ju, YS}, title = {Whole-genome sequences reveal zygotic composition in chimeric twins.}, journal = {HGG advances}, volume = {5}, number = {3}, pages = {100301}, pmid = {38773773}, issn = {2666-2477}, support = {F30 HD106744/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Female ; *Twins, Dizygotic/genetics ; *Zygote/metabolism ; *Whole Genome Sequencing ; Pregnancy ; Chimerism ; Placenta/metabolism ; Male ; Chimera/genetics ; Twins, Monozygotic/genetics ; }, abstract = {While most dizygotic twins have a dichorionic placenta, rare cases of dizygotic twins with a monochorionic placenta have been reported. The monochorionic placenta in dizygotic twins allows in utero exchange of embryonic cells, resulting in chimerism in the twins. In practice, this chimerism is incidentally identified in mixed ABO blood types or in the presence of cells with a discordant sex chromosome. Here, we applied whole-genome sequencing to one triplet and one twin family to precisely understand their zygotic compositions, using millions of genomic variants as barcodes of zygotic origins. Peripheral blood showed asymmetrical contributions from two sister zygotes, where one of the zygotes was the major clone in both twins. Single-cell RNA sequencing of peripheral blood tissues further showed differential contributions from the two sister zygotes across blood cell types. In contrast, buccal tissues were pure in genetic composition, suggesting that in utero cellular exchanges were confined to the blood tissues. Our study illustrates the cellular history of twinning during human development, which is critical for managing the health of chimeric individuals in the era of genomic medicine.}, }
@article {pmid38773521, year = {2024}, author = {Mudavanhu, A and Schols, R and Goossens, E and Nhiwatiwa, T and Manyangadze, T and Brendonck, L and Huyse, T}, title = {One Health monitoring reveals invasive freshwater snail species, new records, and undescribed parasite diversity in Zimbabwe.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {234}, pmid = {38773521}, issn = {1756-3305}, mesh = {Animals ; Zimbabwe/epidemiology ; *Snails/parasitology ; *Trematoda/genetics/classification/isolation &amp; purification/physiology ; Cross-Sectional Studies ; *Introduced Species ; *Fresh Water/parasitology ; One Health ; Humans ; Trematode Infections/parasitology/veterinary/epidemiology ; Biodiversity ; Prevalence ; Schistosomiasis/epidemiology/parasitology/veterinary ; }, abstract = {BACKGROUND: Snail-borne trematodes afflict humans, livestock, and wildlife. Recognizing their zoonotic potential and possible hybridization, a One Health approach is essential for effective control. Given the dearth of knowledge on African trematodes, this study aimed to map snail and trematode diversity, focusing on (i) characterizing gastropod snail species and their trematode parasites, (ii) determining infection rates of snail species as intermediate hosts for medically, veterinary, and ecologically significant trematodes, and (iii) comparing their diversity across endemic regions.<br><br>METHODS: A cross-sectional study conducted in 2021 in Chiredzi and Wedza districts in Zimbabwe, known for high human schistosomiasis prevalence, involved malacological surveys at 56 sites. Trematode infections in snails were detected through shedding experiments and multiplex rapid diagnostic polymerase chain reactions (RD-PCRs). Morphological and molecular analyses were employed to identify snail and trematode species.<br><br>RESULTS: Among 3209 collected snail specimens, 11 species were identified, including schistosome and fasciolid competent snail species. We report for the first time the invasive exotic snail Tarebia granifera in Zimbabwe, which was highly abundant, mainly in Chiredzi, occurring at 29 out of 35 sites. Shedding experiments on 1303 snails revealed a 2.24% infection rate, with 15 trematode species identified through molecular genotyping. Five species were exclusive to Chiredzi: Bolbophorus sp., Schistosoma mansoni, Schistosoma mattheei, Calicophoron sp., and Uvulifer sp. Eight were exclusive to Wedza, including Trichobilharzia sp., Stephanoprora amurensis, Spirorchid sp., and Echinostoma sp. as well as an unidentified species of the Plagiorchioidea superfamily. One species, Tylodelphys mashonensis, was common to both regions. The RD-PCR screening of 976 non-shedding snails indicated a 35.7% trematode infection rate, including&#xa0;the presence of schistosomes (1.1%) Fasciola nyanzae (0.6%). In Chiredzi, Radix natalensis had the highest trematode infection prevalence (33.3%), while in Wedza, R. natalensis (55.4%) and Bulinus tropicus (53.2%) had the highest infection prevalence.<br><br>CONCLUSIONS: Our xenomonitoring approach unveiled 15 trematode species, including nine new records in Zimbabwe. Schistosoma mansoni persists in the study region despite six mass deworming rounds. The high snail and parasite diversity, including the presence of exotic snail species&#xa0;that can impact endemic species and biomedically important trematodes, underscores the need for increased monitoring.}, }
@article {pmid38773413, year = {2024}, author = {Richardson, MA and Nenadic, N and Wingfield, M and McDougall, C}, title = {The development of multiplex PCR assays for the rapid identification of multiple Saccostrea species, and their practical applications in restoration and aquaculture.}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {67}, pmid = {38773413}, issn = {2730-7182}, mesh = {Animals ; *Multiplex Polymerase Chain Reaction/methods ; *Aquaculture/methods ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; *Ostreidae/genetics ; Queensland ; Species Specificity ; Conservation of Natural Resources/methods ; }, abstract = {BACKGROUND: The ecology and biology of oysters (Ostreidae) across the tropics is poorly understood. Morphological plasticity and shared characteristics among oysters have resulted in the misidentification of species, creating challenges for understanding basic species-specific biological information that is required for restoration and aquaculture. Genetic barcoding has proven essential for accurate species identification and understanding species geographic ranges. To reduce the costs of molecular species identification we developed multiplex assays using the cytochrome c oxidase subunit I (COI or cox1) barcoding gene for the rapid identification of five species of oysters within the genus Saccostrea that are commonly found in Queensland, Australia: Saccostrea glomerata, Saccostrea lineage B, Saccostrea lineage F, Saccostrea lineage G, and Saccostrea spathulata (lineage J).<br><br>RESULTS: Multiplex assays were successful in species-specific amplification of targeted species. The practical application of these primers was tested on wild spat collected from a pilot restoration project in Moreton Bay, Queensland, with identified species (S. glomerata, lineage B and lineage G) validated by Sanger sequencing. DNA sampling by extraction of oyster pallial fluid was also tested on adult oysters collected from the Noosa estuary in Queensland to assess whether oysters were able to be identified non-destructively. DNA concentrations as low as 1 ng/ &#x3bc;L still amplified in most cases, allowing for identification, and mortality at 6 weeks post pallial fluid collection was low (3 out of 104 sampled oysters).<br><br>CONCLUSION: These multiplex assays will be essential tools for species identification in future studies, and we successfully demonstrate their practical application in both restoration and aquaculture contexts in Queensland. The multiplex assays developed in this study outline easily replicable methods for the development of additional species-specific primer sets for the rapid identification of other species of Saccostrea found across the Indo-Pacific, which will be instrumental in unravelling the taxonomic ambiguities within this genus in tropical regions.}, }
@article {pmid38769096, year = {2024}, author = {Hermansen, JU and Yin, Y and Rein, ID and Skånland, SS}, title = {Immunophenotyping with (phospho)protein profiling and fluorescent cell barcoding for single-cell signaling analysis and biomarker discovery.}, journal = {NPJ precision oncology}, volume = {8}, number = {1}, pages = {107}, pmid = {38769096}, issn = {2397-768X}, support = {322898//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 19//Stiftelsen Kristian Gerhard Jebsen (Kristian Gerhard Jebsen Foundation)/ ; 328827//Kreftforeningen (Norwegian Cancer Society)/ ; }, abstract = {The microenvironment of hematologic cancers contributes to tumor cell survival and proliferation, as well as treatment resistance. Understanding tumor- and drug-induced changes to the immune cell composition and functionality is therefore critical for implementing optimal treatment strategies and for the development of novel cancer therapies. The liquid nature of peripheral blood makes this organ uniquely suited for single-cell studies by flow cytometry. (Phospho)protein profiles detected by flow cytometry analyses have been shown to correlate with ex vivo drug sensitivity and to predict treatment outcomes in hematologic cancers, demonstrating that this method is suitable for pre-clinical studies. Here, we present a flow cytometry protocol that combines multi-parameter immunophenotyping with single-cell (phospho)protein profiling. The protocol makes use of fluorescent cell barcoding, which means that multiple cell samples, either collected from different donors or exposed to different treatment conditions, can be combined and analyzed as one experiment. This reduces variability between samples, increases the throughput of the experiment, and lowers experimental costs. This protocol may serve as a guide for the use and further development of assays to study immunophenotype and cell signaling at single-cell resolution in normal and malignant cells. The read-outs may provide biological insight into cancer pathogenesis, identify novel drug targets, and ultimately serve as a biomarker to guide clinical decision-making.}, }
@article {pmid38768238, year = {2024}, author = {Shukla, N and Roelle, SM and Snell, JC and DelSignore, O and Bruchez, AM and Matreyek, KA}, title = {Pseudotyped virus infection of multiplexed ACE2 libraries reveals SARS-CoV-2 variant shifts in receptor usage.}, journal = {PLoS pathogens}, volume = {20}, number = {5}, pages = {e1012044}, pmid = {38768238}, issn = {1553-7374}, support = {R21 AI169561/AI/NIAID NIH HHS/United States ; S10 OD021559/OD/NIH HHS/United States ; R21 AI161275/AI/NIAID NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; R21 AI178151/AI/NIAID NIH HHS/United States ; R35 GM142886/GM/NIGMS NIH HHS/United States ; R21 AI156907/AI/NIAID NIH HHS/United States ; }, mesh = {*Angiotensin-Converting Enzyme 2/metabolism/genetics/chemistry ; Humans ; *SARS-CoV-2/genetics ; *Spike Glycoprotein, Coronavirus/genetics/metabolism/chemistry ; *COVID-19/virology/transmission ; Virus Internalization ; Receptors, Virus/metabolism/genetics ; HEK293 Cells ; Viral Pseudotyping ; Mutation ; }, abstract = {Pairwise compatibility between virus and host proteins can dictate the outcome of infection. During transmission, both inter- and intraspecies variabilities in receptor protein sequences can impact cell susceptibility. Many viruses possess mutable viral entry proteins and the patterns of host compatibility can shift as the viral protein sequence changes. This combinatorial sequence space between virus and host is poorly understood, as traditional experimental approaches lack the throughput to simultaneously test all possible combinations of protein sequences. Here, we created a pseudotyped virus infection assay where a multiplexed target-cell library of host receptor variants can be assayed simultaneously using a DNA barcode sequencing readout. We applied this assay to test a panel of 30 ACE2 orthologs or human sequence mutants for infectability by the original SARS-CoV-2 spike protein or the Alpha, Beta, Gamma, Delta, and Omicron BA1 variant spikes. We compared these results to an analysis of the structural shifts that occurred for each variant spike's interface with human ACE2. Mutated residues were directly involved in the largest shifts, although there were also widespread indirect effects altering interface structure. The N501Y substitution in spike conferred a large structural shift for interaction with ACE2, which was partially recreated by indirect distal substitutions in Delta, which does not harbor N501Y. The structural shifts from N501Y greatly influenced the set of animal orthologs the variant spike was capable of interacting with. Out of the thirteen non-human orthologs, ten exhibited unique patterns of variant-specific compatibility, demonstrating that spike sequence changes during human transmission can toggle ACE2 compatibility and potential susceptibility of other animal species, and cumulatively increase overall compatibilities as new variants emerge. These experiments provide a blueprint for similar large-scale assessments of protein compatibility during entry by diverse viruses. This dataset demonstrates the complex compatibility relationships that occur between variable interacting host and virus proteins.}, }
@article {pmid38766256, year = {2024}, author = {Siniscalco, A and Perera, RP and Greenslade, JE and Masters, A and Doll, H and Raj, B}, title = {Barcoding Notch signaling in the developing brain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38766256}, issn = {2692-8205}, support = {DP2 NS131787/NS/NINDS NIH HHS/United States ; R00 HD098298/HD/NICHD NIH HHS/United States ; }, abstract = {Developmental signaling inputs are fundamental for shaping cell fates and behavior. However, traditional fluorescent-based signaling reporters have limitations in scalability and molecular resolution of cell types. We present SABER-seq, a CRISPR-Cas molecular recorder that stores transient developmental signaling cues as permanent mutations in cellular genomes for deconstruction at later stages via single-cell transcriptomics. We applied SABER-seq to record Notch signaling in developing zebrafish brains. SABER-seq has two components: a signaling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control while the recorder accumulates mutations that represent Notch activity in founder cells. We combine SABER-seq with an expanded juvenile brain atlas to define cell types whose fates are determined downstream of Notch signaling. We identified examples wherein Notch signaling may have differential impact on terminal cell fates. SABER-seq is a novel platform for rapid, scalable and high-resolution mapping of signaling activity during development.}, }
@article {pmid38766101, year = {2024}, author = {Toledo-Rodriguez, DA and Veglia, A and Jimenez Marrero, NM and Gomez-Samot, JM and McFadden, CS and Weil, E and Schizas, NV}, title = {Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata, in southwest Puerto Rico.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38766101}, issn = {2692-8205}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {In October 2023, several colonies of an alien soft coral species were reported on shallow reefs in southwest Puerto Rico. The soft coral was identified as a xeniid octocoral (species undetermined), resembling the octocoral Unomia stolonifera, which has invaded and overgrown reefs in Venezuela in recent years. To conclusively characterize the species of the invading xeniid, we employed multilocus barcoding targeting four genes (ND2, mtMutS, COI, and 28S) of three separate colonies across three locations in southwest Puerto Rico. Sequence comparisons with xeniid sequences from GenBank, including those from the genera Xenia and Unomia, indicated a 100% sequence identity (>3,000 bp combined) with the species Xenia umbellata (Octocorallia : Malacalcyonacea : Xeniidae). Xenia umbellata is native to the Red Sea and to our knowledge, this represents the first confirmed case of this species as an invader on Caribbean reefs. Similar to U. stolonifera, X. umbellata is well known for its ability to rapidly overgrow substrate as well as tolerate environmental extremes. In addition, X. umbellata has recently been proposed as a model system for tissue regeneration having the ability to regenerate completely from a single tentacle. These characteristics greatly amplify X. umbellata's potential to adversely affect any reef it invades. Our findings necessitate continued collaborative action between local management agencies and stakeholders in Puerto Rico, as well as neighboring islands, to monitor and control this invasion prior to significant ecological perturbation.}, }
@article {pmid38762544, year = {2024}, author = {Hale, JJ and Matsui, T and Goldstein, I and Mullis, MN and Roy, KR and Ville, CN and Miller, D and Wang, C and Reynolds, T and Steinmetz, LM and Levy, SF and Ehrenreich, IM}, title = {Genome-scale analysis of interactions between genetic perturbations and natural variation.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4234}, pmid = {38762544}, issn = {2041-1723}, support = {R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG010378/HG/NHGRI NIH HHS/United States ; R35 GM130381/GM/NIGMS NIH HHS/United States ; 1R35GM130381//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {*Saccharomyces cerevisiae/genetics ; *Epistasis, Genetic ; *Genome, Fungal ; Genetic Variation ; Genetic Fitness ; CRISPR-Cas Systems ; Phenotype ; DNA Barcoding, Taxonomic ; }, abstract = {Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual's response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.}, }
@article {pmid38761946, year = {2024}, author = {Múrria, C and Wangensteen, OS and Somma, S and Väisänen, L and Fortuño, P and Arnedo, MA and Prat, N}, title = {Taxonomic accuracy and complementarity between bulk and eDNA metabarcoding provides an alternative to morphology for biological assessment of freshwater macroinvertebrates.}, journal = {The Science of the total environment}, volume = {935}, number = {}, pages = {173243}, doi = {10.1016/j.scitotenv.2024.173243}, pmid = {38761946}, issn = {1879-1026}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Invertebrates/genetics/classification ; *Fresh Water ; *Environmental Monitoring/methods ; *Biodiversity ; DNA, Environmental ; Ecosystem ; Biological Monitoring/methods ; }, abstract = {Determining biological status of freshwater ecosystems is critical for ensuring ecosystem health and maintaining associated services to such ecosystems. Freshwater macroinvertebrates respond predictably to environmental disturbances and are widely used in biomonitoring programs. However, many freshwater species are difficult to capture and sort from debris or substrate and morphological identification is challenging, especially larval stages, damaged specimens, or hyperdiverse groups such as Diptera. The advent of high throughput sequencing technologies has enhanced DNA barcoding tools to automatise species identification for whole communities, as metabarcoding is increasingly used to monitor biodiversity. However, recent comparisons have revealed little congruence between morphological and molecular-based identifications. Using broad range universal primers for DNA barcode marker cox1, we compare community composition captured between morphological and molecular-based approaches from different sources - tissue-based (bulk benthic and bulk drift samples) and environmental DNA (eDNA, filtered water) metabarcoding - for samples collected along a gradient of anthropogenic disturbances. For comparability, metabarcoding taxonomic assignments were filtered by taxa included in the standardised national biological metric IBMWP. At the family level, bulk benthic metabarcoding showed the highest congruence with morphology, and the most abundant taxa were captured by all techniques. Richness captured by morphology and bulk benthic metabarcoding decreased along the gradient, whereas richness recorded by eDNA remained constant and increased downstream when sequencing bulk drift. Estimates of biological metrics were higher using molecular than morphological identification. At species level, diversity captured by bulk benthic samples were higher than the other techniques. Importantly, bulk benthic and eDNA metabarcoding captured different and complementary portions of the community - benthic versus water column, respectively - and their combined use is recommended. While bulk benthic metabarcoding can likely replace morphology using similar benthic biological indices, water eDNA will require new metrics because this technique sequences a different portion of the community.}, }
@article {pmid38757413, year = {2024}, author = {Tiono, YV and Prasetyo, AH and Wulanjati, MP and Wink, M and Nurcahyanti, ADR}, title = {Inhibition of oxidative stress of Biancaea sappan (L) Tod. from Java.}, journal = {Natural product research}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/14786419.2024.2355585}, pmid = {38757413}, issn = {1478-6427}, abstract = {Increased reactive oxygen species and advanced glycation end products are often associated with human ageing and degenerative diseases. Biancaea sappan L serves as a medicinal plant and a healthy drinks ingredient in Java. However, the pharmacological investigation of the plant native to this island is still lacking in depth. In the current study, DNA barcoding using the marker gene maturase K (matK), evaluation of the chemical composition, total phenolic content (TPC) and antioxidant properties, antiglycation, anti-β-amyloid, anti-inflammatory, and selective cytotoxic activities were performed. B. sappan shares well-known phytoconstituents with other members of the genus Biancaea. The heartwood ethanol extract possesses the most prominent antioxidant, anti-inflammatory, and anti-β-amyloid effects. The aqueous extract demonstrated a most substantial anti-glycation activity and was rich in phenolics. The ethanol extract from heartwood exhibited the highest cytotoxicity against SW-48, indicating B. sappan heartwood from Java holds promise as antioxidants and may selectively inhibit colorectal cancer.}, }
@article {pmid38756345, year = {2024}, author = {Crabo, LG}, title = {A new noctuid genus and species (Lepidoptera, Noctuidae, Amphipyrinae, Psaphidini, Triocnemidina) from New Mexico and Texas, United States of America.}, journal = {ZooKeys}, volume = {1200}, number = {}, pages = {199-213}, pmid = {38756345}, issn = {1313-2989}, abstract = {Pooleagen. nov. is described for two noctuid species from southwestern United States: Pooleagrandimacula Barnes &amp; McDunnough, comb. nov., previously in Oxycnemis Grote, and Pooleapsaphidoidessp. nov.Poolea is compared to Oxycnemis (Amphipyrinae, Psaphidini, Triocnemidina) and is retained in the same subtribe. Adult moths and male and female genitalia of Poolea species are illustrated along with those of Oxycnemisadvena Grote, the genus type species. Pertinent recent taxonomic changes to Amphipyrinae classification are reviewed.}, }
@article {pmid38751964, year = {2024}, author = {Li, Z and Zhang, F}, title = {Two new species of the genus Cheiracanthium C. L. Koch, 1839 (Araneae, Cheiracanthiidae) from China.}, journal = {ZooKeys}, volume = {1200}, number = {}, pages = {145-157}, pmid = {38751964}, issn = {1313-2989}, abstract = {Two species of the long-legged sac spider genus Cheiracanthium C. L. Koch, 1839 collected from China are diagnosed and described as new to science: Cheiracanthiumbannaensissp. nov. (♂♀) from Yunnan Province and C.bifurcatumsp. nov. (♂♀) from Xinjiang Uyger Autonomous Region. Photos of the habitus and copulatory organs are given. In addition, DNA barcode information of the two new species is provided.}, }
@article {pmid38750233, year = {2024}, author = {Karras, P and Black, JRM and McGranahan, N and Marine, JC}, title = {Decoding the interplay between genetic and non-genetic drivers of metastasis.}, journal = {Nature}, volume = {629}, number = {8012}, pages = {543-554}, pmid = {38750233}, issn = {1476-4687}, mesh = {Animals ; Humans ; *Neoplasm Metastasis/drug therapy/genetics ; *Neoplasms/drug therapy/genetics/pathology ; Single-Cell Analysis ; Multiomics ; Molecular Typing ; Cellular Reprogramming ; }, abstract = {Metastasis is a multistep process by which cancer cells break away from their original location and spread to distant organs, and is responsible for the vast majority of cancer-related deaths. Preventing early metastatic dissemination would revolutionize the ability to fight cancer. Unfortunately, the relatively poor understanding of the molecular underpinnings of metastasis has hampered the development of effective anti-metastatic drugs. Although it is now accepted that disseminating tumour cells need to acquire multiple competencies to face the many obstacles they encounter before reaching their metastatic site(s), whether these competencies are acquired through an accumulation of metastasis-specific genetic alterations and/or non-genetic events is often debated. Here we review a growing body of literature highlighting the importance of both genetic and non-genetic reprogramming events during the metastatic cascade, and discuss how genetic and non-genetic processes act in concert to confer metastatic competencies. We also describe how recent technological advances, and in particular the advent of single-cell multi-omics and barcoding approaches, will help to better elucidate the cross-talk between genetic and non-genetic mechanisms of metastasis and ultimately inform innovative paths for the early detection and interception of this lethal process.}, }
@article {pmid38746545, year = {2024}, author = {Quattrini, AM and McCartin, LJ and Easton, EE and Horowitz, J and Wirshing, HH and Bowers, H and Mitchell, K and González-García, MDP and Sei, M and McFadden, CS and Herrera, S}, title = {Skimming genomes for systematics and DNA barcodes of corals.}, journal = {Ecology and evolution}, volume = {14}, number = {5}, pages = {e11254}, pmid = {38746545}, issn = {2045-7758}, abstract = {Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low-coverage genome sequencing) is a promising method to not only extract high-copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome-skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs and exons from the genome-skimming data and incorporated them with data from previously published target-capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low-cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens.}, }
@article {pmid38746196, year = {2024}, author = {Andriienko, V and Buczek, M and Meier, R and Srivathsan, A and Łukasik, P and Kolasa, MR}, title = {Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38746196}, issn = {2692-8205}, support = {R35 GM124701/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens.<br><br>METHODS: High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals.<br><br>RESULTS: We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species.<br><br>CONCLUSION: Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.}, }
@article {pmid38746155, year = {2024}, author = {Su, C and Chandradoss, KR and Malachowski, T and Boya, R and Ryu, HS and Brennand, KJ and Phillips-Cremins, JE}, title = {MASTR-seq: Multiplexed Analysis of Short Tandem Repeats with sequencing.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.04.29.591790}, pmid = {38746155}, issn = {2692-8205}, support = {R01 MH120269/MH/NIMH NIH HHS/United States ; DP1 MH129957/MH/NIMH NIH HHS/United States ; U01 DA052715/DA/NIDA NIH HHS/United States ; F31 NS129317/NS/NINDS NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; }, abstract = {UNLABELLED: More than 60 human disorders have been linked to unstable expansion of short tandem repeat (STR) tracts. STR length and the extent of DNA methylation is linked to disease pathology and can be mosaic in a cell type-specific manner in several repeat expansion disorders. Mosaic phenomenon have been difficult to study to date due to technical bias intrinsic to repeat sequences and the need for multi-modal measurements at single-allele resolution. Nanopore long-read sequencing accurately measures STR length and DNA methylation in the same single molecule but is cost prohibitive for studies assessing a target locus across multiple experimental conditions or patient samples. Here, we describe MASTR-seq, M ultiplexed A nalysis of S hort T andem R epeats, for cost-effective, high-throughput, accurate, multi-modal measurements of DNA methylation and STR genotype at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, and PCR-free multiplexed barcoding to achieve a >ten-fold increase in on-target read mapping for 8-12 pooled samples in a single MinION flow cell. We provide a detailed experimental protocol and computational tools and present evidence that MASTR-seq quantifies tract length and DNA methylation status for CGG and CAG STR loci in normal-length and mutation-length human cell lines. The MASTR-seq protocol takes approximately eight days for experiments and one additional day for data processing and analyses.<br><br>KEY POINTS: We provide a protocol for MASTR-seq: M ultiplexed A nalysis of S hort T andem R epeats using Cas9-mediated target enrichment and PCR-free, multiplexed nanopore sequencing. MASTR-seq achieves a >10-fold increase in on-target read proportion for highly repetitive, technically inaccessible regions of the genome relevant for human health and disease.MASTR-seq allows for high-throughput, efficient, accurate, and cost-effective measurement of STR length and DNA methylation in the same single allele for up to 8-12 samples in parallel in one Nanopore MinION flow cell.}, }
@article {pmid38744526, year = {2024}, author = {Dreyer, N and Olesen, J and Grygier, MJ and Eibye-Jacobsen, D and Savchenko, AS and Fujita, Y and Kolbasov, GA and Machida, RJ and Chan, BKK and Palero, F}, title = {Novel molecular resources for single-specimen barcoding of enigmatic crustacean y-larvae.}, journal = {Invertebrate systematics}, volume = {38}, number = {}, pages = {}, doi = {10.1071/IS23018}, pmid = {38744526}, issn = {1447-2600}, mesh = {Animals ; *Crustacea/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; Larva/genetics ; Phylogeny ; }, abstract = {Despite discovery more than 100years ago and documented global occurrence from shallow waters to the deep sea, the life cycle of the enigmatic crustacean y-larvae isincompletely understood and adult forms remain unknown. To date, only 2 of the 17 formally described species, all based on larval stages, have been investigated using an integrative taxonomic approach. This approach provided descriptions of the morphology of the naupliar and cyprid stages, and made use of exuvial voucher material and DNA barcodes. To improve our knowledge about the evolutionary history and ecological importance of y-larvae, we developed a novel protocol that maximises the amount of morpho-ecological and molecular data that can be harvested from single larval specimens. This includes single-specimen DNA barcoding and daily imaging of y-nauplii reared in culture dishes, mounting of the last naupliar exuviae on a slide as a reference voucher, live imaging of the y-cyprid instar that follows, and fixation, DNA extraction, amplification and sequencing of the y-cyprid specimen. Through development and testing of a suite of new primers for both nuclear and mitochondrial protein-coding and ribosomal genes, we showcase how new sequence data can be used to estimate the phylogeny of Facetotecta. We expect that our novel procedure will help to unravel the complex systematics of y-larvae and show how these fascinating larval forms have evolved. Moreover, we posit that our protocols should work on larval specimens from a diverse array of moulting marine invertebrate taxa.}, }
@article {pmid38742850, year = {2024}, author = {Neven, LG and Walker, WB and Gowton, C and Carrillo, J}, title = {Using eDNA to play whack-a-mole with invasive species in green yard waste.}, journal = {Journal of economic entomology}, volume = {117}, number = {3}, pages = {918-927}, doi = {10.1093/jee/toae090}, pmid = {38742850}, issn = {1938-291X}, support = {K2530//Washington State Department of Agriculture/ ; }, mesh = {*Introduced Species ; Animals ; *DNA, Environmental/analysis ; Washington ; Insecta/genetics ; British Columbia ; Waste Disposal Facilities ; DNA Barcoding, Taxonomic ; }, abstract = {As large cities begin to overrun their landfill capacities, they begin to look for alternative locations to handle the waste stream. Seeing an opportunity to bring in revenue, rural communities offer to handle municipal waste in their landfills. However, many rural communities are also places of agricultural production, which are vulnerable to attacks by invasive insect species, which could be present in green yard waste, the component of municipal waste most likely to contain agriculturally harmful insect species. We used environmental DNA (eDNA) to determine whether green yard waste could be a pathway for invasive insect species to enter and establish in the landfill-receiving agricultural community. We identified several target species that could be in green yard waste coming from Vancouver, BC, Canada, to Central Washington State, USA. We sampled green yard waste from 3 sites every 2 weeks from June to October in 2019 and 2020. DNA was extracted from the nearly 400 samples and subjected to amplification with COI barcoding primers followed by sequencing to identify target insects in the samples. Sequence analyses identified 3 species from the target list: 2 species that are pests of deciduous tree fruits and a generalist root-feeding crop pest. This eDNA technique was useful in identifying potential invasive species in green yard waste and may prove to be an important tool informing policy on the movement of biological material across borders and stemming the spread of invasive species.}, }
@article {pmid38742184, year = {2024}, author = {Tarkhnishvili, D and Seropian, A and Erhardt, C and Kachlishvili, N and Krammer, HJ and Hein, N}, title = {How dispersal rates depend on the prey capture strategy: A case study of Georgia's spiders.}, journal = {Ecology and evolution}, volume = {14}, number = {5}, pages = {e11372}, pmid = {38742184}, issn = {2045-7758}, abstract = {Large-scale barcoding projects help to aggregate information on genetic variability of multiple species throughout their ranges. Comparing DNA sequences of both non-conspecific and conspecific individuals from distant parts of their ranges helps to compare level of genetic isolation-by-distance patterns in different species and adaptive types. We compared mitochondrial CO1 gene sequences of 223 spiders from Georgia (Caucasus), representing 124 species and eight families, with 3097 homological sequences from spiders mostly from Europe, but also from other parts of the World. In most families, a significant isolation-by distance pattern was observed on family level. On species level, a significant isolation-by-distance was observed in 40 species, although this low proportion is most likely related to a lack of data. Simultaneously, remarkable differences in spatial structure were shown for different species. Although the majority of the studied species have a broad western Palearctic range, web-building spiders from families Araneidae, Theridiidae, and Linyphiidae are less isolated spatially than flower spiders (Thomisidae), jumping spiders (Salticidae), wolf spiders (Lycosidae), sac spiders (Clubionidae), and ground spiders (Gnaphosidae). This pattern is related with more common ballooning in web building than in actively hunting spiders, which commonly remain isolated since preglacial time. Ground spiders build the most isolated populations in the Caucasus.}, }
@article {pmid38741893, year = {2024}, author = {Musa, S and Hemberle, T and Bensch, S and Palinauskas, V and Baltrūnaitė, L and Woog, F and Mackenstedt, U}, title = {Raising the bar: genus-specific nested PCR improves detection and lineage identification of avian haemosporidian parasites.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1385599}, pmid = {38741893}, issn = {2235-2988}, mesh = {Animals ; *Haemosporida/genetics/isolation &amp; purification/classification ; *Polymerase Chain Reaction/methods ; *Protozoan Infections, Animal/diagnosis/parasitology ; Bird Diseases/parasitology/diagnosis ; Birds/parasitology ; Phylogeny ; Sensitivity and Specificity ; Passeriformes/parasitology ; DNA, Protozoan/genetics ; }, abstract = {Avian haemosporidian parasites are useful model organisms to study the ecology and evolution of parasite-host interactions due to their global distribution and extensive biodiversity. Detection of these parasites has evolved from microscopic examination to PCR-based methods, with the mitochondrial cytochrome b gene serving as barcoding region. However, standard PCR protocols used for screening and identification purposes have limitations in detecting mixed infections and generating phylogenetically informative data due to short amplicon lengths. To address these issues, we developed a novel genus-specific nested PCR protocol targeting avian haemosporidian parasites. The protocol underwent rigorous testing utilizing a large dataset comprising blood samples from Malagasy birds of three distinct Passeriformes families. Furthermore, validation was done by examining smaller datasets in two other laboratories employing divergent master mixes and different bird species. Comparative analyses were conducted between the outcomes of the novel PCR protocol and those obtained through the widely used standard nested PCR method. The novel protocol enables specific identification of Plasmodium, Haemoproteus (Parahaemoproteus), and Leucocytozoon parasites. The analyses demonstrated comparable sensitivity to the standard nested PCR with notable improvements in detecting mixed infections. In addition, phylogenetic resolution is improved by amplification of longer fragments, leading to a better understanding of the haemosporidian biodiversity and evolution. Overall, the novel protocol represents a valuable addition to avian haemosporidian detection methodologies, facilitating comprehensive studies on parasite ecology, epidemiology, and evolution.}, }
@article {pmid38740284, year = {2024}, author = {Qin, T and Hernandez, SER and Shiers, J and Crittall, M and Novak, A and Smith, CS}, title = {A decentralized solid compound storage facility managed by a centralized electronic platform at a growing drug discovery company.}, journal = {SLAS technology}, volume = {29}, number = {3}, pages = {100143}, doi = {10.1016/j.slast.2024.100143}, pmid = {38740284}, issn = {2472-6311}, mesh = {*Drug Discovery ; *Drug Storage ; Drug Industry ; }, abstract = {Within a growing drug discovery company, scientists acquire (either through in house synthesis or purchase) then store, retrieve, and ship solid compound samples daily between multiple locations. The efficient management and tracking of this entire process to support drug discovery is a significant challenge. This article describes a decentralized and cost-effective inventory facility that simplifies the solid compound storage and retrieval process. Standardized storage cabinets from the market are utilized, providing a cost-effective physical infrastructure. The cabinets can be distributed across storage rooms at multiple sites and arranged into spaces with a variety of dimensions, allowing the system to be retrofitted into existing facilities and scaled up easily. We can provide storage close to work areas at each location, minimizing both unnecessary movement of staff and transportation of substances. We have applied a systematic barcoding method to the compound batch identifier that correlates with its compound location. This simplifies the compound registration process as well as the process of finding and returning compounds. Additionally, a centralized electronic platform has been employed to store, update and track solid compound information, such as properties, location and quantity. Compound shipment may be initiated from different sites, and a centralized electronic platform assists the information retrieval process, ensuring each location possesses up-to-date information. The electronic platform we present streamlines the management of compound registration, location tracking, weight updates and shipment information, facilitating seamless record sharing among all stakeholders. Every step of the process can be tracked in real time by the project team. The platform can be flexibly configured to adapt to an evolving set of storage locations, with all information and processes being audited.}, }
@article {pmid38739854, year = {2024}, author = {Dos Santos, EL and Xavier, JKAM and Galvão, PLN and Carneiro Nunes, AR and Alegria, OVC and Moreira, ECO and Maia, JGS and Setzer, WN and Figueiredo, PLB and da Silva, JKR}, title = {Volatile Profiles and DNA Barcodes of Myrtaceae Species with Occurrence in the Brazilian Amazon.}, journal = {Chemistry &amp; biodiversity}, volume = {21}, number = {7}, pages = {e202400388}, doi = {10.1002/cbdv.202400388}, pmid = {38739854}, issn = {1612-1880}, support = {//Aromatic Plant Research Center/ ; }, mesh = {*DNA Barcoding, Taxonomic ; Brazil ; *Oils, Volatile/chemistry ; *Myrtaceae/chemistry/genetics ; Plant Leaves/chemistry ; DNA, Plant/genetics ; }, abstract = {Myrtaceae family includes many species with taxonomic challenges, making it one of the most complex families to identify. This study used DNA barcoding to find molecular markers for species authentication based on the Myrtaceae family's chemical composition and genetic diversity. Essential oils and genetic material were extracted from the leaves of six different species: Eugenia uniflora, E. patrisii, Myrcia splendens, Psidium guajava, P. guineense, and Psidium sp. The samples were analyzed based on compound classes and grouped into two categories. Group I included samples with high amounts of oxygenated sesquiterpenes (3.69-76.05 %) and fatty acid derivatives (0.04-43.59 %), such as E. uniflora, Myrcia splendens, and E. patrisii. Group II included samples P. guajava, P. guineense, and Psidium sp., which had a significant content of monoterpene hydrocarbons (0.69-72.35 %), oxygenated sesquiterpenes (8.06-68.1 %), phenylpropanoids (0.45-22.59 %), and sesquiterpene hydrocarbons (0.27-21.84 %). The PsbA-trnH gene sequences had a high genetic variability, allowing the species to be distinguished. A phylogenetic analysis showed two main clusters with high Bootstrap values corresponding to the subtribes Eugeniineae, Myrciinae, and Pimentinae. The results suggest a weak correlation between genetic and chemical data in these Myrtaceae species.}, }
@article {pmid38737823, year = {2024}, author = {Wang, T and Shen, H and Xu, B and Yang, W and Chen, S and Chen, J}, title = {Genome Analysis of Plasmodium falciparum: A Preliminary Observation - Sierra Leone, 2022-2023.}, journal = {China CDC weekly}, volume = {6}, number = {17}, pages = {368-373}, pmid = {38737823}, issn = {2096-7071}, abstract = {Sierra Leone, with a gross domestic product (GDP) per capita below $300 and significant poverty, ranks among the world's least developed countries (LDCs). Despite its modest population of 8.6 million, the nation reports approximately 2.6 million malaria cases annually. Previously, there has been no reporting on the malaria genome data from this country.<br><br>WHAT IS ADDED BY THIS REPORT?: In this study, we present the first reported whole-genome sequence analysis of 19 high parasite-density Plasmodium falciparum isolates from Sierra Leone, providing insights into the genomic epidemiology of this high-prevalence area. We found a high degree of relatedness among infections and substantial genetic diversity, consistent with the gradual reduction in overall case numbers. Moreover, our whole-genome analysis revealed that, beyond drug-resistance genes, gene families related to blood cell invasion, immune evasion, and others are undergoing directional selection. This suggests that the population in Sierra Leone has developed a relatively strong acquired immunity.<br><br>The genomic data not only facilitate the creation of single nucleotide polymorphism barcodes for case tracking but also enable the analysis of evolving transmission dynamics and selection pressures. Additionally, the samples from Sierra Leone exhibited higher selective pressures on resistance genes compared to those from Asia, a trend not commonly observed in other African samples. This suggests that less stringent healthcare systems and inconsistent treatment strategies can subject parasites to increased drug pressure, thereby accelerating the development of resistant strains.}, }
@article {pmid38734639, year = {2024}, author = {Bušić, N and Klobučar, A and Landeka, N and Žitko, T and Vignjević, G and Turić, N and Sudarić Bogojević, M and Merdić, E and Kučinić, M and Bruvo Mađarić, B}, title = {A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species.}, journal = {Parasites &amp; vectors}, volume = {17}, number = {1}, pages = {216}, pmid = {38734639}, issn = {1756-3305}, support = {IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; IP-2016-06-9988//Croatian Science Foundation/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; ZUP-2018-55, 3105-5//Josip Juraj Strossmayer University of Osijek/ ; }, mesh = {*Culicidae/anatomy &amp; histology/classification/genetics ; Mosquito Vectors/anatomy &amp; histology/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; Cyclooxygenase 1/genetics ; DNA, Ribosomal Spacer/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Mosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.<br><br>METHODS: Sampling was carried out in three biogeographical regions of Croatia over six years (2017-2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.<br><br>RESULTS: A total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.<br><br>CONCLUSION: We present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.}, }
@article {pmid38734030, year = {2024}, author = {Stanley, S and Spaulding, CN and Liu, Q and Chase, MR and Ha, DTM and Thai, PVK and Lan, NH and Thu, DDA and Quang, NL and Brown, J and Hicks, ND and Wang, X and Marin, M and Howard, NC and Vickers, AJ and Karpinski, WM and Chao, MC and Farhat, MR and Caws, M and Dunstan, SJ and Thuong, NTT and Fortune, SM}, title = {Identification of bacterial determinants of tuberculosis infection and treatment outcomes: a phenogenomic analysis of clinical strains.}, journal = {The Lancet. Microbe}, volume = {5}, number = {6}, pages = {e570-e580}, pmid = {38734030}, issn = {2666-5247}, support = {75N93019C00071/AI/NIAID NIH HHS/United States ; T32 AI049928/AI/NIAID NIH HHS/United States ; T32 AI007535/AI/NIAID NIH HHS/United States ; T32 GM135014/GM/NIGMS NIH HHS/United States ; U19 AI142793/AI/NIAID NIH HHS/United States ; P01 AI132130/AI/NIAID NIH HHS/United States ; P01 AI143575/AI/NIAID NIH HHS/United States ; T32 HD040128/HD/NICHD NIH HHS/United States ; U19 AI107774/AI/NIAID NIH HHS/United States ; T32 AI132120/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/drug effects ; *Tuberculosis/drug therapy/microbiology ; Vietnam/epidemiology ; *Antitubercular Agents/therapeutic use/pharmacology ; Genome-Wide Association Study ; Treatment Outcome ; Phenotype ; Phylogeny ; Mutation ; Phenomics ; Genotype ; Female ; Adult ; Male ; }, abstract = {BACKGROUND: Bacterial diversity could contribute to the diversity of tuberculosis infection and treatment outcomes observed clinically, but the biological basis of this association is poorly understood. The aim of this study was to identify associations between phenogenomic variation in Mycobacterium tuberculosis and tuberculosis clinical features.<br><br>METHODS: We developed a high-throughput platform to define phenotype-genotype relationships in M tuberculosis clinical isolates, which we tested on a set of 158 drug-sensitive M tuberculosis strains sampled from a large tuberculosis clinical study in Ho Chi Minh City, Viet Nam. We tagged the strains with unique genetic barcodes in multiplicate, allowing us to pool the strains for in-vitro competitive fitness assays across 16 host-relevant antibiotic and metabolic conditions. Relative fitness was quantified by deep sequencing, enumerating output barcode read counts relative to input normalised values. We performed a genome-wide association study to identify phylogenetically linked and monogenic mutations associated with the in-vitro fitness phenotypes. These genetic determinants were further associated with relevant clinical outcomes (cavitary disease and treatment failure) by calculating odds ratios (ORs) with binomial logistic regressions. We also assessed the population-level transmission of strains associated with cavitary disease and treatment failure using terminal branch length analysis of the phylogenetic data.<br><br>FINDINGS: M tuberculosis clinical strains had diverse growth characteristics in host-like metabolic and drug conditions. These fitness phenotypes were highly heritable, and we identified monogenic and phylogenetically linked variants associated with the fitness phenotypes. These data enabled us to define two genetic features that were associated with clinical outcomes. First, mutations in Rv1339, a phosphodiesterase, which were associated with slow growth in glycerol, were further associated with treatment failure (OR 5&#xb7;34, 95% CI 1&#xb7;21-23&#xb7;58, p=0&#xb7;027). Second, we identified a phenotypically distinct slow-growing subclade of lineage 1 strains (L1.1.1.1) that was associated with cavitary disease (OR 2&#xb7;49, 1&#xb7;11-5&#xb7;59, p=0&#xb7;027) and treatment failure (OR 4&#xb7;76, 1&#xb7;53-14&#xb7;78, p=0&#xb7;0069), and which had shorter terminal branch lengths on the phylogenetic tree, suggesting increased transmission.<br><br>INTERPRETATION: Slow growth under various antibiotic and metabolic conditions served as in-vitro intermediate phenotypes underlying the association between M tuberculosis monogenic and phylogenetically linked mutations and outcomes such as cavitary disease, treatment failure, and transmission potential. These data suggest that M&#xa0;tuberculosis growth regulation is an adaptive advantage for bacterial success in human populations, at least in some circumstances. These data further suggest markers for the underlying bacterial processes that contribute to these clinical outcomes.<br><br>FUNDING: National Health and Medical Research Council/A&#x2217;STAR, National Institutes of Allergy and Infectious Diseases, National Institute of Child Health and Human Development, and the Wellcome Trust Fellowship in Public Health and Tropical Medicine.}, }
@article {pmid38732467, year = {2024}, author = {Kim, JH and Doh, EJ and Kim, HY and Lee, G}, title = {Chemical Relationship among Genetically Authenticated Medicinal Species of Genus Angelica.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {38732467}, issn = {2223-7747}, support = {NRF-2021R1A2C1095558//the National Research Foundation of Korea/ ; }, abstract = {The genus Angelica comprises various species utilized for diverse medicinal purposes, with differences attributed to the varying levels or types of inherent chemical components in each species. This study employed DNA barcode analysis and HPLC analysis to genetically authenticate and chemically classify eight medicinal Angelica species (n = 106) as well as two non-medicinal species (n = 14) that have been misused. Nucleotide sequence analysis of the nuclear internal transcribed spacer (ITS) region revealed differences ranging from 11 to 117 bp, while psbA-trnH showed variances of 3 to 95 bp, respectively. Phylogenetic analysis grouped all samples except Angelica sinensis into the same cluster, with some counterfeits forming separate clusters. Verification using the NCBI database confirmed the feasibility of species identification. For chemical identification, a robust quantitative HPLC analysis method was developed for 46 marker compounds. Subsequently, two A. reflexa-specific and seven A. biserrata-specific marker compounds were identified, alongside non-specific markers. Moreover, chemometric clustering analysis reflecting differences in chemical content between species revealed that most samples formed distinct clusters according to the plant species. However, some samples formed mixed clusters containing different species. These findings offer crucial insights for the standardization and quality control of medicinal Angelica species.}, }
@article {pmid38731365, year = {2024}, author = {Ricardo, F and Lopes, ML and Mamede, R and Domingues, MR and Ferreira da Silva, E and Patinha, C and Calado, R}, title = {Combined Use of Fatty Acid Profiles and Elemental Fingerprints to Trace the Geographic Origin of Live Baits for Sports Fishing: The Solitary Tube Worm (Diopatra neapolitana, Annelida, Onuphidae) as a Case Study.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {9}, pages = {}, pmid = {38731365}, issn = {2076-2615}, support = {TC-C10-i01//Desenvolvimento do Projeto de Refor&#xe7;o do Polo de Aveiro (H4)", framed within Measure 10 of Investment TC-C10-i01 - Hub Azul - Rede de Infraestruturas para a Economia Azul, financed by the Recovery and Resilience Plan (PRR) and supported by Fundo Azul of t/ ; + UIDB/50017/2020+ LA/P/0094/2020 + UIDB/50006/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Diopatra neapolitana Delle Chiaje, 1841 (Annelida, Onuphidae) is one of the most exploited polychaete species in European waters, particularly in Ria de Aveiro, a coastal lagoon in mainland Portugal, where the overexploitation of this resource has led to a generalized decline of local populations. In an attempt to reduce the impact of harvesting, several management actions were implemented, but illegal poaching still fuels a parallel economy that threatens the sustainable use of this marine resource. The present study evaluated the combination of fatty acid profiles and elemental fingerprints of the whole body and jaws, respectively, of D. neapolitana collected from four harvesting locations within Ria de Aveiro in order to determine if their geographic origin could be correctly assigned post-harvesting. Results showed that both fatty acid profiles and elemental fingerprints differ significantly among locations, discriminating the geographic origin with higher accuracy when combining these two natural barcodes than when employing each individually. The present work can, therefore, contribute to the implementation of an effective management plan for the sustainable use of this marine resource, making it possible to detect if D. neapolitana was sourced from no-take zones and if it was collected from the place of origin claimed by live bait traders.}, }
@article {pmid38729950, year = {2024}, author = {Cheng, C and Wang, G and Zhu, Y and Wu, H and Zhang, L and Liu, Z and Huang, Y and Zhang, J}, title = {Multiplexed bulk and single-cell RNA-seq hybrid enables cost-efficient disease modeling with chimeric organoids.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3946}, pmid = {38729950}, issn = {2041-1723}, support = {31871453//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Organoids/metabolism ; *Single-Cell Analysis/methods ; *Induced Pluripotent Stem Cells/metabolism/cytology ; Humans ; *Cell Differentiation/genetics ; *RNA-Seq/methods ; Sequence Analysis, RNA/methods ; Macrophages/metabolism/cytology ; Animals ; Single-Cell Gene Expression Analysis ; }, abstract = {Disease modeling with isogenic Induced Pluripotent Stem Cell (iPSC)-differentiated organoids serves as a powerful technique for studying disease mechanisms. Multiplexed coculture is crucial to mitigate batch effects when studying the genetic effects of disease-causing variants in differentiated iPSCs or organoids, and demultiplexing at the single-cell level can be conveniently achieved by assessing natural genetic barcodes. Here, to enable cost-efficient time-series experimental designs via multiplexed bulk and single-cell RNA-seq of hybrids, we introduce a computational method in our Vireo Suite, Vireo-bulk, to effectively deconvolve pooled bulk RNA-seq data by genotype reference, and thereby quantify donor abundance over the course of differentiation and identify differentially expressed genes among donors. Furthermore, with multiplexed scRNA-seq and bulk RNA-seq, we demonstrate the usefulness and necessity of a pooled design to reveal donor iPSC line heterogeneity during macrophage cell differentiation and to model rare WT1 mutation-driven kidney disease with chimeric organoids. Our work provides an experimental and analytic pipeline for dissecting disease mechanisms with chimeric organoids.}, }
@article {pmid38729384, year = {2024}, author = {Dufresnes, C and Ghielmi, S and Halpern, B and Martínez-Freiría, F and Mebert, K and Jelić, D and Crnobrnja-Isailović, J and Gippner, S and Jablonski, D and Joger, U and Laddaga, L and Petrovan, S and Tomović, L and Vörös, J and İğci, N and Kariş, M and Zinenko, O and Ursenbacher, S}, title = {Phylogenomic insights into the diversity and evolution of Palearctic vipers.}, journal = {Molecular phylogenetics and evolution}, volume = {197}, number = {}, pages = {108095}, doi = {10.1016/j.ympev.2024.108095}, pmid = {38729384}, issn = {1095-9513}, mesh = {*Phylogeny ; Animals ; *Viperidae/genetics/classification ; Genetic Variation ; Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; }, abstract = {Despite decades of molecular research, phylogenetic relationships in Palearctic vipers (genus Vipera) still essentially rely on a few loci, such as mitochondrial barcoding genes. Here we examined the diversity and evolution of Vipera with ddRAD-seq data from 33 representative species and subspecies. Phylogenomic analyses of ∼ 1.1 Mb recovered nine major clades corresponding to known species/species complexes which are generally consistent with the mitochondrial phylogeny, albeit with a few deep discrepancies that highlight past hybridization events. The most spectacular case is the Italian-endemic V. walser, which is grouped with the alpine genetic diversity of V. berus in the nuclear tree despite carrying a divergent mitogenome related to the Caucasian V. kaznakovi complex. Clustering analyses of SNPs suggest potential admixture between diverged Iberian taxa (V. aspis zinnikeri and V. seoanei), and confirm that the Anatolian V. pontica corresponds to occasional hybrids between V. (ammodytes) meridionalis and V. kaznakovi. Finally, all analyzed lineages of the V. berus complex (including V. walser and V. barani) form vast areas of admixture and may be delimited as subspecies. Our study sets grounds for future taxonomic and phylogeographic surveys on Palearctic vipers, a group of prime interest for toxinological, ecological, biogeographic and conservation research.}, }
@article {pmid38728918, year = {2024}, author = {Luo, Y and Yang, H and Tao, G}, title = {Systematic review on fingerprinting development to determine adulteration of Chinese herbal medicines.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {129}, number = {}, pages = {155667}, doi = {10.1016/j.phymed.2024.155667}, pmid = {38728918}, issn = {1618-095X}, mesh = {*Drugs, Chinese Herbal/chemistry/analysis ; *Drug Contamination ; *Quality Control ; Chromatography, High Pressure Liquid/methods ; DNA Barcoding, Taxonomic ; }, abstract = {BACKGROUND: It has been a current research hospots using fingerprinting technology for quality control of Chinese herbal medicines (CHMs), which provides a scientific basis for establishment of overall quality control in accordance with the characteristics of CHMs. The fingerprinting technology for CHMs is diverse, and the research field covers many disciplines, such as analytical chemistry, pharmacology, pharmaceutics, biochemistry, and molecular biology.<br><br>PURPOSE: To effectively understand the key areas and future directions of research regarding the fingerprint and adulteration of CHMs.<br><br>METHODS/RESULTS: this paper analyzed 879 articles in this field in the Web of Science Core Collection from 2000 to 2023 with CiteSpace and VOSviewer, and systematically assessed the research process, hotspots, topic distribution among disciplines, etc. The most prominent contributors of fingerprint and adulteration of CHMs research are mainly from China, India, the United States, England, and Brazil. The knowledge domains of fingerprint and adulteration of CHMs research focus mainly on the topics of molecular authentication, DNA barcoding, HPLC, near-infrared spectroscopy, manage data, chemometrics, and electrochemical fingerprinting. Most countries have recognized the pharmaceutical potential of natural products, and have paid more attention to the fingerprint and adulteration of CHMs in the past decade. Future the research tends to focus more on molecular identification and authentication, and electrochemical and chromatographic fingerprinting in controlling the adulteration of CHMs.<br><br>CONCLUSION: This research provides a valuable reference for scholars in related fields to analyze existing research results, understand the development trend, and explore new research directions.}, }
@article {pmid38727924, year = {2024}, author = {Niu, J and Wang, X and Zhou, S and Yue, J and Liu, Z and Zhou, J}, title = {Molecular authentication of commercial "Qian-hu" through the integration of nrDNA internal transcribed spacer 2 and nucleotide signature.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {639}, pmid = {38727924}, issn = {1573-4978}, support = {202205AM070006//Gaoligong Mountain, Forest Ecosystem, Observation and Research Station of Yunnan Province/ ; 31960048//National Natural Science Foundation of China/ ; YNWRQNBJ-2019-208//Ten Thousand Talents Program of Yunnan/ ; 202201AT070118//Department of Science and Technology of Yunnan Province/ ; }, mesh = {*DNA, Plant/genetics ; *DNA Barcoding, Taxonomic/methods ; Drugs, Chinese Herbal/standards ; Apiaceae/genetics/classification ; Medicine, Chinese Traditional/standards ; DNA, Ribosomal Spacer/genetics ; Drug Contamination ; Plants, Medicinal/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Polymerase Chain Reaction/methods ; Nucleotides/genetics/analysis ; }, abstract = {BACKGROUND: Peucedani Radix, also known as "Qian-hu" is a traditional Chinese medicine derived from Peucedanum praeruptorum Dunn. It is widely utilized for treating wind-heat colds and coughs accompanied by excessive phlegm. However, due to morphological similarities, limited resources, and heightened market demand, numerous substitutes and adulterants of Peucedani Radix have emerged within the herbal medicine market. Moreover, Peucedani Radix is typically dried and sliced for sale, rendering traditional identification methods challenging.<br><br>MATERIALS AND METHODS: We initially examined and compared 104 commercial "Qian-hu" samples from various Chinese medicinal markets and 44 species representing genuine, adulterants or substitutes, utilizing the mini barcode ITS2 region to elucidate the botanical origins of the commercial "Qian-hu". The nucleotide signature specific to Peucedani Radix was subsequently developed by analyzing the polymorphic sites within the aligned ITS2 sequences.<br><br>RESULTS: The results demonstrated a success rate of 100% and 93.3% for DNA extraction and PCR amplification, respectively. Forty-five samples were authentic "Qian-hu", while the remaining samples were all adulterants, originating from nine distinct species. Peucedani Radix, its substitutes, and adulterants were successfully identified based on the neighbor-joining tree. The 24-bp nucleotide signature (5'-ATTGTCGTACGAATCCTCGTCGTC-3') revealed distinct differences between Peucedani Radix and its common substitutes and adulterants. The newly designed specific primers (PR-F/PR-R) can amplify the nucleotide signature region from commercial samples and processed materials with severe DNA degradation.<br><br>CONCLUSIONS: We advocate for the utilization of ITS2 and nucleotide signature for the rapid and precise identification of herbal medicines and their adulterants to regulate the Chinese herbal medicine industry.}, }
@article {pmid38722810, year = {2024}, author = {Marshall, WF and Fung, JC}, title = {Modeling homologous chromosome recognition via nonspecific interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {20}, pages = {e2317373121}, pmid = {38722810}, issn = {1091-6490}, support = {R01 GM137126/GM/NIGMS NIH HHS/United States ; R35 GM130327/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Models, Genetic ; Chromosome Pairing ; Drosophila melanogaster/genetics ; Chromosomes ; Drosophila/genetics ; Computer Simulation ; Chromosomes, Insect/genetics/metabolism ; }, abstract = {In many organisms, most notably Drosophila, homologous chromosomes associate in somatic cells, a phenomenon known as somatic pairing, which takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a "specific button" model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, mediated by different proteins that bind to these different regions. Here, we use computational modeling to evaluate an alternative "button barcode" model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. In this model, buttons are nonuniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a nonhomolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. By simulating randomly generated nonuniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.}, }
@article {pmid38721629, year = {2024}, author = {Waki, T and Kumagai, T and Nishino, Y}, title = {Identification of Lepidapedon oregonense as the current world's deepest trematode.}, journal = {Journal of helminthology}, volume = {98}, number = {}, pages = {e38}, doi = {10.1017/S0022149X24000269}, pmid = {38721629}, issn = {1475-2697}, mesh = {Animals ; *Trematoda/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 28S/genetics ; *Phylogeny ; *DNA, Helminth/genetics ; *DNA, Ribosomal/genetics ; Gastropoda/parasitology ; Sequence Analysis, DNA ; Fishes/parasitology ; Fish Diseases/parasitology ; Trematode Infections/parasitology/veterinary ; }, abstract = {The deepest recorded depth for trematodes currently stands at approximately 6200 m. This depth record was achieved solely through sequence datasets of Lepidapedon sp. obtained from a gastropod. Given that trematodes of this genus typically use fish as definitive hosts, the origin of the trematode sequence was thought to be larval stages. However, the specific species remained unclear owing to the absence of reported adult-stage sequences. In the present study, we definitively identified the deepest trematode as Lepidapedon oregonense by comparing 28S ribosomal DNA sequences from adult worms from the macrourid fish Coelorinchus gilberti with data from the gastropod in the previous study.}, }
@article {pmid38718049, year = {2024}, author = {Lokken-Toyli, KL and Aggarwal, SD and Bee, GCW and de Steenhuijsen Piters, WAA and Wu, C and Chen, KZM and Loomis, C and Bogaert, D and Weiser, JN}, title = {Impaired upper respiratory tract barrier function during postnatal development predisposes to invasive pneumococcal disease.}, journal = {PLoS pathogens}, volume = {20}, number = {5}, pages = {e1012111}, pmid = {38718049}, issn = {1553-7374}, mesh = {Animals ; *Pneumococcal Infections/microbiology/immunology ; Mice ; *Streptococcus pneumoniae ; Humans ; Animals, Newborn ; Disease Models, Animal ; Mice, Inbred C57BL ; Respiratory Mucosa/microbiology/metabolism ; Female ; Nasopharynx/microbiology ; }, abstract = {Infants are highly susceptible to invasive respiratory and gastrointestinal infections. To elucidate the age-dependent mechanism(s) that drive bacterial spread from the mucosa, we developed an infant mouse model using the prevalent pediatric respiratory pathogen, Streptococcus pneumoniae (Spn). Despite similar upper respiratory tract (URT) colonization levels, the survival rate of Spn-infected infant mice was significantly decreased compared to adults and corresponded with Spn dissemination to the bloodstream. An increased rate of pneumococcal bacteremia in early life beyond the newborn period was attributed to increased bacterial translocation across the URT barrier. Bacterial dissemination in infant mice was independent of URT monocyte or neutrophil infiltration, phagocyte-derived ROS or RNS, inflammation mediated by toll-like receptor 2 or interleukin 1 receptor signaling, or the pore-forming toxin pneumolysin. Using molecular barcoding of Spn, we found that only a minority of bacterial clones in the nasopharynx disseminated to the blood in infant mice, indicating the absence of robust URT barrier breakdown. Rather, transcriptional profiling of the URT epithelium revealed a failure of infant mice to upregulate genes involved in the tight junction pathway. Expression of many such genes was also decreased in early life in humans. Infant mice also showed increased URT barrier permeability and delayed mucociliary clearance during the first two weeks of life, which corresponded with tighter attachment of bacteria to the respiratory epithelium. Together, these results demonstrate a window of vulnerability during postnatal development when altered mucosal barrier function facilitates bacterial dissemination.}, }
@article {pmid38715571, year = {2024}, author = {Murwani, R and Anggraeni, R and Setiawan, GNA and Astari, PD and Cahyani, NKD and Sibero, MT and Ambariyanto, A}, title = {Lactic Acid Bacteria Isolates and the Microbiome of Cincalok, Tempoyak, and Mandai: A Traditional Fermented Food from Kalimantan Island, Indonesia.}, journal = {International journal of food science}, volume = {2024}, number = {}, pages = {6589766}, pmid = {38715571}, issn = {2314-5765}, abstract = {Indonesia has abundant traditional fermented food with various lactic acid bacteria (LAB), which can be developed into probiotics for pharmaceutical and functional food and feed products. This research is aimed at (1) obtaining and identifying LAB isolates and (2) studying the microbiome (bacterial diversity and abundance) of spontaneously-fermented traditional foods of Kalimantan Island, Cincalok, Tempoyak, and Mandai. To obtain LAB isolates, food samples were serially diluted and inoculated on MRS agar that contained 1% CaCO3 (MRSA). Isolates forming clear zones were purified and identified by DNA barcoding. The microbiome was studied using genomic-sequencing techniques and analysed for taxonomic composition. Seven pure isolates were obtained from Cincalok, two Tempoyak, and one Mandai. DNA barcoding revealed that the Cincalok seven isolates were Staphylococcus carnosus (strain HSP-S16), Tetragenococcus halophilus (FSB201), Corynebacterium phoceense, Vagococcus vulneris (SS1995), Enterococcus faecalis (S11-6), Pisciglobus halotolerans (C01), and Priestia filamentosa (P3.1); two from Tempoyak, Levilactobacillus brevis (E1D3BL1) and Lactiplantibacillus plantarum (UMCC-2996); and one from Mandai, Staphylococcus cohnii (XAAS.x13; non-LAB). The T. halophilus, E. faecalis, P. halotolerans, L. brevis, and L. plantarum belong to LAB. The P. halotolerans from Cincalok and non-LAB in these three fermented foods were the first documented report. The microbiome revealed the dominance of Firmicutes phyla in the fermented foods, with 93% in Cincalok, 89.94% in Tempoyak, and 60.32% in Mandai. On the genus level, Cincalok was dominated by Tetragenococcus 40.33%, Anaerococcus 23.29%, Vagococcus 9.27%, and Lactobacillus 6.84%. Meanwhile, Tempoyak was dominated only by Lactobacillus 89.94%. Mandai were dominated by Lactobacillus 31.97%, Proteus 17.14%, Aerococcus 16.85%, Mangrovibacter 15.15%, and Vagococcus 6.2%. However, Mandai's microbiome LAB was not culturable/isolated on MRSA. The plausibility is that those unculturable LAB require coculturing with other bacteria and additional media components to grow on MRSA. This study is the first report regarding the microbiome of Cincalok, Tempoyak, and Mandai, along with their culturable LAB isolates.}, }
@article {pmid38714853, year = {2024}, author = {Lindenhofer, D and Haendeler, S and Esk, C and Littleboy, JB and Brunet Avalos, C and Naas, J and Pflug, FG and van de Ven, EGP and Reumann, D and Baffet, AD and von Haeseler, A and Knoblich, JA}, title = {Cerebral organoids display dynamic clonal growth and tunable tissue replenishment.}, journal = {Nature cell biology}, volume = {26}, number = {5}, pages = {710-718}, pmid = {38714853}, issn = {1476-4679}, support = {DOC 72/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Organoids/cytology/metabolism ; Humans ; *Cell Lineage ; *Neural Stem Cells/metabolism/cytology ; Brain/cytology/growth &amp; development/metabolism ; Cell Differentiation ; Cell Proliferation ; Clone Cells ; Neurogenesis/genetics ; DNA Barcoding, Taxonomic ; Animals ; }, abstract = {During brain development, neural progenitors expand through symmetric divisions before giving rise to differentiating cell types via asymmetric divisions. Transition between those modes varies among individual neural stem cells, resulting in clones of different sizes. Imaging-based lineage tracing allows for lineage analysis at high cellular resolution but systematic approaches to analyse clonal behaviour of entire tissues are currently lacking. Here we implement whole-tissue lineage tracing by genomic DNA barcoding in 3D human cerebral organoids, to show that individual stem cell clones produce progeny on a vastly variable scale. By using stochastic modelling we find that variable lineage sizes arise because a subpopulation of lineages retains symmetrically dividing cells. We show that lineage sizes can adjust to tissue demands after growth perturbation via chemical ablation or genetic restriction of a subset of cells in chimeric organoids. Our data suggest that adaptive plasticity of stem cell populations ensures robustness of development in human brain organoids.}, }
@article {pmid38714828, year = {2024}, author = {Sipiczki, M and Czentye, K and Kállai, Z}, title = {High intragenomic, intergenomic, and phenotypic diversity in pulcherrimin-producing Metschnikowia yeasts indicates a special mode of genome evolution.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10521}, pmid = {38714828}, issn = {2045-2322}, mesh = {*Metschnikowia/genetics ; *Genome, Fungal ; *Evolution, Molecular ; *Phylogeny ; Genetic Variation ; Phenotype ; DNA, Mitochondrial/genetics ; }, abstract = {In molecular systematics, the delimitation of yeast species is based on the notion that the barcode differences are smaller within species than between them. The most widely used barcodes are segments of the chromosomal repeats coding for ribosomal RNAs that are homogenised in yeasts. The analysis of these segments of the type strains of ten species recently merged in Metschnikowia pulcherrima and 37 new isolates demonstrated that this is not the case in this species. The intragenomic diversity significantly exceeded the threshold gaps used to differentiate related yeast species. Large segments of the D1/D2 domains were not diverse within the genomes and could therefore be used to determine the taxonomic affiliation of the isolates. The genome structures of the isolates were compared by RAPD and the RFLP of the mitochondrial DNA. Both patterns were highly heterogeneous. The sequence analysis of the PUL4 gene (a member of the PUL gene cluster involved in pulcherrimin production) revealed very high intragenomic differences, suggesting that the genomes may be chimerised. Three phenotypic traits related to the antimicrobial antagonism characteristic of the species were also highly diverse and prone to reversible segregation resembling epigenetic processes (silencing and reactivation of regulators) rather than mutations and back-mutations. These features make M. pulcherrima unique among yeasts and indicate that it evolves in a non-standard way.}, }
@article {pmid38712508, year = {2024}, author = {Voorspoels, A and Gevers, J and Santermans, S and Akkan, N and Martens, K and Willems, K and Van Dorpe, P and Verhulst, AS}, title = {Design Principles of DNA-Barcodes for Nanopore-FET Readout, Based on Molecular Dynamics and TCAD Simulations.}, journal = {The journal of physical chemistry. A}, volume = {128}, number = {19}, pages = {3926-3933}, doi = {10.1021/acs.jpca.4c01772}, pmid = {38712508}, issn = {1520-5215}, mesh = {*Molecular Dynamics Simulation ; *DNA/chemistry ; *Nanopores ; *Transistors, Electronic ; }, abstract = {Nanopore field-effect transistor (NP-FET) devices hold great promise as sensitive single-molecule sensors, which provide CMOS-based on-chip readout and are also highly amenable to parallelization. A plethora of applications will therefore benefit from NP-FET technology, such as large-scale molecular analysis (e.g., proteomics). Due to its potential for parallelization, the NP-FET looks particularly well-suited for the high-throughput readout of DNA-based barcodes. However, to date, no study exists that unravels the bit-rate capabilities of NP-FET devices. In this paper, we design DNA-based barcodes by labeling a piece of double-stranded DNA with dumbbell-like DNA structures. We explore the impact of both the size of the dumbbells and their spacing on achievable bit-rates. The conformational fluctuations of this DNA-origami, as observed by molecular dynamics (MD) simulation, are accounted for when selecting label sizes. An experimentally informed 3D continuum nanofluidic-nanoelectronic device model subsequently predicts both the ionic current and FET signals. We present a barcode design for a conceptually generic NP-FET, with a 14 nm diameter pore, operating in conditions corresponding to experiments. By adjusting the spacing between the labels to half the length of the pore, we show that a bit-rate of 78 kbit·s[-1] is achievable. This lies well beyond the state-of-the-art of ≈40 kbit·s[-1], with significant headroom for further optimizations. We also highlight the advantages of NP-FET readout based on the larger signal size and sinusoidal signal shape.}, }
@article {pmid38712231, year = {2025}, author = {Yang, L and Liu, F and Hahm, H and Okuda, T and Li, X and Zhang, Y and Kalyanaraman, V and Heitmeier, MR and Samineni, VK}, title = {Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38712231}, issn = {2692-8205}, support = {P30 CA091842/CA/NCI NIH HHS/United States ; R01 DA056829/DA/NIDA NIH HHS/United States ; R01 DK128475/DK/NIDDK NIH HHS/United States ; R01 DK139386/DK/NIDDK NIH HHS/United States ; }, abstract = {Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons in female mice. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.}, }
@article {pmid38709890, year = {2024}, author = {Li, W and Miller, D and Liu, X and Tosi, L and Chkaiban, L and Mei, H and Hung, PH and Parekkadan, B and Sherlock, G and Levy, SF}, title = {Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries.}, journal = {Nucleic acids research}, volume = {52}, number = {10}, pages = {e47}, pmid = {38709890}, issn = {1362-4962}, support = {R01 AI164530/AI/NIAID NIH HHS/United States ; R01 HG011676/HG/NHGRI NIH HHS/United States ; R01HG011676/NH/NIH HHS/United States ; }, mesh = {*Plasmids/genetics ; *Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Nanopore Sequencing/methods ; }, abstract = {Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.}, }
@article {pmid38709485, year = {2024}, author = {Wang, S and Chi, WY and Au, G and Huang, CC and Yang, JM and Huang, CH}, title = {Reconstructing Signaling Networks Using Biosensor Barcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2800}, number = {}, pages = {189-202}, pmid = {38709485}, issn = {1940-6029}, support = {P50 CA098252/CA/NCI NIH HHS/United States ; R01 GM136711/GM/NIGMS NIH HHS/United States ; S10 OD016374/OD/NIH HHS/United States ; }, mesh = {*Biosensing Techniques/methods ; *Signal Transduction ; Humans ; ErbB Receptors/metabolism/genetics ; }, abstract = {Understanding how signaling networks are regulated offers valuable insights into how cells and organisms react to internal and external stimuli and is crucial for developing novel strategies to treat diseases. To achieve this, it is necessary to delineate the intricate interactions between the nodes in the network, which can be accomplished by measuring the activities of individual nodes under perturbation conditions. To facilitate this, we have recently developed a biosensor barcoding technique that enables massively multiplexed tracking of numerous signaling activities in live cells using genetically encoded fluorescent biosensors. In this chapter, we detail how we employed this method to reconstruct the EGFR signaling network by systematically monitoring the activities of individual nodes under perturbations.}, }
@article {pmid38705596, year = {2024}, author = {Schulz, AR and Rademacher, J and Bockhorn, V and Mei, HE}, title = {Harmonized analysis of PBMC by mass cytometry.}, journal = {Methods in cell biology}, volume = {186}, number = {}, pages = {107-130}, doi = {10.1016/bs.mcb.2024.02.015}, pmid = {38705596}, issn = {0091-679X}, mesh = {Humans ; *Leukocytes, Mononuclear/cytology/immunology ; *Flow Cytometry/methods/standards ; Immunophenotyping/methods ; Single-Cell Analysis/methods ; }, abstract = {Mass cytometry permits the high dimensional analysis of cellular systems at single-cell resolution with high throughput in various areas of biomedical research. Here, we provide a state-of-the-art protocol for the analysis of human peripheral blood mononuclear cells (PBMC) by mass cytometry. We focus on the implementation of measures promoting the harmonization of large and complex studies to aid robustness and reproducibility of immune phenotyping data.}, }
@article {pmid38705192, year = {2024}, author = {van Klink, R}, title = {Delivering on a promise: futureproofing automated insect monitoring methods.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230105}, pmid = {38705192}, issn = {1471-2970}, mesh = {Animals ; Automation/methods ; *Biodiversity ; Entomology/methods/instrumentation/trends ; *Insecta/physiology ; }, abstract = {Due to rapid technological innovations, the automated monitoring of insect assemblages comes within reach. However, this continuous innovation endangers the methodological continuity needed for calculating reliable biodiversity trends in the future. Maintaining methodological continuity over prolonged periods of time is not trivial, since technology improves, reference libraries grow and both the hard- and software used now may no longer be available in the future. Moreover, because data on many species are collected at the same time, there will be no simple way of calibrating the outputs of old and new devices. To ensure that reliable long-term biodiversity trends can be calculated using the collected data, I make four recommendations: (1) Construct devices to last for decades, and have a five-year overlap period when devices are replaced. (2) Construct new devices to resemble the old ones, especially when some kind of attractant (e.g. light) is used. Keep extremely detailed metadata on collection, detection and identification methods, including attractants, to enable this. (3) Store the raw data (sounds, images, DNA extracts, radar/lidar detections) for future reprocessing with updated classification systems. (4) Enable forward and backward compatibility of the processed data, for example by in-silico data 'degradation' to match the older data quality. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, }
@article {pmid38705187, year = {2024}, author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A}, title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230120}, pmid = {38705187}, issn = {1471-2970}, mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; }, abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, }
@article {pmid38705185, year = {2024}, author = {Łukasik, P and Kolasa, MR}, title = {With a little help from my friends: the roles of microbial symbionts in insect populations and communities.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230122}, pmid = {38705185}, issn = {1471-2970}, mesh = {Animals ; *Insecta/microbiology/physiology ; *Symbiosis ; *Microbiota/physiology ; Biodiversity ; }, abstract = {To understand insect abundance, distribution and dynamics, we need to understand the relevant drivers of their populations and communities. While microbial symbionts are known to strongly affect many aspects of insect biology, we lack data on their effects on populations or community processes, or on insects' evolutionary responses at different timescales. How these effects change as the anthropogenic effects on ecosystems intensify is an area of intense research. Recent developments in sequencing and bioinformatics permit cost-effective microbial diversity surveys, tracking symbiont transmission, and identification of functions across insect populations and multi-species communities. In this review, we explore how different functional categories of symbionts can influence insect life-history traits, how these effects could affect insect populations and their interactions with other species, and how they may affect processes and patterns at the level of entire communities. We argue that insect-associated microbes should be considered important drivers of insect response and adaptation to environmental challenges and opportunities. We also outline the emerging approaches for surveying and characterizing insect-associated microbiota at population and community scales. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, }
@article {pmid38705180, year = {2024}, author = {Li, R and Ratnasingham, S and Zarubiieva, I and Somervuo, P and Taylor, GW}, title = {PROTAX-GPU: a scalable probabilistic taxonomic classification system for DNA barcodes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230124}, pmid = {38705180}, issn = {1471-2970}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Algorithms ; Classification/methods ; Computer Graphics ; Animals ; }, abstract = {DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification, advancing on methods that rely solely on sequence similarity. It provides calibrated probabilistic assignments to a partially populated taxonomic hierarchy, accounting for taxa that lack references and incorrect taxonomic annotation. While effective on smaller scales, global application of PROTAX necessitates substantially larger reference libraries, a goal previously hindered by computational barriers. We introduce PROTAX-GPU, a scalable algorithm capable of leveraging the global Barcode of Life Data System (>14 million specimens) as a reference database. Using graphics processing units (GPU) to accelerate similarity and nearest-neighbour operations and the JAX library for Python integration, we achieve over a 1000 × speedup compared with the central processing unit (CPU)-based implementation without compromising PROTAX's key benefits. PROTAX-GPU marks a significant stride towards real-time DNA barcoding, enabling quicker and more efficient species identification in environmental assessments. This capability opens up new avenues for real-time monitoring and analysis of biodiversity, advancing our ability to understand and respond to ecological dynamics. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, }
@article {pmid38705177, year = {2024}, author = {Li, Y and Devenish, C and Tosa, MI and Luo, M and Bell, DM and Lesmeister, DB and Greenfield, P and Pichler, M and Levi, T and Yu, DW}, title = {Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1904}, pages = {20230123}, pmid = {38705177}, issn = {1471-2970}, mesh = {*Arthropods/classification ; *Biodiversity ; Animals ; *DNA, Environmental/analysis ; *Remote Sensing Technology/methods ; Forests ; Animal Distribution ; DNA Barcoding, Taxonomic/methods ; }, abstract = {Arthropods contribute importantly to ecosystem functioning but remain understudied. This undermines the validity of conservation decisions. Modern methods are now making arthropods easier to study, since arthropods can be mass-trapped, mass-identified, and semi-mass-quantified into 'many-row (observation), many-column (species)' datasets, with homogeneous error, high resolution, and copious environmental-covariate information. These 'novel community datasets' let us efficiently generate information on arthropod species distributions, conservation values, uncertainty, and the magnitude and direction of human impacts. We use a DNA-based method (barcode mapping) to produce an arthropod-community dataset from 121 Malaise-trap samples, and combine it with 29 remote-imagery layers using a deep neural net in a joint species distribution model. With this approach, we generate distribution maps for 76 arthropod species across a 225 km[2] temperate-zone forested landscape. We combine the maps to visualize the fine-scale spatial distributions of species richness, community composition, and site irreplaceability. Old-growth forests show distinct community composition and higher species richness, and stream courses have the highest site-irreplaceability values. With this 'sideways biodiversity modelling' method, we demonstrate the feasibility of biodiversity mapping at sufficient spatial resolution to inform local management choices, while also being efficient enough to scale up to thousands of square kilometres. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.}, }
@article {pmid38705075, year = {2024}, author = {Li, X and Liu, R and Zhang, N and Zhao, J and Zhou, Y and Zhou, Q and Gu, Z and Zhang, D}, title = {Carbon nanotubes integrated photonic barcodes in Herringbone Microfluidics for Multiplex Biomarker Quantification.}, journal = {Biosensors &amp; bioelectronics}, volume = {258}, number = {}, pages = {116350}, doi = {10.1016/j.bios.2024.116350}, pmid = {38705075}, issn = {1873-4235}, mesh = {*Nanotubes, Carbon/chemistry ; Humans ; *Biosensing Techniques/instrumentation ; *Biomarkers ; *Lab-On-A-Chip Devices ; Equipment Design ; Aptamers, Nucleotide/chemistry ; Silicon Dioxide/chemistry ; Photons ; Nanoparticles/chemistry ; Microfluidic Analytical Techniques/instrumentation ; }, abstract = {Early monitoring of cardiovascular disease (CVD) is crucial for its treatment and prognosis. Hence, highly specific and sensitive detection method is urgently needed. In this study, we propose a novel herringbone microfluid chip with aptamer functionalized core-shell photonic crystal (PhC) barcode integration for high throughput multiplex CVD detection. Based on the PhC derived from co-assembled carboxylated single-wall carbon nanotubes and silicon dioxide nanoparticles, we obtain core-shell PhC barcodes by hydrogel replicating and partially etching. These core-shell PhC barcodes not only retain the original structural colors coding element, but also fully expose a large number of carboxyl elements in the ore for the probe immobilization. We further combine the functionalized barcodes with herringbone groove microfluidic chip to elucidate its acceptability in testing clinical sample. It is demonstrated that the special design of microfluidic chip can significantly enhance fluid vortex resistance and contact frequency, improving the sample capture efficiency and detection sensitivity. These features indicate that our core-shell PhC barcodes-integrated herringbone microfluidic system possesses great potential for multiplex biomarker detection in clinical application.}, }
@article {pmid38703100, year = {2024}, author = {Molero-Baltanás, R and Mitchell, A and Gaju-Ricart, M and Robla, J}, title = {Worldwide revision of synanthropic silverfish (Insecta: Zygentoma: Lepismatidae) combining morphological and molecular data.}, journal = {Journal of insect science (Online)}, volume = {24}, number = {3}, pages = {}, pmid = {38703100}, issn = {1536-2442}, support = {//the Australian Museum Research Institute/ ; //University of C&#xf3;rdoba/ ; }, mesh = {Animals ; *Phylogeny ; *Insecta/genetics/anatomy &amp; histology/classification ; Female ; Male ; Animal Distribution ; }, abstract = {Synanthropic silverfish are the best-known and most widely distributed insects of the order Zygentoma. However, there is a great gap in the knowledge and confusion about the geographic distribution and the diagnostic characteristics that allow their identification. In this work, we provide an exhaustive and deep analysis of the most common 9 synanthropic silverfish of the world, combining previously published and newly derived morphological and molecular data. Updated descriptions of Ctenolepisma calvum (Ritter, 1910) and Ctenolepisma (Sceletolepisma) villosum (Fabricius, 1775) are included, and morphological remarks, illustrations, and photographs of the remaining synanthropic species are provided to clarify their diagnosis and differentiation among them and from other free-living species. In addition, Ctenolepisma targionii (Grassi and Rovelli, 1889) is synonymized with C. villosum. A molecular phylogeny is presented based on the COI sequences of all the synanthropic species deposited in BOLD and GenBank, with 15 new sequences provided by this study. This has allowed us to detect and correct a series of identification errors based on the lack of morphological knowledge of several species. Moreover, 2 different lineages of Ctenolepisma longicaudatumEscherich, 1905 have also been detected. To help future studies, we also provide a taxonomic interpretation guide for the most important diagnostic characters of the order Zygentoma, as well as an identification key for all the Synanthropic studied species. Finally, an approximation of the global distribution of synanthropic silverfish is discussed. Several new records indicate that the expansion of these species, generally associated with the transport of goods and people, is still far from over.}, }
@article {pmid38703052, year = {2024}, author = {Burg, S and Ovaskainen, O and Furneaux, B and Ivanova, N and Abrahamyan, A and Niittynen, P and Somervuo, P and Abrego, N}, title = {Experimental evidence that root-associated fungi improve plant growth at high altitude.}, journal = {Molecular ecology}, volume = {33}, number = {12}, pages = {e17376}, doi = {10.1111/mec.17376}, pmid = {38703052}, issn = {1365-294X}, support = {101057437//H2020 European Research Council/ ; 101059492//H2020 European Research Council/ ; 856506//H2020 European Research Council/ ; 30865//Research Council of Finland/ ; 336212//Research Council of Finland/ ; 342374//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 346492//Research Council of Finland/ ; }, mesh = {*Altitude ; *Plant Roots/microbiology/growth &amp; development ; *Symbiosis/genetics ; Fungi/genetics ; Plant Development/genetics ; DNA Barcoding, Taxonomic ; Mycorrhizae/genetics/physiology ; }, abstract = {Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root-associated fungi (RAF) along stressful abiotic gradients. We investigate whether variations in RAF community composition along altitudinal gradients influence plant growth at high altitudes, where both plants and fungi face harsher abiotic conditions. We established a translocation experiment between pairs of Bistorta vivipara populations across altitudinal gradients. To separate the impact of shifting fungal communities from the overall influence of changing abiotic conditions, we used a root barrier to prevent new colonization by RAF following translocation. To characterize the RAF communities, we applied DNA barcoding to the root samples. Through the utilization of joint species distribution modelling, we assessed the relationship between changes in plant functional traits resulting from experimental treatments and the corresponding changes in the RAF communities. Our findings indicate that RAF communities influence plant responses to stressful abiotic conditions. Plants translocated from low to high altitudes grew more when they were able to associate with the resident high-altitude RAF compared to those plants that were not allowed to associate with the resident RAF. We conclude that interactions with RAF impact how plants respond to stressful abiotic conditions. Our results provide experimental support that interactions with RAF improve plant stress tolerance to altitudinal stressors such as colder temperatures and less nutrient availability.}, }
@article {pmid38701091, year = {2024}, author = {Aggarwal, S and Walker, FC and Weagley, JS and McCune, BT and Wu, X and Schriefer, LA and Makimaa, H and Lawrence, D and Sridhar, P and Baldridge, MT}, title = {Interferons and tuft cell numbers are bottlenecks for persistent murine norovirus infection.}, journal = {PLoS pathogens}, volume = {20}, number = {5}, pages = {e1011961}, pmid = {38701091}, issn = {1553-7374}, support = {R01 AI139314/AI/NIAID NIH HHS/United States ; R01 AI127552/AI/NIAID NIH HHS/United States ; F32 AI138392/AI/NIAID NIH HHS/United States ; R25 GM103757/GM/NIGMS NIH HHS/United States ; T32 AI007172/AI/NIAID NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Norovirus/physiology ; *Caliciviridae Infections/virology/immunology ; Mice ; *Interferons/metabolism ; Persistent Infection/virology/immunology ; Mice, Inbred C57BL ; Intestinal Mucosa/virology/immunology ; Gastroenteritis/virology ; Virus Replication ; Mice, Knockout ; Immunity, Innate ; Virus Shedding ; }, abstract = {Noroviruses (NoVs) are a leading cause of viral gastroenteritis. Despite global clinical relevance, our understanding of how host factors, such as antiviral cytokines interferons (IFNs), modulate NoV population dynamics is limited. Murine NoV (MNoV) is a tractable in vivo model for the study of host regulation of NoV. A persistent strain of MNoV, CR6, establishes a reservoir in intestinal tuft cells for chronic viral shedding in stool. However, the influence of host innate immunity and permissive cell numbers on viral population dynamics is an open question. We generated a pool of 20 different barcoded viruses (CR6BC) by inserting 6-nucleotide barcodes at the 3' position of the NS4 gene and used this pool as our viral inoculum for in vivo infections of different mouse lines. We found that over the course of persistent CR6 infection, shed virus was predominantly colon-derived, and viral barcode richness decreased over time irrespective of host immune status, suggesting that persistent infection involves a series of reinfection events. In mice lacking the IFN-λ receptor, intestinal barcode richness was enhanced, correlating with increased viral intestinal replication. IL-4 treatment, which increases tuft cell numbers, also increased barcode richness, indicating the abundance of permissive tuft cells to be a bottleneck during CR6 infection. In mice lacking type I IFN signaling (Ifnar1-/-) or all IFN signaling (Stat1-/-), barcode diversity at extraintestinal sites was dramatically increased, implicating different IFNs as critical bottlenecks at specific tissue sites. Of interest, extraintestinal barcodes were overlapping but distinct from intestinal barcodes, indicating that disseminated virus represents a distinct viral population than that replicating in the intestine. Barcoded viruses are a valuable tool to explore the influence of host factors on viral diversity in the context of establishment and maintenance of infection as well as dissemination and have provided important insights into how NoV infection proceeds in immunocompetent and immunocompromised hosts.}, }
@article {pmid38699326, year = {2024}, author = {Zhuang, X and Vo, V and Moshi, MA and Dhede, K and Ghani, N and Akbar, S and Chang, CL and Young, AK and Buttery, E and Bendik, W and Zhang, H and Afzal, S and Moser, D and Cordes, D and Lockett, C and Gerrity, D and Kan, HY and Oh, EC}, title = {Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.04.18.24306052}, pmid = {38699326}, abstract = {Genome sequencing from wastewater has emerged as an accurate and cost-effective tool for identifying SARS-CoV-2 variants. However, existing methods for analyzing wastewater sequencing data are not designed to detect novel variants that have not been characterized in humans. Here, we present an unsupervised learning approach that clusters co-varying and time-evolving mutation patterns leading to the identification of SARS-CoV-2 variants. To build our model, we sequenced 3,659 wastewater samples collected over a span of more than two years from urban and rural locations in Southern Nevada. We then developed a multivariate independent component analysis (ICA)-based pipeline to transform mutation frequencies into independent sources with co-varying and time-evolving patterns and compared variant predictions to >5,000 SARS-CoV-2 clinical genomes isolated from Nevadans. Using the source patterns as data-driven reference "barcodes", we demonstrated the model's accuracy by successfully detecting the Delta variant in late 2021, Omicron variants in 2022, and emerging recombinant XBB variants in 2023. Our approach revealed the spatial and temporal dynamics of variants in both urban and rural regions; achieved earlier detection of most variants compared to other computational tools; and uncovered unique co-varying mutation patterns not associated with any known variant. The multivariate nature of our pipeline boosts statistical power and can support accurate and early detection of SARS-CoV-2 variants. This feature offers a unique opportunity for novel variant and pathogen detection, even in the absence of clinical testing.}, }
@article {pmid38695131, year = {2025}, author = {Ramos, SC and Culver, M}, title = {Integration of Indigenous Research Methodologies, Traditional Ecological Knowledge and molecular scatology in an assessment of mesocarnivore presence, diet and habitat use on Yurok Ancestral Lands.}, journal = {Molecular ecology resources}, volume = {25}, number = {2}, pages = {e13963}, doi = {10.1111/1755-0998.13963}, pmid = {38695131}, issn = {1755-0998}, support = {2010-3-03//The University of Arizona/Sloan Indigenous Graduate Partnership Program/ ; 1906338//National Science Foundation/ ; }, mesh = {Animals ; *Ecosystem ; *Diet ; DNA Barcoding, Taxonomic/methods ; Lynx/genetics/classification/physiology ; Ecology/methods ; Foxes/genetics/classification ; Feeding Behavior ; }, abstract = {Partnerships between Tribes and researchers in wildlife monitoring and application of Traditional Ecological Knowledge (TEK) have taken a variety of forms, and some scholars have noted a need for culturally sensitive approaches. Guided by Indigenous Research Methodologies, this research is coupled with Yurok TEK, or hlkelonah 'ue-megetohl ('to take care of the earth'), enabling an applied, culturally sensitive approach in partnership with the Yurok Tribe. We present results from a molecular scatology study of wildlife within the ancestral territory of the Yurok Tribe. Scats were collected opportunistically on road transects. All samples (N = 132) were analysed via DNA barcoding and results matched to documented 'Oohl 'we-toh (Yurok language) names to determine the depositor species (N = 8). Though there were four focal mesocarnivore species in our study, only bobcat (Chmuuek; Lynx rufus) and gray fox (Wergers; Urocyon cinereoargenteus) were detected as depositor species. Post hoc analyses were conducted to explore distribution, habitat use and selection in a use-availability context, and food habits of these two species. We found almost complete separation of bobcat and gray fox use of transects, as well as indication of partitioning of vegetation cover types and food. We demonstrate an integrated framework of Western and Indigenous sciences that allows the Indigenous researcher to transcend structured academic disciplinary boundaries. Our approach can be modified for partnerships between Tribes, agencies, academics and students for wildlife monitoring in broader geographic regions in various research applications.}, }
@article {pmid38694266, year = {2024}, author = {Ossowska, EA and Moncada, B and Lücking, R and Flakus, A and Rodriguez-Flakus, P and Olszewska, S and Kukwa, M}, title = {Additional new species and new records of the genus Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia.}, journal = {MycoKeys}, volume = {105}, number = {}, pages = {21-47}, pmid = {38694266}, issn = {1314-4049}, abstract = {Four species of the genus Sticta are described as new from Bolivia, based on morphological examination and phylogenetic analysis of the fungal ITS barcoding marker. Additionally, two species are reported as new to Bolivia (their identification confirmed by molecular data) and one previously reported species is confirmed by molecular data for the first time. Detailed morphological and anatomical descriptions are provided for all new species. Two of the new species, S.isidiolobulata Ossowska, B. Moncada, Lücking &amp; Kukwa and S.madidiensis Ossowska, B. Moncada, Lücking &amp; Kukwa belong to clade I, as defined in previous studies. In contrast, S.montepunkuensis Ossowska, B. Moncada, Lücking &amp; Kukwa and S.macrolobata Ossowska, B. Moncada, Lücking &amp; Kukwa, also described here as new to science, belong to clade III. Stictaisidiolobulata has an irregular to suborbicular thallus of medium size, with isidia developing into spathulate lobules, cyanobacterial photobiont and apothecia with entire to weakly-crenate margins. The large irregular thallus of the cyanobacteria-associated S.macrolobata has broad lobes, apothecia with verrucous to tomentose margins and cyphellae with raised margins, whereas S.madidiensis has a medium-sized, palmate to irregular thallus with a stipe, but without vegetative propagules and apothecia. Stictamontepunkuensis has large and irregular thalli with green algae as photobiont, apothecia with crenate to verrucous margins and urceolate cyphellae with a wide pore and a scabrid basal membrane. Two species, S.beauvoisii Delise and S.riparia Merc.-Díaz are reported as new to Bolivia (the latter also as new to South America) and belong to clade III. Stictatomentosa (Sw.) Ach., species confirmed from Bolivia by molecular data, belongs to clade II. Stictabeauvoisii is characterised by a smooth yellowish-brown upper surface with darker apices and abundant, marginal isidia and a brown lower surface with golden-chocolate brown primary tomentum and sparse, golden-brown rhizines. Stictariparia has a strongly branched thallus, with undulate lobes and abundant, marginal, palmate, grey to dark brown phyllidia and greyish-brown lower surface with the primary tomentum absent towards the margins. Stictatomentosa has palmate, bluish thalli with white cilia and abundant, submarginal apothecia and creamy-white lower surface with a sparse, white primary tomentum.}, }
@article {pmid38693183, year = {2024}, author = {Moustafa, MAM and Mohamed, WMA and Chatanga, E and Naguib, D and Matsuno, K and Gofton, AW and Barker, SC and Nonaka, N and Nakao, R}, title = {Unraveling the phylogenetics of genetically closely related species, Haemaphysalis japonica and Haemaphysalis megaspinosa, using entire tick mitogenomes and microbiomes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9961}, pmid = {38693183}, issn = {2045-2322}, support = {16H06431//Japan Society for the Promotion of Science/ ; 19H03118//Japan Society for the Promotion of Science/ ; 19F19097//Japan Society for the Promotion of Science/ ; 20K21358//Japan Society for the Promotion of Science/ ; 20KK0151//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Phylogeny ; *Ixodidae/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Genome, Mitochondrial ; Genetic Variation ; }, abstract = {Ticks have a profound impact on public health. Haemaphysalis is one of the most widespread genera in Asia, including Japan. The taxonomy and genetic differentiation of Haemaphysalis spp. is challenging. For instance, previous studies struggled to distinguish Haemaphysalis japonica and Haemaphysalis megaspinosa due to the dearth of nucleotide sequence polymorphisms in widely used barcoding genes. The classification of H. japonica japonica and its related sub-species Haemaphysalis japonica douglasi or Haemaphysalis jezoensis is also confused due to their high morphological similarity and a lack of molecular data that support the current classification. We used mitogenomes and microbiomes of H. japonica and H. megaspinosa to gain deeper insights into the phylogenetic relationships and genetic divergence between two species. Phylogenetic analyses of concatenated nucleotide sequences of protein-coding genes and ribosomal DNA genes distinguished H. japonica and H. megaspinosa as monophyletic clades, with further subdivision within the H. japonica clade. The 16S rRNA and NAD5 genes were valuable markers for distinguishing H. japonica and H. megaspinosa. Population genetic structure analyses indicated that genetic variation within populations accounted for a large proportion of the total variation compared to variation between populations. Microbiome analyses revealed differences in alpha and beta diversity between H. japonica and H. megaspinosa: H. japonica had the higher diversity. Coxiella sp., a likely endosymbiont, was found in both Haemaphysalis species. The abundance profiles of likely endosymbionts, pathogens, and commensals differed between H. japonica and H. megaspinosa: H. megaspinosa was more diverse.}, }
@article {pmid38690989, year = {2024}, author = {Li, J and Li, M and Wuethrich, A and Guan, R and Zhao, L and Hu, C and Trau, M and Sun, Y}, title = {Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture.}, journal = {Analytical chemistry}, volume = {96}, number = {19}, pages = {7651-7660}, doi = {10.1021/acs.analchem.4c00558}, pmid = {38690989}, issn = {1520-6882}, mesh = {*Extracellular Vesicles/chemistry/metabolism ; *Lung Neoplasms/metabolism ; Humans ; *Spectrum Analysis, Raman ; *Gold/chemistry ; Microelectrodes ; }, abstract = {Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.}, }
@article {pmid38688969, year = {2024}, author = {Blanc-Benigeri, A and Poirier, V and Narango, D and Elliott, KH and Frei, B}, title = {Diet of moulting Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) at a stopover site during fall migration measured with fecal DNA metabarcoding.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {9913}, pmid = {38688969}, issn = {2045-2322}, support = {#522431//Natural Sciences and Engineering Research Council of Canada-Undergraduate Student Research Award (NSERC USRA)/ ; #320544//Graduate Scholarship-Master's (CGS M) award, a Fonds de recherche du Qu&#xe9;bec-Nature et technologies (FRQNT)/ ; }, mesh = {Animals ; *Animal Migration/physiology ; *Songbirds/physiology ; *Diet ; *Feces/chemistry ; DNA Barcoding, Taxonomic/methods ; Seasons ; }, abstract = {Moult and migration are energetically demanding and require adequate nutrition. In some species, individuals may interrupt their fall migration to moult at discrete stopover locations outside of their breeding grounds (i.e., moult-migration) leading to competing nutritional demands for moult and migration. Here, we use DNA barcoding of fecal samples to compare the diet of moulting and actively migrating (post-moult) Swainson's Thrushes (Catharus ustulatus) and Tennessee Warblers (Leiothlypis peregrina) during their fall migration stopover at a large urban greenspace in Montreal, Canada. Diet differed according to moult status, species, and seasonality. Swainson's Thrushes had a broad diet with frequent detections of both insects and berry-producing shrubs; while detections in Tennessee Warblers' diets were mainly arthropods. For both species, more actively migrating individuals consumed fleshy-fruiting plants than moulting individuals. A higher proportion of moulting birds consumed arthropods compared to active migrants, due to either arthropod availability or a dietary preference for proteinaceous foods to grow feathers. Both species and moult classes consumed more native plants than non-native plants later in the season. We show the importance of managing urban greenspaces with native plants and diverse food sources that can provide for the different dietary needs of migratory birds.}, }
@article {pmid38684618, year = {2024}, author = {Wang, X and Zhang, Z and Shi, Y and Man, J and Huang, Y and Zhang, X and Liu, S and He, G and An, K and Amu, L and Chen, W and Liu, Z and Wang, X and Wei, S}, title = {Population identification and genetic diversity analysis of Fritillaria ussuriensis (Fritillaria) based on chloroplast genes atpF and petB.}, journal = {Journal of applied genetics}, volume = {65}, number = {3}, pages = {453-462}, pmid = {38684618}, issn = {2190-3883}, support = {20221156//study on breeding and cultivation technology of precision medicine Bupleurum bupleurum based on molecular anti-counterfeiting technology/ ; 2020110031009385//research project on molecular anti-counterfeiting technology of 4 precision medicinal materials such as Platycodon grandiflorus/ ; 2022YFC3501505//National Key Research and Development Program of China/ ; }, mesh = {*Fritillaria/genetics/classification ; *Haplotypes/genetics ; *Genetic Variation ; Genetics, Population ; DNA Barcoding, Taxonomic ; Genome, Chloroplast/genetics ; Genes, Chloroplast/genetics ; Phylogeny ; DNA, Chloroplast/genetics ; Chloroplasts/genetics ; Evolution, Molecular ; }, abstract = {The chloroplast genomes of five Fritillaria ussuriensis materials from different production areas were comparatively analyzed, atpF and petB were screened as specific DNA barcodes, and the population identification and genetic diversity of F. ussuriensis were analyzed based on them. The F. ussuriensis chloroplast genome showed a total length of 151 515-151 548 bp with a typical tetrad structure and encoded 130 genes. atpF and petB were used to amplify 183 samples from 13 populations, and they could identify 6 and 9 haplotypes, respectively. Joint analysis of the two sequences revealed 18 haplotypes, named H1-H18, with the most widely distributed and most abundant being H4. Ten haplotypes were unique for 7 populations that they could be used to distinguish from others. Haplotype diversity and nucleotide diversity were 0.99 and 2.09 × 10[-3], respectively, indicating the genetic diversity was relatively rich. The results of the intermediary adjacency network showed that H5 was the oldest haplotype, and stellate radiation was centered around it, indicating that population expansion occurred in genuine production areas. This study lays a theoretical foundation for the population identification, genetic evolution, and breed selection of F. ussuriensis.}, }
@article {pmid38683343, year = {2024}, author = {Vences, M and Miralles, A and DeSalle, R}, title = {A Glossary of DNA Barcoding Terms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {561-572}, pmid = {38683343}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; Terminology as Topic ; DNA/genetics ; Humans ; }, abstract = {This chapter provides a reference glossary for the protocols in this volume. We have chosen only the very basic terms in the DNA barcode lexicon to include, and provide clear and concise definitions of these terms. We hope the reader finds this glossary useful.}, }
@article {pmid38683342, year = {2024}, author = {Williams, J and Nash, B and Ghiban, C and Khalfan, M and Hilgert, U and Lauter, S and Yang, CH and Micklos, DA}, title = {Analysis of DNA Barcodes Using DNA Subway.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {551-560}, pmid = {38683342}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; DNA/genetics ; Workflow ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {DNA Subway makes bioinformatic analysis of DNA barcodes classroom friendly, eliminating the need for software installations or command line tools. Subway bundles research-grade bioinformatics software into workflows with an easy-to-use interface. This chapter covers DNA Subway's DNA barcoding analysis workflow (Blue Line) starting with one or more Sanger sequence reads. During analysis, users can view trace files and sequence quality, pair and align forward and reverse reads, create and trim consensus sequences, perform BLAST searches, select reference data, align multiple sequences, and compute phylogenetic trees. High-quality sequences with the required metadata can also be submitted as barcode sequences to NCBI GenBank.}, }
@article {pmid38683341, year = {2024}, author = {Shumskaya, M}, title = {DNA Barcoding for an Undergraduate Class.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {537-550}, pmid = {38683341}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Universities ; DNA/genetics/analysis ; Humans ; Curriculum ; Polymerase Chain Reaction/methods ; }, abstract = {DNA technique is a topic mandatorily covered in a biology and biochemistry undergraduate curriculum. Inquiry-based pedagogy is proven to be the most effective way of learning, and DNA barcoding method allows to merge necessary-to-study experimental techniques such as DNA isolation and purification, PCR, and basic BLAST search into a two- or three-week inquiry-based student project. It also provides a research-based experience to the students, who, when organized in groups, can design their own DNA-barcoding project if they wish. Here, we describe how DNA barcoding can be offered in an undergraduate college or advanced high school settings. This chapter is intended to help college and high school instructors to include DNA barcoding in their classes.}, }
@article {pmid38683340, year = {2024}, author = {Wright, L and Garbarino, J and Marizzi, C}, title = {Engaging Students and Teachers as Community Scientists in DNA Barcoding Initiatives.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {525-535}, pmid = {38683340}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Students ; Humans ; Curriculum ; Faculty ; }, abstract = {Historically, contributions to scientific knowledge have been perceived as something that only professional scientists have the ability to affect. This has led to the belief that scientific pursuits are done not by everyday people but by individuals who have no connection to the communities that their discoveries might impact. DNA barcoding initiatives have the potential to bridge this gap. Community leaders, students, teachers, and other community members can come together with engaged scientists to solve relevant issues that affect them. Over the last 20 years, DNA barcoding has been used successfully in a variety of educational contexts to incorporate original research into school curricula and informal outreach and education programs. DNA barcoding is especially suitable for educational settings because it is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and free and open-access online tools exist that allow participants to contribute high-quality data to international research efforts. DNA barcoding also offers a unique service-learning opportunity, where participants gain both knowledge and confidence in science. This is important because a growing body of evidence suggests that actively conducting research increases student and teacher engagement and retention of students in science. Here, we describe a framework and case studies in different educational settings that can be modeled and adapted to various educational contexts.}, }
@article {pmid38683339, year = {2024}, author = {Pepenella, S and Hackett, J and Fernandez-Marco, C and Petracca, J and Marizzi, C and Nash, B and Micklos, DA}, title = {A Rapid, Equipment-Free DNA Isolation Method for DNA Barcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {517-523}, pmid = {38683339}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; DNA/isolation &amp; purification/genetics ; DNA, Plant/genetics/isolation &amp; purification ; Plants/genetics ; Chromatography/methods ; Lichens/genetics ; }, abstract = {This rapid, equipment-free DNA isolation procedure using chromatography paper is a simple method that can be performed in less than 30 min and requires no wet lab experience. With minimal expense, it offers an affordable alternative for anyone wanting to explore biodiversity. It also provides an excellent option for use in classrooms or other activities that are time limited. The method works best for plants or lichens, producing stable DNA on Whatman® chromatography paper at room temperature, which can be eluted as needed.}, }
@article {pmid38683338, year = {2024}, author = {Wangh, LJ and Rice, JE and Sanchez, JA}, title = {Recent Applications of FastFish-ID.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {503-514}, pmid = {38683338}, issn = {1940-6029}, mesh = {Animals ; *Fishes ; *Sharks ; *DNA Barcoding, Taxonomic/methods ; Animal Fins ; }, abstract = {FastFish-ID via Closed-Tube barcoding is a portable platform for rapid and accurate identification of fish species that was conceived at Brandeis University, commercialized at Thermagenix, Inc., and further improved at Ecologenix, LLC (see Chap. 17 in this volume). This chapter focuses on the use of FastFish-ID for (1) identification of intraspecies variants, (2) quantitative use of FastFish-ID to measure the decay of fresh fish, and (3) use of FastFish-ID for the identification of dried and processed shark fins.}, }
@article {pmid38683337, year = {2024}, author = {Gwiazdowski, R}, title = {Principles for Constructing DNA Barcode Reference Libraries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {491-502}, pmid = {38683337}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Gene Library ; Reference Standards ; DNA/genetics ; Humans ; }, abstract = {All DNA barcode methods rely on reference sequences linked to well-curated voucher specimens. Definitions for and locations of DNA barcode reference libraries are not standardized, and vary throughout the literature. Standardizing, and centralizing reference specimens would provide an unambiguous source, analogous to reference genomes, to reproduce identifications and improve a library. This chapter proposes a working definition of a DNA barcode reference library, consistent with DNA barcode data standards, along with principles and methods to consider when producing or using such a library. These methods allow explicit traceback to sequence-sources which elevate the value of voucher specimens, and create a potential for community curation.}, }
@article {pmid38683336, year = {2024}, author = {O'Brien, TD and Blanco-Bercial, L and Questel, JM and Batta-Lona, PG and Bucklin, A}, title = {MetaZooGene Atlas and Database: Reference Sequences for Marine Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {475-489}, pmid = {38683336}, issn = {1940-6029}, mesh = {Animals ; *Aquatic Organisms/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Ecosystem ; Databases, Genetic ; Databases, Nucleic Acid ; }, abstract = {The MetaZooGene Atlas and Database (MZGdb; https://metazoogene.org/mzgdb/) is an open-access data and metadata portal synchronized with the NCBI GenBank and BOLD data repositories. The MZGdb includes sequences for genes used for the classification and identification of marine organisms based on DNA barcoding and metabarcoding. The focus of the MZGdb is biodiversity of marine ecosystems, including phytoplankton and microbes, zooplankton and invertebrates, fish, and other marine vertebrates (pinnipeds, cetaceans, and sea turtles). DNA sequences currently included are mitochondrial cytochrome oxidase I (COI), 12S, and 16S rRNA, and nuclear 18S and 28S rRNA. The MZGdb provides data and mapping tools for assembling and downloading compilations of reference sequence data that are specific to selected genes, taxonomic groups, and/or ocean regions. An additional feature of the MZGdb is the Atlas which summarizes data coverage and proportional completeness based on statistics of species with available sequences versus species commonly found in each ocean region.This chapter is a collaborative effort of the Scientific Committee for Ocean Research (SCOR) Working Group WG157: MetaZooGene: Toward a new global view of marine zooplankton biodiversity based on DNA metabarcoding and reference DNA sequence databases (https://metazoogene.org).}, }
@article {pmid38683335, year = {2024}, author = {Whitley, BS and Li, Z and Jones, L and de Vere, N}, title = {Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {445-473}, pmid = {38683335}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Plants/genetics ; *DNA, Plant/genetics ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/methods ; Gene Library ; }, abstract = {Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.}, }
@article {pmid38683334, year = {2024}, author = {Ratnasingham, S and Wei, C and Chan, D and Agda, J and Agda, J and Ballesteros-Mejia, L and Boutou, HA and El Bastami, ZM and Ma, E and Manjunath, R and Rea, D and Ho, C and Telfer, A and McKeowan, J and Rahulan, M and Steinke, C and Dorsheimer, J and Milton, M and Hebert, PDN}, title = {BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {403-441}, pmid = {38683334}, issn = {1940-6029}, mesh = {*Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; Software ; DNA/genetics ; }, abstract = {BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.}, }
@article {pmid38683333, year = {2024}, author = {Damaso, N and Elwick, KE and Robertson, JM}, title = {Guidelines for the Analysis of DNA Barcoding/Metabarcoding Sequencing Data and Interpretation of Publicly Available Databases.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {391-402}, pmid = {38683333}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Databases, Nucleic Acid ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Databases, Genetic ; Software ; }, abstract = {This chapter describes procedures for the use of DNA sequence data to obtain and compare taxonomic identification using the public databases GenBank and Barcode of Life Data System (BOLD). The chapter begins by describing procedures used to prepare quality sequences for uploading into GenBank and BOLD. Next, steps used to query the DNA sequences against the public databases are described using GenBank BLAST and BOLD identification engines. Interpretation guidelines for the taxonomic identification assignments are presented. Finally, a procedure for evaluating the accuracy and reliability of sequences from GenBank and BOLD is provided.}, }
@article {pmid38683332, year = {2024}, author = {Phillips, JD and Griswold, CK and Young, RG and Hubert, N and Hanner, RH}, title = {A Measure of the DNA Barcode Gap for Applied and Basic Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {375-390}, pmid = {38683332}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Coleoptera/genetics/classification ; DNA/genetics/analysis ; Species Specificity ; }, abstract = {DNA barcoding has largely established itself as a mainstay for rapid molecular taxonomic identification in both academic and applied research. The use of DNA barcoding as a molecular identification method depends on a "DNA barcode gap"-the separation between the maximum within-species difference and the minimum between-species difference. Previous work indicates the presence of a gap hinges on sampling effort for focal taxa and their close relatives. Furthermore, both theory and empirical work indicate a gap may not occur for related pairs of biological species. Here, we present a novel evaluation approach in the form of an easily calculated set of nonparametric metrics to quantify the extent of proportional overlap in inter- and intraspecific distributions of pairwise differences among target species and their conspecifics. The metrics are based on a simple count of the number of overlapping records for a species falling within the bounds of maximum intraspecific distance and minimum interspecific distance. Our approach takes advantage of the asymmetric directionality inherent in pairwise genetic distance distributions, which has not been previously done in the DNA barcoding literature. We apply the metrics to the predatory diving beetle genus Agabus as a case study because this group poses significant identification challenges due to its morphological uniformity despite both relative sampling ease and well-established taxonomy. Results herein show that target species and their nearest neighbor species were found to be tightly clustered and therefore difficult to distinguish. Such findings demonstrate that DNA barcoding can fail to fully resolve species in certain cases. Moving forward, we suggest the implementation of the proposed metrics be integrated into a common framework to be reported in any study that uses DNA barcoding for identification. In so doing, the importance of the DNA barcode gap and its components for the success of DNA-based identification using DNA barcodes can be better appreciated.}, }
@article {pmid38683331, year = {2024}, author = {Mahmoud, MAB}, title = {Classification of DNA Sequence Based on a Non-gradient Algorithm: Pseudoinverse Learners.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {359-373}, pmid = {38683331}, issn = {1940-6029}, mesh = {*Algorithms ; *Neural Networks, Computer ; DNA/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA/methods ; Humans ; Deep Learning ; }, abstract = {This chapter proposes a prototype-based classification approach for analyzing DNA barcodes that uses a spectral representation of DNA sequences and a non-gradient neural network. Biological sequences can be viewed as data components with higher non-fixed dimensions, which correspond to the length of the sequences. Through computational procedures such as one-hot encoding, numerical encoding plays an important role in DNA sequence evaluation (OHE). However, the OHE method has some disadvantages: (1) It does not add any details that could result in an additional predictive variable, and (2) if the variable has many classes, OHE significantly expands the feature space. To address these shortcomings, this chapter proposes a computationally efficient framework for classifying DNA sequences of living organisms in the image domain. A multilayer perceptron trained by a pseudoinverse learning autoencoder (PILAE) algorithm is used in the proposed strategy. The learning control parameters and the number of hidden layers do not have to be specified during the PILAE training process. As a result, the PILAE classifier outperforms other deep neural network (DNN) strategies such as the VGG-16 and Xception models.}, }
@article {pmid38683330, year = {2024}, author = {Bergmann, T}, title = {CAOS-R: Character-Based Barcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {347-357}, pmid = {38683330}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; }, abstract = {CAOS-Barcoding is a culmination of traditional taxonomy and modern DNA barcoding. CAOS identifies taxa by diagnostic characters as is done in traditional taxonomy and produces an identification matrix for taxon discrimination similar to DNA barcoding distance matrices. Here, I describe how to set up the CAOS-Barcoder and CAOS-Classifier software, which input data is needed, and how to interpret the output data. With the CAOS-Barcoder, single marker or concatenated data can be processed into diagnostic barcodes for taxon discrimination. The CAOS-Classifier can use the diagnostic barcodes for specimen identification.}, }
@article {pmid38683329, year = {2024}, author = {Ramanan, V and Sarkar, IN}, title = {Characteristic Attribute Organization System (CAOS): Identifying Classification Rules Based on Phylogenetically Organized Sequences.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {335-345}, pmid = {38683329}, issn = {1940-6029}, mesh = {*Phylogeny ; *Software ; Computational Biology/methods ; Algorithms ; Sequence Alignment/methods ; }, abstract = {Classification is a technique that labels subjects based on the characteristics of the data. It often includes using prior learned information from preexisting data drawn from the same distribution or data type to make informed decisions per each given subject. The method presented here, the Characteristic Attribute Organization System (CAOS), uses a character-based approach to molecular sequence classification. Using a set of aligned sequences (either nucleotide or amino acid) and a maximum parsimony tree, CAOS will generate classification rules for the sequences based on tree structure and provide more interpretable results than other classification or sequence analysis protocols. The code is accessible at https://github.com/JuliaHealth/CAOS.jl/ .}, }
@article {pmid38683328, year = {2024}, author = {Puillandre, N and Miralles, A and Brouillet, S and Fedosov, A and Fischell, F and Patmanidis, S and Vences, M}, title = {Species Delimitation and Exploration of Species Partitions with ASAP and LIMES.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {313-334}, pmid = {38683328}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Biodiversity ; Phylogeny ; Species Specificity ; Animals ; Genetic Speciation ; }, abstract = {DNA barcoding plays an important role in exploring undescribed biodiversity and is increasingly used to delimit lineages at the species level (see Chap. 4 by Miralles et al.). Although several approaches and programs have been developed to perform species delimitation from datasets of single-locus DNA sequences, such as DNA barcodes, most of these were not initially provided as user-friendly GUI-driven executables. In spite of their differences, most of these tools share the same goal, i.e., inferring de novo a partition of subsets, potentially each representing a distinct species. More recently, a proposed common exchange format for the resulting species partitions (SPART) has been implemented by several of these tools, paving the way toward developing an interoperable digital environment entirely dedicated to integrative and comparative species delimitation. In this chapter, we provide detailed protocols for the use of two bioinformatic tools, one for single locus molecular species delimitation (ASAP) and one for statistical comparison of species partitions resulting from any kind of species delimitation analyses (LIMES).}, }
@article {pmid38683327, year = {2024}, author = {Fedosov, A and Puillandre, N and Fischell, F and Patmanidis, S and Miralles, A and Vences, M}, title = {DNA Barcode-Based Species Diagnosis with MolD.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {297-311}, pmid = {38683327}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; Biodiversity ; }, abstract = {Rapid biodiversity loss sets new requirements for taxonomic research, prompting updating some long-established practices to maximize timely documentation of species before they have gone extinct. One of the crucial procedures associated with the description of new taxa in Linnean taxonomy is assigning them a diagnosis, which is an account of the specific features of the taxon, differentiating it from already described species. Traditionally, diagnostic characters have been morphological, but especially in the case of morphologically cryptic species, molecular diagnoses become increasingly important. In this chapter, we provide detailed protocols for molecular taxon diagnosis with the bioinformatic tool MolD which is available as open-source Python code, command-line driven binary, GUI-driven executable for Windows and Mac, and Galaxy implementation. MolD identifies diagnostic combinations of nucleotides (DNCs) in addition to single (pure) diagnostic sites, enabling users to base DNA diagnoses on a minimal number of diagnostic sites necessary for reliable differentiation of taxa.}, }
@article {pmid38683326, year = {2024}, author = {Vences, M and Patmanidis, S and Fedosov, A and Miralles, A and Puillandre, N}, title = {iTaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {281-296}, pmid = {38683326}, issn = {1940-6029}, mesh = {*Software ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA/genetics ; }, abstract = {The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.}, }
@article {pmid38683325, year = {2024}, author = {Sanchez, JA and Rice, JE and Wangh, LJ}, title = {Recent Advances in Closed-Tube Barcoding for FastFish-ID.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {267-278}, pmid = {38683325}, issn = {1940-6029}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; Seafood ; Polymerase Chain Reaction/methods ; DNA, Mitochondrial/genetics ; Fisheries ; }, abstract = {FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process.}, }
@article {pmid38683323, year = {2024}, author = {Liu, R and Wang, Y and Yao, X and Liu, C}, title = {Generating 2D Barcode for DNA Barcode Sequences.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {239-246}, pmid = {38683323}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; DNA/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {DNA barcode sequence is a short DNA sequence representing a sample from a particular species. The commonly used DNA barcodes are at least 200 bps long. This large number of characters cannot be encoded in two-dimensional codes for sample recognition and tracking. In the present study, we described a method that can be used to compress the DNA sequences and then generate the corresponding QR code. With the large numbers of software and hardware, the QR code can be used efficiently for printing, labeling, and scanning.}, }
@article {pmid38683322, year = {2024}, author = {Srivathsan, A and Meier, R}, title = {Scalable, Cost-Effective, and Decentralized DNA Barcoding with Oxford Nanopore Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {223-238}, pmid = {38683322}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods/economics ; *Nanopore Sequencing/methods ; Cost-Benefit Analysis ; High-Throughput Nucleotide Sequencing/methods/economics ; Software ; Gene Library ; Sequence Analysis, DNA/methods/economics ; Workflow ; DNA/genetics ; }, abstract = {DNA barcodes are useful in biodiversity research, but sequencing barcodes with dye termination methods ("Sanger sequencing") has been so time-consuming and expensive that DNA barcodes are not as widely used as they should be. Fortunately, MinION sequencers from Oxford Nanopore Technologies have recently emerged as a cost-effective and efficient alternative for barcoding. MinION barcodes are now suitable for large-scale species discovery and enable specimen identification when the target species are represented in barcode databases. With a MinION, it is possible to obtain 10,000 barcodes from a single flow cell at a cost of less than 0.10 USD per specimen. Additionally, a Flongle flow cell can be used for small projects requiring up to 300 barcodes (0.50 USD per specimen). We here describe a cost-effective laboratory workflow for obtaining tagged amplicons, preparing ONT libraries, sequencing amplicon pools, and analyzing the MinION reads with the software ONTbarcoder. This workflow has been shown to yield highly accurate barcodes that are 99.99% identical to Sanger barcodes. Overall, we propose that the use of MinION for DNA barcoding is an attractive option for all researchers in need of a cost-effective and efficient solution for large-scale species discovery and specimen identification.}, }
@article {pmid38683321, year = {2024}, author = {Ivanov, V and Lee, KM and Mutanen, M}, title = {ddRAD Sequencing and DNA Barcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {213-221}, pmid = {38683321}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Polymorphism, Single Nucleotide ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; Gene Library ; Humans ; }, abstract = {Double-digest restriction site-associated DNA sequencing is a library preparation protocol that enables capturing variable sites across the genome including single-nucleotide polymorphisms (SNPs). These SNPs can be utilized to gain evolutionary insights into patterns observed in DNA barcodes, to infer population structure and phylogenies, to detect gene flow and introgression, and to perform species delimitation analyses. The protocol includes chemically shearing genomic DNA with restriction enzymes, unique tagging, size selection, and amplification of the resulting DNA fragments. Here we provide a detailed description of each step of the protocol, as well as information on essential equipment and common issues encountered during laboratory work.}, }
@article {pmid38683320, year = {2024}, author = {Seth, S and Bhattacharya, A}, title = {DNA Barcodes Using a Dual Nanopore Device.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {197-211}, pmid = {38683320}, issn = {1940-6029}, support = {R21 HG011236/HG/NHGRI NIH HHS/United States ; }, mesh = {*Nanopores ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; DNA/chemistry/genetics ; }, abstract = {We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.}, }
@article {pmid38683319, year = {2024}, author = {Sethi, S and Wijesinghe, KM and Dhakal, S}, title = {Single-Molecule FRET-Based Multiplexed Detection.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {183-195}, pmid = {38683319}, issn = {1940-6029}, mesh = {*Fluorescence Resonance Energy Transfer/methods ; *Single Molecule Imaging/methods ; *Fluorescent Dyes/chemistry ; Biosensing Techniques/methods ; Humans ; }, abstract = {Single-molecule multiplexed detection is a high-promise toolkit for the expanding field of biosensing and molecular diagnostics. Among many single-molecule techniques available today for biomarker sensing including fluorescence, force, electrochemical, spectroscopic, barcoding, and other techniques, fluorescence-based approaches are arguably the most widely used methods due to their high sensitivity, selectivity, and readily available fluorophore-labeling schemes for a wide variety of biomolecules. However, multiplexed imaging using fluorescence techniques has proven to be challenging due to the sophisticated labeling schemes often requiring multiple FRET (fluorescence resonance energy transfer) pairs and/or excitation sources, which lead to overlapping signals and complicate data analysis. Here, we describe a single-molecule FRET method that enables multiplexed analysis while still using only one FRET pair, and thus the described approach is a significant step forward from conventional FRET methods.}, }
@article {pmid38683317, year = {2024}, author = {Elwick, KE and Damaso, N and Robertson, JM}, title = {DNA Barcoding and Metabarcoding Protocols for Species Identification.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {155-169}, pmid = {38683317}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; *Plants/genetics ; Insecta/genetics/classification ; Fungi/genetics/classification ; Sequence Analysis, DNA/methods ; Gene Library ; DNA/genetics ; }, abstract = {The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.}, }
@article {pmid38683316, year = {2024}, author = {David, A and Deepa Arul Priya, J and Gautam, A}, title = {DNA Sequencing Technologies and DNA Barcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {139-154}, pmid = {38683316}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Biodiversity ; DNA/genetics ; Animals ; }, abstract = {DNA barcodes are short, standardized DNA segments that geneticists can use to identify all living taxa. On the other hand, DNA barcoding identifies species by analyzing these specific regions against a DNA barcode reference library. In its initial years, DNA barcodes sequenced by Sanger's method were extensively used by taxonomists for the characterization and identification of species. But in recent years, DNA barcoding by next-generation sequencing (NGS) has found broader applications, such as quality control, biomonitoring of protected species, and biodiversity assessment. Technological advancements have also paved the way to metabarcoding, which has enabled massive parallel sequ.encing of complex bulk samples using high-throughput sequencing techniques. In future, DNA barcoding along with high-throughput techniques will show stupendous progress in taxonomic classification with reference to available sequence data.}, }
@article {pmid38683315, year = {2024}, author = {Hyman, O and Cass, A and Enke, R and Storm, A and Nash, B}, title = {Cost-Effective DNA Extraction for DNA Barcoding Diverse Biological Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {129-137}, pmid = {38683315}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *DNA/genetics/isolation &amp; purification ; *Cost-Benefit Analysis ; Polymerase Chain Reaction/methods ; Plants/genetics ; }, abstract = {DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.}, }
@article {pmid38683314, year = {2024}, author = {Hackett, J and Pepenella, S and Marco, CF and Bodt, L and Grajales, LR and Petracca, J and Burke, J and Mayle, A and Nash, B and Micklos, DA}, title = {Simple, Robust Invertebrate DNA Barcoding: Chelex-Based DNA Extraction and Optimized COI Amplification.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {119-127}, pmid = {38683314}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; *Polymerase Chain Reaction/methods ; Invertebrates/genetics/classification ; DNA/genetics/isolation &amp; purification ; }, abstract = {Chelex-based DNA extractions are well suited for student DNA barcoding research because they are simple, safe, and inexpensive and can be performed without specialized laboratory equipment, allowing them to be performed in classrooms or at home. Extracted DNA is stable in Chelex solution for at least a week at ambient temperature, allowing collection of DNA samples from remote students. These extractions provide quality DNA for many taxa and are optimal for barcoding invertebrates, especially in combination with novel cytochrome c oxidase I (COI) primer cocktails and PCR cycling conditions.}, }
@article {pmid38683313, year = {2024}, author = {Brower, AVZ and DeSalle, R}, title = {DNA Barcodes in Taxonomic Descriptions.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {105-115}, pmid = {38683313}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; Software ; DNA/genetics ; Animals ; Phylogeny ; }, abstract = {This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).}, }
@article {pmid38683312, year = {2024}, author = {Miralles, A and Puillandre, N and Vences, M}, title = {DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {77-104}, pmid = {38683312}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Animals ; Species Specificity ; }, abstract = {Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.}, }
@article {pmid38683311, year = {2024}, author = {Hubert, N and Phillips, JD and Hanner, RH}, title = {Delimiting Species with Single-Locus DNA Sequences.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {53-76}, pmid = {38683311}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Phylogeny ; *Algorithms ; Software ; Biodiversity ; Sequence Analysis, DNA/methods ; Haplotypes/genetics ; }, abstract = {DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The "Materials" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.}, }
@article {pmid38683310, year = {2024}, author = {Ahrens, D}, title = {Species Diagnosis and DNA Taxonomy.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {33-52}, pmid = {38683310}, issn = {1940-6029}, mesh = {*DNA/genetics ; DNA Barcoding, Taxonomic/methods ; Classification/methods ; Phylogeny ; Species Specificity ; }, abstract = {The use of DNA has helped to improve and speed up species identification and delimitation. However, it also provides new challenges to taxonomists. Incongruence of outcome from various markers and delimitation methods, bias from sampling and skewed species distribution, implemented models, and the choice of methods/priors may mislead results and also may, in conclusion, increase elements of subjectivity in species taxonomy. The lack of direct diagnostic outcome from most contemporary molecular delimitation approaches and the need for a reference to existing and best sampled trait reference systems reveal the need for refining the criteria of species diagnosis and diagnosability in the current framework of nomenclature codes and good practices to avoid nomenclatorial instability, parallel taxonomies, and consequently more and new taxonomic impediment.}, }
@article {pmid38683309, year = {2024}, author = {Schindel, DE and Page, RMP}, title = {Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2744}, number = {}, pages = {7-32}, pmid = {38683309}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Entrepreneurship ; Humans ; Inventions ; }, abstract = {This chapter on the history of the DNA barcoding enterprise attempts to set the stage for the more scholarly contributions in this volume by addressing the following questions. How did the DNA barcoding enterprise begin? What were its goals, how did it develop, and to what degree are its goals being realized? We have taken a keen interest in the barcoding movement and its relationship to taxonomy, collections, and biodiversity informatics more broadly considered. This chapter integrates our two different perspectives on barcoding. DES was the Executive Secretary of the Consortium for the Barcode of Life from 2004 to 2017, with the mission to support the success of DNA barcoding without being directly involved in generating barcode data. RDMP viewed barcoding as an important entry into the landscape of biodiversity data, with many potential linkages to other components of that landscape. We also saw it as a critical step toward the era of international genomic research that was sure to follow. Like the Mercury Program that paved the way for lunar landings by the Apollo Program, we saw DNA barcoding as the proving grounds for the interdisciplinary and international cooperation that would be needed for success of whole-genome research.}, }
@article {pmid38681421, year = {2024}, author = {Halue, G and Chieochanthanakij, R and Kittipanyaworakun, T and Passorn, P and Kaewboonsert, D and Tharavichitkul, T and Banjongjit, A and Kanjanabuch, T and Eiam-Ong, S}, title = {Peritonitis Caused by Various Species of Diaporthe in Peritoneal Dialysis Patients: A Plant Pathogen to Human Infection.}, journal = {Cureus}, volume = {16}, number = {3}, pages = {e57016}, pmid = {38681421}, issn = {2168-8184}, abstract = {Peritonitis caused by dematiaceous molds is uncommon but poses a significant threat to patients undergoing peritoneal dialysis (PD), leading to high mortality and morbidity. This report highlights three cases of peritonitis caused by three distinct species of Diaporthe (D. amygdali, D. eucalyptorum, and D. phaseolorum), initially unidentified through conventional culture methods. The nucleotide sequences of internal transcribed spacer regions (ITS), 18S nuclear ribosomal small subunit (SSU), and 28S nuclear ribosomal large subunit (LSU) of the ribosomal DNA gene correctly identified the isolates. Despite early catheter removal and administration of appropriate antifungal medications, all patients experienced fatal outcomes. DNA barcoding emerges as a valuable tool for accurately diagnosing species within the genus of pathogenic microbes, aiding in identifying the root causes of infections. It emphasizes the importance of strict adherence to aseptic techniques during PD exchanges to prevent peritonitis caused by plant-borne pathogens.}, }
@article {pmid38680524, year = {2024}, author = {Kermek, D and Pischiutta, N and Hlebec, D and Sivec, I and Kučinić, M}, title = {Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e121398}, pmid = {38680524}, issn = {1314-2828}, abstract = {In Medvednica Nature Park, near Croatia's capital Zagreb, urbanisation significantly impacts the fauna. Comprehensive field research has never been conducted in this area, despite the presence of diverse microhabitats and the discovery of several rare species previously unknown in the Croatian fauna. This study provides the Park with first insight into the genetic and morphological diversity of stoneflies, one of the most endangered groups of organisms. Phylogenetic reconstructions and species delineation methods revealed intraspecific haplotype variation in most species (e.g. Brachypteraseticornis, Isoperlagrammatica and Leuctrabraueri), except for Leuctraprima. Additionally, our study has identified isolated populations that merit further in-depth investigation concerning morphology, genetics and ecology.}, }
@article {pmid38678568, year = {2024}, author = {Gallaccio, G and Wang, M and Schlickeiser, S and Kunkel, D and Böttcher, C and Fernández-Zapata, C}, title = {Protocol to characterize immune cell subpopulations in cerebrospinal fluid of patients with neuroinflammatory diseases using mass cytometry.}, journal = {STAR protocols}, volume = {5}, number = {2}, pages = {103038}, pmid = {38678568}, issn = {2666-1667}, mesh = {Humans ; *Flow Cytometry/methods ; *Neuroinflammatory Diseases/cerebrospinal fluid/immunology ; Single-Cell Analysis/methods ; Biomarkers/cerebrospinal fluid ; Cerebrospinal Fluid/cytology/immunology ; }, abstract = {Phenotypic and compositional changes of immune cells in cerebrospinal fluid (CSF) can be used as biomarkers to help diagnose and track disease activity for neuroinflammatory and neurodegenerative diseases. Here, we present a workflow to perform high-dimensional immune profiling at single-cell resolution using cytometry by time-of-flight (CyTOF) on cells isolated from the CSF of patients with neuroinflammation. We describe steps for sample collection and preparation, barcoding to allow for multiplexing, and downstream data analysis using R. For complete details on the use and execution of this protocol, please refer to Fernández-Zapata et al.[1].}, }
@article {pmid38676334, year = {2024}, author = {Rong, Q and Deng, Y and Chen, F and Yin, Z and Hu, L and Su, X and Zhou, D}, title = {Polymerase-Based Signal Delay for Temporally Regulating DNA Involved Reactions, Programming Dynamic Molecular Systems, and Biomimetic Sensing.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {20}, number = {35}, pages = {e2400142}, doi = {10.1002/smll.202400142}, pmid = {38676334}, issn = {1613-6829}, support = {32141003//National Natural Science Foundation of China/ ; }, mesh = {*DNA/chemistry/metabolism ; *DNA-Directed DNA Polymerase/metabolism ; *Biomimetics/methods ; Molecular Dynamics Simulation ; Biosensing Techniques/methods ; Nanotechnology/methods ; }, abstract = {Complex temporal molecular signals play a pivotal role in the intricate biological pathways of living organisms, and cells exhibit the ability to transmit and receive information by intricately managing the temporal dynamics of their signaling molecules. Although biomimetic molecular networks are successfully engineered outside of cells, the capacity to precisely manipulate temporal behaviors remains limited. In this study, the catalysis activity of isothermal DNA polymerase (DNAP) through combined use of molecular dynamics simulation analysis and fluorescence assays is first characterized. DNAP-driven delay in signal strand release ranged from 10[0] to 10[2] min, which is achieved through new strategies including the introduction of primer overhangs, utilization of inhibitory reagents, and alteration of DNA template lengths. The results provide a deeper insight into the underlying mechanisms of temporal control DNAP-mediated primer extension and DNA strand displacement reactions. Then, the regulated DNAP catalysis reactions are applied in temporal modulation of downstream DNA-involved reactions, the establishment of dynamic molecular signals, and the generation of barcodes for multiplexed detection of target genes. The utility of DNAP-based signal delay as a dynamic DNA nanotechnology extends beyond theoretical concepts and achieves practical applications in the fields of cell-free synthetic biology and bionic sensing.}, }
@article {pmid38674379, year = {2024}, author = {Zhang, S and Han, S and Bi, D and Yang, J and Ge, W and Ye, Y and Gao, J and Dai, C and Kan, X}, title = {Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective.}, journal = {Genes}, volume = {15}, number = {4}, pages = {}, pmid = {38674379}, issn = {2073-4425}, support = {BK20211078//the Basic Research Program of Natural Science Foundation of Jiangsu Province of China/ ; NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; }, mesh = {*Phylogeny ; *Sedum/genetics ; Genome, Plastid ; Evolution, Molecular ; Genetic Variation ; Codon Usage ; Genome, Plant ; Base Composition/genetics ; }, abstract = {Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.}, }
@article {pmid38674377, year = {2024}, author = {Kan, J and Zhang, S and Wu, Z and Bi, D}, title = {Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics.}, journal = {Genes}, volume = {15}, number = {4}, pages = {}, pmid = {38674377}, issn = {2073-4425}, support = {BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province (Grant no. BK20211078)/ ; RCYX20200714114538196//the Science Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20220818103212025//the Shenzhen Fundamental Research Program/ ; 2021QN02N792//the Guangdong Pearl River Talent Program/ ; }, mesh = {*Phylogeny ; *Plastids/genetics ; Codon Usage ; Genome, Plastid/genetics ; Evolution, Molecular ; }, abstract = {The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.}, }
@article {pmid38672767, year = {2024}, author = {Vankova, L and Vanek, D}, title = {Capillary-Electrophoresis-Based Species Barcoding of Big Cats: CR-mtDNA-Length Polymorphism.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, pmid = {38672767}, issn = {2075-1729}, support = {VJ01010026//Ministry of Interior Czech Republic/ ; }, abstract = {This study aimed to provide an overview of the methodological approach used for the species determination of big cats. The molecular system described herein employs mitochondrial DNA control region (CR-mtDNA)-length polymorphism in combination with highly sensitive and precise capillary electrophoresis. We demonstrated that the described CR-mtDNA barcoding system can be utilized for species determination where the presence of biological material from big cats is expected or used as a confirmatory test alongside Sanger or massive parallel sequencing (MPS). We have also addressed the fact that species barcoding, when based on the analysis of mtDNA targets, can be biased by nuclear inserts of the mitochondrial genome (NUMTs). The CR-mtDNA barcoding system is suitable even for problematic and challenging samples, such as hair. CR-mtDNA-length polymorphisms can also distinguish hybrids from pure breeds.}, }
@article {pmid38671234, year = {2024}, author = {Rios-Willars, E and Chirinos-Arias, MC}, title = {Mfind: a tool for DNA barcode analysis in angiosperms and its relationship with microsatellites using a sliding window algorithm.}, journal = {Planta}, volume = {259}, number = {6}, pages = {134}, pmid = {38671234}, issn = {1432-2048}, mesh = {*Microsatellite Repeats/genetics ; *DNA Barcoding, Taxonomic/methods ; *Algorithms ; *Magnoliopsida/genetics ; DNA, Plant/genetics ; }, abstract = {Mfind is a tool to analyze the impact of microsatellite presence on DNA barcode specificity. We found a significant correlation between barcode entropy and microsatellite count in angiosperm. Genetic barcodes and microsatellites are some of the identification methods in taxonomy and biodiversity research. It is important to establish a relationship between microsatellite quantification and genetic information in barcodes. In order to clarify the association between the genetic information in barcodes (expressed as Shannon's Measure of Information, SMI) and microsatellites count, a total of 330,809 DNA barcodes from the BOLD database (Barcode of Life Data System) were analyzed. A parallel sliding-window algorithm was developed to compute the Shannon entropy of the barcodes, and this was compared with the quantification of microsatellites like (AT)n, (AC)n, and (AG)n. The microsatellite search method utilized an algorithm developed in the Java programming language, which systematically examined the genetic barcodes from an angiosperm database. For this purpose, a computational tool named Mfind was developed, and its search methodology is detailed. This comprehensive study revealed a broad overview of microsatellites within barcodes, unveiling an inverse correlation between the sumz of microsatellites count and barcodes information. The utilization of the Mfind tool demonstrated that the presence of microsatellites impacts the barcode information when considering entropy as a metric. This effect might be attributed to the concise length of DNA barcodes and the repetitive nature of microsatellites, resulting in a direct influence on the entropy of the barcodes.}, }
@article {pmid38670414, year = {2024}, author = {Lattos, A and Makri, V and Papadopoulos, DK and Gourzioti, E and Pagonis, C and Georgoulis, I and Karagiannis, D and Theodorou, JA and Michaelidis, B and Giantsis, IA and Feidantsis, K}, title = {Molecular characterization of Lernathropus kroyeri from intensive aquaculture and pathophysiology of infested sea bass.}, journal = {Fish &amp; shellfish immunology}, volume = {149}, number = {}, pages = {109576}, doi = {10.1016/j.fsi.2024.109576}, pmid = {38670414}, issn = {1095-9947}, mesh = {Animals ; *Bass/immunology ; *Copepoda/physiology/genetics ; *Fish Diseases/immunology/parasitology ; *Aquaculture ; *Phylogeny ; Greece ; Ectoparasitic Infestations/veterinary/parasitology/immunology ; }, abstract = {The copepod Lernathropus kroyeri constitutes one of the major parasites for the Mediterranean aquaculture, infesting the sea bass Dicentrarchus labrax causing thus disruptions of growth performance and occasionally mortalities. Despite the large spread and the high frequency of this parasite in mariculture farms of Eastern Mediterranean, L. kroyeri genetic profile from aquaculture as well as the pathophysiological response of D. labrax have not been studied so far. Keeping this in mind, in the present study we investigated the L. kroyeri infestation on D. labrax from two farms in Greece, examining both healthy and heavy parasitized individuals. Assays included histopathology, phylogenetic reconstruction of the parasite and physiological response of the fish by the means of antioxidant, inflammatory metabolic and stress related gene expression analysis at both mRNA and protein levels. Genetic analysis indicated that L. kroyeri composes a monophyletic group, highly phylogenetically distant from other congeneric groups. Heavy infested D. labrax witnessed a significantly increased immune response that further led to oxidative stress and metabolic alterations. Overall, our results demonstrate the, seasonally independent, high infestation of this parasitic copepods, which continue to affect Mediterranean intensive aquaculture systems.}, }
@article {pmid38670101, year = {2024}, author = {Holze, H and Talarmain, L and Fennell, KA and Lam, EY and Dawson, MA and Vassiliadis, D}, title = {Analysis of synthetic cellular barcodes in the genome and transcriptome with BARtab and bartools.}, journal = {Cell reports methods}, volume = {4}, number = {5}, pages = {100763}, pmid = {38670101}, issn = {2667-2375}, mesh = {*Transcriptome ; *Single-Cell Analysis/methods ; Humans ; *High-Throughput Nucleotide Sequencing ; Software ; DNA Barcoding, Taxonomic/methods ; Genome/genetics ; Cell Lineage/genetics ; Gene Expression Profiling/methods ; Computational Biology/methods ; Animals ; }, abstract = {Cellular barcoding is a lineage-tracing methodology that couples heritable synthetic barcodes to high-throughput sequencing, enabling the accurate tracing of cell lineages across a range of biological contexts. Recent studies have extended these methods by incorporating lineage information into single-cell or spatial transcriptomics readouts. Leveraging the rich biological information within these datasets requires dedicated computational tools for dataset pre-processing and analysis. Here, we present BARtab, a portable and scalable Nextflow pipeline, and bartools, an open-source R package, designed to provide an integrated end-to-end cellular barcoding analysis toolkit. BARtab and bartools contain methods to simplify the extraction, quality control, analysis, and visualization of lineage barcodes from population-level, single-cell, and spatial transcriptomics experiments. We showcase the utility of our integrated BARtab and bartools workflow via the analysis of exemplar bulk, single-cell, and spatial transcriptomics experiments containing cellular barcoding information.}, }
@article {pmid38667952, year = {2024}, author = {Guerra-Mateo, D and Cano-Lira, JF and Fernández-Bravo, A and Gené, J}, title = {Sunken Riches: Ascomycete Diversity in the Western Mediterranean Coast through Direct Plating and Flocculation, and Description of Four New Taxa.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {4}, pages = {}, pmid = {38667952}, issn = {2309-608X}, support = {PID2021-128068NB-100//Ministeri de Ci&#xe8;ncia Innovaci&#xf3; i Universitats/ ; }, abstract = {The Mediterranean Sea stands out as a hotspot of biodiversity, whose fungal composition remains underexplored. Marine sediments represent the most diverse substrate; however, the challenge of recovering fungi in culture hinders the precise identification of this diversity. Concentration techniques like skimmed milk flocculation (SMF) could represent a suitable solution. Here, we compare the effectiveness in recovering filamentous ascomycetes of direct plating and SMF in combination with three culture media and two incubation temperatures, and we describe the fungal diversity detected in marine sediments. Sediments were collected at different depths on two beaches (Miracle and Arrabassada) on the Spanish western Mediterranean coast between 2021 and 2022. We recovered 362 strains, and after a morphological selection, 188 were identified primarily with the LSU and ITS barcodes, representing 54 genera and 94 species. Aspergillus, Penicillium, and Scedosporium were the most common genera, with different percentages of abundance between both beaches. Arrabassada Beach was more heterogeneous, with 42 genera representing 60 species (Miracle Beach, 28 genera and 54 species). Although most species were recovered with direct plating (70 species), 20 species were exclusively obtained using SMF as a sample pre-treatment, improving our ability to detect fungi in culture. In addition, we propose three new species in the genera Exophiala, Nigrocephalum, and Queenslandipenidiella, and a fourth representing the novel genus Schizochlamydosporiella. We concluded that SMF is a useful technique that, in combination with direct plating, including different culture media and incubation temperatures, improves the chance of recovering marine fungal communities in culture-dependent studies.}, }
@article {pmid38667369, year = {2024}, author = {Aguado-Aranda, P and Ricarte, A and Nedeljković, Z and Hauser, M and Kelso, S and Sainz-Escudero, L and Skevington, JH and Marcos-García, M&#xc1;}, title = {Unveiling the Mainland vs. Insular Variability of the Eumerus barbarus Species Group (Diptera: Syrphidae) in the Western Mediterranean Basin.}, journal = {Insects}, volume = {15}, number = {4}, pages = {}, pmid = {38667369}, issn = {2075-4450}, support = {PRE2019-087508//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades (Spain)/ ; PGC2018-095851-A-C65//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades (Spain)/ ; IME 2022//Institut Menorqu&#xed; d'Estudis (Spain)/ ; }, abstract = {Comprising nearly 300 described species, Eumerus Meigen, 1822, is one of the most speciose syrphid genera worldwide, and its taxonomic diversity is remarkable in the Mediterranean basin. The Eumerus barbarus (Coquebert, 1804) group consists of four species in the western Mediterranean. Although the phenotypic variability of this species group has been commented on in previous studies, it has never been contrasted with molecular data. In the present work, the morphological variation found in 300+ specimens of this species group from the western Mediterranean is explored and tested against the COI mitochondrial DNA (mtDNA). The highest phenotypic disparity was found in E. barbarus and Eumerus sulcitibius Rondani 1868. The integrative approach has not revealed cryptic diversity within the species E. barbarus but in E. sulcitibius. As a result, a new species close to E. sulcitibius was discovered, Eumerus sardus Aguado-Aranda, Ricarte &amp; Hauser sp. n., from Sardinia, Italy. The new insular species is here described, illustrated, and discussed. A total of twenty-three haplotypes of COI mtDNA were identified amongst the analyzed Mediterranean specimens of E. barbarus, whereas two and five haplotypes were distinguished in the Iberian specimens of E. sulcitibius and Eumerus gibbosus van Steenis, Hauser &amp; van Zuijen, 2017, respectively. Moreover, the first known barcodes of E. gibbosus and Eumerus schmideggeri van Steenis, Hauser &amp; van Zuijen, 2017 were obtained, and the distribution ranges of all species are mapped. An updated dichotomous key to the males of the E. barbarus group from the western Mediterranean is provided.}, }
@article {pmid38667358, year = {2024}, author = {Wang, L and Wu, H and He, W and Lai, G and Li, J and Liu, S and Zhou, Q}, title = {Diversity of Parasitoid Wasps and Comparison of Sampling Strategies in Rice Fields Using Metabarcoding.}, journal = {Insects}, volume = {15}, number = {4}, pages = {}, pmid = {38667358}, issn = {2075-4450}, support = {2023KJ113//the Agricultural Science and Technology Innovative and Promotion Program of Guangdong Province/ ; }, abstract = {A comprehensive and precise evaluation of Arthropoda diversity in agricultural landscapes can enhance biological pest control strategies. We used Malaise traps and sweep nets to collect insects from three double-cropping paddy fields. DNA was extracted from the ethanol preservative of the Malaise traps and from tissue samples of selected parasitoid wasps. This was followed by amplification using DNA barcoding primers to prepare high-throughput sequencing libraries. We annotated a total of 4956 operational taxonomic units (OTUs), encompassing 174 genera and 32 families of parasitoid wasps. The ethanol filter method efficiently captured a wide range of information. However, the method has low resolution and may result in a reduced estimate of species abundance. Additional insect species were also identified in the parasitoid samples. This suggests that high throughput sequencing from adult parasitoid wasps can also detect host species, enabling a better understanding of host species and providing insights into food webs.}, }
@article {pmid38666586, year = {2024}, author = {Wang, J and Zhang, T and Gao, Z and Wei, M and Jia, Y and Tong, X and Hu, F and Zhao, YS}, title = {Two-Dimensional Lanthanide Metal-Organic Framework Heterostructures for Noninvasively Photoresponsive High-Security Photonic Barcodes.}, journal = {ACS applied materials &amp; interfaces}, volume = {16}, number = {18}, pages = {23576-23584}, doi = {10.1021/acsami.4c02440}, pmid = {38666586}, issn = {1944-8252}, abstract = {Stimuli-responsive micro/nanoscale photonic barcodes show great capacity for encryption and anticounterfeiting technologies due to multiple authentications, yet their application is commonly restricted by invasive stimuli. Herein, we report noninvasive light-stimulated high-security photonic barcodes based on spatially assembled photoresponsive two-dimensional (2D) 1,3,5-benzenetribenzoate (BTB)@Ln-MOF host-guest heterostructures. The photoluminescence (PL) spectra information on BTB@Ln-MOF heterostructures could be precisely controlled by the different wavelengths of ultraviolet (UV) light trigger. By using the PL properties and 2D heterostructures as cryptographic primitives, spatially resolved smart photonic barcodes based on both spectral and graphical coding are realized in BTB@Ln-MOF host-guest materials. These results will pave an avenue for the development of smart stimuli-responsive photonic barcodes for anticounterfeiting applications.}, }
@article {pmid38665980, year = {2023}, author = {Li, GS and Leal-Dutra, CA and Cuesta-Maté, A and Conlon, BH and Peereboom, N and Beemelmanns, C and Aanen, DK and Rosendahl, S and de Beer, ZW and Poulsen, M}, title = {Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution.}, journal = {Persoonia}, volume = {51}, number = {}, pages = {257-279}, pmid = {38665980}, issn = {0031-5850}, abstract = {The genus Podaxis was first described from India by Linnaeus in 1771, but several revisions of the genus have left the taxonomy unclear. Forty-four Podaxis species names and nine intraspecific varieties are currently accepted, but most fungarium specimens are labelled Podaxis pistillaris. Recent molecular analyses based on barcoding genes suggest that the genus comprises several species, but their status is largely unresolved. Here we obtained basidiospores and photographs from 166 fungarium specimens from around the world and generated a phylogeny based on rDNA internal transcribed spacer ITS1,5.8S and ITS2 (ITS), and a phylogenomic analysis of 3 839 BUSCO genes from low-coverage genomes for a subset of the specimens. Combining phylogenetics, phylogenomics, morphology, ecology, and geographical distribution, spanning 250 years of collections, we propose that the genus includes at least 16 unambiguous species. Based on 10 type specimens (holotype, paratype, and syntype), four recorded species were confirmed, P. carcinomalis, P. deflersii, P. emerici, and P. farlowii. Comparing phylogenetic analysis with described species, including morphology, ecology, and distribution, we resurrected P. termitophilus and designated neotypes, epitypes, or lectotypes for five previously described species, P. aegyptiacus, P. africana, P. beringamensis, P. calyptratus, and P. perraldieri. Lastly, based on phylogenies and morphology of type material, we synonymized three reported species, P. algericus, P. arabicus, and P. rugospora with P. pistillaris, and described five new species that we named P. desolatus, P. inyoensis, P. mareebaensis, P. namaquensis, and P. namibensis. Citation: Li GS, Leal-Dutra CA, Cuesta-Maté A, et al. 2023. Resolution of eleven reported and five novel Podaxis species based on ITS phylogeny, phylogenomics, morphology, ecology, and geographic distribution. Persoonia 51: 257-279. doi: 10.3767/persoonia.2023.51.07.}, }
@article {pmid38665977, year = {2023}, author = {Crous, PW and Costa, MM and Kandemir, H and Vermaas, M and Vu, D and Zhao, L and Arumugam, E and Flakus, A and Jurjević, &#x17d; and Kaliyaperumal, M and Mahadevakumar, S and Murugadoss, R and Shivas, RG and Tan, YP and Wingfield, MJ and Abell, SE and Marney, TS and Danteswari, C and Darmostuk, V and Denchev, CM and Denchev, TT and Etayo, J and Gené, J and Gunaseelan, S and Hubka, V and Illescas, T and Jansen, GM and Kezo, K and Kumar, S and Larsson, E and Mufeeda, KT and Piątek, M and Rodriguez-Flakus, P and Sarma, PVSRN and Stryjak-Bogacka, M and Torres-Garcia, D and Vauras, J and Acal, DA and Akulov, A and Alhudaib, K and Asif, M and Balashov, S and Baral, HO and Baturo-Cieśniewska, A and Begerow, D and Beja-Pereira, A and Bianchinotti, MV and Bilański, P and Chandranayaka, S and Chellappan, N and Cowan, DA and Custódio, FA and Czachura, P and Delgado, G and De Silva, NI and Dijksterhuis, J and Dueñas, M and Eisvand, P and Fachada, V and Fournier, J and Fritsche, Y and Fuljer, F and Ganga, KGG and Guerra, MP and Hansen, K and Hywel-Jones, N and Ismail, AM and Jacobs, CR and Jankowiak, R and Karich, A and Kemler, M and Kisło, K and Klofac, W and Krisai-Greilhuber, I and Latha, KPD and Lebeuf, R and Lopes, ME and Lumyong, S and Maciá-Vicente, JG and Maggs-Kölling, G and Magistà, D and Manimohan, P and Martín, MP and Mazur, E and Mehrabi-Koushki, M and Miller, AN and Mombert, A and Ossowska, EA and Patejuk, K and Pereira, OL and Piskorski, S and Plaza, M and Podile, AR and Polhorský, A and Pusz, W and Raza, M and Ruszkiewicz-Michalska, M and Saba, M and Sánchez, RM and Singh, R and Śliwa, L and Smith, ME and Stefenon, VM and Strasiftáková, D and Suwannarach, N and Szczepańska, K and Telleria, MT and Tennakoon, DS and Thines, M and Thorn, RG and Urbaniak, J and van der Vegte, M and Vasan, V and Vila-Viçosa, C and Voglmayr, H and Wrzosek, M and Zappelini, J and Groenewald, JZ}, title = {Fungal Planet description sheets: 1550-1613.}, journal = {Persoonia}, volume = {51}, number = {}, pages = {280-417}, pmid = {38665977}, issn = {0031-5850}, abstract = {Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.}, }
@article {pmid38665369, year = {2024}, author = {Sun, W and Wei, Z and Gu, Y and Wang, T and Liu, B and Yan, Y}, title = {Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1328080}, pmid = {38665369}, issn = {1664-462X}, abstract = {Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.}, }
@article {pmid38661214, year = {2024}, author = {Ylagan, M and Xu, Q and Kowalski, J}, title = {TTSBBC: triplex target site biomarkers and barcodes in cancer.}, journal = {Nucleic acids research}, volume = {52}, number = {W1}, pages = {W547-W555}, pmid = {38661214}, issn = {1362-4962}, support = {//University of Texas Dell Medical School Research Funds/ ; }, mesh = {Humans ; *DNA/chemistry/genetics/metabolism ; *Neoplasms/genetics/metabolism ; Software ; Biomarkers, Tumor/genetics/metabolism ; Oligonucleotides/chemistry ; Binding Sites ; Nucleic Acid Conformation ; DNA Barcoding, Taxonomic/methods ; }, abstract = {The technology of triplex-forming oligonucleotides (TFOs) provides an approach to manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a unique intermolecular triple-helix DNA structure through Hoogsteen hydrogen bonding. This targeting by TFOs is site-specific and the locations TFOs bind are referred to as TFO target sites (TTS). Triplexes have been observed to selectively influence gene expression, homologous recombination, mutations, protein binding, and DNA damage. These sites typically feature a poly-purine sequence in duplex DNA, and the characteristics of these TTS sequences greatly influence the formation of the triplex. We introduce TTSBBC, a novel analysis and visualization platform designed to explore features of TTS sequences to enable users to design and validate TTSs. The web server can be freely accessed at https://kowalski-labapps.dellmed.utexas.edu/TTSBBC/.}, }
@article {pmid38660246, year = {2024}, author = {Lin, T and Liu, D and Guan, Z and Zhao, X and Li, S and Wang, X and Hou, R and Zheng, J and Cao, J and Shi, M}, title = {CRISPR screens in mechanism and target discovery for AML.}, journal = {Heliyon}, volume = {10}, number = {8}, pages = {e29382}, pmid = {38660246}, issn = {2405-8440}, abstract = {CRISPR-based screens have discovered novel functional genes involving in diverse tumor biology and elucidated the mechanisms of the cancer pathological states. Recently, with its randomness and unbiasedness, CRISPR screens have been used to discover effector genes with previously unknown roles for AML. Those novel targets are related to AML survival resembled cellular pathways mediating epigenetics, synthetic lethality, transcriptional regulation, mitochondrial and energy metabolism. Other genes that are crucial for pharmaceutical targeting and drug resistance have also been identified. With the rapid development of novel strategies, such as barcodes and multiplexed mosaic CRISPR perturbation, more potential therapeutic targets and mechanism in AML will be discovered. In this review, we present an overview of recent progresses in the development of CRISPR-based screens for the mechanism and target identification in AML and discuss the challenges and possible solutions in this rapidly growing field.}, }
@article {pmid38659825, year = {2024}, author = {Simon, JJ and Fowler, DM and Maly, DJ}, title = {Multiplexed, multimodal profiling of the intracellular activity, interactions, and druggability of protein variants using LABEL-seq.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38659825}, issn = {2692-8205}, support = {R01 GM086858/GM/NIGMS NIH HHS/United States ; R01 GM145011/GM/NIGMS NIH HHS/United States ; }, abstract = {Multiplexed assays of variant effect are powerful tools for assessing the impact of protein sequence variation, but are limited to measuring a single protein property and often rely on indirect readouts of intracellular protein function. Here, we developed LAbeling with Barcodes and Enrichment for biochemicaL analysis by sequencing (LABEL-seq), a platform for the multimodal profiling of thousands of protein variants in cultured human cells. Multimodal measurement of ~20,000 variant effects for ~1,600 BRaf variants using LABEL-seq revealed that variation at positions that are frequently mutated in cancer had minimal effects on folding and intracellular abundance but could dramatically alter activity, protein-protein interactions, and druggability. Integrative analysis of our multimodal measurements identified networks of positions with similar roles in regulating BRaf's signaling properties and enabled predictive modeling of variant effects on complex processes such as cell proliferation and small molecule-promoted degradation. LABEL-seq provides a scalable approach for the direct measurement of multiple biochemical effects of protein variants in their native cellular context, yielding insight into protein function, disease mechanisms, and druggability.}, }
@article {pmid38656593, year = {2024}, author = {Al-Sarar, AS and Abobakr, Y and Alzabib, AA and Saleh, AA}, title = {First Report on Banana Weevil, Cosmopolites sordidus (Germar 1823) (Coleoptera: Curculionidae), an Exotic Economically Important Pest from Saudi Arabia.}, journal = {Neotropical entomology}, volume = {53}, number = {3}, pages = {461-468}, pmid = {38656593}, issn = {1678-8052}, support = {2-17-04-001-0040//National Plan for Science, Technology and Innovation/ ; }, mesh = {Animals ; *Weevils/classification ; Saudi Arabia ; *Musa/parasitology ; Female ; Male ; }, abstract = {We report the first record of the occurrence of the banana weevil, Cosmopolites sordidus (Germar, 1823) (Coleoptera: Curculionidae), an economically important pest of bananas (Musa spp.), from Fifa Mountains in Saudi Arabia. Moreover, we recorded the first observation of damage caused to bananas by C. sordidus in a banana farm in Jazan Province, southwestern Saudi Arabia, in March 2022. Molecular characterization using DNA sequences of the mitochondrial COI gene confirmed the morphological identification of C. sordidus. This discovery is considered a warning notice to prevent the potential establishment and spread of this dangerous pest in the banana cultivation regions in Saudi Arabia. Therefore, it is recommended that detection and monitoring of banana weevil should be undertaken in Saudi banana farms in order to restrict the dissemination of this weevil to other banana cultivation areas.}, }
@article {pmid38656472, year = {2024}, author = {Yuan, JM and Su, J and Zhang, ZH and Sun, B and Jiao, XL and Zhang, X and Zhai, YP and Chen, YJ}, title = {Initial study and phylogenetic analysis of hard ticks (Acari: Ixodidae) in Nantong, China along the route of avian migration.}, journal = {Experimental &amp; applied acarology}, volume = {92}, number = {4}, pages = {871-883}, pmid = {38656472}, issn = {1572-9702}, support = {MS2023092//Research Project Foundation of Nantong Health Commission/ ; }, mesh = {Animals ; China ; *Ixodidae/genetics/classification/physiology ; *Phylogeny ; *Electron Transport Complex IV/genetics/analysis ; *Animal Migration ; *Birds ; RNA, Ribosomal/genetics/analysis ; Nymph/growth &amp; development/classification/genetics/physiology ; Arthropod Proteins/genetics/analysis ; DNA, Ribosomal Spacer/analysis ; }, abstract = {The growing concern about migratory birds potentially spreading ticks due to global warming has become a significant issue. The city of Nantong in this study is situated along the East Asia-Australasian Flyway (EAAF), with numerous wetlands serving as roosting sites for migratory birds. We conducted an investigation of hard ticks and determined the phylogenetic characteristics of tick species in this city. We utilized three different genes for our study: the mitochondrial cytochrome oxidase subunit 1 (COX1) gene, the second internal transcribed spacer (ITS2), and the mitochondrial small subunit rRNA (12 S rRNA) gene. The predominant tick species were Haemaphysalis flava (H. flava) and Haemaphysalis longicornis (H. longicornis). Additionally, specimens of Haemaphysalis campanulata (H. campanulata) and Rhipicephalus sanguineus (R. sanguineus) were collected. The H. flava specimens in this study showed a close genetic relationship with those from inland provinces of China, as well as South Korea and Japan. Furthermore, samples of H. longicornis exhibited a close genetic relationship with those from South Korea, Japan, Australia, and the USA, as well as specific provinces in China. Furthermore, R. sanguineus specimens captured in Nantong showed genetic similarities with specimens from Egypt, Nigeria, and Argentina.}, }
@article {pmid38656420, year = {2024}, author = {Oyuntsetseg, D and Nyamgerel, N and Baasanmunkh, S and Oyuntsetseg, B and Urgamal, M and Yoon, JW and Bayarmaa, GA and Choi, HJ}, title = {The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia.}, journal = {Botanical studies}, volume = {65}, number = {1}, pages = {11}, pmid = {38656420}, issn = {1817-406X}, support = {P2023-4591//National University of Mongolia/ ; KNA1-2-42, 22-2//Korea National Arboretum/ ; 2023R1A6C101B022//Korea Basic Science Institute/ ; }, abstract = {BACKGROUND: Swertia banzragczii and S. marginata are important medicinal species in Mongolia. However, their taxonomic positions and genetic backgrounds remain unknown. In this study, we explored the complete chloroplast genomes and DNA barcoding of these species and compared them with those of closely related species within the subgenus to determine their taxonomic positions and phylogenetic relationships.<br><br>RESULT: The chloroplast genomes of S. banzragczii and S. marginata encoded 114 genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 16 genes contained a single intron, and 2 genes had two introns. Closely related species had a conserved genome structure and gene content. Only differences in genome length were noticed, which were caused by the expansion and contraction of the inverted repeat (IR) region and loss of exons in some genes. The trnH-GUG-psbA and trnD-GUC-trnY-GUA intergenic regions had high genetic diversity within Swertia plastomes. Overall, S. banzragczii and S. marginata are true species and belong to the subgenus Swertia.<br><br>CONCLUSIONS: These results provide valuable genetic and morphological information on rare and subendemic Swertia species in Mongolia, which can be used for further advanced studies on the Swertia genus.}, }
@article {pmid38655012, year = {2024}, author = {Ståhls, G}, title = {Pelecocera (Pelecocera) tricincta and Pelecocera (Chamaesyrphus) caledonica (Diptera, Syrphidae) reared from Rhizopogon fungal host in Finland.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e118563}, pmid = {38655012}, issn = {1314-2828}, abstract = {MtDNA COI barcodes have frequently been used in identification to associate an unknown life stage in insects with a known species. This study reports the discovery of hoverfly larvae in the fungal fruit bodies of Rhizopogonluteolus Fr. &amp; Nordholm, 1817 in Finland. The identity of the larvae was firstly resolved using mtDNA COI barcodes generated from the larvae and tree-based identification confirming the species Pelecocera (Pelecocera) tricincta Meigen, 1822 and Pelecocera (Chamaesyrphus) caledonica (Collin, 1940) (Diptera, Syrphidae). Obtained pupae were reared into adult flies and produced the same two species. The morphological features of these mycophagous larvae are compared with those of other fungus-feeding hoverfly species. This study confirms Rhizopogonluteolus as fungal host for these Pelecocera species in the Western Palaearctic Region.}, }
@article {pmid38655011, year = {2024}, author = {Kim, S and Čkrkić, J and Tomanović, &#x17d; and Sohn, JH and Lim, J and Kim, H}, title = {A new species of genus Monoctonus (Hymenoptera, Braconidae, Aphidiinae) from South Korea.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e119476}, pmid = {38655011}, issn = {1314-2828}, abstract = {BACKGROUND: The genus Monoctonus Haliday, 1833 is a small group which consists of 24 species worldwide. In South Korea, Chang and Youn (1983) recorded one species, M.similis Starý &amp; Schlinger, 1967, but the evidence for identification of this species is doubtful and further confirmation is required (personal communication with Prof. Jong-Cheol Paik).<br><br>NEW INFORMATION: An additional Monoctonus species is recorded as new to science from South Korea. Descriptions and illustrations of the new species -Monoctonuskoreanus sp. nov. - are provided, together with its mitochondrial cytochrome c oxidase subunit I (COI) data and phylogenetic position. A key to the female of the two species present in Korea is provided.}, }
@article {pmid38652658, year = {2024}, author = {Cheng, YL and Banu, MA and Zhao, W and Rosenfeld, SS and Canoll, P and Sims, PA}, title = {Multiplexed single-cell lineage tracing of mitotic kinesin inhibitor resistance in glioblastoma.}, journal = {Cell reports}, volume = {43}, number = {5}, pages = {114139}, pmid = {38652658}, issn = {2211-1247}, support = {R01 NS118513/NS/NINDS NIH HHS/United States ; U01 CA168426/CA/NCI NIH HHS/United States ; S10 OD032433/OD/NIH HHS/United States ; R01 NS103473/NS/NINDS NIH HHS/United States ; U01 CA272610/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Glioblastoma/pathology/genetics/metabolism/drug therapy ; *Kinesins/metabolism/antagonists &amp; inhibitors/genetics ; *Drug Resistance, Neoplasm/drug effects/genetics ; Animals ; *Single-Cell Analysis ; *Cell Lineage/drug effects ; Mice ; Brain Neoplasms/pathology/genetics/drug therapy/metabolism ; Cell Line, Tumor ; Mitosis/drug effects ; }, abstract = {Glioblastoma (GBM) is a deadly brain tumor, and the kinesin motor KIF11 is an attractive therapeutic target with roles in proliferation and invasion. Resistance to KIF11 inhibitors, which has mainly been studied in animal models, presents significant challenges. We use lineage-tracing barcodes and single-cell RNA sequencing to analyze resistance in patient-derived GBM neurospheres treated with ispinesib, a potent KIF11 inhibitor. Similar to GBM progression in patients, untreated cells lose their neural lineage identity and become mesenchymal, which is associated with poor prognosis. Conversely, cells subjected to long-term ispinesib treatment exhibit a proneural phenotype. We generate patient-derived xenografts and show that ispinesib-resistant cells form less aggressive tumors in vivo, even in the absence of drug. Moreover, treatment of human ex vivo GBM slices with ispinesib demonstrates phenotypic alignment with in vitro responses, underscoring the clinical relevance of our findings. Finally, using retrospective lineage tracing, we identify drugs that are synergistic with ispinesib.}, }
@article {pmid38646932, year = {2024}, author = {Saranholi, BH and França, FM and Vogler, AP and Barlow, J and Vaz de Mello, FZ and Maldaner, ME and Carvalho, E and Gestich, CC and Howes, B and Banks-Leite, C and Galetti, PM}, title = {Testing and optimizing metabarcoding of iDNA from dung beetles to sample mammals in the hyperdiverse Neotropics.}, journal = {Molecular ecology resources}, volume = {24}, number = {5}, pages = {e13961}, doi = {10.1111/1755-0998.13961}, pmid = {38646932}, issn = {1755-0998}, support = {1989427//University of Bristol (PolicyBristol, SYNPAM)/ ; ProjectBIOCLIMATE//BNP Paribas Foundation (Climate and Biodiversity Initiative)/ ; 2258319//Cabot Seedcorn 2023 (Voices of Amazonia)/ ; 303524/2019-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 406767/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 420254/2018-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441257/2023-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441573/2020-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441659/2016-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 1777136//University of Bristol (Liv Sidse Jansen Memorial Foundation, FOR-TRAITS)/ ; NE/S011811/1//Natural Environment Research Council/ ; 170839//Climate and Net Zero Impact Awards (Scaling-up TAOCA)/ ; MR/X032949/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Coleoptera/genetics/classification ; *Mammals/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; Biodiversity ; Metagenomics/methods ; DNA/genetics ; Feces/chemistry ; }, abstract = {Over the past few years, insects have been used as samplers of vertebrate diversity by assessing the ingested-derived DNA (iDNA), and dung beetles have been shown to be a good mammal sampler given their broad feeding preference, wide distribution and easy sampling. Here, we tested and optimized the use of iDNA from dung beetles to assess the mammal community by evaluating if some biological and methodological aspects affect the use of dung beetles as mammal species samplers. We collected 403 dung beetles from 60 pitfall traps. iDNA from each dung beetle was sequenced by metabarcoding using two mini-barcodes (12SrRNA and 16SrRNA). We assessed whether dung beetles with different traits related to feeding, nesting and body size differed in the number of mammal species found in their iDNA. We also tested differences among four killing solutions in preserving the iDNA and compared the effectiveness of each mini barcode to recover mammals. We identified a total of 50 mammal OTUs (operational taxonomic unit), including terrestrial and arboreal species from 10 different orders. We found that at least one mammal-matching sequence was obtained from 70% of the dung beetle specimens. The number of mammal OTUs obtained did not vary with dung beetle traits as well as between the killing solutions. The 16SrRNA mini-barcode recovered a higher number of mammal OTUs than 12SrRNA, although both sets were partly non-overlapping. Thus, the complete mammal diversity may not be achieved by using only one of them. This study refines the methodology for routine assessment of tropical mammal communities via dung beetle 'samplers' and its universal applicability independently of the species traits of local beetle communities.}, }
@article {pmid38646006, year = {2024}, author = {Banerjee, P and Dey, G and Maity, JP and Stewart, KA and Sharma, RK and Chan, MWY and Lee, K and Chen, CY}, title = {The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P. maculata (Golden apple snails) across Taiwan.}, journal = {Ecology and evolution}, volume = {14}, number = {4}, pages = {e11268}, pmid = {38646006}, issn = {2045-7758}, abstract = {The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.}, }
@article {pmid38645306, year = {2024}, author = {Lammertse, E and Li, S and Kendall, J and Kim, C and Morris, P and Ranade, N and Levy, D and Wigler, M and Brouzes, E}, title = {Magnetically functionalized hydrogels for high-throughput genomic applications.}, journal = {Advanced materials technologies}, volume = {9}, number = {2}, pages = {}, pmid = {38645306}, issn = {2365-709X}, support = {R01 CA181595/CA/NCI NIH HHS/United States ; }, abstract = {Single-cell genomics has revolutionized tissue analysis by revealing the genetic program of individual cells. The key aspect of the technology is the use of barcoded beads to unambiguously tag sequences originating from a single cell. The generation of unique barcodes on beads is mainly achieved by split-pooling methods, which are labor-intensive due to repeated washing steps. Towards the automation of the split-pooling method, we developed a simple method to magnetize hydrogel beads. We show that these hydrogel beads provide increased yields and washing efficiencies for purification procedures. They are also fully compatible with single-cell sequencing using the BAG-Seq workflow. Our work opens the automation of the split-pooling technique, which will improve single-cell genomic workflows.}, }
@article {pmid38643988, year = {2024}, author = {Nathans, JF and Ayers, JL and Shendure, J and Simpson, CL}, title = {Genetic Tools for Cell Lineage Tracing and Profiling Developmental Trajectories in the Skin.}, journal = {The Journal of investigative dermatology}, volume = {144}, number = {5}, pages = {936-949}, pmid = {38643988}, issn = {1523-1747}, support = {K08 AR075846/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; *Cell Lineage ; Animals ; *Cell Differentiation ; Skin/cytology ; Stem Cells/cytology ; Cell Proliferation ; Regeneration/physiology ; }, abstract = {The epidermis is the body's first line of protection against dehydration and pathogens, continually regenerating the outermost protective skin layers throughout life. During both embryonic development and wound healing, epidermal stem and progenitor cells must respond to external stimuli and insults to build, maintain, and repair the cutaneous barrier. Recent advances in CRISPR-based methods for cell lineage tracing have remarkably expanded the potential for experiments that track stem and progenitor cell proliferation and differentiation over the course of tissue and even organismal development. Additional tools for DNA-based recording of cellular signaling cues promise to deepen our understanding of the mechanisms driving normal skin morphogenesis and response to stressors as well as the dysregulation of cell proliferation and differentiation in skin diseases and cancer. In this review, we highlight cutting-edge methods for cell lineage tracing, including in organoids and model organisms, and explore how cutaneous biology researchers might leverage these techniques to elucidate the developmental programs that support the regenerative capacity and plasticity of the skin.}, }
@article {pmid38642645, year = {2024}, author = {Alloun, W and Berkani, M and Shavandi, A and Beddiar, A and Pellegrini, M and Garzia, M and Lakhdari, D and Ganachari, SV and Aminabhavi, TM and Vasseghian, Y and Muddapur, U and Chaouche, NK}, title = {Harnessing artificial intelligence-driven approach for enhanced indole-3-acetic acid from the newly isolated Streptomyces rutgersensis AW08.}, journal = {Environmental research}, volume = {252}, number = {Pt 3}, pages = {118933}, doi = {10.1016/j.envres.2024.118933}, pmid = {38642645}, issn = {1096-0953}, mesh = {*Streptomyces/genetics/metabolism ; *Artificial Intelligence ; *Indoleacetic Acids/metabolism ; *RNA, Ribosomal, 16S/genetics ; Algeria ; Phylogeny ; }, abstract = {Indole-3-acetic acid (IAA) derived from Actinobacteria fermentations on agro-wastes constitutes a safer and low-cost alternative to synthetic IAA. This study aims to select a high IAA-producing Streptomyces-like strain isolated from Lake Oubeira sediments (El Kala, Algeria) for further investigations (i.e., 16S rRNA gene barcoding and process optimization). Subsequently, artificial intelligence-based approaches were employed to maximize IAA bioproduction on spent coffee grounds as high-value-added feedstock. The specificity was the novel application of the Limited-Memory Broyden-Fletcher-Goldfarb-Shanno Box (L-BFGS-B) optimization algorithm. The new strain AW08 was a significant producer of IAA (26.116 ± 0.61 μg/mL) and was identified as Streptomyces rutgersensis by 16S rRNA gene barcoding and phylogenetic inquiry. The empirical data involved the inoculation of AW08 in various cultural conditions according to a four-factor Box Behnken Design matrix (BBD) of Response surface methodology (RSM). The input parameters and regression equation extracted from the RSM-BBD were the basis for implementing and training the L-BFGS-B algorithm. Upon training the model, the optimal conditions suggested by the BBD and L-BFGS-B algorithm were, respectively, L-Trp (X1) = 0.58 %; 0.57 %; T° (X2) = 26.37 °C; 28.19 °C; pH (X3) = 7.75; 8.59; and carbon source (X4) = 30 %; 33.29 %, with the predicted response IAA (Y) = 152.8; 169.18 μg/mL). Our findings emphasize the potential of the multifunctional S. rutgersensis AW08, isolated and reported for the first time in Algeria, as a robust producer of IAA. Validation investigations using the bioprocess parameters provided by the L-BFGS-B and the BBD-RSM models demonstrate the effectiveness of AI-driven optimization in maximizing IAA output by 5.43-fold and 4.2-fold, respectively. This study constitutes the first paper reporting a novel interdisciplinary approach and providing insights into biotechnological advancements. These results support for the first time a reasonable approach for valorizing spent coffee grounds as feedstock for sustainable and economic IAA production from S. rutgersensis AW08.}, }
@article {pmid38641660, year = {2024}, author = {Reicher, A and Reiniš, J and Ciobanu, M and Růžička, P and Malik, M and Siklos, M and Kartysh, V and Tomek, T and Koren, A and Rendeiro, AF and Kubicek, S}, title = {Pooled multicolour tagging for visualizing subcellular protein dynamics.}, journal = {Nature cell biology}, volume = {26}, number = {5}, pages = {745-756}, pmid = {38641660}, issn = {1476-4679}, support = {ERC-CoG-772437//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LS21-01//Vienna Science and Technology Fund (Wiener Wissenschafts-, Forschungs- und Technologiefonds)/ ; }, mesh = {Humans ; *Proteomics/methods ; Machine Learning ; Microscopy, Fluorescence/methods ; Cell Line, Tumor ; }, abstract = {Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.}, }
@article {pmid38637345, year = {2024}, author = {Patil, GS and Pinto, N and Nath, R and Goswami, M}, title = {Decoding the molecular phylogenetics of ornamental catfishes (siluriformes) of North East India using DNA barcoding approach.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {528}, pmid = {38637345}, issn = {1573-4978}, support = {BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR16430/NER/95/201/2015//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; Humans ; *Catfishes/genetics ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; DNA ; India ; }, abstract = {BACKGROUND: Catfishes (order Siluriformes) are among the most diverse and widely distributed fish groups in the world. They are not only used for human consumption but are also a major part of the ornamental fish trade. Being a Biodiversity Hotspot, the North Eastern Region of India is home to a diverse population of ornamental fishes. Catfishes contain a humongous number of species; in this study, the authors have tried to elucidate the phylogenetic relationship of some important ornamental catfishes found in North East India using DNA barcodes.<br><br>METHODS AND RESULTS: In this study, we have tried to explore the phylogenetic history of 13 species (41 specimens) of ornamental catfishes spanning 12 genera and 9 families of Siluriformes using DNA barcoding. Pairwise genetic distances using Kimura 2-Parameter (K2P) were calculated at intra-specific and inter-specific levels. A Neighbor-Joining tree was constructed to understand the phylogenetic relationship among the nine different catfish families. All the specimens under this study clustered with their respective species under the same family and formed three sub-clades. However, Olyra longicaudata, belonging to the Bagridae family, did not cluster with other species from the same family. In this study, the authors have suggested a revision of the classification of O. longicaudata back to its original family, Olyridae.<br><br>CONCLUSIONS: In this study, the maximum intraspecific genetic distance of 0.03 and the minimum interspecific genetic distance of 0.14 were observed among the species. Therefore, it is evident that there is a barcoding gap among the species, which helped in the correct identification of the species. Thus, DNA barcoding helped complement the phenetic approach and also revealed a different phylogenetic relationship among the catfishes belonging to the Bagridae family.}, }
@article {pmid38635627, year = {2024}, author = {Chevée, V and Hullahalli, K and Dailey, KG and Güereca, L and Zhang, C and Waldor, MK and Portnoy, DA}, title = {Temporal and spatial dynamics of Listeria monocytogenes central nervous system infection in mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {17}, pages = {e2320311121}, pmid = {38635627}, issn = {1091-6490}, support = {R25 GM140276/GM/NIGMS NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; R01 AI027655/AI/NIAID NIH HHS/United States ; F31 AI156949/AI/NIAID NIH HHS/United States ; P01 AI063302/AI/NIAID NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Listeria monocytogenes/physiology ; *Listeriosis/microbiology ; Brain/microbiology ; *Central Nervous System Infections ; }, abstract = {Listeria monocytogenes is a bacterial pathogen that can cause life-threatening central nervous system (CNS) infections. While mechanisms by which L. monocytogenes and other pathogens traffic to the brain have been studied, a quantitative understanding of the underlying dynamics of colonization and replication within the brain is still lacking. In this study, we used barcoded L. monocytogenes to quantify the bottlenecks and dissemination patterns that lead to cerebral infection. Following intravenous (IV) inoculation, multiple independent invasion events seeded all parts of the CNS from the blood, however, only one clone usually became dominant in the brain. Sequential IV inoculations and intracranial inoculations suggested that clones that had a temporal advantage (i.e., seeded the CNS first), rather than a spatial advantage (i.e., invaded a particular brain region), were the main drivers of clonal dominance. In a foodborne model of cerebral infection with immunocompromised mice, rare invasion events instead led to a highly infected yet monoclonal CNS. This restrictive bottleneck likely arose from pathogen transit into the blood, rather than directly from the blood to the brain. Collectively, our findings provide a detailed quantitative understanding of the L. monocytogenes population dynamics that lead to CNS infection and a framework for studying the dynamics of other cerebral infections.}, }
@article {pmid38634956, year = {2024}, author = {Chakraborty, M and Kaur, J and Gunjan,  and Kathpalia, M and Kaur, N}, title = {Clinical relevance of glycosylation in triple negative breast cancer: a review.}, journal = {Glycoconjugate journal}, volume = {41}, number = {2}, pages = {79-91}, pmid = {38634956}, issn = {1573-4986}, mesh = {Female ; Humans ; Biomarkers, Tumor/metabolism ; Clinical Relevance ; Glycosylation ; *Triple Negative Breast Neoplasms/metabolism ; }, abstract = {Glycosylation alterations in TNBC have significant implications for tumor behavior, diagnosis, prognosis, and therapeutic strategies. Dysregulated glycosylation affects cell adhesion, signaling, immune recognition, and response to therapy in TNBC. Different types of glycosylation, including N-linked glycosylation, O-linked glycosylation, glycosphingolipid glycosylation, mucin-type glycosylation, and sialylation, play distinct roles in TNBC. The "barcoding" method based on glycosylation sites of the membrane type mannose receptor (MR) shows promise in accurately distinguishing breast cancer subtypes, including TNBC. Alpha-L-fucosidase 1 (FUCA1) and Monocarboxylate transporter 4 (MCT4) have been identified as potential diagnostic and prognostic markers for TNBC. The glycosylation status of PD-L1 impacts the response to immune checkpoint blockade therapy in TNBC. Inhibiting fucosylation of B7H3 enhances immune responses and improves anti-tumor effects. Targeting glycosylated B7H4 and modulating estrogen metabolism through glycosylation-related mechanisms are potential therapeutic strategies for TNBC. Understanding the role of glycosylation in TNBC provides insights into disease mechanisms, diagnosis, and potential therapeutic targets. Further research in this field may lead to personalized treatment approaches and improved outcomes for TNBC patients.}, }
@article {pmid38633369, year = {2024}, author = {Kang, S and Choi, P and Maile-Moskowitz, A and Brown, CL and Gonzalez, RA and Pruden, A and Vikesland, PJ}, title = {Highly Multiplexed Reverse-Transcription Loop-Mediated Isothermal Amplification and Nanopore Sequencing (LAMPore) for Wastewater-Based Surveillance.}, journal = {ACS ES&amp;T water}, volume = {4}, number = {4}, pages = {1629-1636}, pmid = {38633369}, issn = {2690-0637}, abstract = {Wastewater-based surveillance (WBS) has gained attention as a strategy to monitor and provide an early warning for disease outbreaks. Here, we applied an isothermal gene amplification technique, reverse-transcription loop-mediated isothermal amplification (RT-LAMP), coupled with nanopore sequencing (LAMPore) as a means to detect SARS-CoV-2. Specifically, we combined barcoding using both an RT-LAMP primer and the nanopore rapid barcoding kit to achieve highly multiplexed detection of SARS-CoV-2 in wastewater. RT-LAMP targeting the SARS-CoV-2 N region was conducted on 96 reactions including wastewater RNA extracts and positive and no-target controls. The resulting amplicons were pooled and subjected to nanopore sequencing, followed by demultiplexing based on barcodes that differentiate the source of each SARS-CoV-2 N amplicon derived from the 96 RT-LAMP products. The criteria developed and applied to establish whether SARS-CoV-2 was detected by the LAMPore assay indicated high consistency with polymerase chain reaction-based detection of the SARS-CoV-2 N gene, with a sensitivity of 89% and a specificity of 83%. We further profiled sequence variations on the SARS-CoV-2 N amplicons, revealing a number of mutations on a sample collected after viral variants had emerged. The results demonstrate the potential of the LAMPore assay to facilitate WBS for SARS-CoV-2 and the emergence of viral variants in wastewater.}, }
@article {pmid38632506, year = {2024}, author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ}, title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {380}, pmid = {38632506}, issn = {1471-2164}, mesh = {Animals ; *Borrelia/genetics ; DNA ; *Microbiota ; Multilocus Sequence Typing ; Orientia ; *Orientia tsutsugamushi/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rodentia/genetics ; Saudi Arabia ; *Scrub Typhus/epidemiology/microbiology ; *Trombiculidae/genetics/microbiology ; *Wolbachia/genetics ; }, abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.<br><br>RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.<br><br>CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.}, }
@article {pmid38631624, year = {2024}, author = {Hu, H and Liu, L and Wei, XY and Duan, JJ and Deng, JY and Pei, DS}, title = {Revolutionizing aquatic eco-environmental monitoring: Utilizing the RPA-Cas-FQ detection platform for zooplankton.}, journal = {The Science of the total environment}, volume = {929}, number = {}, pages = {172414}, doi = {10.1016/j.scitotenv.2024.172414}, pmid = {38631624}, issn = {1879-1026}, mesh = {*Zooplankton ; *Environmental Monitoring/methods ; Animals ; CRISPR-Cas Systems ; DNA, Environmental/analysis ; Nucleic Acid Amplification Techniques/methods ; Recombinases/metabolism ; }, abstract = {The integration of recombinase polymerase amplification (RPA) with CRISPR/Cas technology has revolutionized molecular diagnostics and pathogen detection due to its unparalleled sensitivity and trans-cleavage ability. However, its potential in the ecological and environmental monitoring scenarios for aquatic ecosystems remains largely unexplored, particularly in accurate qualitative/quantitative detection, and its actual performance in handling complex real environmental samples. Using zooplankton as a model, we have successfully optimized the RPA-CRISPR/Cas12a fluorescence detection platform (RPA-Cas-FQ), providing several crucial "technical tips". Our findings indicate the sensitivity of CRISPR/Cas12a alone is 5 × 10[9] copies/reaction, which can be dramatically increased to 5 copies/reaction when combined with RPA. The optimized RPA-Cas-FQ enables reliable qualitative and semi-quantitative detection within 50 min, and exhibits a good linear relationship between fluorescence intensity and DNA concentration (R[2] = 0.956-0.974***). Additionally, we developed a rapid and straightforward identification procedure for single zooplankton by incorporating heat-lysis and DNA-barcode techniques. We evaluated the platform's effectiveness using real environmental DNA (eDNA) samples from the Three Gorges Reservoir, confirming its practicality. The eDNA-RPA-Cas-FQ demonstrated strong consistency (Kappa = 0.43***) with eDNA-Metabarcoding in detecting species presence/absence in the reservoir. Furthermore, the two semi-quantitative eDNA technologies showed a strong positive correlation (R[2] = 0.58-0.87***). This platform also has the potential to monitor environmental pollutants by selecting appropriate indicator species. The novel insights and methodologies presented in this study represent a significant advancement in meeting the complex needs of aquatic ecosystem protection and monitoring.}, }
@article {pmid38629445, year = {2024}, author = {Fiedler, S and Frenzel, F and Würth, C and Tavernaro, I and Grüne, M and Schweizer, S and Engel, A and Resch-Genger, U}, title = {Interlaboratory Comparison on Absolute Photoluminescence Quantum Yield Measurements of Solid Light Converting Phosphors with Three Commercial Integrating Sphere Setups.}, journal = {Analytical chemistry}, volume = {96}, number = {17}, pages = {6730-6737}, pmid = {38629445}, issn = {1520-6882}, abstract = {Scattering luminescent materials dispersed in liquid and solid matrices and luminescent powders are increasingly relevant for fundamental research and industry. Examples are luminescent nano- and microparticles and phosphors of different compositions in various matrices or incorporated into ceramics with applications in energy conversion, solid-state lighting, medical diagnostics, and security barcoding. The key parameter to characterize the performance of these materials is the photoluminescence/fluorescence quantum yield (Φf), i.e., the number of emitted photons per number of absorbed photons. To identify and quantify the sources of uncertainty of absolute measurements of Φf of scattering samples, the first interlaboratory comparison (ILC) of three laboratories from academia and industry was performed by following identical measurement protocols. Thereby, two types of commercial stand-alone integrating sphere setups with different illumination and detection geometries were utilized for measuring the Φf of transparent and scattering dye solutions and solid phosphors, namely, YAG:Ce optoceramics of varying surface roughness, used as converter materials for blue light emitting diodes. Special emphasis was dedicated to the influence of the measurement geometry, the optical properties of the blank utilized to determine the number of photons of the incident excitation light absorbed by the sample, and the sample-specific surface roughness. While the Φf values of the liquid samples matched between instruments, Φf measurements of the optoceramics with different blanks revealed substantial differences. The ILC results underline the importance of the measurement geometry, sample position, and blank for reliable Φf data of scattering the YAG:Ce optoceramics, with the blank's optical properties accounting for uncertainties exceeding 20%.}, }
@article {pmid38629305, year = {2024}, author = {Fening, KO and Okyere, SO and Forchibe, EE and Layodé, BFR and Richmond, TE and Agboyi, LKBA and Afreh-Nuamah, K and Wamonje, FO}, title = {First report of Leucinodes africensis and Leucinodes laisalis on Solanum aethiopicum and Solanum melongena in farmer's fields in southern Ghana.}, journal = {Bulletin of entomological research}, volume = {114}, number = {3}, pages = {359-373}, doi = {10.1017/S0007485324000154}, pmid = {38629305}, issn = {1475-2670}, mesh = {Animals ; Ghana ; *Moths/physiology ; *Solanum ; Male ; *Solanum melongena/parasitology ; }, abstract = {The eggplant fruit and shoot borer (EFSB) is a devastating pest of eggplants (Solanum aethiopicum L. and Solanum melongena L.) in Ghana, causing significant economic losses. Although initially thought to be the Leucinodes orbonalis Guenee species found in Asia, recent European and Mediterranean Plant Protection Organization reports suggest its absence in Africa. However, eight Leucinodes species have been recently described in Africa, including two new species, Leucinodes africensis sp. n. and Leucinodes laisalis Walker, which were intercepted in eggplant fruits exported from Ghana to the United Kingdom. Despite the reported absence of L. orbonalis in Africa, it remains on the pest list of Ghana as a species known to attack eggplants. To accurately determine the identity of the EFSB complex occurring on eggplant in Southern Ghana, molecular and morphological taxonomic tools were employed, and adult male populations were monitored in on-farm conditions. Our results revealed the presence of two EFSB species, L. africensis and L. laisalis, in the shoot and fruits of eggplants, with L. africensis being the dominant species and widely distributed in Southern Ghana. Notably, L. africensis males were attracted to the pheromone lure of L. orbonalis despite the two species being biologically distinct. This study provides crucial information on correctly identifying the EFSB species attacking eggplants in Southern Ghana and has significant implications for developing management interventions against these pests and their effects on international eggplant trade.}, }
@article {pmid38621699, year = {2024}, author = {Grisendi, A and Calzolari, M and Defilippo, F and Torri, D and Marzani, K and Dottori, M and Bonilauri, P and Maioli, G}, title = {MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF AMBLYOMMA SCUTATUM (ACARI: IXODIDAE) ACCIDENTALLY INTRODUCED IN ITALY.}, journal = {The Journal of parasitology}, volume = {110}, number = {2}, pages = {155-158}, doi = {10.1645/20-69}, pmid = {38621699}, issn = {1937-2345}, mesh = {Animals ; *Ixodidae/genetics ; Amblyomma ; *Tick Infestations/epidemiology/veterinary ; *Ticks ; Italy ; *Lizards ; }, abstract = {Eight ticks were found in Comacchio (FE), Italy parasitizing a young black iguana (Ctenosaura similis) that had been accidentally transported in a commercial plant container from Costa Rica. Specimens were identified morphologically as Amblyomma scutatum and then confirmed by the barcoding of the mitochondrial cytochrome c oxidase subunit 1 gene. Amblyomma scutatum is a common tick known to infest reptiles in Central America, Mexico, and Venezuela, but not in Europe. In Italy, the possibility for this tick to become endemic is unlikely because of the absence of its principal hosts. Nevertheless, this finding confirms the high risk of introducing exotic species that is linked with global commerce and therefore the need for veterinary control of shipments.}, }
@article {pmid38621643, year = {2024}, author = {Liu, Z and Zeng, H and Xiang, H and Deng, S and He, X}, title = {Achieving single-cell-resolution lineage tracing in zebrafish by continuous barcoding mutations during embryogenesis.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {51}, number = {9}, pages = {947-956}, doi = {10.1016/j.jgg.2024.04.004}, pmid = {38621643}, issn = {1673-8527}, mesh = {Animals ; *Zebrafish/genetics/embryology ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; *Embryonic Development/genetics ; *Mutation/genetics ; Phylogeny ; DNA Barcoding, Taxonomic ; Germ Cells/cytology/metabolism ; Embryo, Nonmammalian/cytology ; }, abstract = {Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology. However, existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis. A recently developed method, a substitution mutation-aided lineage-tracing system (SMALT), successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster. Here, we implement the SMALT system in zebrafish, recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos. Leveraging this system, we reconstruct four cell lineage trees for zebrafish fin cells, encompassing both original and regenerated fin. Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%. Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins. Through multiple times sampling germ cells from the same individual, we show the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors. Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues, providing valuable insights into development and disease in zebrafish.}, }
@article {pmid38617833, year = {2024}, author = {Ge, X and Wang, C and Pei, W and Tang, Y and Liu, W and Yan, C}, title = {New descriptions of the larval and pupal stages of Orthocladiusnitidoscutellatus and Psectrocladiusnevalis from Xizang, China (Diptera, Chironomidae).}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e121952}, pmid = {38617833}, issn = {1314-2828}, abstract = {BACKGROUND: Tibetan Plateau is one of the most typical areas of biodiversity in the world because of its unique environmental and regional units, which breed unique biological communities and concentrate on many unique and rare wild animals and plants. Research on Chironomidae in the Tibetan Plateau is relatively weak. At present, the identification of Chironomidae species mainly depends on male adults, while identification of larvae and pupae is relatively difficult and there is less research on them.<br><br>NEW INFORMATION: During the investigations of insect diversity in the Tibetan Plateau, larval and pupal stages of Orthocladiusnitidoscutellatus Lundstr&#xf6;m, 1915 and Psectrocladiusnevalis Akhrorov, 1977 were described and illustrated. Matching and identification of larval and pupal stages were based on DNA barcodes. Neighbour-joining trees were reconstructed, based on known Orthocladius and Psectrocladius COI DNA barcodes, respectively.}, }
@article {pmid38617287, year = {2024}, author = {Scherer, M and Singh, I and Braun, M and Szu-Tu, C and Kardorff, M and Rühle, J and Frömel, R and Beneyto-Calabuig, S and Raffel, S and Rodriguez-Fraticelli, A and Velten, L}, title = {Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38617287}, issn = {2692-8205}, support = {K99 HL146983/HL/NHLBI NIH HHS/United States ; }, abstract = {Current approaches to lineage tracing of stem cell clones require genetic engineering or rely on sparse somatic DNA variants, which are difficult to capture at single-cell resolution. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a droplet-based method for transgene-free lineage tracing, and apply it to study hematopoiesis, capturing hundreds of clonal trajectories across almost 100,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation. Applied to unperturbed hematopoiesis, we describe an overall decline of clonal complexity during murine ageing and the expansion of rare low-output stem cell clones. In aged human donors, we identified expanded hematopoietic clones with and without genetic lesions, and various degrees of clonal complexity. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing at scale.}, }
@article {pmid38615893, year = {2024}, author = {Merivaara, A and Puranen, J and Sadeghi, A and Zashikhina, N and Pirskanen, L and Lajunen, T and Terasaki, T and Auriola, S and Vellonen, KS and Urtti, A}, title = {Barcode lipids for absolute quantitation of liposomes in ocular tissues.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {370}, number = {}, pages = {1-13}, doi = {10.1016/j.jconrel.2024.04.023}, pmid = {38615893}, issn = {1873-4995}, mesh = {Animals ; *Liposomes ; *Vitreous Body/metabolism ; *Aqueous Humor/metabolism ; *Lipids/chemistry ; *Retina/metabolism ; Male ; Rats ; Eye/metabolism ; Mass Spectrometry ; Chromatography, Liquid ; Rats, Sprague-Dawley ; Tissue Distribution ; }, abstract = {Lipid-based drug formulations are promising systems for improving delivery of drugs to ocular tissues, such as retina. To develop lipid-based systems further, an improved understanding of their pharmacokinetics is required, but high-quality in vivo experiments require a large number of animals, raising ethical and economic questions. In order to expedite in vivo kinetic testing of lipid-based systems, we propose a barcode approach that is based on barcoding liposomes with non-endogenous lipids. We developed and evaluated a liquid-chromatography-mass spectrometry method to quantify many liposomes simultaneously in aqueous humor, vitreous, and neural retina at higher than ±20% precision and accuracy. Furthermore, we showed in vivo suitability of the method in pharmacokinetic evaluation of six different liposomes after their simultaneous injection into the rat vitreal cavity. We calculated pharmacokinetic parameters in vitreous and aqueous humor, quantified liposome concentrations in the retina, and quantitated retinal distribution of the liposomes in the rats. Compared to individual injections of the liposome formulations, the barcode-based study design enabled reduction of animal numbers from 72 to 12. We believe that the proposed approach is reliable and will reduce and refine ocular pharmacokinetic experiments with liposomes and other lipid-based systems.}, }
@article {pmid38614287, year = {2024}, author = {Lu, Q and Tian, Q and Gu, W and Yang, CX and Wang, DJ and Yi, TS}, title = {Comparative genomics on chloroplasts of Rubus (Rosaceae).}, journal = {Genomics}, volume = {116}, number = {3}, pages = {110845}, doi = {10.1016/j.ygeno.2024.110845}, pmid = {38614287}, issn = {1089-8646}, mesh = {*Phylogeny ; *Rubus/genetics ; *Genomics ; Genome, Chloroplast ; Chloroplasts/genetics ; Microsatellite Repeats ; Evolution, Molecular ; RNA, Transfer/genetics ; Codon Usage ; }, abstract = {Rubus, the largest genus in Rosaceae, contains over 1400 species that distributed in multiple habitats across the world, with high species diversity in the temperate regions of Northern Hemisphere. Multiple Rubus species are cultivated for their valuable fruits. However, the intrageneric classification and phylogenetic relationships are still poorly understood. In this study, we sequenced, assembled, and characterized 17 plastomes of Rubus, and conducted comparative genomics integrating with 47 previously issued plastomes of this genus. The 64 plastomes of Rubus exhibited typical quadripartite structure with sizes ranging from 155,144 to 156,700 bp, and contained 132 genes including 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. All plastomes are conservative in the gene order, the frequency of different types of long repeats and simple sequence repeats (SSRs), the codon usage, and the selection pressure of protein-coding genes. However, there are also some differences in the Rubus plastomes, including slight contraction and expansion of the IRs, a variation in the numbers of SSRs and long repeats, and some genes in certain clades undergoing intensified or relaxed purifying selection. Phylogenetic analysis based on whole plastomes showed that the monophyly of Rubus was strongly supported and resolved it into six clades corresponding to six subgenera. Moreover, we identified 12 highly variable regions that could be potential molecular markers for phylogenetic, population genetic, and barcoding studies. Overall, our study provided insight into plastomic structure and sequence diversification of Rubus, which could be beneficial for future studies on identification, evolution, and phylogeny in this genus.}, }
@article {pmid38613982, year = {2024}, author = {Zhang, J and Zheng, T and Helalat, SH and Yesibolati, MN and Sun, Y}, title = {Synthesis of eco-friendly multifunctional dextran microbeads for multiplexed assays.}, journal = {Journal of colloid and interface science}, volume = {666}, number = {}, pages = {603-614}, doi = {10.1016/j.jcis.2024.04.061}, pmid = {38613982}, issn = {1095-7103}, mesh = {*Dextrans/chemistry ; *Microspheres ; Particle Size ; Surface Properties ; Humans ; Cytokines/analysis ; Click Chemistry ; Porosity ; Mice ; Animals ; Green Chemistry Technology ; }, abstract = {There has been an increasing demand for simultaneous detection of multiple analytes in one sample. Microbead-based platforms have been developed for multiplexed assays. However, most of the microbeads are made of non-biodegradable synthetic polymers, leading to environmental and human health concerns. In this study, we developed an environmentally friendly dextran microbeads as a new type of multi-analyte assay platform. Biodegradable dextran was utilized as the primary material. Highly uniform magnetic dextran microspheres were successfully synthesized using the Shirasu porous glass (SPG) membrane emulsification technique. To enhance the amount of surface functional groups for ligand conjugation, we coated the dextran microbeads with a layer of dendrimers via a simple electrostatic adsorption process. Subsequently, a unique and efficient click chemistry coupling technique was developed for the fluorescence encoding of the microspheres, enabling multiplexed detection. The dextran microbeads were tested for 3-plex cytokine analysis, and exhibited excellent biocompatibility, stable coding signals, low background noise and high sensitivity.}, }
@article {pmid38612346, year = {2024}, author = {Vella, A and Vella, N}, title = {The First Report of Pennella (Crustacea: Copepoda) Infesting Stenella coeruleoalba Stranded in Malta: Morphological and Genetic Analyses.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {7}, pages = {}, pmid = {38612346}, issn = {2076-2615}, support = {I18LU06-01//University of Malta/ ; }, abstract = {Here, we document the stranding of a striped dolphin Stenella coeruleoalba (Meyen, 1833) (Mammalia: Delphinidae), which was found dead in Maltese waters in July 2020. The stranded dolphin exhibited a severe infestation of the mesoparasitic copepod, Pennella balaenoptera Koren and Danielssen, 1877 (Copepoda: Pennelidae). Parasites of this genus represent the largest known mesoparasites to infest cetaceans. Under normal circumstances, cetaceans may have a few P. balaenoptera individuals attached to them, but cetaceans with compromised health are more prone to heavy infestations. The identification of the parasite was accomplished through morphological and genetic analyses. This incident highlights the significance of monitoring mesoparasitic infestations, offering valuable insights into the health of cetacean populations and emphasizing the potential implications for conservation efforts in the region.}, }
@article {pmid38612257, year = {2024}, author = {Graziosi, G and Lupini, C and Gobbo, F and Zecchin, B and Quaglia, G and Pedrazzoli, S and Lizzi, G and Dosa, G and Martini, G and Terregino, C and Catelli, E}, title = {Genetic Diversity of Avian Influenza Viruses Detected in Waterbirds in Northeast Italy Using Two Different Sampling Strategies.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {7}, pages = {}, pmid = {38612257}, issn = {2076-2615}, support = {Project no. PE00000007, INF-ACT//Ministero dell'Universit&#xe0; e della Ricerca/ ; }, abstract = {Avian influenza viruses (AIVs), which circulate endemically in wild aquatic birds, pose a significant threat to poultry and raise concerns for their zoonotic potential. From August 2021 to April 2022, a multi-site cross-sectional study involving active AIV epidemiological monitoring was conducted in wetlands of the Emilia-Romagna region, northern Italy, adjacent to densely populated poultry areas. A total of 129 cloacal swab samples (CSs) and 407 avian faecal droppings samples (FDs) were collected, with 7 CSs (5.4%) and 4 FDs (1%) testing positive for the AIV matrix gene through rRT-PCR. A COI-barcoding protocol was applied to recognize the species of origin of AIV-positive FDs. Multiple low-pathogenic AIV subtypes were identified, and five of these were isolated, including an H5N3, an H1N1, and three H9N2 in wild ducks. Following whole-genome sequencing, phylogenetic analyses of the hereby obtained strains showed close genetic relationships with AIVs detected in countries along the Black Sea/Mediterranean migratory flyway. Notably, none of the analyzed gene segments were genetically related to HPAI H5N1 viruses of clade 2.3.4.4b isolated from Italian poultry during the concurrent 2021-2022 epidemic. Overall, the detected AIV genetic diversity emphasizes the necessity for ongoing monitoring in wild hosts using diverse sampling strategies and whole-genome sequencing.}, }
@article {pmid38609853, year = {2024}, author = {Kuijpers, L and Hornung, B and van den Hout-van Vroonhoven, MCGN and van IJcken, WFJ and Grosveld, F and Mulugeta, E}, title = {Split Pool Ligation-based Single-cell Transcriptome sequencing (SPLiT-seq) data processing pipeline comparison.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {361}, pmid = {38609853}, issn = {1471-2164}, mesh = {*Transcriptome ; *Computational Biology ; Data Analysis ; }, abstract = {BACKGROUND: Single-cell sequencing techniques are revolutionizing every field of biology by providing the ability to measure the abundance of biological molecules at a single-cell resolution. Although single-cell sequencing approaches have been developed for several molecular modalities, single-cell transcriptome sequencing is the most prevalent and widely applied technique. SPLiT-seq (split-pool ligation-based transcriptome sequencing) is one of these single-cell transcriptome techniques that applies a unique combinatorial-barcoding approach by splitting and pooling cells into multi-well plates containing barcodes. This unique approach required the development of dedicated computational tools to preprocess the data and extract the count matrices. Here we compare eight bioinformatic pipelines (alevin-fry splitp, LR-splitpipe, SCSit, splitpipe, splitpipeline, SPLiTseq-demultiplex, STARsolo and zUMI) that have been developed to process SPLiT-seq data. We provide an overview of the tools, their computational performance, functionality and impact on downstream processing of the single-cell data, which vary greatly depending on the tool used.<br><br>RESULTS: We show that STARsolo, splitpipe and alevin-fry splitp can all handle large amount of data within reasonable time. In contrast, the other five pipelines are slow when handling large datasets. When using smaller dataset, cell barcode results are similar with the exception of SPLiTseq-demultiplex and splitpipeline. LR-splitpipe that is originally designed for processing long-read sequencing data is the slowest of all pipelines. Alevin-fry produced different down-stream results that are difficult to interpret. STARsolo functions nearly identical to splitpipe and produce results that are highly similar to each other. However, STARsolo lacks the function to collapse random hexamer reads for which some additional coding is required.<br><br>CONCLUSION: Our comprehensive comparative analysis aids users in selecting the most suitable analysis tool for efficient SPLiT-seq data processing, while also detailing the specific prerequisites for each of these pipelines. From the available pipelines, we recommend splitpipe or STARSolo for SPLiT-seq data analysis.}, }
@article {pmid38608184, year = {2024}, author = {Laojun, S and Changbunjong, T and Abdulloh, A and Chaiphongpachara, T}, title = {Geometric morphometrics to differentiate species and explore seasonal variation in three Mansonia species (Diptera: Culicidae) in central Thailand and their association with meteorological factors.}, journal = {Medical and veterinary entomology}, volume = {38}, number = {3}, pages = {325-340}, doi = {10.1111/mve.12720}, pmid = {38608184}, issn = {1365-2915}, support = {//Suan Sunandha Rajabhat University/ ; }, mesh = {Animals ; Thailand ; *Seasons ; *Culicidae/anatomy &amp; histology/classification ; Male ; DNA Barcoding, Taxonomic ; Female ; Species Specificity ; }, abstract = {Mansonia mosquito species are recognised as a significant vector of human pathogens, primarily transmitting the filarial nematode, Brugia malayi. In central Thailand, the three most prevalent Mansonia species are Mansonia annulifera, Mansonia indiana and Mansonia uniformis. This study explored the influence of seasonal changes on the phenotypic variation of these Mansonia species in central Thailand using the geometric morphometrics (GM). To ensure accurate species identification, we integrated GM techniques with DNA barcoding, examining distinctions in both phenotype and genotype among the species. The intraspecific genetic divergence ranged from 0.00% to 1.69%, whereas the interspecific genetic divergence ranged from 10.52% to 16.36%. The clear distinction between intra- and interspecific distances demonstrated the presence of a barcoding gap, confirming the successful differentiation of the three Mansonia mosquito species through DNA barcoding. Similarly, the interspecies GM assessment for classifying Mansonia species demonstrated a high degree of accuracy, with an overall performance of 98.12%. Exploring seasonal variation in the three Mansonia species revealed wing variations across different seasons, and pronounced variations appearing in the cool season. Regarding their association with meteorological factors, Ma. annulifera and Ma. uniformis showed significant positive correlations with temperature (p < 0.05), and Ma. uniformis also displayed a significant negative correlation with atmospheric pressure (p < 0.05). The insights from this study will deepen our understanding of the adaptive patterns of Mansonia mosquitoes in Thailand's central region, paving the way for enhanced disease surveillance related to these vectors.}, }
@article {pmid38607945, year = {2024}, author = {Cai, L and Lin, L and Lin, S and Wang, X and Chen, Y and Zhu, H and Zhu, Z and Yang, L and Xu, X and Yang, C}, title = {Highly Multiplexing, Throughput and Efficient Single-Cell Protein Analysis with Digital Microfluidics.}, journal = {Small methods}, volume = {8}, number = {12}, pages = {e2400375}, doi = {10.1002/smtd.202400375}, pmid = {38607945}, issn = {2366-9608}, support = {21927806//National Natural Science Foundation of China/ ; 22204132//National Natural Science Foundation of China/ ; 22293031//National Natural Science Foundation of China/ ; 2022YFB3205600//National Key Research and Development Program of China/ ; 20720210001//Fundamental Research Funds for the Central Universities/ ; 20720220005//Fundamental Research Funds for the Central Universities/ ; SSMU-ZLCX20180701//Innovative research team of high-level local universities in Shanghai/ ; }, mesh = {*Single-Cell Analysis/methods ; Humans ; Microfluidics/methods/instrumentation ; Proteins/analysis/chemistry ; Microfluidic Analytical Techniques/instrumentation/methods ; Lab-On-A-Chip Devices ; }, abstract = {Proteins as crucial components of cells are responsible for the majority of cellular processes. Sensitive and efficient protein detection enables a more accurate and comprehensive investigation of cellular phenotypes and life activities. Here, a protein sequencing method with high multiplexing, high throughput, high cell utilization, and integration based on digital microfluidics (DMF-Protein-seq) is proposed, which transforms protein information into DNA sequencing readout via DNA-tagged antibodies and labels single cells with unique cell barcodes. In a 184-electrode DMF-Protein-seq system, ≈1800 cells are simultaneously detected per experimental run. The digital microfluidics device harnessing low-adsorbed hydrophobic surface and contaminants-isolated reaction space supports high cell utilization (>90%) and high mapping reads (>90%) with the input cells ranging from 140 to 2000. This system leverages split&amp;pool strategy on the DMF chip for the first time to overcome DMF platform restriction in cell analysis throughput and replace the traditionally tedious bench-top combinatorial barcoding. With the benefits of high efficiency and sensitivity in protein analysis, the system offers great potential for cell classification and drug monitoring based on protein expression at the single-cell level.}, }
@article {pmid38607148, year = {2024}, author = {Cheng, H and Qu, J and Mao, W and Chen, S and Dong, H}, title = {Continuous-Wave Pumped Monolayer WS2 Lasing for Photonic Barcoding.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, pmid = {38607148}, issn = {2079-4991}, support = {61925506, 12374297, 62305078//National Natural Science Foundation of China/ ; TD2020002//Hangzhou Science and Technology Bureau of Zhejiang Province/ ; 23XD1404500//Academic/Technology Research Leader Program of Shanghai/ ; }, abstract = {Micro/nano photonic barcoding has emerged as a promising technology for information security and anti-counterfeiting applications owing to its high security and robust tamper resistance. However, the practical application of conventional micro/nano photonic barcodes is constrained by limitations in encoding capacity and identification verification (e.g., broad emission bandwidth and the expense of pulsed lasers). Herein, we propose high-capacity photonic barcode labels by leveraging continuous-wave (CW) pumped monolayer tungsten disulfide (WS2) lasing. Large-area, high-quality monolayer WS2 films were grown via a vapor deposition method and coupled with external cavities to construct optically pumped microlasers, thus achieving an excellent CW-pumped lasing with a narrow linewidth (~0.39 nm) and a low threshold (~400 W cm[-2]) at room temperature. Each pixel within the photonic barcode labels consists of closely packed WS2 microlasers of varying sizes, demonstrating high-density and nonuniform multiple-mode lasing signals that facilitate barcode encoding. Notably, CW operation and narrow-linewidth lasing emission could significantly simplify detection. As proof of concept, a 20-pixel label exhibits a high encoding capacity (2.35 × 10[108]). This work may promote the advancement of two-dimensional materials micro/nanolasers and offer a promising platform for information encoding and security applications.}, }
@article {pmid38606447, year = {2024}, author = {Mwamula, AO and Kwon, OG and Kwon, C and Kim, YS and Kim, YH and Lee, DW}, title = {A Revision of the Phylogeny of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as Inferred from Ribosomal and Mitochondrial DNA.}, journal = {The plant pathology journal}, volume = {40}, number = {2}, pages = {171-191}, pmid = {38606447}, issn = {1598-2254}, support = {//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; 321001-03//Ministry of Agriculture, Food and Rural Affairs/ ; }, abstract = {Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.}, }
@article {pmid38605363, year = {2024}, author = {Pellecchia, S and Franchini, M and Viscido, G and Arnese, R and Gambardella, G}, title = {Single cell lineage tracing reveals clonal dynamics of anti-EGFR therapy resistance in triple negative breast cancer.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {55}, pmid = {38605363}, issn = {1756-994X}, support = {23162//My First AIRC grant/ ; }, mesh = {Humans ; *Triple Negative Breast Neoplasms/drug therapy/genetics/metabolism ; Afatinib/pharmacology/therapeutic use ; Cell Lineage ; ErbB Receptors ; Signal Transduction ; Protein Kinase Inhibitors/pharmacology/therapeutic use ; Cell Line, Tumor ; }, abstract = {BACKGROUND: Most primary Triple Negative Breast Cancers (TNBCs) show amplification of the Epidermal Growth Factor Receptor (EGFR) gene, leading to increased protein expression. However, unlike other EGFR-driven cancers, targeting this receptor in TNBC yields inconsistent therapeutic responses.<br><br>METHODS: To elucidate the underlying mechanisms of this variability, we employ cellular barcoding and single-cell transcriptomics to reconstruct the subclonal dynamics of EGFR-amplified TNBC cells in response to afatinib, a tyrosine kinase inhibitor (TKI) that irreversibly inhibits EGFR.<br><br>RESULTS: Integrated lineage tracing analysis revealed a rare pre-existing subpopulation of cells with distinct biological signature, including elevated expression levels of Insulin-Like Growth Factor Binding Protein 2 (IGFBP2). We show that IGFBP2 overexpression is sufficient to render TNBC cells tolerant to afatinib treatment by activating the compensatory insulin-like growth factor I receptor (IGF1-R) signalling pathway. Finally, based on reconstructed mechanisms of resistance, we employ deep learning techniques to predict the afatinib sensitivity of TNBC cells.<br><br>CONCLUSIONS: Our strategy proved effective in reconstructing the complex signalling network driving EGFR-targeted therapy resistance, offering new insights for the development of individualized treatment strategies in TNBC.}, }
@article {pmid38602321, year = {2024}, author = {Cai, Y and Chen, T and Cai, Y and Liu, J and Yu, B and Fan, Y and Su, J and Zeng, Y and Xiao, X and Ren, L and Tang, Y}, title = {Surface protein profiling and subtyping of extracellular vesicles in body fluids reveals non-CSF biomarkers of Alzheimer's disease.}, journal = {Journal of extracellular vesicles}, volume = {13}, number = {4}, pages = {e12432}, pmid = {38602321}, issn = {2001-3078}, support = {82171776//National Natural Science Foundation of China/ ; 82101429//National Natural Science Foundation of China/ ; 81971300//National Natural Science Foundation of China/ ; JCYJ20180228162815750//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20190806164203496//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; JCYJ20210324103213037//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; KCXFZ20201221173213036//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; ZDSYS20190902093401689//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; }, mesh = {Humans ; Mice ; Animals ; *Alzheimer Disease/diagnosis/metabolism ; *Extracellular Vesicles/metabolism ; Biomarkers/metabolism ; Mice, Transgenic ; Membrane Proteins/metabolism ; *Body Fluids/metabolism ; }, abstract = {Noninvasive and effortless diagnosis of Alzheimer's disease (AD) remains challenging. Here we report the multiplexed profiling of extracellular vesicle (EV) surface proteins at the single EV level in five types of easily accessible body fluids using a proximity barcoding assay (PBA). A total of 183 surface proteins were detected on the EVs from body fluids collected from APP/PS1 transgenic mice and patients with AD. The AD-associated differentially expressed EV proteins could discriminate between the control and AD/AD model samples with high accuracy. Based on machine learning predictive models, urinary EV proteins exhibited the highest diagnostic potential compared to those on other biofluid EVs, both in mice and humans. Single EV analysis further revealed AD-associated EV subpopulations in the tested body fluids, and a urinary EV subpopulation with the signature proteins PLAU, ITGAX and ANXA1 could diagnose patients with AD in blinded datasets with 88% accuracy. Our results suggest that EVs and their subpopulations from noninvasive body fluids, particularly urine, are potential diagnostic biomarkers for AD.}, }
@article {pmid38601700, year = {2024}, author = {Adao, DEV and Rivera, WL}, title = {Subtype-host patterns and genetic differentiation of Blastocystis sp. in the Philippines.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e29019}, pmid = {38601700}, issn = {2405-8440}, abstract = {Blastocystis sp. is a gastrointestinal protozoan commonly encountered in humans and animals. Specificity to certain hosts may be associated with 38 known subtypes (STs) and 8 nonmammalian and avian STs (NMASTs). This can be determined by analyzing ST-host associations, ST-allele data, genetic variability analyses, and fixation index (FST) with sufficient data present. Thus, newly acquired and previously published data on Blastocystis sp. STs and NMASTs from the Philippines were compiled to determine the following: (1) ST-host associations, (2) ST-allele diversity per ST in certain hosts/sources, (3) intrasubtype diversity of certain STs found in different hosts using genetic variability analysis, and (4) comparison of similarities between specific ST populations to determine if these are the same circulating populations using FST. A total of 448 samples subtyped using both sequence-tagged site primers and the 600-bp barcoding region of the Blastocystis sp. SSU rRNA gene were analyzed in this study. Patterns of association for the Philippine samples were similar to those from neighboring Southeast Asian countries and around the world: ST1-ST4 were found in humans but ST3 was the most common, ST5 were found in pigs, and ST6 and ST7 were found in poultry. Blastocystis sp. from humans are mostly the same ST alleles (ST3 allele 34 and ST1 allele 4) while 3-5 ST alleles were found in the most common STs in pigs, macaques, and poultry. Also, ST1, ST3, ST5, and NMAST I are undergoing population expansion according to genetic variability analyses through possible addition of new alleles based on ST-allele diversity. Moreover, FST shows the same circulating population of ST1 in humans, pigs, and water indicating a possible waterborne route of cross-transmission. In contrast, ST3 found in humans possibly come from the same circulating population and is genetically distinct from those in nonhuman sources.}, }
@article {pmid38601032, year = {2024}, author = {Cardinali, I and Ceccarelli, M}, title = {Molecular and cytogenetic analyses in Geranium macrorrhizum L. wild Italian plants.}, journal = {Royal Society open science}, volume = {11}, number = {4}, pages = {240035}, pmid = {38601032}, issn = {2054-5703}, abstract = {Geranium macrorrhizum L. is a herbaceous species native to southern Europe and was introduced in central Europe and North America. It is also widely distributed in Italy. In this study, molecular and cytogenetic analyses were carried out on 22 wild plants, collected in central and southern Italy, compared with five cultivated plants, with the main purpose to identify those living near the Marmore waterfalls in central Italy, recently described as the new species Geranium lucarinii. Four barcoding markers (rbcL, matK, trnH-psbA intergenic spacer and internal transcribed spacer region) were sequenced and their variability among the plants was evaluated. Chromosome numbers were determined and 45S rDNA was physically mapped by fluorescence in situ hybridization. Moreover, genomic affinity between wild and cultivated plants was evaluated by genomic in situ hybridization. The results of this study supported that all the plants belong to G. macrorrhizum, including the Marmore population. Barcoding analyses showed a close similarity among the wild plants, and a differentiation, although not significant, between the wild plants on one hand and the cultivated plants on the other. Integrated studies focusing on morphological, genetic and ecological characterization of a larger number of wild populations would allow us to know the extent of the variability within the species.}, }
@article {pmid38600958, year = {2024}, author = {Visagie, CM and Yilmaz, N and Kocsubé, S and Frisvad, JC and Hubka, V and Samson, RA and Houbraken, J}, title = {A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species.}, journal = {Studies in mycology}, volume = {107}, number = {}, pages = {1-66}, pmid = {38600958}, issn = {0166-0616}, abstract = {The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. Taxonomic novelties: New sections: Aspergillus section Dichlaena Visagie, Kocsubé &amp; Houbraken. New series: Aspergillus series Annuorum J.J. Silva, B.T. Iamanaka, Frisvad. New species: Aspergillus annui J.J. Silva, M.H.P. Fungaro, Frisvad, M.H. Taniwaki &amp; B.T. Iamanaka; Aspergillus saccharicola J.J. Silva, Frisvad, M.H.P. Fungaro, M.H. Taniwaki &amp; B.T. Iamanaka. New combinations: Aspergillus lentisci (Durieu &amp; Mont.) Visagie, Malloch, L. Kriegsteiner, Samson &amp; Houbraken; Xerochrysium coryli (Crous &amp; Decock) Visagie &amp; Houbraken. Citation: Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024). A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1-66. doi: 10.3114/sim.2024.107.01.}, }
@article {pmid38599628, year = {2024}, author = {Diver, P and Ward, BA and Cunliffe, M}, title = {Physiological and morphological plasticity in response to nitrogen availability of a yeast widely distributed in the open ocean.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38599628}, issn = {1574-6941}, support = {772584/ERC_/European Research Council/International ; }, mesh = {*Nitrogen/metabolism ; *Seawater/microbiology ; *Nitrates/metabolism ; Atlantic Ocean ; Yeasts/metabolism/genetics/growth &amp; development ; Ammonium Compounds/metabolism ; Urea/metabolism ; }, abstract = {Yeasts are prevalent in the open ocean, yet we have limited understanding of their ecophysiological adaptations, including their response to nitrogen availability, which can have a major role in determining the ecological potential of other planktonic microbes. In this study, we characterized the nitrogen uptake capabilities and growth responses of marine-occurring yeasts. Yeast isolates from the North Atlantic Ocean were screened for growth on diverse nitrogen substrates, and across a concentration gradient of three environmentally relevant nitrogen substrates: nitrate, ammonium, and urea. Three strains grew with enriched nitrate while two did not, demonstrating that nitrate utilization is present but not universal in marine yeasts, consistent with existing knowledge of nonmarine yeast strains. Naganishia diffluens MBA_F0213 modified the key functional trait of cell size in response to nitrogen concentration, suggesting yeast cell morphology changes along chemical gradients in the marine environment. Meta-analysis of the reference DNA barcode in public databases revealed that the genus Naganishia has a global ocean distribution, strengthening the environmental applicability of the culture-based observations. This study provides novel quantitative understanding of the ecophysiological and morphological responses of marine-derived yeasts to variable nitrogen availability in vitro, providing insight into the functional ecology of yeasts within pelagic open ocean environments.}, }
@article {pmid38598919, year = {2024}, author = {Sidstedt, M and Gynnå, AH and Kiesler, KM and Jansson, L and Steffen, CR and Håkansson, J and Johansson, G and Österlund, T and Bogestål, Y and Tillmar, A and Rådström, P and Ståhlberg, A and Vallone, PM and Hedman, J}, title = {Ultrasensitive sequencing of STR markers utilizing unique molecular identifiers and the SiMSen-Seq method.}, journal = {Forensic science international. Genetics}, volume = {71}, number = {}, pages = {103047}, doi = {10.1016/j.fsigen.2024.103047}, pmid = {38598919}, issn = {1878-0326}, mesh = {Humans ; *Microsatellite Repeats ; *High-Throughput Nucleotide Sequencing ; *DNA Fingerprinting/methods ; Alleles ; Multiplex Polymerase Chain Reaction ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Machine Learning ; Genetic Markers ; }, abstract = {Massively parallel sequencing (MPS) is increasingly applied in forensic short tandem repeat (STR) analysis. The presence of stutter artefacts and other PCR or sequencing errors in the MPS-STR data partly limits the detection of low DNA amounts, e.g., in complex mixtures. Unique molecular identifiers (UMIs) have been applied in several scientific fields to reduce noise in sequencing. UMIs consist of a stretch of random nucleotides, a unique barcode for each starting DNA molecule, that is incorporated in the DNA template using either ligation or PCR. The barcode is used to generate consensus reads, thus removing errors. The SiMSen-Seq (Simple, multiplexed, PCR-based barcoding of DNA for sensitive mutation detection using sequencing) method relies on PCR-based introduction of UMIs and includes a sophisticated hairpin design to reduce unspecific primer binding as well as PCR protocol adjustments to further optimize the reaction. In this study, SiMSen-Seq is applied to develop a proof-of-concept seven STR multiplex for MPS library preparation and an associated bioinformatics pipeline. Additionally, machine learning (ML) models were evaluated to further improve UMI allele calling. Overall, the seven STR multiplex resulted in complete detection and concordant alleles for 47 single-source samples at 1 ng input DNA as well as for low-template samples at 62.5 pg input DNA. For twelve challenging mixtures with minor contributions of 10 pg to 150 pg and ratios of 1-15% relative to the major donor, 99.2% of the expected alleles were detected by applying the UMIs in combination with an ML filter. The main impact of UMIs was a substantially lowered number of artefacts as well as reduced stutter ratios, which were generally below 5% of the parental allele. In conclusion, UMI-based STR sequencing opens new means for improved analysis of challenging crime scene samples including complex mixtures.}, }
@article {pmid38598453, year = {2024}, author = {Hussain, A and Kakar, A and Naseem, M and Kamran, K and Ullah, Z and Shehla, S and Obaid, MK and Ahmed, N and Khan, Q and Liaqat, I}, title = {Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300903}, pmid = {38598453}, issn = {1932-6203}, mesh = {Humans ; Animals ; Bees/genetics ; Pakistan ; *Parks, Recreational ; DNA Barcoding, Taxonomic/methods ; Insecta/genetics ; *Hymenoptera/genetics ; Plants/genetics ; }, abstract = {The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).}, }
@article {pmid38590889, year = {2024}, author = {Askari, H and Soleimanian-Zad, S and Kadivar, M and Shahbazi, S}, title = {Creating a novel genetic diversity of Trichoderma afroharzianum by γ-radiation for xylanase-cellulase production.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e28349}, pmid = {38590889}, issn = {2405-8440}, abstract = {Creating novel sources of a microbial strain using induced mutation can increase enzyme production for industrial use. According to this, we have developed a mutant strain of Trichoderma afroharzianum by Co[60] gamma irradiation. Trichoderma mutants were isolated from an optimum dose of 250 Gy. The qualitative and quantitative screening were used for evaluating their enzyme production and the DNA barcoding method was used to identify the best Trichoderma mutant isolates. The highest cellulase (exo-glucanase, endoglucanase, β-glucosidase, and total cellulase) and xylanase activities were observed in superior mutant isolates of Trichoderma afroharzianum NAS107-M44 and Trichoderma afroharzianum NAS107-M82, which is approximately 1.6-2.5 times higher than its parent strain, respectively. The electrophoretic pattern of proteins showed that the exo-glucanase I, endo-glucanase III, and the xylanase I enzymes hydrolyzed the corn bran, synergistically. Overall, gamma irradiation-induced mutation could be an expedient technique to access such superior mutants for the bioconversion of corn bran wastes.}, }
@article {pmid38589809, year = {2024}, author = {Stelbrink, B and von Rintelen, T and Marwoto, RM and Salzburger, W}, title = {Mitogenomes do not substantially improve phylogenetic resolution in a young non-model adaptive radiation of freshwater gastropods.}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {42}, pmid = {38589809}, issn = {2730-7182}, mesh = {Humans ; Animals ; Phylogeny ; *Genome, Mitochondrial/genetics ; *Gastropoda/genetics ; Ecosystem ; Lakes ; }, abstract = {BACKGROUND: Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups.<br><br>RESULTS: Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression.<br><br>CONCLUSIONS: This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.}, }
@article {pmid38588740, year = {2024}, author = {Rund, H and Wanzenböck, J and Dobrovolny, S and Kurmayer, R}, title = {Relating target fish DNA concentration to community composition analysis in freshwater fish via metabarcoding.}, journal = {The Science of the total environment}, volume = {927}, number = {}, pages = {172281}, doi = {10.1016/j.scitotenv.2024.172281}, pmid = {38588740}, issn = {1879-1026}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Fishes/genetics ; *Fresh Water ; *Biodiversity ; Environmental Monitoring/methods ; DNA/analysis ; }, abstract = {Metabarcoding has been widely accepted as a useful tool for biodiversity assessment based on eDNA. The method allows for the detection of entire groups of organisms in a single sample, making it particularly applicable in aquatic habitats. The high sensitivity of the molecular approaches is especially beneficial in detecting elusive and rare fish species, improving biodiversity assessments. Numerous biotic and abiotic factors that affect the persistence and availability of fish DNA in surface waters and therefore affecting species detectability, have been identified. However, little is known about the relationship between the total fish DNA concentration and the detectability of differential abundant species. In this study three controlled mock-community DNA samples (56 individual samples) were analyzed by (i) metabarcoding (MiSeq) of 12S rDNA (175 bp) and by (ii) total freshwater fish DNA quantification (via qPCR of 12S rDNA). We show that the fish DNA quantity affects the relative abundance of species-specific sequences and the detectability of rare species. In particular we found that samples with a concentration between 1000 pg/μL down to 10 pg/μL of total fish DNA revealed a stable relative frequency of DNA sequences obtained for a specific fish species, as well as a low variability between replicates. Additionally, we observed that even in complex mock-community DNA samples, a total fish DNA concentration of 23 pg/μL was sufficient to reliably detect all species in every replicate, including three rare species with proportions of ≤0.5 %. We also found that the DNA barcode similarity between species can affect detectability, if evenness is low. Our data suggest that the total DNA concentration of fish is an important factor to consider when analyzing and interpreting relative sequence abundance data. Therefore, the workflow proposed here will contribute to an ecologically and economically efficient application of metabarcoding in fish biodiversity assessment.}, }
@article {pmid38588628, year = {2024}, author = {Xue, W and Wang, L and Yi, K and Sun, L and Ren, H and Bian, F}, title = {Hepatocellular carcinoma biomarkers screening based on hydrogel photonic barcodes with tyramine deposition amplified ELISA.}, journal = {Biosensors &amp; bioelectronics}, volume = {255}, number = {}, pages = {116270}, doi = {10.1016/j.bios.2024.116270}, pmid = {38588628}, issn = {1873-4235}, mesh = {Humans ; Hydrogels/chemistry ; *Carcinoma, Hepatocellular/diagnosis ; *Biosensing Techniques/methods ; *Liver Neoplasms/diagnosis ; Biomarkers, Tumor ; Enzyme-Linked Immunosorbent Assay ; Tyramine ; }, abstract = {Hepatocellular carcinoma (HCC), as one of the most lethal cancers, significantly impacts human health. Attempts in this area tends to develop novel technologies with sensitive and multiplexed detection properties for early diagnosis. Here, we present novel hydrogel photonic crystal (PhC) barcodes with tyramine deposition amplified enzyme-linked immunosorbent assay (ELISA) for highly sensitive and multiplexed HCC biomarker screening. Because of the abundant amino groups of acrylic acid (AA) component, the constructed hydrogel PhC barcodes with inverse opal structure could facilitate the loading of antibody probes for subsequent detection of tumor markers. By integrating tyramine deposition amplified ELISA on the barcode, the detection signal of tumor markers has been enhanced. Based on these features, it is demonstrated that the hydrogel PhC barcodes with tyramine deposition amplified ELISA could realize highly sensitive and multiplexed detection of HCC-related biomarkers. It was found that this method is flexible, sensitive and accurate, suitable for multivariate analysis of low abundance tumor markers and future cancer diagnosis. These features make the newly developed PhC barcodes an innovation platform, which possesses tremendous potential for practical application of low abundance targets.}, }
@article {pmid38587185, year = {2024}, author = {Saunders, SH and Ahmed, AM}, title = {ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.}, journal = {Nucleic acids research}, volume = {52}, number = {8}, pages = {e43}, pmid = {38587185}, issn = {1362-4962}, mesh = {*Escherichia coli/genetics ; *Oligonucleotides/genetics ; *Plasmids/genetics ; Integrases/genetics/metabolism ; Genome, Bacterial/genetics ; Genetic Engineering/methods ; Gene Knockout Techniques ; Transcription Factors/genetics/metabolism ; }, abstract = {Microbiology and synthetic biology depend on reverse genetic approaches to manipulate bacterial genomes; however, existing methods require molecular biology to generate genomic homology, suffer from low efficiency, and are not easily scaled to high throughput. To overcome these limitations, we developed a system for creating kilobase-scale genomic modifications that uses DNA oligonucleotides to direct the integration of a non-replicating plasmid. This method, Oligonucleotide Recombineering followed by Bxb-1 Integrase Targeting (ORBIT) was pioneered in Mycobacteria, and here we adapt and expand it for Escherichia coli. Our redesigned plasmid toolkit for oligonucleotide recombineering achieved significantly higher efficiency than λ Red double-stranded DNA recombineering and enabled precise, stable knockouts (≤134 kb) and integrations (≤11 kb) of various sizes. Additionally, we constructed multi-mutants in a single transformation, using orthogonal attachment sites. At high throughput, we used pools of targeting oligonucleotides to knock out nearly all known transcription factor and small RNA genes, yielding accurate, genome-wide, single mutant libraries. By counting genomic barcodes, we also show ORBIT libraries can scale to thousands of unique members (>30k). This work demonstrates that ORBIT for E. coli is a flexible reverse genetic system that facilitates rapid construction of complex strains and readily scales to create sophisticated mutant libraries.}, }
@article {pmid38586055, year = {2024}, author = {Franco-Enzástiga, &#xda; and Inturi, NN and Natarajan, K and Mwirigi, JM and Mazhar, K and Schlachetzki, JCM and Schumacher, M and Price, TJ}, title = {Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38586055}, issn = {2692-8205}, support = {R01 NS111929/NS/NINDS NIH HHS/United States ; U19 NS130608/NS/NINDS NIH HHS/United States ; }, abstract = {Gene expression is influenced by chromatin architecture via controlled access of regulatory factors to DNA. To better understand gene regulation in the human dorsal root ganglion (hDRG) we used bulk and spatial transposase-accessible chromatin technology followed by sequencing (ATAC-seq). Using bulk ATAC-seq, we detected that in females diverse differentially accessible chromatin regions (DARs) mapped to the X chromosome and in males to autosomal genes. EGR1/3 and SP1/4 transcription factor binding motifs were abundant within DARs in females, and JUN, FOS and other AP-1 factors in males. To dissect the open chromatin profile in hDRG neurons, we used spatial ATAC-seq. The neuron cluster showed higher chromatin accessibility in GABAergic, glutamatergic, and interferon-related genes in females, and in Ca[2+]- signaling-related genes in males. Sex differences in transcription factor binding sites in neuron-proximal barcodes were consistent with the trends observed in bulk ATAC-seq data. We validated that EGR1 expression is biased to female hDRG compared to male. Strikingly, XIST, the long-noncoding RNA responsible for X inactivation, hybridization signal was found to be highly dispersed in the female neuronal but not non-neuronal nuclei suggesting weak X inactivation in female hDRG neurons. Our findings point to baseline epigenomic sex differences in the hDRG that likely underlie divergent transcriptional responses that determine mechanistic sex differences in pain.}, }
@article {pmid38585983, year = {2024}, author = {Shepherdson, JL and Granas, DM and Li, J and Shariff, Z and Plassmeyer, SP and Holehouse, AS and White, MA and Cohen, BA}, title = {Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38585983}, issn = {2692-8205}, support = {F30 EY033640/EY/NEI NIH HHS/United States ; R01 GM092910/GM/NIGMS NIH HHS/United States ; DP2 CA290639/CA/NCI NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; R21 HG012146/HG/NHGRI NIH HHS/United States ; }, abstract = {Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.}, }
@article {pmid38585727, year = {2024}, author = {Sarhan, MS and Filosi, M and Maixner, F and Fuchsberger, C}, title = {Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38585727}, issn = {2692-8205}, support = {R01 HG009976/HG/NHGRI NIH HHS/United States ; }, abstract = {Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation at https://pypi.org/project/taxonize-gb/ and on GitHub https://github.com/msabrysarhan/taxonize_genbank. It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).}, }
@article {pmid38583817, year = {2024}, author = {Afifi, MAM and Azab, AM and Ali, E and Ghazy, A and El-Tabakh, MAM}, title = {DNA barcoding, phylogeography and evolutionary dynamics of Chrysichthys auratus.}, journal = {Gene}, volume = {917}, number = {}, pages = {148448}, doi = {10.1016/j.gene.2024.148448}, pmid = {38583817}, issn = {1879-0038}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Phylogeography ; *Phylogeny ; *Haplotypes ; Evolution, Molecular ; Genetic Variation ; Goldfish/genetics/classification ; Gene Flow ; Electron Transport Complex IV/genetics ; }, abstract = {This study embarked on an exploration into the genetic structure and evolutionary history of the Chrysichthys auratus species, leveraging PCR amplification, phylogenetic trees, and haplotype networks. Specific DNA segments were successfully amplified and visualized through electrophoresis. Newly obtained sequences were Bank into GenBank and given accession numbers (OR730807-OR730808-OR730809). The Neighbor-Joining method provided insights into the evolutionary relationships among taxa, further augmented by bootstrap values and the Tamura 3-parameter method. A comprehensive geographical haplotype network showcased pronounced genetic differentiation, especially between remote populations. Nonetheless, shared haplotypes between proximate regions indicated either ancestral genetic connections or ongoing gene flow. Employing the COI-DNA barcodes, an in-depth understanding of intra- and inter-populational genetic diversity was achieved. The study's findings unravel the intricate genetic landscape and evolutionary dynamics of C. auratus, offering novel perspectives into its demographic history across its vast native habitat.}, }
@article {pmid38580715, year = {2024}, author = {Mikhaylova, V and Rzepka, M and Kawamura, T and Xia, Y and Chang, PL and Zhou, S and Paasch, A and Pham, L and Modi, N and Yao, L and Perez-Agustin, A and Pagans, S and Boles, TC and Lei, M and Wang, Y and Garcia-Bassets, I and Chen, Z}, title = {Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7988}, pmid = {38580715}, issn = {2045-2322}, mesh = {Humans ; Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Genomics ; DNA/genetics ; Genome, Human ; }, abstract = {In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2-200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2-200 kb targets using a short-read sequencer.}, }
@article {pmid38578268, year = {2024}, author = {Quail, MA and Corton, C and Uphill, J and Keane, J and Gu, Y}, title = {Identifying the best PCR enzyme for library amplification in NGS.}, journal = {Microbial genomics}, volume = {10}, number = {4}, pages = {}, pmid = {38578268}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Polymerase Chain Reaction/methods ; *Saccharomyces cerevisiae ; Gene Library ; *DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Background. PCR amplification is a necessary step in many next-generation sequencing (NGS) library preparation methods [1, 2]. Whilst many PCR enzymes are developed to amplify single targets efficiently, accurately and with specificity, few are developed to meet the challenges imposed by NGS PCR, namely unbiased amplification of a wide range of different sizes and GC content. As a result PCR amplification during NGS library prep often results in bias toward GC neutral and smaller fragments. As NGS has matured, optimized NGS library prep kits and polymerase formulations have emerged and in this study we have tested a wide selection of available enzymes for both short-read Illumina library preparation and long fragment amplification ahead of long-read sequencing.We tested over 20 different hi-fidelity PCR enzymes/NGS amplification mixes on a range of Illumina library templates of varying GC content and composition, and find that both yield and genome coverage uniformity characteristics of the commercially available enzymes varied dramatically. Three enzymes Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) 'Equinox' and Takara Ex Premier were found to give a consistent performance, over all genomes, that mirrored closely that observed for PCR-free datasets. We also test a range of enzymes for long-read sequencing by amplifying size fractionated S. cerevisiae DNA of average size 21.6 and 13.4 kb, respectively.The enzymes of choice for short-read (Illumina) library fragment amplification are Quantabio RepliQa Hifi Toughmix, Watchmaker Library Amplification Hot Start Master Mix (2X) 'Equinox' and Takara Ex Premier, with RepliQa also being the best performing enzyme from the enzymes tested for long fragment amplification prior to long-read sequencing.}, }
@article {pmid38577158, year = {2024}, author = {Veselovsky, VA and Boldyreva, DI and Olekhnovich, EI and Klimina, KM and Babenko, VV and Zakharevich, NV and Larin, AK and Morozov, MD and Zoruk, PY and Sergiev, PV and Dontsova, OA and Maev, IV and Novik, TS and Kotlobay, AA and Lazarev, VN and Lagarkova, MA}, title = {Effect of the consumption of brazzein and monellin, two recombinant sweet-tasting proteins, on rat gut microbiota.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1362529}, pmid = {38577158}, issn = {2296-861X}, abstract = {Sweet-tasting proteins (SPs) are proteins of plant origin initially isolated from tropical fruits. They are thousands of times sweeter than sucrose and most artificial sweeteners. SPs are a class of proteins capable of causing a sweet taste sensation in humans when interacting with the T1R2/T1R3 receptor. SP thaumatin has already been introduced in the food industry in some countries. Other SPs, such as monellin and brazzein, are promising products. An important stage in researching SPs, in addition to confirming the absence of toxicity, mutagenicity, oncogenicity, and allergenic effects, is studying their influence on gut microbiota. In this paper we describe changes in the composition of rat gut microbiota after six months of consuming one of two recombinant SPs-brazzein or monellin. A full length 16S gene sequencing method was used for DNA library barcoding. The MaAsLin2 analysis results showed noticeable fluctuations in the relative abundances of Anaerocella delicata in brazzein-fed rat microbiota, and of Anaerutruncus rubiinfantis in monellin-fed rat microbiota, which, however, did not exceed the standard deviation. The sucrose-fed group was associated with an increase in the relative abundance of Faecalibaculum rodentium, which may contribute to obesity. Overall, prolonged consumption of the sweet proteins brazzein and monellin did not significantly change rat microbiota and did not result in the appearance of opportunistic microbiota. This provides additional evidence for the safety of these potential sweeteners.}, }
@article {pmid38575088, year = {2024}, author = {Li, P and Zhao, Z and Li, Z and Zeng, R and Li, W}, title = {Distinguishing features of Prunus humilis, P. japonica, P. pedunculata seeds and their adulterant based on DNA barcoding, morphological characterization, and chemical profiles.}, journal = {Fitoterapia}, volume = {175}, number = {}, pages = {105942}, doi = {10.1016/j.fitote.2024.105942}, pmid = {38575088}, issn = {1873-6971}, mesh = {*Seeds/chemistry ; *DNA Barcoding, Taxonomic ; *Prunus/chemistry/classification/genetics ; *Phylogeny ; Amygdalin ; Flavonoids/analysis ; Drug Contamination ; China ; Phytochemicals ; }, abstract = {Pruni Semen, the dried ripe seed of Prunus humilis, P. japonica, or P. pedunculata as recorded in the Chinese Pharmacopoeia, has been widely used in pharmaceutical and food industries. The adulteration of the marketed product with morphologically similar plants of the same genus has led to variable product quality and clinical effectiveness. This study systematically investigated the phylogenetic relationships, morphological traits, and chemical profiles of 37 Pruni Semen samples from planting bases, markets, and fields. DNA barcoding could successfully distinguish the genuine and counterfeit Pruni Semen, and the results indicated that there was almost no authentic Pruni Semen available in the market. The samples were divided into "big seed" (P. pedunculata and P. salicina seeds) and "small seed" (P. humilis, P. japonica, P. tomentosa, and P. avium seeds) categories based on morphology results. The notable discrepancy in the chemical characteristics of "big seed" and "small seed" was that "small seeds" were rich in flavonoids and low in amygdalin, whereas "big seeds" were the opposite. Furthermore, principal component analysis and clustered heatmap analysis verified the distinguishing features of "big seed" and "small seed" based on morphological and chemical characteristics. This study suggested that a combination of DNA barcoding and morphological and chemical characteristics can aid in the identification and quality evaluation of authentic and adulterated Pruni Semen. These findings may help standardize Pruni Semen available in the market and protect the rights and interests of customers.}, }
@article {pmid38574082, year = {2024}, author = {Tiktak, GP and Gabb, A and Brandt, M and Diz, FR and Bravo-Vásquez, K and Peñaherrera-Palma, C and Valdiviezo-Rivera, J and Carlisle, A and Melling, LM and Cain, B and Megson, D and Preziosi, R and Shaw, KJ}, title = {Genetic identification of three CITES-listed sharks using a paper-based Lab-on-a-Chip (LOC).}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300383}, pmid = {38574082}, issn = {1932-6203}, mesh = {Animals ; *Sharks/genetics ; Endangered Species ; Seafood ; Meat ; DNA/genetics ; }, abstract = {Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.}, }
@article {pmid38572806, year = {2024}, author = {Ang, YS and Yung, LL}, title = {Protein-to-DNA Converter with High Signal Gain.}, journal = {ACS nano}, volume = {18}, number = {15}, pages = {10454-10463}, doi = {10.1021/acsnano.3c11435}, pmid = {38572806}, issn = {1936-086X}, mesh = {*DNA/genetics/chemistry ; Nucleic Acid Amplification Techniques/methods ; *Biosensing Techniques/methods ; }, abstract = {DNA isothermal amplification techniques have been applied extensively for evaluating nucleic acid inputs but cannot be implemented directly on other types of biomolecules. In this work, we designed a proximity activation mechanism that converts protein input into DNA barcodes for the DNA exponential amplification reaction, which we termed PEAR. Several design parameters were identified and experimentally verified, which included the choice of enzymes, sequences of proximity probes and template strand via the NUPACK design tool, and the implementation of a hairpin lock on the proximity probe structure. Our PEAR system was surprisingly more robust against nonspecific DNA amplification, which is a major challenge faced in existing formats of the DNA-based exponential amplification reaction. The as-designed PEAR exhibited good target responsiveness for three protein models with a dynamic range of 4-5 orders of magnitude down to femtomolar input concentration. Overall, our proposed protein-to-DNA converter module led to the development of a stable and robust configuration of the DNA exponential amplification reaction to achieve high signal gain. We foresee this enabling the use of protein inputs for more complex molecular evaluation as well as ultrasensitive protein detection.}, }
@article {pmid38569896, year = {2024}, author = {Weile, J and Ferra, G and Boyle, G and Pendyala, S and Amorosi, C and Yeh, CL and Cote, AG and Kishore, N and Tabet, D and van Loggerenberg, W and Rayhan, A and Fowler, DM and Dunham, MJ and Roth, FP}, title = {Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {4}, pages = {}, pmid = {38569896}, issn = {1367-4811}, support = {R01 GM132162/GM/NIGMS NIH HHS/United States ; R01 HL164675/HL/NHLBI NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Gene Library ; Genotype ; Cluster Analysis ; *Software ; }, abstract = {MOTIVATION: Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.<br><br>RESULTS: Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or nonunique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.<br><br>Pacybara, freely available at https://github.com/rothlab/pacybara, is implemented using R, Python, and bash for Linux. It runs on GNU/Linux HPC clusters via Slurm, PBS, or GridEngine schedulers. A single-machine simplex version is also available.}, }
@article {pmid38568891, year = {2024}, author = {D'Ercole, J and Dapporto, L and Opler, P and Schmidt, CB and Ho, C and Menchetti, M and Zakharov, EV and Burns, JM and Hebert, PDN}, title = {A genetic atlas for the butterflies of continental Canada and United States.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300811}, pmid = {38568891}, issn = {1932-6203}, mesh = {Animals ; United States ; *Butterflies/genetics ; Phylogeography ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; Haplotypes ; Genetic Variation ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between ge