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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@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 & 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.

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.

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.},
}

*DNA Barcoding, Taxonomic/methods
*Precision Medicine
Humans
*Molecular Diagnostic Techniques
*DNA/genetics
Animals

@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 & 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.},
}

*Lichens/microbiology/classification
*Ascomycota/genetics/classification/isolation & purification/physiology
Metagenomics
Symbiosis
Phylogeny
Computer Simulation
Metagenome

@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 & Yadav sp. nov., D. heingangensis Tiwari & Yadav sp. nov., D. leibiensis Tiwari & Yadav sp. nov., and D. laichingensis Tiwari & Yadav sp. nov.

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.

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.},
}

Animals
*Oligochaeta/classification/genetics
India
Phylogeny
Biodiversity
Ecosystem
Electron Transport Complex IV/genetics

@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 & 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 & 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 & 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.},
}

Animals
*Mustelidae/physiology
*DNA Barcoding, Taxonomic
*Feces/chemistry
Japan
Seasons
*Feeding Behavior/physiology
Diet/veterinary

@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.

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.

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.

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&D Program of China/ ; BK20220089//Distinguished Young Scholars of Jiangsu Province/ ; BE2022322//Key R&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.},
}

*Promoter Regions, Genetic
*Escherichia coli/genetics
*Deep Learning
Gene Expression Regulation, Bacterial
Gene Library

@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.

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.

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.

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 & Zhang, 1996, Hogna jiafui Peng, Yin, Zhang & Kim, 1997 and Hogna arborea Lo, Wei & Cheng, 2023) have been recorded in China.

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.},
}

*DNA Barcoding, Taxonomic/methods
*Cinnamomum zeylanicum/genetics/classification
DNA, Plant/genetics
*Food Contamination/analysis
*Cinnamomum/genetics

@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//Muséum 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.},
}

Animals
*Oligochaeta
*Biodiversity
*Rainforest
Ecosystem
French Guiana
Soil
Tropical Climate

@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.},
}

*Cell Differentiation/genetics
*Cell Lineage/genetics
*Single-Cell Analysis/methods
Clone Cells/cytology
Algorithms
Animals
Hematopoietic Stem Cells/cytology/metabolism
Humans
Mice
Stochastic Processes

@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.},
}

*Metabolomics/methods
*Zingiberaceae/metabolism/classification/genetics/chemistry
Gas Chromatography-Mass Spectrometry
Phylogeny
*Oils, Volatile
*Volatile Organic Compounds/metabolism/analysis
DNA Barcoding, Taxonomic

@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.},
}

*In Situ Hybridization, Fluorescence/methods
*RNA/genetics/analysis
Humans
Animals
*Single Molecule Imaging/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.},
}

*Estuaries
*DNA Barcoding, Taxonomic
*Biodiversity
*Environmental Monitoring
Animals
Seasons
*Wetlands
Plankton
*Zooplankton/classification/genetics
Fishes/classification

@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.},
}

Animals
*DNA Barcoding, Taxonomic/methods
India
Phylogeny
*Psychodidae/genetics/classification
Electron Transport Complex IV/genetics
*DNA, Mitochondrial/genetics

@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.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Diptera/genetics/classification
Algorithms

@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.},
}

*DNA Barcoding, Taxonomic
China
*Seeds/genetics
Biodiversity
*Plants/genetics/classification
Ecosystem

@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.},
}

Animals
*Animals, Wild/virology/blood
*Culicidae/virology/physiology
Swine
Deer/blood/virology
Florida
Turkeys/blood
DNA Barcoding, Taxonomic

@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, Innovación 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 & 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.},
}

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

@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-Démo//Bpifrance/ ; REGE-NETHER 639888//Union Nationale des Aveugles et Déficients 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.},
}

*High-Throughput Nucleotide Sequencing/methods/standards
Gene Library
*DNA Barcoding, Taxonomic/methods
*Sequence Analysis, DNA/methods
Humans
Polymerase Chain Reaction
DNA

@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.

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 ≥ 4x UMI-family size, umiVar achieved exceptionally low error rates, ranging from 7.4×10[-7] to 7.5×10[-5]. Even when including mixed consensus reads (duplex & simplex), error rates remained low, between 6.1×10[-6] and 9×10[-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.

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.

METHODS: Specimens of Arenosetella were collected from the Mediterranean, Aegean, and Black Sea coasts of Türkiye. 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.

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.

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.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Electron Transport Complex IV/genetics
Turkey
Phylogeny
*Copepoda/genetics/classification
Haplotypes
Genetic Variation
*DNA, Ribosomal Spacer/genetics

@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.},
}

*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

@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 & 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.

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).

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.

RESULTS: DNA barcoding using five markers (trnH-psbA, matK, rpoC1, rbcL, and ITS) successfully amplified sequences of 930 bp, 1520 bp, 2295 bp, 1910 bp, and 1630 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 cm vs. 5.02 cm), and greater total phenolic content (31.92 mg/g vs. 28.95 mg/g). Agronomically, CACH-W showed superior plant height, spike weight, and seed yield (1003.83 kg/feddan vs. 606.46 kg/feddan), making it a promising candidate for cultivation and breeding.

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 & 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.},
}

*Boswellia/genetics/classification
*Genome, Plastid
*Evolution, Molecular
Phylogeny
Genetic Variation

@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.},
}

Animals
*Environmental Monitoring/methods
*Fishes/classification
*DNA, Environmental/analysis
Biodiversity
Rivers/chemistry
DNA Barcoding, Taxonomic
Israel
Ecosystem
Fresh Water

@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 & 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.},
}

Humans
*Drug Resistance, Neoplasm/drug effects/genetics
*Lung Neoplasms/drug therapy/pathology/genetics/metabolism
ErbB Receptors/antagonists & 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

@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.

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&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.

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).

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.

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.},
}

Phylogeny
*Basidiomycota/genetics/classification
Asia, Southeastern
DNA, Fungal/genetics
Europe

@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 & 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.},
}