@article {pmid42345750,
year = {2026},
author = {Zhang, D and Liu, P and Lu, X and Hao, H and Sun, H and Nie, Z and Ren, S},
title = {COI DNA Barcoding of Six Schizothoracine Fishes from the Tarim River Basin, Xinjiang, China: Implications for Species Delimitation and Phylogenetic Relationships.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345750},
issn = {2079-7737},
support = {TDZKBS202540//Tarim University/ ; TDZKPY202608//Tarim University/ ; TCYC2024//Tarim University/ ; 32460920//National Natural Science Foundation of China/ ; TDZKSS202310//Tarim University/ ; },
abstract = {To test the performance of COI-based DNA barcoding in species delimitation, we amplified and sequenced the mitochondrial COI gene from six Schizothoracine fishes endemic to Xinjiang, China. We then characterized the COI gene dataset, quantified genetic divergence, and inferred phylogenetic relationships using distance-based approaches. Morphological examination supported clear phenotypic differentiation among taxa. In particular, Diptychus maculatus can be readily distinguished from the densely scaled Schizothorax species by having a single pair of barbels and relatively sparse scales. The COI gene sequences showed an evident AT bias (55.1%), consistent with patterns reported for teleost mitochondrial genomes. Across all samples, 11 haplotypes were identified. Pairwise comparisons indicated a maximum interspecific divergence of 15.296%, whereas the smallest interspecific distance (0.262%) occurred between Schizothorax barbatus and Schizothorax irregularis. Species-delimitation analyses and phylogenetic reconstruction supported D. maculatus and A. laticeps as distinct mitochondrial lineages, whereas S. biddulphi, S. eurystomus, S. irregularis, and S. barbatus were not fully resolved by COI gene. The shared haplotypes and low genetic distances among the four Schizothorax species may reflect recent divergence, incomplete lineage sorting, or historical gene flow. Overall, COI gene barcoding is effective for distinguishing the major lineages in this dataset, especially D. maculatus and A. laticeps.},
}

@article {pmid42347167,
year = {2026},
author = {Lopez Garcia, AV and Jolley, KA and Parfitt, KM and Hashish, A and Sato, Y and El-Gazzar, M and Nunez-Garcia, J and Fearnley, C and Sheppard, SK and Maiden, MCJ and Anjum, MF},
title = {A standardized core genome multilocus sequence typing and life identification number barcoding framework for global Pasteurella multocida surveillance and outbreak investigation.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001733},
pmid = {42347167},
issn = {2057-5858},
mesh = {*Pasteurella multocida/genetics/classification/isolation & purification ; *Multilocus Sequence Typing/methods/standards ; Disease Outbreaks ; Animals ; *Genome, Bacterial ; *Pasteurella Infections/epidemiology/microbiology/veterinary ; *DNA Barcoding, Taxonomic/methods ; Humans ; },
abstract = {Effective pathogen surveillance requires robust typing systems for outbreak detection and understanding transmission dynamics, evolutionary patterns, host colonization and disease progression. Pasteurella multocida is a globally distributed pathogen that infects mammals and birds, causing a variety of diseases. Despite its significance to public and animal health, genotypic characterization of this species remains limited, impeding effective surveillance and control strategies. To address this, we developed a core genome multilocus sequence typing (cgMLST) scheme and a complementary life identification number (LIN) barcoding system for P. multocida. The cgMLST scheme was developed and validated using 1,233 core genes identified from 1,593 genomes sourced from more than 8 host species across all continents, spanning collections from 1922 to 2024. Genomes included publicly available assemblies from PubMLST, newly sequenced isolates from the Animal and Plant Health Agency (APHA) and assemblies from Iowa State University. The cgMLST scheme assigned core genome sequence types (cgSTs) to 1,554 of the 1,593 genomes (97.55%), identifying 1,304 unique cgSTs and improving resolution compared to the 2 currently available 7-locus MLST schemes. Based on pairwise allelic differences, 12 thresholds were defined to establish the LIN barcoding system, a hierarchical and stable nomenclature enabling multi-level clustering. Application of the cgMLST-based Life Identification number code to independent outbreak datasets confirmed the scheme's ability to delineate outbreak clusters and distinguish unrelated isolates. This standardized typing framework provides a robust approach for strain classification, population structure analysis, vaccine target identification and global surveillance of P. multocida. Integration into the PubMLST platform ensures open access and facilitates global collaboration in the molecular epidemiology of this pathogen.},
}

*Pasteurella multocida/genetics/classification/isolation & purification
*Multilocus Sequence Typing/methods/standards
Disease Outbreaks
Animals
*Genome, Bacterial
*Pasteurella Infections/epidemiology/microbiology/veterinary
*DNA Barcoding, Taxonomic/methods
Humans

@article {pmid42349067,
year = {2026},
author = {Yuan, G and Steyert, M and Nowakowski, TJ},
title = {Lineage tracing in human cortical development.},
journal = {Current opinion in genetics & development},
volume = {100},
number = {},
pages = {102506},
doi = {10.1016/j.gde.2026.102506},
pmid = {42349067},
issn = {1879-0380},
abstract = {How progenitor lineage relationships shape the cellular diversity and organization of the human cortex remains a central question in developmental neuroscience. Lineage tracing provides a framework for understanding how developmental trajectories generate this diversity by capturing cellular history rather than static molecular identity, revealing progenitor fate potential, temporal regulation of developmental competence, and spatial patterns of clonal organization. In this review, we examine advances in prospective viral barcoding, clustered regularly interspaced short palindromic repeats (CRISPR)-based evolvable lineage recording, and retrospective inference from endogenous somatic mutations, highlighting how these complementary approaches are reshaping our understanding of human cortical development. We discuss evidence that human cortical progenitors exhibit expanded fate potential, prolonged temporal control of lineage output, and regionally patterned lineage dispersion, distinct from canonical rodent models. We further consider how integrating lineage information with molecular profiling and genetic perturbation enables causal dissection of developmental programs. Finally, we explore how disrupted lineage dynamics contribute to neurodevelopmental disorders, suggesting disease mechanisms as deviations in developmental trajectories. Recognizing lineage dynamics as an organizing principle will be essential for linking developmental ancestry to cortical organization and disease vulnerability.},
}

@article {pmid42349934,
year = {2026},
author = {Thipphet, K and Sanit, S and Limsopatham, K and Horpaopan, S and Chaiwong, T and Moophayak, K and Vitta, A and Phuwanatsarunya, P and Kunlanantakun, J and Watanasak, K and Photo, M and Kanta, W and Kurahashi, H and Sukontason, KL and Bunchu, N},
title = {Ultrastructure of mouthpart and terminalia in Musca crassirostris (Diptera: Muscidae) with molecular confirmation from Thailand.},
journal = {Journal of medical entomology},
volume = {63},
number = {3},
pages = {},
doi = {10.1093/jme/tjag097},
pmid = {42349934},
issn = {1938-2928},
support = {//Naresuan University (NU)/ ; //National Science, Research/ ; R2566B041//Innovation Fund (NSRF)/ ; 040/2568//Faculty of Medicine, Chiang Mai University/ ; },
mesh = {Animals ; Female ; Mouth/ultrastructure ; Microscopy, Electron, Scanning ; Thailand ; *Muscidae/ultrastructure/genetics/anatomy & histology ; Electron Transport Complex IV/genetics ; Male ; DNA Barcoding, Taxonomic ; Insect Proteins/genetics/analysis ; },
abstract = {Musca crassirostris Stein, 1903 (Diptera: Muscidae) is a medically and veterinary important hematophagous fly whose feeding activity causes significant irritation and blood loss in livestock and is occasionally associated with human myiasis. Although this species is widely distributed and epidemiologically relevant, its feeding-related functional morphology and genital diagnostic characters have remained insufficiently documented at the ultrastructural level. Here, we present the first comprehensive scanning electron microscopy (SEM)-based characterization of the labellar feeding apparatus and male and female terminalia of M. crassirostris, integrating stereomicroscopy and mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding for species confirmation. SEM images revealed well-developed prestomal teeth and serrated pseudotracheal structures, features directly associated with hematophagous feeding. Distinctive genital characters are also present and facilitate accurate species identification. The COI barcoding confirmed species identity with complete concordance among BOLD, GenBank, and species delimitation analyses, providing new reference data for Southeast Asian populations. By linking ultrastructural morphology with feeding function and diagnostic utility, this study establishes a robust morphological-molecular framework that advances current understanding of M. crassirostris and supports its identification and surveillance in medical and veterinary entomology.},
}

Animals
Female
Mouth/ultrastructure
Microscopy, Electron, Scanning
Thailand
*Muscidae/ultrastructure/genetics/anatomy & histology
Electron Transport Complex IV/genetics
Male
DNA Barcoding, Taxonomic
Insect Proteins/genetics/analysis

@article {pmid42350001,
year = {2026},
author = {Ghaderi, A and Shirdel, B and Shakerian, S},
title = {Strategic analysis of electronic prescriptions in Iran: a qualitative study.},
journal = {BMJ open},
volume = {16},
number = {6},
pages = {e101872},
doi = {10.1136/bmjopen-2025-101872},
pmid = {42350001},
issn = {2044-6055},
mesh = {Iran ; Humans ; Qualitative Research ; *Electronic Prescribing/statistics & numerical data ; Attitude of Health Personnel ; Interviews as Topic ; Pharmacists ; },
abstract = {OBJECTIVES: This study aims to examine the electronic prescription programme in Iran by thoroughly identifying the key strengths, weaknesses, opportunities and threats (SWOT) associated with its implementation and utilisation among healthcare stakeholders.

DESIGN: A thematic analysis was adopted, with data systematically examined through the SWOT analytical framework.

SETTING: Hospital, pharmacy, specialised clinic, insurance affiliated clinic in Iran.

PARTICIPANTS: Participants consisted of four groups involved in implementing the electronic prescription programme, including physicians, pharmacists, nurses and hospital administrative employees. Moreover, research participants were selected using a purposive sampling approach and sampling continued until data saturation was reached.

METHODS: Semistructured interviews were employed for data collection. The data analysis steps were systematically executed using Braun and Clarke's six-phase thematic analysis approach. Within the study's conceptual framework based on SWOT analysis, themes and codes were categorised into positive (strengths, opportunities) and negative (weaknesses, threats) drivers. In addition, the method proposed by Lincoln and Guba was employed to endorse the data credibility.

RESULTS: Overall, data saturation was reached with 25 participants and two major themes and four minor themes. The 'strengths' theme comprised patient safety, economic efficiency, information sharing, remote access and drug list accessibility. The 'weaknesses' theme encompassed internet and electricity dependency, resistance to implementation, numerous platforms and diverse insurer schemes and frequent changes in insurance company tariffs. The 'opportunities' theme consisted of health system networking, clarifying processes, eliminating drug intermediaries, improving health service quality, enhancing data banks, expediting drug monitoring and improving technological infrastructures in the health field. Ultimately, the 'threats' theme involved confidential information access and misuse, damaged drug barcodes, incorrect data recording, patient dissatisfaction and government financial burden.

CONCLUSIONS: Due to the fact that the challenges and benefits associated with this system vary across countries depending on their technical and non-technical capacities and infrastructures, the findings of the current research can contribute to promoting the system within our country.},
}

Iran
Humans
Qualitative Research
*Electronic Prescribing/statistics & numerical data
Attitude of Health Personnel
Interviews as Topic
Pharmacists

@article {pmid42353493,
year = {2026},
author = {Yan, MC and Yao, ZY},
title = {Morphological and Molecular Data Reveal Two New Cryptic Spider Species of the Pholcus yichengicus Species Group (Araneae, Pholcidae) from Central China.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/ani16121884},
pmid = {42353493},
issn = {2076-2615},
support = {32170461//National Natural Science Foundation of China/ ; },
abstract = {Two new cryptic species from central China, belonging to the Pholcus yichengicus species group, were identified using an integrative approach combining morphological and three molecular species delimitation methods, and incorporating data from five related previously described species. These two new species are named Pholcus chengkousp. nov. and P. yanansp. nov. DNA barcodes were generated for the two new species to calculate p-distances and K2P distances, thus confirming their identities alongside the five previously described species. Additionally, revised diagnoses for the five previously described species and a distribution map encompassing all the species discussed are provided.},
}

@article {pmid42353773,
year = {2026},
author = {Li, Z and Luo, M and Zhu, M and Bai, Y},
title = {From Molecular Visualization to Spatial Landscapes: Engineering the Next Generation of In Situ Hybridization.},
journal = {Genes},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/genes17060616},
pmid = {42353773},
issn = {2073-4425},
mesh = {Animals ; *In Situ Hybridization/methods ; Humans ; Spatial Transcriptomics ; In Situ Hybridization, Fluorescence/methods ; },
abstract = {In situ hybridization (ISH) has undergone a rapid evolution from a low-throughput histological staining technique to a diverse family of modern methods for sensitive, specific and multiplexed molecular detection in intact cells and tissues, and to a cornerstone technology for image-based spatial transcriptomics. This transformation has been driven by advances in probe design, signal amplification, cyclic imaging, combinatorial barcoding, automated fluidics and computational decoding, which together allow RNA molecules to be measured within preserved cellular and tissue architecture. In this review, we examine the molecular and engineering principles that underlie modern ISH methods and their extension into ISH-based spatial profiling, with emphasis on hybridization chain reaction, branched-DNA amplification, SABER-FISH, rolling-circle-amplification-based approaches, seqFISH, MERFISH, RAEFISH and selected commercial implementations. We discuss how sensitivity, specificity, tissue compatibility, optical crowding, imaging burden, cost, reproducibility and computational uncertainty shape the practical use of each method. Sequencing-based spatial capture platforms are not reviewed comprehensively, but are considered where comparative benchmarks help clarify trade-offs in spatial resolution, transcriptome breadth, tissue area or analytical interpretation. We also consider how recent benchmarking and standardization efforts are beginning to define quantitative criteria for comparing platforms, and how advances in segmentation, barcode decoding, spatial integration and cell-cell communication analysis convert raw images into biological insight. Finally, we highlight applications in targeted transcript detection, tissue-based validation, neuroscience, cancer, developmental biology, non-model organisms and spatial functional genomics, where modern ISH methods and ISH-based spatial profiling provide information that bulk and dissociated single-cell approaches cannot capture. Together, these developments trace how ISH has expanded from targeted molecular visualization into a broad methodological framework for in situ detection and spatially resolved transcriptomic analysis.},
}

Animals
*In Situ Hybridization/methods
Humans
Spatial Transcriptomics
In Situ Hybridization, Fluorescence/methods

@article {pmid42355274,
year = {2026},
author = {Williams, PH and Alonso-Alonso, P and Arbetman, M and Françoso, E and Ghisbain, G and Huang, J and Orr, MC and Ren, ZX and Streinzer, M and Thanoosing, C and Vandame, R and Waite, M and Brace, S},
title = {Evolutionary Tree for All Bumblebee Species World-Wide Estimated by Combining Information from Fast-Evolving Genes, Slow-Evolving Genes, and Genomic Data (Apidae, Bombus).},
journal = {Insects},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/insects17060540},
pmid = {42355274},
issn = {2075-4450},
support = {2026PVC0122//Chinese Academy of Science's President's International Fellowship Initiative/ ; CARS-KXJ5//China Agriculture Research System-Bee funding for bumblebee taxonomy 2007-2026/ ; },
abstract = {Evolutionary trees are of central importance in biology to develop explanatory frameworks for many kinds of studies, including studies of behaviour, ecology, and conservation. Since the last major estimate of evolutionary relationships among many bumblebee species two decades ago, there have been revisions to their taxonomy, descriptions of new species, and sequencing of many rarer species. By combining: (1) earlier data mostly from slow-evolving nuclear genes as a backbone tree; with (2) new data from fast-evolving mitochondrial COI barcodes to resolve more of the twigs on the tree, including sequences obtained from rare old specimens with ancient DNA techniques; as well as (3) the results from broader genomic data for resolving deep relationships, we make a Bayesian estimate of evolutionary relationships with BEAST 2 among all 289 published and accepted extant bumblebee species, an increase of more than 29% of the species on the previous largest tree. The new tree will serve as a framework for future comparative studies that should enable broader insights into the evolution and ecology of all bumblebees. We illustrate this with an analysis of the evolution of some male morphological characters related to male mate-searching behaviour. We also present a novel map of spatial variation in net diversification rates among bumblebee species world-wide, which indicates an especially rapid net diversification within the more recent Mesoamerican and South American faunas.},
}

@article {pmid42355325,
year = {2026},
author = {Huang, DG and Tang, HC and Tsai, CW},
title = {Seasonal Population Dynamics of Mosquitoes in Taipei, Taiwan.},
journal = {Insects},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/insects17060592},
pmid = {42355325},
issn = {2075-4450},
abstract = {Mosquito-borne diseases pose a significant public health concern globally; however, data on mosquito population dynamics in Taipei, Taiwan are limited and outdated. Updated information on species composition and seasonal abundance is crucial for enhancing vector surveillance and informing effective control strategies. In this study, to investigate the seasonal dynamics of mosquito populations in Taipei, Taiwan, adult females were collected biweekly from June 2023 to May 2025 using CDC light traps baited with ultraviolet light and dry ice. Species identification was performed based on morphological characteristics, and morphologically challenging Culex mosquito species were further confirmed using cytochrome c oxidase I barcoding. Mosquito surveillance from June 2023 to May 2025 yielded 1926 females representing 31 species. Of these, Culex quinquefasciatus, Culex pipiens molestus, Aedes albopictus, and Culex tritaeniorhynchus accounted for over 90% of all specimens. These dominant species exhibited distinct seasonal patterns: Cx. quinquefasciatus occurred year-round, Cx. pipiens molestus predominated during winter and spring, while Ae. albopictus and Cx. tritaeniorhynchus populations peaked in summer. Furthermore, spatial heterogeneity in both mosquito abundance and species composition was noted among the study sites. Monitoring the composition and seasonal dynamics of mosquito species is essential for understanding the epidemiology of mosquito-borne pathogens. These insights can inform more effective and targeted vector control strategies for reducing disease transmission. Such ecological insights can also support One Health approaches by linking human, animal, and environmental factors that influence the transmission of mosquito-borne diseases.},
}

@article {pmid42355339,
year = {2026},
author = {Inoue, H},
title = {A New Trioza Species (Hemiptera: Triozidae) from Japan Associated with Urtica (Urticaceae).},
journal = {Insects},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/insects17060606},
pmid = {42355339},
issn = {2075-4450},
support = {JP25850035//Japan Society for the Promotion of Science/ ; },
abstract = {A nettle-feeding psyllid of the genus Trioza (Hemiptera: Triozidae) was discovered in Hokkaido, northern Japan. Although the European species Trioza urticae has been reported from Japan in several databases and publications, these records are based on erroneous literature citations rather than examined specimens. Adult and immature materials collected from Urtica platyphylla were examined morphologically and analysed using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The Japanese species is closely related to Palaearctic T. urticae and Nearctic T. albifrons but is consistently distinguishable by several adult and immature morphological characters. In addition, COI sequences show large interspecific divergence (≥12%) among the three species, supporting its distinct taxonomic status. The Japanese species is therefore described as Trioza miyatakei sp. nov., and Japan is formally excluded from the distribution range of T. urticae. These results indicate that records of T. urticae in East Asia surrounding Japan require re-examination using both morphology and DNA barcoding. A diagnostic key to all known Urtica-feeding species of Trioza worldwide is provided. Furthermore, the Chinese species Triozopsis huai Li, 2011 is transferred to Trioza as Trioza huai (Li, 2011) comb. nov.},
}

@article {pmid42355380,
year = {2026},
author = {Mintara, R and Wannasingha, W and Jaroenchaiwattanachote, C and Jumpato, W and Namtaku, S and Inkhavilay, K and Thanee, I and Pramual, P},
title = {Diversity and Host Blood Meal Analysis of Culicoides (Diptera: Ceratopogonidae) from Laos.},
journal = {Insects},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/insects17060647},
pmid = {42355380},
issn = {2075-4450},
support = {6806008//Mahasarakham University/ ; },
abstract = {Many biting midge species of the genus Culicoides Latreille are significant pests and vectors that transmit diverse parasites to humans and other animals. However, knowledge of these hematophagous insects in Laos remains limited, with the most recent information reported more than four decades ago. In this study, we investigated Culicoides species diversity, DNA barcoding and host blood sources using specimens collected across seven provinces in northern, central, and southern Laos. A total of 4592 specimens were collected, comprising 3095 females and 1497 males. Morphological identification, complemented by DNA barcode analysis, revealed 26 species (24 named and 2 unnamed), including five (three named and two unnamed) new country records. Culicoides peregrinus was the most abundant species, representing 25.7% (1179 individuals), followed by C. oxystoma at 23.8% (1093 individuals), and C. arakawae/C. mahasarakhamense, which together comprised 18.5% (849 individuals) of the total specimens. DNA barcode analysis demonstrated that this genetic marker is effective for species identification of Culicoides in Laos. Of the 115 COI sequences, 103 (89.6%) were successfully matched with conspecifics in the BOLD database. Cryptic genetic diversity was detected in three species, C. clavipalpis, C. palpifer, and C. huffi, with two, two, and three divergent lineages, respectively. Host blood meal analysis revealed that chickens and domestic water buffalo were the most common blood sources for the investigated Culicoides species. These findings provide important baseline information for future studies on the pest and vectorial roles of Culicoides in Laos.},
}

@article {pmid42357136,
year = {2026},
author = {Aiture, N and Kanayev, A and Mussina, R and Kyzdarova, D and Sultangaliyeva, G and Sapakhova, Z},
title = {Morphology, Taxonomy, Geographic Distribution, Genetic Diversity, and Phylogenomics of the Genus Tulipa L.: A Comprehensive Review.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/plants15121817},
pmid = {42357136},
issn = {2223-7747},
abstract = {The genus Tulipa L. is a common group of ornamental plants, characterized by high morphological variability and a complex taxonomy. Despite considerable interest in this group, assessments of its species composition remain inconclusive, as evidenced by discrepancies between contemporary taxonomic sources. The number of recognized taxa varies across major taxonomic databases, including Plants of the World Online, World Flora Online, and Euro+Med PlantBase, reflecting ongoing taxonomic revisions and differences in species concepts. In terms of distribution patterns, 7.6% are widely distributed taxa across transcontinental regions, 28.0% occur across multiple countries within a continent, and 66.9% are range-restricted taxa. The latter group includes 4.2% transnational endemics, 44.1% single-country endemics, 8.5% single-region endemics, and 10.2% single-site endemics. Recent taxonomic and evolutionary studies of Tulipa increasingly rely on molecular approaches, particularly DNA barcoding and chloroplast genome analyses, which have improved phylogenetic resolution and species delimitation in several cases. However, truly comprehensive studies combining morphological, cytogenetic, and molecular datasets remain limited and are typically restricted to individual taxa or species complexes rather than the genus as a whole. Modern molecular genetic studies demonstrate the high informativeness of both nuclear and plastid markers for studying the phylogeny, systematics, and genetic diversity of Tulipa species. Natural populations of Tulipa are under pressure from anthropogenic factors and climate change, resulting in reduced range and habitat degradation. According to the International Union for Conservation of Nature Red List of Threatened Species, among 118 taxa of the genus Tulipa, T. sprengeri Baker is classified as Extinct in the Wild, 5.9% as Critically Endangered, 5.9% as Endangered, 8.5% as Vulnerable, 11.9% as Near Threatened, and 11.0% as Least Concern. The use of exclusively national assessments to determine species extinction risk may be insufficiently objective, whereas global assessments provide a more informative and reliable approach for evaluating conservation status. In this review, we combine investigations of the morphology, taxonomy, and geographic diversity; population genetic structure and molecular diversity; and molecular phylogenetics and plastome-based genomics of the genus Tulipa. Furthermore, the review examines current challenges and future research prospects, emphasizing that studies of the genus Tulipa should integrate morphological, genomic, and ecological approaches to refine taxonomy and conserve genetic resources.},
}

@article {pmid42357915,
year = {2026},
author = {Luo, X and Sun, R and Qiu, XM and Lin, Y},
title = {Integration pathway of environmental DNA technology into the environmental impact assessment system.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {37},
number = {6},
pages = {2094-2102},
doi = {10.13287/j.1001-9332.202606.034},
pmid = {42357915},
issn = {1001-9332},
mesh = {*DNA, Environmental/analysis ; *Environmental Monitoring/methods ; *Ecosystem ; *Conservation of Natural Resources ; Rivers ; China ; Environment ; },
abstract = {Amid comprehensive fishing bans and the continuous advancement of major infrastructure projects, the implementation of Technical Guidelines for Ecological Impact Assessment (HJ 19-2022) faces three contradictions: restrictions on traditional survey methods, insufficient efficiency in large-scale ecological assessment, and lack of historical data. Environmental DNA (eDNA) technology, with the advantages of high sensitivity, non-invasiveness and high-throughput capabilities, offers a new pathway to resolve these dilemmas. We systematically analyzed the unique value of eDNA in addressing the core contradictions in ecological impact assessment (EIA), and proposed a three-level collaborative implementation framework - "screening-locking, verification-qualification, monitoring-tracking". Drawing on the environmental impact assessments of the Fuling to Fengdu Waterway Regulation Project on the Upper Yangtze River and the tender announcement of the Yangzhong Reach Phase Ⅱ (Emergency Regulation) Project, we embedded eDNA technology into the entire EIA process. It critically addressed the bottlenecks in three aspects: the standardization of full-process eDNA workflows, the completeness of native aquatic organism reference gene databases, and the development of quantitative models linking eDNA concentration to biomass. Accordingly, an institutional integration support system was constructed, centered on a national technical specification for eDNA monitoring in aquatic ecological surveys and whole-process quality control, underpinned by a national aquatic eDNA barcode reference database and independent third-party data quality verification. Through an eDNA dynamic monitoring network, the dynamic optimization of ecological conservation redlines and the precision of ecological-environmental access lists could be promoted, thereby achieving a strategic shift from "static delineation" to "dynamic monitoring" and from "passive assessment" to "proactive early warning". Systematically integrating eDNA techno-logy into the environmental impact assessment system would be a crucial pathway to enhance ecological governance capabilities.},
}

*DNA, Environmental/analysis
*Environmental Monitoring/methods
*Ecosystem
*Conservation of Natural Resources
Rivers
China
Environment

@article {pmid42335153,
year = {2026},
author = {Santana, DJ and Shepard, DB and Carvalho, PS and Müller, MMP and Assis, CL and Feio, RN},
title = {A new species of Dendropsophus (Anura, Hylidae) of the D. ruschii group from the Atlantic Forest in Serra da Mantiqueira, Minas Gerais, Brazil.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351087},
pmid = {42335153},
issn = {1932-6203},
mesh = {Animals ; Brazil ; *Anura/classification/genetics/anatomy & histology ; *Forests ; Phylogeny ; DNA, Mitochondrial/genetics ; Species Specificity ; },
abstract = {The Dendropsophus ruschii species group currently comprises two species with disjunct distributions between the Atlantic Forest and the Amazon. Based on an integrative approach combining morphological, acoustic, and molecular data (mtDNA barcoding), we describe a new species from the Serra da Mantiqueira, Minas Gerais, Brazil. Dendropsophus liliae sp. nov. is diagnosed by its small size, rounded digital discs, presence of a calcar appendage, dark red iris, and a distinct white stripe from the snout to the upper eyelid. This discovery expands the known diversity of the group and represents its most inland record within the Atlantic Forest.},
}

Animals
Brazil
*Anura/classification/genetics/anatomy & histology
*Forests
Phylogeny
DNA, Mitochondrial/genetics
Species Specificity

@article {pmid42335171,
year = {2026},
author = {Yang, X and Yi, S and Wei, X and Zheng, G and Wu, L and Zhang, L and Ouyang, G and He, S and Yang, X and Yang, F},
title = {Rapid Detection of Hemoglobinopathy Variants Using One-Step Library Preparation and Nanopore Sequencing.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvag072},
pmid = {42335171},
issn = {1530-8561},
support = {2023A1515110676//Guangdong Basic and Applied Basic Research Foundation/ ; 2024B03J1036//Science and Technology Program of Guangzhou/ ; },
abstract = {BACKGROUND: Third-generation sequencing (TGS) enables comprehensive detection of rare hemoglobin (Hb) variants due to its long-read capability. However, library preparation is often labor-intensive and time-consuming. This study developed a novel one-step library preparation (OSLP) method for TGS. By integrating barcode sequences into target-specific primers, the approach enables immediate barcoding on amplification, streamlining identification of hemoglobinopathy variants.

METHODS: A retrospective set of DNA samples (n = 455; 394 adult, 61 prenatal) underwent OSLP targeting of the HBA2/1, HBG2/1, HBD, and HBB genes on the Qitan Nanopore platform for variant and structural variation detection. Samples were divided into validation and application cohorts based on prior testing with multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing alongside Gap-polymerase chain reaction (GAP-PCR)/reverse dot blot (RDB).

RESULTS: In the validation cohort, OSLP-TGS showed 100% concordance with routine methods (MLPA, Sanger, GAP-PCR, RDB), including 294 samples for α-globin genotyping [8 structural variants (SVs), 17 single nucleotide variants (SNVs)/insertions-deletions (indels)], 138 for β-globin genotyping (4 SVs, 22 SNVs/indels), and 61 prenatal samples for combined genotyping. The method directly spanned breakpoints and determined cis/trans configurations. In the application cohort, OSLP-TGS-Nanopore identified additional variants not covered by routine genotyping: 9 extra α-globin SNVs in 16/100 samples and 8 extra β-globin SNVs in 33/256 samples. Notably, 3 samples with the -SEA deletion harbored co-inherited novel variants, explaining their disproportionately low Hb A2 levels.

CONCLUSIONS: The OSLP-TGS-Nanopore assay provides an efficient, comprehensive solution for detecting rare hemoglobinopathy variants, with a framework extendable to population screening for diverse genetic disorders.},
}

@article {pmid42337406,
year = {2026},
author = {Poma-Soto, F and Van Droogenbroeck, H and Soulliaert, B and Giridhar, M and Behr, J and Sabzalipoor, H and Somoza, M and Mestdagh, P and Vandesompele, J},
title = {Benchmarking DNA barcode decoding strategies under high error rates.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06540-x},
pmid = {42337406},
issn = {1471-2105},
support = {460736965//Deutsche Forschungsgemeinschaft/ ; 101115134//European Innovation Council Pathfinder Challenge: DNA-based digital data storage/ ; GOA009-22 BOF//Universiteit Gent/ ; G0AI925N//Fund for Scientific Research Flanders/ ; F/2024/2755//Stichting Tegen Kanker/ ; },
abstract = {BACKGROUND: DNA barcoding enables multiplexed identification of biomolecules in pooled sequencing experiments, with broad applications including spatial transcriptomics. Photolithographic synthesis of high-density barcode arrays achieves library sizes exceeding [Formula: see text] unique sequences but introduces error rates of 10-20% per nucleotide through substitutions, insertions, and deletions. Classical error-correcting codes cannot scale to such library sizes while maintaining robust error correction under these conditions.

METHODS: We benchmarked three computational barcode decoding approaches-Columba (FM-index-based lossless alignment), QUIK (k-mer filtering with GPU acceleration), and RandomBarcodes (trimer-based triage with GPU parallelization)-across simulated and empirical datasets. Simulations spanned barcode lengths of 28-36 nt, library sizes of 21,000-85,000 barcodes, and error rates of 9-32%. Real sequencing data were generated from photolithographically synthesized arrays at three printing density levels.

RESULTS: Under medium error rates (~23%), QUIK achieved the highest recall (87-89%) while maintaining precision [Formula: see text], outperforming RandomBarcodes (recall 56%, precision [Formula: see text]) and Columba (recall 35%, precision 98-100%). QUIK demonstrated superior scalability, processing 59,620 reads/second on a single GPU compared to RandomBarcodes (68 reads/second) and Columba (1550 reads/second with 8 CPU threads). Barcode length strongly influenced accuracy: 34-nt barcodes enabled 75% recall at 99.97% precision with QUIK, compared to 60% recall with 32-nt barcodes. On real data from a 42,000-spot subarray with 36-nt barcodes, QUIK managed a 57% assignment rate with perfect precision, versus 52% (Columba, precision 99.96) and 50% (RandomBarcodes, precision 99.82).

CONCLUSIONS: QUIK provides the optimal balance of speed, accuracy, and scalability for high-density spatial transcriptomics applications under realistic synthesis error conditions. Barcode lengths [Formula: see text] nt are recommended for applications requiring [Formula: see text] read recovery at [Formula: see text] precision.},
}

@article {pmid42339374,
year = {2026},
author = {De Corte, D and Hubot, N and Patterson, C and Holt, B and Mills, S and Long, S and McQuillan, JS},
title = {Nanopore sequencing dataset of marine rocky shoreline microbial communities from the UK's first marine citizen science week event.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112966},
pmid = {42339374},
issn = {2352-3409},
abstract = {In March of 2025 the UK's first Marine Citizen Science Week recruited Citizen Scientists from around the country to participate in a series of activities exploring the ecology and biodiversity of rocky shorelines at sites on the northeast and southwest coastlines of England. To investigate the 'unseen' microbial biodiversity the organisers instructed participants to collect microorganisms from seawater using sterile pressure driven filtration units; these were sent to a laboratory for DNA extraction and metabarcoding analysis. DNA was extracted from material collected on the filter membranes and used in PCR amplification to generate 16S rRNA gene amplicons (bacterial) and 18S rRNA gene amplicons (protozoal). Each amplicon was ligated with a unique barcode and compiled into sequencing libraries, which were sequenced using Oxford Nanopore Technologies' MinION platform. The data sets for 16S rRNA gene amplicon sequencing and 18S rRNA gene amplicon sequencing reads have been uploaded as raw fastq files to the publicly accessible NCBI Sequencing Read Archive. The data sets provide an overview of the bacterial and eukaryotic microbial communities present in seawater collected from two geographically distinct rocky shore environments.},
}

@article {pmid42341749,
year = {2026},
author = {Hawkins, AG and Shapiro, JA and Spielman, SJ and Mejia, DS and Venkatesh Prasad, D and Ichihara, N and Yakovets, A and Gottlieb, AM and Wheeler, KG and Bethell, CJ and Foltz, SM and O'Malley, J and Greene, CS and Taroni, JN},
title = {The Single-Cell Pediatric Cancer Atlas: Data portal and open-source tools for single-cell transcriptomics of pediatric tumors.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101283},
doi = {10.1016/j.xgen.2026.101283},
pmid = {42341749},
issn = {2666-979X},
abstract = {The Single-Cell Pediatric Cancer Atlas (ScPCA) Portal is a resource for uniformly processed single-cell and single-nucleus RNA sequencing (RNA-seq) data and de-identified metadata from pediatric tumor samples. Originally comprising data from 10 projects funded by Alex's Lemonade Stand Foundation (ALSF), the Portal currently contains summarized gene expression data for over 700 samples across 55 cancer types from ALSF-funded and community-contributed datasets. Downloads include expression data as SingleCellExperiment or AnnData objects containing raw and normalized counts, principal-component analysis (PCA) and uniform manifold approximation and projection (UMAP) coordinates, automated cell-type annotations, and copy-number variation estimates, along with summary reports. Some samples have additional data from bulk RNA-seq, spatial transcriptomics, and/or feature barcoding (e.g., CITE-seq) included in the download. All data on the Portal were uniformly processed using scpca-nf, an efficient and open-source Nextflow workflow that uses alevin-fry to quantify gene expression. Comprehensive documentation, including file descriptions and a getting-started guide, are available online.},
}

@article {pmid42343934,
year = {2026},
author = {Bellot, S and Bourobou, DN and Quintero-Berns, C and Csiba, L and Gasson, P and McBride, B and Ilondea, BA and Bouka, GUD and Ebanyenle, E and Moundounga, CG and Ricker, M and Yarwoah, P and Zanguim Tchoutezou, GH and Lisingo, J and Deklerck, V},
title = {Leveraging target enrichment and genome skimming (Hyb-Seq) of herbarium collections to unlock timber DNA barcoding.},
journal = {Applications in plant sciences},
volume = {14},
number = {3},
pages = {e70063},
pmid = {42343934},
issn = {2168-0450},
abstract = {PREMISE: DNA barcoding for timber species identification requires comprehensive reference datasets, informative DNA barcodes, and cost-effective protocols. We developed a workflow leveraging Hyb-Seq (target capture sequencing and genome skimming) to address these challenges, and we tested it on four genera from the mahogany family (Meliaceae).

METHODS: We sequenced up to 350 nuclear and 177 plastid loci from 132 herbarium specimens representing leaf samples of 22 species. We determined the DNA barcoding potential of each locus by looking at species recovery and monophyly in gene trees. We then selected 13 short regions (candidate barcodes) within high-potential loci and tested their PCR amplification and Sanger sequencing on wood DNA.

RESULTS: Three candidate barcodes emerged as the most reliably sequenced from wood DNA and as providing the most accurate species-level identifications, with species monophyly rates above 80%. Failure to obtain sequences from some wood DNA extracts was more often associated with potential DNA impurity (as inferred from DNA color) than with DNA degradation.

DISCUSSION: Our reference data and candidate barcodes provide a foundation to support the DNA barcoding of mahogany and its relatives. Our workflow illustrates how the wealth of Hyb-Seq data currently generated from global herbaria may be leveraged to monitor plant diversity.},
}

@article {pmid42344524,
year = {2026},
author = {Ahn, E and Baek, I and Kandpal, L and Zhang, D and Kirubakaran, S and Lim, S and Bhatt, J and Kim, MS and Park, S and Meinhardt, LW},
title = {Optimizing the genomic bit budget: an information-theoretic framework for trait-enriched genotyping and stratified screening in Theobroma cacao.},
journal = {Horticulture research},
volume = {13},
number = {7},
pages = {uhag106},
pmid = {42344524},
issn = {2662-6810},
abstract = {High-throughput genotyping has revolutionized horticultural breeding, yet the efficient utilization of genomic data remains a bottleneck for germplasm curation and downstream selection. Translating complex genomic information into cost-effective and readily applicable tools for clonally propagated crops requires a shift from maximizing marker density to optimizing information content. Here, we reinterpret cacao (Theobroma cacao L.) genotyping as an information-allocation problem and introduce an information-theoretic framework for designing minimalist, trait-enriched single nucleotide polymorphism (SNP) barcodes. Using a diverse international collection from Trinidad (ICGT) and an independent field trial in Puerto Rico (USDA-ARS Tropical Agriculture Research Station), we compress a 500+ SNP panel into a 32-marker 'CacaoCipher' barcode that preserves pairwise genetic distance structure at coarse resolution while retaining trait-aligned signal for pod index and related yield components. Barcode-space axes correlate with agronomic traits measured across environments in a limited overlap subset, supporting the portability of key signals beyond the training setting. We further quantify a heuristic 'genomic bit budget', showing how information is allocated across unique identification, ancestry structure, and trait variation. Together, this framework converts cacao germplasm from an analog collection of names into a compact digital code and provides a general template for designing low-cost, high-information marker panels for germplasm quality control and stratified screening in clonally propagated crops. One-sentence summary We introduce a 'genomic bit budget' framework to design a minimalist 32-SNP barcode that supports germplasm quality control, coarse ancestry screening, and trait-aligned stratification with limited cross-environment portability.},
}

@article {pmid42344937,
year = {2026},
author = {Enguídanos García, A and Cuesta-Porta, V and Abrego L, J and Almanza, M and Alvelo Villegas, KZ and Antaneda H, J and Bonner, L and Carpintero, OJ and Collado, GN and Córdoba González, D and Díaz Vergara, M and Guerra-Lima, ZI and Noriega, JD and de León Herrera, DS and Domingo, AI and Durán, O and Garrido-Trujillo, A and González, Y and Justo Riverol, SC and Guerrero Romero, A and León Correoso, N and Molina, LEP and Montalvo, E and Pérez-González, CM and Rivera, M and Vásquez Acosta, JL and Vásquez, M and Vega-Atencio, A and Zhuo, W and Galià-Camps, C},
title = {Bridging genetic knowledge gaps in a biodiversity hotspot through conservation training.},
journal = {Bioscience},
volume = {76},
number = {6},
pages = {563-568},
pmid = {42344937},
issn = {0006-3568},
abstract = {The Mesoamerican biodiversity hotspot is extraordinarily rich, yet most invertebrate genetic diversity remains invisible, hampering effective conservation planning amid accelerating biodiversity loss. How can this hidden diversity be revealed while simultaneously building local scientific capacity? Panama BioResearch, a hands-on molecular course, addressed this issue by embedding DNA barcoding within training and conservation contexts. Participants collected terrestrial and marine invertebrates across three protected areas and generated 158 DNA barcode sequences, two-thirds of which represented first genetic records for their species. Comparisons with public databases revealed striking under-representation of Mesoamerican taxa, especially non-iconic groups with key ecosystem roles. Barcoding also enabled the rapid detection of two invasive species, prompting immediate management responses. Beyond documenting biodiversity, this experience demonstrates that small, low-cost educational initiatives can produce actionable data, foster local expertise, and inform conservation priorities. Embedding molecular tools in education provides a scalable model for linking research, training, and management in species-rich but data-deficient regions.},
}

@article {pmid42344953,
year = {2026},
author = {Marquisseau, A and Ollivier, M and Klopp, C and Pascal, G and Pornon, A and Escaravage, N and Sarthou, V and Sarthou, JP and Pichon, M},
title = {16S rRNA sequence dataset for the identification of the French hoverflies (Diptera, Syrphidae).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e189822},
pmid = {42344953},
issn = {1314-2828},
abstract = {With ongoing biodiversity loss, a wide range of taxa are being monitored to support the implementation of conservation measures aimed at preventing their decline. Effective monitoring requires the development of robust and scalable tools and methods. Amongst these, DNA barcoding and metabarcoding have emerged as powerful and widely adopted approaches for tracking biodiversity. To achieve high taxonomic resolution in molecular-based monitoring, the use of multiple DNA markers is often essential. In this study, we focused on Syrphidae, a family that plays a key role in ecological networks. Alongside bees, hoverflies are remarkable pollinators within the order Diptera. Furthermore, larvae of the subfamily Syrphinae are widely regarded as beneficial in agricultural contexts, contributing to the biological control of pest populations. Mainland France, with its temperate climate, is a hotspot for Syrphidae diversity, hosting 566 species whose biological and ecological traits are thoroughly documented in the Syrph the Net 2024 database. France currently holds the highest recorded number of Syrphidae species in Europe. We produced a set of 16S rRNA sequences for Syrphidae, well suited for environmental biomonitoring applications. A total of 713 specimens from the private collection of specialist entomologists, representing 352 species across 14 tribes, were sequenced. Using a customised validation workflow, 561 sequences covering 316 species were retained, representing approximately 60% of the French hoverfly fauna. For 166 species, the 16S rRNA marker successfully discriminates specimens at the species level, including morphologically challenging genera such as Paragus, Melanostoma and Microdon. For the remaining 150 species in the dataset, the 16S rRNA marker enables identification at the genus level, though species-level resolution would require additional specimens to be sequenced. This study represents a first step towards the development of a comprehensive multi-marker reference library for French Syrphidae.},
}

@article {pmid42331962,
year = {2026},
author = {Benzahra, H and Mrabti, I and Grijja, H and Azenzem, R and Kubaa, RA and Afechtal, M and Selmaoui, K},
title = {First report of Penicillium ulaiense causing whisker mold on postharvest citrus fruits in Morocco.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-56301-2},
pmid = {42331962},
issn = {2045-2322},
abstract = {Between February 2024 and June 2025, surveys conducted in northwestern Morocco revealed citrus fruits (Citrus sinensis and Citrus × limon) showing atypical postharvest decay symptoms, characterized by dark, water-soaked lesions with zonation and coremia-like structures. These symptoms were detected at only two sites, with a low incidence of 1.6% in the orchard and 0.5% in market samples. Five fungal isolates were obtained from symptomatic tissues on potato dextrose agar (PDA). Morphological characterization identified all isolates as Penicillium ulaiense, based on colony and micromorphological features consistent with published descriptions. Two representative isolates (BH_B1 and BH_E2) were selected for molecular analyses. Sequencing of the ITS region and the β-tubulin (BenA) gene showed 99-100% identity with reference P. ulaiense sequences, and the concatenated alignment comprised 804 base pairs. Phylogenetic analyses placed the Moroccan isolates within a well-supported P. ulaiense clade, clearly distinct from closely related species such as P. italicum and P. expansum. Pathogenicity assays reproduced typical symptoms on C. sinensis fruits, with progressive lesion development and successful re-isolation of the pathogen, confirming its pathogenic role under experimental conditions. This study reports, for the first time, the occurrence of Penicillium ulaiense associated with postharvest whisker mold symptoms on citrus fruits in Morocco. It provides new insights into postharvest citrus pathogens in Morocco and establishes a basis for future investigations on the occurrence and epidemiology of this species.},
}

@article {pmid42332099,
year = {2026},
author = {Pohl, M and Laukamp, T and Caspers, M and Paczkowski, S and Buellesbach, J},
title = {Sharply Contrasting Chemotypes Coincide with Aggression and Divergence in Cryptic African Carpenter Ant Populations.},
journal = {Journal of chemical ecology},
volume = {52},
number = {4},
pages = {},
pmid = {42332099},
issn = {1573-1561},
mesh = {Animals ; *Ants/genetics/physiology/chemistry/classification ; *Aggression ; *Hydrocarbons/chemistry/metabolism/analysis ; Phylogeny ; DNA Barcoding, Taxonomic ; Behavior, Animal ; },
abstract = {Cryptic differentiation poses a significant challenge to taxonomy, particularly in morphologically conserved lineages whose divergence is not immediately apparent. In eusocial insects like ants, where species boundaries are often maintained through chemical rather than morphological differentiation, integrative methodologies are essential for resolving taxonomic complexity. Here, we present compelling evidence for the recent divergence of African carpenter ants initially identified as Camponotus maculatus into two distinct sub-populations. This divergence is supported through an integrative approach combining chemical, behavioral, and genetic analyses. Most strikingly, we identify two sharply contrasting chemotypes characterized by categorically different cuticular hydrocarbon (CHC) profiles that unambiguously separate the investigated ant populations. Concordantly, behavioral assays reveal that worker ants consistently exhibit aggression toward individuals with opposing chemotypes, while displaying affiliative behaviors toward shared chemotypes irrespective of colony affiliation. Genetic barcoding further corroborates these findings, indicated by phylogenetic clusters largely corresponding with the two chemotypes. Our results highlight the primary role of chemical differentiation within morphologically indistinguishable populations to resolve cryptic sub-population structures. These findings also provide valuable insights into potential early-stage chemical differentiation mechanisms in eusocial insect populations.},
}

Animals
*Ants/genetics/physiology/chemistry/classification
*Aggression
*Hydrocarbons/chemistry/metabolism/analysis
Phylogeny
DNA Barcoding, Taxonomic
Behavior, Animal

@article {pmid42334270,
year = {2026},
author = {Huo, B and Zhang, Z and Li, G},
title = {Dual Adjacent Capture Probe-Induced Hybridization Chain Reaction in a Cyclic Array Reactor for Rapid and Sensitive Fluorescence Detection of Norovirus in Aquatic Food.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.6c02150},
pmid = {42334270},
issn = {1520-6882},
abstract = {Norovirus (NoV) is a leading global cause of foodborne illness, necessitating the development of rapid and sensitive detection methods. However, conventional proximity ligation assays (PLA) often suffer from limited sensitivity and poor compatibility with array-based analysis. Here, we present a novel detection strategy that integrates a proximity-ligation hybridization chain reaction with catalytic hairpin assembly (NPLA-HCR/CHA) and a multidirectional cyclic fluorescence detection system (MDCFS). In this design, protein targets are first converted into amplifiable DNA barcodes via NPLA-HCR/CHA, enabling exponential signal amplification. The MDCFS device, employing electronic fluorinated liquid spacers, enables cyclic array-based readout with enhanced sensitivity. Specific lectin- and antibody-based probes were designed to ensure selective recognition of NoV capsid protein VP1. Signal amplification is achieved through proximity-activated hybridization chain reaction and catalytic hairpin assembly. For practical samples, this method demonstrated a detection limit of 0.15 pg·mL[-1] (approximately 8.51 × 10[3] copies·mL[-1]) and a linear range of 0.50-50 pg·mL[-1] (approximately 2.84 × 10[4] to 2.84 × 10[6] copies·mL[-1]), exhibiting high selectivity and accuracy comparable to those of real-time polymerase chain reaction (RT-PCR). The combination of NPLA-HCR/CHA with MDCFS thus provides a powerful platform for ultrasensitive, multiplexed, and array-compatible detection of NoV, offering significant potential for applications in public health monitoring and food safety assurance.},
}

@article {pmid42328678,
year = {2026},
author = {Ontaneda-Gallegos, R and Moreno-Coellar, EA and García-Ruilova, AB and Salazar-Buenaño, F and Poveda-Proaño, E and Reyes-Barriga, D and Lojan-Cueva, P and Polo, M and Donoso, DA and Barragán, Á},
title = {Carpenter bees (Apidae: Xylocopa) of Ecuador: distribution, DNA barcodes and plant interactions.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21345},
pmid = {42328678},
issn = {2167-8359},
mesh = {Animals ; Bees/classification/genetics/physiology ; Ecuador ; *DNA Barcoding, Taxonomic ; *Plants ; Biodiversity ; },
abstract = {Knowledge of the diversity and ecology of carpenter bees (Xylocopa) in Ecuador remains limited and scattered. Here, we present the first updated assessment of Xylocopa across Ecuador, including continental Ecuador and the Galápagos Archipelago, based on the examination of 1,351 specimens from museum collections, published records and citizen science observations. Twenty-two DNA (COI) barcodes were generated for ten species to support accurate identification. In total, 16 Xylocopa species were recorded, including three newly reported species for the country: X. ornata, X. metallica, and X. nigrocincta. Six morphotypes could not be confidently assigned to any described species, suggesting the presence of undescribed or cryptic taxa. An identification key to the subgenera and species of Xylocopa in Ecuador is also provided. Flower-visitation data was recorded for seven bee species across 60 plant taxa belonging to 26 families. By combining traditional data sources with citizen science observations, this study provides essential baseline information on the diversity, distribution, and ecological interactions of Xylocopa in Ecuador. Observed intraspecific phenotypic variation highlights the need for continued morphological and molecular research.},
}

Animals
Bees/classification/genetics/physiology
Ecuador
*DNA Barcoding, Taxonomic
*Plants
Biodiversity

@article {pmid42329233,
year = {2026},
author = {Ayala-Velastegui, D and Mortimer, TD and Siceloff, AT and Shariat, NW},
title = {NanoPop: Nanopore amplicon sequencing of Salmonella virulence genes to characterize complex mixed serovar populations using k-mers to overcome high sequencing error rates.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
doi = {10.1099/mgen.0.001743},
pmid = {42329233},
issn = {2057-5858},
mesh = {*Nanopore Sequencing/methods ; Animals ; *Salmonella enterica/genetics/classification/pathogenicity ; Serogroup ; Serotyping/methods ; *Salmonella/genetics/classification/pathogenicity ; Virulence/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Virulence Factors/genetics ; },
abstract = {Salmonella enterica comprises over 2,600 genetically distinct serovars, of which 20 are associated with 70% of human illnesses. In food animal production systems, including poultry, mixed serovars commonly exist. Therefore, culture-based approaches that rely on selecting colonies can underestimate serovar complexity in a sample. Recent advances in molecular deep serotyping methods like CRISPR-SeroSeq provide a high resolution of Salmonella populations in a single sample but are still time-consuming. This project aimed to develop a faster serotyping approach using the Oxford Nanopore Technology (ONT) platform. A database was built containing the alleles of two conserved Salmonella virulence genes, fimH (n=91 sequences) and sseL (n=91 sequences), from a total of 1,160 genomes that represent 36 serovars (including polyphyletic lineages for 11 of these serovars). To test the sensitivity of the assay, bacterial cultures of three serovars of concern (Typhimurium, Enteritidis and Infantis) were mixed in tenfold ratios with serovar Kentucky. Both genes were amplified, barcoded with the ONT native barcoding kit, pooled and sequenced with a MinION device, followed by basecalling, demultiplexing and filtering for length and quality. To overcome high sequencing error rates and still resolve serovars with a low relative abundance, we used two tools: Emu, a published alignment and sequence likelihood algorithm that has been applied to ONT 16S rRNA gene sequencing, and NanoPop, a method developed here. NanoPop relies on a generated database of sliding window 15-mer sequences (n=6,322) across SNPs in all fimH and sseL alleles and parsing ONT sequencing reads against these 15-mers. Emu and NanoPop each detected background serovars present at 1% or higher. Finally, these methods were applied to real-world samples from pre- and post-harvest poultry samples and compared to CRISPR-SeroSeq outputs. NanoPop is beneficial because it calls unknown or untypeable salmonellae, while Emu forces a match with an allele in the database, potentially calling incorrect serovars. While Salmonella was used as a bacterial model for this study, this method has potential application to other micro-organisms.},
}

*Nanopore Sequencing/methods
Animals
*Salmonella enterica/genetics/classification/pathogenicity
Serogroup
Serotyping/methods
*Salmonella/genetics/classification/pathogenicity
Virulence/genetics
High-Throughput Nucleotide Sequencing/methods
*Virulence Factors/genetics

@article {pmid42331214,
year = {2026},
author = {Kibet, CJ and Kuchta, R and Kundid, P and Selbach, C and Leontovyč, R and Bulantová, J and Soldánová, M},
title = {Bringing order to chaos: A new classification of avian schistosomes and their genetic lineages in the context of swimmer's itch.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104904},
doi = {10.1016/j.ijpara.2026.104904},
pmid = {42331214},
issn = {1879-0135},
abstract = {Schistosomes are parasitic flatworms that infect birds and mammals, including humans, using gastropods as intermediate hosts. Despite their ecological and medical importance, the taxonomy of avian schistosomes is poorly understood due to morphological similarity and patchy molecular data. Here, we present the global synthesis of AS diversity integrating all available sequence data for three genetic markers (cox1, ITS1-5.8S-ITS2 and 28S rDNA) with newly obtained samples from snails and birds across Europe. Among the markers, cox1 proved to be the most sensitive and reliable for species delimitation and is recommended as the primary barcode for future studies. We identified 25 molecularly confirmed species, representing 29% of the 85 nominal species worldwide, and a further 52 unnamed genetic lineages that may correspond to morphologically known but molecularly unconfirmed species or represent new species. In Europe, we have recognised seven named species and 12 genetic lineages, including six newly discovered lineages based on material obtained from our field collections. To facilitate uniform taxonomy and comparative research, we propose a standardised molecular framework for naming undescribed avian schistosome lineages. Although the morphology of avian schistosome cercariae offers limited taxonomic resolution due to high interspecific similarity, two distinct morphotypes were identified that generally correspond to infections in lymnaeid and planorbid snail hosts.},
}

@article {pmid42317022,
year = {2026},
author = {Zhao, P and Liu, Q and Ou, M and Liu, H and Liu, Y and Wang, J and Yang, M and Chen, Z and Cai, W},
title = {Mainland diversification and recent island lineages in the reduviid genus Tapirocoris: an integrative taxonomic framework with four new species.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70302},
pmid = {42317022},
issn = {1744-7917},
support = {32270474//National Natural Science Foundation of China/ ; 31730086//National Natural Science Foundation of China/ ; AD23026043//Guangxi Natural Science Foundation/ ; },
abstract = {The assassin bug genus Tapirocoris Miller, 1954 (Hemiptera: Reduviidae: Harpactorinae: Dicrotelini) is distributed in southern China and adjacent regions. However, gradual morphological variation among its members has long complicated species delimitation and obscured the understanding of their phylogenetic relationship and evolutionary history. Here, we apply an integrative taxonomic framework to revise the classification of Tapirocoris and to reconstruct its spatio-temporal diversification history. Based on mitochondrial COI DNA barcode sequences from 94 specimens collected across 26 localities, multiple species-delimitation methods and phylogenetic inference consistently recovered seven well-supported evolutionary lineages, including three previously known species and four newly described species: T. hainanensis Zhao & Cai, sp. nov., T. rufus Zhao & Cai, sp. nov., T. taiwanensis Zhao & Cai, sp. nov., and T. yuensis Zhao & Cai, sp. nov. Geometric morphometric analyses further confirmed that these lineages are morphologically diagnosable. Divergence time estimation may indicate an early Miocene crown origin of Tapirocoris (∼21.48 Ma), and discrete phylogeographic reconstruction is consistent with repeated range shifts between the South China hilly region and the Yunnan-Guizhou Plateau, forming a mainland diversification backbone. Subsequent directional dispersal events likely contributed to the emergence of insular endemic species in Hainan and Taiwan during the Pleistocene. These interpretations are based primarily on mitochondrial COI data and would benefit from further validation using multilocus or nuclear genomic datasets. In addition, we provide an updated key to the species of Tapirocoris and a world catalogue of the tribe Dicrotelini, establishing practical taxonomic resources and a broader systematic framework for future research.},
}

@article {pmid42318773,
year = {2026},
author = {Isiye, E and Olmeda, AV and Curran, T and O'Neill, D and De Waal, T and Barry, G and O'Hanlon, A and O'Shaughnessy, J and England, M and Zintl, A and O'Meara, D},
title = {Design and optimisation of rapid real-time PCR assays for the detection of key Culicoides species.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70088},
pmid = {42318773},
issn = {1365-2915},
support = {//Department of Agriculture, Food and the Marine, Ireland/ ; },
abstract = {In extensive surveillance programmes of Culicoides biting midges (Diptera: Ceratopogonidae), morphological identification can be time-consuming and difficult, while DNA barcoding, although highly accurate, may not be cost-effective or suitable for rapid analysis, as it requires individual specimen processing. To address these limitations, we developed a rapid screening method using real-time PCR assays with either SYBR Green or hydrolysis probe-based detection chemistries. Species-specific primers and, where necessary, hydrolysis probes were designed based on the updated sequences of the ITS2 region of seven Culicoides species. The specificity and efficiency of these assays were validated both in silico and through real-time PCR testing on target and non-target Culicoides species, tested individually and as mixed-species samples. The new real-time PCR assays detect the presence of key species including C. obsoletus, C. scoticus, C. chiopterus, C. dewulfi, C. pulicaris, C. punctatus and C. impunctatus in pools of specimens. The molecular techniques developed in this study provide a valuable tool for accurate and high-throughput Culicoides surveillance, which can be used for year-round monitoring of adult midges in traps, larvae and in environmental samples, potentially revealing novel insights into the spatial and temporal turnover of Culicoides species. These methods can be applied to large-scale vector screening programmes involving pooled samples, addressing the limitations of previously described methods used in midge surveillance.},
}

@article {pmid42319209,
year = {2026},
author = {Parsons, DAJ and Vos, RA and Price, BW},
title = {BeeGees: A High-Throughput Protein-Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70170},
pmid = {42319209},
issn = {1755-0998},
support = {101059492//European Commission/ ; 22.00173//Swiss State Secretariat for Education, Research and Innovation/ ; 24.00054//Swiss State Secretariat for Education, Research and Innovation/ ; //UK Research and Innovation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; Workflow ; *Metagenomics/methods ; },
abstract = {Natural history collections are unparalleled archives of global biodiversity, yet most specimens remain molecularly uncharacterised due to the technical challenges of historical DNA (hDNA), including degradation, low endogenous content and contamination. Genome skimming offers a scalable alternative to PCR-based barcoding, but existing bioinformatic workflows are not optimised for the heterogeneous, metagenomic nature of museum-derived data. Here we present BeeGees (Barcode Extraction and Evaluation from Genome Skims), a high-performance computing (HPC) integrated, Snakemake-based workflow designed for protein-guided recovery and validation of mitochondrial and plastid barcode genes from degraded short-read genome sequences. BeeGees integrates dual read pre-processing, systematic per-sample parameter sweeps, sequential consensus cleaning to remove contaminant sequences and rigorous structural and taxonomic validation against curated reference databases. We benchmarked BeeGees on 1518 museum specimen-derived genome skims spanning eight phyla. The workflow completed in approximately 120 h (< 5 min per sample) on HPC infrastructure. When excluding sequencing failures (< 1 M reads), validated COI barcodes were recovered for 73.2% of specimens (1050/1435). Barcode recovery success was influenced by endogenous content, preservation quality and parameter choice rather than raw read count alone, highlighting the importance of systematic parameter optimisation. Sequential consensus cleaning eliminated ambiguous bases and reduced chimeric artefacts, proving essential for robust museomic analyses. BeeGees provides a reproducible, scalable framework for high-throughput barcode recovery and biodiversity genomics and reference gap-filling initiatives from natural history collections. The BeeGees pipeline is available at: https://github.com/bge-barcoding/BeeGees/.},
}

*DNA Barcoding, Taxonomic/methods
Museums
Animals
*High-Throughput Nucleotide Sequencing/methods
*Computational Biology/methods
Workflow
*Metagenomics/methods

@article {pmid42319452,
year = {2026},
author = {Lei, F and Liang, Q and Yuan, X and Liu, Q and Zhang, Y and Xie, T and Wang, L and Zhu, B},
title = {IBS-CNN: a novel computer vision-based kinship classification model for high-density SNP microarray.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42319452},
issn = {1437-1596},
support = {82293652//National Natural Science Foundation of China/ ; 82293650//National Natural Science Foundation of China/ ; 82572152//National Natural Science Foundation of China/ ; },
abstract = {This study addresses multiple challenges in applying forensic genealogy to Chinese populations by exploring novel kinship classification strategies based on machine learning (ML) and deep learning (DL). Utilizing Infinium Asian Screening Array (ASA) microarray integrated with Han Chinese reference data from the 1000 Genomes Project, we simulated 70,000 pairs of first- to fifth-degree relatives and unrelated individuals while experimentally validating data from Han Chinese volunteers from 19 pedigrees, including corresponding kinship pairs across all degrees and unrelated individuals. We systematically evaluated the performance of shared identity-by-descent (IBD) segment analysis, likelihood ratio (LR) method, and kinship coefficient approaches. Innovatively, we developed a multi-feature ML model incorporating IBD distribution statistics, LR values, and kinship coefficients. Concurrently, we created an IBS-CNN model for image recognition by integrating computer vision with identity-by-state (IBS) theory. With pairwise SNP genotypes color-encoded by their IBS status, an IBS-CNN model for IBS heatmap recognition was created. Results demonstrate that the IBS-CNN model (https://github.com/Rarapie/IBS-CNN) showed advantages over the common methods and ML models: it directly processes images converted from VCF files while exhibiting greater robustness to data heterogeneity. The IBS-CNN approach achieved robust real-data accuracy (94.56%) while supporting input of IBS barcode heatmaps that exclusively represent IBS status of paired samples, establishing a data transmission format more secure and storage-efficient than raw DNA data.},
}

@article {pmid42321208,
year = {2026},
author = {King, JJ and Mowla, A and Kretzmann, JA and Bhalla, N and Sugianto, G and Norret, M and Kadolsky, UD and Iqbal, M and Saxena, A and Amos, SE and Choi, YS and Kennedy, BF and Iyer, KS and Smith, NM and Evans, CW},
title = {Single-cell RNA sequencing profiles drug activity within spatially engineered 3D cultures.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74587-8},
pmid = {42321208},
issn = {2041-1723},
abstract = {Spatial transcriptomic techniques provide a wealth of information useful in guiding drug development, while three-dimensional (3D) cell cultures have demonstrated power in accelerating drug approvals. However, techniques for robust spatial analysis of 3D cultures are limited. Here, we present a transfection-based method for constructing cellular spheroids through a layer-by-layer approach, in which DNA barcodes encode the spatial positioning of cells. Our technique facilitates multiplex single-cell RNA sequencing, providing spatial maps of gene expression and drug response, while correlative imaging reveals the locations of barcoded cell populations and quantifies local tissue elasticity. We show that model HeLa 3D spheroids display heterogeneous responses to drugs, which may arise through diffusion gradients of the drug, or from differences in metabolism, nutrient supply, and cellular stressors. The ability to create spatially encoded cellular assemblies may help to reveal spatial variation in gene expression within 3D culture models.},
}

@article {pmid42324848,
year = {2026},
author = {Santos-Perdomo, I and Salces-Castellano, A and Moraza, ML and Mateos, E and Muñoz-Barrera, A and González-Montelongo, R and Suárez, D and Vega-Pita, N and Falcón-López, L and Lorenzo-Salazar, JM and Flores, C and Arribas, P and Andújar, C},
title = {Integrating Megabarcoding and Metabarcoding to Unlock Diversity and Distribution Data Shortfalls in Dark Taxa.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70166},
doi = {10.1111/1755-0998.70166},
pmid = {42324848},
issn = {1755-0998},
support = {CGL2015-74178-JIN//Agencia Estatal de Investigación/ ; PID2021-126883NA-I00//Agencia Estatal de Investigación/ ; PID2022-143291NB-I00//Agencia Estatal de Investigación/ ; RYC2020-029196-I//Agencia Estatal de Investigación/ ; RYC2021-034291-I//Agencia Estatal de Investigación/ ; TESIS2022010039//Agencia Canaria de Investigación, Innovación y Sociedad de la Información/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; Spain ; Phylogeography ; High-Throughput Nucleotide Sequencing/methods ; Genetic Variation ; *Metagenomics/methods ; Soil ; },
abstract = {Persistent biodiversity data shortfalls undermine our capacity to detect species, map their distributions and characterize their spatial genetic structure, limiting robust biogeographic analyses and the development of effective conservation strategies. This particularly affects hyperdiverse invertebrate groups where hidden diversity remains largely undocumented. This study develops and demonstrates the potential of an integrated high-throughput sequencing (HTS) framework to improve the representation of hidden diversity in regional species inventories and to help close critical gaps in our understanding of species distributions and genetic diversity from a conservation biogeography perspective. Focusing on the Canary Islands (Spain), the workflow combines megabarcoding of more than 4000 mesofauna specimens to generate a curated species-level molecular reference library with community DNA metabarcoding of 168 soil samples. This approach enables consistent taxonomic assignment across insular landscapes and increases the spatial and genetic resolution of occurrence data. We identified 145 species of mites and springtails, including 49 species newly recorded for the archipelago and numerous genetically distinct lineages likely representing undescribed taxa, highlighting all the biodiversity that remains to be described. Integration of the barcode library with metabarcoding data produced 1440 species occurrences, revealing extensive distributional gaps, multiple range expansions and strong within-island phylogeographic structuring, indicating prevalent diversification at fine spatial scales. These results highlight a deep, taxonomically broad underestimation of soil biodiversity and demonstrate that this integrative approach provides a transferable model for advancing the biogeography, evolutionary understanding and conservation of dark and cryptic taxa across broad taxonomic and conservation-relevant contexts.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Biodiversity
Spain
Phylogeography
High-Throughput Nucleotide Sequencing/methods
Genetic Variation
*Metagenomics/methods
Soil

@article {pmid42324862,
year = {2026},
author = {Gomez-Olivieri, LR and Schiavi-Ehrenhaus, LJ and Jabloñski, M and Buffone, MG and Luque, GM},
title = {A Scalable Flow Cytometry Assay to Evaluate CatSper-mediated Ca[2+] Influx Triggered by High-K[+]/High-pH Stimulation in Mouse Sperm.},
journal = {Andrology},
volume = {},
number = {},
pages = {},
doi = {10.1111/andr.70294},
pmid = {42324862},
issn = {2047-2927},
support = {//Male Contraceptive Initiative: Sokal Innovation Award 2020/ ; PICT 2021-00031//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2020-00098//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2021-00014//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIBAA 2022-100368//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; 2024//Florencio Fiorini/ ; },
abstract = {BACKGROUND: The sperm-specific Ca[2+] channel CatSper is essential for male fertility, as it mediates Ca[2+] influx required for sperm hyperactivation. Because of its restricted expression in sperm and crucial role in fertilization, CatSper represents a promising target for the development of nonhormonal male contraceptives. However, its structural complexity and the absence of functional heterologous expression systems have limited inhibitor discovery.

OBJECTIVES: To develop a scalable and multiplexed flow cytometry assay to identify compounds capable of blocking CatSper activity in mammalian sperm.

MATERIALS AND METHODS: The assay relies on the stimulation of CatSper by exposing live mouse sperm to a high-K[+]/high-pH solution (K8.6), which induces membrane depolarization and intracellular alkalinization, triggering Ca[2+] entry through CatSper. Changes in intracellular Ca[2+] levels were monitored using the fluorescent indicator Fluo-4. To increase throughput and minimize variability, this assay was combined with fluorescent cell barcoding, which assigns each sperm sample a unique fluorescent signature, enabling the simultaneous acquisition of multiple conditions within a single tube. Additionally, a compound pooling strategy was implemented to further improve assay efficiency, allowing the rapid identification of active compounds within a library. The assay was validated using CatSper1 knockout sperm and known pharmacological inhibitors.

RESULTS: Fluorescent cell barcoding greatly reduced acquisition time and reagent consumption by allowing multiple experimental conditions to be pooled and analyzed simultaneously within a single acquisition. The compound pooling strategy facilitated large-scale screening experiments. Validation confirmed that both genetic deletion and pharmacological blockade of CatSper abolish the K8.6-induced Ca[2+] response.

CONCLUSION: These results establish a robust, scalable, and high-throughput screening platform for identifying novel CatSper blockers and potential male contraceptive candidates.},
}

@article {pmid42326861,
year = {2026},
author = {Jahani, R and Chen, J and Kong, J and Zhou, S and Zheng, H and Munusamy, S and Guan, X},
title = {From Gold to Polymer: Latex Bead-Assisted CRISPR-Cas12a Platform for Next-Generation Protein Diagnostics.},
journal = {ACS measurement science au},
volume = {6},
number = {3},
pages = {728-735},
pmid = {42326861},
issn = {2694-250X},
abstract = {Sensitive and accurate detection of protein biomarkers in clinical samples is crucial for early disease diagnosis and monitoring treatment outcomes. Although gold nanoparticle (AuNP)-assisted CRISPR-Cas12a biosensors have shown promise, their practical applications have been restricted by limitations of AuNPs, such as costly and complex synthesis, tendency to aggregate, and nonspecific adsorption of various unwanted species. To address these limitations, herein, we report a CRISPR-Cas12a-based fluorescence biosensor for the detection of a well-established and clinically significant inflammatory biomarker, interleukin-6 (IL-6), which employs latex beads instead of AuNPs as a transducer and signal amplifier. By the combined use of IL-6 detection antibody-functionalized magnetic beads, dual-functionalized latex beads, which carry both IL-6 detection antibodies and multiple dsDNA strands per antibody molecule, and the Cas12a-crRNA system, our method was able to detect IL-6 with a limit of detection (LOD) reaching as low as 0.76 pg/mL. Moreover, our sensor was highly selective: nontarget proteins such as human serum albumin (HSA), bovine serum albumin (BSA), C-reactive protein (CRP), procalcitonin (PCT), and IL-2β would not interfere with the detection of IL-6. In addition, the practical application of this sensor was assessed by successfully analyzing simulated serum samples. This study shows that latex beads can serve as an alternative to gold nanoparticles for CRISPR-based protein diagnostics. This approach improves stability and specificity while maintaining a high level of sensitivity for early disease diagnosis.},
}

@article {pmid42327020,
year = {2026},
author = {Schizas, NV and Toledo-Rodriguez, DA and Jimenez Marrero, NM and Veglia, AJ and Sáez, JE and Estrada, RE and Pérez, AM and Del Carmen Luguera González, Y and Muñoz-Maravilla, JD and Weil, E and McFadden, CS},
title = {The invasive soft coral Xenia umbellata has been confirmed in Cuban waters.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.08.730793},
pmid = {42327020},
issn = {2692-8205},
abstract = {Octocoral colonies with unusual morphology were detected in September 2022 and October 2023 in two coastal areas east of Havana, Cuba, and tentatively identified as Unomia stolonifera. U. stolonifera is an invasive octocoral from the Indo-Pacific that was first reported in the Caribbean off Venezuela in the 2000's, where it has spread rapidly, smothering coral reefs and substantially altering benthic communities. After obtaining tissue samples from a Cuban octocoral colony, we re-examined the specimen using molecular barcoding of three mitochondrial regions (16S/ND2, mtMutS, COI) and the nuclear large ribosomal subunit (28S rRNA), and we unequivocally identified it as Xenia umbellata. X. umbellata , a native of the Red Sea, was first identified in southern Puerto Rico in October 2023 and has since been found in various marine ecosystems along the southern coast of the island. The presence of either invasive octocoral species in Cuba or elsewhere in the Caribbean would be of a serious environmental concern due to their documented tolerance, totipotentiality, propagation capacity and significant negative interactions with local benthic fauna. Attempts to eradicate the invasive soft coral colonies from Cuban waters have been initiated with apparent success, helping to control further expansion. The most likely introduction pathway is the accidental or intentional releases from the aquarium trade but transport via ballast water cannot be ruled out. We cannot discount the possibility of independent invasion events from different routes to Puerto Rico and Cuba occurring within a year of each other. Propagation from Cuba to Puerto Rico, or vice versa, which we consider highly improbable, would likely imply that soft coral populations may also have been established on Hispaniola but have remained undetected in the Dominican Republic and Haiti to date.},
}

@article {pmid42327120,
year = {2026},
author = {Weber, JM and Shrader, CR and Shapiro, DB and Truong, KT and Sposato, AL and Adler, FR and Gagnon, JA},
title = {Clonal dynamics deviate from neutral drift in zebrafish spermatogenesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.08.730911},
pmid = {42327120},
issn = {2692-8205},
abstract = {Spermatogonial stem cells (SSCs) maintain male fertility, but how their clonal dynamics change with age remains poorly understood. Here, we use in vivo CRISPR barcoding in zebrafish to label SSCs and track their contributions to sperm production through monthly sampling across the fertile lifespan. We find that only a subset of embryonic germ cells contributes to adult sperm production and that the relative contributions of individual clones shift dramatically over time. To interpret these dynamics, we developed a mathematical model that quantifies clonal drift rates and formally tests neutral versus non-neutral hypotheses. Most SSC clones show significant evidence of drift, yet their dynamics are inconsistent with a neutral model where clones have equal fitness and their dynamics are driven solely by random chance. Instead, we observe heterogeneous clonal dynamics, including a positive relationship between clone size and drift rate. Together, these findings demonstrate that SSC clonal dynamics are non-neutral across the zebrafish reproductive lifespan with important implications for allele transmission.},
}

@article {pmid42327221,
year = {2026},
author = {Xu, Y and Park, HC and Li, J and Liu, Y and Lih, TM and Lee, CY and Li, X and Zhang, H},
title = {SPOTTER: Automated Tissue-Barcoding Platform for Spatial Proteomics and Phosphoproteomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.08.730901},
pmid = {42327221},
issn = {2692-8205},
abstract = {Spatial proteomics aims to characterize proteome in situ with regional resolution, linking molecular states to tissue architecture and microenvironments. While recent advances have expanded our access to spatially resolved proteomics, major barriers in scalability and throughput remain. Building on our prior SPOT (Spatial Proteomics through On-site Tissue-protein-labeling) framework [1] , we introduce SPOTTER, a customizable robotic platform that enables automated, micron-scale spatial barcoding directly on intact tissue sections. SPOTTER barcodes proteins by labeling tissue proteins in situ to encode spatial origin across the whole tissue section. This strategy enables unbiased whole-tissue proteome mapping and, for the first time, spatial phosphoproteome profiling from intact sections. Coupled with high-resolution LC-MS/MS, SPOTTER achieves deep proteome and phosphoproteome coverage while preserving histological integrity. By replacing labor-intensive laser capture microdissection workflows and low-plex antibody arrays, SPOTTER provides a scalable route to high-plex spatial proteomics, resolving spatially distinct regions within a single experiment.},
}

@article {pmid42327304,
year = {2026},
author = {Liu, DD and Eastman, AE and Womack-Gambrel, NL and Kim, CN and He, JQ and Raj, S and Reilly, E and Sinha, R and Uchida, N and Chau, K and Ohene-Gambill, BF and Thapa, S and Nasajpour, E and Belk, JA and Neff, NF and Jaiswal, S and Phillips, HW and Chambers, M and Petritsch, CK and Grant, GA and Prolo, LM and Hooper, JE and Nowakowski, TJ and Weissman, IL},
title = {Isolation of postnatal human neural stem cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.11.731596},
pmid = {42327304},
issn = {2692-8205},
abstract = {While it was once thought that neurogenesis is complete by birth, it is now apparent that the human brain continues to generate new neurons postnatally, at least into childhood. While much attention has been focused on postnatally-born neurons, their presumed progenitor - the postnatal neural stem cell (NSC) - remains poorly characterized. Using index sorting, we identify and prospectively isolate two subsets of NSCs from the postnatal human brain, and describe their differentiation dynamics using clonal barcoding and in vivo xenotransplantation. We demonstrate an A2B5 [+] EGFR [+] population biased towards interneuron and oligodendrocyte fates (NINO), and an A2B5 [-] EGFR [hi] population biased towards an astrocyte fate (NAC). Profiling of human brains across lifespan shows that the frequency of NSCs declined exponentially across the first two decades of life, but stabilized thereafter, still present in the brains of donors as old as 90 years. Our study provides a framework for the functional study of postnatal human NSCs and their potential roles in development, aging, and disease.},
}

@article {pmid42328324,
year = {2026},
author = {Zhao, W and Jiang, Q and Zhou, X and Ye, Z and Bao, W and Wu, J and Zhang, Y},
title = {Corrigendum to "Optimization of a magnetic bead-based DNA extraction method combined with 12S rRNA barcoding for species traceability in fish oil products" [Food Chem. Mol. Sci. 12 (2026) 100408].},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100412},
doi = {10.1016/j.fochms.2026.100412},
pmid = {42328324},
issn = {2666-5662},
abstract = {[This corrects the article DOI: 10.1016/j.fochms.2026.100408.].},
}

@article {pmid42310468,
year = {2026},
author = {Danno, T and Nakamura, S and Taguchi, S and Fujii, Y and Teshima, T and Sato, Y and Kawai, T and Kobayashi, Y and Nagaoka, K and Ueda, Y and Matoba, R and Kakimi, K and Kume, H},
title = {High Sensitivity ctDNA Analysis Using a Novel Panel and NOIR-SS Technology for Monitoring Advanced Urothelial Carcinoma.},
journal = {Cancer medicine},
volume = {15},
number = {6},
pages = {e72045},
pmid = {42310468},
issn = {2045-7634},
support = {23K08731//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Circulating Tumor DNA/blood/genetics ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Biomarkers, Tumor/genetics/blood ; Mutation ; Aged ; Middle Aged ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; },
abstract = {Advanced urothelial carcinoma (aUC) has a poor prognosis, and real-time monitoring of treatment response remains clinically challenging. Circulating tumor DNA (ctDNA) has emerged as a promising non-invasive biomarker that may reflect tumor burden and molecular response. In this study, we analyzed ctDNA dynamics using a urothelial carcinoma-specific mutation panel and the non-overlapping integrated read sequencing system (NOIR-SS), a high-fidelity deep sequencing platform incorporating molecular barcoding for enhanced analytical sensitivity. Tumor tissue and serial plasma samples were collected from 15 patients with aUC treated with dose-dense methotrexate, vinblastine, doxorubicin, and cisplatin (ddMVAC). The custom panel targeted hotspot mutations in TP53, FGFR3, KRAS/HRAS, and the TERT promoter. Based on tumor-derived mutations, a tumor-informed approach was used to track ctDNA in plasma. ctDNA was detectable in 10 of 15 patients prior to ddMVAC and showed a trend toward association with total tumor volume, especially in cases with liver metastases. In contrast, ctDNA detection was limited in cases with only pulmonary metastases. Longitudinal changes in variant allele frequency largely mirrored treatment response, although discrepancies were observed in two cases, likely reflecting subclonal resistance. While the NOIR-SS-based assay proved sensitive and informative, limitations include the cost and time required for sequencing, potential temporal discordance between tissue and plasma sampling, and the absence of correction for clonal hematopoiesis of indeterminate potential. Overall, ctDNA profiling using this targeted panel and NOIR-SS suggested the feasibility of sensitive, non-invasive molecular monitoring in aUC, and may have future clinical applicability if validated prospectively in larger cohorts.},
}

Humans
*Circulating Tumor DNA/blood/genetics
Female
*High-Throughput Nucleotide Sequencing/methods
Male
*Biomarkers, Tumor/genetics/blood
Mutation
Aged
Middle Aged
Antineoplastic Combined Chemotherapy Protocols/therapeutic use

@article {pmid42310833,
year = {2026},
author = {Han, S and Kang, T and Lee, SG and Shin, S},
title = {First record of the forensically important genus Protopiophila Duda (Diptera: Piophilidae) from South Korea and an integrative framework for forensic identification.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70383},
pmid = {42310833},
issn = {1556-4029},
support = {3344-20250035//Seoul National University/ ; RS-2021-NR060088//National Research Foundation of Korea/ ; RS-2021-NR061223//National Research Foundation of Korea/ ; NIBR202507101//National Institute of Biological Resources/ ; },
abstract = {The family Piophilidae is of significant forensic importance due to its association with late-stage decomposition; however, the Korean piophilid fauna remains poorly studied, lacking comprehensive morphological and molecular data. This study reports the first record of the genus Protopiophila Duda from South Korea. Five male specimens were collected and identified as Protopiophila contecta (Walker) based on morphological characters. We provide the first detailed illustrations and descriptions of the previously poorly documented male internal genitalia and a new identification key to the South Korean piophilids. To complement the morphological data, mitochondrial cytochrome c oxidase subunit I (COI) barcodes were generated and analyzed. The neighbor-joining tree showed that the four Korean specimens formed a distinct, well-supported clade, clearly separated from the congeners P. latipes and P. litigata. This study establishes an integrative framework for identifying P. contecta, adding a fourth forensically relevant piophilid species to the Korean entomofauna. These morphological and molecular data provide a crucial reference for future forensic investigations in the region.},
}

@article {pmid42313827,
year = {2026},
author = {Nguyen, DT and Ho, LT},
title = {Leaf beetle diversity on a Southeast Asian continental island: Taxonomy, DNA barcoding, and preliminary evolutionary insights from Cat Ba Island, Vietnam.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0351706},
doi = {10.1371/journal.pone.0351706},
pmid = {42313827},
issn = {1932-6203},
mesh = {Animals ; *Coleoptera/genetics/classification ; *DNA Barcoding, Taxonomic ; Vietnam ; Phylogeny ; *Biodiversity ; Genetic Variation ; Islands ; *Evolution, Molecular ; Electron Transport Complex IV/genetics ; },
abstract = {Continental shelf islands in Southeast Asia remain poorly studied with respect to insect diversity and evolutionary history. Here, we provide an integrative assessment of species diversity, DNA barcode variation, diversification dynamics, and historical biogeography of leaf beetles (Coleoptera: Chrysomelidae) on Cat Ba Island, northern Vietnam. Based on field surveys, 36 morphospecies operational taxonomic units (OTUs) belonging to 30 genera and five subfamilies were documented, with Galerucinae representing the most species-rich lineage. DNA barcoding of the mitochondrial COI gene generated 31 Barcode Index Numbers (BINs), most of which represent new records in the Barcode of Life Data System, highlighting substantial undocumented genetic diversity. COI-based analyses were further used to explore broad temporal and evolutionary patterns. Within this exploratory framework, divergence-time estimation under a relaxed molecular clock suggests that major lineages may have originated during the early-middle Miocene, predating the formation of the present-day island. Diversification analyses support relatively constant rates through time with low inferred extinction, consistent with expectations for continental shelf island systems shaped by repeated connectivity and isolation. Model-based biogeographic analyses indicate predominantly localized ancestral ranges, with Cat Ba Island and adjacent mainland regions playing recurrent roles in the assembly of the fauna. Together, these results provide baseline taxonomic and genetic data for a poorly known insular insect assemblage while offering a preliminary evolutionary context that should be interpreted with caution and that can serve as a foundation for future biodiversity monitoring and comparative studies in dynamic island-mainland systems.},
}

Animals
*Coleoptera/genetics/classification
*DNA Barcoding, Taxonomic
Vietnam
Phylogeny
*Biodiversity
Genetic Variation
Islands
*Evolution, Molecular
Electron Transport Complex IV/genetics

@article {pmid42315143,
year = {2026},
author = {Taniguchi, M and Hardy, G and Xu, W},
title = {Integrative identification of insect flower visitors associated with avocado flowering in Western Australia.},
journal = {Environmental entomology},
volume = {55},
number = {3},
pages = {},
doi = {10.1093/ee/nvag067},
pmid = {42315143},
issn = {1938-2936},
support = {//Australian Government Research Training Program (RTP)/ ; //Murdoch University/ ; },
mesh = {Animals ; *Persea/growth & development ; Western Australia ; Flowers/growth & development ; *Pollination ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/analysis ; Bees/classification/physiology ; Phylogeny ; },
abstract = {Accurate identification of insect flower visitors is fundamental for understanding crop pollination systems and supporting sustainable production. In Western Australia, avocado (Persea americana Mill.) production relies heavily on insect visitation, yet the taxonomic identity of native flower-visiting taxa remains poorly resolved. This study provides the first integrative identification of insects associated with avocado flowering in Western Australia using a combination of morphological examination and mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. Insects were collected from commercial avocado orchards in Carabooda and Pemberton during the flowering seasons of 2019-2021. Besides honeybees, morphological assessment identified 5 dominant native bee taxa, primarily within Lasioglossum (Halictidae), and 3 hoverfly taxa (Syrphidae). DNA barcoding confirmed species-level identities for Lasioglossum lanarium (Smith), L. castor (Smith), and the syrphids Simosyrphus grandicornis (Macquart) and Eristalis tenax (Lannaeus) (≥99% to 100% sequence similarity). In contrast, COI sequences from 3 additional Lasioglossum lineages showed lower similarity to available reference records (eg 96%, 91%, and 94%) and are therefore treated conservatively as Lasioglossum sp. 3 to 5 (morphospecies) rather than assigned species-level names. Overall, 73% of putative avocado flower-visitor taxa were shared between regions, indicating a broadly consistent core assemblage across contrasting climatic zones. By clarifying the taxonomic identity and reporting confidence of key avocado-associated taxa, this study provides a baseline for future work evaluating visitation dynamics, pollen transfer, and management strategies in Australian avocado orchards.},
}

Animals
*Persea/growth & development
Western Australia
Flowers/growth & development
*Pollination
DNA Barcoding, Taxonomic
Electron Transport Complex IV/analysis
Bees/classification/physiology
Phylogeny

@article {pmid42315282,
year = {2026},
author = {Ho, HC and Huang, JF and Smith, DG},
title = {Two new species of the eel genus Facciolella from Taiwan, northwestern Pacific Ocean (Anguilliformes: Nettastomatidae).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70538},
pmid = {42315282},
issn = {1095-8649},
abstract = {Two new species of the duckbill eel genus Facciolella are described based on specimens collected off Taiwan, representing the first record of the genus in the western Pacific Ocean. Facciolella bicolor sp. nov., based on three types, is most similar to F. smithi in having a bicoloured body and trunk, and can be distinguished by more preanal lateral-line pores and preanal vertebrae and a combination of characters. Facciolella punctatus sp. nov., based on six type specimens, is distinct in having a pale body and scattered black dots, and a combination of characters. The DNA barcoding analysis also supports the establishment of both new species. Detailed descriptions and figures are provided. The leptocephali found in the Pacific Ocean are also discussed.},
}

@article {pmid42305150,
year = {2026},
author = {Gherbawy, YA and Al-Harthi, H and El-Dawy, E and Gaber, M and Pet, I and Wang, L and Hu, P and Hussein, M},
title = {The molecular revolution in fungal diagnostics: bridging gaps across clinical, agricultural, and environmental mycology.},
journal = {Mycology},
volume = {17},
number = {2},
pages = {350-377},
pmid = {42305150},
issn = {2150-1203},
abstract = {Fungi play essential roles in human health, agriculture, and ecosystems, yet their diversity has long been underestimated due to reliance on morphology and culture. Molecular innovations-DNA barcoding, multilocus and whole-genome sequencing, NGS, and rapid nucleic acid diagnostics (qPCR, LAMP, CRISPR/Cas)-have revolutionized fungal taxonomy and detection. The ITS region now serves as a universal barcode, often complemented by other loci or genomic data. High-throughput and portable tools enable near real-time identification, supported by AI-driven bioinformatics for species recognition and resistance prediction. Despite progress, challenges remain in database accuracy, primer design, and standardization. Integrating molecular taxonomy, AI, and global collaboration promises scalable, reliable frameworks for fungal surveillance and control across clinical, agricultural, and environmental domains.},
}

@article {pmid42306980,
year = {2026},
author = {Liu, R and Song, J and Liu, S and Yang, X and Wang, K and Xie, N and Zhang, K and Han, D and Huang, J},
title = {Weight-Controllable Biobarcode Probes for Multi-input Breast Cancer Diagnosis.},
journal = {Nano letters},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.nanolett.6c01955},
pmid = {42306980},
issn = {1530-6992},
abstract = {DNA-based molecular classifiers have emerged as a promising strategy for precise cancer diagnosis, offering a superior alternative to invasive biopsy detection. However, current DNA-computation-dependent molecular classifiers remain limited by complex pathways and cumbersome weight assignment procedures. To address this, we developed weight-controllable biobarcode probes (WBPs) that enable programmable signal amplification via precise stoichiometric regulation of barcode strands versus nonbarcode strands. These probes demonstrated robust performance in the weighted molecular computation. Using these WBPs, we performed fluorescence-based analog-to-digital signal conversion, enabling the representation of 128 combinations across up to seven targets. By integrating three miRNA inputs trained in silico machine learning, we constructed a WBP-based molecular classifier that can distinguish breast cancer patients from healthy individuals, achieving an accuracy of 84.00% on clinical serum samples. This work expands the scope of biobarcode technology from single-target detection to logical analysis of multiple targets, establishing a scalable and noninvasive platform for precision cancer diagnosis.},
}

@article {pmid42308124,
year = {2026},
author = {Brauburger, S and Schmidt, T and Bošković, F and Keyser, UF},
title = {Label Type Influence on DNA Translocation Velocity in Solid-State Nanopores.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.6c05303},
pmid = {42308124},
issn = {1936-086X},
abstract = {Solid-state nanopores enable single-molecule detection of long double-stranded nucleic acids and can resolve the position of site-specific molecular labels attached to a DNA carrier. These labels are employed in many applications, such as molecular barcoding, protein mapping, and structure-based DNA data storage. Often, it is implicitly assumed that these labels do not significantly perturb molecular transport through the pore. However, the magnitude of such perturbations and their potential impact on positional readout remain largely unquantified. Here, we systematically quantify how dense molecular labeling affects the translocation time of DNA carriers in solid-state nanopores using glass nanopipettes with diameters of 8-12 nm, exceeding the physical size of the labels. We employ multiple 7.2 kbp DNA carriers, each bearing up to 60 labels of a given type, including DNA nanostructures, monovalent streptavidin, and 20 kDa polyethylene glycol (PEG). Despite carrier-level differences in mass of up to 83% and charge of up to 23%, all labels produce only modest changes in global translocation time, remaining within ±15%, which is below intrameasurement variability (∼20%). This corresponds to a total velocity change of <0.25% per label. Analysis of the timing of label-associated spikes reveals that the velocity profile throughout the translocation is preserved across label types. It also indicates that 40-70% of the observed global translocation-time shift occurs while labeled regions pass through the pore, despite these regions comprising only 20% of the carrier. However, because global translocation times change only weakly and relative label positions remain largely unaffected, molecular barcoding and protein-positioning assays can generally be performed without label-specific velocity corrections under the conditions studied.},
}

@article {pmid42308418,
year = {2026},
author = {Schaeper, D and Chowdhury, U and Janga, SC},
title = {Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {3},
pages = {},
doi = {10.1093/bib/bbag323},
pmid = {42308418},
issn = {1477-4054},
mesh = {Humans ; Single-Cell Gene Expression Analysis ; *Single-Cell Analysis/methods ; *Transcriptome ; High-Throughput Nucleotide Sequencing/methods ; Animals ; Sequence Analysis, RNA/methods ; Gene Expression Profiling/methods ; },
abstract = {Advancements in single-cell RNA sequencing (scRNA-seq) techniques have expanded the study of cellular heterogeneity and transcriptional dynamics. Early methods relied on manual cell isolation followed by barcode introduction, but subsequent approaches integrated automated cell isolation with cellular barcoding to increase throughput. While most current single-cell RNA-seq methods aim to capture transcripts at the single-cell level in a high-throughput manner using short-read sequencing, such efforts frequently prevent assignment of full-length transcripts to individual cells, limiting insight into isoform diversity and complete mutational profiles. Recent advances in long-read sequencing accuracy are starting to enable integration of full-length transcript coverage with high-throughput barcoding. This review traces the evolution of scRNA-seq from early manual isolation methods to today's high-throughput short-read droplet- and combinatorial barcoding-based platforms. Then, the review discusses recent advances stemming from the adaptation of high-throughput scRNA-seq protocols for use with long-read sequencing and addresses key challenges such as accurate barcode identification despite lower base-calling accuracy and efforts to compensate for reduced throughput relative to short-read technologies. In parallel, the review highlights the development of computational tools tailored to long-read scRNA-seq, including methods for cell barcode and unique molecular index recovery, variant detection, and complete end-to-end workflows, emphasizing both their shared and unique advantages. Finally, applications of long-read scRNA-seq are shown to provide novel insights, spanning cancer genomics, neurology, early development, and disease contexts. By integrating technical, computational, and biological perspectives, the transformative potential of long-read scRNA-seq is shown, advancing our understanding of cellular heterogeneity.},
}

Humans
Single-Cell Gene Expression Analysis
*Single-Cell Analysis/methods
*Transcriptome
High-Throughput Nucleotide Sequencing/methods
Animals
Sequence Analysis, RNA/methods
Gene Expression Profiling/methods

@article {pmid42297842,
year = {2026},
author = {Fantinelli, AC and Dos Santos, N and Junior, CER and de Carvalho, DEV and da Costa, RC and Porto-Foresti, F and Utsunomia, R},
title = {DNA-based identification uncovers the illegal trade of sea cucumbers from Brazil.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31971-6},
pmid = {42297842},
issn = {2045-2322},
support = {2024/01575-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {The illegal trade of sea cucumbers is widespread, driven by high international demand, particularly in Asia, where they are valued as culinary delicacies and for use in traditional medicine. Although domestic consumption in Brazil is limited, illegal harvesting for export is a growing concern, with unregulated fisheries posing a threat to local populations. In 2023, the Brazilian Institute of Environment and Renewable Natural Resources (IBAMA) seized dried sea cucumber specimens at Guarulhos International Airport. Using DNA barcoding with the Cytochrome C Oxidase I (COI) gene, we identified 18 specimens as Holothuria grisea and 22 as Isostichopus badionotus. Although both species are currently listed as "Least Concern" by the IUCN globally, the unregulated nature of this trade raises concerns about potential overexploitation, especially given the ecosystems they inhabit are increasingly vulnerable to habitat degradation and unsustainable practices. Additionally, the absence of H. grisea sequences in public genetic databases required us to collect fresh specimens to complete the analysis, underscoring the need for expanded molecular repositories. Open access to molecular repositories is a cornerstone of modern scientific progress, serving as a critical infrastructure for collaborative research. By providing unrestricted availability of standardized molecular data, these repositories not only prevent redundant investigations and optimize the use of research resources but also reinforce the robustness and reproducibility of scientific findings through independent validation. Furthermore, this democratization of knowledge levels the scientific playing field, enabling institutions of varying sizes and from diverse geographical locations to contribute equitably to the global research endeavor. Consequently, open access to these databases maximizes the return on public investment in science and significantly accelerates the pace of discovery in critical fields such as drug development and materials science. Our findings highlight the effectiveness of molecular tools in identifying illegally traded species, even in degraded forms, and emphasize the importance of stricter monitoring to protect biodiversity.},
}

@article {pmid42297870,
year = {2026},
author = {Piasecki, W and Mathieu-Bégné, E and Boxshall, GA and Panicz, R and Eljasik, P},
title = {An integrative redescription of the copepod Tracheliastes polycolpus (Lernaeopodidae) based on ultrastructure, COI barcoding, and Palearctic distribution.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57840-4},
pmid = {42297870},
issn = {2045-2322},
support = {RID/SP/0045/2024/01//Ministerstwo Edukacji i Nauki/ ; },
abstract = {Tracheliastes polycolpus is one of the most widely reported parasitic copepods of Palearctic freshwater fishes. Despite nearly two centuries of citations in fish-disease literature, its morphology, taxonomy, and genetic identity have remained insufficiently resolved and summarized. We provide an integrative redescription based on scanning electron microscopy (SEM) and mitochondrial cytochrome c oxidase subunit I (COI) barcoding of specimens collected from the type host Leuciscus idus in Lake Dąbie, Poland. Molecular identity was confirmed by PCR using universal COI primers, with phylogenetic reconstruction under the GTR + I + G4 model. SEM examination revealed fine-scale features of all cephalothoracic appendages and genital processes. Secondary denticles on the antennal endopod and exopod are demonstrated to constitute reliable diagnostic characters within the genus Tracheliastes. Vestigial thoracic legs, each surrounded by concentric cuticular patches of distinct ultrastructure, are documented for the first time in this species. This study presents the first COI sequences for T. polycolpus (GenBank: PQ520502-PQ520503), only the second for the genus, confirming its distinct genetic identity and close relationship to T. maculatus. A maximum-likelihood phylogeny places T. polycolpus firmly within the Lernaeopodidae. Based on morphological reassessment and historical evidence, T. chondrostomi and T. mourkii are synonymized with T. polycolpus, reducing the number of valid species in the genus. A revised genus diagnosis is provided.},
}

@article {pmid42300515,
year = {2026},
author = {Tengan, BM and Armbruster, MR and Agongo, J and Arnatt, CK and Edwards, JL},
title = {Barcoding for isobaric tagging of carboxylic acids and amines metabolites.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6an00437g},
pmid = {42300515},
issn = {1364-5528},
abstract = {Conventional isobaric platforms in metabolomic analyses are designed to label a single functional group, typically primary amines. This specificity restricts the range of detectable analytes in a single injection, limiting overall chemical coverage of metabolites, and potentially reducing the depth of biological insight. Using a proof-of-concept 2-plex isobaric barcode tagging scheme, amine-containing metabolites are selectively labeled using acid barcode tags. Acid-containing metabolites (carboxylate) are derivatized using amine barcode tags. This allows for broad coverage of two metabolite classes in a single injection in a 30-minute LC gradient. These barcode tags undergo double fragmentation to generate cyclized products and distinct reporter ions that are specific to each metabolite class, enabling accurate quantitation. This tagging scheme also serves as an untargeted approach for identifying metabolites not present in the user's metabolic library. Tagged acid and tagged amine analytes are mixed at ratios of 1 : 2 : 5 : 10 using various amounts of Escherichia coli lysate to produce a 10-fold linear dynamic range, an average linearity (R[2]) of 0.99, and an average RSD of 2.64%. Metabolic changes in amine and carboxylic acid metabolism of genetic knockout PanC and wild-type Escherichia coli were characterized using this method.},
}

@article {pmid42302391,
year = {2026},
author = {Fei, L and Maksimovic, J and Oshlack, A},
title = {barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag397},
pmid = {42302391},
issn = {1367-4811},
abstract = {MOTIVATION: A 'clone' encompasses a progenitor cell and its progeny cells. Tracking clonal composition as cells differentiate or evolve is useful in many fields. Various single-cell lineage tracing (clonal tracking) technologies use unique DNA barcodes that are passed from progenitor cells to their offspring. The barcode count for each sample indicates cell number in clones. However, analysis of barcode count data is often bespoke and relies on visualisations and heuristics. A generalized workflow for preprocessing and robust statistical analysis of barcode count data across protocols is needed.

RESULTS: We introduce barbieQ, a Bioconductor R package for analysing barcode count data across groups of samples. It provides data-driven quality control and filtering, extensive visualisations, and two statistical tests: 1) Differential barcode proportion (differences in proportions between sample groups), and 2) Differential barcode occurrence (differences in presence/absence odds between groups). Both tests handle complex experimental designs using regression models and rigorously account for sample-to-sample variability. We validated both tests on semi-simulated, real data and a case study, demonstrating that they hold their size, are sufficiently powered to detect true differences, and outperform existing approaches.

AVAILABILITY: barbieQ is available on Bioconductor at https://doi.org/10.18129/B9.bioc.barbieQ.

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

@article {pmid42304004,
year = {2026},
author = {Skrutl, L and Chavan, A and Sintsova, A and Ceppi, I and Ropp, CJ and Sunagawa, S and Cejka, P and Jagannathan, M},
title = {Meiotic pairing through barcode-like satellite DNA repeats.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74398-x},
pmid = {42304004},
issn = {2041-1723},
support = {310030_189131//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 320030_228043//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_207588//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_205199//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
abstract = {During meiosis, chromosomes must find, pair, and synapse with their homologous partners in the crowded milieu of the nucleus. Although homology detection generally relies on recombination, pairing can occur in its absence, suggesting alternative mechanisms. Here, we show that the barcode-like arrangement of non-coding satellite DNA repeats facilitates homologue pairing during meiosis. Using satellite DNA deletion, duplication, and translocation strains, we demonstrate that repeat mismatches perturb meiotic pairing, particularly at centromeres and pericentromeres. Notably, pairing defects are also observed in the progeny of D. melanogaster natural populations that have diverged in their satellite DNA content. In the absence of satellite DNA homology, pairing is antagonised by the HORMAD protein, Mad2, while a Pachytene checkpoint 2 (Pch2)-dependent meiotic delay restores pairing. In addition, compromised meiotic pairing is strongly correlated with mid-oogenesis cell death, a quality control mechanism that likely culls defective oocytes to prevent chromosome mis-segregation and aneuploidy. Taken together, our findings reveal an important role for satellite DNA repeats during meiotic homology detection. We propose that this repeat-based pairing mechanism exerts an underappreciated selective pressure, constraining the divergence of rapidly evolving satellite DNA within interbreeding natural populations.},
}

@article {pmid42290941,
year = {2026},
author = {Steding, H and Dörpmund, N and Herbst, J and Sauer, M and Maetzig, T},
title = {Lentiviral rescue of UMPS auxotrophy enables drug-free selection and stable vector expression.},
journal = {Molecular therapy. Advances},
volume = {34},
number = {2},
pages = {201761},
pmid = {42290941},
issn = {3117-387X},
abstract = {Retroviral gene transfer remains a cornerstone of biomedical research and gene therapy, yet its effectiveness is occasionally compromised by low transduction efficiency, transgene silencing, and the reduced fitness of engineered cells. Although antibiotic-based selection systems can enrich transduced populations in vitro, their use in vivo is limited by safety and regulatory constraints. To overcome these challenges, we present a drug-free selection strategy based on uridine-5'-monophosphate synthase (UMPS) auxotrophy. Efficient UMPS disruption via CRISPR-Cas9 rendered cells dependent on uridine supplementation for survival and concomitantly enabled the selection of knockout cells based on their acquired resistance to the chemotherapeutic prodrug 5-fluoroorotic acid. Lentiviral reconstitution of UMPS restored uridine independence, and enabled the formation of >90% gene-marked cells within 7-14 days upon uridine removal. Likewise, splitting UMPS into its two functional domains-orotate phosphoribosyltransferase (OPRT) and orotidine-5'-monophosphate decarboxylase (ODC)-for expression from separate vectors promoted the effective selection of double-transduced cells under auxotrophic conditions. Apart from robust cell enrichment, long-term stabilization of transgene-expressing cells without pharmacological intervention could be demonstrated and was superior to antibiotic selection. Our work thus establishes UMPS auxotrophy-rescue as a versatile platform for both in vitro and possibly in vivo applications, offering a safe and scalable alternative to conventional drug-based selection methods.},
}

@article {pmid42291507,
year = {2026},
author = {Félix-Oliveira, PH and Prazeres, JFSA and Ferro, LO and Antunes, ACA and Lima, CF and Neves, DSS and Fonseca, EO and Miranda, LS and Momoli, RS and Souza-Motta, CM and Bensch, K and Crous, PW and Bezerra, JDP},
title = {Cladosporium from caves of the Brazilian savannah (Cerrado) and the description of six new species.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e191673},
pmid = {42291507},
issn = {2210-6340},
abstract = {Caves are important but understudied reservoirs of fungal diversity, particularly for genera such as Cladosporium (Cladosporiales, Dothideomycetes). This study aimed to characterise the richness of Cladosporium species from six caves in the Brazilian savannah (Cerrado) using an integrative approach combining morphology and multi-locus phylogenetic analyses (ACT, ITS, RPB2, TEF1-α, and TUB). To improve species recognition in Cladosporium, selected ex-type strains were studied, for which RPB2 and TUB barcodes were also sequenced. Species were delimited using morphology and phylogenetic inferences, supplemented by the pairwise homoplasy index (PHI) test to evaluate species boundaries. Twenty-three species were identified among 94 Cladosporium isolates. The polyphasic approach resulted in the description of six new species: five in the C. cladosporioides complex (C. carsi, C. lacerdae, C. mambaiense, C. nogueirae, and C. propiciense) and one in the C. sphaerospermum complex (C. mesquitapaivae). Additionally, analyses based on morphology, genealogical concordance phylogenetic species recognition (GCPSR), and the PHI test resulted in the synonymisation of C. ribis and C. speluncae under C. bambusicola, C. brigadeirense under C. puris, and C. marinisedimentum under C. sphaerospermum. Among the previously known species identified, 11 represent new records for cave environments, with C. bambusicola being the most frequent (29.17%). These findings substantially expand the known diversity of Cladosporium in Neotropical caves, highlighting the Brazilian Cerrado as a hotspot of mycodiversity. Furthermore, ACT, RPB2, TEF1-α, and TUB are proposed as the primary phylogenetic barcodes for distinguishing closely related Cladosporium species, particularly within the C. cladosporioides complex. This study further emphasises the necessity of using a polyphasic approach to achieve accurate taxonomic resolution among Cladosporium species, trace their distribution in caves, and help to understand their ecology.},
}

@article {pmid42297823,
year = {2026},
author = {Adler, KM and Xu, H and Gladstein, AC and Irizarry-Negron, VM and Robertson, MR and Doerig, KR and Petrov, DA and Winslow, MM and Feldser, DM},
title = {Tumor suppressor genotype influences the extent and mode of immunosurveillance in lung cancer.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74023-x},
pmid = {42297823},
issn = {2041-1723},
support = {R01-CA262619-04//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01-CA-279698-01)//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {The impact of cancer driving mutations on immunosurveillance throughout tumor development remains poorly understood. To better understand the contribution of tumor genotype to immunosurveillance, we generated and validated lentiviral-based vectors that create increasingly immunogenic neoantigens. This vector system is compatible with autochthonous Cre-regulated cancer models, CRISPR/Cas9-mediated somatic genome editing, and tumor barcoding. Here, we show that in the context of oncogenic KRAS-driven lung cancer and strong neoantigen expression, tumor suppressor genotype dictates the degree of immune cell recruitment, positive selection of tumors with neoantigen silencing, and tumor outgrowth. By quantifying the impact of 11 commonly inactivated tumor suppressor genes on tumor growth across neoantigenic contexts, we show that the growth-promoting effects of tumor suppressor gene inactivation correlate with increasing sensitivity to immunosurveillance. Importantly, some genotypes also dramatically changed sensitivity to immunosurveillance independently of their growth-promoting effects. We propose a model of immunoediting in which tumor suppressor gene inactivation works in tandem with neoantigen expression to shape tumor immunosurveillance and immunoediting such that the same neoantigens uniquely modulate tumor immunoediting depending on the genetic context.},
}

@article {pmid40622487,
year = {2025},
author = {Soorni, A and Golchini, MM},
title = {Complete Chloroplast genome of Mentha aquatica reveals hypervariable regions and resolves phylogenetic position within the genus Mentha.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {677},
pmid = {40622487},
issn = {1573-4978},
abstract = {BACKGROUND: The genus Mentha (Lamiaceae) encompasses economically and medicinally important aromatic herbs, yet its taxonomy remains complex due to frequent hybridization, polyploidy, and morphological plasticity. Chloroplast (cp.) genomes emerged as powerful tools for resolving phylogenetic relationships, but no complete cp. genome of Mentha aquatica from Iran has been available. METHODS AND RESULTS: In this study, we sequenced and assembled the first complete cp. genome of M. aquatica from Iran using Illumina sequencing. The resulting circular genome measured 152,077 bp and exhibited a typical quadripartite structure, consisting of a large single-copy region (83,212 bp), a small single-copy region (17,665 bp), and two inverted repeats (25,600 bp each). Annotation revealed 132 functional genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Comparative analyses with other Mentha species showed conserved gene content but detected structural variations at IR-LSC/SSC boundaries, particularly in the positioning of rps19 and trnN. Nucleotide diversity (Pi) analysis identified hypervariable regions, with ycf1 and *rpl2-trnH* displaying the highest polymorphism, suggesting their potential as DNA barcodes. Phylogenetic reconstruction based on complete cp. genomes placed M. aquatica in a strongly supported clade with M. canadensis, indicating recent divergence, while the broader Mentha lineage formed a monophyletic group distinct from related genera. The ycf1 locus demonstrated high discriminatory power, generating phylogenies consistent with whole-genome analyses, whereas rpl14 provided limited resolution. CONCLUSIONS: This study established a foundational genomic resource for M. aquatica, advancing phylogenetic and biogeographic research within Mentha, and highlighted the utility of cp. genomes and hypervariable loci for species identification and evolutionary studies in this taxonomically challenging genus.},
}

@article {pmid42281790,
year = {2025},
author = {von Gries, SC and Awad, J and Talamas, EJ and McMechan, AJ and Koch, RL and Lindsey, ARI},
title = {Synopeas ruficoxum Buhl (Hymenoptera, Platygastridae) is a natural enemy of soybean gall midge, Resseliella maxima Gagné (Diptera, Cecidomyiidae).},
journal = {Journal of Hymenoptera research},
volume = {98},
number = {},
pages = {721-742},
pmid = {42281790},
issn = {1070-9428},
abstract = {Platygastridae (Hymenoptera) is known as a 'dark taxon' as it is highly diverse and understudied. Within Platygastridae, one of the largest genera is Synopeas Förster, species of which parasitize Cecidomyiidae (Diptera). This study identifies a new host association between these two families, with Synopeas ruficoxum Buhl as the second reported parasitoid of soybean gall midge, Resseliella maxima Gagné. Parasitoids were reared from soybean stems infested with R. maxima collected in Nebraska, USA. Furthermore, PCR assays confirmed that R. maxima larvae are parasitized by S. ruficoxum in the field. All S. ruficoxum specimens were female, suggesting that this may be an asexually reproducing population. We found that some, but not all, S. ruficoxum were infected with a bacterium, Wolbachia, known to mediate asexual reproduction in other insects, suggesting other factors may be responsible for the all-female population. Publicly available barcoding data allowed us to determine that S. ruficoxum is also present in Eastern Canada, which is beyond the known geographic range of R. maxima. This suggests that S. ruficoxum has other hosts or that the geographic range of R. maxima is broader than currently documented. A redescription and diagnostic data for S. ruficoxum are provided, advancing the ability to use this parasitoid for biological control of R. maxima.},
}

@article {pmid42282734,
year = {2026},
author = {Vaidya, CM and Carpenter, MC and Abdullah, L and Kolling, FW and Huang, YH and Song, L and Ackerman, ME},
title = {RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.29.728810},
pmid = {42282734},
issn = {2692-8205},
abstract = {Single-cell long-read sequencing (LRS) techniques enable the analysis of full transcript sequences within a cell. However, the high error rate inherent to LRS introduces computational challenges for parsing information like cell barcode, and custom workflows are often required to handle complex read layouts, such as split combinatorial barcodes. We introduce an error-robust, read-structure agnostic demultiplexer (RAD). In RAD, users can easily specify read structure, such as adapter sequence and barcode relative position, and can rapidly extract these elements for each read. In addition to finding the barcode, RAD implements efficient barcode correction strategies for scenarios of knowing or not knowing the full barcode whitelist or having paired short-read single-cell sequencing data for a short whitelist. In synthetic and real-world benchmarks, RAD is faster and achieves significantly higher sensitivity than existing pipelines while having comparable precision. We show RAD can be applied to high-definition long-read spatial transcriptomic data and demonstrate single cell and spatial analysis of B cell isotype and secretion states.},
}

@article {pmid42282937,
year = {2026},
author = {Miller, J and Kratzer, CA and Griswold, C},
title = {Description of a new Andean species of widow spider (Araneae, Theridiidae, Latrodectus).},
journal = {ZooKeys},
volume = {1281},
number = {},
pages = {49-67},
pmid = {42282937},
issn = {1313-2989},
abstract = {We describe a new species of widow spider (Araneae, Theridiidae, Latrodectus) from the Andean region. DNA barcode sequences are provided. The species is documented from museum specimens across Peru and identified from photographs on iNaturalist, extending its inferred distribution into Ecuador, Bolivia, and Chile. We integrate specimen and citizen-science occurrences to generate a species distribution model using WorldClim bioclimatic variables, predicting highest suitability along temperate to high-elevation Andean regions. We discuss the utility and limitations of citizen-science imagery for delimiting and mapping species and summarize available information on clinical aspects of envenomation in Peru associated with the local "lucacha" widow spider.},
}

@article {pmid42284698,
year = {2026},
author = {Piffaretti, D and Consoli, C and Rossi, D},
title = {Analysis of cell-free DNA in lymphomas: from sample collection to genotyping and minimal residual disease monitoring.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024015609},
pmid = {42284698},
issn = {2473-9537},
abstract = {Circulating tumor DNA (ctDNA) is increasingly investigated in lymphomas because it enables non-invasive molecular profiling, longitudinal assessment of clonal evolution, and quantification of minimal residual disease (MRD), which reflects residual tumor burden and treatment response and serves as a clinically validated prognostic biomarker. The clinical utilities of ctDNA include supporting diagnosis, enabling early detection of relapse, and resolving ambiguous imaging findings. Current approaches for ctDNA assessment in lymphomas include droplet digital PCR, immunoglobulin clonotype sequencing, hybrid-capture next-generation sequencing with unique molecular identifiers or duplex barcoding, and phased sequencing. Establishing ctDNA as a clinical-grade assay requires rigorous quality control and standardization across all technical steps, from blood collection and plasma processing to cfDNA extraction, quantification, and analytically validated genotyping and MRD measurement. Large prospective trials and international standardization efforts are underway to define ctDNA-based MRD assessment as a reproducible and clinically actionable tool in lymphoma care. In this review, we outline key pre-analytical and analytical workflows for ctDNA assessment in lymphomas and discuss unresolved challenges and future directions in the field.},
}

@article {pmid42285896,
year = {2026},
author = {Upshur, IF and Yang, CS and Lahondère, C},
title = {Spotted lanternfly honeydew as a sugar source for mosquitoes.},
journal = {Journal of medical entomology},
volume = {63},
number = {3},
pages = {},
doi = {10.1093/jme/tjag086},
pmid = {42285896},
issn = {1938-2928},
support = {//Department of Biochemistry/ ; VA160160//USDA NIFA/ ; //Virginia Tech New Faculty Start-up Funds/ ; #8080-21000-001-00D//USDA-ARS Areawide Pest Management Program/ ; },
mesh = {Animals ; *Culicidae/physiology ; *Diptera/physiology/genetics ; DNA Barcoding, Taxonomic ; Feeding Behavior ; Introduced Species ; *Sugars/metabolism ; Hemiptera ; },
abstract = {Spotted lanternflies and mosquitoes are among the most concerning invasive insects, which have introduced a myriad of public health, social, economic, and agricultural problems. In addition to their characteristic blood-feeding behavior, mosquitoes exhibit frequent sugar-feeding activity, targeting a diverse range of sugar sources. Spotted lanternflies are ravenous sap-feeders and, as a result, produce large aggregates of honeydew, a sugary excreta. Here, we used spotted lanternfly honeydew-specific DNA barcoding to determine that both invasive and native mosquito species feed on spotted lanternfly honeydew in the field. The implications and applications of these findings for invasive interspecies interactions and disease vector management are discussed.},
}

Animals
*Culicidae/physiology
*Diptera/physiology/genetics
DNA Barcoding, Taxonomic
Feeding Behavior
Introduced Species
*Sugars/metabolism
Hemiptera

@article {pmid42288376,
year = {2026},
author = {Hepler, JR and Ohler, B and Schutze, IX and Hull, JJ and Cooper, WR},
title = {Parasitism of Spissistilus festinus (Hemiptera: Membracidae) by Halictophagus jordani (Strepsiptera: Halictophagidae) in Arizona alfalfa fields.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/jisesa/ieag046},
pmid = {42288376},
issn = {1536-2442},
support = {# 2020-22620-023-000-D//United States Department of Agriculture Agricultural Research Service CRIS/ ; },
mesh = {Animals ; Male ; Female ; Arizona ; *Wasps/physiology ; Medicago sativa ; *Host-Parasite Interactions ; Larva/parasitology/physiology/growth & development ; Sex Ratio ; },
abstract = {Sweep net samples taken from alfalfa fields in Arizona contained 3-cornered alfalfa hopper, Spissistilus festinus (Say), abundantly stylopized by an unknown strepsipteran parasitoid. Targeted sampling of S. festinus was conducted over a 2-wk period from October to November to determine the rate of parasitism and identify the parasitoid. Adult male parasitoids were reared for morphological identification. Additionally, representative male, female, and larval parasitoids were identified through COI barcoding gene sequencing. Strepsiptera were determined to be Halictophagus jordani (Pierce), previously reported only from eastern Texas and Louisiana, United States. All adult S. festinus and mature H. jordani were sexed and counted, and all apparently unstylopized hoppers were dissected to look for internal parasitoid larvae. Parasitism rates, parasitoid loads, and parasitoid sex ratios of both host sexes were compared. Overall, of 3,791 S. festinus examined, 1,092 (28.8%) bore mature H. jordani protruding between abdominal segments. A further 613 (16.2%) were found to contain internal larvae upon dissection, yielding a total stylopization rate of 45.0%. Male and female hoppers did not differ significantly in mature male, female, or total parasitoid load, though female hoppers were significantly more likely to be parasitized than male hoppers. Parasitoid infrapopulations showed evidence of segregation by parasitoid sex, but no relationship was detected between infrapopulation sex ratio and host sex. The size of an infrapopulation strongly predicted its sex ratio, which became more male-skewed with increasing size. These findings indicate that H. jordani is more widely distributed than previously believed and suggest its potential role in the biological control of S. festinus.},
}

Animals
Male
Female
Arizona
*Wasps/physiology
Medicago sativa
*Host-Parasite Interactions
Larva/parasitology/physiology/growth & development
Sex Ratio

@article {pmid42288377,
year = {2026},
author = {Figueroa, A and Baca, SM and Rosati, JY and Hernandez, R and Musah, RA},
title = {Untargeted metabolomics for chemotaxonomy of blow fly pupae (Diptera: Calliphoridae) supported by DNA barcoding.},
journal = {Journal of medical entomology},
volume = {63},
number = {3},
pages = {},
doi = {10.1093/jme/tjag075},
pmid = {42288377},
issn = {1938-2928},
support = {2020-MU-MU-0016//National Institute of Justice, Office of Justice Programs/ ; 15PNIJ-24-GG-01567-RESS//National Institute of Justice, Office of Justice Programs/ ; //U.S. Department of Justice/ ; PG010892//Department of Justice/ ; },
mesh = {Animals ; *Calliphoridae/classification/chemistry/genetics/metabolism/growth & development ; Pupa/chemistry/classification/growth & development/metabolism/genetics ; *DNA Barcoding, Taxonomic ; *Forensic Entomology/methods ; *Metabolomics/methods ; Mass Spectrometry ; },
abstract = {In forensics, accurate species identification of necrophagous insects retrieved from decomposing remains is critical for estimating the postmortem interval (PMI). Blow flies (Diptera: Calliphoridae) are typically the earliest colonizers to arrive on carrion. Because juvenile life stages are morphologically similar across species, forensic entomologists traditionally rear the eggs, larvae, and pupae to adulthood to ensure a definitive identification based on features of the adults, in a process that is time-consuming and relies heavily on specimen viability. This study presents a rapid, high-throughput identification method for forensically significant blow fly pupae utilizing direct analysis in real time-high-resolution mass spectrometry (DART-HRMS) coupled with chemometrics. A prediction model was developed for 11 species of necrophagous blow fly pupae across seven genera of Calliphoridae: Calliphora, Chrysomya, Cochliomyia, Cynomya, Lucilia, Phormia, and Protophormia. It was built using 220 species-validated test samples, and tested with 115 external validation samples. Leave-one-out cross validation accuracies of 97.27% and 98.26%, respectively, were observed for the test and validation datasets. Species identities were independently verified via DNA barcoding with cytochrome c oxidase I. These results demonstrate that DART-HRMS can successfully identify pupae-a historically underutilized developmental stage in forensic casework-based upon their unique metabolome signatures. This work provides critical forensic resources for the utilization of pupae that may facilitate PMI estimations, even for non-viable specimens.},
}

Animals
*Calliphoridae/classification/chemistry/genetics/metabolism/growth & development
Pupa/chemistry/classification/growth & development/metabolism/genetics
*DNA Barcoding, Taxonomic
*Forensic Entomology/methods
*Metabolomics/methods
Mass Spectrometry

@article {pmid42288656,
year = {2026},
author = {Labrousse, P and Russell, H and Stetson, D and Powalowska-Pickton, PK and Anton, KA and Litovchenko, M and Lowy-Gallego, E and Lovell, A and Hackinger, S and Stolarek-Januszkiewicz, M and Balmforth, BW and Hadfield, J},
title = {Enrichment of mutated DNA enables ultra-sensitive ctDNA detection in NSCLC using shallow targeted sequencing.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57421-5},
pmid = {42288656},
issn = {2045-2322},
abstract = {Liquid biopsy assays using next-generation sequencing have emerged as a promising tool in cancer diagnostics to aid detection of minimal residual disease (MRD) and treatment monitoring. A key concern is the trade-off between sensitivity and sequencing depth, with ultra-sensitive techniques suffering from high costs. To this end, we sought to evaluate the analytical performance of Enspyre, a novel ctDNA enrichment method with the potential to achieve ultra-high sensitivity at a significantly reduced sequencing depth. Tumour and, where available, matched normal tissue from 8 lung cancer patients underwent whole-genome sequencing to identify somatic variants. Custom capture panels designed against patient-specific variants were used to run the Enspyre assay on 72 samples (9 per subject) consisting of patient-derived plasma diluted into a background of healthy donor plasma. An additional 8 healthy donor samples were run as negative controls. Plasma samples were analysed using a proprietary algorithm to estimate ctDNA levels in each sample. Enspyre reached 100% (6/6) detection rate down to 10 parts per million (ppm) and was able to call MRD in samples as low as 5 ppm, while maintaining a false positive rate of zero. This was achieved despite very low DNA input (median: 7.67 ng), without the use of molecular barcodes for error suppression and a median of only 9.6 million read pairs per sample. Given its low sequencing requirements, Enspyre could make liquid biopsy-based MRD and treatment monitoring more accessible by bringing down costs and allowing for use of smaller benchtop sequencing machines. While larger studies are needed to robustly establish the assay's analytical performance, the results described here showcase Enspyre's promise in cancer diagnostics.},
}

@article {pmid42290255,
year = {2026},
author = {Sekine, H and Ota, Y and Toshino, S and Nitta, M and Yamamoto, G and Fukumori, H and Yamazaki, D and Takano, T and Waki, T},
title = {Insights into the life cycles of trematodes infecting pelagic gastropods in Japan.},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e60},
doi = {10.1017/S0022149X26101564},
pmid = {42290255},
issn = {1475-2697},
mesh = {Animals ; Japan ; *Trematoda/classification/genetics/growth & development/physiology ; *Gastropoda/parasitology ; *Life Cycle Stages ; Metacercariae/genetics/classification/growth & development ; Phylogeny ; Electron Transport Complex IV/analysis/genetics ; RNA, Ribosomal, 28S/genetics/analysis ; Host-Parasite Interactions ; },
abstract = {Pelagic gastropods, including holoplanktonic and neustonic species, have been considered potential sources of trematodes that parasitize marine fishes. However, the taxonomy and life cycles of metacercariae detected in pelagic gastropods remain poorly understood. This study examined metacercaria infections in 10 species of pelagic gastropods (N = 415) collected from Japanese coastal waters between 2016 and 2025. Metacercariae were detected in four pelagic gastropod species and were identified as seven trematode species based on molecular analyses of the 28S ribosomal RNA and cytochrome c oxidase subunit 1 regions. In holoplanktonic gastropods, six species within the family Lepocreadiidae were molecularly identified as Cephalolepidapedon saba, Prodistomum orientale, Prodistomum sp., Opechona sp., Preptetos sp., and Lepocreadiidae gen. sp., all of which represent new host-parasite records. A metacercaria molecularly identified as Dinurus tornatus (Hemiuridae) was detected in the neustonic gastropod Glaucus atlanticus. These results confirm that pelagic gastropods can act as the second intermediate or paratenic hosts and suggest predator-prey relationships with marine fishes. In addition, rediae obtained from benthic gastropods (cowries) were examined molecularly and identified as Prodistomum sp., thereby clarifying aspects of its life cycle.},
}

Animals
Japan
*Trematoda/classification/genetics/growth & development/physiology
*Gastropoda/parasitology
*Life Cycle Stages
Metacercariae/genetics/classification/growth & development
Phylogeny
Electron Transport Complex IV/analysis/genetics
RNA, Ribosomal, 28S/genetics/analysis
Host-Parasite Interactions

@article {pmid42269616,
year = {2026},
author = {Schaefer, NK and Pavlovic, BJ and Schmitz, MT and Pollen, AA},
title = {CellBouncer, a unified toolkit for single-cell demultiplexing and ambient RNA analysis, reveals hominid mitochondrial incompatibilities.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {101275},
doi = {10.1016/j.xgen.2026.101275},
pmid = {42269616},
issn = {2666-979X},
abstract = {Pooled processing, in which cells from multiple sources are cultured or captured together, is increasingly popular for droplet-based single-cell sequencing studies. This design allows efficient scaling of experiments, isolation of cell-intrinsic differences, and mitigation of batch effects. We present CellBouncer, a computational toolkit for demultiplexing and analyzing single-cell sequencing data from pooled experiments. We demonstrate that CellBouncer can separate and quantify multi-species and multi-individual cell mixtures, identify unknown mitochondrial haplotypes in cells, assign treatments from lipid-conjugated barcodes or CRISPR single-guide RNAs, and infer pool composition, outperforming existing methods. We introduce methods to quantify ambient RNA contamination per cell, infer individual donors' contributions to the ambient RNA pool, and determine a consensus doublet rate harmonized across data types. Applying these tools to tetraploid composite cells, we identify a competitive advantage of human over chimpanzee mitochondria across ten cell fusion lines and provide evidence for inter-mitochondrial incompatibility and mito-nuclear incompatibility between species.},
}

@article {pmid42270853,
year = {2026},
author = {Umer, S and Muhammad, K and Sajjad, S and AlHusnain, L and AlKahtani, MDF and Majid, A and Ali, H and Ullah, I and Zeb, A and Ali, S and Khalili, A and Yang, SH and Fiaz, S and Attia, KA},
title = {DNA barcoding and phylogenetic insights into the selected endemic flora of the Western Himalayas.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42270853},
issn = {2045-2322},
abstract = {The Himalayan region is recognized as one of the world's major biodiversity hotspots due to its remarkable altitudinal variation, high species richness, and exceptional endemism. Despite its ecological significance, the endemic flora of the western Himalayas remains insufficiently explored at the molecular level. This study aimed to evaluate the performance of multiple nuclear and chloroplast DNA barcode loci (ITS2, rbcL, trnH-psbA, trnA, trnV, rpoB, ycf3, and rbcLa) for the identification and phylogenetic assessment of 32 endemic and threatened plant species representing 31 genera and 24 families from the western Himalayan region of Pakistan, such as Thalictrum secundum Edgew. Aquilegia pubiflora Wall. ex Royle, Anemone obtusiloba D.Don and Delphinium cashmerianum Royle of family (Ranunculaceae), Pimpinella stewartii (C.B. Clarke) Nasir (Umbeliferaceae), Bistorta amplexicaulis (D.Don) Greene, and Bistorta affinis (D.Don) Greene (Polygonaceae) Abelia triflora R.Br. ex Wall. And Lonicera japonica Thunb. (Caprifoliaceae), Aesculus indica (Wall. ex Cambess.) Hook. (Sapindaceae), Arisaema utile Nakai (Araceae), Coriaria nepalensis Wall. (Coriaraceae), Desmodium elegans DC (Papilionacea), Daphne papyracea Wall. ex Steud. (Thymelaceae), Epimedium elatum C.Morren. (Berberidaceae), Galium tetraphyllum. Nazim. & Ehrend. (Rubiaceae), Bupleurum lanceolatum Wall. ex August. and Heracleum polyadenum Franchet (Apiaceae), Impatiens edgeworthii Hook.f. (Balsaminaceae), Incarvillea emodi Chatterjee (Bignoniaceae), Potentilla erecta (L.) Raeusch., Cotoneaster frigidus var. affinis (Lindl.) Wenz., and Spiraea hazarica R.Parker (Rosaceae), Phytolacca latbenia (Moq.) H.Walter. (Phytolaccaceae), Rhamnus parvifolius Bunge. (Rhamnaceae), Thymus linearis Benth. (Lamiaceae), Jasminum leptophyllum Wall. ex G.Don (Oleaceae), Rhododendron lepidotum Wall. ex Hook.f. (Ericaceae), Swertia ciliata Roxb. ex Fleming. (Gentianaceae), Zanthoxylum armatum DC. (Rutaceae), Dioscorea balcanica Kosanin (Dioscoreaceae), and Deutzia staminea R.Br. ex Wall. (Hydrangeaceae). Among the tested markers, rbcL showed the highest PCR amplification (100%) and sequencing success (96%), followed by trnH-psbA (100% amplification, 80% sequencing success), whereas ITS2 exhibited comparatively lower sequencing efficiency (52%). BLAST analysis demonstrated ≥ 97% sequence identity for most taxa, and best Match/Best Close Match analysis indicated higher discrimination efficiency for rbcL and trnH-psbA compared with other loci. Multilocus phylogenetic analysis further confirmed taxonomic placement at the family, genus, and species levels. Overall, this study demonstrates that a multilocus DNA barcoding approach provides reliable species authentication and phylogenetic resolution for endemic Himalayan flora, contributing valuable molecular reference data to global databases and supporting conservation and taxonomic efforts in this biodiversity-rich yet understudied region.},
}

@article {pmid42271498,
year = {2026},
author = {Plumbom, I and Obermayer, B and Raspe, R and Pascual-Reguant, A and Theurillat, I and Pentimalli, TM and Hsieh, YH and Gil, M and Dietrich, C and Seeger-Zografakis, M and Quedenau, C and Wilde, J and Braeuning, C and Fischer, C and Schuelke, M and Seitz, V and Ludwig, LS and Eggert, A and Rajewsky, N and Borodina, T and Beule, D and Altmueller, J and Radbruch, H and Hauser, AE and Conrad, T},
title = {circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42271498},
issn = {1756-994X},
abstract = {Monitoring T cell repertoires in human tissues provides important insights into immune response mechanisms in cancer, infectious diseases, and autoimmunity. However, retrieving VDJ information from single-cell and spatial transcriptomics workflows with 3'-barcoding of cDNA remains resource-intensive or requires specialized sequencing equipment. Here, we introduce circVDJ-seq for simplified and cost-efficient T cell receptor (TCR) profiling from 3'-directed workflows like single-cell or single-nucleus RNA sequencing, ATAC + RNA multi-omics, and spatial transcriptomics. Application of circVDJ-seq to freshly resected neuroblastomas and postmortem lymph nodes affected by pneumonia or COVID-19 reveals distinct immune microenvironments and T cell clonality patterns, highlighting broad utility across diverse clinical contexts.},
}

@article {pmid42274516,
year = {2026},
author = {Fang, B and Zhang, Z and Ding, Y and Cheng, J and Yang, J and Zhai, J and Chen, X and Elsayed, AK and Tokuda, M and Yang, D and Liu, Y and Meier, R and Wang, Q and Li, X},
title = {Urban Filter vs. Natural Refuge: Divergent Diptera Community Assembly Mechanisms-Evidence from Beijing, China.},
journal = {Biology},
volume = {15},
number = {11},
pages = {},
pmid = {42274516},
issn = {2079-7737},
abstract = {Urbanization can act as a powerful ecological filter, restructuring biodiversity through species loss, replacement, and altered resource pathways. While urban green spaces (UGS) are recognized as potential biodiversity refuges, the effectiveness and mechanisms for conserving insect diversity across the urban-to-natural gradient remain poorly understood. Here, we combine full-season Malaise trapping (April-November) with MinION-based DNA barcoding to test two predictions about how urbanization reshapes Diptera communities across five sites in Haidian District, Beijing, ranging from residential areas and urban parks to a nearby shallow mountain reserve (BWM). Based on 5528 barcoded individuals, we identified 686 putative species from 39 families. As predicted, β-diversity between urban and mountain sites was overwhelmingly driven by species turnover rather than nestedness, demonstrating that cities do not simply receive subsets of the surrounding fauna but actively reassemble communities. This filtering effect was, however, trophic-guild specific. Detritivores showed the highest replacement, consistent with a shift from natural to anthropogenic resource subsidies, while predators/parasitoids exhibited significant nested loss, aligning with their hypothesized sensitivity at higher trophic levels. Vegetation structure further clarified these patterns: vegetation density, not plant species richness, was the primary bottom-up driver for herbivore and predator/parasitoid diversity, whereas detritivores were decoupled from living plant biomass. These findings demonstrate that urban and near-natural habitats maintain distinct species pools via guild-specific assembly pathways, highlighting the need for guild-specific conservation strategies for urban biodiversity conservation. Extending beyond compositional analysis, we propose a temporal-abundance framework, classifying species by persistence and abundance, as a diagnostic tool for assessing ecological integrity and guiding conservation in urbanizing landscapes.},
}

@article {pmid42277314,
year = {2026},
author = {Zhang, J and Zhang, J and Shull, P and Park, C and Sun, S and Najafi, B and Wang, C},
title = {Daily activity patterns from wearable accelerometry predict physical frailty and concern about falling.},
journal = {NPJ digital medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41746-026-02863-4},
pmid = {42277314},
issn = {2398-6352},
support = {62303496, 62573441//National Natural Science Foundation of China/ ; D250403003//Shenzhen Medical Research Fund, China/ ; 2025A1515011729//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {Physical frailty and concern about falling are interrelated geriatric conditions that significantly impair mobility, limit daily activity, and reduce life quality among older adults. Traditional methods for assessing frailty and fall concern rely heavily on questionnaires such as the Fried Frailty Phenotype (FFP) and the Falls Efficacy Scale-International (FES-I). These tools, although clinically established, are subjective, require professional administration, and cannot capture the mutual influence between the two conditions. In this study, we propose a wearable-sensor-based, objective framework that simultaneously predicts physical frailty status and level of concern about falling by analyzing real-world activity patterns. We collected continuous chest acceleration data from 146 participants over a 48-hour period using a pendant sensor. These activity sequences were transformed into barcodes and analyzed using global complexity metrics (e.g., single- and multi-scale entropy) and local sequential dynamics via bidirectional LSTM networks. A multi-task deep learning model with attention mechanisms was proposed to jointly predict frailty and fall concern. Our model achieved high predictive performance for both tasks, achieving F1 scores of 93.12% for physical frailty and 86.27% for concern about falling. This study provides the first joint modeling of physical frailty and concern about falling using long-term real-world accelerometry data.},
}

@article {pmid42278215,
year = {2026},
author = {Cavallo, M and Diaf, A and Milanesi, G and Biggiogera, M and Casali, C},
title = {Resolving Sub-Nuclear Architecture from Compartments to Functional Domains.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27114680},
pmid = {42278215},
issn = {1422-0067},
support = {Fondo Ricerca Giovani (FRG)//University of Pavia/ ; },
mesh = {*Cell Nucleus/ultrastructure/metabolism/genetics ; Humans ; Animals ; Chromatin/metabolism/ultrastructure ; Microscopy, Electron/methods ; RNA/metabolism ; },
abstract = {The cell nucleus is a highly dynamic and complex organelle that orchestrates fundamental cellular processes through its spatial organization. Far from being merely the repository of genetic information, it acts as a regulatory hub whose architecture profoundly influences transcription, RNA maturation and genome maintenance. Dissecting such a multilayered organization requires approaches that integrate molecular profiling with spatially resolved technologies capable of capturing nuclear architecture in situ. In this Review, we discuss classical and emerging imaging strategies that are transforming our understanding of nuclear organization across scales, from multiplexed and super-resolution light microscopy to barcoding-based spatial methods, live-cell imaging, and ultrastructural electron microscopy. Together, these methods are providing crucial insights into the localization and dynamics of RNAs and genomic regions within distinct compartments revealing how nuclear architecture governs genome function.},
}

*Cell Nucleus/ultrastructure/metabolism/genetics
Humans
Animals
Chromatin/metabolism/ultrastructure
Microscopy, Electron/methods
RNA/metabolism

@article {pmid42280754,
year = {2026},
author = {Pan, J and Fang, C and Anwar, T and Ma, K},
title = {Genetic Diversity and SNP-Based Fingerprinting of 94 Pumpkin Cultivars: Database Establishment and Population Analysis.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/plants15111717},
pmid = {42280754},
issn = {2223-7747},
support = {[2025]028//Shanghai Academy of Agricultural Sciences/ ; },
abstract = {Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders' rights enforcement. Despite the established utility of SNP markers as the gold standard for genetic analysis, a dedicated high-resolution molecular database for modern pumpkin cultivars remains unavailable. To address this gap, we conducted whole-genome resequencing (WGS) on 94 representative pumpkin cultivars (spanning C. moschata, C. maxima, and C. pepo). Clean reads were mapped to the Cucurbita maxima reference genome. We employed a stringent pipeline to identify genomic variants and utilized STRUCTURE software, Principal Component Analysis (PCA), and Neighbor-Joining (NJ) trees to evaluate population stratification. Linkage disequilibrium (LD) decay and DNA fingerprinting barcodes were also developed. A total of 8,873,150 high-quality variants were identified, including 7,345,007 SNPs and 1,528,143 InDels, with an average SNP density of 21,281.50 SNPs/Mb. Population analysis consistently categorized the 94 cultivars into two primary subpopulations (G1 and G2). The first two PCs accounted for 74.06% of the total genetic variance. Further analysis revealed that G1 possessed a more complex genetic architecture and slower LD decay compared to G2, suggesting distinct selection histories. Finally, we screened for highly informative biallelic SNPs to construct a DNA fingerprinting database, enabling precise sample discrimination through unique chromatic barcodes. This study fills a critical gap in pumpkin genomics by establishing a high-density SNP database and a robust fingerprinting system. These resources provide a definitive tool for variety certification, seed purity testing, and the advancement of molecular-assisted breeding in pumpkin.},
}

@article {pmid42281569,
year = {2026},
author = {Piwowarczyk, R and Wiśniewska, K and Rewicz, T and Olbrycht, T and Salata, S and Fateryga, AV and Nicewicz, Ł and Depa, Ł and Zając, K and Masarovič, R and Celary, W and Mielczarek, Ł and Mátis, A},
title = {A multiverse of trophic networks and coevolutionary trajectories among holoparasitic Orobanchaceae and their animal associates: a global perspective.},
journal = {PhytoKeys},
volume = {275},
number = {},
pages = {209-297},
pmid = {42281569},
issn = {1314-2011},
abstract = {Holoparasitism, in achlorophyllous, fully heterotrophic plants, is one of the most peculiar symbioses in the plant world. In particular, holoparasites from Orobanchaceae, the largest parasitic plant family, have evolved unique visual and olfactory signals in the plant kingdom, and thus play a key role in the evolution of animal-plant adaptations. Holoparasitism offers excellent case studies of the effects of a specialised interaction on multiple aspects of plant ecology and evolution, including pollination, herbivory, and speciation. In this paper, we present the first global study of these interactions using morphological and molecular tools, summarising almost 20 years of field studies. These observations were supplemented with literature data and internet sources, ultimately encompassing more than 1370 observations from 76 countries in Europe, America, Africa, Asia, and Australia. We found data on animals interacting with 130 species of 16 holoparasitic genera from the Orobanchaceae family. This study represents the first comprehensive study of animals which use these plants as food, shelter, hunting grounds, or part of their development cycles. Our work has resulted in recognising 667 animal species from 34 orders, 163 families, and 434 genera, with a predominance of arthropods (91% of species recorded) followed mainly by gastropods (ca. 4%), mammals (2%), birds and reptiles (0.6% each). Besides the combination of different pollinator and herbivore species, parasitic plants also attract a range of other animals, such as carnivores and parasitoids, creating a habitat with multitrophic and multilayered relationships. Our research sheds light on the intricate interactions mediated by parasitic plants and animals, opening the path for further elucidating the ecological and evolutionary drivers of holoparasite diversity and their broader ecological role.},
}

@article {pmid42015157,
year = {2026},
author = {Yang, P and Ma, R and Zeng, J and Li, L and Peng, J and Zhou, M and Qu, M and Li, X and Lai, T and Zhou, W and Wu, Y and Lu, Y and Zhang, Y},
title = {Simple and rapid profiling of tumor EVs for differential diagnosis of NSCLC via orthogonal barcode-driven CRISPR/Cas12a.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {42015157},
issn = {1477-3155},
support = {82172374//National Natural Science Foundation of China/ ; 2023GDRC005//Chongqing Science and technology joint major funding program/ ; 2022CDJYGRH-010//Natural Science Foundation Project of Chongqing, Chongqing Science and Technology Commission/ ; 2021M693730//China Postdoctoral Science Foundation/ ; },
abstract = {UNLABELLED: Tumor-derived extracellular vesicles (tEVs), a class of nanoscale vesicles actively released by malignant cells, have emerged as attractive biomarkers for non-invasive cancer diagnosis. However, their clinical translation remains challenging due to low abundance, molecular heterogeneity, and the requirement for multiplexed surface marker discrimination. Here, we report a dual aptamer-mediated CRISPR/Cas12a-assisted sensing platform (DA-CAS) for rapid and orthogonally programmable dual-marker profiling of tEVs, enabling differential diagnosis of non-small cell lung cancer (NSCLC) using only 10 µL of plasma within 100 min. The DA-CAS system integrates proximity ligation-based dual-marker recognition with hyperbranched rolling circle amplification (HRCA) to generate programmable DNA barcodes, which selectively trigger Cas12a trans-cleavage in an orthogonal manner. Using EpCAM and PD-L1 as representative surface markers, the platform achieves subtype-specific detection of NSCLC-derived tEVs with minimal background activation and a detection limit as low as 75 particles/mL. Moreover, a portable lateral flow readout enables accurate, instrument-free visual detection at concentrations down to 406 particles/mL. Under the condition of free-ultracentrifugation, clinical validation using a cohort of 45 plasma samples demonstrated a sensitivity of 97%, specificity of 88%, and overall diagnostic accuracy of 96%, outperforming conventional ELISA assays and multi-marker serum panels in both analytical sensitivity and subtype resolution. In addition, this platform demonstrated preliminary potential for discriminating between benign and malignant lung diseases and for dynamically monitoring radiotherapeutic responses. The orthogonal barcode design effectively eliminates inter-channel crosstalk and enzymatic interference, enabling orthogonal dual-target recognition with high subpopulation specificity. Overall, DA-CAS provides a robust, rapid, and point-of-care-compatible strategy for tEV-based cancer diagnostics, offering strong translational potential for non-invasive tumor profiling and dynamic immune status monitoring.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12951-026-04465-4.},
}

@article {pmid42258901,
year = {2026},
author = {Chadd, EF and Kumsa, B and Caicedo-Quiroga, L and Linton, YM},
title = {DNA barcoding reveals novel biodiversity in ticks (Acari: Ixodida: Ixodidae) of Ethiopia.},
journal = {Veterinary parasitology},
volume = {346},
number = {},
pages = {110828},
doi = {10.1016/j.vetpar.2026.110828},
pmid = {42258901},
issn = {1873-2550},
abstract = {Identification of hard ticks (Acari: Ixodida: Ixodidae) is problematic due to inconsistent diagnostic characters, sexual dimorphism, individual variation, and vast morphological differences among life stages, as well as distortion through blood feeding. DNA barcoding has proven useful in delineating tick species, but available genetic databases are littered with misleading mis-identifications, hindering tick-borne disease mitigation strategies. Efforts are needed to generate high quality reference sequences from expertly identified and morphologically vouchered samples. To date, 56 species of hard ticks are reported from Ethiopia. Here, we subsampled and e-vouchered exemplars of 22 expert-validated hard tick species from 25,343 total ticks collected on a range of livestock from five regions across Ethiopia. We successfully sequenced the barcoding region of the mitochondrial cytochrome c oxidase subunit I (COI) for 208 individual ticks, representing 21 of these target taxa (The COI gene of one tick species, Haemaphysalis parmata, was not able to be amplified). Our data suggest the presence of 29 species-level groupings among the 21 morphologically identified taxa successfully sequenced, an increase of 38%, reiterating the gaps and challenges of accurate tick identification in Ethiopia, as well as the greater East Africa region. Here we report novel hidden diversity in Amblyomma variegatum, Hyalomma truncatum, Rhipicephalus lunulatus, and Rh. praetextatus in Ethiopia, and provide the first expertly-verified mtDNA COI barcodes for Hae. aciculifer and Rh. bergeoni. Molecular confirmation of the presence of Hy. marginatum in Ethiopia is documented for the first time. Dorsal and ventral photographic vouchers are provided for examples of all known and newly discovered COI barcodes sequenced in this study, enhancing accuracy in future taxonomic and ecologic studies of ticks in Ethiopia and across East Africa. This validated barcoding resource improves tick-borne disease surveillance across East Africa, and provides a framework for broader vector-borne disease biosurveillance efforts.},
}

@article {pmid42263684,
year = {2026},
author = {Jia, Y and Sun, D and Weir, JA and Liu, X and Russell, AJC and Kim, Y and Thom, N and Marrero, G and Kumar, V and Chen, F and Camargo, FD},
title = {SPACE-seq integrates spatial transcriptomics and lineage tracing in native tissues.},
journal = {Cell stem cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.stem.2026.05.017},
pmid = {42263684},
issn = {1875-9777},
abstract = {Understanding how cells change state, interact with their neighbors, and organize into tissues requires recording of cellular lineage history in native spatial context. Here, we present SPACE-seq (spatial tracing enabled by CRISPR-based barcodes and slide-seq), a versatile platform that integrates CRISPR-based lineage recording with spatial transcriptomics to jointly resolve lineage, cell state, and tissue architecture at near-cellular resolution in situ. Using SPACE-seq, we uncovered intratumor transcriptional diversification among clonally related cells and identified tumor-stroma crosstalk that reciprocally reshapes behaviors of both malignant and stromal populations, which we further experimentally validated. Beyond disease, SPACE-seq revealed a narrow developmental window in which hepatoblast dispersion contributes to spatially confined lineage compartments that prefigure liver lobar architecture. Together, these results highlight the broad applicability and adaptability of SPACE-seq to uncover previously inaccessible principles of cellular organization, lineage dynamics, and tissue patterning.},
}

@article {pmid42265178,
year = {2026},
author = {Yan, R and Abdullah, and Sammad, A and Li, H and Fu, M and Cui, Y and Heidari, P and Tian, X},
title = {Complete chloroplast genomes of four Triumfetta species obtained from herbarium specimens: comparative analysis and identification of a synapomorphic inversion.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57295-7},
pmid = {42265178},
issn = {2045-2322},
support = {82474031//the National Natural Science Foundation of China/ ; },
abstract = {The genus Triumfetta L. (Malvaceae) comprises about 177 species, several of which are of medicinal importance. However, genomic resources for this genus remain limited, with only ten chloroplast (cp.) genomes published to date. Here, we report the sequencing and de novo assembly of complete cp. genomes for four Triumfetta species (Triumfetta annua L., Triumfetta cordifolia A.Rich., Triumfetta lappula L., and Triumfetta rhomboidea Jacq.) using the Illumina NovaSeq 6000 platform. Our objectives were to characterize cp. genome features, conduct comparative analyses with previously reported species, identify polymorphic loci, and reconstruct a preliminary phylogeny. The cp. genomes exhibited the typical quadripartite structure, ranging from 159,245 to 160,604 bp, and contained 112 unique genes (78 protein-coding, 30 tRNA, and 4 rRNA). Comparative analysis revealed a six-gene synapomorphic inversion (trnC, petN, psbM, trnD, trnY, and trnE) in the large single-copy (LSC) region. Codon usage analysis revealed a strong bias toward A/T-ending codons (RSCU > 1). Leucine was the most abundant amino acid, while cysteine was the least abundant. Simple sequence repeat analysis identified 63-81 repeats, with a predominance of mononucleotide A/T repeats. Nucleotide substitution analysis revealed a transition bias across all regions (Ts/Tv > 1), most pronounced in the LSC (Ts/Tv = 1.29-1.35). Seven highly polymorphic loci were identified as potential DNA barcoding candidates, including two intergenic spacers (trnL-ccsA, ndhD-psaC), and five coding regions (clpP, rpl22, ycf1, rpl23, and ndhI). This study provides genomic resources for Triumfetta taxonomy, highlighting key structural variations and identifying molecular markers with potential applications in taxonomic research.},
}

@article {pmid42265211,
year = {2026},
author = {Xiao, Y and Bai, Z and Zou, Z and Ye, C and Tao, B and Zheng, Z and Chen, YM and Zou, Z and Jiang, L and Zhao, L and Fan, Y and Gao, Y and Fan, R and He, C},
title = {Spatially resolved m[6]A profiling using m[6]A-ARTR-DBiT.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {42265211},
issn = {1548-7105},
support = {RM1HG008935//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; RC2DK139552//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01HG013495//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; UH3CA257393//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54CA274509//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA245313//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54AG076043//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U54AG079759//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1MH128876//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; },
abstract = {N[6]-methyladenosine (m[6]A) on RNA plays diverse regulatory roles, yet its spatial distribution within tissues remains largely unexplored. Here we introduce m[6]A-ARTR-DBiT, a spatial m[6]A profiling assay that leverages reverse-transcription-based detection and deterministic barcoding in tissue to map transcriptome-wide m[6]A distribution while preserving native tissue context. Applying m[6]A-ARTR-DBiT to mouse embryonic tissues and adult brains generates spatially resolved m[6]A landscapes and reveals region-associated m[6]A features across different functional domains. Pairwise comparison of spatial m[6]A profiles with spatial transcriptomes uncovers positive correlations between m[6]A levels and the expression of its methyltransferases and binding proteins, which also enables systematic identification of tissue-region-specific epitranscriptomic regulation. In the mouse hippocampus, m[6]A-ARTR-DBiT allows for high-resolution mapping of m[6]A organization within fine-scale tissue structures. Together, m[6]A-ARTR-DBiT provides a platform for interrogating RNA modification distribution within intact tissue sections, offering insights into the link between spatially patterned m[6]A deposition and gene regulation.},
}

@article {pmid42265602,
year = {2026},
author = {Yan, R and Sammad, A and Shah, SA and Vallada, A and Tian, X and Abdullah, },
title = {Comparative chloroplast genomics of 22 species of Sida (Malvaceae) reveals structural conservation, adaptive evolution, and preliminary phylogenetic structure.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09208-z},
pmid = {42265602},
issn = {1471-2229},
abstract = {BACKGROUND: The genus Sida L. (Malvoideae, Malvaceae) comprises 275 species with a near-cosmopolitan distribution. Persistent taxonomic uncertainties, driven by morphological complexity and low resolution of traditional molecular markers, hinder systematic understanding of the genus. Chloroplast (cp) genomes provide genome-scale data capable of resolving these taxonomic uncertainties, but genomic resources for Sida remain limited. Here, we substantially expand cp genome sampling, perform comparative and selection analyses, identify candidate loci for species discrimination and phylogenetic inference, and conduct phylogenomic inference to clarify infrageneric relationships.

RESULTS: We sequenced and de novo assembled the complete cp genomes of Sida cordata (Burm.f.) Borss.Waalk. and Sida rhombifolia L., and assembled cp genomes of 18 additional species de novo from publicly available raw sequencing reads. Together with two previously reported cp genomes, 22 cp genomes were subjected to comparative and phylogenetic analyses. Genome sizes ranged from 159,706 to 160,513 base pairs (bp), comprising a large single-copy region (88,771-89,551 bp), inverted repeats (IRa/IRb; 25,288-25,640 bp), and a small single-copy region (19,863-20,294 bp). Each genome contained 113 unique genes (79 protein-coding, 30 tRNAs, 4 rRNAs). Comparative analyses revealed conserved gene order, guanine-cytosine content, codon usage, and simple sequence repeat composition, as well as a consistent transition bias in substitution patterns across all Sida species. Gene-level selection analyses identified episodic positive selection in psaB, psbB, rbcL, and rps8, while site-level analyses detected positive selection at specific codons in rbcL and ycf1. Ten highly polymorphic loci with elevated nucleotide diversity and low missing data were identified as candidates for species identification and phylogenetic inference, including psbT-psbN, ndhD-psaC, psaC-ndhE, rps15-ycf1, and psaI. Phylogenetic analysis of the 22 species resolved two strongly supported clades: a monophyletic endemic Australian lineage and a broadly distributed Asian/pantropical lineage.

CONCLUSIONS: Our findings reveal conserved cp genome structure across 22 Sida cp genomes, identify polymorphic loci as potential barcodes, and resolve two clades (an endemic Australian lineage and a widespread Asian/pantropical lineage), demonstrating the value of whole-cp genome data. However, due to sampling limitations and sole reliance on the maternally inherited cp genome, we recommend that future studies refine biogeographic inferences using denser taxon sampling and nuclear genomic data.},
}

@article {pmid42269100,
year = {2026},
author = {Panich, J and Awad, D and Waggoner, M and Hallam, M},
title = {Determining whether barcodes on investigational compounded sterile products are scannable by an IV workflow management system.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxag165},
pmid = {42269100},
issn = {1535-2900},
abstract = {PURPOSE: The goals of this project were to determine (1) what proportion of compounded sterile product investigational products (CSP IPs) stocked by our institution's investigational drug service have barcodes, and (2) whether CSP IPs that do have barcodes contain a number that is usable by our institution's IV workflow management system. A secondary goal was to determine sponsor willingness to embed a drug identifier in the barcodes.

SUMMARY: A survey of the site's inventory was conducted to identify CSP IPs. The vials were examined to determine if they contained a barcode, and if so, scanning was performed to determine what number was embedded in each barcode. In addition, sponsors of vials with barcodes were queried about whether they would be willing to embed a drug identifier, while sponsors with no barcodes were queried about their willingness to add barcodes.

CONCLUSION: The study found that 66.9% of the CSP IP vials contained barcodes. However, the numbers embedded in the barcodes on most of these IPs varied from vial to vial. The structure of the numbers embedded in each barcode did not match the GS1-128 structure seen on FDA-approved products, and there was no usable drug identifier in any barcode in the opinion of the team's informatics pharmacist.},
}

@article {pmid42254670,
year = {2026},
author = {Jeong, KH and Harms, D and Kim, S},
title = {Korean dragon pseudoscorpions revisited: a taxonomic review of Allochthonius (Pseudoscorpiones: Pseudotyrannochthoniidae) Chamberlin, 1929 with three new species.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21332},
pmid = {42254670},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; Republic of Korea ; Species Specificity ; *Arachnida/classification ; },
abstract = {Allochthonius (Pseudoscorpiones: Pseudotyrannochthoniidae) is a genus widely distributed throughout East Asia. In Korea, only three species in this genus have been recorded to date: Allochthonius buanensis Lee, 1982; Allochthonius coreanus Morikawa, 1970; and Allochthonius opticus Ellingsen, 1907. Here, we review the Korean fauna of Allochthonius and describe three new species for the country: Allochthonius jungsuni sp. nov., Allochthonius maximus sp. nov., and Allochthonius rufimanus sp. nov. We also exclude Allochthonius opticus -a species originally described from Japan-from the country record and redescribe two Korean recorded species, Allochthonius buanensis and Allochthonius coreanus. Following up on our previous taxonomic work that elevated several subspecies of Japanese pseudotyrannochthoniids originally described by Kuniyasu Morikawa to species level, we elevate eight former subspecies to full species rank: A. ishikawai deciclavatus Morikawa, 1956 = A. deciclavatus Morikawa, 1956, stat. nov., A. ishikawai ishikawai Morikawa, 1954 = A. ishikawai Morikawa, 1954, A. ishikawai kyushuensis Morikawa, 1960 = A. kyushuensis Morikawa, 1960, stat. nov., A. ishikawai shiragatakiensis Morikawa, 1954 = A. shiragatakiensis Morikawa, 1954, stat. nov., A. ishikawai uenoi Morikawa, 1956 = A. uenoi Morikawa, 1956, stat. nov., and A. ishikawai uyamadensis Morikawa, 1954 = A. uyamadensis Morikawa, 1954, stat. nov.; A. opticus opticus Ellingsen, 1907 = A. opticus Ellingsen, 1907, and A. opticus troglophilus Morikawa, 1956 = A. troglophilus Morikawa, 1956, stat. nov.. This elevates the total number of Allochthonius species from 40 to 43, of which five species are presently known from the Korean Peninsula.},
}

Animals
Phylogeny
Republic of Korea
Species Specificity
*Arachnida/classification

@article {pmid42256146,
year = {2026},
author = {Wu, L and Huang, Z and Ren, X and Yao, H and Li, M and Deng, A and Li, Y and Lian, S and Men, L and Zhang, Z},
title = {Comparative Analysis of Lepidopteran Community Structure Using DNA Metabarcoding: Warm-Temperate Forest Versus Grass-Shrub Ecotones in Pangquangou National Nature Reserve.},
journal = {Ecology and evolution},
volume = {16},
number = {6},
pages = {e73738},
pmid = {42256146},
issn = {2045-7758},
abstract = {Lepidoptera is a widely geographically distributed insect order that plays crucial ecological roles in forest and grass-shrub ecosystems as both pollinators and herbivores. This study compared Lepidoptera species composition and diversity between semi-arid forest and grass-shrub ecosystems in northern China's Pangquangou National Nature Reserve to provide scientific insights for biodiversity conservation and pest management. Nine representative plots (five forest and four grass-shrub) were established, and Lepidoptera communities were analyzed using an integrated approach combining DNA metabarcoding, DNA barcoding, and classical morphological methods. A total of 2944 individuals were collected, representing 453 species from 80 genera and 31 families, with an 82% cross-method species identification match. Despite being more time-consuming, metabarcoding offers a clear advantage for large-scale biodiversity monitoring due to its extremely low per-sample cost (up to 79.2% of costs saved compared to traditional morphological methods and 87.3% of costs saved compared to DNA barcoding). However, morphological validation remains necessary to ensure accurate identification. Dominant families showed higher relative abundance in forests (85.07%) than in grass-shrub areas (75.18%). Alpha diversity, assessed via the Shannon-Wiener index, exhibited no significant difference between ecosystems (p = 0.72). Beta diversity analysis also indicated comparable community compositions, though differences were not statistically significant (p = 0.332). Five dominant families (Noctuidae, Notodontidae, Geometridae, Erebidae, and Nymphalidae) were shared between ecosystems, while Lasiocampidae occurred exclusively in forests. Notably, metabarcoding data accurately reflected species composition and abundance, facilitated precise prediction of caterpillar pest outbreaks, and supported targeted control measures. This study confirms that DNA metabarcoding, when supplemented with morphological verification, is a robust tool for Lepidoptera biodiversity assessment. Our findings provide reliable solutions for ecosystem monitoring and pest management, underscoring the method's potential for large-scale biodiversity studies.},
}

@article {pmid42256186,
year = {2026},
author = {Elefánti, S and Lasley, R and Paulay, G and Pfaller, JB},
title = {Planes on a Snake? On the Identities of Crab Larvae Rafting on Sea Snakes.},
journal = {Ecology and evolution},
volume = {16},
number = {6},
pages = {e73742},
pmid = {42256186},
issn = {2045-7758},
abstract = {Rafting on surface-drifting flotsam or pelagic animals may represent an important behavioral strategy for larval transport and recruitment among brachyuran crabs. For some, like crabs of the genus Planes (Grapsidae), rafting has even become an adult lifestyle. After a 2012 study reported high numbers of unidentified grapsid megalopae rafting on pelagic sea snakes (Hydrophis platurus) off Pacific Costa Rica, we hypothesized their identity to be Planes minutus, which are commonly found rafting on flotsam and sea turtles in the area. To test the "Planes on a snake" hypothesis, we sequenced barcoding genes (CO1 and/or 16S) for 106 individual megalopae collected from sea snakes and compared with those of known species in the region. Three distinct species were detected, and all were in the predominately inter- to supratidal family Grapsidae: Pachygrapsus socius, Goniopsis pulchra, and Grapsus grapsus. No Planes were detected. While the "Planes on a snake" hypothesis was refuted, our results suggest that larval rafting may be a successful strategy for recruitment in inter- and supratidal grapsid crabs, but not other inter- to supratidal crabs nor Planes. The prevalence of larval rafting only in grapsid crabs suggests that the behavior may have provided the necessary precursor for the evolution of an obligate rafting species, like Planes.},
}

@article {pmid42256783,
year = {2026},
author = {He, Y and Wang, X and Yan, X and Liu, W and Jiang, Y and Ai, C and Sheng, J and Zhang, X and Wang, S},
title = {A morphological and phylogenetic analysis of dematiaceous hyphomycete strains of Distoseptispora (Distoseptisporaceae, Distoseptisporales) and Kirschsteiniothelia (Kirschsteiniotheliaceae, Pleosporales) in southern China.},
journal = {MycoKeys},
volume = {133},
number = {},
pages = {41-66},
pmid = {42256783},
issn = {1314-4049},
abstract = {Dematiaceous hyphomycetes are widely distributed throughout the world. They can live either saprophytically or parasitically and are commonly found growing on dead wood, in soil, and in aquatic environments. During an ongoing survey of saprophytic fungi in multiple southern provinces of China, two Distoseptispora-like and one Kirschsteiniothelia-like strains were isolated from decaying wood. Five barcodes (i.e., ITS, SSU, LSU, RPB2, and TEF1) were amplified and sequenced. Of these markers, ITS, LSU, RPB2, and TEF1 were selected for Distoseptispora, whereas ITS, LSU, and SSU were used for Kirschsteiniothelia. Based on maximum likelihood (ML) and Bayesian inference (BI) phylogenetic analyses, combined with morphological characteristics, three new species, Distoseptispora linchunlingensis, D. xinganensis, and Kirschsteiniothelia guiyangensis, are proposed. This study provides detailed illustrations, phylogenetic trees, and morphological descriptions to clarify the taxonomic status of the three new species, thereby improving our understanding of the diversity of dematiaceous hyphomycetes in Hainan, Guangxi, and Guizhou provinces, China.},
}

@article {pmid42245506,
year = {2026},
author = {Fernandes Sousa, T and Gwinner, R and Santos da Silva, IJ and Dos Santos Castro, G and Vasconcelos da Costa, G and de Filippi, MCC and Athayde Sobrinho, C and Yamagishi, MEB and Eiji Hanada, R and Muniz, AW and Fayad, FR and Koolen, HHF and da Silva, GF},
title = {Isolation and characterization of Trichoderma from Amazonian white-water river sediments with descriptions of five new species and new records from Brazil.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1778622},
pmid = {42245506},
issn = {1664-302X},
abstract = {Trichoderma is a cosmopolitan genus widely used in agriculture due to its beneficial traits that promote plant growth and provide sustainable crop protection. Over 450 valid Trichoderma species have been described, with increasing whole-genome data showing extensive enzymatic repertoires and biosynthetic potential. However, the Amazonian biome remains underexplored for Trichoderma diversity despite its megadiversity. In this study, 44 Trichoderma strains were isolated from sediments collected during a systematic expedition along three major white-water Amazonian rivers (Juruá, Madeira, and Purus). Initial molecular barcoding using tef1-α sequences identified 14 species, with Trichoderma lentiforme being ubiquitously distributed across all three river systems. Isolates exhibiting <97% sequence identity to known species underwent comprehensive polyphasic characterization, including multi-locus phylogenetic analyses (tef1-α and rpb2), morphological studies, biocontrol assays, and comparative genomics. This approach led to the description of five novel species (Trichoderma madeiraense, Trichoderma labreaense, Trichoderma tapauaense, Trichoderma submersum, and Trichoderma juburiaense). It established the first records of Trichoderma cyanodichotomus and Trichoderma awajun for Brazil. All newly described species demonstrated strong antagonistic activity against major phytopathogens, with T. juburiaense TM67 achieving >95% mycelial growth inhibition against multiple Colletotrichum species. Comparative genomic analyses revealed diverse CAZyme arsenals enriched in glycoside hydrolases associated with mycoparasitism (GH16, GH18, GH72) and lignocellulose degradation, with T. labreaense TM26 exhibiting particularly high chitinase content and T. juburiaense TM67 showing elevated β-glucanase levels. Genome mining identified biosynthetic gene clusters encoding bioactive secondary metabolites, including verticillins, ilicicolins, chaetoglobosins, harzianopyridone, and brefeldin A, compounds with established antifungal, antibacterial, and cytotoxic activities. This study provides a taxonomic and genomic survey of Trichoderma from Amazonian white-water river sediments, describing five novel species and highlighting this frontier ecosystem as an important but undersampled source of fungal biodiversity.},
}

@article {pmid42246005,
year = {2026},
author = {Orcel, E and Sentausa, E and Hage, H and Louis, K and Taha, M and Bellais, S and Villain, A and Beloeil, L and Sijmons, S and Devos, N and Saliou, A},
title = {UMI-guided single locus sequence typing method for phylotyping Cutibacterium acnes from skin samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1807759},
pmid = {42246005},
issn = {2235-2988},
mesh = {Humans ; *Skin/microbiology ; Skin Microbiome ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Molecular Typing/methods ; *Propionibacteriaceae/genetics/classification/isolation & purification ; *Bacterial Typing Techniques/methods ; },
abstract = {INTRODUCTION: Cutibacterium acnes is a dominant member of the human skin microbiota and displays substantial strain-level diversity with relevance for skin health and disease. However, accurate characterization of C. acnes lineages directly from skin samples remains challenging due to low biomass, host DNA contamination, and limitations of short-read sequencing.

METHODS: Here, we present SLST-Seq, a culture-independent approach based on single-locus sequence typing (SLST), enabling strain-level profiling of C. acnes from low-input skin-strip samples. SLST-Seq adapts the LUMI-Seq® synthetic long-read sequencing technology to the C. acnes SLST marker, combining unique molecular identifier barcoding with de novo assembly to reconstruct full-length SLST sequences with high accuracy.

RESULT: Method performance was validated using single-isolate controls, defined genomic DNA mixtures, spike-in dilution series, and run-specific controls, demonstrating high specificity, quantitative accuracy across a wide range of target-to-background DNA ratios, and strong run-to-run reproducibility. Applied to skin-strip samples from healthy volunteers, SLST-Seq generated robust SLST profiles and revealed marked inter-individual variability, with donor-specific community structures largely conserved between face and back skin sites.

DISCUSSION: Overall, SLST-Seq provides a sensitive and scalable framework for in situ analysis of C. acnes population structure and supports high-resolution studies of skin microbiome composition from challenging clinical samples.},
}

Humans
*Skin/microbiology
Skin Microbiome
DNA, Bacterial/genetics
Phylogeny
Sequence Analysis, DNA
*Molecular Typing/methods
*Propionibacteriaceae/genetics/classification/isolation & purification
*Bacterial Typing Techniques/methods

@article {pmid42247036,
year = {2026},
author = {Sahraoui, N and Belkahia, H and Ben Said, M and Boukert, R and Ben Ali, S and Denis, F},
title = {Global cytochrome c oxidase subunit I analysis reveals mitochondrial conservation in Camelus dromedarius with clear interspecific separation from other camelids.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42247036},
issn = {1573-4978},
abstract = {BACKGROUND: The mitochondrial cytochrome c oxidase subunit I (COI) gene is widely used as a DNA barcoding marker; however, its ability to discriminate closely related camelid species and capture intraspecific variation in Camelus dromedarius remains insufficiently assessed at a global scale.

METHODS AND RESULTS: In this study, we sequenced COI from 20 Algerian dromedaries and combined these data with publicly available sequences covering the same fragment, along with representative sequences from the six other extant camelid species and Bos taurus as an outgroup. Sequence alignment, diversity indices, and neutrality tests were performed using DnaSP, while genetic distances and phylogenetic relationships were inferred using Maximum Likelihood under the Tamura-Nei model. Analysis of 136 C. dromedarius COI sequences (625 bp) revealed only five polymorphic sites and four genotypes worldwide, with very low genotype diversity (Gd = 0.277), nucleotide diversity (π = 0.00145), and mean nucleotide differences (k = 0.905). The Algerian genotypes (G1 and G2) fell within this limited variation, showing ≥ 99.2% identity and minimal genetic distances (≤ 0.008) relative to reference sequences. In contrast, interspecific distances between dromedaries and other camelids were substantially higher (≈ 0.014-0.188). Phylogenetic analysis recovered well-supported clades corresponding to C. dromedarius, Bactrian camels, and New World camelids, with no overlap between intra- and interspecific variation.

CONCLUSIONS: These findings indicate that the COI region is highly conserved within C. dromedarius but remains effective for species discrimination. The inclusion of Algerian sequences supports the low mitochondrial diversity of dromedaries and suggests a recent shared maternal ancestry across their global range.},
}

@article {pmid42247922,
year = {2026},
author = {Xiao, W and Di, Y and Chu, X and Liu, X},
title = {Assessing the effectiveness of DNA barcoding in shark identification.},
journal = {Forensic science international},
volume = {387},
number = {},
pages = {113043},
doi = {10.1016/j.forsciint.2026.113043},
pmid = {42247922},
issn = {1872-6283},
abstract = {The conservation status of shark populations has become increasingly concerning, with many species at risk of extinction, largely due to the shark fin trade. Effective conservation and regulation of illegal shark fin trading require accurate identification of shark species from samples. However, traditional DNA barcoding techniques have shown certain limitations during their application. To overcome these issues, this study systematically analyzed shark cytochrome c oxidase subunit I (COI) gene sequences, focusing on the distribution of genetic distances among shark populations and the investigation of DNA barcode gaps at the species level. Our results revealed that the current public shark COI dataset contains inaccuracies, including mislabeled barcodes and species misidentifications. In response, a curated and high-quality reference database for shark species identification was established. Analysis of genetic divergence showed considerable variation in both intraspecific and interspecific distances was observed across different sharks, with 149 out of 353 species displaying clear barcode gaps. Identification thresholds were also found to vary among species. Additionally, twelve COI primer pairs were evaluated, with those developed by Inoue et al. showing superior performance on degraded samples. Application of COI barcoding to 258 shark fin specimens successfully identified the majority of samples, although it failed to discriminate among four closely related species. In contrast, 16S rRNA markers improved resolution, and instances of COI misidentification were attributed to errors within the database. Notably, a significant data imbalance remains, with 56 shark species represented by only a single COI sequence and 208 species lack any reliable reference barcodes. This study not only curated and established a comprehensive DNA barcode library for shark species identification but also evaluated the effectiveness of various primers, offering a valuable framework to standardize species identification procedures.},
}

@article {pmid42251169,
year = {2026},
author = {Singh, K and Thundat, T and Goyal, A},
title = {Three-dimensional transient thermal barcode for waste plastic identification.},
journal = {Communications engineering},
volume = {},
number = {},
pages = {},
doi = {10.1038/s44172-026-00703-7},
pmid = {42251169},
issn = {2731-3395},
abstract = {Low global recycling rates of plastics are constrained by the lack of rapid, accurate, and scalable technologies for waste sorting. Here we report a standoff Transient Thermal Barcode (TTB) technique that identifies plastics using their mid-infrared (IR) absorption-induced thermal signatures. When the IR irradiation wavenumber matches a polymer absorption band in the molecular fingerprint regime, the non-radiative decay produces localized heating, yielding a transient hotspot that can be recorded with a thermal camera. Scanning with a tunable mid-IR source produces thermal spectra that closely track conventional FTIR spectrum. We show that a set of six mid-IR wavelengths can generate distinct thermal barcodes that enable the unique identification of all six major commercially relevant plastic classes in waste plastics. These results show the potential of mid-IR based non-contact plastic identification according to their resin codes for automated sorting in recycling.},
}

@article {pmid42243387,
year = {2026},
author = {Fox, B and Paulini, K and Chahal, J and Łypaczewski, P},
title = {Same-day tagmentation PCR-based whole genome sequencing of bacteriophage genomes from a single plaque without DNA extraction.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55253-x},
pmid = {42243387},
issn = {2045-2322},
support = {195796/CAPMC/CIHR/Canada ; },
abstract = {DNA sequencing is at the core of genome characterization, proteomics, and identification of novel organisms. For microorganisms such as bacteriophages, sequencing their DNA can provide key insights into their tropism, infectivity, and virulence. There remains however a critical lack of rapid sequencing techniques with the traditional process of replating and incubating individual plaques, collecting lysate, extracting DNA, preparing the DNA library, and sequencing that is labor intensive. Herein, we demonstrate the use of an adapted Nanopore Rapid PCR Barcoding protocol to sequence bacteriophage genomes via tagmentation and PCR amplification of crude plaque material, bypassing classical phage amplification, filtration and DNA extraction. When applied to our phage collection, this technique provided genome assemblies with 99.88-100% (mean 99.97%) average nucleotide identity (ANI) scores when compared to the traditional methods involving phage amplification, extraction, and sequencing using Illumina. This PCR-based approach is however not suitable for studying phage DNA modifications, akin to sequencing by synthesis, although developed for Oxford Nanopore Technologies sequencing which traditionally allows for interrogation modified bases. The optimization of bacteriophage identification by the technique of tagmentation directly to isolated plaques can enable same-day plaque-to-sequence workflows for novel phages, as demonstrated here in a proof-of-concept evaluation of 14 plaque genomes.},
}

@article {pmid42241193,
year = {2026},
author = {Khan, N and Mishra, AK and Das, A},
title = {DNA barcoding and mitochondrial genetic diversity of mosquito vectors from central India.},
journal = {Journal of vector borne diseases},
volume = {},
number = {},
pages = {},
doi = {10.4103/jvbd.jvbd_52_26},
pmid = {42241193},
issn = {0972-9062},
abstract = {BACKGROUND OBJECTIVES: Accurate discrimination of mosquito vectors is essential for entomological surveillance in India, where multiple Anopheles, Aedes and Culex species transmit malaria, lymphatic filariasis and arboviral diseases. However, routine species identifications are challenged by cryptic and morphologically similar taxa. Furthermore, population genetic information of major mosquito vectors remains elusive.

METHODS: A total of 265 adult mosquitoes representing 21 species from four mosquito genera and one non-mosquito dipteran genus (Chironomus) used as an outgroup, were collected from indoor and outdoor resting habitats in selected districts of Madhya Pradesh and Chhattisgarh. Mosquitoes were identified morphologically using standard keys and a mobile identification application. Subsets of specimens representing major genera and putative vector and non-vector taxa were subjected to PCR amplification and sequencing of the cox1 and ITS2 genes that are known to be genetic barcodes for mosquitoes. DNA sequences of these two genes were analyzed for inter- and intra-specific divergence, and phylogenetic clustering and genetic diversity.

RESULTS: The cox1 marker showed 100% amplification success and reliably separated most species and genera, although it failed to fully resolve certain closely related taxa, particularly within Anopheles and culicine groups. In contrast, ITS2 amplification success was lower (~50%) but provided complementary resolution for selected species complexes that clarified ambiguous morphological assignments and improved discrimination of selected species complexes in combination with cox1 . Phylogenetic analyses recovered largely congruent species-level clustering across both markers, highlighting both the strengths and limitations of each marker for operational surveillance. Furthermore, mitochondrial diversity analyses revealed high haplotype diversity in Anopheles species with limited genetic differentiation between populations, suggesting weak population structure.

INTERPRETATION CONCLUSION: The combined use of morphology with cox1 and ITS2 sequencing enhances species identification and phylogenetic resolution in diverse mosquito vectors. While cox1 serves as a robust primary barcode for routine surveillance, ITS2 provides additional resolution for cryptic taxa., However, population genetic inferences based on mitochondrial data alone should be interpreted cautiously. These findings support the strengthening of molecularly informed vector surveillance pipelines and backup more precise, evidence-based vector control in endemic settings.},
}

@article {pmid42241959,
year = {2026},
author = {Shin, J and Cho, J and Shin, Y and Kim, H and Heo, C},
title = {Selection and qualification of standard test organisms for BWMS type-approval testing.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108172},
doi = {10.1016/j.marenvres.2026.108172},
pmid = {42241959},
issn = {1879-0291},
abstract = {Seasonal and regional variability of natural plankton assemblages can constrain biological validity in BWMS land-based type-approval testing, particularly when challenge-water concentrations fall below regulatory requirements. This study proposes an evidence-based workflow to select and qualify standard test organisms (STOs) for the ≥10 μm to <50 μm and ≥50 μm size classes. Survivor records from full-scale type-approval tests were first used to prioritize taxa that persist through treatment and subsequent handling. Four candidates were finalized: two centric diatoms for the ≥10 μm to <50 μm class (Stephanocyclus meneghinianus and Actinocyclus sp.) and two zooplankton for the ≥50 μm class (Moina macrocopa and Tigriopus sp.). Taxonomic assignments were supported by DNA barcoding, and regulatory compliance was evaluated using minimum-dimension measurements under practical microscopy views. All candidates consistently satisfied the relevant size thresholds. Operational feasibility was assessed through routine maintenance, showing stable culture growth for diatoms (OD750) and maintained or increasing total abundance for zooplankton. Control-holding performance under test-relevant conditions was examined during short-term dark holding across freshwater, brackish, and marine waters over the protocol temperature range (5-35 °C) for up to 5 days. The ≥10 μm to <50 μm candidates remained above the minimum required concentration throughout the holding period, whereas the ≥50 μm candidates were more sensitive under extreme conditions but remained viable under typical holding durations and non-extreme temperatures. Collectively, the finalized candidates provide practical STO options that combine size compliance, routine maintainability, and control-holding validity for reproducible challenge-water preparation in land-based type-approval testing.},
}

@article {pmid42242218,
year = {2026},
author = {Kim, H and Xu, C and Washington, C and Shi, C and Lowman, M and Kebschull, JM},
title = {POINTseq: Cell-type-specific barcoding reveals single-cell projection architecture of the mouse dopaminergic system.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2026.05.005},
pmid = {42242218},
issn = {1097-4199},
abstract = {Neural circuits are shaped by the diverse axonal branching patterns of neurons across different cell types. To map these patterns, here we introduce POINTseq (projections of interest by sequencing), a barcoded connectomics method for rapid, cell-type-specific mapping of thousands of single-cell projections per animal. POINTseq leverages viral pseudotyping and cell-type-specific infection to integrate MAPseq-style high-throughput barcoded projection mapping with the established viral-genetic neural circuit analysis toolbox. We validated POINTseq by mapping genetically and projection-defined cell populations in the mouse motor cortex. We then used POINTseq to reconstruct the brain-wide projections of 5,902 individual dopaminergic neurons in the ventral tegmental area (VTA) and substantia nigra pars compacta (SNc). These neurons fall into >25 connectomic cell types, vastly exceeding the known diversity of dopaminergic cells, and form stereotyped projection motifs that may mediate parallel dopamine signaling. These data constitute the anatomical substrate on which the diverse functions of dopamine in the brain are built.},
}

@article {pmid42242343,
year = {2026},
author = {Cabrera, A and Lee, TD and Yao, AY and Tyson, J and Kolehmainen, K and Singh, I and Cheung, M and Lee, MK and Su, LD and Chahil, N and Tsang, F and Iwasawa, S and Stewart, Q and Fraser, E and Snyman, LP and Prystajecky, N and Savage, J and Morshed, MG and Hogan, CA},
title = {Comparative Diagnostic Evaluation of Microscopy and Targeted Next-generation Sequencing of the Barcoding Gene Cytochrome oxidase subunit I for Tick Identification in British Columbia, 2021-2023.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104897},
doi = {10.1016/j.ijpara.2026.104897},
pmid = {42242343},
issn = {1879-0135},
abstract = {Tick surveillance protocols in public health laboratories have traditionally relied on microscopy for species identification. However, recognition of emerging species with overlapping morphology, loss of expertise, and new technologies have highlighted the need for complementary testing approaches. We performed a comparative diagnostic evaluation assessing accuracy of next-generation sequencing targeting the barcoding portion of cytochrome oxidase subunit I (COI) against traditional microscopy for tick identification. A total of 306 Dermacentor and Ixodes ticks were included in the study. Overall agreement between the methods was >90%. Molecular testing highlighted the challenges with identifying ticks to the species level by morphology alone, especially for rare and/or emerging species. Molecular testing proved useful as a quality assurance tool for microscopy and highlighted the need for targeted continuing education to strengthen morphological analysis expertise. Finally, the COI NGS workflow demonstrated feasibility for integration into routine laboratory sequencing workflows. Our findings support the utility of COI sequencing as a complementary diagnostic approach in reference laboratories where tick identification and surveillance are performed.},
}

@article {pmid41965426,
year = {2026},
author = {Montes-Ortiz, L and Mis Avila, PC and Zawal, A and Elías-Gutíerrez, M and Martínez-Burgos, M and Canto-Mis, KL and Gómez-Rivera, ÁS and Morales, FC and Poot Haw, ME and Śmietana, P},
title = {Water mite larvae (Hydrachnidia, Arrenurus) parasitism of Anopheles albimanus and An. vestitipennis in a Mexican Neotropical region, including parasite descriptions.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41965426},
issn = {2045-2322},
support = {RID/SP/0045/2024/01//Minister of Science under the "Regional Excellence Initiative" Program for 2024-2027/ ; },
abstract = {Parasitic interactions between water mite larvae (Acari: Hydrachnidia) and mosquitoes (Diptera: Culicidae) remain poorly understood, especially in the Neotropical region. Given the medical significance of mosquito hosts, this ecological relationship has garnered attention for its potential to contribute to natural population regulation and influence mosquito vectorial capacity. However, accurate species identification is essential to deepen our understanding of this interaction. In this study, a total of 565 female Anopheles albimanus and 216 Anopheles vestitipennis were collected in Quintana Roo, Mexico, as part of vector-borne disease prevention and control activities. A total of 26 water mite larvae were recorded, from the 21 parasitized mosquitoes, yielding a prevalence of 2.83% in An. albimanus and 2.31% in An. vestitipennis. To identify the mite specimens, we employed a combination of morphological analysis using scanning electron microscopy (SEM) and DNA barcoding, leveraging previously constructed DNA libraries from the region. The water mites were identified as Arrenurus sp. and Arrenurus federicoi. This study represents the first record of these mosquito species being parasitized by water mites in the Neotropical region. Furthermore, it is the first to employ a multifaceted approach, incorporating both DNA analysis and morphology, to accurately identify both the mosquito host and the parasitic water mite larva.},
}

@article {pmid42229351,
year = {2026},
author = {Xiong, W and Zhang, J and Zhai, X and Ma, J and Chen, Z and Gao, Y and Wang, F and Li, H and Huang, X and Chen, Y and Zhou, K and Zhan, A},
title = {Nursery pressures in megacities: Interplay of anthropogenic disturbance and natural drivers in shaping ichthyoplankton community dynamics in urbanized coasts.},
journal = {Journal of environmental management},
volume = {410},
number = {},
pages = {130101},
doi = {10.1016/j.jenvman.2026.130101},
pmid = {42229351},
issn = {1095-8630},
abstract = {Coastal ecosystems worldwide are increasingly exposed to multiple pressures driven by rapid urbanization and global change. These interacting stressors can significantly alter key ecological processes and ecosystem functioning. However, their effects on ecologically and economically important early-life fish assemblages (i.e., ichthyoplankton) remain insufficiently understood in highly urbanized coastal zones. Improving our understanding of how multiple stressors influence ichthyoplankton diversity is therefore critical for advancing ecosystem-based conservation and management strategies. Here, we combined seasonal field surveys with DNA barcoding to resolve the spatiotemporal dynamics and environmental drivers of fish eggs and larvae across four coastal zones in the Guangdong-Hong Kong-Macao Greater Bay Area. From over 150,000 individuals, we identified 74 egg and 71 larval taxa, revealing exceptionally high β-diversity (βjac > 0.95) dominated by species turnover. Shenzhen Bay and the Pearl River Estuary supported consistently high egg and larval abundance and were identified as key nursery hotspots, despite that community composition exhibited strong seasonal shifts. Multivariate modeling and variance partitioning showed that nutrient-related and organic-pollution-related water-quality gradients were significantly associated with ichthyoplankton community variation, along with spatial and seasonal factors. Structural equation models further indicated that nutrient-related gradients were negatively associated with local β-diversity, potentially reflecting reduced community distinctiveness under nutrient-enriched conditions. Interestingly, eggs and larvae showed stage-specific environmental sensitivities: egg assemblages were mainly shaped by depth, salinity, and phosphate, whereas larvae responded strongly to temperature, nitrate and nitrite, and petroleum hydrocarbons. Collectively, our findings demonstrate that nutrient enrichment and organic loading are key environmental drivers shaping ichthyoplankton community variation in coastal nursery habitats adjacent to megacities. These results underscore the importance of integrating nutrient and organic-pollution management with nursery-habitat protection to enhance fish recruitment success and conserve biodiversity in the face of accelerating urbanization.},
}

@article {pmid42232583,
year = {2026},
author = {Masango, N and Dos Santos, QM and Avenant-Oldewage, A},
title = {Taxonomic revision of Rhabdochona (Rhabdochona) esseniae Mashego, 1990 and Rhabdochona (Rhabdochona) gendrei Campana-Rouget, 1961 in Labeobarbus spp. from the Vaal River, South Africa.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {30},
number = {},
pages = {101233},
pmid = {42232583},
issn = {2213-2244},
abstract = {During standard parasitological surveys in the Vaal River, South Africa, nematodes were collected from Labeobarbus aeneus (Burchell, 1822) and Labeobarbus kimberleyensis (Gilchrist and Thompson, 1913). No adult nematodes had been reported from these fishes before; thus, the specimens were studied using integrated taxonomic approaches to identify them. This involved combining light microscopy (LM), scanning electron microscopy (SEM), genetic characterisation (18S rDNA, 28S rDNA, and CO1 mtDNA), and multivariate statistical analyses, applying several of these approaches to the same specimen to obtain more holistic information. Two morphotypes were observed and identified as Rhabdochona (Rhabdochona) esseniae Mashego, 1990 and Rhabdochona (Rhabdochona) gendrei Campana-Rouget, 1961. These taxa could be distinguished using several morphological characteristics, some of which have not been previously reported for these species. These included morphology of the vagina, sublabia, mucron, and eggs (revised), which complemented the previously established use of right spicule morphology and left spicule length as characteristic features. Morphological differences between R. (R.) esseniae and R. (R.) gendrei were supported by distinct haplotypes for all gene regions utilised, confirmed through integrated approaches and hologenophore material. Additionally, deirids are reported for the first time for R. (R.) esseniae. Both nematode species were collected from L. aeneus and L. kimberleyensis, with co-infections also observed, representing new host and locality (Vaal-Orange River system) records for R. (R.) esseniae and R. (R.) gendrei. As mixed infections were recorded in both host fishes, and reanalysis of the R. (R.) esseniae type series revealed that a male paratype represented R. (R.) gendrei, the diligent revision of rhabdochonids in Africa is advised. The use of integrative taxonomy, as implemented here, with the same specimen used for microscopy (SEM and LM) and genetic characterisation, was crucial for differentiating taxa and identifying diagnostic morphology in this study and should be considered in future studies of Rhabdochona spp.},
}