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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid41584737,
year = {2026},
author = {Suh, H and Seo, CW and Park, KH and Yoo, S and Kim, D and Cho, Y and Lim, YW},
title = {Hidden diversity of crust-like Sebacinaceae (Sebacinales, Agaricomycetes) in Asia.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e168486},
pmid = {41584737},
issn = {2210-6340},
abstract = {Crust-like Sebacinaceae, comprising the genera Helvellosebacina, Sebacina, and Tremelloscypha, represent the only ectomycorrhizal lineage within the Sebacinaceae family. However, species delimitation within this group remains challenging because of their cryptic lifestyles, inconspicuous morphological traits, and limited taxonomic annotation. To address these limitations, we investigated crust-like Sebacinaceae in Asia by integrating two datasets: specimen-derived (barcoding) sequence data and root-associated metabarcoding data. A high diversity of crust-like Sebacinaceae species was uncovered, most of which did not match any previously described taxa. Multigene phylogenetic analyses (ITS, LSU, and rpb2) based on basidiomata identified eleven distinct species, of which six are proposed here as new to science. In parallel, metabarcoding data revealed additional crust-like Sebacinaceae species and confirmed their ectomycorrhizal association with Pinus and Quercus species. These findings advance our understanding of crust-like Sebacinaceae diversity and ecology in previously unexplored regions.},
}

@article {pmid41579861,
year = {2026},
author = {Wang, J and Suh, JM and Woo, BJ and Navickas, A and Garcia, K and Yin, K and Fish, L and Cavazos, T and Hänisch, B and Markett, D and Hirst, GL and Brown-Swigart, L and Esserman, LJ and van 't Veer, LJ and Goodarzi, H},
title = {Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102577},
doi = {10.1016/j.xcrm.2025.102577},
pmid = {41579861},
issn = {2666-3791},
abstract = {From extrachromosomal DNA to neo-peptides, reprogramming of cancer genomes leads to the emergence of cancer state-specific molecules. Here, we systematically identify and characterize a large repertoire of orphan non-coding RNAs (oncRNAs), a class of cancer-emergent small RNAs, across 32 tumor types. We show that oncRNA binary presence-absence patterns represent a digital molecular barcode that captures cancer type and subtype identities. Importantly, this barcode is partially accessible from the cell-free space as cancer cells secrete a subset of oncRNAs. Leveraging large-scale in vivo genetic screens in xenografted mice, we functionally identify driver oncRNAs in multiple tumor types. In a retrospective study across 192 breast cancer patients, we show that oncRNAs are reliably detected in blood and that changes in cell-free oncRNA burden predict both short-term and long-term clinical outcomes. Together, we establish that oncRNAs have potential roles in tumor progression and clinical utility in liquid biopsies for tumor-naive minimum residual disease monitoring.},
}

@article {pmid41578609,
year = {2026},
author = {Zhao, B and Andermann, T},
title = {Properties and Limitations of eDNA Substrates for Terrestrial Animal Monitoring.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70096},
pmid = {41578609},
issn = {1755-0998},
support = {2023-05366//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab & Wallenberg Data Driven Life Science Program/ ; },
mesh = {Animals ; *DNA, Environmental/genetics/isolation & purification ; *Environmental Monitoring/methods ; *Biodiversity ; },
abstract = {Environmental DNA (eDNA) constitutes a valuable tool for monitoring terrestrial animal diversity, but outcomes are affected by multiple factors. Among these factors, the choice of sampling substrate and method is especially important and must be aligned with research objectives. We reviewed 245 published studies that utilise eDNA for terrestrial animal monitoring and compiled an overview of the most frequently used environmental substrates. Based on the reviewed literature, we provide a key description of each substrate, as well as its particular properties and limitations related to the detection of animal species across different spatial and temporal scales. We categorise these substrates into three groups: abiotic substrates (soil, water, air, sediment), biotic substrates (invertebrate samples, plant tissues, spiderwebs) and direct-evidence substrates (scat, footprints, shelters, feeding sites). In addition, we identify several key challenges with the interpretation of eDNA-based biodiversity monitoring, including false negatives and false positives, as well as the dynamics of spatial and temporal deviations. The latter concepts, which we propose and define in this review, describe the temporal and spatial discrepancies between the DNA source and its detection in a given sample. We reflect on how these temporal and spatial deviations are expected to affect eDNA data extracted from the different types of substrates and how knowledge of these dynamics can inform effective and accurate biomonitoring. In summary, this review provides a decision basis for designing terrestrial eDNA monitoring studies by summarising the properties and limitations of different substrates and contextualising the interpretation of results in light of substrate-specific challenges.},
}

Animals
*DNA, Environmental/genetics/isolation & purification
*Environmental Monitoring/methods
*Biodiversity

@article {pmid41577483,
year = {2026},
author = {Betts, MM and Hultin, EA and Hallerman, EM and Maurakis, EG and Frimpong, EA},
title = {Embryonic selfish-herding blurs the line between brood parasitism and mutualism for communal-breeding stream fishes.},
journal = {Ecology},
volume = {107},
number = {1},
pages = {e70302},
doi = {10.1002/ecy.70302},
pmid = {41577483},
issn = {1939-9170},
support = {2039692//National Science Foundation/ ; //National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Symbiosis ; *Nesting Behavior/physiology ; Reproduction/physiology ; *Cyprinidae/physiology/embryology ; *Embryo, Nonmammalian/physiology ; Rivers ; Female ; Male ; },
abstract = {Mutualisms are complex, interspecific relationships, which sometimes create "selfish-herds" as individuals of each species compete to maximize their own fitness. Nest association, where individuals of different species spawn on a nest created by a host species, is a reproductive interaction characteristic of some minnows (Leuciscidae) and is considered mutualistic despite mimicking the behavior labeled "brood parasitism." We studied the spawning behaviors of bluehead chub (Nocomis leptocephalus) and its nest associates, testing the hypothesis that bluehead chub exploits the selfish-herd dynamic in a novel manner by arranging embryos within its nest to maximize the survival of its own offspring at the expense of the nest associates' offspring. Our results show that embryos were not uniformly distributed within a nest, as one section representing one-sixth of the nest's total volume contained a disproportionate percentage of embryos (x¯ = 40.0% ± 6.1% SE). We found three-quarters of host embryos within deeper nest sections safer from embryo predators, whereas only a third of all associate embryos were found in the same sections. These results support our hypothesis that male Nocomis leptocephalus create "embryonic selfish-herds" within their nests. This is the first study to document the existence of embryonic selfish-herds, a phenomenon that warrants the reexamination of some vertebrate reproductive interactions labeled as brood parasitism.},
}

Animals
*Symbiosis
*Nesting Behavior/physiology
Reproduction/physiology
*Cyprinidae/physiology/embryology
*Embryo, Nonmammalian/physiology
Rivers
Female
Male

@article {pmid41574122,
year = {2026},
author = {Asiri, MMA and Ali, MA and Alwahibi, MS and Ahmed, SS and Rahman, MO and Mahato, R and Faisal, M and Kim, SY and Lee, J},
title = {The First Complete Chloroplast Genome of Lycium shawii: Genomic Architecture, Molecular Phylogenetics and Evolutionary Insights.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72972},
pmid = {41574122},
issn = {2045-7758},
abstract = {Lycium shawii Roem. & Schult., a stress-resilient medicinal plant native to the deserts of Saudi Arabia, possesses notable bioactive compounds used in traditional medicine for treating inflammation, oxidative stress, and other ailments. However, its chloroplast (Cp) genome has not previously been sequenced or described, limiting accurate molecular identification and phylogenetic resolution. In this study, we present the first complete Cp genome of L. shawii. The plastome spans 155,936 bp and is organized into a large single-copy (LSC) region (86,608 bp), a small single-copy (SSC) region (18,430 bp), and two inverted repeats regions (IRA and IRB), each spanning 25,449 bp. A total of 128 genes were annotated, comprising 84 protein-coding genes, 36 tRNAs, and eight rRNAs. Comparative genomic analyses revealed conservation of genome structure without major rearrangements across Solanaceae. Forty simple sequence repeats (SSRs) and 50 oligonucleotide repeats were identified, with mononucleotides (38) as the dominant SSR type, and forward repeats as the most common among longer repeats. RNA-editing sites were unevenly distributed, with the highest proportion in the LSC region (48%), followed by the SSC (29%) and IRs (23%). Nucleotide diversity analysis highlighted atpI, rbcL, and accD within the LSC region as hypervariable loci suitable for DNA barcoding. Plastome-wide phylogenetic reconstruction confirmed the placement of L. shawii within the tribe Lycieae of the subfamily Solanoideae. Molecular dating analysis suggested its emergence around 1.40 MYA, during the Calabrian stage of the Cenozoic era. This study provides the first Cp genome resource for L. shawii, offering new perspectives for evolutionary and comparative genomics within Solanaceae.},
}

@article {pmid41568947,
year = {2026},
author = {Robino, E and Perret, A and Noel, C and Haffner, P and Intertaglia, L and Richard, M and Descamps, N and Sellier, A and Onillon, L and Lebaron, P and Destoumieux-Garzón, D and Charrière, GM},
title = {Diversity and varying predation capacities of culturable Amoebozoae against opportunistic vibrios in contrasting Mediterranean coastal environments.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0113825},
doi = {10.1128/spectrum.01138-25},
pmid = {41568947},
issn = {2165-0497},
abstract = {Free-living amoebae (FLA) are ubiquitous and can be found in many environments including soil, freshwater, and marine environments. They feed on various microorganisms and can play an important role in the food web and its dynamics. We previously described that FLA belonging to the Vannella genus isolated from oyster farms in the Thau lagoon in France are able to establish stable interactions with Vibrionaceae, suggesting they can play a role in pathogen dynamics. To further investigate the ecological interactions between FLA and Vibrionaceae in Mediterranean coastal waters, we conducted monthly sampling for 1 year at three contrasting sites. FLA populations were isolated from water and sediment samples on different bacterial lawns, including Escherichia coli or Vibrio tasmaniensis, Vibrio crassostreae, and Vibrio harveyi. Diversity analysis by v4-18S barcoding revealed distinct communities between fractions and sites. The Vannellidae were found significantly enriched in the water, whereas Paramoebidae were found enriched in the sediments. Additionally, uneven distribution of Vexilliferidae, Vermistellae, and, to a lesser extent, Acanthamoebidae and Subulatomonas contrasted between sampling sites. Selection of grazers on different bacterial lawns revealed that V. tasmaniensis inhibits the growth of most Vannellidae, whereas V. crassostreae inhibits the growth of Paramoebidae. These differences were further confirmed functionally using isolates belonging to each Amoebozoa taxonomic group. Overall, our results highlight the need for more comprehensive studies of the diversity and population dynamics of Amoebozoa in marine environments and indicate that the role of these diversified grazers in shaping Vibrio communities is complex and still poorly characterized.IMPORTANCEAlthough they can play an important role in shaping bacterial communities and as intracellular niches for potential pathogens, the diversity and ecology of free-living amoebae (FLA) in marine environments are still poorly characterized. Very few studies have used systematic approaches to unravel the population dynamics and ecological variations of FLA in different environments. Our study in marine coastal environments highlights that FLA taxonomic groups can harbor habitat preferences and have different predation capacities, suggesting that FLA-bacteria interactions need to be considered at different taxonomic levels to uncover generalist versus specialist adaptations.},
}

@article {pmid41568902,
year = {2026},
author = {Li, H and Dong, Q and Guo, J and Hu, E and Li, Y and Shan, R and Zhang, L and Zhao, D and Guo, H and Qian, G},
title = {A Smart-Perception Rare Earth MOF.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e21289},
doi = {10.1002/adma.202521289},
pmid = {41568902},
issn = {1521-4095},
support = {52302200//National Natural Science Foundation of China/ ; 52402206//National Natural Science Foundation of China/ ; 12574443//National Natural Science Foundation of China/ ; 52472173//National Natural Science Foundation of China/ ; LQ23E020004//Natural Science Foundation of Zhejiang Province/ ; LQN25E020013//Natural Science Foundation of Zhejiang Province/ ; 2024-3-029//Key Projects of Jinhua Science and Technology Burea/ ; },
abstract = {Smart responsive luminescent materials have attracted considerable scientific and technological interest owing to their broad optoelectronic applications. However, issues such as single responsive mode, inadequate spectral coverage, and poor environmental adaptability still hinder their diversified development. Herein, we propose the concept of smart multi-stimuli responsive scintillator (SMRS) and fabricate a new series of rare earth metal-organic frameworks (RE-MOFs) with active and passive perception capabilities. Such RE-MOFs exhibit excellent scintillation performances, including high relative light yield (max ∼ 42,200 photons MeV[-1]), low dose rate detection limit (min ∼ 128.2 nGyair s[-1]), and great photostability. Systematic modulation of RE[3+] contents endows MOFs with tunable broadband luminescence, thereby ensuring the passive perception. The distinct photo- and radio-luminescent mechanisms lead to significant spectral contrasts under UV and X-ray irradiation. Furthermore, RE-MOFs demonstrate thermal-stimuli responsive luminescent variation since heat will influence the energy transfer processing among the organic and inorganic units. As a result, RE-MOFs autonomously produce active luminescent perception toward both irradiation and thermal stimuli. These SMRSs exhibit great potential in in situ optical imaging and high-security photonic barcodes (the widest spectral range among MOFs for photonic encoding). This study establishes a new paradigm for smart MOF-based scintillators for an advanced intelligent perception system.},
}

@article {pmid41568360,
year = {2026},
author = {Hupało, K and Sassor, C and Fuhren, MM and Buchner, D and Grabner, D and Sures, B},
title = {Assessing whole-host homogenisation as a new tool for parasite detection and identification.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {9},
number = {},
pages = {100348},
pmid = {41568360},
issn = {2667-114X},
abstract = {Despite their importance in ecosystem functioning, parasites remain the most neglected components of biodiversity monitoring. This neglect is partly due to the methodological challenges associated with their detection and identification. Current traditional morphological and molecular approaches are time-consuming, labour-intensive, and require specialised expertise. Here, we explore a novel approach of deriving parasite information through whole-host homogenisation followed by DNA-based identification of its parasite biota. Our goal was to validate whether the approach is feasible and if it could become a complementary method for studying parasites, providing a time-efficient solution allowing for a holistic parasite scan with limited taxonomic expertise. To test the method's efficiency, we analysed five specimens of European eel as model hosts. Their parasites were identified morphologically, and then all the parasites and the entire host tissue were homogenised together using a commercial blender. Molecular identification of the morphologically detected parasites was conducted using DNA barcoding with parasite-specific primers. Following homogenisation and DNA-based identification, we successfully detected all parasite taxa identified during morphological analyses, even including instances where they had not been detected morphologically. A notable exception were acanthocephalans, which showed low levels of molecular detection. Despite certain limitations, the detection of parasites directly from the whole-host homogenate shows high potential for efficient and accurate parasite detection, in some cases even surpassing morphological identification. The further development of the method, particularly through exploration of DNA metabarcoding, could improve the reliability of parasite assessments and facilitate parasite detection, which could aid in proper parasite recognition.},
}

@article {pmid41568027,
year = {2026},
author = {Fusari, LM and Höcherl, A and Chimeno, C and Baranov, V},
title = {A new species and record of Xestochironomus Sublette & Wirth, 1972 (Diptera, Chironomidae) from the Dominican Republic, with males and females associated by DNA barcode.},
journal = {ZooKeys},
volume = {1266},
number = {},
pages = {219-230},
pmid = {41568027},
issn = {1313-2989},
abstract = {We describe a new species of Xestochironomus Sublette & Wirth, 1972 and provide notes on X. luteifurcatus Sublette & Wirth, 1972 from the Dominican Republic. The adult male and female of Xestochironomus digitulus sp. nov. are also described and illustrated. The male and female of X. luteifurcatus are redescribed. Males of the new species can be easily distinguished from congeners by the following combination of characters: the abdomen of both sexes bears cross bands; the anal point is long, slender; the male gonostylus has a slightly bifurcated apex; and there is a thumb-like lobe at the apex of the gonostylus.},
}

@article {pmid41566400,
year = {2026},
author = {Jiang, WJ and Cai, K and Sun, Y and Liu, A and Zhu, H and Gao, R and Zhong, C and Wei, N and Lai, F and Fei, T and Wang, YJ and Zheng, X and Xu, M and Wu, HJ},
title = {Harmonizing single-cell 3D genome data with STARK and scNucleome.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03938-x},
pmid = {41566400},
issn = {1474-760X},
abstract = {Single-cell three-dimensional genome sequencing (sc3DG-seq) reveals genome regulation and heterogeneity in various biological processes, but a universal analysis tool is lacking. Here we present STARK, a versatile toolkit for processing, quality control, and analysis of diverse sc3DG-seq data. Utilizing STARK, we benchmark 15 technologies, quantitatively comparing their strengths and limitations. We also develop EmptyCells to filter empty barcodes and introduce Spatial Structure Capture Efficiency (SSCE) to assess chromatin structure capture quality. Additionally, we establish scNucleome, a uniformly processed repository of sc3DG-seq datasets, to serve as a foundational resource for future 3D genome research.},
}

@article {pmid41565766,
year = {2026},
author = {Wu, B and Yang, X and Cai, Y and Wan, S and Liu, J and Xing, J and Chen, X and Zhang, J and Jin, Y and Yu, A and Yang, L},
title = {Proteomic profiling of single extracellular vesicles as a promising new approach for the diagnosis and treatment modality of advanced ovarian cancer.},
journal = {NPJ precision oncology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41698-026-01271-x},
pmid = {41565766},
issn = {2397-768X},
support = {82274266//National Natural Science Foundation of China/ ; 82505319//National Natural Science Foundation of China/ ; 2026ZL0202//The Traditional Chinese Medicine Science and Technology Project of Zhejiang Province/ ; },
abstract = {This study utilized a novel Proximity Barcoding Assay to perform high-resolution proteomic profiling of individual plasma extracellular vesicles from 85 patients with advanced high-grade serous ovarian carcinoma (OC) and 95 healthy controls (HC). Single-EV analysis identified 119 differentially expressed proteins and 17 distinct EV subpopulations. Cluster 7 (enriched in integrins ITGB3, ITGB1, and ITGA6) was significantly elevated in OC plasma (4.47% in HC vs. 14.79-15.82% in OC). Machine learning (SVM-RFE, LASSO, Random Forest) identified a diagnostic panel (ITGA6, ITGB2, ILK) achieving exceptional accuracy in distinguishing OC from HC (AUC = 0.999 training; 1.000 validation). Furthermore, risk models incorporating specific protein signatures effectively stratified patients by platinum sensitivity/resistance (9-protein panel: ILK, CDCP1, CD86, CLDN4, CLEC1B, CDHR5, CLDN11, JAM2, FOLH1), lymph node metastasis status (7-protein panel: APOE, CD28, CLDN4, FOLH1, ITGAL, JAML, ULBP3), and post-surgical residual disease burden (4-protein panel: CD44, CLMP, ITGA4, AMIGO1), with Cluster 13 (ITGB1-high) also significantly associated with residual disease. This work demonstrates the power of single-EV proteomics combined with machine learning for non-invasive diagnosis and clinical outcome assessment in advanced ovarian cancer, though the absence of early-stage patients limits its applicability for early detection.},
}

@article {pmid41563521,
year = {2026},
author = {Dela Cruz, JWR and Malit, EPB and Patanindagat, CY and Arevalo, CFL and Manalo, AJI and Boongaling, DDG and Ramos, JDA},
title = {Electron microscopy and molecular phylogenetic characterization of the allergenic dust mite species Suidasia pontifica (Acari: Suidasiidae).},
journal = {Experimental & applied acarology},
volume = {96},
number = {2},
pages = {12},
pmid = {41563521},
issn = {1572-9702},
mesh = {Animals ; Female ; Male ; Allergens ; Arthropod Proteins/genetics ; Electron Transport Complex IV/genetics ; *Microscopy, Electron ; Philippines ; *Phylogeny ; *Pyroglyphidae/classification/genetics ; },
abstract = {The clinical significance of house dust mites (HDMs) as sources of allergens for medical diagnostics, allergen-specific immunotherapy, and allergology research is dependent on accurate morphological and molecular data analysis for species identification and characterization. Here, we report the species identification and allergenicity of a tropical HDM, Suidasia pontifica (Sp), via morphological-molecular characterization tandem and IgE ELISA, respectively. Electron microscopy of monocultures of HDM samples collected from Laguna, Philippines, revealed different traits related to chaetotaxy, cuticle pattern, and body anatomy. Genus-specific characters such as the length of the scapular setae, cuticle patterns, vertical setae, ω1 setae, along with species-specific traits such as short dorsal setae, long h3 setae, average c1 to c1 verrucae count, presence of sclerotized bursa copulatrix (female), and c3 setae size, suggest that the sample identity is Sp. In addition, PCR amplification from the HDM monoculture genomic DNA and bidirectional sequencing of the 18S and COI gene markers were performed. Sequences were subjected to sequence assembly, consensus acquisition, sequence alignment, and phylogenetic inference. The COI gene showed an exact match and phylogenetic attachment of the sample assembly to Sp, confirming the species-level identification, corroborated with morphological data. Furthermore, 18S gene character analysis was able to prove phylogenetic demarcation of the Sp 18S gene from the sister species S. nesbitti and other allergenic sarcoptiform species. Our molecular phylogenetic analysis, which is strongly supported by electron microscopy data, indicates the identity of our monocultures as Sp. Interestingly, the Sp allergenicity profile of allergic patients and controls (n = 200) suggests 47% IgE-binding reactivity, confirming its allergenicity and clinical importance among atopic patients. This study emphasizes the resolving power of the morphological-molecular phylogenetic approach and IgE-reactivity to objectively verify Sp species identity and allergenicity for downstream immunological studies.},
}

Animals
Female
Male
Allergens
Arthropod Proteins/genetics
Electron Transport Complex IV/genetics
*Microscopy, Electron
Philippines
*Phylogeny
*Pyroglyphidae/classification/genetics

@article {pmid41562469,
year = {2026},
author = {Wan, Z and Xu, C and Wang, Y and Song, L and Yuan, W and Chen, M and Gong, R and Zhang, XE},
title = {An AND-Logic Gate-Based Biosensor for Simultaneous Detection of SARS-CoV-2 Nucleic Acids and Nucleocapsid Proteins.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c07321},
pmid = {41562469},
issn = {1520-6882},
abstract = {Nucleic acids and proteins are recognized as gold standard biomarkers for disease diagnosis and pathogen detection. However, conventional single-analyte detection methods remain susceptible to false positives caused by manual operational errors or sample contamination, thereby undermining diagnostic reliability and increasing the burden on healthcare systems. To address this limitation, we developed a one-pot isothermal amplification and CRISPR-Cas cooperative system (OIACS) that functions as an AND-logic gate biosensor for the simultaneous detection of SARS-CoV-2 RNA and nucleocapsid protein. Unlike conventional methods relying solely on CRISPR RNA (crRNA) recognition, the OIACS employs antibody-mediated target binding with blocker release for target recognition, offering increased flexibility in assay design for different targets. A universal Cas12a-targetable DNA barcode is generated via strand displacement isothermal amplification, enabling signal amplification upon dual-target recognition. The OIACS assay exhibited practical utility by reliably detecting SARS-CoV-2 transcription- and replication-competent virus-like-particles at 5000 copies/mL, and the limit of detection was determined to be as low as 1698 copies/mL, highlighting its robustness and potential for clinical diagnosis.},
}

@article {pmid41561880,
year = {2025},
author = {Zucco, Z and Cava, S and Bonacci, T and Scalercio, S},
title = {Effectiveness of DNA Barcoding Libraries Boosted through Taxonomy: the Case of a Neglected Taxon within an Underexplored Region.},
journal = {Zoological studies},
volume = {64},
number = {},
pages = {e49},
pmid = {41561880},
issn = {1810-522X},
abstract = {In recent decades, taxonomy has been significantly improved by integrating molecular techniques with classical morphological methods, leading to the discovery of cryptic species. On the other hand, molecular datasets by themselves are ineffective in several types of research without basic taxonomic studies, as the ecological and biological roles of a given species cannot be determined without an accurate name. DNA barcoding libraries are widely used as identification tools by non-specialists to overcome the taxonomic impediment, but they fail when basic taxonomic studies are insufficient and faunistic inventories are lacking. South European microlepidoptera are poorly studied, with the exception of a few families such as Depressariidae. We tested the effectiveness of the DNA barcoding library for this family to identify 174 specimens collected in southern Italy, where faunistic studies are very limited. All specimens were successfully barcoded, and 95% of them were assigned to 47 species, 43 of which correspond to a Barcode Index Number (BIN). Four additional species shared a BIN but were still clearly separated into different clusters at within-BIN resolution. Only seven specimens belonging to four BINs remain unnamed, and ad hoc studies are needed to clarify their status. The regional fauna was enriched by 37 species, three of which are new for the Italian mainland and 21 for peninsular Italy, demonstrating the usefulness of the DNA barcoding library in assessing local diversity and overcoming the taxonomic impediment. Improving taxonomic studies is crucial for utilizing molecular datasets to depict ongoing macroecological dynamics, highlight species richness trends, and identify changes in species assemblages.},
}

@article {pmid41560697,
year = {2026},
author = {Xue, Y and Su, J and Chao, Y and Liu, L and Lin, X and Xiang, Y and Ho, MK and Su, Z and Chen, J and Luo, Z and Lin, C and Luo, R and Aurich, T and Wu, J and Cheung, KSC and Huang, Y and Ho, JWK and Sugimura, R},
title = {Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18084},
doi = {10.1002/advs.202518084},
pmid = {41560697},
issn = {2198-3844},
support = {//Hong Kong Research Grant Council/ ; N_HKU731/21//NSFC/RGC Joint Research Scheme/ ; 2023A1515011265//Guangdong Natural Science Fund/ ; SGDX2021082310356025//Shenzhen-Hong Kong-Macau Technology Research Programme/ ; //InnoHK initiative of the Innovation and Technology Commission of the Hong Kong Special Administrative Region Government/ ; },
abstract = {Lineage tracing at single-cell resolution is vital for mapping cell fate decisions, yet synthetic barcoding faces limitations in precision, diversity, and toxicity-especially in human pluripotent stem cells (hPSCs). Here, we repurpose naturally occurring somatic mutations in mitochondrial transcripts from single-cell RNA sequencing as endogenous genetic barcodes. By enriching mitochondrial reads and applying a robust computational pipeline, we identified clonally informative variants to trace hematopoietic lineage emergence from hPSCs during early embryogenesis. Integrating mitochondrial barcoding with synthetic lineage tracing, we modeled embryonic tissue development and reconstructed the transcriptional logic and regulatory networks driving fate specification using a dynamical systems model. Extending this approach to spatial transcriptomics, we mapped the clonal architecture of human embryonic organoids, revealing spatial zonation orchestrated by NOTCH-mediated crosstalk between stromal cells and hematopoietic progenitors. This multimodal strategy links clonal dynamics with niche-driven fate decisions, offering a scalable, non-invasive method to dissect tissue organization in development and disease. Together, our work establishes a scalable, non-invasive multimodal framework that leverages endogenous mitochondrial DNA variants to reconstruct high-resolution spatiotemporal clonal dynamics and decode niche-driven fate decisions in a human stem cell-derived model. This approach provides a powerful strategy for dissecting tissue self-organization in development and disease.},
}

@article {pmid39113372,
year = {2025},
author = {Anbalagan, R and Srivastava, PK and Baruah, K and Krishnan, J},
title = {Insecticide resistance status and bar-coding of dengue vectors in three districts of Tamil Nadu, India.},
journal = {Journal of vector borne diseases},
volume = {62},
number = {1},
pages = {51-59},
doi = {10.4103/JVBD.JVBD_79_24},
pmid = {39113372},
issn = {0972-9062},
mesh = {India/epidemiology ; Animals ; *Insecticide Resistance ; *Aedes/drug effects/genetics/classification ; *Mosquito Vectors/genetics/drug effects/classification ; Phylogeny ; *Insecticides/pharmacology ; Dengue/transmission ; Female ; Malathion/pharmacology ; DDT/pharmacology ; },
abstract = {BACKGROUND OBJECTIVES: Occurrence and distribution of vector population are crucial for entomological study in context of prevention, control and elimination of vector-borne diseases. To update some entomological aspects the study was undertaken in three districts of Tamil Nadu state namely Kumbakonam, Nagapattinam and Thriuvarur. The objective of the study was to understand the prevalence of mosquitoes; to assess insecticide resistance and phylogenetic analysis of dengue vectors (Aedes aegypti and Ae. albopictus).

METHODS: The immature stages of mosquitoes were collected from different localities by standard WHO methods marking with GPS and mapping was done using ArcGIS 10.4 software for all three districts. Insecticide resistance test was conducted using WHO susceptibility test kits. The F1 generation of female adult mosquitoes of Ae. aegypti and Ae. albopictus were exposed to DDT 4% and malathion 5% with the control paper of Risella oil and olive oil, respectively. Further, genomic DNA of individual mosquito was isolated, and sequencing was done through Eurofins, Bangalore, India. The FASTA sequence was analyzed and phylogenic tree was constructed using the Maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software (version 10.0).

RESULTS: A total 5307 specimens were collected through expanded survey in all three study areas. The collection yielded 16 species from six genera of mosquitoes. In total collection, Ae. albopictus was the dominant species in Kumbakonam and Thiruvarur districts and Ae. aegypti was dominant in Nagapattinam. The predominant breeding sources were discarded tyres with rainwater, plastic cups, coconut shells, aluminum vessels, sliver containers, bottles, grinding stones and earthen pots. The study revealed high pupal indices in all three study areas. Insecticide resistance monitoring revealed possible resistance in Ae. aegypti against DDT in all three districts whereas against malathion, possible resistance was recorded in Kumbakonam and Nagapattinam and Thiruvarur district, the species was found to be susceptible. Ae. albopictus showed resistance against DDT in all three districts but susceptible to malathion. The sequences obtained for dengue vectors showed 99% similar with GenBank. The phylogenetic tree was constructed using COI region sequences. Certainly, we observed the different genetic relationship among Ae. aegypti and Ae. albopictus between the study areas.

INTERPRETATION CONCLUSION: The study confirmed the presence of Ae. aegypti and Ae. albopictus in all three districts. The study further revealed that these vectors are susceptible to malathion but resistant to DDT. The continued surveillance of dengue vector and monitoring of insecticide resistance will strengthen the control programme for appropriate vector control measurements.},
}

India/epidemiology
Animals
*Insecticide Resistance
*Aedes/drug effects/genetics/classification
*Mosquito Vectors/genetics/drug effects/classification
Phylogeny
*Insecticides/pharmacology
Dengue/transmission
Female
Malathion/pharmacology
DDT/pharmacology

@article {pmid41559823,
year = {2026},
author = {Harl, J and Himmel, T and Pacheco, MA and Weissenböck, H},
title = {New mitochondrial genomes of parasites belonging to the Leucocytozoon toddi and Haemoproteus nisi groups (Haemosporida, Apicomplexa).},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07244-0},
pmid = {41559823},
issn = {1756-3305},
support = {P37076//FWF Austrian Science Fund/ ; NSF-DEB 2146653//US National Science Foundation/ ; },
abstract = {BACKGROUND: Avian haemosporidians are single-celled eukaryotic parasites of vertebrates that require dipteran vectors for transmission. The genera Plasmodium, Haemoproteus and Leucocytozoon currently comprise over 5000 parasite lineages based on a 478-bp section of the mitochondrial cytochrome b gene, which is the standard DNA barcode for avian haemosporidians. The mitochondrial genomes of apicomplexan parasites are highly condensed, with a length of approximately 6000 bp, containing three coding genes (cytochrome c oxidase subunit I, cytochrome c oxidase subunit III and cytochrome b) and dispersed fragments of the small and large ribosomal RNA (rRNA) genes. Since the mitochondrial genomes are relatively conserved, they are valuable markers for studying the phylogenetic relationships between haemosporidian parasites. However, until recently, mitochondrial genomes were unavailable for parasites of the Haemoproteus nisi and Leucocytozoon toddi species groups, which are exclusive to accipitriform raptors and strongly diverged from other Haemoproteus and Leucocytozoon parasites.

METHODS: We screened 171 accipitriform raptors from Austria and Germany using new primers targeting the cytochrome b gene of a previously neglected L. toddi clade. We also developed a new primer assay that enables the amplification and sequencing of the complete mitochondrial genomes of haemosporidian parasites. This process involved long-range PCRs with lineage-specific primers placed within the cytochrome b gene, followed by five nested PCRs targeting conserved sequence regions.

RESULTS: Screening the accipitriform raptors revealed 10 new L. toddi group lineages. We sequenced 18 mitochondrial genomes belonging to five H. nisi group, nine L. toddi group, and two other Leucocytozoon lineages. Phylogenetic analyses based on mt genome sequences placed the L. toddi lineages within the genus Leucocytozoon, but the results did not support a monophyly of the genus Haemoproteus.

CONCLUSIONS: The new nested PCR approach with lineage-specific primers used for the long-range PCRs described herein successfully enabled the sequencing of the complete mitochondrial genomes, even in samples with mixed infections. The mitochondrial genomes of the H. nisi and L. toddi group lineages are highly valuable for resolving the phylogenetic relationships of the order Haemosporida since these parasites belong to clades distinct from other Haemoproteus and Leucocytozoon parasites.},
}

@article {pmid41555650,
year = {2026},
author = {Han, EL and Kim, D and Murray, AM and Mrksich, K and Hamilton, AG and Tang, S and Yoo, S and Zhu, AT and Tong, ER and Palanki, R and Hall, ML and Bedingfield, SK and Mitchell, MJ},
title = {High-Throughput In Vivo Screening Identifies Structural Factors Driving mRNA Lipid Nanoparticle Delivery to the Brain.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c19138},
pmid = {41555650},
issn = {1936-086X},
abstract = {Achieving systemic nonviral delivery of large nucleic acids such as mRNA to the brain is challenging due to high off-target delivery and the blood-brain barrier (BBB), a cellular barrier which prevents most nucleic acids in circulation from entering the brain. Ionizable lipid nanoparticles (LNPs) are a promising class of nanocarriers to facilitate the delivery of mRNA, as their highly modular nature enables fine-tuning of the LNP formulation for targeted delivery applications. In this work, we explore the role of ionizable lipid chemical structure and lipid molar ratios within the LNP formulation on mRNA delivery to and transfection of the brain. We utilize a high-throughput in vivo screening approach based on mRNA barcoding to study a large library of LNPs made with systematically varied ionizable lipid structures, amounts of ionizable lipid, and amounts of lipid-polyethylene glycol (PEG). We find that ionizable lipids with longer tail structures and linear amine cores can facilitate mRNA delivery to the mouse brain, and ultimately identify a specific ionizable lipid, C14-306, that facilitates brain transfection coupled with reduced liver transfection compared to an FDA-approved benchmark formulation. Furthermore, the lead LNP formulated with C14-306 is able to increase neuronal transfection and facilitate Cre-mediated recombination in the brain. Finally, safety analyses demonstrate that the lead LNP does not induce BBB leakage, increases in serum inflammatory cytokine levels, or increases in serum liver enzyme levels. Overall, our work highlights the utility of molecular barcoding for high-throughput screening of LNPs for delivery to the brain and suggests several design principles to guide the engineering of next-generation brain-tropic LNPs.},
}

@article {pmid41552826,
year = {2025},
author = {Kashuri, M and Ikrar, T and Sutriyo, and Mun'im, A and Yanuar, A},
title = {Evidence-based production framework for herbal medicine regulation in Indonesia.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1730273},
pmid = {41552826},
issn = {1663-9812},
abstract = {This narrative review synthesizes 2015-2025 evidence on evidence-based production (EBP) of herbal medicines with emphasis on advanced production technologies, omics-enabled authentication, quality by design (QbD), and regulatory harmonization relevant to Indonesia. We map how in vitro root culture, bioreactor scale-up, elicitation/metabolic engineering, and nanotechnology address supply variability and improve consistency; how DNA barcoding/metabarcoding and metabolomics with chemometrics underpin identity and chemical reproducibility; and how ASEAN/WHO initiatives enable 'loose harmonization' while preserving traditional diversity. We argue for a two-key batch-release specification (genomic × metabolite) and validated omics workflows within GLP to strengthen traceability, with real-world evidence and digital pharmacovigilance extending safety monitoring post-market. We translate these elements into an actionable framework for the Indonesian FDA (BPOM) to operationalize EBP through regulation, cross-sector training, and reliance pathways, positioning Indonesia as a regional hub for evidence-based herbal regulation.},
}

@article {pmid41551611,
year = {2025},
author = {Yu, S and Luo, Y and Dang, T and Peng, C and Gan, Q and Liang, Y and Yu, J and Long, P and Zhou, W and Dai, D},
title = {A single-sEV analysis identifies plasma EPCAM[+] sEVs as a biomarker for early diagnosis and monitoring postoperative remission of thyroid cancer.},
journal = {Extracellular vesicles and circulating nucleic acids},
volume = {6},
number = {4},
pages = {982-999},
pmid = {41551611},
issn = {2767-6641},
abstract = {Aim: Small extracellular vesicles (sEVs) are promising noninvasive biomarkers for several malignancies, including thyroid carcinoma (TC). However, their heterogeneity is frequently overlooked in bulk-level analyses. Methods: Plasma samples from TC and healthy controls (HC) were collected for a proximity-dependent barcoding assay (PBA) to identify plasma sEV biomarkers at the single-sEV level. We screened the potential biomarkers using the Panel260 (the panel that detects 260 proteins) of PBA in Cohort 1, and validated them using Panel550 (the panel that detects 550 proteins) in Cohort 2. Results: Plasma exosome counts were significantly elevated in TC compared with those in HC in both Cohort 1 and Cohort 2. Receiver operating characteristic curve analysis showed that sEV counts exhibited an area under the curve > 0.75 in both cohorts. The sEV proteomic analysis revealed that sEV epithelial cell adhesion molecule (EPCAM) levels were significantly increased, whereas claudin-11, integrin alpha X, and lymphocyte-activating 3 were significantly decreased in TC compared with HC. The increase in EPCAM in the plasma and tumor tissues was confirmed by enzyme-linked immunosorbent assay and immunohistochemistry analyses, respectively. The sEV subpopulation analysis further demonstrated that EPCAM[+] sEVs were significantly elevated in TC compared with HC in both cohorts. The reduction in sEV counts was observed in 18 out of 20 patients after the operation. The decrease in EPCAM[+] sEVs was observed in 20 patients with TC post-operatively, whereas the reduction in the conventional biomarker serum thyroglobulin (Tg) was observed in 14 patients. TC-derived plasma sEVs promoted TC cell proliferation, migration, invasion, and TC xenograft growth. Conclusion: EPCAM[+] sEVs could serve as a promising biomarker for the early diagnosis of TC and perform better in monitoring post-operative remission of TC than serum Tg.},
}

@article {pmid41551220,
year = {2025},
author = {Réblová, M and Nekvindová, J and Hernández-Restrepo, M and Hradilová, M and Kolařík, M},
title = {Phylogeny, taxonomy and geographic distribution of novel and known fungi with holoblastic-denticulate conidiogenesis in Rhamphoriales and Pleurotheciales (Sordariomycetes).},
journal = {Persoonia},
volume = {55},
number = {},
pages = {277-311},
pmid = {41551220},
issn = {0031-5850},
abstract = {As part of a broader survey of lignicolous saprobic fungi, we investigated fungal taxa from the class Sordariomycetes displaying holoblastic-denticulate conidiogenesis, a distinct developmental process and phylogenetically informative trait. Although these fungi appear morphologically similar in culture, they represent distinct evolutionary lineages. This taxonomic study integrates comparative morphological analyses, phylogenetic reconstruction of five nuclear markers, and analysis of biogeographical patterns through environmental DNA data to introduce novel taxa in the Pleurotheciales and Rhamphoriales. A new genus and species Echinodenticula allantospora and three new species, Phaeoisaria parallela, Rhamphoriopsis cuprea and Rh. denticulata, are described. A rarely encountered species Rhamphoria separata is reported, along with its previously undocumented asexual morph. Furthermore, we successfully demonstrate the utility of two protein-coding genes, rpb2 and tef1, as complementary barcodes for distinguishing closely related Phaeoisaria species. Our findings highlight the significance of holoblastic-denticulate conidiogenesis as a diagnostic feature of the Rhamphoriales and a prevalent trait in the Pleurotheciales. An unknown ascomycete that produced only sterile mycelium in culture is described here as Melanocrypta curvata and placed at an incertae sedis position within the Sordariomycetes. Additionally, we present short-read whole-genome sequencing data for the ex-type strains of the newly described species, providing a valuable genomic resource for future taxonomic, phylogenetic, and functional studies. Environmental DNA data from the GlobalFungi database bring new perspective into the biogeographical patterns of Phaeoisaria, Rhamphoria, and Rhamphoriopsis. The distribution of E. allantospora and M. curvata remains poorly understood, as no records for these species were found in GlobalFungi. This study provides new insights into the molecular systematics, taxonomy, and biogeography of the Rhamphoriales and Pleurotheciales, and highlights the role of environmental DNA metabarcoding in uncovering fungal diversity and distribution patterns. Citation: Réblová M, Nekvindová J, Hernández-Restrepo M, Hradilová M, Kolařík M (2025). Phylogeny, taxonomy and geographic distribution of novel and known fungi with holoblastic-denticulate conidiogenesis in Rhamphoriales and Pleurotheciales (Sordariomycetes). Persoonia 55: 277-311. doi: 10.3114/persoonia.2025.55.08.},
}

@article {pmid41550687,
year = {2026},
author = {Back, J and Bang, HW},
title = {A new genus of Orthopsyllidae Huys, 1990 (Copepoda, Harpacticoida) from the Pacific Ocean.},
journal = {ZooKeys},
volume = {1266},
number = {},
pages = {137-192},
pmid = {41550687},
issn = {1313-2989},
abstract = {This study reports the discovery of four new benthic harpacticoids from Korean waters in the Pacific Ocean. The harpacticoids were collected using SCUBA or a grab sampler and sorted using a stereomicroscope for both molecular and morphological analysis. The study employed standard DNA sequencing methods (COI and 18S rRNA) and detailed morphological characterization through microscopy and scanning electron microscopy. As a result, three new species belonging to the family Orthopsyllidae and classified as a new genus were discovered. Although the new genus lacks brush setae on leg 1, a diagnostic feature of Orthopsyllidae, it shares similarities with other orthopsyllids in characters such as the large thorn-like process on the antennule, leg 5, and sexual dimorphism. This finding necessitates an expanded diagnosis of Orthopsyllidae to reflect the characters of the new genus based on the three new species. In addition, a new species belonging to the genus Orthopsyllus was discovered. This study is the first to describe a new species of Orthopsyllus from Korea, where the genus has not been previously reported at the species level. This study provides a key for classifying genera and species within the Orthopsyllidae family.},
}

@article {pmid41546775,
year = {2026},
author = {Debnath, R and Rajmohana, K and Dinesh, KP},
title = {A new species of Telenomus Haliday (Hymenoptera: Scelionidae) and a novel host association with Creatonotos transiens (Walker) (Lepidoptera: Erebidae) in India.},
journal = {Systematic parasitology},
volume = {103},
number = {1},
pages = {5},
pmid = {41546775},
issn = {1573-5192},
support = {CRG/2021/005047//DST-SERB, Govt. of India/ ; },
mesh = {Animals ; India ; *Moths/parasitology ; Species Specificity ; *Wasps/classification/anatomy & histology/genetics ; DNA Barcoding, Taxonomic ; Host-Parasite Interactions ; Phylogeny ; Female ; *Hymenoptera/classification/anatomy & histology/genetics ; Male ; },
abstract = {Telenomus hexodon Debnath & Rajmohana sp. nov. (Hymenoptera: Scelionidae), is described as new to science. The species was reared from eggs of the polyphagous pest Clouded Tiger moth, Creatonotos transiens (Walker) (Lepidoptera: Erebidae). This represents the first record of an insect parasitoid association with C. transiens. Host identity was confirmed through DNA barcoding, while the parasitoid was characterized using an integrative taxonomic approach combining morphological and molecular data. Further, a checklist of Telenomus species reported from India is provided.},
}

Animals
India
*Moths/parasitology
Species Specificity
*Wasps/classification/anatomy & histology/genetics
DNA Barcoding, Taxonomic
Host-Parasite Interactions
Phylogeny
Female
*Hymenoptera/classification/anatomy & histology/genetics
Male

@article {pmid41546422,
year = {2026},
author = {Tang, Q and Yu, H and Hou, J and Jiang, M and Zhang, Z and Wang, J and Zhang, M and Han, D and Guo, P},
title = {Spatial Mapping of Membrane Protein Interactions Using a DNA Origami Rubbing.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e13795},
doi = {10.1002/anie.202513795},
pmid = {41546422},
issn = {1521-3773},
support = {XDB1020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 22304176//National Natural Science Foundation of China/ ; 32341017//National Natural Science Foundation of China/ ; 22225402//National Natural Science Foundation of China/ ; 22374132//National Natural Science Foundation of China/ ; 2024R01005//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang Province/ ; KF2101//State Key Laboratory of Fine Chemicals, Dalian University of Technology/ ; },
abstract = {Revealing the protein-protein interactions (PPIs) of membrane proteins is as challenging as their structural reconstruction, primarily because the molecular structures and related PPIs of membrane proteins are highly dependent on the bio-membrane where they are situated. DNA origami offers a platform for manipulating molecules with nanoscale precision. Herein, we used a square-like DNA origami, refer to as DNA origami rubbing, to map the two-dimensional distribution of membrane proteins in situ. Through artificial models and cell studies, we correlated the efficiency of barcode recording of DNA origami rubbings with the distance between adjacent proteins, and we observed that the frequency of adjacent proteins mapped by DNA origami rubbings was correlated to the abundance of the bait protein. We demonstrated that the DNA origami rubbing was able to reflect the distribution change of adjacent proteins caused by adding the ligand of bait protein. Our results suggested that the DNA origami rubbing can serve as a powerful tool in the field of protein interactomics.},
}

@article {pmid41544931,
year = {2026},
author = {Romariz, APPL and da Silva, DT and Benassi, JC and Leonel, JAF and Spada, JCP and Rodrigues, CMF and Pérez, HAG and de Almeida Paula, NF and Teixeira, MMG and de Sousa Oliveira, TMF and Buzetti, WAS},
title = {Water buffaloes (Bubalus bubalis): potential reservoirs of trypanosomatids in endemic areas.},
journal = {Parasitology international},
volume = {},
number = {},
pages = {103242},
doi = {10.1016/j.parint.2026.103242},
pmid = {41544931},
issn = {1873-0329},
abstract = {Trypanosomatids are protozoan parasites that include the genera Trypanosoma and Leishmania, which infect a wide range of mammalian species, including humans and ruminants. This study aimed to assess the presence of Trypanosomatid parasites in water buffaloes (Bubalus bubalis) using molecular techniques. Blood samples and conjunctival swabs from the right and left eyes were collected from 100 buffaloes (44 females and 56 males). PCR analysis detected Trypanosomatids in 32% (32/100) of the buffaloes: 29% (29/100) tested positive for DNA extracted from blood, and 4% (4/100) tested positive from conjunctival swab samples. Using the Fluorescent Fragment Length Barcoding (FFLB) technique, 38% (38/100) of blood samples were positive for Trypanosomatids, with 35% (35/100) identified as Trypanosoma theileri and 3% (3/100) as Trypanosoma vivax. Direct sequencing and analysis of PCR amplicons from four buffaloes revealed that three samples matched 100% with Trypanosoma theileri, while one matched 100% with Leishmania infantum. Our findings confirm that buffaloes can serve as hosts for Trypanosomatids and support previous observations that these parasites are often underdiagnosed. This is the first report of Leishmania infantum DNA in buffalo conjunctival swabs in Brazil and the first detection of Trypanosoma vivax DNA in buffaloes in the city of Andradina and in São Paulo state. These findings underscore the need for further studies to clarify the role of buffaloes in the epidemiology and dissemination of trypanosomatids in livestock populations.},
}

@article {pmid41542514,
year = {2026},
author = {Hornick, AC and Walters, LC and Dobson, CS and Gaglione, SA and Birnbaum, ME},
title = {Interrogating antiviral antibody responses with multiplexed, high-throughput serum assays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.03.697501},
pmid = {41542514},
issn = {2692-8205},
abstract = {The COVID-19 pandemic underscored the importance of rapidly analyzing antibody responses against emerging viruses. Existing techniques, however, are limited in their ability to probe antibodies' recognition of multiple native-conformation antigens simultaneously. To increase the throughput and multiplexability of antibody profiling, we developed A ntibody R eactivity C haracterization by A ntibody- D ependent E nhancement (ARCADE). This assay employs an antigen-agnostic Fc receptor-expressing cell line and a library of antigen-displaying, genetically barcoded lentiviruses that, when mixed with serum, infect cells and integrate their barcodes at rates reflecting the relative abundances and affinities of the antigen-specific antibodies present. Verified using sera from COVID-19-convalescent and - vaccinated donors, ARCADE delivers insights that align with and expand upon those offered by established immunoassays, highlighting, for example, how an mRNA-based vaccine elicits broader and stronger antibody responses than an adenovirus vector-based vaccine. ARCADE can comprehensively assess how infection and vaccination impact antiviral antibody repertoires over time and across patient populations.},
}

@article {pmid41542380,
year = {2026},
author = {Vallin, H and Fraser, M and Pakeman, RJ and Hipperson, H},
title = {Evaluating the Quantitative Accuracy and Application of DNA Metabarcoding for Dietary Reconstruction in Ruminants.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72878},
pmid = {41542380},
issn = {2045-7758},
abstract = {DNA metabarcoding offers a powerful, non-invasive tool to identify dietary composition with high taxonomic resolution, yet its quantitative accuracy and bias remain a well-recognised limitation across taxa and sample types. This universal challenge is particularly evident in herbivores, where plant material introduces additional amplification constraints. This study evaluates the accuracy of DNA metabarcoding in reconstructing the diets of sheep under controlled feeding trials involving high and low digestibility forage, using two widely used plant DNA barcodes (ITS2 and trnL). A secondary trial tested the detectability and proportional representation of a target species, Medicago sativa, when added to the diet in varying amounts (1%, 5%, 10%). ITS2 provided greater species-level resolution, while trnL showed broader taxonomic coverage but reduced precision. Both markers distinguished diet treatments effectively; however, faecal DNA showed proportional discrepancies from vegetation input, particularly under low-digestibility conditions. M. sativa was reliably detected even at 1% inclusion but was consistently overrepresented in sequence reads. Our findings highlight the strengths and limitations of DNA metabarcoding for herbivore diet studies and underscore the importance of marker choice and the effects of differential digestion biases. These findings demonstrate the need for multi-marker approaches and calibration controls in dietary studies, especially when quantitative interpretation is required. Despite limitations in quantitative accuracy, faecal DNA metabarcoding provides valuable insights into herbivore diet composition and preferences, with future refinements expected to improve its resolution and reliability for ecological monitoring and grazing management.},
}

@article {pmid41541251,
year = {2025},
author = {Wu, Y and Liu, R and Wang, WJ and Li, DZ and Burgess, KS and Yu, WB and Wang, H},
title = {High species discrimination in Pedicularis (Orobanchaceae): Plastid genomes and traditional barcodes equally effective via parsimony-informative sites.},
journal = {Plant diversity},
volume = {47},
number = {6},
pages = {920-930},
pmid = {41541251},
issn = {2468-2659},
abstract = {Complete plastid genomes have been proposed as potential "super-barcodes" for plant identification and delineation, particularly in cases where standard DNA barcodes may be insufficient. However, few studies have systematically addressed how taxonomic complexity, especially in rapidly radiating lineages with intricate evolutionary histories, might influence the efficacy of plastome-scale barcodes. Pedicularis is a hyperdiverse genus in the Himalaya-Hengduan Mountains, and previous studies have demonstrated high discriminatory power of the standard barcodes within this genus. Therefore, Pedicularis serves as a model for investigating the key plastome-sequence characteristics and biological phenomena that determine species-discrimination capacity. In this study, we evaluated 292 plastomes representing 96 Pedicularis species to compare the discriminatory power of complete plastid genomes with of standard DNA barcodes. Our results revealed that the traditional standard barcode combination (nrITS + matK + rbcL + trnH-psbA) achieved the highest discrimination rates (81.25%), closely followed by the plastid large single copy (LSC) region (80.21%), then by full plastome, the supermatrix of protein-coding genes, and hypervariable regions (79.17%). Notably, the matK and ycf1 gene alone could discriminate 78.13% of species. Key determinants of species discrimination by integrating alignment length (AL) and the proportion of parsimony-informative sites (PPIS), as well as conserved genes under relaxed selection exhibiting stronger discriminatory capacity. Unlike previous studies that demonstrated superior discrimination rates of plastome-scale barcodes, this study reveals a notable exception of minimal differences between traditional DNA and plastome-scale barcodes that appearing linked to Pedicularis' specific biological habits and potentially reflecting unique evolutionary patterns in the plastid genome.},
}

@article {pmid41540123,
year = {2026},
author = {Enninful, A and Zhang, Z and Klymyshyn, D and Ingalls, M and Yang, M and Zong, H and Bai, Z and Farzad, N and Su, G and Baysoy, A and Nam, J and Lu, Y and Bao, S and Deng, S and Zhang, NR and Braubach, O and Xu, ML and Ma, Z and Fan, R},
title = {Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41540123},
issn = {1548-7105},
support = {U54CA274509//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA245313//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54CA268083//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; UH3CA257393//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; RF1MH128876//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54AG079759//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54AG076043//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; RM1MH132648//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01CA294514//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2245575//Center for Selective C-H Functionalization, National Science Foundation/ ; 2245575//Center for Selective C-H Functionalization, National Science Foundation/ ; 2345215//National Science Foundation (NSF)/ ; 2245575//National Science Foundation (NSF)/ ; },
abstract = {Spatially mapping the transcriptome and proteome in the same tissue section can profoundly advance our understanding of cellular heterogeneity and function. Here we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multimodal spatial omics approach combining sequencing-based spatial transcriptomics and multiplexed protein imaging on the same section, enabling both single-cell-resolution cell typing and transcriptome-wide interrogation of biological pathways. DBiTplus utilizes spatial barcoding and RNase H-mediated cDNA retrieval, preserving tissue architecture for multiplexed protein imaging. We developed computational pipelines to integrate these modalities, allowing imaging-guided deconvolution to generate single-cell-resolved spatial transcriptome atlases. We demonstrate DBiTplus across diverse samples including frozen mouse embryos, and formalin-fixed paraffin-embedded human lymph nodes and lymphoma tissues, highlighting its compatibility with challenging clinical specimens. DBiTplus uncovered mechanisms of lymphomagenesis, progression and transformation in human lymphomas. Thus, DBiTplus is a unified workflow for spatially resolved single-cell atlasing and unbiased exploration of biological mechanisms in a cell-by-cell manner at transcriptome scale.},
}

@article {pmid41539929,
year = {2026},
author = {Li, X and Zheng, J and Fang, X and Gao, W and Chen, H and Liu, Z and Li, C and Zhang, R},
title = {Multiple microRNAs analysis based on DNAzyme cascade DNA fiber barcodes for cell typing.},
journal = {Biosensors & bioelectronics},
volume = {},
number = {},
pages = {118383},
doi = {10.1016/j.bios.2026.118383},
pmid = {41539929},
issn = {1873-4235},
abstract = {Accurate tumor subtyping through multiplex miRNA profiling is critical for precision medicine but remains challenging due to limitations in current methods, including cross-reactivity, cost, and stability. Herein, we present a DNAzyme-powered DNA fiber barcode platform that combines G-quadruplex (G4)/hemin catalysis, miRNA-responsive displacement, and polydopamine (PDA)-mediated fluorescence modulation for sensitive and specific miRNA detection. The system operates via a target-dependent "switch": in the absence of target miRNAs, G4/hemin DNAzymes catalyze dopamine (DA) oxidation into PDA that efficiently quench fluorescence through Förster resonance energy transfer (FRET); when target miRNAs are present, they competitively binding to the capture strands on DNA fibers with higher affinity, displacing the G4 structures, inhibiting DNAzyme formation and preserving the fluorescence signal, with fluorescence intensity showing a positive correlation with target concentration. This mechanism enables dual qualitative and quantitative analysis with a broad linear range (50 pM-100 nM) and low detection limits (5.50 pM). Key advantages include stable, tunable G4/hemin transduction, enhanced kinetics and signal-to-noise through synergistic displacement-quenching, and multicolor barcoding for one-pot multiplex miRNA detection. Validated against qPCR with high concordance, this platform overcomes existing technical barriers to enable robust miRNA-based cell typing classification and precision diagnostics.},
}

@article {pmid41539305,
year = {2026},
author = {Kurochkin, I and Altman, AR and Caiado, I and Pértiga-Cabral, D and Halitzki, E and Minaeva, M and Zimmermannová, O and Henriques-Oliveira, L and Klein, D and Nair, M and Oliveira, D and Cajal, LR and Knittel, R and Feick, C and Ringnér, M and Martin, M and Cirovic, B and Pires, CF and Rosa, FF and Sitnicka, E and Theis, FJ and Pereira, CF},
title = {A combinatorial transcription factor screening platform for immune cell reprogramming.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101457},
doi = {10.1016/j.cels.2025.101457},
pmid = {41539305},
issn = {2405-4720},
abstract = {Direct reprogramming of immune cells holds promise for immunotherapy but is constrained by limited knowledge of transcription factor (TF) networks. Here, we developed REPROcode, a combinatorial single-cell screening platform to identify TF combinations for immune cell reprogramming. We first validated REPROcode by inducing type-1 conventional dendritic cells (cDC1s) with multiplexed sets of 9, 22, and 42 factors. With cDC1-enriched TFs, REPROcode enabled identification of optimal TF stoichiometry, fidelity enhancers, and regulators of cDC1 states. We then constructed an arrayed lentiviral library of 408 barcoded immune TFs to explore broader reprogramming capacity. Screening 48 TFs enriched in dendritic cell subsets yielded myeloid and lymphoid phenotypes and enabled the construction of a TF hierarchy map to guide immune reprogramming. Finally, we validated REPROcode's discovery power by inducing natural killer (NK)-like cells. This study deepens our understanding of immune transcriptional control and provides a versatile toolbox for engineering immune cells to advance immunotherapy.},
}

@article {pmid41538080,
year = {2026},
author = {Juhász, A and Makaula, P and Cunningham, LJ and Nkolokosa, C and Archer, J and Jones, S and Namacha, G and Chammudzi, P and Mainga, B and Lally, D and Kayuni, SA and LaCourse, EJ and O'Ferrall, AM and Musaya, J and Stothard, JR},
title = {One Health insights into local transmission of zoonotic Schistosoma mattheei in southern Malawi.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1941},
pages = {},
doi = {10.1098/rstb.2024.0519},
pmid = {41538080},
issn = {1471-2970},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Malawi/epidemiology ; *Schistosoma/genetics/physiology ; *Schistosomiasis/transmission/veterinary/parasitology/epidemiology ; Cattle ; Humans ; *Zoonoses/transmission/parasitology/epidemiology ; *Cattle Diseases/parasitology/transmission/epidemiology ; Snails/parasitology ; Goats ; *One Health ; *Goat Diseases/parasitology/transmission/epidemiology ; Praziquantel/therapeutic use ; Prevalence ; Haplotypes ; },
abstract = {Schistosoma mattheei is a zoonotic schistosome species in central and southern Africa and is of increasing public health concern in southern Malawi. To gain insight into its local transmission, we investigated the biology of Schistosoma mattheei in southern Malawi, integrating epidemiological, environmental and genetic data within a One Health framework. Cattle, goats, humans and snails were surveyed, with DNA barcoding revealing nine mitochondrial S. mattheei haplotypes. Two haplotypes were shared across species, indicating cross-host transmission. Infected snails were detected year-round, with seasonal variation linked to vegetation cover (Normalized Difference Vegetation Index (NDVI)). Praziquantel (40 mg kg-1) treatment in selected cattle herds reduced infection prevalence over 12 weeks. These findings highlight the zoonotic potential of S. mattheei and the need for integrated control strategies. This article is part of the Royal Society Science+ meeting issue 'Parasite evolution and impact in action: exploring the importance and control of hybrid schistosomes in Africa and beyond'.},
}

Animals
Malawi/epidemiology
*Schistosoma/genetics/physiology
*Schistosomiasis/transmission/veterinary/parasitology/epidemiology
Cattle
Humans
*Zoonoses/transmission/parasitology/epidemiology
*Cattle Diseases/parasitology/transmission/epidemiology
Snails/parasitology
Goats
*One Health
*Goat Diseases/parasitology/transmission/epidemiology
Praziquantel/therapeutic use
Prevalence
Haplotypes

@article {pmid41538056,
year = {2026},
author = {Rehman, U and Sarfraz, M and Bibi, F and Noor, A and Ullah, M and Tarafder, E and Shinwari, ZK},
title = {DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {2},
pages = {40},
pmid = {41538056},
issn = {1572-9699},
mesh = {*DNA Barcoding, Taxonomic/methods/trends ; *Phylogeny ; *Agaricales/genetics/classification ; Genomics/methods ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; Metabolomics ; },
abstract = {Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.},
}

*DNA Barcoding, Taxonomic/methods/trends
*Phylogeny
*Agaricales/genetics/classification
Genomics/methods
Genome, Fungal
High-Throughput Nucleotide Sequencing
Metabolomics

@article {pmid41536623,
year = {2026},
author = {Noenrimnong, C and Suttinun, C and Tungpairojwong, N and Boonsoong, B},
title = {Taxonomic insights into the diversity of Cloeon Leach, 1815 (Ephemeroptera, Baetidae) in Thailand.},
journal = {ZooKeys},
volume = {1266},
number = {},
pages = {1-39},
pmid = {41536623},
issn = {1313-2989},
abstract = {Four species of the genus Cloeon have previously been reported in Thailand: C. bicolor Kimmins, 1947, C. bimaculatum Eaton, 1885, C. harveyi (Kimmins, 1947) and C. marginale Hagen, 1858. However, since 1961, no systematic studies or investigations of this genus have been conducted in that country. This study reviews Cloeon Leach, 1815 in Thailand and investigates five species-C. bengalense, C. bicolor, C. harveyi, C. rubellum, and C. viridulum-based on morphological, molecular, and taxonomic analyses. Three species (C. bengalense, C. rubellum, and C. viridulum) are recorded for the first time in Thailand, and C. rubellum is described for the first time as a mature nymph and adult female. Additionally, the egg chorionic surface of all five species is described for the first time, and its use is demonstrated for species identification in Thailand. A key to the species of Cloeon in Thailand is provided based on the egg structure, mature nymph, and adult female and male.},
}

@article {pmid41536601,
year = {2025},
author = {Schmidt-Stohn, G and Bellanger, JM and Brandrud, TE and Bidaud, A and Oertel, B and Saar, G and Ballarà, J and Carteret, X and Reyes García, JDD and Dondl, M and Ploch, S and Thines, M and Dima, B},
title = {The big brown Telamonia unlocked: four new species in Cortinarius section Bovini (Agaricales, Basidiomycota) and a revised taxonomy of bovinoid Cortinarii.},
journal = {Persoonia},
volume = {55},
number = {},
pages = {1-57},
pmid = {41536601},
issn = {0031-5850},
abstract = {In this study, we describe four species of Cortinarius subgen. Telamonia sect. Bovini as new to science: Cortinarius acutipes, C. cepiformis, C. schistaceus and C. sericeovelatus. We also provide updated descriptions and synonymies for several known species in the section, including C. pachypus (formerly C. terribilis and C. pseudobulbosus), C. sordescens (neotypified here), C. turgidulus and C. urbis-veteris, as well as for C. hillieri, here supported as a genuine Bovini member. In addition, through DNA sequencing of its holotype, we fix here the interpretation of C. aprinus, the iconic member of a difficult group of large, fleshy, grey brown Telamonia species often referred to as Aprini or Sordescentes. We also update the taxonomy of C. diffractosuavis (sect. Sordescentes) and C. testaceomicaceus (sect. Exsulares), to yield a most comprehensive overview of phylogenetically supported "bovinoid" species from deciduous forests on calcareous soils of Europe. The habitat and distribution of all treated species are presented, and a tentative identification key is also proposed. Citation: Schmidt-Stohn G, Bellanger J-M, Brandrud TE, Bidaud A, Oertel B, Saar G, Ballarà J, Carteret X, Reyes García JdD, Dondl B, Ploch S, Thines M, Dima B (2025). The big brown Telamonia unlocked: four new species in Cortinarius section Bovini (Agaricales, Basidiomycota) and a revised taxonomy of bovinoid Cortinarii. Persoonia 55: 1-57. doi: 10.3114/persoonia.2025.55.01.},
}

@article {pmid41535733,
year = {2026},
author = {Wang, Y and Liu, H and Zhao, D and Wang, S and Wang, J and Chi, X and Zhang, C and Wang, T and Lyu, C and Kang, C and Sun, J and Guo, L and Huang, L},
title = {Assessment of suitable cultivation area for Paris polyphylla var. chinensis and var. yunnanensis under anthropogenic disturbance based on ensemble modeling and germplasm identification.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-08010-7},
pmid = {41535733},
issn = {1471-2229},
support = {2023YFC3503801//National Key Research and Development Program of China/ ; },
}

@article {pmid41534951,
year = {2026},
author = {Lichtner, V and Irnazarow, A and Bush, S and Dowding, D and Elphick, P and Franklin, BD and Jani, YH and Songhurst, M},
title = {Complexities and capabilities of Scan4Safety in NHS hospitals: a qualitative study of a national demonstrator site.},
journal = {BMJ health & care informatics},
volume = {33},
number = {1},
pages = {},
doi = {10.1136/bmjhci-2024-101366},
pmid = {41534951},
issn = {2632-1009},
mesh = {Qualitative Research ; Humans ; *State Medicine ; Interviews as Topic ; United Kingdom ; *Hospitals ; Patient Safety ; },
abstract = {OBJECTIVES: Data standards and barcoding technologies are implemented in hospitals to uniquely identify objects, people and locations; streamline the management of supplies and inventories; improve efficiency; reduce waste and improve patient safety and quality of care. This study examined the implementation of the Scan4Safety programme at one NHS demonstrator site to understand the hospital experience of adopting these standards, barcoding and related technologies.

METHODS: Exploratory case study design, informed by information infrastructure theory, at one Scan4Safety demonstrator site. Semi-structured interviews were conducted with internal and external stakeholders (n=19), and 67 documents related to the Scan4Safety programme were identified. Interview transcripts and documents underwent thematic analysis.

RESULTS: Key enablers for Scan4Safety included allocated funding, government role/regulation, executive buy-in/wide stakeholder involvement, patient focus, agile/adaptive approach and data linkage. Challenges were both internal and external, mainly pertaining to data quality, work-as-done and trade-offs. Mechanisms of anticipated positive outcomes and potential risks were also identified.

DISCUSSION: Scan4Safety benefits are delivered through tracking and tracing capabilities, and automating data capture, alerts and data linkages. For traceability of devices, the benefits depend on the extent to which items are tracked in inventory and consistent barcode scanning at the point of care.

CONCLUSIONS: Linked standards for identification of patients, products, places and procedures, across supplies and hospital processes, constitute a wide-ranging information infrastructure with the potential for significant value to patients and the whole health system.},
}

Qualitative Research
Humans
*State Medicine
Interviews as Topic
United Kingdom
*Hospitals
Patient Safety

@article {pmid41532186,
year = {2026},
author = {Mur, M and Kavčič, A and Jagodič, U and Podlipec, R and Humar, M},
title = {Two-Photon 3D Printing of Functional Microstructures Inside Living Cells.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e19286},
doi = {10.1002/adma.202519286},
pmid = {41532186},
issn = {1521-4095},
support = {851143//HORIZON EUROPE European Research Council/ ; N1-0362//The Slovenian Research and Innovation Agency/ ; P1-0099//The Slovenian Research and Innovation Agency/ ; },
abstract = {3D printing is transforming manufacturing and biomedicine, yet it has not been demonstrated inside living cells. Additionally, there is no method to deliver micron-scale, free-standing solid microstructures directly into the cytosol of non-phagocytic cells. Here, both of these challenges are addressed by fabricating custom-shaped polymeric microstructures directly inside living cells using two-photon polymerization. A bio-compatible photoresist is injected into cells and selectively polymerized with a femtosecond laser, creating intracellular structures with submicron resolution. Structures of various shapes are printed in live cells, including a 10 μ m $\umu {\rm m}$
elephant, barcodes for cell tracking, diffraction gratings for remote readout, and microlasers. The printed structures in cells can affect the cell biology. The demonstrated top-down intracellular biofabrication approach, combined with functional photoresists, may enable new applications in intracellular sensing, biomechanical manipulation, bioelectronics, and targeted drug delivery. These embedded structures could provide novel control over the intracellular environment, allowing engineering of cellular properties beyond natural limits and genetic engineering.},
}

@article {pmid41366305,
year = {2025},
author = {Tsafack, DT and Monamele, CG and Koro Koro, F and Essengue, LLM and Mounchili-Njifon, A and Esso, L and Njankouo Ripa, M and Touoyem, PI and Mouliem, JLM and Tamoufe, U and Moumbeket-Yifomnjou, MH and Njouom, R},
title = {Whole-genome analysis of influenza A(H1N1)pdm09 viruses in Cameroon (2019-2024) using nanopore sequencing.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {53},
pmid = {41366305},
issn = {1471-2334},
abstract = {BACKGROUND: Since 2019, Cameroon has reported a high number of seasonal influenza cases caused by the A(H1N1)pdm09 subtype, which remained the predominant global strain as of 2024.

METHODS: To characterize the evolutionary dynamics of circulating A(H1N1)pdm09 viruses, whole-genome sequencing was conducted using Oxford Nanopore Technologies, with multiplexing native barcode expansion kits. DNA repair and end preparation were performed using the NEBNext Ultra II End-Repair/dA-tailing kit. Phylogenetic trees for HA genes segments were inferred using the maximum likelihood (ML) method implemented in IQ-TREE v3.0.1under the LG + F + G4 substitution model. Additionally, Mutation analysis was performed across all eight gene segments using MEGA with A/Wisconsin/67/2022 (A/H1N1pdm09) serving as the reference strain. Identified amino acid substitutions were annotated and their potential phenotypic effects were evaluated using FluSurver.

RESULTS: All Cameroonian A(H1N1)pdm09 strains from 2019 to 2024 belonged to subclade 6B.1A.5a.2a. Phylogenetic analysis revealed annual divergence from Northern Hemisphere vaccine strains, suggesting a mismatch with locally circulating variants. Several functionally relevant mutations were identified in the viral genes, including A3L, A214T, and F12V in HA; R159K and A267V in PA; A241E and T137A in M2; I42L and V7I in NS1; and I84V and I33V in PB1. Many of these mutations have been associated with increased virulence. In addition, amino acid substitutions were observed in the NA protein at V13I, S200N, L339S, S37T, V80M, and I163V, relative to the 2024 vaccine strain A/Wisconsin/67/2022.Overall, the number of amino acid mutations between circulating strains and the vaccine strain was notably high, indicating that local viruses may be evolving away from the vaccine strain selected for the 2023–2024 season.

CONCLUSIONS: These findings underscore the ongoing genetic evolution of the influenza A(H1N1)pdm09 virus in Cameroon and highlight the importance of local genomic data into the selection of WHO vaccine candidate strains for the Northern Hemisphere.

CLINICAL TRIAL NUMBER: Not applicable.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-12284-5.},
}

@article {pmid41531910,
year = {2026},
author = {Muirberry, J and Lancaster, LT},
title = {Global Changes in Lepidopteran Phylogenetic Diversity Across Space and Time.},
journal = {Ecology and evolution},
volume = {16},
number = {1},
pages = {e72557},
doi = {10.1002/ece3.72557},
pmid = {41531910},
issn = {2045-7758},
abstract = {Amidst increasing reports of insect declines, it is ever more important to understand spatial and temporal insect diversity patterns and processes. Phylogenetic diversity (PD) is an important biodiversity metric in that it relates strongly to ecosystem processes, and it can be estimated more accurately from opportunistic occurrence data than other elements of biodiversity. Here, we assess recent changes across global variation in Lepidopteran PD, to discover overall patterns, their repeatability across regions and environmental drivers. We assess global, spatiotemporal variation in PD, as compared to null expectations given sampling effort, determining how such variation relates to region, space, time and environment. Our analysis is based on 374,749 gene sequence accessions from the barcode of life database (BOLD), representing 3158 species assemblages, spanning 62 years. We find that global variation in PD of Lepidopteran species assemblages has significantly increased over time at high latitudes while remaining relatively unchanged near the equator. This pattern exhibits parallelism across global regions, with the strongest increases in PD towards the present observed in high-latitude communities in North America and Asia, in lowland sites in Europe, and across the African continent. In contrast, PD has declined through time in wetter portions of Australasia and in Africa and South America. Our reported patterns likely reflect changes in Lepidopteran responses to tropical habitat loss and widespread range expansions to higher latitudes. However, changing clines in DNA barcoding strategies could also play a role. Detecting spatiotemporal patterns of change in PD at the global scale is enabled by the increasing use of genetic markers in taxonomy. Our replicated findings provide confidence in biogeographic interpretation, yet increased metadata on sub-sampling decisions would aid future interpretation of biodiversity trends using ecological genomics synthesis.},
}