@article {pmid41775217,
year = {2026},
author = {Zheng, M and Gao, M and Zhang, Z and Song, X},
title = {Integrating DNA barcoding and machine learning for species identification: Comparative genomics and codon usage bias of chloroplasts in Gentiana sect. Cruciata.},
journal = {Journal of plant physiology},
volume = {319},
number = {},
pages = {154730},
doi = {10.1016/j.jplph.2026.154730},
pmid = {41775217},
issn = {1618-1328},
abstract = {This study integrates chloroplast genome comparison, codon usage analysis, machine learning, and DNA barcoding to elucidate the phylogeny, genetic diversity, and species identification of Gentiana Sect. Cruciata. Perform chloroplast genome analysis using IRscope (boundary analysis), MISA (SSR detection), and mVISTA (variation alignment). Based on ChiPlot, CodonW, and CUSP analysis, factors influencing codon preference and usage patterns were studied. Molecular identification based on ITS2, matK, ITS, psbA-trnH barcode with BLOG, WEKA machine learning algorithms. Chloroplast SSRs dominated by A/T repeats; non-coding regions exhibited higher variability. Codon bias driven by natural selection, with A/U preference at the third position. ITS2 showed the highest discrimination power (matK > ITS > psbA-trnH). Machine learning (J48/SMO classifiers) achieved 83.33%-100% accuracy using four barcodes. This study provides theoretical foundations for conservation, medicinal quality control, and resource authentication of the Gentiana Sect. Cruciata.},
}

@article {pmid41775031,
year = {2026},
author = {Chen, C and Gao, H and Zhang, X and Fu, Y and Yang, S and Wu, G and Zheng, J and Chen, P and Chen, Z},
title = {Human umbilical cord mesenchymal stem cell-derived small extracellular vesicles accelerate diabetic wound healing by reprogramming fibroblast subpopulations and delivering pro-regenerative cargos.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {52},
number = {4},
pages = {107910},
doi = {10.1016/j.burns.2026.107910},
pmid = {41775031},
issn = {1879-1409},
abstract = {BACKGROUND: Diabetic wound healing is complex and challenging. Human umbilical cord mesenchymal stem cell-derived small extracellular vesicles (hUC-MSC-sEVs) play a crucial role in tissue repair, but their specific mechanisms in diabetic wounds remain unclear.

METHODS: hUC-MSC-sEVs were isolated via tangential flow filtration and size-exclusion chromatography. Fibroblast proliferation was assessed using the CCK-8 assay. In vivo, the therapeutic effectiveness of hUC-MSC-sEVs in diabetic wound healing was evaluated by measuring wound-closure rates and by conducting histologic analyses. Single-cell transcriptomic sequencing (scRNA-seq) and bulk RNA sequencing were exploited to elucidate the mechanisms by which hUC-MSC-sEVs mediated the healing of diabetic wounds. Finally, we implemented the Proximity Barcoding Assay (PBA) technology to characterize the sEV subpopulations.

RESULTS: hUC-MSC-sEVs were isolated and shown to dose-dependently amplify fibroblast proliferation. In diabetic mice, topical application accelerated wound closure via expedited re-epithelialization, robust neovascularization, and immunomodulation. scRNA-seq revealed alterations in the skin microenvironment following sEVs treatment, identifying and validating via immunofluorescence the presence of four fibroblast subpopulations. Among these, Trps1[+] fibroblasts were demonstrated to be the principal drivers of reparative lineage commitment through reprogrammed ligand-receptor crosstalk. PBA analysis resolved sEVs into 11 distinct subpopulations. Integrated bioinformatics highlighted a key ITGB1-enriched sEV subpopulation, whose interaction network was fibroblast-specific, with FLNA implicated as a key downstream signaling node in fibroblasts linking this sEV subpopulation to phenotypic modulation.

CONCLUSION: Our study revealed that hUC-MSC-sEVs accelerated diabetic wound healing through a dual mechanism: by reprogramming fibroblast subpopulations and by delivering pro-regenerative cargos (via functionally distinct sEV subpopulations enriched with immunomodulatory and reparative factors). These findings elucidate the molecular and cellular basis for hUC-MSC-sEV efficacy and provide a novel theoretical foundation for EV-based therapies in diabetic wound repair.},
}

@article {pmid41769403,
year = {2026},
author = {Vieira, LMC and Pacheco, MA and Escalante, AA and Braga, EM},
title = {Morphological description and near-complete mitochondrial genome of Haemoproteus (Parahaemoproteus) trarotraro n. sp.: a widely distributed species reported in Brazilian falcons.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20653},
pmid = {41769403},
issn = {2167-8359},
abstract = {Haemosporida are vector-borne parasitic protozoa known to be present in birds of most avian orders. However, despite their perceived diversity using DNA barcode approaches, describing and delimiting species is challenging, particularly for those parasites found in non-passerine birds. In this study, we describe Haemoproteus trarotraro n. sp., a species found in two Falconiform hosts, the Crested Caracara (Caracara plancus plancus, type host) and the Yellow-headed Caracara (Daptrius chimachima chimachima), both sampled in Brazil at a wildlife rehabilitation center using microscopy and molecular tools. Haemoproteus trarotraro n. sp. is distinguished from the two other haemoproteid species described in Falconiformes, H. brachiatus and H. tinnunculi , by the absence of gametocytes that fully encircle the host-cell nucleus, and by the presence of numerous small vacuoles scattered throughout the cytoplasm of macrogametocytes. Both the partial cytb gene and the mtDNA genome for this new species are reported. The sequencing of the cytb barcode fragment revealed that H. trarotraro n. sp. reported here corresponds to a Haemoproteus sp. haplotype (GenBank Accession (AF465594) lineage POLPLA01 in Malavi) previously reported from Caracara plancus cheriway in Florida, USA. Although it diverges by only 2% at the cytb level from H. tinnunculi and H. brachiatus, H. trarotraro n. sp. is not a sister lineage to these taxa. Instead, phylogenetic analyses place it within a distinct but closely related, well-supported clade comprising lineages infecting American Kestrels (Falco sparverius). This study contributes, through an integrative taxonomic approach, to the ongoing discussion about species delimitation within the order Haemosporida.},
}

@article {pmid41769190,
year = {2026},
author = {Al-Jamal, FF and Abuassaf, RA and Abusara, OH and Zihlif, M and Deeb, AA and Al-Rshaidat, MMD},
title = {Ethanolic extracts from deep marine sponges: A new frontier in antibacterial discovery from the Jordanian Gulf of Aqaba.},
journal = {Biomedical reports},
volume = {24},
number = {4},
pages = {44},
pmid = {41769190},
issn = {2049-9442},
abstract = {The urgent need for new antibiotics to counter bacterial resistance has led to renewed interest in marine natural products. The present study evaluated the antibacterial potential of ethanolic extracts from three deep-sea sponges: Stelletta sp., Dactylospongia cf. elegans (D. cf. elegans) and Axinella sp., which were collected from the Gulf of Aqaba off the coast of Jordan. Antibacterial activity was assessed against Gram-negative and Gram-positive bacteria using the well diffusion method, followed by determination of the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC). Only D. cf. elegans exhibited potent activity, which was limited to Gram-positive bacteria and showed inhibition zones of 7 to 21 mm and MIC and MBC values of 1 and 2 mg/ml, respectively. Stelletta sp. showed no detectable activity, and Axinella sp. displayed minimal effects. DNA barcoding (28S rRNA) confirmed that all three species belong to the class Demospongiae. LC-MS/MS analysis of the extract from D. cf. elegans identified bioactive constituents, including bolinaquinone, dactyloquinone, gallic acid and caffeic acid, which are compounds known for antibacterial properties and likely contributed to the observed activity. Thus, D. cf. elegans could be a promising source of antibacterial agents against Gram-positive pathogens and warrants further evaluation of the mechanisms involved, its toxicity, and its effects in vivo.},
}

@article {pmid41766972,
year = {2026},
author = {Yi, JS and Jung, YS and Cho, A and Lim, HS and Chang, MI},
title = {Comparative evaluation of conventional, real-time, and ultrafast real-time PCR assays for accurate identification of Euphausia pacifica.},
journal = {Food science and biotechnology},
volume = {35},
number = {4},
pages = {1041-1050},
pmid = {41766972},
issn = {2092-6456},
abstract = {In this study, a species-specific primer was developed for the cytochrome c oxidase subunit I (COI) region to identify krill species in processed foods. Optimal conditions for qualitative conventional PCR, real-time PCR (RT-PCR), and ultrafast RT-PCR were established by adjusting annealing temperature, primer concentration, and annealing time. Specificity and sensitivity were established by adjusting annealing temperature, primer concentration, and annealing time. Specificity and sensitivity were established by analyzing the presence or absence of a specific band and the limit of detection. The concentration was validated as 0.001 ng/μL for RT-PCR and ultrafast RT-PCR as well as 0.005 ng/μL for conventional PCR. All validation items, including false-negative and false-positive rates, were performed according to the Codex Alimentarius guidelines. Among 14 commercial products tested, E. pacifica was identified in a salted fermentation product of Korean origin through ultrafast RT-PCR, offering a rapid, sensitive tool for regulatory seafood authentication.},
}

@article {pmid41761779,
year = {2026},
author = {Smith, N and Cohen, M and Tracey, L and Alipaz, J and Loh, C and King, D and Pulyani, N and Auzins, R and Gray, E and Taylor, S and Rai, R and Kao, S and Fazekas de St Groth, B and McGuire, H},
title = {Mass Cytometry Workflow to Achieve High-Dimensional Immunophenotyping in Resource-Limited or Decentralized Environments.},
journal = {Current protocols},
volume = {6},
number = {3},
pages = {e70335},
pmid = {41761779},
issn = {2691-1299},
support = {2014538//National Health and Medical Research Council/ ; },
abstract = {Globally, regional and remote communities are burdened by both an increased prevalence and worse prognosis of many infectious and chronic diseases. However, largely owing to logistical challenges, these communities are under-represented in clinical trials and research studies. As individuals from rural communities experience unique environmental exposures and risk factors for disease, immune phenotyping data collected from metropolitan populations may not be broadly generalizable. To address this, we present a workflow that enables the inclusion of resource-limited sites in high-parameter mass cytometry studies. In this approach, whole blood (WB) or peripheral blood mononuclear cells (PBMCs) are collected, stained fresh for surface antigens, and cryopreserved at the collection site. Samples are then shipped to the central site for further processing, including neutrophil depletion, fixation, barcoding, intracellular staining, and data acquisition. Importantly, the WB staining approach does not require specialized equipment such as centrifuges and is therefore feasible to perform in a resource-limited environment. A support protocol details steps for data preprocessing and cleanup. We present example data demonstrating the application of this workflow to determine immune differences between eight patients with late-stage lung cancer and four healthy blood donors. Overall, this workflow may improve access to underserved communities and facilitate, for the first time, the scalability of immune phenotyping studies to harness geographically dispersed clinical centers. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation and staining of PBMCs for cytometry Basic Protocol 2: Preparation and staining of whole blood for cytometry Basic Protocol 3: Fixation, permeabilization, intracellular staining, and data acquisition for blood sample immunophenotyping Support Protocol: Data preprocessing and cleanup.},
}

@article {pmid41761051,
year = {2026},
author = {Klaiklueng, N and Bootsongkorn, W and Sarasombath, PT and Ruenchit, P and Wongkamchai, S},
title = {DNA barcoding and geometric morphometry of tabanid flies (Diptera: Tabanidae) in Thailand and a new record of a Thai horse fly.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.70058},
pmid = {41761051},
issn = {1365-2915},
support = {//Siriraj Research Development Fund/ ; },
abstract = {Tabanid flies are gaining high medical and veterinary importance due to their role as a vector of many pathogens. In the present study, a total of 3760 female tabanid flies were collected from Narathiwat and Phayao provinces of Thailand. All were identified using the morphological method, DNA barcoding and wing geometric morphometric (WGM) analysis. Eight species were identified, and among them, Tabanus tenens is a new recorded Thai horse fly. Morphologically, 2178 and 1559 females from Narathiwat and Phayao were identified at the species level, including Chrysops dispar, Chrysops fasciatus, Tabanus griseilineis, Tabanus rufiscutellatus and Tabanus minimus. The other 23 females were identified at the level of the genus (Tabanus spp.) only. Among these, DNA barcoding was further identified as Tabanus tenens, Tabanus rubidus and Tabanus striatus. The landmark-based WGM analysis was used to differentiate the samples from Narathiwat, and the results showed the efficacy of this approach in differentiating the four species of tabanids, achieving an overall accuracy score of 99%. Additionally, the data derived from wing landmarks of samples collected in Narathiwat were used as reference materials for identification of the tabanid fly collected from Phayao, and the finding revealed efficacy of the reference materials. Together, this study demonstrated that DNA barcoding is a reliable tool for the identification of tabanid fly species, while WGM analysis could be a complementary tool. The barcode sequences and WGM data generated in this study can serve as a valuable reference material to identify new field samples from other regions of Thailand. Altogether, this study updated the species list of tabanid flies in Thailand, particularly in the Narathiwat and Phayao provinces, using various integrative identification tools.},
}

@article {pmid41760925,
year = {2026},
author = {Rodriguez-Fraticelli, AE and Parreno, V},
title = {Charting single-cell lineages with synthetic and natural barcodes.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {41760925},
issn = {1471-0064},
abstract = {Across our lifespan, cells divide and differentiate to create the functional units of all organs, yet with age and cancer a small number of cellular families (clones) will rule the fate of the organism. Advances in synthetic and natural barcoding methods now enable cellular ancestries to be reconstructed with unprecedented single-cell resolution. These single-cell lineage-tracing studies are leading to a re-evaluation of long-standing paradigms in development, ageing and cancer biology and are revealing the underpinnings of phenotypic heterogeneity for various cellular functions, including regeneration and stress responses. Despite remaining methodological challenges, progress continues towards multimodal tracing methods that combine spatial, genetic, epigenetic and transcriptomic information. The future transition of clonal analysis into the clinic may eventually help detect, predict and prevent disease progression.},
}

@article {pmid41759133,
year = {2026},
author = {Kondratov, AP and Vereshchagin, VY and Pogiba, AY and Volinsky, AA},
title = {Transparent multilayer polymer films for hidden marking of reflective containers.},
journal = {Optics letters},
volume = {51},
number = {5},
pages = {1215-1218},
doi = {10.1364/OL.585073},
pmid = {41759133},
issn = {1539-4794},
abstract = {Counterfeit production remains a major socio-economic challenge, and one effective countermeasure is the hidden marking of polymer packaging. When polarized light reflects from mirror-like containers wrapped in anisotropic, transparent shrink films, it generates vivid multicolor effects used for both open and covert labeling. These optical features have been observed across various anisotropic films, revealing a surprising dependence of color and transparency on film scale. Additionally, hidden barcodes can be embedded within internal film layers and later read using polarized light, offering a robust method for product authentication.},
}

@article {pmid41758996,
year = {2026},
author = {Yin, K and Lin, S and Yang, C},
title = {Metabolic RNA Labeling-Enabled Time-Resolved Single-Cell RNA Sequencing.},
journal = {Accounts of chemical research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.accounts.6c00010},
pmid = {41758996},
issn = {1520-4898},
abstract = {ConspectusGene expression of cells is a highly heterogeneous and dynamic program that changes over time in various biological processes such as embryogenesis, disease progression, and response to stimuli. Understanding the molecular mechanisms of heterogeneous and dynamic gene expression is crucial for advancing our knowledge of health and disease. The recent development of single-cell RNA sequencing (scRNA-seq) technologies has offered a great opportunity to dissect cellular heterogeneity by profiling the transcriptomes of individual cells. However, scRNA-seq captures only static snapshots of gene expression and fails to temporally resolve the RNA dynamics. Therefore, the rapid changes in transcription, the coordinated regulation of RNA synthesis and degradation rates, and the cellular interactions driving cell fate decisions remain poorly understood. In the past few years, metabolic RNA labeling-based scRNA-seq has emerged as a cutting-edge chemical tool to tackle these challenges. Nucleoside analogs are applied to label newly transcribed RNAs and distinguish them from pre-existing RNAs. This time-resolved technology unbiasedly captures the true RNA dynamics for thousands of genes in each of the individual cells, providing unprecedented insight into the regulation of heterogeneous and dynamic gene expression in diverse biological processes.In this Account, we highlight the recent advances achieved by our group and other laboratories in metabolic RNA labeling-enabled time-resolved scRNA-seq. First, we summarize the recent development of time-resolved scRNA-seq by integrating metabolic RNA labeling (e.g., 4-thioridine labeling) with various scRNA-seq platforms. We highlight our size-exclusion and locally quasi-static hydrodynamics-based Well-TEMP-seq method, which greatly improves the performance of time-resolved scRNA-seq (higher throughput, higher cell barcoding efficiency, and RNA recovery rate) and lowers the cost. Next, we extend the labeling strategy from single nucleoside labeling to double nucleoside labeling and develop scDUAL-seq The sequential (pulse-pulse) labeling by two different nucleosides in scDUAL-seq addresses the limitation of single nucleoside labeling in the simultaneous monitoring of RNA synthesis and degradation processes and accurate measurement of RNA kinetics. The ability of scDUAL-seq to discriminate between different cell states also allows the unveiling of the interplay between RNA synthesis and degradation that controls distinct RNA regulatory strategy transitions during dynamic processes. Then, we discuss the further development of in vivo metabolic RNA labeling-based scRNA-seq by our laboratory (Dyna-vivo-seq) and others, which advances the time-resolved scRNA-seq studies from cultured cells to animal models. This innovation opens new avenues to reveal single-cell RNA dynamics in living organisms. Finally, we introduce our attempts to integrate time-resolved scRNA-seq with spatial transcriptomics, adding a spatial dimension to temporal RNA dynamics. This new paradigm allows the dissection of the spatiotemporal regulation of gene expression and cell fate decisions through cell-cell interactions in the tissue microenvironment, which holds great promise for biomedical applications.Our perspectives on the current limitations of the chemical tools for single-cell RNA dynamics profiling and the future directions for improvement are also provided. We anticipate that this Account will inspire chemists to develop advanced chemical tools to profile the heterogeneous and dynamic gene expression programs and offer transformative insights into the molecular landscape of RNA dynamics in health and disease.},
}

@article {pmid41756968,
year = {2026},
author = {Iwaszkiewicz-Eggebrecht, E and Granqvist, E and Nowak, KH and Valdivia, C and Buczek, M and Srivathsan, A and Hartop, E and Miraldo, A and Roslin, T and Tack, AJM and Łukasik, P and Meier, R and Ronquist, F},
title = {Accuracy of occurrence and abundance estimates from insect metabarcoding.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.20.707016},
pmid = {41756968},
issn = {2692-8205},
abstract = {1. DNA metabarcoding-high-throughput sequencing of barcode regions from bulk samples-has become a key tool for insect biodiversity assessment. Yet, how methodological choices affect the accuracy of metabarcoding data remains insufficiently explored. In this paper, we ask: (1) How does the lysis method (non-destructive lysis vs. destructive homogenization) affect community recovery? (2) How comprehensively does metabarcoding capture species richness? (3) To what extent can spike-ins improve abundance estimates? (4) How accurately can species abundances be estimated?2. We evaluated the accuracy of insect metabarcoding using 4,749 bulk samples from a large-scale biodiversity survey subjected to mild lysis. Of these samples, 856 were also homogenized, allowing a systematic comparison of the effect of alternative treatments. To potentially improve abundance estimates, we added six biological spike-ins (i.e., foreign insects) to all samples, and two synthetic spike-ins (artificial DNA fragments) to the homogenization treatment. In addition, we established the contents of 15 samples by individually barcoding all specimens, enabling direct assessment of occurrence and abundance estimates.3. Our results revealed consistent differences between destructive and non-destructive treatments. While both methods reliably detected the majority of species, small and soft-bodied taxa were more often recovered after mild lysis than after homogenization, while the reverse was true for heavily sclerotized, hairy, and large taxa. Using biological spike-ins for calibration reduced the variance in read numbers per specimen considerably, especially in homogenized samples, while synthetic spike-ins were less effective. In a Bayesian analysis, where species data were matched to the best-fitting spike-in calibration curve, accurate abundance estimates (+/-1 individual) were obtained for 72.9% of species occurrences.4. Our results show that it is possible to obtain reasonably accurate abundance estimates from metabarcoding data, and that mild lysis and homogenization result in different taxon-specific biases in terms of occurrence data, with neither method outperforming the other. Accuracy is improved by homogenization rather than mild lysis of samples, and by the use of biological rather than synthetic spike-ins. Together, these findings provide a major step towards robust, quantitative biodiversity monitoring using DNA-metabarcoding.},
}

@article {pmid41755823,
year = {2026},
author = {Lu, H and Chen, J and Yang, J and Ma, J and Wang, C and Qian, J and Zhang, ZH and Chen, Q and He, MY and Lin, J},
title = {Emergence of Radiochromic Metal-Organic Frameworks for Information Encryption via Dual-Stimuli Responses.},
journal = {JACS Au},
volume = {6},
number = {2},
pages = {1079-1088},
pmid = {41755823},
issn = {2691-3704},
abstract = {Secure information encryption is paramount in modern society for data protection, anticounterfeiting, and confidential communication. Here, we report the first demonstration of radiochromic metal-organic frameworks (MOFs) for high-security information encryption, leveraging their unique X-ray-induced chromic responses. Three thorium-based MOFs (Htpc⊂TOF, Hmpc⊂TOF, and Hpybz⊂TOF) were rationally constructed by embedding distinct pyridine-derived guest molecules within a robust layered Th6(μ3-O)4(μ3-OH)4(HCOO)12(DMF)2·2DMF host framework. Remarkably, upon X-ray irradiation, each framework exhibits well-defined and distinguishable color transformations, including purple for Htpc⊂TOF, yellow for Hmpc⊂TOF, and green for Hpybz⊂TOF, while Htpc⊂TOF additionally responds to ultraviolet (UV) light, enabling dual-stimuli activation. This hierarchical, sequential chromic switching facilitates multilevel decryption, significantly enhancing encryption complexity and thwarting unauthorized access. Proof-of-concept demonstrations, including barcodes, QR codes, and 3D color matrices, illustrate the potential of these MOFs for spatially encoded, temporally controlled, and multidimensional information encryption. The frameworks exhibit excellent chemical, thermal, and radiative stability, maintaining structural integrity under different conditions, including high dose ionizing radiation, heating to 200 °C, and prolonged water exposure. Collectively, these findings establish a new paradigm for robust, stimuli-responsive MOFs, marking the first use of radiochromism in advanced information encryption technology.},
}

@article {pmid41755527,
year = {2026},
author = {Faria, TC and Ohara, WM and Monteiro, ILP and Oliveira, C},
title = {A new Hyphessobrycon (Characiformes: Acestrorhamphidae) of the Hyphessobrycon agulha lineage of Hyphessobryconinae from the lower Aripuanã basin, Brazil, with comments about the lineage.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70379},
pmid = {41755527},
issn = {1095-8649},
support = {2011/50282-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2013/22473-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2020/13433-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/00242-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306054/2006-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441128/2020-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Pro-Reitoria de Pesquisa, Universidade de São Paulo/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {A new species of Hyphessobrycon is described from a tributary of Rio Jatuarana, lower Rio Aripuanã basin, Rio Madeira basin, Apuí, Amazonas. The new species is part of the Hyphessobrycon agulha lineage, with the typical midlateral narrow black stripe immediately followed dorsally by an iridescent stripe. Its phylogenetic position is corroborated by the DNA barcoding methodology, which also indicates the new species as closely related to Hyphessobrycon ericae and Hyphessobrycon ribeiroi, with both possessing very distinct colour patterns. The new species can be distinguished from all species of Hyphessobrycon by the association of a well-defined and horizontally elongated humeral blotch with a ventral diffuse expansion, a conspicuous caudal peduncle blotch restricted to the ventral half of the caudal peduncle and proximal half of mid rays of caudal fin, the presence of a red midlateral stripe dorsal to the iridescent stripe and lateral-line scale counts.},
}

@article {pmid41754359,
year = {2026},
author = {Gawhari, AMH and Culham, A and Ellmouni, FY and Alghamdi, AA and Jury, SL and El-Banhawy, A},
title = {Resolving Species Limits and Evolutionary Distinctiveness of the Libyan Endemic Arbutus pavarii (Ericaceae) Using Multilocus DNA Barcoding and Phylogenetic Analyses.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/plants15040653},
pmid = {41754359},
issn = {2223-7747},
abstract = {The taxonomic status of Arbutus pavarii Pamp., a rare and geographically restricted species endemic to northeastern Libya, has long been debated, with some treatments considering it a synonym of A. unedo. To resolve this uncertainty, we applied an integrative molecular framework that combined multilocus DNA barcoding, phylogenetic inference, and multivariate statistical analyses. Five barcode loci-nrITS, matK, rbcL, trnH-psbA, and rps16-were analyzed using barcode-gap diagnostics, TaxonDNA identification tests, and single-locus and concatenated phylogenetic analyses. Barcode-gap analyses based on Kimura 2-parameter distances revealed clear and reproducible separation between intra- and interspecific variation for A. pavarii, particularly for nrITS and the concatenated multilocus dataset, whereas conserved plastid loci showed limited discriminatory power when used individually. Phylogenetic reconstructions consistently recovered A. pavarii as a strongly supported monophyletic lineage, distinct from A. unedo and other Mediterranean congeners, with congruent topologies across the nuclear, plastid, and combined datasets. Multivariate analyses, including principal component analysis and heatmap clustering, further corroborate the genetic cohesion and distinctiveness of A. pavarii samples. Collectively, these results provide robust molecular evidence supporting the recognition of Arbutus pavarii as a distinct evolutionary lineage, rather than an intraspecific variant of A. unedo. This study established a reproducible multilocus framework for species delimitation in Arbutus and highlighted the importance of integrating nuclear and plastid markers to resolve complex taxonomic relationships. The clarified taxonomic status of A. pavarii has important implications for biodiversity assessment and conservation planning in the Mediterranean region, particularly in the Cyrenaican floristic province.},
}

@article {pmid41752622,
year = {2026},
author = {Fang, Y and Luo, W and van Achterberg, C and Chen, X and Tang, P},
title = {DNA Barcodes and Morphology Reveal Five New Species of Phanerotoma (Hymenoptera, Braconidae, Cheloninae) from China.},
journal = {Insects},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/insects17020219},
pmid = {41752622},
issn = {2075-4450},
support = {2023FY100200//the Science & Technology Fundamental Resources Investigation Program of China/ ; 2022FY202100//the Science & Technology Fundamental Resources Investigation Program of China/ ; 32070467//the General Program of National Natural Science Foundation of China/ ; },
abstract = {The genus Phanerotoma Wesmael, 1838 (Hymenoptera, Braconidae, Cheloninae, Phane- rotomini) is distributed across all six major zoogeographical regions, with the highest species diversity recorded in the Palaearctic Region. DNA barcoding provides a robust method for species identification, yet its effectiveness for the genus Phanerotoma is limited by the scarcity of reliable, species-level data from specific regions in public databases. This gap makes it essential to contribute comprehensive genetic resources to advance taxonomic research. This study presents a comprehensive COI dataset of 92 sequences for the genus Phanerotoma, employing both the Automatic Barcode Gap Discovery (ABGD) method for species delimitation and the bPTP model for phylogenetic inference. The integrated analytical approach revealed 18 distinct species, including five new species; all species new to science are described and illustrated, and updates of the most recent key to the Chinese species are included.},
}

@article {pmid41751624,
year = {2026},
author = {Chen, S and Wang, M and Lu, X and Sun, Y and Ma, M},
title = {Assembly of the Delphinium densiflorum Chloroplast Genome and Comparative Genomics Within Delphinium.},
journal = {Genes},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/genes17020240},
pmid = {41751624},
issn = {2073-4425},
support = {(Grant No. 2024-ZJ-T02).//the Qinghai Provincial Science and Technology Program/ ; },
abstract = {Background/Objectives: Chloroplast genomes are essential for understanding the systematics and adaptive evolution of alpine plants, yet genomic data for high-altitude Delphinium species remain scarce. Delphinium densiflorum, a medicinal plant endemic to the Qinghai-Tibet Plateau, exhibits notable high-altitude adaptations, but its plastome features and evolutionary position are still unclear. This study aims to assemble and characterize its complete chloroplast genome and clarify its phylogenetic placement within Delphinium. Methods: Using Illumina NovaSeq data, we de novo assembled the D. densiflorum plastome, annotated it with CPGAVAS2, and compared it with 12 published Ranunculaceae plastomes. We analyzed IR-boundary dynamics, genome-wide sequence variation, and codon-usage bias and constructed a maximum-likelihood phylogeny based on 69 shared protein-coding genes. Results: The plastome is 154,161 bp (GC 38.24%) with a canonical quadripartite structure, encoding 131 genes (87 CDS, 8 rRNA, 37 tRNA). An IR expansion into the SSC region yields the shortest SSC reported among the compared Delphinium species and produces unique structural variants. Photosynthetic genes are extremely conserved (nucleotide diversity Pi ≤ 0.01), whereas several loci (e.g., ycf1 and psaC) are highly divergent (Pi ≥ 0.05). Codon usage shows a strong bias toward AU-ending triplets. Phylogenetically, D. densiflorum forms a 100%-bootstrap clade with other high-altitude congeners, supporting the non-monophyly of Delphinium. Conclusions: This study delineates the plastome architecture and putative adaptive signatures of D. densiflorum, identifies robust candidate loci for DNA barcoding, and provides molecular evidence for taxonomic revision and conservation strategies in Delphinium.},
}

@article {pmid41748820,
year = {2026},
author = {Yildiz, U and Lobato-Moreno, S and Claringbould, A and Bauersachs, HG and Servaas, NH and Vlachou, EP and Arnold, C and Campos-Fornés, V and Prummel, KD and Zaugg, JB and Noh, KM and Marttinen, M},
title = {Single-cell ultra-high-throughput multiplexed chromatin accessibility and gene expression sequencing (SUM-seq).},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {41748820},
issn = {1750-2799},
abstract = {Single-cell epigenome and transcriptome profiling enables the dissection of gene regulatory networks, offering a powerful approach to characterize cellular heterogeneity and regulatory landscapes of cell states. Here we describe a single-cell ultra-high-throughput multiplexed sequencing (SUM-seq) assay for scalable and cost-effective simultaneous profiling of chromatin accessibility and gene expression in single nuclei. SUM-seq combines sample-specific accessible DNA and mRNA in situ barcoding with droplet-based microfluidic barcoding, introducing sample multiplexing and means to resolve multinucleated droplets for multiomic single-cell library preparation. In comparison with existing methods for multimodal profiling of chromatin accessibility and gene expression from the same cell, SUM-seq offers increased throughput and an unmatched multiplexing capability. This permits substantial scaling of the number of samples and nuclei assayed in one experiment, adhering to the needs of large-scale atlas projects, time-course experiments and perturbation screens while considerably reducing costs. We provide guidelines for experimental design and sample handling to accommodate various settings and sample types. Moreover, we discuss potential applications and provide guidelines for data processing. From sample collection to library preparation, the assay can be completed in 2-3 days, followed by sequencing and 1 day of data processing. Although the protocol can be implemented by researchers with general molecular biology skills, prior experience with single-cell assays is recommended.},
}

@article {pmid41747370,
year = {2026},
author = {Jin, C and Li, W and Liu, B and Cao, LQ and Stefan, SM and Yuan, L and Yu, X and Shi, L and Yu, H},
title = {Emerging trends and converging evidence in tumor evolution: A comprehensive review.},
journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy},
volume = {86},
number = {},
pages = {101380},
doi = {10.1016/j.drup.2026.101380},
pmid = {41747370},
issn = {1532-2084},
abstract = {BACKGROUND: Tumor evolution is a spatiotemporal dynamic process orchestrated by the interplay of genetic mutations, epigenetic reprogramming, and bidirectional microenvironmental interactions, which collectively generate the phenotypic diversity necessary for cancer progression, metastasis, and therapeutic resistance. Foundational models - linear, branched, neutral, and parallel evolution - provide complementary, albeit incomplete, frameworks to illustrate how tumors diversify through the accumulation of gradual mutations or catastrophic genomic events (e.g., chromosomal instability, disruptions in topologically associating chromatin domains). The applicability of each model is context-dependent, shaped by the specific selective pressures present across space and time. These evolutionary processes are fundamental to clonal heterogeneity, immune evasion, and the establishment of adaptive cellular ecosystems.

CONTENT: Somatic mutations, including single-base substitutions and structural variations, function as evolutionary barcodes that trace tumor lineage. Beyond the genetic code, epigenetic dysregulation-encompassing DNA hypermethylation that silences tumor suppressors and dynamic RNA modifications (e.g., m6A) that fine-tune mRNA stability-confers a layer of phenotypic plasticity. This allows for rapid, often reversible, adaptation to therapeutic and microenvironmental stresses without altering the underlying DNA sequence, thereby generating non-genetic heterogeneity. Non-coding RNAs, including microRNAs that post-transcriptionally fine-tune gene expression and circular RNAs that can function as miRNA sponges or encode peptides, comprise a critical regulatory network. They orchestrate oncogenic signaling, metastasis, and immune suppression, often in response to signals from the tumor microenvironment, thereby integrating diverse cues to shape evolutionary trajectories. The tumor microenvironment transcends a passive supportive role to act as a dynamic and decisive orchestrator of evolution: hypoxia stabilizes HIFs to drive angiogenic and metabolic reprogramming; lactate accumulation in acidic niches polarizes immunosuppressive macrophages; and neural-tumor crosstalk promotes perineural invasion. These bi-directional interactions create distinct ecological niches that exert spatially heterogeneous selection pressures, fundamentally shaping the clonal landscape. Treatment pressures (e.g., chemotherapy, radiotherapy, immunotherapy, etc.) impose evolutionary bottlenecks, selecting resistant clones and fostering cross-resistance through shared pathways. Emerging technologies - single-cell sequencing, spatial multi-omics, and liquid biopsies - now decode intra-tumoral heterogeneity, map cellular ecosystems, and monitor clonal dynamics in real time and multiple dimensions.

CONCLUSION: Integrating evolutionary models with multi-omics data reveals the complexity of tumor adaptation, emphasizing the need for temporally adaptive therapeutic strategies. Current preclinical models inadequately recapitulate human tumor-microenvironment interactions, necessitating advanced systems to bridge this translational gap. Looking forward, the convergence of artificial intelligence and dense, longitudinal biomarker profiling holds the potential to move personalized oncology beyond static genomic matching. The future lies in refining dynamic interventions that simultaneously target the dual pillars of malignancy: the molecular hallmarks of cancer cells and the ecological hallmarks of the tumor ecosystem, thereby aiming to control the process of evolution itself.},
}

@article {pmid41747097,
year = {2026},
author = {Hernández-Navarro, E and Velázquez-Machorro, V and Álvarez-Manjarrez, J},
title = {Two new species of Tulostoma from the tropical dry forest of Mexico.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/00275514.2025.2604592},
pmid = {41747097},
issn = {1557-2536},
abstract = {Mexican dry ecosystems, mainly tropical dry forests, harbor a vast and largely undiscovered fungal diversity. The stalked puffballs of Tulostoma (Basidiomycota: Agaricales) are highly cryptic, necessitating detailed and expert examination to accurately distinguish the species. A revision of the MEXU national fungarium and recent sampled specimens revealed fruiting bodies that did not match any known species. This led us to propose T. parvirufula and T. chamelensis as new species. Six collections were morphologically characterized using two microscopy techniques: light and scanning electron microscopy. DNA was extracted, the nuc rDNA internal transcribed spacer region ITS15.8S-ITS2 (ITS barcode) and D1-D2 domains of the nuc 28S rDNA were amplified and sequenced. Phylogenetic analyses were conducted using maximum likelihood and Bayesian inference methods, incorporating sequences from previous studies. Tulostoma chamelensis is distinguished by its medium-sized spore sac, a hyphal exoperidium that persists at the base, a tubular ostiole, and verrucose to subreticulate basidiospores. Tulostoma parvirufula is characterized by minute spore sacs, a tubular ostiole, a hyphal exoperidium, a reddish-brown endoperidium, and spiny basidiospores. Phylogenetic analyses place both species in a sister clade to clade 11, alongside other taxa with tubular ostioles and coarsely ornamented basidiospores, further expanding our understanding of the Tulostoma genus and its diversity in dry ecosystems.},
}

@article {pmid41745449,
year = {2026},
author = {Majnarić, I and Jelkić, M and Morić, M and Hajdek, K},
title = {Print Quality Assessment of QR Code Elements Achieved by the Digital Thermal Transfer Process.},
journal = {Journal of imaging},
volume = {12},
number = {2},
pages = {},
pmid = {41745449},
issn = {2313-433X},
abstract = {The new European Regulation (EU) 2025/40 includes provisions on modern packaging and packaging waste. It defines the use of image QR codes on packaging (items 71 and 161) and in personal documents, making line barcodes a thing of the past. The definition of a QR code is precisely specified in ISO/IEC 18004:2024. However, their implementation in printing systems is not specified and remains an important factor for their future application. Digital foil printing is a completely new hybrid printing process for applying information to highly precise applications such as QR codes, security printing, and packaging printing. The technique is characterized by a combination of two printing techniques: drop-on-demand UV inkjet followed by thermal transfer of black foil. Using a matte-coated printing substrate (Garda Matt, 300 g/m[2]), Konica Minolta KM1024 LHE Inkjet head settings, and a transfer temperature of 100 °C, the size of the square printing elements in QR codes plays a decisive role in the quality of the decoded information. The aim of this work is to investigate the possibility of realizing the basic elements of the QR code image (the profile of square elements and the success of realizing a precisely defined surface) with a variation in the thickness of the UV varnish coating (7, 14 and 21 µm), realized using the MGI JETvarnish 3DS digital machine. The most commonly used rectangular elements with a surface area of 0.01 cm[2] were tested: 0.06 cm[2], 0.25 cm[2], 1 cm[2], 4 cm[2], and 16 cm[2]. The results showed that the imprint quality is uneven for the smallest elements (square elements with base lengths of 0.1 cm and 0.25 cm). The effect is especially visible with a minimum UV varnish application of 7 μm (1 drop). By increasing the amount of UV varnish and the application thickness to 14 μm (2 drops) and 21 μm (3 drops), respectively, a significantly more stable, even reproduction of the achromatic image is achieved. The highest technical precision was achieved with a UV varnish thickness of 21 μm.},
}

@article {pmid41744646,
year = {2026},
author = {Kim, K and Kwon, J and Kim, K and Jang, MH},
title = {Assessment of Freshwater Unionidae Using Environmental DNA Metabarcoding in Lentic Ecosystems: Implications for Spatial Sampling Strategies.},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
pmid = {41744646},
issn = {2079-7737},
support = {3010133703901//Konju National University industry-university cooperation foundation/ ; },
abstract = {Environmental DNA (eDNA) metabarcoding has become a powerful, non-invasive method for detecting aquatic organisms. However, optimal sampling strategies for benthic taxa in lentic ecosystems remain unclear. This study evaluated the effectiveness of eDNA metabarcoding in detecting freshwater Unionidae mussels in lake water columns and examined their spatial and seasonal distribution patterns. We validated a mini-barcode primer targeting the mitochondrial 16S rDNA of unionid mussels through controlled laboratory experiments and field tests, confirming reliable amplification and accurate taxonomic assignment of freshwater bivalve DNA. Field surveys were conducted in four lakes within the Nakdong River basin, where eDNA samples were collected from littoral zones and from surface, mid-, and bottom layers of central lake areas during autumn and winter. Metabarcoding analysis identified 79 amplicon sequence variants (ASVs) representing four unionid taxa, with Cristaria plicata and Sinanodonta lauta comprising the majority of reads and ASVs. Overall, the number of Unionidae eDNA reads showed no significant seasonal differences, but there was notable spatial variation among sampling locations. Read numbers were significantly lower in littoral zones compared to central lake areas, with no significant differences detected among depth layers within the central zones. Species-specific analyses revealed contrasting spatial patterns: C. plicata had higher read abundance in mid- and bottom layers, while S. lauta was more frequently detected in surface and littoral samples. These findings suggest that the distribution of freshwater mussel eDNA in lakes is primarily influenced by spatial factors related to habitat preference and hydrodynamic mixing, rather than by seasonal variation during stable periods. This study offers practical insights for designing effective eDNA sampling strategies for benthic invertebrates in lentic ecosystems.},
}

@article {pmid41744641,
year = {2026},
author = {He, L and Wang, P and Wang, Z and Kong, L and Ma, J and Huang, S and Pan, M and Yang, K and Liu, W and Ma, W and Liu, X},
title = {Comparative Analysis of Morphological, Molecular, and Physicochemical Markers to Evaluate Trollius ledebouri Rchb. as a Potential Alternative Source to Trollius chinensis Bunge for High-Quality Flos Trollii Supplements.},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biology15040332},
pmid = {41744641},
issn = {2079-7737},
support = {2021YFD1600901//WeiMa/ ; 2024yjscx021//LianqingHe/ ; },
abstract = {Trollius chinensis Bunge (TCB), a perennial Ranunculaceae herb, produces Flos Trollii-dried flowers with medicinal properties including heat clearing, detoxification, and relieving oral/throat discomfort, eye pain, and cold-induced fever. TCB is mainly cultivated in northern China, while Trollius ledebouri Rchb. (TLR), distributed in Heilongjiang's Great Xing'an Mountains, is morphologically similar to TCB. However, their regulatory statuses are inconsistent, and comprehensive comparative studies are lacking. This study adopted morphological assessment, microscopy, DNA barcoding, and physicochemical analysis to explore whether TLR could be a potential alternative source of Flos Trollii. Key differences were identified: TLR's sepals are shorter than petals, whereas TCB's sepals and petals are nearly equal in length; TLR has brown secretory structures absent in TCB. Genetic distance analysis showed high conservation in ITS2 and trnL-trnF sequences between the two species, but psbA-trnH sequence divergence exceeded the 0.05 threshold. HPLC quantification revealed that TLR contained slightly higher levels of orientin and vitexin than TCB. HPLC quantification revealed that TLR contained slightly higher levels of orientin (5.370-5.377 mg/g) and vitexin (1.954-2.053 mg/g) compared to TCB (orientin: 4.493-4.620 mg/g; vitexin: 1.361-1.451 mg/g). Collectively, TLR exhibits comparable flavonoid content and holds potential as an alternative Flos Trollii source. Given the limited bioactive compounds analyzed, future research should conduct comprehensive metabolomic profiling to fully evaluate its phytochemical composition and medicinal value. These data establish chemotaxonomic markers for Trollius authentication in herbal medicine.},
}

@article {pmid41744630,
year = {2026},
author = {Badry, A and Al-Qahtni, AH and Al-Salem, AM and Al Balawi, MS and Mesfer, F and Allahyani, WS and Alqahtani, AR},
title = {DNA Barcoding and Phylogenetic Relationship of Parabuthus liosoma (Ehrenberg, 1828) (Scorpiones: Buthidae) in Saudi Arabia.},
journal = {Biology},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biology15040321},
pmid = {41744630},
issn = {2079-7737},
abstract = {(1) Background. Parabuthus liosoma is one of the largest buthid scorpion species and is endemic to Saudi Arabia and Yemen. This study provides the first DNA barcoding and phylogenetic analysis of P. liosoma from Saudi Arabia, contributing to global efforts in arachnid molecular identification and biodiversity documentation. (2) Methods. The whole genome was extracted from nine adult individuals of P. liosoma, collected from Farasan Island, southwest of Saudi Arabia. A portion of the mitochondrial DNA, specifically, the cytochrome oxidase subunit I gene (COI) sequences, was amplified and sequenced and subjected to genetic and phylogenetic analyses. (3) Results. The DNA barcoding results revealed a high level of genetic variability within P. liosoma, aiding in species identification and supporting its utility as a molecular tool for scorpion taxonomy. In addition, our results reveal a monophyletic relationship among Parabuthus species, with a clear distinction between Arabian and African lineages. (4) Conclusions. This study highlights the effectiveness of DNA barcoding as a reliable tool for species identification and taxonomy and enhances our knowledge of the evolutionary history and geographic distribution of Parabuthus scorpions. However, further research is required to elucidate the complex phylogenetic relationships within this genus.},
}

@article {pmid41743990,
year = {2026},
author = {Takács, AS and Stark, W and Szabóky, C and Bozsó, M and Kőszegi, K and Lendvai, G and Richter, I and Sramkó, G and Jordán, S},
title = {Coleophora cytisicolella sp. nov., a new species (Lepidoptera, Coleophoridae), from Austria and Hungary bred from Chamaecytisus austriacus.},
journal = {ZooKeys},
volume = {1269},
number = {},
pages = {265-281},
pmid = {41743990},
issn = {1313-2989},
abstract = {We describe Coleophora cytisicolella sp. nov. (Lepidoptera: Coleophoridae), a new species from material collected in Austria and Hungary during recent fieldwork. The collected specimens were found only in these countries within the Pannonian Biogeographical Region, and were exclusively associated with Chamaecytisus austriacus (L.) Link (Fabaceae). The taxonomic status of the new species was determined by applying traditional macro- and micromorphological methods and genetic analysis, including genitalia examinations and DNA barcoding (cytochrome c oxidase subunit I). In addition to the results of morphological comparisons and genetic analysis, we present further information on the habitat, life history, and larval food plant of this species. Our results revealed that the examined individuals belong to a species new to science, which is a member of the Coleophora genistae Stainton, 1857 species group, and described here as C. cytisicolella sp. nov. Based on the molecular results, the closest relative of the new taxon is Coleophora bruttia, a species described from southern Italy. Although the examined barcoding sequence poorly differentiated these taxa, the micromorphological features of the genitalia revealed their separate status.},
}

@article {pmid41743792,
year = {2025},
author = {Ren, Y and Wei, GW},
title = {Interpretability and Representability of Commutative Algebra, Algebraic Topology, and Topological Spectral Theory for Real-World Data.},
journal = {Advanced intelligent discovery},
volume = {},
number = {},
pages = {},
pmid = {41743792},
issn = {2943-9981},
abstract = {While recent years have witnessed a fast growth in mathematical artificial intelligence (AI). One of the most successful mathematical AI approaches is topological data analysis via persistent homology (PH) that provides explainable AI by extracting multiscale structural features from complex datasets. Interpretability is crucial for world models, the new frontier in AI that can understand and simulate reality. This article investigates the interpretability and representability of three foundational mathematical AI methods, PH, persistent Laplacians (PL) derived from topological spectral theory, and persistent commutative algebra (PCA) rooted in Stanley-Reisner theory. We apply these methods to a set of data, including geometric shapes, synthetic complexes, fullerene structures, and biomolecular systems to examine their geometric, topological, and algebraic properties. PH captures topological invariants such as connected components, loops, and voids through persistence barcodes. PL extends PH by incorporating spectral information, quantifying topological invariants, geometric stiffness, and connectivity via harmonic and nonharmonic spectra. PCA introduces algebraic invariants such as graded Betti numbers, facet persistence, and f / h -vectors, offering combinatorial, topological, geometric, and algebraic perspectives on data over scales. Comparative analysis reveals that while PH offers computational efficiency and intuitive visualization, PL provides enhanced geometric sensitivity, and PCA delivers rich algebraic interpretability. Together, these methods form a hierarchy of mathematical representations, enabling explainable and generalizable AI for real-world data.},
}

@article {pmid41743667,
year = {2026},
author = {Sarieva, K and Kagermeier, T and Lysenkov, V and Castagnetti, F and Yentuer, Z and Becker, K and Matilainen, J and Casadei, N and Mayer, S},
title = {Comparing the impact of sample multiplexing approaches for single-cell RNA-sequencing on downstream analysis using cerebellar organoids.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114780},
pmid = {41743667},
issn = {2589-0042},
abstract = {Multiplexing overcomes limited throughput in single-cell RNA sequencing (scRNA-seq). Commercial strategies include Parse Biosciences combinatorial barcoding (Parse) and 10x Genomics CellPlex with microfluidic capture (10x). It is currently unknown how these techniques differ when characterizing complex tissues. Cerebellar organoids are a highly relevant model for studying cerebellar evolution, development, and disease. Yet, their extensive characterization through scRNA-seq is ongoing. Therefore, we compared the two multiplexing techniques using cerebellar organoids. While both strategies demonstrated technical reproducibility and revealed comparable cellular diversity, we found more stressed cells in 10x than in Parse. Additionally, Parse covered a higher gene biotype diversity and showed lower mitochondrial and ribosomal protein-coding transcript fractions. In summary, we demonstrate that both techniques provide similar insight into cerebellar organoid biology, but the flexibility of experimental design, capture of long transcripts, and the level of cell stress caused by the two workflows differ.},
}

@article {pmid41742753,
year = {2026},
author = {Schuster, K and Torun, S and Kainz, I and Schwarz-Blankart, M and Hinrichs, J and Steliopoulos, P and Oellig, C},
title = {Spectral Similarity Score (SSS)-Barcoding for the Quality Control of LACTEM Emulsifiers by High-Performance Thin-Layer Chromatography.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11928},
pmid = {41742753},
issn = {1520-5118},
abstract = {LACTEM emulsifiers are widely applied in the food industry to adjust and improve techno-functional properties of food products. The study introduces a high-performance thin-layer chromatography-fluorescence detection (HPTLC-FLD) fingerprint method for the similarity assessment of these emulsifiers using a straightforward barcoding approach based on the concept of spectral similarity scores (SSS), referred to as SSS-barcoding. Analysis of 21 LACTEM emulsifiers showed similarities between two emulsifiers as low as 67%, despite the same product labeling. The method also revealed batch-to-batch variability. Limitations were identified when applying the method to fatty matrices. Finally, partial least-squares regression (PLSR) was applied as a proof-of-concept to predict the techno-functional properties of aerosol whipping cream, such as drainage, apparent viscosity, foam firmness, particle size (D90,3), and overrun, from the densitometric data.},
}

@article {pmid41742734,
year = {2026},
author = {Musiol, M and Grabner, D and Díaz-Morales, D and Nachev, M and Descamps, S and Fonteneau, F and Sures, B and Carravieri, A},
title = {Diversity of helminths parasitising North-East Atlantic and Antarctic seabirds.},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e22},
doi = {10.1017/S0022149X26101163},
pmid = {41742734},
issn = {1475-2697},
abstract = {Seabirds are largely used as indicators of Ocean health and are final hosts of several helminth parasites. However, the helminth fauna of seabirds is still poorly studied. Here, we quantified the diversity of gastrointestinal parasites in 52 individuals belonging to 10 seabird species with different habitat preferences and feeding strategies from the North-East Atlantic and Antarctica. Fresh carcasses were collected in Northern France and at Svarthamaren (Dronning Maud Land, Antarctica), helminth parasites were extracted from the gastrointestinal tract, and were identified by morphological inspection and DNA barcoding. In total, we identified 13 helminth taxa. North-East Atlantic seabirds hosted parasites from four helminth groups (Acanthocephala, Cestoda, Nematoda, Trematoda), while Antarctic seabirds hosted Acanthocephala and Cestoda only. The largest parasite diversity was found in northern fulmars Fulmarus glacialis (9 species), European shags Gulosus aristotelis (5 species), razorbills Alca torda (4 species), and black-legged kittiwakes Rissa tridactyla (4 species). Co-infections with multiple parasite species in single hosts were common. Oceanic diving species were found to be the most parasite-poor, with common guillemots Uria aalge and Atlantic puffins Fratercula arctica hosting no parasites. In contrast, oceanic surface-feeding seabirds had a large parasite diversity, which notably included trematodes, and was comparable to that of coastal species. To the best of our knowledge, this study identified 9 new host-parasite associations: Andracantha sp. in northern fulmars and south polar skuas Stercorarius maccormicki, C. septentrionale in northern fulmars and black-legged kittiwakes, a species of Microphallidae in black-legged kittiwakes, Cardiocephaloides longicollis in European shags, Cryptocotyle lingua in Sandwich terns Thalasseus sandvicensis, and a clophyllidean species in south polar skuas and Antarctic petrels Thalassoica antarctica.},
}

@article {pmid41741043,
year = {2026},
author = {González, MA and Mateus, TL and Rodrigues, FT and Martins, F and Martínez-Calabuig, N and Saldaña, A and Panadero, R and Estruch, J and Bravo-Barriga, D and Carrera-Faja, L},
title = {New records of Lipoptena andaluciensis (Diptera: Hippoboscidae) in the Iberian Peninsula with a pictorial key of the genus.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {68},
number = {},
pages = {101428},
doi = {10.1016/j.vprsr.2026.101428},
pmid = {41741043},
issn = {2405-9390},
abstract = {Since its first description in southern Spain, Lipoptena andaluciensis (Diptera: Hippoboscidae) has drawn increasing attention due to its uncertain origin and distribution. In this study, we report new records of L. andaluciensis from geographically distant regions, including the Castelo Branco district in Portugal and three different northern Spanish provinces (Lérida, Tarragona, and Aragón). A total of 26 specimens, identified as unwinged L. andaluciensis based on morphological traits and COI barcoding, were collected between 2022 and 2024 during several field surveys on red deer (Cervus elaphus) and roe deer (Capreolus capreolus). Additionally, Lipoptena cervi and Hippobosca equina were also collected on hosts. These recent records, indicate that the species may have been previously overlooked or misidentified, underscores the need for enhanced taxonomic resolution and expanded surveillance. To facilitate accurate identification, we provide a pictorial key to distinguish among the six European Lipoptena species, with special emphasis on Lipoptena fortisetosa, L. cervi, and L. andaluciensis. We also highlight the importance of combining detailed morphological and molecular analyses of both recent and historical specimens to prevent misidentifications and to better understand the biogeography of this emerging species.},
}

@article {pmid41741041,
year = {2026},
author = {Kunprom, C and Wannasingha, W and Pramual, P},
title = {Diversity, abundance and host blood meal of mosquitoes (Diptera: Culicidae) from different habitat types in Thailand.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {68},
number = {},
pages = {101427},
doi = {10.1016/j.vprsr.2026.101427},
pmid = {41741041},
issn = {2405-9390},
abstract = {This study investigated diversity, abundance, host blood sources and haemosporidian parasite infection of mosquitoes (Diptera: Culicidae) collected from 25 sites across Thailand, representing three habitat types: livestock shelters, commercial farms and natural areas. A total of 757 specimens were collected, with the highest abundance observed in livestock shelters (n = 654), followed by farms (n = 67) and natural areas (n = 36). Identification based on morphology and DNA barcode revealed 23 mosquito species, with the genus Culex being the most abundance representing >50% (379 of 757) of the total collected specimens. High diversity and abundance in livestock shelters, due to high density of the host blood sources and also our sampling biased because specimens were collected mostly (17 of 25 collections) from this habitat type. In contrast, natural areas had lower mosquito abundance, possibly due to fewer hosts and fluctuating environmental factors. The findings highlight that habitat type and host availability significantly influence mosquito community structure and thereby potentially influencing pathogen transmission dynamics. Host blood meal analysis using mitochondrial cytochrome b indicated that cattle are the most preferable host blood source of these mosquito species. Haemosporidian parasites were detected in nine mosquito specimens, of three Culex mosquito species. Six were identified as Plasmodium juxtanucleare, one was P. gallinaceum and two were Leucocytozoon caulleryi. These results provide baseline data to guide targeted vector surveillance and control strategies in Thailand.},
}

@article {pmid41741040,
year = {2026},
author = {Nallan, K and Ayyavu, V and Ayyanar, E and Thiruppathi, B and Ramalingam, R and Rahi, M and Rajaiah, P},
title = {DNA barcoding identifies hard tick (Acari: Ixodidae) species infesting domesticated animals in Tamil Nadu, South India.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {68},
number = {},
pages = {101425},
doi = {10.1016/j.vprsr.2026.101425},
pmid = {41741040},
issn = {2405-9390},
abstract = {The diverse and vast ecological landscapes of India support a rich diversity of ticks, many of which are known vectors of a wide range of pathogens. Accurate identification of tick species is critical for incriminating specific vectors involved in pathogen transmission. The present study aims to generate DNA barcodes using molecular markers for the identification of tick fauna from Tamil Nadu, southern India, where molecular taxonomic studies remain limited. A total of 57 specimens representing 12 different species were subjected to DNA barcoding using cytochrome c oxidase subunit I (COI) and internal transcribed spacer 2 (ITS2). Polymerase chain reaction (PCR) assays targeting the COI gene were successful in 7 species from four genera: Haemaphysalis, Hyalomma, Rhipicephalus, and Amblyomma. Similarly, 6 species from two genera, Rhipicephalus and Haemaphysalis, were successfully amplified using the ITS2 gene marker. Further analysis of inter-species diversity based on COI markers across eight species revealed better resolution compared to ITS2 markers. Inter-species distances of 16%, 15%, 14%, and 13% were recorded among four Rhipicephalus species using both markers, with the highest genetic divergence (16%) observed between R. microplus and R. sanguineus. The lowest inter-species divergence was 6% (COI) and 1% (ITS2), observed between R. microplus and R. annulatus. To our knowledge, this study provides the first DNA barcode records based on COI for Hyalomma anatolicum and Amblyomma integrum, and based on ITS2 for Rhipicephalus annulatus and Haemaphysalis intermedia from India. In conclusion, for four Rhipicephalus and two Haemaphysalis species, the dual-marker barcoding approach effectively complements conventional identification methods by resolving ambiguities arising from morphological similarities among tick species in this region.},
}

@article {pmid41740420,
year = {2026},
author = {Wei, X and Cai, L and Li, N and Fang, Y and Wang, J and Zhu, Y},
title = {High-throughput screening of bladder cancer exosome biomarkers by barcodes integrated herringbone microfluidics.},
journal = {Biosensors & bioelectronics},
volume = {302},
number = {},
pages = {118545},
doi = {10.1016/j.bios.2026.118545},
pmid = {41740420},
issn = {1873-4235},
abstract = {Bladder cancer (BC) ranks among the most prevalent urological malignancieswith high mortality, driving an urgent need for efficient, non-invasive diagnostic methods. In this work, we developed an integrated microfluidic platform that combines herringbone mixers with photonic crystal (PhC)-encoded, core-shell hydrogel microcarriers for efficient exosome enrichment and multiplexed biomarker detection. The core-shell hydrogel microcarriersoffer stable structural color barcoding immune to assay conditions and a substantiallyexpanded surface area for enhanced sensitivity. Concurrently, the herringbone structures generate controlled microturbulence, significantly improving fluid mixing and extending target-probe contact time. By employing this platform to profile a panel of six proteomic biomarkers derived from bladder cancer exosomes, we demonstrate efficient high-throughput analysisof urinary exosomal signatures. The platform thus shows excellent diagnostic performance, offering a promising approach for the early detection and monitoring of BC in clinical practice.},
}

@article {pmid41736984,
year = {2026},
author = {Seymour, M and Wong, K},
title = {Seasonality, Moisture, and Host Community Structure of Haemaphysalis Ticks in a Subtropical Urban Mosaic in Hong Kong, China.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73140},
pmid = {41736984},
issn = {2045-7758},
abstract = {Ticks (Ixodida) are ecologically and epidemiologically important parasites, yet their diversity, host associations, and environmental drivers remain poorly resolved in many parts of the world, including subtropical and urban Hong Kong. Here, we combined wet-season spatial surveys (23 sites in 2023) with monthly temporal sampling (four sites across 11 months in 2024) to characterize the spatiotemporal dynamics of ticks in Hong Kong. Ticks were collected using standardized drags, CO[2] traps, and opportunistic sampling; adults were identified morphologically and validated via COI barcoding. Vertebrate host use was inferred through iDNA metabarcoding of tick abdomens. Our findings provide the first documented widespread occurrence of Haemaphysalis hystricis and Haemaphysalis formosensis in Hong Kong. Additionally, we provide initial insights into local life stage-specific seasonality dynamics, whereby adult peaks in late winter-spring, nymphs are elevated in the cool dry months, and larvae noticeably surge during the wet season. In assessing the potential environmental drivers, adult abundance was most strongly associated with moisture (relative humidity and dew point). Presence-only models suggested additional contributions from porcupine (Hystrix spp.) occurrence and temperature. iDNA analysis suggests primarily mammalian host feeding (73.7%), specficially wild boar (Sus spp.) and porcupines being the most frequent (43.4%), with additional detections of civets, dogs, cattle, and several bird families. In general, H. hystricis exhibited a broader host spectrum than H. formosensis. Overall, these results indicate that moisture availability and mammal host communities influence Haemaphysalis tick distributions across Hong Kong's mosaic landscape. Future consideration should be made for expanding spatial and temporal surveillance, integrating microhabitat moisture and host density data, and coupling ecological surveys with pathogen screening to inform One Health surveillance and management.},
}

@article {pmid41736983,
year = {2026},
author = {Seidensticker, MT and Bullington, LS and Morales, SE and Ramsey, PW},
title = {A Regional DNA Barcode Library for Northern Rocky Mountain Arthropods to Support Biodiversity and Molecular Ecological Research.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73150},
pmid = {41736983},
issn = {2045-7758},
abstract = {Arthropod DNA barcode reference libraries have advanced ecological research but remain incomplete in many areas, including the western United States. To improve coverage in the Northern Rocky Mountains, we developed the MPG Ranch Arthropod Library (MPG-AL), a cytochrome oxidase I (COI) DNA barcode reference library for local arthropods in west-central Montana. From 2017 to 2019, we collected 86,533 specimens from various habitats, generating 52,270 DNA barcodes for arthropod taxa from 38 orders, 389 families, 1668 genera, and 1793 species. A comparison of the MPG-AL taxonomic coverage with a combined dataset of publicly accessible Montana arthropod DNA barcodes in the Barcode of Life Database (BOLD) and Montana Natural Heritage Program occurrence records revealed that the MPG-AL added references representing 5154 Barcode Index Numbers (BINs) to BOLD. These additions mark a 280% increase for Montana arthropod DNA barcodes, including 1140 new BINs for taxa previously lacking reference barcode sequences in BOLD. The MPG-AL provides a substantial foundation for establishing a comprehensive arthropod DNA barcode database in the Northern Rocky Mountain ecoregion. However, many taxa still lack reference barcode sequences, particularly in large, diverse insect orders. Future barcoding efforts are encouraged to expand regional taxonomic coverage through targeted sampling and collaborations with regional entomological collections. A comprehensive regional arthropod DNA barcode library will enhance our understanding of arthropod population trends and trophic relationships in the western United States amid persistent threats such as climate change, habitat loss, pesticides, and invasive species.},
}

@article {pmid41736977,
year = {2026},
author = {Castellanos-Galindo, GA and Robertson, DR and Bravo, V and Saltonstall, K and Sanchez, P and Morales, L and Cahill, R and Torchin, ME},
title = {First Confirmed Record of a Bull Shark in Lake Gatun, the Freshwater Body of the Panama Canal.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73114},
pmid = {41736977},
issn = {2045-7758},
abstract = {Bull Sharks are circumtropical top predators able to tolerate a wide range of salinity conditions that include freshwater. In several areas of Central America this species is known to migrate upstream in rivers and is commonly found in freshwater. The Panama Canal, an engineered system critical for global shipping, has experienced repeated marine fish incursions into Lake Gatun, the freshwater portion of the system, since it opened over 100 years ago. With increased numbers of species and abundance of these marine migrants into the system it is surprising that no credible reports of Bull Sharks have been made to date. Here we present the first confirmed report of a Bull Shark captured in Lake Gatun, 30 km from the Pacific entrance of the Canal. Analyzing its DNA barcode and vertebral morphometrics and chemistry, we were able to infer the origin (Pacific Ocean), the total length and age (120-150 cm, 2-3 year old) and likely pupping of this shark in low salinity areas adjacent to the Canal. The recent capture of more bull sharks by the artisanal fisher who collected the study shark and a video of sharks at the seaward entrance to the new Pacific locks indicates that there is the potential for increased contact between Pacific and Atlantic Bull Shark populations through the Panama Canal.},
}

@article {pmid41736754,
year = {2026},
author = {Han, MH and Chang, JS and Tan, JK and Yeap, SK and Ng, WL and Yong, YS},
title = {A double agent? Unveiling the chemical profile of the pathogenic fungus Pyrrhoderma noxium as an endophyte in true mangroves.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20826},
pmid = {41736754},
issn = {2167-8359},
mesh = {*Endophytes/chemistry/isolation & purification/genetics ; Plant Leaves/microbiology ; Phylogeny ; Tandem Mass Spectrometry ; Chromatography, Liquid ; *Plant Diseases/microbiology ; *Rhizophoraceae/microbiology ; Wetlands ; },
abstract = {Pyrrhoderma noxium, commonly referred to as the brown root rot pathogen, has previously been recognized as a pathogenic species. However, it has been largely overlooked for its capability to produce useful bioactive compounds. In this study, we report for the first time that the fungus has been isolated as an endophytic fungus (EF) from the leaves of true mangrove plant species, and chemically profiled the fungal isolates to identify potential bioactive compounds. Three P. noxium isolates (AA2AA, BG3BA and SA2AA) were successfully identified via DNA barcoding and were subjected to methanolic extraction prior to chemical profiling via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Despite proximity of the host plants, our results, comprising morphological characteristics, phylogenetic analysis, and the Jaccard Similarity Index based on the detected compounds showed that AA2AA and SA2AA possess greater similarity compared to any of them with BG3BA. Compounds produced by the P. noxium isolates were classified into six main classes (i.e., amino acids and peptides, aromatics, terpenoids, phenolics, other lipids, and other alkaloids) and these compounds are believed to facilitate the equilibrium in endophyte-host interactions. According to literature, the identified compounds from the P. noxium isolates have previously been reported to possess anticancer, antioxidant, anti-inflammatory, antibacterial, antifungal, and antiviral activities, indicating significant potential for pharmaceutical applications. Besides, the chemical profiles of the P. noxium isolates determined in this study may serve as a reference for subsequent research on the biological control of P. noxium infection.},
}

*Endophytes/chemistry/isolation & purification/genetics
Plant Leaves/microbiology
Phylogeny
Tandem Mass Spectrometry
Chromatography, Liquid
*Plant Diseases/microbiology
*Rhizophoraceae/microbiology
Wetlands

@article {pmid41736749,
year = {2026},
author = {Hestetun, JT and Lanzén, A and Kongsrud, JA and Alvestad, T and Johansen, PO and Dahlgren, TG},
title = {Metabarcoding and targeted barcoding can enhance Norwegian Continental Shelf macrofauna species inventories.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20849},
pmid = {41736749},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Norway ; *Biodiversity ; Electron Transport Complex IV/genetics ; RNA, Ribosomal, 18S/genetics ; *Aquatic Organisms/genetics/classification ; },
abstract = {Metabarcoding of bulk community samples is a powerful tool to characterize marine softbottom macrofaunal communities, but high-quality taxonomic assignment is dependent on adequate sequence coverage in taxonomic databases. Here, our main aim was to advance metabarcoding as a complement to benthic morphological taxonomy in biodiversity inventories on the Norwegian Continental Shelf (NCS). We used morphological taxonomy, barcoding, and metabarcoding for two objectives, namely to (1) increase macrofauna barcode coverage for a selection of species, and (2) provide an in-depth comparison of morphology and metabarcoding data from mock bulk samples of softbottom macrofauna. We used morphological taxonomy to identify 257 morphotaxa from 32 sieved grab sampling stations at eight areas on the NCS. For the first objective (barcoding), 45 species (95 specimens) were selected from these 32 stations based on incomplete sequence coverage in online repositories, obtaining barcodes for 25 (cytochrome oxidase subunit 1, COI), 35 (18S rDNA), and 24 (28S rDNA) species. Results typically showed an increase in taxonomic assignment of 4-5 ranks in the subsequent metabarcoding data for these particular species. For the second objective (metabarcoding), mock bulk samples with a known taxonomic composition including Annelida, Arthropoda, Mollusca and a single brachiopod, were sequenced using the COI and 18S rDNA V1-V2 partitions from a subset of eight stations from three of the areas. COI Barcode of Life Data System (BOLD) and MIDORI2 assignment with some additional manual sequence curation recovered 100 distinct species-rank taxa compared to 120 species-rank taxa (152 taxa total) from morphology based taxonomic identification. Assignment of 18S rDNA using SILVA recovered 29 unique species including 13 not found in the COI data. Annelida, Arthropoda, and Mollusca were all well-represented in metabarcoding data, and abundance biases were associated with disparate species in a range of clades. Taxonomic congruence was high at high rank, but in some cases species assignments resolved as genus only or sibling species to those identified by morphological taxonomy even when present in one of the databases used. Potential explanations include species genotype variation, putative species complexes and remnant sequencing artifacts. The study findings show the potential of metabarcoding in an area with relatively high taxonomic database coverage. Integrating metabarcoding datasets can increase biodiversity inventory pace and uncover hidden biodiversity, but performance is dependent on database coverage, highlighting the importance of barcoding efforts in biodiversity studies, and metabarcoding-based inventories need to be critically examined by taxonomic expertise.},
}

*DNA Barcoding, Taxonomic/methods
Animals
Norway
*Biodiversity
Electron Transport Complex IV/genetics
RNA, Ribosomal, 18S/genetics
*Aquatic Organisms/genetics/classification

@article {pmid41732722,
year = {2026},
author = {Englund, M and Hancock, G and Laiho, E and Mappes, J and Sihvonen, P and Söderholm, M and Turunen, A and Lee, KM},
title = {Quantitative image analysis applied to revise the taxonomy of the Palearctic Earophila badiata species group (Lepidoptera: Geometridae: Larentiinae).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20620},
pmid = {41732722},
issn = {2167-8359},
mesh = {Animals ; Male ; Female ; Phylogeny ; *Moths/anatomy & histology/classification/genetics ; DNA Barcoding, Taxonomic ; Wings, Animal/anatomy & histology ; Finland ; Sex Characteristics ; DNA, Mitochondrial/genetics ; X-Ray Microtomography ; },
abstract = {The geometrid moth Earophila badiata (Denis & Schiffermüller, 1775), which occurs widely in the Palearctic realm, has rapidly filled a large gap in its range across southern Finland during the past two decades, prompting a re-evaluation of its taxonomy. Using an integrative taxonomic approach including a quantitative wing image analysis combined with genitalia morphology and mitochondrial DNA barcoding (mtCOI) analyses, we reassessed the status of the described taxa within the E. badiata species group. Quantitative analysis of forewing colours revealed strong sexual dimorphism and significant effects of specimen wear and age on colouration, but no consistent morphological differences between the nominotypical subspecies E. badiata badiata and taxon E. badiata fennokarelica (Kaisila, 1945). Comparative genitalia morphology, including micro-CT imaging, showed no diagnostic differences among closely related E. badiata, E. kolomietsi Vasilenko, 2003, and E. pseudobadiata Vasilenko, 2007, supporting the synonymy of these taxa. Molecular phylogeny and haplotype analysis confirmed monophyly among Eurasian samples with low genetic divergence (<0.63%), but implying a distinct lineage for North African E. badiata tellensis (Herbulot, 1957). Based on these findings, we propose synonymizing E. kolomietsi and E. pseudobadiata with E. badiata syn. n. and classify the E. badiata taxon fennokarelica as a morphological form of E. badiata below the subspecific rank. Our results challenge the current subspecies delineation and support a revision of taxonomic boundaries within this group, highlighting the value of integrative taxonomy for resolving complex relationships among closely related species.},
}

Animals
Male
Female
Phylogeny
*Moths/anatomy & histology/classification/genetics
DNA Barcoding, Taxonomic
Wings, Animal/anatomy & histology
Finland
Sex Characteristics
DNA, Mitochondrial/genetics
X-Ray Microtomography

@article {pmid41732445,
year = {2026},
author = {Prasetyo, DB and Vallecillo, T and Krupa, E and Gratiaux, J and Vol, A and Loyer, M and Martinet, JP and Di Brasi, Q and Vongphayloth, K and Mathieu, B and Boyer, S and Izri, A and Gay, F and Depaquit, J},
title = {Taxonomic assessment of phlebotomine sand flies in Southeast Asia based on records from Cambodia.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {9},
number = {},
pages = {100356},
pmid = {41732445},
issn = {2667-114X},
abstract = {Previously considered a leishmaniasis-free region, Southeast Asia has reported emerging cases over the past 20 years. This has renewed interest in the primary vectors, the phlebotomine sand flies. However, information on these vectors in Southeast Asia, particularly in Cambodia, remains scarce. To update distribution records and assess species diversity, CDC light traps were deployed to collect sand flies at 16 locations across several provinces of Cambodia in 2011 and 2014. A total of 940 sand flies were collected and identified both morphologically and molecularly using cytochrome b as a marker gene. Species identification revealed the presence of four genera and 10 species. The predominant species was Grassomyia sp. (21.9%), followed by Sergentomyia sylvatica (21.4%) and Sergentomyia iyengari Group (16.7%). Generally identified as Grassomyia indica, the Grassomyia specimens found in this study exhibited morphological disparities, although genetic analysis showed homogeneity with Gr. indica from other countries. Sergentomyia iyengari and Sergentomyia barraudi each displayed two distinct groups based on both morphological and genetic analyses, suggesting that different species within these complexes are present in Cambodia. Further investigation of these species complexes is warranted, since genomic evidence suggests the existence of previously undescribed species in this region.},
}

@article {pmid41730944,
year = {2026},
author = {Nascimento, CL and Tonge, DP and Tripet, F},
title = {In silico DNA barcoding surpasses whole genome sequencing for species identification from vector surveillance pools.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-39937-y},
pmid = {41730944},
issn = {2045-2322},
}

@article {pmid41730100,
year = {2026},
author = {Liang, C and Li, Q and Chen, B and Zhai, T and Luo, X and Yang, Y and Qian, J and Zhao, D and Luo, S and Wang, F and Li, Q and Shen, J and Fan, C},
title = {Reactive oxygen species-resistant ultrastable super-resolution DNA framework dots.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {9},
pages = {e2514438123},
doi = {10.1073/pnas.2514438123},
pmid = {41730100},
issn = {1091-6490},
support = {2023YFB3208200//the national key R&D program of China/ ; T2188102//the national natural science foundation of China/ ; },
mesh = {*Reactive Oxygen Species/chemistry/metabolism ; *DNA/chemistry ; Humans ; Fluorescent Dyes/chemistry ; Photobleaching ; Green Fluorescent Proteins/chemistry ; Microscopy, Fluorescence/methods ; *Quantum Dots/chemistry ; },
abstract = {Nanoconfinement as observed in natural (e.g. green fluorescent protein, GFP) or artificial (metal-organic or covalent organic frameworks) systems effectively modulates chemical and physical properties of encapsulated molecules for various photonic, electronic, or catalytic applications. Inspired by GFP's barrel-like peptide scaffold, which stabilizes the chromophore within a confined space, here we develop photobleaching-resistant super-resolution DNA framework (SDF) dots that enables programmable confinement of various types of fluorophores within the inner cavity resembling GFP. We find that SDF dots are resistant to reactive oxygen species-induced photobleaching due to the shielding effects of DNA frameworks. SDF dots with four fluorophores labeling inside of the cavity leads to ~1.8-fold enhancement in photostability compared to the corner labeling, whereas ~50-fold enhancement compared to single fluorophore labeled on double-stranded DNA. These ultrastable SDF dots are readily adaptable for super-resolution imaging including stimulated emission depletion (STED) and structured illumination microscopy (SIM) imaging. We realize STED imaging of live cell membranes over 30 min. We further construct ultrastable super-resolution SIM barcodes that can distinguish eighteen colored barcodes with a spatial resolution of ~70 nm. This strategy provides a versatile platform for engineering ultrastable fluorescent probes for advancing super-resolution imaging and single-particle tracking in biophysics and biomedical research.},
}

*Reactive Oxygen Species/chemistry/metabolism
*DNA/chemistry
Humans
Fluorescent Dyes/chemistry
Photobleaching
Green Fluorescent Proteins/chemistry
Microscopy, Fluorescence/methods
*Quantum Dots/chemistry

@article {pmid41729925,
year = {2026},
author = {Lan, L and Mao, J and Mao, B and Liu, S and Li, T and Zhou, X and Lei, H and Wu, S and Chen, J and Zhang, X},
title = {Intraspecific identification of Actinidia eriantha Benth. based on chloroplast genes.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0342803},
pmid = {41729925},
issn = {1932-6203},
mesh = {Genome, Chloroplast ; *DNA Barcoding, Taxonomic/methods ; *Actinidia/genetics/classification ; Haplotypes ; Phylogeny ; *Genes, Chloroplast ; *Chloroplasts/genetics ; },
abstract = {OBJECTIVE: This study aimed to identify specific DNA barcodes based on the chloroplast genome of Actinidia eriantha Benth. and to utilize these barcodes for the identification of germplasm resources from different geographic origins.

METHODS: The chloroplast genome of A. eriantha samples were sequenced using the Illumina NovaSeq PE150 platform. Specific highly variable regions were identified through mVISTA alignment and nucleotide diversity analysis. Haplotypes of samples from various regions were further analyzed based on the selected DNA barcode candidate fragments.

RESULTS: The complete chloroplast genomes of three A. eriantha from different locations were 156,955-157,100 bp in length and exhibited a typical quadripartite circular structure, with 88 genes annotated in each genome. Comparative analyses with mVISTA and nucleotide diversity indices identified matK, trnK(UUU), ycf1, and the atpH_atpI intergenic spacer as candidate regions for specific DNA barcodes. Among these, trnK(UUU), ycf1, and atpH_atpI were selected for further analysis based on PCR amplification efficiency. Sequencing of these three regions across 223 samples from 21 locations in six provinces revealed 7, 10, and 39 polymorphic sites, respectively, which defined 6, 4, and 6 haplotypes. A combined analysis of the three loci identified 56 polymorphic sites and 12 distinct haplotypes (Hap1-Hap12), with pairwise genetic distances ranging from 0 to 1.96%. Six haplotypes were found to be unique to specific geographic regions, suggesting their potential as molecular markers for tracing the geographic origin of A. eriantha.

CONCLUSION: The chloroplast gene regions trnK(UUU), ycf1, and atpH_atpI, identified through comparative chloroplast genomics, serve as effective DNA barcodes for the intraspecific identification of A. eriantha germplasm. These markers provide a molecular basis for future efforts in geographic origin tracing, germplasm conservation, and breeding of this species.},
}

Genome, Chloroplast
*DNA Barcoding, Taxonomic/methods
*Actinidia/genetics/classification
Haplotypes
Phylogeny
*Genes, Chloroplast
*Chloroplasts/genetics

@article {pmid41728918,
year = {2026},
author = {Summerbell, RC and Scott, JA},
title = {Dermatophyte speciation processes reconciled with current phylogenetic species concepts.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myag017},
pmid = {41728918},
issn = {1460-2709},
abstract = {The family Arthrodermataceae, the dermatophytes and allies, ancestrally began with Ascomycetous bifactorial sexual cycles built into an ecology that also featured considerable clonal propagation via conidia. When keratinolytic capabilities made ecological crossover to dermatopathogenicity possible, that conventional cycle, requiring moist, deposited keratinous material, could only be maintained by pathogens infecting animals burrowing or denning in habitats with soil. Lineages adapted to animals not nesting in soil became established clonally from representatives of single mating types. They became transformed in morphology and physiology, tending to develop reduced conidiation and more exogenous growth factor requirements in addition to retaining specific host adaptations. Viewing this speciation process through the lens of population biology tools designed for interbreeding populations can give a distorted picture, since the often ecologically neutral factors considered, like spacer regions, introns, restriction sites and single nucleotide polymorphisms, likely have a slower rate of change over time than the directly adaptive factors enabling these unifactorial radiate host switching events. The current state of species concepts in the dermatophytes and related, mostly nonpathogenic dermatophytoids is reviewed in light of this contrast of perspectives. Practical steps that can be taken in the clinical laboratory to make accurate identifications based on accurate species concepts are addressed. Some species concepts are supported in lineages that have previously reduced to lower rank, such as Trichophyton indotineae, T. interdigitale, and T. soudanense. The diversity of internal transcribed spacer barcodes in T. tonsurans suggests that research into clinical differences among genotypes is warranted.},
}

@article {pmid41728369,
year = {2026},
author = {},
title = {Correction to "A Barcoding-Based Scat-Analysis Assessment of Eurasian Otter Lutra lutra Diet on Kinmen Island".},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73144},
doi = {10.1002/ece3.73144},
pmid = {41728369},
issn = {2045-7758},
abstract = {[This corrects the article DOI: 10.1002/ece3.7712.].},
}

@article {pmid41728022,
year = {2026},
author = {Shi, Y and Liu, P and Yao, Y and Liu, K},
title = {A new spider species of Scytodes Latreille, 1804 from Jiangxi Province, southern China (Araneae, Scytodidae).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e181164},
pmid = {41728022},
issn = {1314-2828},
abstract = {BACKGROUND: Despite the increasing discovery of new spider species in Jiangxi Province, most are entelegynes or mygalomorphs, with haplogyne spiders being seldom reported. However, during a decade-long survey of spiders in Jinggangshan National Nature Reserve, two species of Scytodes were identified, including one known species, S. liui Wang, 1994 and one new species.

NEW INFORMATION: A new species, Scytodes tanjiashui Liu, sp. nov., is described from Jinggangshan National Nature Reserve, Jiangxi Province, China. Morphological illustrations, SEM pictures, ink drawing, DNA barcode, photos of live specimens and a distribution map are given. The total number of the known species of Scytodes from China is raised to 11.},
}

@article {pmid41727160,
year = {2026},
author = {Mojumder, A and Nguyen, KW and Sullivan, CS},
title = {Divergent Fates of Kidney-Resident Polyomaviruses: Stable Shedding Versus Near-Silent Persistence.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.12.705499},
pmid = {41727160},
issn = {2692-8205},
abstract = {Polyomaviruses establish long-term infection in the kidney and are intermittently shed in urine. However, the relationship between kidney-resident viral genomes and urinary shedding during persistent infection remains poorly defined. Using a genetically barcoded murine polyomavirus library, we tracked thousands of viral lineages in vivo by pairing longitudinal urine sampling with endpoint barcode sequencing of kidney tissue in four mice. Across all animals, kidney infection consistently resolved into two stable viral populations, with near-silent persistence as the dominant fate. Most kidney-resident barcodes were never detected in late urine at late stages of infection, even though many reached substantial abundance within the kidney, demonstrating that kidney viral genome levels alone do not predict urinary shedding. In contrast, only a small minority of kidney barcodes contributed disproportionately to urine virus output at late timepoints, and these barcodes exhibited stable longitudinal behavior, with repeated detection in urine over time and markedly higher peak urine abundance than late non-shed or random barcode controls. Shedding behavior was not explained by input virus stock abundance, barcode sequence features, predicted miRNA targeting, or ongoing reseeding from blood or other tissues. Instead, barcodes that ultimately dominated late urine already showed elevated urine detection early after infection, indicating that shedding fate is established early and maintained throughout persistent infection. Together, these findings reveal that persistent kidney infection is a structured reservoir composed of a large population of deeply restricted viral genomes and a smaller, stable subset that repeatedly produces urine-detectable viruses, with concurrent smoldering infections and latency-like restriction representing one possible model to explain the sharply different probabilities of shedding among kidney-resident genomes.},
}

@article {pmid41726901,
year = {2026},
author = {Gao, T and Weng, C and Johnson, I and Poeschla, M and Gudera, J and King, E and Rouya, C and Donovan, A and Bourke, L and Shao, Y and Marquez, E and Tyagi, R and Zon, LI and Weissman, JS and Sankaran, VG},
title = {Modeling mitochondrial inheritance enables high-precision single-cell lineage tracing in humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.12.705660},
pmid = {41726901},
issn = {2692-8205},
abstract = {Somatic mutations in mitochondrial DNA (mtDNA) provide natural barcodes that enable engineering-free lineage tracing in human tissues, but the complex dynamics of mtDNA inheritance across cell divisions and incomplete sampling of mtDNA introduce uncertainty in reconstructed lineages. Here, we present MitoDrift, a probabilistic framework that integrates Wright-Fisher drift dynamics with sparse single-cell measurements to produce confidence-refined lineage trees enriched for accurate clonal relationships. Validation with gold-standard lentiviral barcoding and whole-genome sequencing demonstrates that MitoDrift outperforms existing tree reconstruction methods in precision while maintaining high clonal recovery, enabling robust analyses linking lineage to cell state. Applying MitoDrift to human hematopoiesis reveals an age-associated decline in clonal diversity with differential impact across cell types and identifies heritable regulatory programs in hematopoietic stem cells in vivo, linking AP-1/stress-associated programs to clonal expansions. In multiple myeloma, MitoDrift captures therapy-associated clonal remodeling undetectable by copy number analysis, revealing phenotypic transitions and linking gene regulatory programs to differential drug sensitivity. Collectively, MitoDrift enables high-precision lineage tracing at scale and establishes quantitative lineage-state analysis in primary human tissues, linking clonal history to transcriptional and epigenetic programs in tissue homeostasis, aging, and disease.},
}

@article {pmid41725736,
year = {2026},
author = {Vargas, HA},
title = {A new species of Aristotelia Hübner (Lepidoptera, Gelechiidae, Aristoteliinae) from northern Chile.},
journal = {ZooKeys},
volume = {1269},
number = {},
pages = {199-210},
pmid = {41725736},
issn = {1313-2989},
abstract = {Aristotelia Hübner, [1825] (Lepidoptera, Gelechiidae, Aristoteliinae) is a widely distributed moth genus comprising 153 described species, many of which have striking forewings. The variation in genitalia morphology among some members suggests that, as currently circumscribed, the genus is probably not monophyletic. The only Chilean species of Aristotelia previously described inhabits the central region of the country. A second Chilean representative, Aristotelia aguilensis sp. nov., is described and illustrated based on adults reared from larvae collected on Hoffmannseggia minor (Phil.) Ulibarri (Fabaceae) in the Atacama Desert. The genetic divergence between DNA barcode sequences of the new species was 0.3% (K2P), while it ranged from 11% to 17.1% for other members of the genus. This study reveals a new piece of the Aristotelia puzzle, adds a new member to the poorly known gelechiid fauna of northern Chile, and highlights the need to continue fieldwork to reveal the moth diversity that remains overlooked in underexplored Neotropical environments.},
}

@article {pmid41721431,
year = {2026},
author = {Sun, C and Sun, Q and Li, J and Zhang, J and Cai, Y and Yan, J and Chang, Q and Li, P and Hu, C},
title = {Migratory bird species as the primary contributors to wildlife collisions: a case study at Shanghai Pudong International Airport, China.},
journal = {BMC zoology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40850-026-00257-3},
pmid = {41721431},
issn = {2056-3132},
}

@article {pmid41716782,
year = {2026},
author = {Montes-Rodríguez, JM and Holguin, CM and Parra-Gómez, A and Marchant, S},
title = {Morphological and molecular identification of symphylans (Myriapoda, Symphyla) from Colombian pineapple crops, with descriptions of two new species.},
journal = {ZooKeys},
volume = {1268},
number = {},
pages = {281-324},
pmid = {41716782},
issn = {1313-2989},
abstract = {Symphylans are soil-dwelling arthropods that can cause significant damage to agricultural crops, particularly pineapple. Despite their economic importance, their taxonomy and biodiversity remain poorly understood in Colombia, and the Neotropics. Here the symphylan species associated with pineapple crops were investigated in Santander, Colombia, the country's largest pineapple-producing region. Symphylans were sampled from four commercial pineapple fields using baited pitfall traps. Morphological examination and DNA barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene were used to identify the collected specimens. Six symphylan morphospecies were identified, including four Hanseniella and two Symphylella. The molecular analysis revealed four distinct genetic clades within the sequenced specimens. The integration of morphological and molecular data resolved initial taxonomic uncertainties, indicating that some previously separated morphospecies represent intraspecific morphological variation. Our results conclude that Hanseniella cf. unguiculata is the predominant species in pineapple crops, accounting for 95.9% of records. Additionally, two new species are described: Hanseniella chocoita sp. nov. and Hanseniella lebrijana sp. nov. A revised dichotomous key for the identification for Hanseniella species present in South America is also provided. This study provides valuable insights into the symphylan species inhabiting Colombian pineapple crops and emphasizes the need for further research to fully understand their diversity and evolutionary relationships.},
}

@article {pmid41716582,
year = {2026},
author = {Fujisawa, T and Imai, T},
title = {Performance and Limitations of Out-Of-Distribution Detection for Insect DNA Barcoding.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73112},
pmid = {41716582},
issn = {2045-7758},
abstract = {Successful applications of DNA barcoding rely on the accurate taxonomic identification of sequence fragments. When biological surveys with DNA barcoding target underexplored biological communities, sequence-based identification is often conducted using incomplete databases that do not fully cover the regional species pool. Consequently, specimens to be identified may include species not present in reference databases. Such unknown or "out-of-distribution" samples can cause misidentification if left undetected. A similarity cutoff is commonly used to detect out-of-distribution samples before taxonomic assignment, but its effectiveness has not been carefully studied. In this study, we evaluated the performance of out-of-distribution detection for DNA barcoding with genetic distance and deep learning metrics. Using extensively sampled datasets of multiple insect taxa, we measured the performance of identification and out-of-distribution detection under conditions in which genetic variations in species were sufficiently sampled. Although identification with DNA barcoding is a highly accurate process, even with short noisy fragments, out-of-distribution detection was more susceptible to a reduction in performance due to sequence noise and a lack of diagnosable characters. When fragments shorter than 300 bp were used for out-of-distribution detection, large performance reductions were observed irrespective of detection methods. Our results provide guidelines for designing unknown-proof identification procedures by determining factors affecting out-of-distribution detection performance.},
}

@article {pmid41716275,
year = {2026},
author = {Pfeufer, EE and Groben, G and Harrison, L and Quang Thu, P and Widmer, T and Puig, AS},
title = {Oomycetes found in wild and cultivated areas of Vietnam.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1606112},
pmid = {41716275},
issn = {1664-302X},
abstract = {To determine the diversity of oomycetes in Vietnam, particularly in the presumed center of origin of most Phytophthora taxa, isolates were collected from rivers, agricultural soils, and forested areas. Species identification was performed using sequences from the internal transcribed spacer (ITS) and cytochrome 2 oxidase (cox2) regions of the genome. Of the 245 isolates included in this study, the majority (66.5%) were identified as Phytopythium spp., followed by Phytophthora spp. (31%) and Pythium spp. (2.4%). The most prevalent species were Phytopythium vexans and Phytophthora cinnamomi, accounting for 51.8 and 24.5%, respectively, of all isolates obtained. A total of 17 isolates were identified as belonging to multiple undescribed species. From agricultural soils, only one isolate each of Phytophthora and Pythium was obtained, with the remaining 93% belonging to the genus Phytopythium. This study shows that natural and agricultural areas in Vietnam harbor a wide diversity of oomycetes, including several undescribed species. The identification of oomycete species in a center of origin will help identify potential emerging pathogens that can become a threat to U.S. agriculture.},
}

@article {pmid41715976,
year = {2026},
author = {Alcantara, SG and Juanico, CST and Ordynets, A and Fernandez, MC and Yambot, AV},
title = {DNA barcoding for identification of ichthyofauna in Pantabangan Dam, Nueva Ecija, Philippines.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/24701394.2026.2631395},
pmid = {41715976},
issn = {2470-1408},
abstract = {The present study established the first molecular-based inventory of nine freshwater fish species from Pantabangan Dam, a genetically unexplored fishery resource in Nueva Ecija, Central Luzon region of the Philippines. Forty mitochondrial cytochrome c oxidase I (COI) sequences were generated representing nine species, eight families and six orders of fishes, providing potential application in biodiversity assesment and management. In all cases, sequence analysis yielded low intraspecific divergence and a high interspecific genetic distance was observed in the Nearest Neighbor Distance analysis. Neighbor-Joining and Maximum Likelihood phylogenetic trees recovered a monophyletic species-level clades supported by high bootstrap values. Out of the nine species identified, three were native species in the Philippines (Leiopotherapon plumbeus, Glossogobius aureus and Clarias batrachus). Two species (Micropterus floridanus and Coptodon zillii) have been recorded for the first time in the dam, indicating the need to review how monitoring protocols can be enhanced by combining morphological assessment and molecular identification. The generated sequences can be used as a baseline data for the conservation of endemic species and formulation of management decisions on the invasive fishes. Overall, our study confirmed the efficiency of DNA barcoding in species delineation and offered a new framework for fish management in the dam.},
}

@article {pmid41612194,
year = {2026},
author = {Ballandras, V and McNamara, L and Carolan, JC and Pichon, A and Byrne, S},
title = {Whole genome sequencing of 18 economically important aphid pests with photographic vouchers for taxonomic validation.},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {41612194},
issn = {2730-6844},
abstract = {OBJECTIVES: Accurate molecular identification in insect monitoring programs relies on validated genomic references, yet many pest species remain underrepresented or incorrectly annotated in public databases. This Data Note provides a curated genomic resource for 18 economically important aphid pests. For each species, we generated whole-genome shotgun sequences and captured high-resolution photographic vouchers of the sequenced individuals to ensure taxonomic verification. Specimens were collected from field or suction trap networks to incorporate intraspecific variation. This dataset will support the development of reliable DNA barcoding, metabarcoding, and mitochondrial metagenomic assays, and contribute to improved reference libraries for aphid pest surveillance.

DATA DESCRIPTION: This dataset includes whole-genome shotgun sequencing data for 18 agriculturally important aphid pest species selected from suction trap monitoring programs. Specimens were morphologically identified using standard aphid identification keys, and diagnostic traits were documented with high-resolution Leica Flexacam C3 images to provide taxonomic verification. For each species, pooled individuals (up to 15 per species) were used for DNA extraction using the Monarch[®] Genomic DNA Purification Kit. Illumina 150 bp paired-end sequencing (10.1–22.7 Gb per species) was performed by Novogene. These data enable extraction of Cytochrome Oxidase I (COI) barcodes, mitochondrial genomes, and associated endosymbiont sequences.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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