@article {pmid42652530,
year = {2026},
author = {Liang, Z and Ren, K and Sun, B and Xie, T},
title = {Global DNA Barcoding of Sigara (Hemiptera: Corixidae) Reveals Cryptic Species Formation and Climatic-Niche Divergence.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
pmid = {42652530},
issn = {2075-4450},
support = {2022-LHYJ-02-0102//The Yangtze River Joint Research Phase II Program/ ; },
abstract = {The genus Sigara Fabricius, 1775 (Hemiptera: Corixidae) is an important freshwater bioindicator, but its conservative morphology complicates traditional species identification. This study combines DNA barcoding, traditional taxonomy, and climatic factors within an integrative framework to provide new insights into species delimitation. We analyzed cytochrome c oxidase subunit I (COI) sequences from 501 Sigara specimens collected from 15 countries, including 95 newly generated COI barcodes. Our integrated approach included phylogenetic analyses, genetic distance assessments, and ecological niche modeling. The results revealed remarkable diversity, with sequences clustering into 46 Barcode Index Numbers (BINs). COI genetic distances showed a pronounced bimodal pattern, with most intraspecific divergences below 1% and interspecific divergences mainly ranging from 8-16%, while the few intermediate divergences (4-8%) suggested potential cryptic diversity or recent species divergence. Most morphologically defined species corresponded to distinct molecular lineages, supporting traditional taxonomy, whereas some morphospecies exhibited genetic discordance potentially associated with species divergence. Integrative analyses revealed that climatic factors, particularly isothermality and seasonal temperature and precipitation, are major drivers of Sigara MOTU distributions, highlighting the important role of climate in shaping their geographic patterns. These findings indicate that although COI barcodes are not sufficient to define the species boundaries of Sigara alone, they provide a key entry point for the accurate division of species, which in turn promotes the development of molecular tools for freshwater ecological monitoring and conservation.},
}

@article {pmid42653170,
year = {2026},
author = {Rodionov, AV and Machs, EM and Romanova, EL and Dyomin, AG and Shulzhenko, IN and Gnutikov, AA and Nosov, NN and Shneyer, VS and Kalugin, YG},
title = {Nuclear Ribosomal ITS1-5.8S rDNA-ITS2 Region as a Phylogenetic Marker for Selenicereus grandiflorus and Related Species (Cactaceae: Cactoideae: Phyllocacteae).},
journal = {International journal of molecular sciences},
volume = {27},
number = {16},
pages = {},
pmid = {42653170},
issn = {1422-0067},
support = {state assignment topic number: 124020100075-2//The Ministry of Education and Science of the Russian Federation/ ; },
mesh = {*Phylogeny ; *Cactaceae/genetics/classification ; *DNA, Ribosomal Spacer/genetics ; *RNA, Ribosomal, 5.8S/genetics ; *DNA, Ribosomal/genetics ; Base Sequence ; Sequence Analysis, DNA ; Genetic Markers ; },
abstract = {The nuclear ITS1-5.8S rDNA-ITS2 region is among the most widely used markers for phylogenetic studies in plants. We sequenced the ITS1-5.8S rDNA-ITS2 region in several species of Selenicereus, two species of Deamia and Epiphyllum chrysocardium. The newly generated sequences were found to be more closely related to ITS and 5.8S rDNA sequences from representatives of other cactus tribes than to the Selenicereus ITS sequences previously deposited in GenBank by research group O. Plume. Importantly, all these sequences retained three conserved motifs of the 5.8S rRNA gene that are commonly used to distinguish functional copies from pseudogenes. Then we analyzed available genome assemblies representing 12 species of Cactaceae. In contrast to the ribotypes identified in this study, the previously reported 5.8S rDNA variants in the assembled genomes of Selenicereus and Carnegiea were represented by a single copy flanked by highly degraded 18S and 28S rDNA sequences. Phylogenetic analyses based on the newly generated ITS sequences and Genbank data supported the monophyly of the subtribes Hylocereinae, Rhipsalideae, and Trichocereinae, as well as the tribes Rhipsalideae, Notocacteae, and Cylindropuntieae. These results demonstrate that the functional ITS1-5.8S rDNA-ITS2 region represents an informative marker for phylogenetic studies within the Cactaceae.},
}

*Phylogeny
*Cactaceae/genetics/classification
*DNA, Ribosomal Spacer/genetics
*RNA, Ribosomal, 5.8S/genetics
*DNA, Ribosomal/genetics
Base Sequence
Sequence Analysis, DNA
Genetic Markers

@article {pmid42653357,
year = {2026},
author = {Rodionov, AV and Kalugin, YG and Romanova, EL and Zhurbenko, PM and Punina, EO and Dyomin, AG and Shulzhenko, IN and Gnutikov, AA and Nosov, NN},
title = {Intragenomic and Interspecific Polymorphism of 35S rDNA Internal Transcribed Spacer 1 (ITS1) in Selenicereus and Related Species (Cactaceae: Cactoideae: Phyllocacteae).},
journal = {International journal of molecular sciences},
volume = {27},
number = {16},
pages = {},
pmid = {42653357},
issn = {1422-0067},
support = {124020100136-0//The Ministry of Education and Science of the Russian Federation/ ; },
mesh = {*Cactaceae/genetics/classification ; *Polymorphism, Genetic ; *DNA, Ribosomal Spacer/genetics ; Phylogeny ; },
abstract = {Locus-specific Illumina NGS was used to analyze the polymorphism of the partial 18S rDNA, spacer ITS1, and partial 5.8S rDNA sequences across 25 cactus species (53 accessions) of the subtribes Hylocereinae and Echinocereinae. To ensure data reliability, only ribotypes (zero-radius operational taxonomic units, ZOTUs) with a minimum read depth of 10 reads within each genome-read pool were retained. A single ribotype was identified in 18 analyzed genomes. In 23 accessions, two or three ribotypes were detected, typically consisting of a major ribotype (98-99%) and one or two minor ribotypes. In the remaining samples, two distinct ribotypes were present in approximately equal proportions, suggesting that these individuals are recent hybrids. Ribotype patterns clearly distinguish the genus Deamia from Selenicereus, Hylocereus, and Epiphyllum. Putative pseudogenes with deletions in the 18S and 5.8S rDNA, as well as deletions and insertions in the ITS1 spacers, were detected. Their abundance was generally low (usually <1%), except in two Deamia species (5-15%). In ITS1 of some minor ribotypes, deletions eliminated cleavage sites B1, B2, and A3, which are important for pre-rRNA processing. Consequently, the products of these putative pseudogenes could not participate in ribosome formation. In addition, pseudogenic copies exhibited a strong transition bias and A/T enrichment in the ITS1 region.},
}

*Cactaceae/genetics/classification
*Polymorphism, Genetic
*DNA, Ribosomal Spacer/genetics
Phylogeny

@article {pmid42657007,
year = {2026},
author = {De la Sota, A and Hidalgo, M and Estivals, G and Faustino-Fuster, D and Meza-Vargas, V and Caminade, P and Bêche, L and Britzke R, R and Steinke, D and Hubert, N},
title = {Delimiting Andean catfish species of the families Astroblepidae and Loricariidae (Ostariophysi, Siluriformes) in the Peruvian Andes using DNA barcodes.},
journal = {ZooKeys},
volume = {1290},
number = {},
pages = {59-84},
pmid = {42657007},
issn = {1313-2989},
abstract = {The Amazon Basin, the largest on Earth, hosts an exceptionally rich fish fauna shaped by its ancient evolutionary history, vast environmental heterogeneity, and steep altitudinal gradient. Despite this diversity, major taxonomic gaps persist, including the Linnean shortfall-the large number of undescribed species-and the Wallacean shortfall, reflecting limited knowledge of species distributions. During the past two decades, DNA barcoding using the mitochondrial COI gene has helped uncover substantial cryptic diversity in Amazonian fishes, particularly along the Andean slope, where Siluriformes exhibit striking levels of undocumented diversity. In this study, we investigated catfish communities from the families Astroblepidae and Loricariidae in the headwaters of the Madre de Dios and Huallaga rivers in Peru, spanning elevations from 500 to 2,500 m. Using DNA barcoding and multiple species-delimitation methods, we identified 27 MOTUs, most of which could not be assigned to recognized species. Our aim was to examine diversity patterns, species co-occurrence, and phylogenetic community structure along the Andean slope. This framework allows us to evaluate how ecological processes-such as competition, niche partitioning, and ecological specialization-shape community assembly. Combined with evidence of close phylogenetic relationships among MOTUs, our results highlight the likely importance of in situ diversification in driving species turnover and structuring catfish biodiversity across Andean elevational gradients.},
}

@article {pmid42642597,
year = {2026},
author = {Veerappa, A and Guda, C},
title = {A Framework for Analyzing the Epigenetic and Transcriptomic Landscape of Cancers Using Single-Cell Multiomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3005},
number = {},
pages = {241-281},
pmid = {42642597},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; Humans ; Multiomics/methods ; *Neoplasms/genetics ; *Epigenesis, Genetic ; *Transcriptome ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling/methods ; Gene Expression Regulation, Neoplastic ; *Epigenomics/methods ; Chromatin/genetics/metabolism ; Computational Biology/methods ; },
abstract = {Single-cell approaches to study gene regulation using multi-modal data (sc-Multiome), such as genomes, transcriptomes, and chromatin accessibility of tumor cells, offer great insights into the development trajectory. By enabling high-resolution barcoding, single-cell isolation facilitates the detection of subpopulations, uncovers molecular mechanisms, and characterizes cell types to reveal cellular heterogeneity within complex tissues. The pipeline for analyzing multiome data includes four main steps: processing Single-Cell Multiome ATAC + Gene Expression sequencing data, gene expression analysis using Seurat, chromatin accessibility analysis and the joint embedding of the expression and accessibility data using SnapATAC2. Here, we outline a comprehensive protocol for joint embedding of chromatin accessibility and transcriptomic data using best practices developed in our laboratories, along with detailed parameter tuning at each step to fully leveraging this pipeline. This approach enhances our understanding of the intricate tumor microenvironment and aids in determining cellular landscape. This chapter focuses on the integration of single-cell multi-omics methodologies, emphasizing their utility in cancer research.},
}

*Single-Cell Analysis/methods
Humans
Multiomics/methods
*Neoplasms/genetics
*Epigenesis, Genetic
*Transcriptome
Single-Cell Gene Expression Analysis
Gene Expression Profiling/methods
Gene Expression Regulation, Neoplastic
*Epigenomics/methods
Chromatin/genetics/metabolism
Computational Biology/methods

@article {pmid42642982,
year = {2026},
author = {Li, P and Xiao, R and Li, F and Bu, X and Cao, F and Wang, J and Guo, Z},
title = {Siglec Ligand Profiling on Extracellular Vesicles Reveals a Cancer-Related Signature with Immunosuppressive Function in Pancreatic Cancer.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e75407},
doi = {10.1002/smll.75407},
pmid = {42642982},
issn = {1613-6829},
support = {NSFC 32301194//National Natural Science Foundation of China/ ; ZR2022QC165//Natural Science Foundation of Shandong Province/ ; ZR2023QH008//Natural Science Foundation of Shandong Province/ ; ZR2026LMB034//Natural Science Foundation of Shandong Province/ ; ZR2023QC090//Natural Science Foundation of Shandong Province/ ; tsqn202507391//Taishan Scholars Foundation/ ; },
abstract = {Cancer-derived extracellular vesicles (EVs) act as systemic carriers of functional sialic acids and participate in local or distant immune escape via the Siglec pathway. Therefore, assessing the expression of Siglec ligands on EVs can facilitate the exploration of novel cancer biomarkers and enable the evaluation of circulating sialic acid-mediated immunosuppression. However, the structural complexity and functional redundancy of Siglec ligands pose challenges for evaluating their collective role in immune evasion. Here, an adjustable Siglec-DNA barcoding platform is established for multiplexed detection of four Siglec ligands on EVs, thereby enabling the simultaneous profiling of multiple ligand-receptor pairs in a single competitive assay. EV Siglec ligand signatures show statistical differences between cancer and normal groups, as quantified by the Siglec-DNA platform in cell lines and clinical samples, highlighting their potential for pancreatic cancer discrimination. Specific types of Siglec ligands on EVs also inactivate natural killer (NK) cells and T cells in co-culture, demonstrating their immunosuppressive potential. These findings uncover a novel, systemic mechanism of immune inhibition mediated by sialic acids, and also offer new insights into how EVs modulate cancer immunity.},
}

@article {pmid42644667,
year = {2026},
author = {Muñoz-Sánchez, AH and Contreras-Negrete, G and Zaldívar-Riverón, A and Colín, RT and Zakharov, EV and López-Vaamonde, C and Hernández-López, A},
title = {High-Throughput DNA Barcoding Reveals Multi-Trophic Networks of Plants, Leafminers and Parasitoids in a Tropical Dry Forest.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70183},
pmid = {42644667},
issn = {1755-0998},
support = {58548//Consejo Nacional de Ciencia y Tecnología/ ; //the European Union via the FEDER program FONDS EUROPEEN DE DEVELOPPEMENT REGIONAL - PROGRAMME OPERATIONNEL FEDER - FSE 2014-2020 CONSEIL REGIONAL CENTRE-VAL DE LOIRE/ ; CBF 2025 G576//SECIHTI/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Forests ; Tropical Climate ; Mexico ; Sequence Analysis, DNA ; Plant Leaves/parasitology ; *Insecta/classification/genetics/physiology ; *Plants/genetics/classification/parasitology ; },
abstract = {Tropical dry forests host highly diverse insect communities and complex trophic interactions, yet these networks remain difficult to resolve using conventional molecular or rearing-based approaches. Here, we integrate long-read DNA barcoding, non-target sequence co-amplification, and host plant taxonomy to reconstruct tri-trophic interactions among leaf-mining insects, their host plants, and associated parasitoids in a Mexican tropical dry forest. Using Single Molecule, Real-Time (SMRT) sequencing on the PacBio Sequel IIe platform, we generated high-fidelity barcodes from individual leaf-miner larvae and from parasitoid larvae and pupae recovered from leaf mines. From 253 specimens, we obtained 214 sequences, and identified 83 operational taxonomic units including leaf-mining Lepidoptera, Diptera, Coleoptera, and their hymenopteran parasitoids, plus 31 non-target sequences. Of the 214 sequences, 69 were parasitoid wasps (32.2%). Of these, 40 were obtained from parasitoids dissected directly from leaf mines, while 29 were co-amplified from leaf-miner samples, demonstrating that SMRT-based co-amplification allows detection of parasitism without rearing. Our analysis revealed 156 trophic interaction types and 247 interaction events. Network analyses showed a highly modular tripartite network, with module structure primarily driven by host plant identity and a reduced set of influential leaf-miner and parasitoid taxa. Bipartite networks supported the hypothesis that interactions are more strongly compartmentalized between leafminers and host plants than at higher trophic levels. These results demonstrate that long-read DNA barcoding with co-amplification detection provides a scalable framework for reconstructing multi-trophic interactions from individual specimens, overcoming key limitations of rearing-based methods and enabling robust biodiversity and ecological network assessments in species-rich ecosystems.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Forests
Tropical Climate
Mexico
Sequence Analysis, DNA
Plant Leaves/parasitology
*Insecta/classification/genetics/physiology
*Plants/genetics/classification/parasitology

@article {pmid42646098,
year = {2026},
author = {Wei, S and Mi, Y and Zhang, X and Qi, B and Wang, W and Wang, Q and Shi, D and Li, Y},
title = {Exploration of the Potential Suitable Distribution Range of the Lyophyllum decastes Complex in High-Altitude Cold Regions of Southwest China.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {8},
pages = {},
pmid = {42646098},
issn = {2309-608X},
abstract = {Climate change may alter the abiotic conditions associated with macrofungal occurrence, but projections for taxonomically unresolved species complexes require cautious interpretation. Here, we used an AICc-optimized MaxEnt model to characterize the climate-defined aggregate suitability envelope of records assigned to the Lyophyllum decastes (Fr.) Singer complex in Sichuan, Yunnan, and Xizang, Southwest China, under current conditions and four RCP scenarios for the 2050s and 2070s. After spatial thinning, 70 occurrence records compiled from field surveys and published sources were modeled with correlation-filtered bioclimatic variables. The optimized model showed high discrimination for the pooled occurrence dataset (mean AUC > 0.95), and mean temperature of the coldest quarter had the largest contribution (50.8%). Projected changes differed between scenarios, with increasing fragmentation and reductions in highly suitable climate space under several futures. These outputs do not represent a lineage-resolved species distribution, as the occurrence records were not uniformly verified by molecular barcodes, and the model omits host availability, vegetation, soil, land use, dispersal, and other biotic processes. We therefore interpret the maps as a hypothesis-generating, aggregate climatic envelope for the complex that can guide stratified field surveys, molecular sampling, and habitat monitoring rather than as direct evidence of taxon-specific physiological tolerances or realized distributions.},
}

@article {pmid42648135,
year = {2026},
author = {Remelli, S and Ducci, L and Filonzi, L and Pinardi, R and Rizzo, P and Celico, F and Scanferla, E and Pianu, M and Menta, C},
title = {Rethinking ecotoxicological paradigms: microbial-mediated tolerance and life-history trade-offs of Folsomia candida in hydrocarbon-contaminated groundwater.},
journal = {Chemosphere},
volume = {411},
number = {},
pages = {145072},
doi = {10.1016/j.chemosphere.2026.145072},
pmid = {42648135},
issn = {1879-1298},
abstract = {The ecological relevance of soil invertebrates in contaminated groundwater systems remains largely unexplored, particularly under chronic exposure to petroleum-derived compounds. Here, we provide the first evidence of stable colonization and functional persistence of the model collembolan Folsomia candida within a hydrocarbon-polluted aquifer in Gaeta (central Italy). Long-term monitoring (2019-2023) revealed persistent groundwater contamination, with ethyl tert-butyl ether (ETBE) > 10,000 μg/L and total petroleum hydrocarbons (TPH) > 1000 μg/L. Despite these extreme conditions, F. candida populations were consistently detected on the water surface of quiescent piezometers and taxonomically confirmed via COI DNA barcoding. To disentangle tolerance and potential adaptive responses, we performed ecotoxicological bioassays using three populations (laboratory control, native contaminated population, and a depurated lineage) across aqueous and soil exposure scenarios with site-specific groundwater. Survival remained high (>70%) across all treatments which indicates a limited acute toxicity of ETBE-dominated mixtures. In contrast, reproduction was significantly stimulated under contaminated conditions, suggesting a shift from toxic to trophic effects mediated by hydrocarbon-associated microbial communities, including Aeromonas and Sulfuricurvum, likely providing both nutritional subsidy and oviposition substrates. However, under soil conditions, this enhanced reproductive output was coupled with reduced body length, revealing a contamination-driven life-history trade-off between reproduction and somatic growth. These results demonstrate that organism-microbe-contaminant interactions can modulate ecotoxicological outcomes beyond direct toxicity paradigms, enabling persistence and even functional exploitation of polluted environments. Our findings redefine the ecological boundaries of Collembola and support their use as bioindicators of hydrocarbon contamination pathways across terrestrial and groundwater interfaces, with implications for risk assessment frameworks in subsurface ecosystems.},
}

@article {pmid42649521,
year = {2026},
author = {Ji, Q and He, S and Lai, S and Long, S and Jing, X and Lu, Y},
title = {Molecular identification of Hypoderma sinense cutaneous myiasis in a child from a cattle-raising pastoral region of China: a case report.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {42649521},
issn = {1348-8945},
abstract = {BACKGROUND: Human cutaneous myiasis caused by Hypoderma sinense is rarely reported and may be mistaken for common bacterial skin disease.

CASE PRESENTATION: A 3-year-old boy from a livestock-raising pastoral region of China presented with multiple painful subcutaneous nodules that had not responded to topical antibacterial treatment. Marked eosinophilia, elevated total IgE, and linear ultrasonographic structures raised suspicion of parasitic infestation. A larva was removed intact from the posterior neck lesion through a pre-existing punctum under local anesthesia. Whole-genome shotgun sequencing followed by de novo assembly generated a 16,888-bp mitochondrial contig containing a complete COI barcode region, supporting identification of the larva as H. sinense. At the one-month follow-up, the pain and subcutaneous nodules had resolved.

CONCLUSIONS: This case highlights the importance of considering cutaneous myiasis in children from livestock-raising regions with painful, treatment-resistant subcutaneous nodules and demonstrates the diagnostic value of ultrasonography, minimally invasive larval extraction, and molecular identification.},
}

@article {pmid42652432,
year = {2026},
author = {Zafar, MI and Wang, S and Liu, Q and Hassan, J and Shafique, T and Liu, Y},
title = {Habitat-Driven Insect Community Structure in an Arid Agroecosystem of Xinjiang, China: Integrated Light-Trap Monitoring and DNA Barcoding Evidence.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080777},
pmid = {42652432},
issn = {2075-4450},
support = {KH0394//Science and Technology Project of the Fourth Division of the Xinjiang Production and Construction Corps/ ; },
abstract = {Research on insect biodiversity in arid and semi-arid agroecosystems of Central Asia remains limited, hindering the development of effective insect conservation strategies and integrated pest management (IPM) programs. This study examined insect community structure, diversity, and seasonal dynamics across three habitat types in Kekedala City, in the autonomous region of Ili Kazakh, Xinjiang, China. Solar-powered ultraviolet LED light traps (350-420 nm) were used for sampling from April to August 2024. A total of 63,090 individuals of 83 species, 57 families and 72 genera of insects were collected. Diversity indices calculated using the complete species dataset showed highest diversity in the riparian corridor (L3: H' = 3.42, D = 0.962, S = 62), intermediate diversity in the agro-horticultural garden (L2: H' = 3.18, D = 0.948, S = 54), and lowest diversity in the xerophytic shrubland (L1: H' = 2.97, D = 0.935, S = 47). A supplementary analysis targeted a shared core assemblage of 17 species, defined as taxa captured at all three sampling sites with cumulative total abundances ranging from 50 to 100 individuals. This subset exhibited near-uniform diversity metrics across habitats (H' = 2.83, D = 0.941, Pielou's evenness J' ≈ 1.0), a pattern driven by the prevalence of habitat generalists rather than capturing site-specific full community diversity. Two abundant pest species, Helicoverpa armigera (Hübner, 1808) (cotton bollworm, 5209 individuals, 8.3% of total) and Oryctes rhinoceros (Linnaeus, 1758) (rhinoceros beetle, 5206 individuals, 8.2% of total), both peaked in abundance in July-August; O. rhinoceros is associated with local ornamental and date palm plantings in the study area. In total, 15 major pest species were recorded. Mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding confirmed two new national insect records for China: Stethoconus pyri (Mella, 1861) (Hemiptera: Anthocoridae) and Pinacoplus didymogramma (Hampson, 1907) (Lepidoptera: Noctuidae). This study provides the first comprehensive baseline inventory of the insect fauna of Kekedala City. Descriptive ordination analyses suggest that habitat vegetation complexity may exert a stronger filtering effect on insect assemblage composition than the relatively small seasonal variation in temperature and humidity observed during the sampling period. As only a single trap was deployed within each habitat with no within-site replication, all cross-habitat community patterns reported herein are strictly descriptive and require validation via replicated field sampling in future research.},
}

@article {pmid42652433,
year = {2026},
author = {Zhao, J and Xu, Q and Chi, G and Zhang, S and Yu, R and Zhao, S and Gao, Q and Yang, Z and Xu, G},
title = {Species-Specific COI Primers for Rapid Molecular Identification of Leucoptera malifoliella.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080778},
pmid = {42652433},
issn = {2075-4450},
support = {2026KJCXZX-SGS-9//Hebei Academy of Agriculture and Forestry Sciences/ ; HBCT2024150208//Science and Technology Innovation Project of Hebei Agriculture Research System/ ; },
abstract = {Leucoptera malifoliella (Lepidoptera: Lyonetiidae) is a quarantine pest of apple and other Rosaceae fruit trees whose range is expanding into new territories. Its minute size and morphological overlap with closely related Lyonetiidae make routine identification unreliable, especially for larvae and damaged specimens. We compared COI sequences from six common small Lepidoptera species found in orchards and designed the species-specific primer pair SXW-F/SXW-R. The resulting polymerase chain reaction (PCR) assay amplifies an ~500 base pairs (bp) fragment exclusively from L. malifoliella; no product was detected in any of five non-target species. The reaction tolerates annealing temperatures of 50-58 °C and consistently detects the target across all life stages (first- to third-instar larvae, pupae, adults) and all adult tissues tested (antennae, head-thorax, abdomen, wings, legs). Detection sensitivity reaches 0.03 ng/μL-approximately one-thousandth of the DNA content of a single adult. This is the first species-specific COI (SS-COI) method reported for L. malifoliella. It furnishes a rapid, specific, and sensitive diagnostic tool for quarantine inspection, field monitoring, and integrated pest management (IPM) programs.},
}

@article {pmid42652468,
year = {2026},
author = {Xie, TY and Zhang, Y and Chen, YZ and Liu, Z and Lin, XL},
title = {DNA Barcoding Reveals Hidden Genetic Diversity and Environmental Correlates of Lineage Differentiation in Neozavrelia Goetghebuer & Thienemann, 1941 (Diptera: Chironomidae).},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080814},
pmid = {42652468},
issn = {2075-4450},
support = {12110600000018003910//the Ministry of Natural Resources' High-Level Scientific and Technological Innovation Talent Cul-tivation Program/ ; 41502021//National Natural Science Foundation of China/ ; 12111300000018001-14//the Innovative Research Project on the Laboratory of Geo-Specimens Study and Testing at the Ge-ological Museum of China/ ; },
abstract = {Species delimitation and biodiversity assessment in Chironomidae are frequently hindered by morphological conservatism and widespread cryptic diversity. Neozavrelia (Diptera: Chironomidae), a genus inhabiting specialized freshwater microhabitats such as springs and hygropetric seepages, remains poorly understood with respect to its genetic diversity and the environmental processes underlying lineage differentiation. Clarifying lineage diversity is a prerequisite for evaluating the ecological factors associated with genetic differentiation. In this study, we compiled a global COI DNA barcode dataset comprising 137 sequences from newly generated specimens and publicly available records in the Barcode of Life Data Systems (BOLD). Genetic diversity was evaluated using neighbor-joining (NJ) analysis and Automatic Barcode Gap Discovery (ABGD), whereas environmental and geographic drivers of genetic differentiation were assessed using Mantel tests, distance-based redundancy analysis (db-RDA), variation partitioning, and hierarchical partitioning. A total of 26 molecular operational taxonomic units (MOTUs) were identified, with most lineages forming well-supported clades in the NJ tree. Genetic differentiation was significantly associated with both environmental and geographic distances, although environmental variables explained a substantially greater proportion of the observed variation. Hierarchical partitioning identified slope, annual cloud cover, mean precipitation amount of the coldest quarter, and frost frequency as the principal environmental predictors of lineage differentiation. Our findings reveal substantial COI genetic diversity within Neozavrelia and suggest that environmental heterogeneity, particularly variation in water availability and thermal conditions, is significantly associated with lineage differentiation. This study expands the global COI DNA barcode reference library for Neozavrelia and provides new insights into ecological and evolutionary factors associated with diversification in freshwater chironomids.},
}

@article {pmid42652502,
year = {2026},
author = {Santiago-Calvo, Y and de Paz, V and Bastin, S and Fusu, L and Baños-Picón, L and Flores-Pérez, D and Pozo-Romero, MI and Asensio-S-Manzanera, MC},
title = {Parasitoid Diversity and Biological Control of Bactericera tremblayi and Bactericera trigonica (Hemiptera: Psylloidea) in Horticultural Crops in Spain.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080848},
pmid = {42652502},
issn = {2075-4450},
support = {ASOPROFIT 001 - PDRCYL (2014-2022) Sub. 16.2//ASOPROFIT 001/ ; HORTICCROP 013 - PPAC (2023-2027) Int. CYL7162//HORTICCROP 013/ ; },
abstract = {Biological control using parasitoids is a key strategy for managing psyllid pests in horticultural crops. This study investigated the parasitoid complex associated with Bactericera tremblayi and Bactericera trigonica, two economically important psyllid pests of leek and carrot, respectively, in Castile and León (Spain). Nymphs of both psyllid species were collected and reared to assess parasitism; emerging parasitoids were identified morphologically and by DNA barcoding. A total of 969 parasitized nymphs were collected, from which 291 parasitoids emerged, including Tamarixia pronomus, Tamarixia tremblayi, Syrphophagus herbidus, Syrphophagus cf. taeniatus, Cheiloneurus sp. and Encyrtidae sp. Tamarixia pronomus is reported here for the first time as parasitoids of B. tremblayi while T. tremblayi, S. herbidus, and S. cf. taeniatus are newly recorded as parasitoids of B. trigonica. Moreover, the two Syrphophagus species represent the first records of this genus for Spain. The COI barcode sequences were generated for T. pronomus, T. tremblayi and S. cf. taeniatus. The parasitism rate of S. herbidus on B. trigonica reached a maximum of 23.18%. No significant differences in parasitism by Tamarixia species were observed between the two Bactericera hosts. Maximum parasitism rates recorded were 32.43% for T. pronomus on B. trigonica, and approximately 11-12% for T. tremblayi on both host species. Total parasitism of B. tremblayi in leek crops reached up to 70%, whereas parasitism of B. trigonica in carrot remained generally low and poorly synchronized with pest population dynamics. These results highlight a diverse parasitoid complex with substantial natural control of B. tremblayi and variable but lower impact on B. trigonica, underscoring the relevance of habitat and temporal factors for conservation biological control in these agroecosystems.},
}

@article {pmid42652511,
year = {2026},
author = {Xie, T and Chai, L and Zhang, N and Wang, N and Ge, X and Yan, C},
title = {A DNA Barcode Reference Library for Trichoptera of Jingpo Lake: Taxonomic Diversity and Molecular Identification Basics.},
journal = {Insects},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/insects17080857},
pmid = {42652511},
issn = {2075-4450},
support = {32400357//National Natural Science Foundation of China/ ; },
abstract = {Jingpo Lake in Northeast China is a vital aquatic ecosystem, yet it lacks baseline molecular data for its insects. Trichoptera (caddisflies) are excellent ecological bioindicators, but their accurate identification is often hindered by morphological similarities, life-stage limitations, and insufficient DNA barcode records. To address this gap, this study combined morphological identification with DNA barcoding to establish a local reference database. From 285 collected adult caddisflies, 105 representative specimens were selected for genetic analysis. The survey identified 22 species across 9 families, revealing four new records for China and six for Heilongjiang Province. Analyses confirmed the high efficacy of the COI marker, demonstrating low intraspecific genetic divergence (0.78%) and high interspecific divergence (17.80%), with a clear barcode gap separating all examined species. Species accumulation curves indicated robust sampling of the main genera, although expanded collection efforts could still uncover additional species. In conclusion, this study provides a valuable DNA barcode reference library for Trichoptera in the Jingpo Lake region. It establishes foundational data for regional biodiversity inventories and future ecological monitoring based on environmental DNA (eDNA) or metabarcoding approaches.},
}

@article {pmid42633069,
year = {2026},
author = {Duffy, GA and Wainwright, JA and Gonzalez, BC and Bond, T and Jamieson, AJ},
title = {Two new species of Princaxelia (Crustacea, Amphipoda, Pardaliscidae) from hadal depths of the Tonga and Mariana trenches (Pacific Ocean).},
journal = {ZooKeys},
volume = {1289},
number = {},
pages = {303-334},
pmid = {42633069},
issn = {1313-2989},
abstract = {Princaxelia Dahl, 1959, is a genus containing predatory pardaliscid amphipods, typically captured in small numbers from hadal trenches (> 6,000 m ocean depth). Here, two new species, Princaxelia malohi Duffy & Wainwright, sp. nov. and Princaxelia kahat Duffy & Wainwright, sp. nov., are added to the genus based on key morphological features to bring the total number of species of Princaxelia to seven. DNA barcodes at the 16S and COI region are also provided for all type specimens where possible to add to the limited but growing number available. Princaxelia malohi sp. nov. was described from five specimens captured using baited landers between 8,200-8,350 m water depth in the Tonga Trench. They exhibit the first identified record of Princaxelia from this hadal feature. Key diagnostic features include the presence of two plumose setae on the inner plate of maxilla 1 and one projection near the base of the dactylus in gnathopods 1 and 2. The second species, Princaxelia kahat sp. nov., is described from between 8,000-8,964 m in the Mariana Trench, and is the second species described from this hadal feature. Key diagnostic features for this species include the presence of six plumose setae on the inner plate of maxilla 1, and three to four projections near the base of the dactylus in gnathopod 1, and four to five projections on the base of the dactylus in gnathopod 2. A morphological matrix and key to the genus is updated to aid in future identification of species of Princaxelia and notes on in situ observations are also included.},
}

@article {pmid42633071,
year = {2026},
author = {Likhitrakarn, N and Golovatch, SI and Srisonchai, R and Thi, S and Chhin, S and Lou, V and Sinovas, P and Jirapatrasilp, P and Sutcharit, C and Panha, S and Seesamut, T},
title = {Integrated taxonomy of two new species of the millipede genus Plusioglyphiulus Silvestri, 1923 from Cambodia (Diplopoda, Spirostreptida).},
journal = {ZooKeys},
volume = {1289},
number = {},
pages = {237-269},
pmid = {42633071},
issn = {1313-2989},
abstract = {Two new sympatric cavernicolous species of the millipede genus Plusioglyphiulus Silvestri, 1923, are described from Battambang Province, northwestern Cambodia: Plusioglyphiulus parviserratus Likhitrakarn & Seesamut, sp. nov. and Plusioglyphiulus battambangensis Likhitrakarn & Seesamut, sp. nov. Both new taxa are diagnosed based on an integrated taxonomic approach combining morphological features and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences from a previous study. Plusioglyphiulus parviserratus sp. nov. is distinguished from all congeners by having the male leg 1 telopodite distinctly 2-segmented with a rudimentary, knob-like second telopoditomere, the anterior gonopod coxosternal processes long, slender, and regularly curved anteriorly, resembling a bird's head, and a unique micro-serrate upper margin of the broad flagellum process. In contrast, P. battambangensis sp. nov. is characterized by a distinct carinotaxic formula of the collum, a significantly smaller second telopoditomere on the male leg 1, a slender, elongated, paramedian coxal process of the posterior gonopod, and a narrow, smooth-margined flagellum process. The two new species are separated from each other by an interspecific COI p-distance of 10.3% and show divergences of 9.6-9.9% from their closest known relatives, all lying well within the stable range observed for species boundaries in the Cambalopsidae and therefore strongly supporting their independent specific status. Beyond traditional descriptions, this study evaluates the resolution efficiency and practical limitations of multiple imaging modalities, including the standard transmission light photography, traditional line drawings, scanning electron microscopy, and micro-computed tomography scanning. While 3DµCT reconstructions provide powerful, non-destructive visualizations of external somatic architectures, we demonstrate that current in-situ tomographic data remain insufficient for resolving the highly condensed, tightly appressed gonopodial microscopic characters, thereby emphasizing the continued necessity of physical dissection and SEM in cambalopsid taxonomy. These findings increase the number of Plusioglyphiulus species currently known to occur in Cambodia to six, highlighting the significant, yet severely understudied, cavernicolous diplopod diversity in the country's extensive karst systems. An updated identification key to all six Cambodian Plusioglyphiulus species is provided. These discoveries underscore the critical need for continued taxonomic exploration and the implementation of conservation strategies for the imperiled limestone karst ecosystems in the region.},
}

@article {pmid42633869,
year = {2026},
author = {Hong, O and Mayor, T and Joshi, J},
title = {Peptide barcoding: an alternative to the phenotype-genotype problem.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2026.08.007},
pmid = {42633869},
issn = {1876-4347},
abstract = {Barcoding methods are powerful tools for screening large libraries and have successfully been employed using DNA-centric approaches for over two decades. Yet despite the central role of proteins in most biological processes, protein-based barcoding methods have only recently emerged as a viable alternative. In this review we summarize recent advances in peptide barcoding and highlight its diverse applications, including screening of binding affinity, lipid nanoparticles, mRNA untranslated regions, and designed protein libraries. We discuss key challenges in barcode design, library construction, and mass spectrometry methods for accurate, scalable, and high-throughput screening. We propose that peptide barcoding represents a conceptual shift in genotype-phenotype mapping and will play an increasingly important role in AI-driven protein engineering, delivery technologies, and synthetic biology.},
}

@article {pmid42635227,
year = {2026},
author = {Noman, AA and Sashittal, P},
title = {Sensitivity analysis of cell fate trajectories from single-cell transcriptomics.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {Supplement_2},
pages = {},
pmid = {42635227},
issn = {1367-4811},
support = {//Virginia Tech/ ; },
mesh = {Single-Cell Gene Expression Analysis ; *Single-Cell Analysis/methods ; *Cell Differentiation/genetics ; Animals ; *Transcriptome ; Gene Regulatory Networks ; Mice ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; *Gene Expression Profiling/methods ; },
abstract = {SUMMARY: Cell differentiation is a dynamic process in which cells traverse through high-dimensional gene expression space under the influence of gene regulatory networks and environmental cues. Recent advances in single-cell RNA sequencing (scRNA-seq) have enabled us to measure high-resolution snapshots of this dynamic process. Several computational methods have been developed to reconstruct cellular flow maps from these snapshots, revealing the trajectories taken by cells in gene expression space. While existing methods provide increasingly detailed descriptions of cellular trajectories, the stability of these trajectories to perturbations is largely unexplored. As such, it remains unclear how robust inferred trajectories are to perturbations, which genes most strongly influence long-term fate outcomes, and where instability arises between competing fate commitments. While sensitivity and stability analysis tools from dynamical systems theory provide a principled way to study the stability of differentiation trajectories, existing approaches are not designed for the high-dimensionality and sparsity of scRNA-seq data. Here, we introduce FateSens, a sensitivity-based computational framework for analyzing gene regulatory dynamics using flow maps derived from scRNA-seq data. FateSens performs sensitivity analysis of differentiation trajectories derived from scRNA-seq data to identify regulatory genes and fate boundaries. To demonstrate its utility, we applied FateSens to study neutrophil-monocyte differentiation using scRNA-seq data of mouse hematopoiesis. While FateSens relies only on transcriptomic measurements, this dataset also contains lineage tracing barcodes that provide ground-truth fate relationships. Our results show that FateSens accurately recovers regulators consistent with known biology and identifies fate boundaries that are supported by lineage tracing data.

We implement FateSens in Python 3, with an open-source implementation available at: https://github.com/sashittal-group/FateSens.},
}

Single-Cell Gene Expression Analysis
*Single-Cell Analysis/methods
*Cell Differentiation/genetics
Animals
*Transcriptome
Gene Regulatory Networks
Mice
Sequence Analysis, RNA/methods
*Computational Biology/methods
*Gene Expression Profiling/methods

@article {pmid42637706,
year = {2026},
author = {He, Q and Zhao, LH and Xu, HE},
title = {Arrestins as programmable integrators of GPCR signaling: structural microstates, spatiotemporal logic, and therapeutic control.},
journal = {Cell discovery},
volume = {12},
number = {1},
pages = {},
pmid = {42637706},
issn = {2056-5968},
support = {32130022, 82495184,82121005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371255, 32071203//National Natural Science Foundation of China (National Science Foundation of China)/ ; 23ZR1475200//Natural Science Foundation of Shanghai (Natural Science Foundation of Shanghai Municipality)/ ; },
abstract = {Arrestins were originally defined as terminators of G protein-coupled receptor (GPCR) signaling, yet structural and mechanistic advances now reveal them as programmable, spatiotemporal integrators of cellular signaling. Recent cryo-electron microscopy studies have revealed a diverse spectrum of GPCR-arrestin engagement modes, including core-, tail-, loop-, side-engaged, and membrane-anchored conformations, across GPCR classes and arrestin isoforms. These structures reveal that arrestin recruitment operates as a conditional, allosterically regulated process rather than a binary on-off switch. The selection of the arrestin microstate is governed by layered regulatory inputs, including GPCR kinase-dependent phosphorylation barcodes, membrane and lipid cofactors, and isoform-specific mechanics, which together define the signaling geometry, duration, and subcellular localization. This structural logic provides a mechanistic foundation for biased signaling, noncanonical endosomal signaling, and GPCR-independent arrestin functions. Importantly, emerging therapeutic strategies, including intracellular allosteric modulators and molecular glues, demonstrate that arrestin signaling can be reprogrammed by directly sculpting transducer assemblies rather than ligand efficacy alone. Here, we synthesize recent structural, biochemical, and physiological insights to outline how arrestins decode regulatory inputs into signaling outcomes and how this knowledge enables the development of next-generation, structure-guided GPCR therapeutics.},
}

@article {pmid42630299,
year = {2026},
author = {Schaub, D and Lessing, A and Meyer, F and Stockinger, P and Estévez-Gay, M and Eichenberger, M and von Haugwitz, G and Gloger, A and Scheuermann, J and Buller, R},
title = {A tailored CoA ligase-N-acyltransferase cascade for on-DNA amide bond formation gives access to broad substrate scope.},
journal = {Nature catalysis},
volume = {9},
number = {8},
pages = {834-847},
pmid = {42630299},
issn = {2520-1158},
abstract = {DNA-encoded chemical library (DEL) technology is a powerful tool in early-stage drug discovery. Although widely applied in industry and academia, challenges persist in generating DELs with high quality and chemical diversity. Low yields in building-block incorporation, limited selectivity and, most importantly, DNA damage from harsh reaction conditions compromise library quality, reduce signal-to-noise in affinity selections and ultimately hinder drug discovery. Here we show that tailored enzymes can be harnessed for the effective construction of molecular diversity on DNA under mild conditions. Targeting amide bond formation, we designed a cascade of complementary coenzyme A ligases and rationally tailored N-acyltransferases to access a broad amide scope on-DNA (>120 examples), identifying structural elements that optimize the biocatalysts' DNA compatibility in the process. Integrating the enzymatic cascade with chemical synthesis led to the construction of a diverse DEL without damage to the DNA barcode, highlighting the biocatalysts' applicability for early scaffold construction and late-stage functionalization.},
}

@article {pmid42629163,
year = {2026},
author = {Chen, Z and Zhang, B and Tang, L and Gong, F and Wan, L and Ma, L},
title = {Bayesian inference of lineage trees by joint analysis of single-cell multimodal lineage-tracing data with BiLinT.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281460.125},
pmid = {42629163},
issn = {1549-5469},
abstract = {The advent of single-cell lineage-tracing technologies has enabled the simultaneous profiling of gene expression and lineage barcodes. However, accurate, high-resolution reconstruction of cell lineage trees remains challenging because most existing approaches treat these modalities separately and therefore fail to fully exploit their complementary information. Here we present BiLinT, a Bayesian framework that jointly models multimodal single-cell lineage-tracing data for lineage tree reconstruction. BiLinT integrates barcode evolution (a continuous-time Markov chain) with gene expression dynamics (an Ornstein-Uhlenbeck process) within a unified probabilistic model. Across synthetic and real datasets, BiLinT provides accurate lineage-tree reconstruction and reveals differentiation-associated clonal structure and developmental fate biases.},
}

@article {pmid42623401,
year = {2026},
author = {Castillo, AH and Jacobs, S and Steinke, D and Smith, MA},
title = {Assessment of leaf-litter invertebrate biodiversity using high throughput sequencing.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0347811},
pmid = {42623401},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *Plant Leaves ; DNA Barcoding, Taxonomic/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Invertebrates/genetics/classification ; DNA, Environmental/genetics ; Ecosystem ; },
abstract = {Leaf litter ecosystems and their fauna are largely understudied, despite their critical ecological roles. Here, we investigate challenges associated with estimating biodiversity in terrestrial leaf litter. Current methodologies for biodiversity assessment are fraught with limitations; amongst the most significant is a decline in taxonomic expertise, complicating the process of species identification and the significant costs associated with species-level morphological identifications. DNA barcoding employs molecular markers to identify animal species, and the mitochondrial gene cytochrome c oxidase I (COI) is the agreed upon standard for animals. DNA metabarcoding facilitates the identification of multiple species without necessitating taxonomic expertise. Recent studies indicate that environmental DNA (eDNA) may exhibit greater sensitivity compared to taxonomic identifications completed on animals collected using traditional methods (e.g., pitfall traps, pan traps). To test whether eDNA methodology works in a real-world scenario, we sampled leaf litter across a temperate forest/field ecotone. Leaf litter was dried, ground and processed to extract environmental DNA. We evaluated multiple DNA extraction protocols to test their relative efficacy. We found that the Qiagen Blood and Tissue Kit was the most effective at recovering invertebrate diversity and found that there were notable differences in the biodiversity recovered between forest and field habitats. Temperature emerged as a significant factor influencing the composition of the communities observed. Our methodology is applicable across various environments for efficient biodiversity assessment and would be particularly beneficial for monitoring pests and invasive species. Our approach offers a cost-effective and timely alternative to conventional biodiversity assessment methods and underscores the significance of accurate assessment methodologies for leaf litter communities.},
}

Animals
*Biodiversity
*Plant Leaves
DNA Barcoding, Taxonomic/methods
*High-Throughput Nucleotide Sequencing/methods
*Invertebrates/genetics/classification
DNA, Environmental/genetics
Ecosystem

@article {pmid42625985,
year = {2026},
author = {Shankar, M and Moorthy, M and Shetty, A and Gurusiddaiah, SC},
title = {Potential diagnostic role of urinary exosomal microRNAs in immunoglobulin A nephropathy: A case-control study.},
journal = {World journal of nephrology},
volume = {15},
number = {3},
pages = {119882},
pmid = {42625985},
issn = {2220-6124},
abstract = {BACKGROUND: The most common type of primary glomerulonephritis is immunoglobulin A nephropathy (IgAN), which can eventually cause end-stage kidney disease among individuals. A kidney biopsy, which is invasive and has risks of mortality or morbidity, is currently the "gold standard" for diagnosis. Urinary exosomes contain abundant, well-preserved microRNAs (miRNAs), which are small, non-coding endogenous RNAs that may be used as non-invasive biomarkers. Studies on urinary exosomal miRNA profiles for the diagnosis of IgAN are rare.

AIM: To examine the profile of urinary exosomal miRNAs in Indian individuals diagnosed with IgAN.

METHODS: Over a period of 4 years (2020-2024), fifty biopsy-confirmed IgAN patients, fifty healthy controls, and fifty disease controls (DC) were recruited. Urinary exosomes were first discovered and then utilized for miRNA extraction. The nCounter[®] Human v3 miRNA Expression Assay, a digital multiplex technique that evaluates 798 unique miRNA barcodes, was used to further analyze the extracted miRNAs. After the least absolute shrinkage and selection operator feature selection identified candidate miRNAs, logistic regression and the CombiROC algorithm were used.

RESULTS: The average age of patients diagnosed with IgAN was 36.32 years, with a standard deviation of 3.07 years. The average proteinuria was 2.69 ± 0.64 g/day, and the average creatinine level was 2.26 ± 0.318 mg/dL. Nine candidate miRNAs - hsa-miR-4532, hsa-miR-4488, hsa-miR-3158-3p, hsa-miR-151b, hsa-miR-3195, hsa-miR-1289, hsa-miR-20a-5p, hsa-miR-20b-5p, hsa-miR-32-5p, and hsa-miR-525-3p - successfully differentiate IgAN cases from both healthy and DC, exhibiting under the curve values of 0.7, 1, and 0.8 for healthy controls, DC, and IgAN cases, respectively. When compared to healthy and DC, a combination of just two miRNAs - hsa-miR-4532 and hsa-miR-548a-3p - was found to be sufficiently effective for detecting IgAN, with an area under the curve > 0.8.

CONCLUSION: Our investigation involving Indian participants revealed a marked alteration in the urinary exosomal miRNA patterns among individuals with IgAN compared to both healthy subjects and those with other kidney diseases, demonstrating the effectiveness of miRNAs in the non-invasive diagnosis of IgAN.},
}

@article {pmid42627892,
year = {2026},
author = {Zhang, Y and Zhu, Y and Zhang, Y and Peng, S and Wu, D and Li, W and Ji, T and Chen, S and Lin, Y and Yang, H and Guo, Y and Li, B and Liu, C and Situ, B and Yan, X and Zheng, L},
title = {Orthogonal DNA barcoding enables subpopulation-resolved extracellular vesicle miRNA profiling.},
journal = {Science advances},
volume = {12},
number = {34},
pages = {eaef8133},
pmid = {42627892},
issn = {2375-2548},
mesh = {Humans ; *MicroRNAs/genetics/metabolism ; *Extracellular Vesicles/genetics/metabolism ; Gene Expression Profiling ; *DNA Barcoding, Taxonomic/methods ; *Stomach Neoplasms/genetics/pathology/metabolism ; ErbB Receptors/genetics ; Cell Line, Tumor ; Gene Expression Regulation, Neoplastic ; Biomarkers, Tumor/genetics ; },
abstract = {Extracellular vesicle-associated microRNAs (EV-miRNAs) hold promise for liquid biopsy, but their clinical utility is hindered by EV heterogeneity. Here, we report DEEPER, a DNA-encoded orthogonal recognition platform for selective barcoding of tumor-derived EV subpopulations and in situ miRNA profiling. DEEPER uses four aptamers targeting Cluster of Differentiation 44 (CD44), Epidermal Growth Factor Receptor‌ (EGFR), Human Epidermal Growth Factor Receptor 2‌ (HER2), and ‌Programmed Death-Ligand 1(PD-L1) to generate orthogonal barcodes that distinguish 15 EV subpopulations. Barcoded EVs then undergo targeted membrane fusion with liposome probes, enabling sensitive in situ analysis of subpopulation-specific miRNAs. In a 60-sample cohort of patients with gastric cancer (GC) and healthy donors (HDs), DEEPER identified a high-performing signature, GC-EV miRNA Prime, comprising EGFR[+], EGFR[+]HER2[+], and EGFR[+]HER2[+]CD44[+] EVs, which achieved 98.3% diagnostic accuracy. The same profiling framework also assessed tumor invasiveness with 95.5% accuracy. Mechanistic studies further showed that these EV-miRNAs contribute to tumor progression. In summary, DEEPER not only confirmed the clinical application value of EV-miRNA-based liquid biopsy but also provided unique insights through the EV subpopulations into the mechanisms driving cancer development.},
}

Humans
*MicroRNAs/genetics/metabolism
*Extracellular Vesicles/genetics/metabolism
Gene Expression Profiling
*DNA Barcoding, Taxonomic/methods
*Stomach Neoplasms/genetics/pathology/metabolism
ErbB Receptors/genetics
Cell Line, Tumor
Gene Expression Regulation, Neoplastic
Biomarkers, Tumor/genetics

@article {pmid42623365,
year = {2026},
author = {Bouchet, VMP and Francescangeli, F and Sousa, SHM and de Jesus, MSDS and Pawlowski, J and Frontalini, F},
title = {Taxonomy-free approach overcomes the gaps in ecological knowledge: The case of foraminiferal metabarcoding applied to environmental impact assessment.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0356357},
pmid = {42623365},
issn = {1932-6203},
mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Geologic Sediments/chemistry ; DNA, Environmental/genetics ; *Environmental Monitoring/methods ; Ecosystem ; Zinc/analysis ; Ecology ; },
abstract = {Environmental DNA (eDNA) metabarcoding has emerged as a cost- and time-efficient alternative to traditional morpho-taxonomic methods for benthic foraminiferal inventories. However, the prevalence of soft-walled monothalamous taxa of unknown ecology, which are largely underrepresented in the barcode reference database, limits the accuracy of eDNA studies. Taxonomy-free approaches, which bypass species-level assignment, may overcome these constraints. Here, we use the case study of the Armida gas platform to confirm the potential of the taxonomy-free framework for ecological quality assessment. As highlighted in a PCA, stations located near the platform (i.e., from 0 to 125 m) exhibited significantly higher concentrations of Zn and Ba in the sediment, while stations farther away appeared unpolluted. Molecular indices based on diversity, e.g., ecological quality ratio (EQR) calculated from exp(H'bc), and a taxonomy-free adaptation of Foram-AMBI (Foram-gAMBI) were applied, with barium serving as an independent indicator for ecological group assignment. The indices EQR (morphology), gEQR and Foram-gAMBI (eDNA) were significantly correlated with Zn and/or Ba, while Foram-AMBI (morphology) did not show any significant meaningful correlation. These results are confirmed by the inferred ecological quality statuses which revealed a clear improvement in benthic habitat quality with increasing distance from the platform when assessed with molecular indices (poor to good for gEQR and moderate to good for Foram-gAMBI), while morphological indices, particularly Foram-AMBI, failed to capture this trend. The weak agreement between morphological and molecular indices is likely due to the greater number of Molecular Operational Taxonomic Units (275) than morphospecies (31), including abundant soft-walled monothalamous foraminifera detected only by eDNA. By adopting a taxonomy-free approach to compute Foram-gAMBI, we can fully exploit the metabarcoding dataset without relying on prior taxonomic or ecological knowledge. Our findings demonstrate the robustness and accuracy of taxonomy-free metabarcoding approaches for monitoring benthic ecosystem health using benthic foraminifera in impacted marine environments.},
}

*Foraminifera/genetics/classification
*DNA Barcoding, Taxonomic/methods
Geologic Sediments/chemistry
DNA, Environmental/genetics
*Environmental Monitoring/methods
Ecosystem
Zinc/analysis
Ecology

@article {pmid42620142,
year = {2026},
author = {Solanky, D and Low, C and Hathaway, CL and Cherne, S and Brown, E and Palanee-Phillips, T and Barnabas, RV and Bhattacharyya, RP and Berdy, B and Livny, J},
title = {Phased amplicon multiplex sequencing for cost-effective detection of high-risk human papillomavirus from cervical samples.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.27.26359029},
pmid = {42620142},
abstract = {Access to accurate cost-effective technologies for typing high-risk human papillomaviruses (hrHPV) is critical to expand cervical cancer screening and inform vaccination strategies. Compared with clinical-standard quantitative polymerase chain reaction (qPCR) assays, HPV genotyping by next-generation sequencing (NGS) provides greater flexibility, scalability, and genotype specificity. We have developed a method for HPV genotyping, HPV Phased Amplicon Multiplex Sequencing (PhAM-Seq), that uses combinatorial barcoding of amplicons with short, variable-length inline sequences to enable higher throughput and lower per-sample costs than conventional amplicon sequencing approaches. We evaluated HPV PhAM-Seq using degenerate and type-specific primers targeting the L1 and E6-E7 gene loci in a blinded cohort of 170 cervical samples previously typed by the Seegene Anyplex II HPV28 Detection qPCR assay. Across eight common hrHPV types (HPV16, 18, 31, 33, 35, 45, 52, and 58), HPV PhAM-Seq demonstrated >80% overall agreement with qPCR using degenerate L1-targeting primers, with the highest sensitivity for HPV16, 31, 33, and 58. Sensitivity for HPV35, 45, and 52 improved to 85% or greater with type-specific primers targeting genes E6/E7. Parallel processing and sequencing enables a single technician to assay hundreds of samples per week at a reagent cost of around $10 USD per sample, with laboratory automation and sequencing on higher-output platforms enabling further scaling and cost reduction to a scale amenable to population-level surveillance. We include a detailed SOP; tools for primer design, sequencing library construction, and sample tracking; and all scripts needed for data analysis to ensure HPV PhAM-Seq can be readily implemented for scalable, cost-effective hrHPV genotyping or extended to other similar applications.},
}

@article {pmid42621361,
year = {2026},
author = {Hsu, YF},
title = {Sun moths in the genus Epicroesa (Lepidoptera, Heliodinidae) associated with Ceodes umbellifera, with description of a new species from Taiwan.},
journal = {ZooKeys},
volume = {1289},
number = {},
pages = {203-214},
pmid = {42621361},
issn = {1313-2989},
abstract = {The association of two heliodinid moths with Ceodes umbellifera is documented for the first time: Epicroesa thiasarcha Meyrick, 1907 from Australia and E. bellatula sp. nov. from Taiwan. The two share similar wing patterns and genitalia, but they can be separated by diagnostic features of adults and immatures. The p-distance of COI barcodes was over 9% between samples of the two taxa, lending support to their recognition as distinct species. The considerable geographical separation between these morphologically similar yet genetically diverged species suggests that either both may have broader distributions than currently recognized, or additional undescribed species may occur in the large gap between Australia and Taiwan.},
}

@article {pmid42622428,
year = {2026},
author = {Baker, CS and Colpus, M and Gentry, J and Hall, A and Roghi, E and Webster, H and Drummond, B and Cooper, R and Thai, H and Westhead, J and Turner, R and Peto, TEA and Fowler, PW and Morgan, M and Crook, DW},
title = {Validation of an optimized Oxford Nanopore sequencing workflow versus Illumina for mycobacteria from primary MGIT culture.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0140226},
doi = {10.1128/spectrum.01402-26},
pmid = {42622428},
issn = {2165-0497},
abstract = {UNLABELLED: Illumina short-read sequencing of primary Mycobacterial Growth Indicator Tube (MGIT) cultures is an established approach for mycobacterial genomic characterization but relies on labor-intensive workflows and centralized sequencing facilities. Oxford Nanopore Technologies (ONT) offers long-read sequencing and is increasingly being explored for in-house implementation in diagnostic laboratories; however, low DNA yields from primary MGIT cultures frequently limit standard PCR-free ONT workflows, restricting routine implementation. We developed and evaluated a semi-automated DNA extraction and Rapid PCR Barcoding workflow for ONT sequencing and compared its performance with Illumina for species identification and Mycobacterium tuberculosis complex (MTBC) single-nucleotide polymorphism (SNP) detection. A platform-agnostic bioinformatics pipeline was used for human read removal, taxonomic assignment, and MTBC genomic characterization. The time required to achieve reliable species identification was assessed by subsampling ONT data at 1, 6, and 72 h. Concordance between ONT and Illumina for species classification was 98.3% (95% CI: 95.8%-99.5%), with all discordant classifications attributable to potential mixed infections. MTBC SNP concordance was high, with a mean of 0.3 and a median of 0 SNP differences between platforms after masking. Reliable species identification was achieved for 233/237 (98.3%) samples within 6 h of sequencing, with no incorrect primary species assignments. These findings demonstrate that an optimized PCR-amplified ONT workflow provides a practical approach for routine in-house genomic characterization of primary MGIT cultures, achieving high concordance with Illumina while addressing a major barrier to ONT implementation in diagnostic laboratories.

IMPORTANCE: Rapid genomic characterization of mycobacterial infections is important for timely patient management, infection control, and public health surveillance. However, many diagnostic laboratories rely on referral of positive cultures to regional reference centers for sequencing, introducing delays associated with transport, batching, and processing. Although Oxford Nanopore Technologies (ONT) can support local sequencing, implementation has been limited by the low DNA yields typically obtained from primary Mycobacterial Growth Indicator Tube (MGIT) cultures and the absence of practical workflows suitable for routine diagnostic laboratories. In this study, we developed and validated a semi-automated DNA extraction and PCR-based ONT workflow designed to support implementation in routine diagnostic laboratories. The workflow generated genomic results highly concordant with Illumina sequencing while overcoming a major barrier to ONT implementation by enabling reliable sequencing from low-yield MGIT-derived DNA. This approach supports routine in-house genomic characterization of mycobacterial cultures and has the potential to reduce turnaround times and dependence on external sequencing services.},
}

@article {pmid42608964,
year = {2026},
author = {Hey, L and Chen, C and Xu, T and Cowell, E and Langlet, D and Methou, P},
title = {Widespread Association of Ciliates Colonizing Gills of Shrimps Inhabiting Vents and Seeps Across the Pacific Ocean.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {5},
pages = {e70115},
pmid = {42608964},
issn = {1550-7408},
support = {ANR-17-EURE-0015//ISblue project, Interdisciplinary Graduate School for the Blue Planet/ ; ANR-22-POCE-0007//National Research Agency/ ; 23K05942//Japan Society for the Promotion of Science/ ; 16309324//General Research Funds (GRFs) & Collaborative Research Fund (CRF) of the Hong Kong SAR government/ ; 16100425//General Research Funds (GRFs) & Collaborative Research Fund (CRF) of the Hong Kong SAR government/ ; C2013-22G//General Research Funds (GRFs) & Collaborative Research Fund (CRF) of the Hong Kong SAR government/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability of The Hong Kong University of Science and Technology/ ; 2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; YK23-16S//Cooperative Research Program of Atmosphere and Ocean Research Institute/ ; SIP//Council for Science, Technology, and Innovation (CSTI), Japan/ ; FKt231024//Schmidt Ocean Institute/ ; NSF OCE 1635219//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Gills/parasitology ; Pacific Ocean ; *Ciliophora/classification/genetics/isolation & purification/physiology/ultrastructure ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Symbiosis ; Microscopy, Electron, Scanning ; DNA, Ribosomal/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Bacterial symbiosis is well-documented in chemosynthesis-based ecosystems, but associations with microeukaryotes remain overlooked. In this study, using scanning electron microscopy and 18S rDNA barcoding, we investigate the presence, diversity, and biogeographic patterns of ciliate epibionts associated with two deep-sea caridean families: Alvinocarididae and Thoridae. We identified a widespread lineage of ciliates colonizing the gills of different alvinocaridid species, extending their previously known distribution in freshwater and coastal habitats to deep ocean down to 3388 m. These ciliates form a distinct clade related to coastal Chonotrichia, but show clear genetic divergence from the previously described species. Geographic divergence of these ciliate populations was observed across the Pacific Ocean, with no evident structure related to their host species. These chonotrichian ciliates exhibited variation in occurrence across host species, individuals, and regions, indicating a facultative association with their hosts. In contrast, the thorid shrimps harbored rare and phylogenetically diverse ciliates. More rarely, we found ciliates related to known parasitic lineages hosted by both shrimp families, with signs of immune response (black gills) in some individuals colonized by these ciliates. Our results reveal previously overlooked protist-crustacean associations in chemosynthetic ecosystems and highlight the ecological and biogeographic importance of this group in the deep ocean.},
}

Animals
*Gills/parasitology
Pacific Ocean
*Ciliophora/classification/genetics/isolation & purification/physiology/ultrastructure
Phylogeny
RNA, Ribosomal, 18S/genetics
Symbiosis
Microscopy, Electron, Scanning
DNA, Ribosomal/genetics/chemistry
Sequence Analysis, DNA

@article {pmid42610891,
year = {2026},
author = {Tian, R and Kang, Q and Dai, X and Ding, Y and Chen, A and Zhang, P and Yang, C},
title = {Ortho-Fusion Metaboliprobe for Sensitive and Specific In Situ Detection of Metabolites in Tumor-Derived Exosomes.},
journal = {Analytical chemistry},
volume = {98},
number = {32},
pages = {23572-23583},
doi = {10.1021/acs.analchem.6c01961},
pmid = {42610891},
issn = {1520-6882},
support = {SHSMU-ZLCX20212601//Innovative Research Team of High-level Local University in Shanghai/ ; 22374028//National Natural Science Foundation of China/ ; 22374097//National Natural Science Foundation of China/ ; 2022YFA1305200//National Key Research and Development Program of China/ ; },
mesh = {*Exosomes/metabolism/chemistry ; Humans ; *Prostatic Neoplasms/metabolism/diagnosis ; Tetraspanin 30/metabolism/chemistry ; Male ; Aptamers, Nucleotide/chemistry/metabolism ; Cell Line, Tumor ; *Biomarkers, Tumor/metabolism ; *Adenosine Triphosphate/analysis/metabolism ; Epithelial Cell Adhesion Molecule/metabolism ; Liposomes/chemistry ; },
abstract = {Small molecule metabolites carried by exosomes have emerged as promising biomarkers for cancer liquid biopsy. However, their clinical application is hindered by the complexity of blood components, the difficulty in distinguishing tumor-derived exosome subpopulations, and the low abundance of metabolites. Here, we develop an Ortho-Fusion Metaboliprobe for the in situ detection of small molecule metabolites in tumor-derived exosomes with high specificity and sensitivity. The Ortho-Fusion Metaboliprobe employs a dual allosteric aptamer system targeting CD63 and EpCAM to form an orthogonal labeling barcode on the surface of tumor-derived exosomes, enabling precise discrimination of tumor exosome subpopulations from complex biological backgrounds. Following orthogonal labeling, liposomes functionalized with complementary DNA tags recognize this barcode via zipper hybridization, triggering targeted membrane fusion between the liposome and the exosome. This fusion event delivers the encapsulated Au NFs-based metabolite detection probes into the exosomal lumen, where they react with target metabolites and generate amplified fluorescent signals for sensitive and specific in situ detection. Using this assay, we successfully detected ATP and spermine in exosomes derived from prostate cancer cell lines and clinical plasma samples. Both metabolite markers effectively distinguished prostate cancer patients from benign controls, demonstrating the clinical potential of this assay. This strategy offers a powerful tool for the analysis of small molecule metabolites in tumor-derived exosomes and holds significant promise for early cancer diagnosis and screening.},
}

*Exosomes/metabolism/chemistry
Humans
*Prostatic Neoplasms/metabolism/diagnosis
Tetraspanin 30/metabolism/chemistry
Male
Aptamers, Nucleotide/chemistry/metabolism
Cell Line, Tumor
*Biomarkers, Tumor/metabolism
*Adenosine Triphosphate/analysis/metabolism
Epithelial Cell Adhesion Molecule/metabolism
Liposomes/chemistry

@article {pmid42611350,
year = {2026},
author = {Karendi, MG and Ndungu, CN and Mbadi, EM and Wanga, VO and Nyamvula, HM and Kaigongi, MM and Hu, GW},
title = {Comparative chloroplast genomics and phylogenomic insights into the genus Zehneria (Cucurbitaceae).},
journal = {Genetica},
volume = {154},
number = {1},
pages = {},
pmid = {42611350},
issn = {1573-6857},
support = {32270228, 31970211//National Natural Science Foundation of China,/ ; ZL202203601//Survey of Wildlife Resources in Key Areas of Tibet,/ ; 2019QZKK0502//Tibetan Plateau Scientific Expedition and Research (STEP) program,/ ; 151853KYSB20190027//nternational Partnership Program of Chinese Academy of Sciences,/ ; },
mesh = {*Phylogeny ; *Genome, Chloroplast ; *Cucurbitaceae/genetics/classification ; Codon Usage ; Genomics ; Evolution, Molecular ; Microsatellite Repeats ; },
abstract = {The genus Zehneria (Cucurbitaceae) presents significant taxonomic challenges due to morphological similarities among species and a lack of resolution in molecular studies. In this study, we sequenced and assembled the chloroplast genomes of seven African Zehneria species collected from Kenya, complementing a previously published accession (Zehneria sp. MZ427944.1), to establish a comprehensive plastome-based framework for the genus. The plastomes ranged from 157,150 to 157,365 bp and exhibited a conserved quadripartite structure, with 130-132 annotated genes, including 86-87 protein-coding genes, 36-37 tRNAs, and 8 rRNAs. Structural variation, particularly in non-coding regions and inverted repeat boundaries, was observed, with eight hypervariable loci providing potential targets for molecular marker development. Simple sequence repeat (SSR) analysis revealed a predominance of A/T mononucleotides across species. Codon usage analysis revealed a strong AT-bias across all species, with codons ending in A or U accounting for 72.2% of synonymous codon preferences. Selective pressure analysis identified eight protein-coding genes with Ka/Ks ratios exceeding 1.0, including psaJ and rps8, proposed as candidate molecular barcodes pending further validation. Phylogenomic analysis of 79 protein-coding genes strongly supported the monophyly of Zehneria (ML bootstrap = 96-100%; PP = 1.0), with one node showing slightly reduced support (BS = 96%), and enhanced resolution of interspecific relationships compared to prior studies using fewer loci. This work offers novel insights into genomic diversity and evolutionary history of sampled Zehneria species, providing a critical molecular resource for future taxonomic and phylogenetic studies within Cucurbitaceae. Broader taxon sampling, particularly from Asian lineages, will be necessary to fully resolve interspecific relationships across the genus.},
}

*Phylogeny
*Genome, Chloroplast
*Cucurbitaceae/genetics/classification
Codon Usage
Genomics
Evolution, Molecular
Microsatellite Repeats

@article {pmid42612742,
year = {2026},
author = {Hoyos-López, R and Fernández, N and Gallego-Gómez, JC},
title = {Mosquito-host blood-meal networks reveal potential arboviral bridge pathways in Colombian Caribbean mangroves.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108288},
doi = {10.1016/j.actatropica.2026.108288},
pmid = {42612742},
issn = {1873-6254},
abstract = {Mosquito-host feeding networks shape the ecological routes through which arboviruses may move from enzootic cycles toward human-exposure compartments, yet these networks remain largely uncharacterized in Colombian Caribbean mangroves. We analyzed blood-fed female mosquitoes collected in La Balsa, San Bernardo del Viento (Córdoba, Colombia), between 2011 and 2014 to infer a molecular blood-meal-based interaction network. Of 496 blood-fed females from nine mosquito species, 437 amplified by CytB and/or COI PCR and 396 yielded high-quality sequences suitable for host identification, resolving 31 vertebrate host taxa. Birds dominated successful host assignments (275/396; 69.4%), whereas human feeding was concentrated in Aedes aegypti (HBI = 0.75; 95% CI: 0.47-0.91) and Aedes scapularis (HBI = 0.22; 95% CI: 0.09-0.45). Bray-Curtis clustering identified an ornithophagic Culex guild, an exploratory mixed mammal-bird bridge grouping, and an anthropophagic/mammalophagic Aedes guild, with bootstrap support of 84.6%, 47.4%, and 98.3%, respectively. The directed, weighted network contained 40 nodes and 63 feeding links, with high topological complexity (0.9621) and central bridge nodes including Cx. erraticus, Ma. titillans, De. atlanticus, and Ps. confinnis. Complementary R/bipartite analysis indicated a generalist but partially structured network: connectance = 0.2258, generality = 7.0 host taxa per mosquito species, vulnerability = 2.03 mosquito species per host taxon, H2' = 0.421, QuanBiMo Q = 0.378, NODF = 29.73, and weighted NODF = 19.83. Arbovirus screening of these blood-fed specimens was negative, so the network should be interpreted as a map of potential ecological pathways rather than confirmed transmission. Low HBI outside the anthropophagic guild and high non-human host use are consistent with a dilution-effect hypothesis in intact mangroves, while the identified bridge pathways highlight mosquito-host relationships that could connect enzootic and peridomestic compartments if viral circulation increases or habitat structure changes.},
}

@article {pmid42613581,
year = {2026},
author = {Jiang, Q and Yin, J and Han, X and Yong, J and Sun, R and Liu, M and Wang, W and Wang, Y and Song, M and Xiang, B and Yu, H},
title = {Authentication of the Botanical Origins of Curcumae Radix Based on DNA Barcoding and HS-GC-IMS.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {40},
number = {21},
pages = {e70160},
doi = {10.1002/rcm.70160},
pmid = {42613581},
issn = {1097-0231},
support = {2440STCZB2617//Ministry of Industry and Information Technology 2024 Key Special Projects/ ; 25ZXZSSS00280//Science and Technology Program of Tianjin/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Gas Chromatography-Mass Spectrometry/methods ; *Curcuma/genetics/chemistry/classification ; DNA, Plant/genetics ; Volatile Organic Compounds/analysis ; Principal Component Analysis ; *Drugs, Chinese Herbal/chemistry ; Discriminant Analysis ; },
abstract = {RATIONALE: As a classic multiorigin herbal medicine, the precise authentication of Curcumae Radix (Yujin) is crucial for ensuring market standardization and clinical efficacy. Given the complexity of herbal materials, single-method identification often lacks the resolution required to distinguish between closely related species or handle degraded with significant DNA degradation.

METHODS: A two-dimensional analytical strategy was applied to 24 batches of Curcumae Radix samples. This approach combined ITS2 DNA barcoding for genetic identification with headspace gas chromatography-ion mobility spectrometry (HS-GC-IMS) to analyze volatile organic compound (VOC) profiles. The resulting HS-GC-IMS data were processed using chemometric tools, including principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), to compare and differentiate the decoction pieces.

RESULTS: The results demonstrated that while ITS2 DNA barcoding effectively identified Curcuma kwangsiensis S. G. Lee et C. F. Liang, it failed to discriminate between the closely related species Curcuma longa L. and Curcuma phaeocaulis Val. and was ineffective for DNA-degraded samples of Curcuma wenyujin Y. H. Chen et C. Ling. Conversely, HS-GC-IMS successfully established distinct VOC fingerprints for each source. When coupled with chemometric analysis, this method pinpointed specific interspecific discriminatory biomarkers that allowed for clear differentiation where genetic barcoding fell short.

CONCLUSION: By integrating stable genetic information with volatile chemical fingerprints, this study establishes a complementary two-dimensional identification system. This strategy provides an innovative and reliable solution for the botanical authentication and quality control of Curcumae Radix, offering a broadly applicable paradigm for the precise identification of other complex herbal materials.},
}

*DNA Barcoding, Taxonomic/methods
*Gas Chromatography-Mass Spectrometry/methods
*Curcuma/genetics/chemistry/classification
DNA, Plant/genetics
Volatile Organic Compounds/analysis
Principal Component Analysis
*Drugs, Chinese Herbal/chemistry
Discriminant Analysis

@article {pmid42619821,
year = {2026},
author = {Bennett, A and Moore, R and Herbold, CW and Hanson, TE},
title = {A Sample to Results Workflow for Compositional Analysis of Multiplexed Amplicon Sequencing Experiments.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.28.741237},
pmid = {42619821},
issn = {2692-8205},
abstract = {UNLABELLED: Microbial communities play key roles in the transformation and cycling of elements ranging from required macronutrients to toxic metalloids. Next-generation sequencing has been applied across multiple ecosystems to probe the interplay of microbial community structure and functional potential with respect to elemental cycling. Shotgun metagenomics collects marker gene sequences without amplification and is costly for large numbers of samples and deep coverage. Conversely, amplicon sequencing of taxonomic marker genes, e.g. 16S and 18S rRNA, is cost-effective for large numbers of samples, but provides limited functional insight. A middle ground between the two approaches is needed to analyze community structure and functional potential within a sample while remaining cost-effective with high throughput. To address this need, we developed a standardized workflow for multiplexed amplicon sequencing from sample collection through data analysis for diverse sample types, including freshwater, sediments, and soils, that produces data and publication-ready figures for multiple taxonomic and functional genes for carbon, nitrogen, phosphorus, sulfur, and arsenic cycling for each sample analyzed. The workflow's utility was shown by analyzing 11 taxonomic and functional gene amplicons sequenced from 25 samples with high technical replicate similarity. The workflow is named CAMASE for C ompositional A nalysis of M ultiplex A mplicon S equencing E xperiments. This proof-of-concept shows that CAMASE economically produces standard amplicon sequencing outputs (ASV/OTU counts and taxonomy, PCA, and relative abundance plots) for hundreds of amplicon by sample combinations and provides specific recommendations for implementation.

GRAPHICAL ABSTRACT: Samples are collected in a preservative and material collected on filters prior to DNA extraction. Target gene amplicons are produced in parallel with internal barcodes enabling sequencing in a single run followed by compositional data analysis. All wet lab protocols, code markdowns, and templates for required metadata files are available at https://hansonlabgit.dbi.udel.edu/aprange/CAMASE . Created in BioRender. Bennett, A. (2026) https://BioRender.com/ymnojt0.},
}

@article {pmid42620021,
year = {2026},
author = {Husain, K and Flagg, L and Pincus, D and Murugan, A},
title = {A DNA-barcoded Luria-Delbrück assay resolves mechanisms of adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.08.03.742544},
pmid = {42620021},
issn = {2692-8205},
abstract = {When populations encounter a harsh new environment, they adapt in many different ways - from spontaneous genetic changes to transient non-genetic plasticity. Distinguishing between mechanisms of adaptation is often difficult, as the key events are rare and hard to observe directly. Here, we introduce HiDenSeq, a Luria-Delbrück assay that uses DNA barcoding and deep sequencing to resolve the Luria-Delbrück distribution - the statistics of adaptation to a new environment - over four orders of magnitude. At this statistical depth, the shape of the distribution encodes the underlying adaptive mechanism. We find that DNA mismatch repair mutants shift the distribution's scale without changing its shape, indicating their only effect is as mutator alleles. A pulse of UV mutagenesis, however, adds a second, statistically distinguishable mode atop the spontaneous background, showing that different mechanisms of adaptation can be quantified directly from the distribution. By sampling rare-event statistics with DNA barcodes, HiDenSeq provides a general method for studying mechanisms of adaptation in evolving populations from microbes to cancers.},
}

@article {pmid42607675,
year = {2026},
author = {Piras, A and Galvagno, F and Pizzini, L and Nunziante, M and Fletcher, SJ and Grassi, E and Bertotti, A and Primo, L and Celani, A and Puliafito, A},
title = {Inference of lineage hierarchies, growth, and drug response mechanisms in cancer cell populations without tracking.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101566},
doi = {10.1016/j.crmeth.2026.101566},
pmid = {42607675},
issn = {2667-2375},
abstract = {Lineage hierarchies and plasticity regulate development and tissue homeostasis, while diverted lineage dynamics and aberrant phenotypic plasticity are among the causes of incomplete drug response and resistance in cancer. Knowing the dynamics of phenotypically heterogeneous populations is therefore central to understanding growth regulation principles and to rationally design therapeutic approaches anticipating drug-tolerant states. While lineage inference can be addressed by barcoding technologies, these approaches often yield average clonal behaviors that neglect the underlying phenotypic plasticity of individual cells. Directly observing single-ancestor pedigrees in multi-type populations remains an experimental challenge. To address these difficulties, we developed a method to infer active phenotypic transitions in a multi-type tumor or clone and to quantify them, solely relying on counting cell-type abundances. We demonstrate the effectiveness of our approach to address cancer phenotypic heterogeneity and drug tolerance in silico. We then perform experiments on cancer cell populations and infer growth mechanisms and transition probabilities.},
}

@article {pmid42600172,
year = {2026},
author = {Schallhart, S and Grimm, J and Holzinger, WE and Huber, E and Klar, N and Kunz, G and Schäffer, S and Schlosser, L and Thalinger, B and Koblmüller, S},
title = {Filling DNA barcode gaps in Central European Auchenorrhyncha: a new reference library and Oxford Nanopore Technologies-based species identification.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2026-0009},
pmid = {42600172},
issn = {1480-3321},
abstract = {Terrestrial arthropods are declining in most ecosystems, creating a need for efficient and scalable biodiversity monitoring tools. DNA-barcoding enables high-throughput species identification but is constrained by incomplete reference libraries for many taxa. Here, we expand the DNA barcode database for Austrian Auchenorrhyncha by combining morphological identification with Sanger-sequenced COI barcodes. A total of 1 304 specimens representing 394 species were successfully barcoded, resulting in 384 Barcode Index Numbers (BINs), including 73 newly established BINs. Elevated intraspecific COI divergence and BIN discordance in several taxa reveal species complexes and missing barcode gaps. The expanded reference library was applied to Auchenorrhyncha from Malaise trap samples collected at an agricultural lowland and an alpine site and analyzed using a high-throughput Oxford Nanopore Technologies (ONT) workflow. The improved reference library substantially increased assignment success and taxonomic resolution. Finally, we compared the ONT barcoding results from Malaise trap catches with morphology-based identifications from single-event suction sampling. Both approaches detected similar proportions of species, and differences in species composition likely reflect sampling- and method-specific biases. Overall, this study advances the development of a comprehensive DNA barcode reference library for Central European Auchenorrhyncha and underscores the importance of regionally curated databases and complementary approaches for biodiversity assessments.},
}

@article {pmid42602933,
year = {2026},
author = {Kandaurova, E and Novák, J and Náhlovský, J and Perglerová, A and Jewell, JB and Vorel, A and Munclinger, P and Tůmová, P and Hampl, V},
title = {Gut protist diversity in Eurasian beavers (Castor fiber) revealed by metabarcoding.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {31},
number = {},
pages = {101270},
pmid = {42602933},
issn = {2213-2244},
abstract = {Gut protists are an important part of the microbial community that is often overlooked or limited to certain "flagship" species, mainly parasites. This also applies to Eurasian beavers (Castor fiber), which act as aquatic engineers in riparian habitats and have been identified as potential reservoirs of the well-known intestinal protist parasite - Giardia intestinalis. In this study, we focus on exploring protistan diversity in Eurasian beavers from freshly collected stool samples using molecular methods, including targeted barcoding of specific parasitic groups (Giardia, Cryptosporidium and Microsporidia) and general metabarcoding of the V4 region of 18S rRNA on the Illumina MiSeq platform. Two individuals were tested positive for Cryptosporidium spp. using the targeted barcoding. The metabarcoding approach revealed that the gut community was predominantly composed of gut commensals, Blastocystis, and trichomonads, found in every individual. More detailed investigation of Blastocystis confirmed the potential existence of a specific beaver subtype. Colpodellids and parasitic Eimeria spp. were only occasionally present. Geographic location of the host, unlike sex, has a significant impact on gut microbiota composition, though more research is needed due to limited sampling. Finally, we tested a new primer set for amplifying the V4 region of 18S rRNA, which shows promise for improving the detection of Metamonada protists in the gut samples.},
}

@article {pmid42603972,
year = {2026},
author = {Buckley, TR and Dopheide, A and Ward, D and Dhami, M},
title = {Prospects for Complete DNA Barcode Coverage of the New Zealand Insect Fauna.},
journal = {Journal of the Royal Society of New Zealand},
volume = {56},
number = {4},
pages = {e70078},
pmid = {42603972},
issn = {1175-8899},
abstract = {The accurate identification of insects supports conservation, biosecurity and ecological monitoring. However, morphological identification is constrained by taxonomic complexity, undescribed diversity, and limited expertise. DNA barcoding can alleviate some of these challenges and complement morphological identification, if reference data are comprehensive and reliable. We assessed the taxonomic, geographic and elevational coverage of New Zealand insect DNA barcodes using taxonomic names from the New Zealand Organisms Register, published estimates of undescribed species richness, and DNA barcode metadata. Only 18% of described native and exotic insect species currently have DNA barcodes, with higher coverage for exotic (59%) than native species (12%). DNA barcode coverage varies from complete in several single-species orders to very low in hyperdiverse orders such as Coleoptera (7%) and Diptera (5%), while moderately diverse aquatic orders reach 31%-91% coverage. Low elevation and populated regions are overrepresented in the DNA barcode data, and many species identifications are based on bioinformatic approaches rather than taxonomic or diagnostic expertise. Despite these biases, we propose that a complete national DNA barcode library for described insect species is highly achievable given access to well-curated insect collections and species name databases for tracking progress. Complete DNA barcoding of undescribed species will be more challenging and will require targeting underrepresented taxa, geographic regions and elevations. Sampling will need to incorporate field surveys with bulk specimen collection, environmental DNA, museomic approaches and expert-verified identifications. Completing this library will strengthen New Zealand's regional and national-scale biodiversity monitoring using environmental DNA, with important contributions to biosecurity and conservation outcomes.},
}

@article {pmid42604164,
year = {2026},
author = {Liu, YF and Zhao, WJ and Yang, X and Li, LK and Huang, YX and Wang, X},
title = {Two new species of Conostigmus Dahlbom, 1858 (Hymenoptera, Megaspilidae) from Xizang Autonomous Region, China.},
journal = {ZooKeys},
volume = {1287},
number = {},
pages = {321-334},
pmid = {42604164},
issn = {1313-2989},
abstract = {The genus Conostigmus Dahlbom, 1858 (Hymenoptera: Megaspilidae) is the most species-rich genus within the family Megaspilidae, with a worldwide distribution and important ecological roles as parasitoids. Based on morphological evidence, two new species of the genus, namely Conostigmus vitreus sp. nov. and Conostigmus obsidianus sp. nov., are described and illustrated from Xizang Autonomous Region, China. An updated key to the Chinese species of Conostigmus is provided. This study contributes additional new taxa to the fauna of Conostigmus in Xizang, further enriching the knowledge of the Himalayan Megaspilidae fauna.},
}

@article {pmid42597991,
year = {2026},
author = {Lee, WK and Kim, SJ},
title = {New records of three vent-endemic scale worms (Annelida, Polynoidae) from the northern Central Indian Ridge fill regional distributional gaps.},
journal = {ZooKeys},
volume = {1287},
number = {},
pages = {273-289},
pmid = {42597991},
issn = {1313-2989},
abstract = {The tribe Lepidonotopodini (Polychaeta, Polynoidae) consists of 61 species in 12 genera. Species in this tribe lack eyes and lateral antennae and exhibit pronounced sexual dimorphism; some have external branchiae. Here, we report new records of three species of Lepidonotopodini-Cladopolynoe jiaolongae, Photinopolynoe kaireiensis, and Themis longqiensis-from hydrothermal vents on the northern Central Indian Ridge (nCIR) based on morphological characteristics and COI barcodes. Morphological characters missing in the original description papers are also provided here to complement and refine these species' diagnoses. The COI barcodes of all three species showed low intraspecific divergence (0.00-1.55%), substantially lower than interspecific divergence within the genus (7.77-24.47%). These findings expand the known distribution ranges and clarify the species boundaries of these taxa in nCIR vent fields. Consequently, this study contributes to a better understanding of regional biodiversity and helps establish biological baselines for environmental management within the contract areas.},
}

@article {pmid42595963,
year = {2026},
author = {Zeng, CX and Zhou, MY and Twyford, AD and Gao, LM and Zhang, ZY and Ji, YH and Li, HT and Ma, PF and Yu, WB and Mo, ZQ and Zuo, ZY and Huang, W and Yi, TS and Yang, JB and Hollingsworth, PM and Li, DZ},
title = {Plant species identification by genome skimming across the vascular plant tree of life.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71494},
pmid = {42595963},
issn = {1469-8137},
support = {32120103003//the National Natural Science Foundation of China/ ; 32370245//the National Natural Science Foundation of China/ ; 2021FY100200//Science and Technology Basic Resources Investigation Program of China/ ; 2023YFA0915800//Science and Technology Basic Resources Investigation Program of China/ ; },
abstract = {Accurate species identification is essential for biodiversity conservation and sustainable use, yet standard plant DNA barcoding often fails to achieve species-level resolution. We present a large-scale empirical evaluation of genome skimming as a tool to improve plant species discrimination. Using standardised data from 1969 individuals representing 475 species from 32 genera across major lineages of the vascular plant tree of life, we compare conventional plastid + internal transcribed spacer (ITS) barcodes with genome skimming approaches. Standard barcoding using rbcL, matK, trnH-psbA and ITS resolved about half of species (49.3%), with six genera showing < 25% species discrimination. By contrast, genome skimming enabled the recovery of complete plastid genomes, yielding 57.6% species discrimination. It also generated sufficient nuclear genomic data for additional resolution from k-mer analysis, achieving 66.8% species discrimination - an average gain of 17.5% over standard barcodes - while eliminating cases of extreme failure (< 25% resolution). The recovery of complete plastomes and ribosomal DNAs from genome skims also ensures backward compatibility with existing barcode datasets. Our results demonstrate that genome skimming provides data that substantially improves species-level resolution across diverse plant lineages and offers a scalable, high-throughput approach for building comprehensive reference resources to support global biodiversity initiatives.},
}

@article {pmid42595975,
year = {2026},
author = {Al-Shammari, AS},
title = {Integrated environmental, phytochemical, and genetic assessment of Avicennia marina populations along the Arabian Gulf coast of eastern Saudi Arabia.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42595975},
issn = {1471-2229},
mesh = {*Avicennia/genetics/chemistry/metabolism ; Saudi Arabia ; *Phytochemicals/analysis ; Gas Chromatography-Mass Spectrometry ; Genetic Variation ; },
abstract = {BACKGROUND: Avicennia marina dominates mangrove communities along the hypersaline Arabian Gulf, yet links among local habitat conditions, secondary metabolite profiles, and genetic structure remain poorly characterized. This study examined four A. marina stands-Tarout (P1), Saihat (P2), Al Qatif (P3), and Safwa (P4)-near Dammam, eastern Saudi Arabia, integrating field observations, water and pore-soil physico-chemical analyses, GC-MS/MS profiling, SCoT markers, and rbcL barcoding.

RESULTS: Sites differed strongly in stand structure, water chemistry, and sediment ion loading, with Tarout, Saihat, and Safwa exhibiting marine-hypersaline waters and Al Qatif more dilute, high-alkalinity conditions but highly saline sediments. GC-MS/MS revealed 27 compounds and a shared flavonoid-rich baseline dominated by 7,3',4',5'-tetramethoxyflavanone, superimposed on distinct site-specific terpenoid and phenolic signatures. SCoT markers detected moderate nuclear diversity and clear genetic differentiation among populations, while rbcL sequences, though conservative, resolved low but informative chloroplast structuring.

CONCLUSIONS: Collectively, the environmental, chemical, and molecular evidence indicates that A. marina in this region comprises a mosaic of locally differentiated, genetically structured stands with distinct chemotypes, providing a preliminary basis for managing these stands as locally differentiated conservation units rather than a single homogeneous resource.},
}

*Avicennia/genetics/chemistry/metabolism
Saudi Arabia
*Phytochemicals/analysis
Gas Chromatography-Mass Spectrometry
Genetic Variation

@article {pmid42594714,
year = {2026},
author = {Fikri, E and Eldin Khair, AS},
title = {Discussion on "Infectious medical waste characterization using X-ray transmission with Machine learning".},
journal = {Waste management (New York, N.Y.)},
volume = {225},
number = {},
pages = {115807},
doi = {10.1016/j.wasman.2026.115807},
pmid = {42594714},
issn = {1879-2456},
abstract = {This article is a discussion on the non-contact automated characterization framework for infectious healthcare waste by Vielsack et al. (2026). Two critical scientific and operational boundaries are critically analyzed while recognizing their pioneering combination of X-ray transmission (XRT) and machine learning in field conditions. First, single-energy XRT technology limitations hinder fine-grained polymer discrimination; overlapping attenuation profiles cannot differentiate high-value recyclable polymers from problematic polyvinyl chloride (PVC), risking contamination of downstream mechanical recycling. Second, the deployment of the model is hampered by structural barriers to transferability, such as systemic waste co-mingling, non-standardized disposal vessels and the absence of centralized institutional registers within developing countries, which were exposed in the disciplined field trial by the 38.2 % database matching failure. To realize global validity, this letter puts forward the paradigm shift from broad batch identification (e.g., RFID, barcodes) to definitive material quantification through: three-dimensional tomographic sensing (specifically prioritizing limited-angle computed tomography over standard two-dimensional configurations), digital procurement data-harmonization, and indelible manufacturing-stage tracking mechanisms (QR/RFID).},
}

@article {pmid42587938,
year = {2026},
author = {Marmin, L and Ruby, F and Philipp, P},
title = {Detecting Plant-Based Food Fraud Using Nanopore Metabarcoding: A Proof-of-Concept Study.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
pmid = {42587938},
issn = {2304-8158},
abstract = {Food products containing plant ingredients are particularly vulnerable to economically motivated adulteration (EMA), which poses risks to consumer trust and regulatory compliance. While traditional methods-such as microscopy, chemical profiling or targeted PCR-struggle to detect adulterants in processed food products or complex mixes, DNA metabarcoding offers a non-targeted, high-throughput alternative. This study presents a nanopore sequencing-based technique that is easy to implement, cost-effective and sufficiently sensitive to detect substitutions, with a focus on spices and herbal teas as model matrices. The method was evaluated using eight single-species reference samples and five commercial multi-ingredient products. It reliably detected undeclared contaminants (e.g., mint in oregano) and species substitutions. Compared to single-barcode approaches, the combination of ITS2 + matK + trnH-psbA markers achieved higher sensitivity. The proposed workflow requires minimal infrastructure and a 2-4-day turnaround time. However, factors such as DNA degradation in highly processed foods, database gaps, and biological diversity limited detection in some cases. These findings demonstrate the workflow's potential as a first-line screening tool for food authenticity testing, aligning with requirements such as EU regulation 1169/2011 on food labelling or the FDA's Economically Motivated Adulteration (EMA) program. Future work should validate the method against regulatory thresholds and expand testing to a broader variety of species and matrices.},
}

@article {pmid42588852,
year = {2026},
author = {Chaichit, S and Phrutivorapongkul, A and Arunotayanun, W and Intharuksa, A},
title = {Integrated ITS2 DNA Barcoding and LC-QTOF/MS Metabolomics for Authentication of Ngueak Pla Mo (Acanthus spp.) and Differentiation of Pharmacopoeial Species from A. montanus L.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
pmid = {42588852},
issn = {2223-7747},
support = {214531, FRB690042/0162//Fundamental Fund 2026 (214531), Chiang Mai University, and also Thailand Science Research and Innovation (TSRI) (FRB690042/0162)/ ; },
abstract = {Ngueak Pla Mo is a Thai medicinal crude drug derived from the pharmacopoeial Acanthus species A. ebracteatus Vahl and A. ilicifolius L.; however, morphological similarity and the occurrence of non-pharmacopoeial substitutes such as A. montanus (Nees) T. Anderson may complicate authentication and quality control. This study aimed to develop an integrated molecular-chemical approach for differentiating pharmacopoeial Ngueak Pla Mo species from A. montanus. Twenty authenticated Acanthus samples were analyzed using ITS2 DNA barcoding, including nucleotide variation, pairwise genetic distance, barcode gap, haplotype network, phylogenetic analysis, and predicted ITS2 secondary structure. Representative samples were further examined by untargeted LC-QTOF/MS metabolite profiling combined with hierarchical clustering, PCA, PLS-DA, VIP analyses, fold-change evaluation, and specificity scoring. ITS2 analyses clearly separated A. montanus from A. ebracteatus and A. ilicifolius, supported by diagnostic sequence variation, positive barcode gaps, distinct haplotypes, phylogenetic clustering, and secondary-structure differences, whereas A. ebracteatus and A. ilicifolius could not be reliably differentiated from each other at the species level using ITS2. LC-QTOF/MS profiling revealed species-consistent metabolite patterns and prioritized gallic acid, catechol, 3,4-dihydroxybenzoic acid, trigonelline, and ursolic acid as preliminary candidate markers for A. montanus discrimination. These results indicate that combining ITS2 barcoding with metabolite profiling provides complementary evidence for Ngueak Pla Mo authentication and supports future quality-control development.},
}

@article {pmid42589208,
year = {2026},
author = {Malewski, T and Matić, S and Bilska, AG and Cucu, MA and Miozzi, L and Mello, A and Skwiercz, A and Oszako, T and Nowakowska, JA},
title = {Primer-Less Species Identification Throughout Fungal (Tuber magnatum), Plant (Corylus avellana) and Animal (Eisenia fetida) Kingdoms by Direct RNA Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
pmid = {42589208},
issn = {1422-0067},
mesh = {Animals ; *Fungi/genetics/classification ; *Sequence Analysis, RNA/methods ; Phylogeny ; },
abstract = {Accurate species identification is essential for biodiversity studies, ecological monitoring, and biosecurity, but current molecular approaches rely on PCR amplification, which requires universal primers. Here, we evaluated the possibility of primer-free species identification via direct RNA sequencing (dRNA-seq) by using Oxford Nanopore Technology (ONT). Total RNA isolated from three major eukaryotic kingdoms-fungal (Tuber magnatum Picco 1788), plant (Corylus avellana L. 1753), and animal (Eisenia fetida Savigny 1826) specimens-was sequenced without reverse transcription and PCR amplification. Taxonomic assignments based on similarity to ribosomal nuclear (fungi and animals) and chloroplast (plant) transcripts enabled reliable host species identification. Ribosomal RNA reads dominated the datasets and supported accurate identification of the target organisms, while additional sequences revealed associated microbiota and co-occurring taxa. Notably, dRNA-seq successfully detected symbiotic bacteria in E. fetida and latent fungal infection in C. avellana, highlighting the method sensitivity. However, the complex organization of nuclear ribosomal gene clusters may complicate taxonomic assignment in plants, underscoring the need for improved analytical pipelines. Overall, our results provide proof of concept that dRNA-seq enables primer-independent species identification while simultaneously providing insights into the host microbiomes. Direct sequencing of naturally present RNA molecules generated sufficient sequence information for species identification across different taxonomic kingdoms, indicating the technical feasibility of the developed technique. Further validation using larger biological datasets and direct comparisons with conventional sequencing methods will determine its wider applicability as an innovative and complementary species identification approach.},
}

Animals
*Fungi/genetics/classification
*Sequence Analysis, RNA/methods
Phylogeny

@article {pmid42592693,
year = {2026},
author = {Raviraj, T and Yu, CL and Intharuksa, A and Lai, SC and Tenderly, VF and Loo, YC and Chen, PW and Wang, SW and Purnomo, KA and Kulandhaivel, SR and Renadi, S and Lirio, S and Cheng, YB and Yang, YL and Hwang, TL and Chang, FR and Korinek, M},
title = {Discovery of VEGFR-2 Inhibitors From Leonurus japonicus via Integrated Genetic Authentication, Molecular Networking, and In Silico Analysis.},
journal = {Archiv der Pharmazie},
volume = {359},
number = {8},
pages = {e70249},
pmid = {42592693},
issn = {1521-4184},
support = {NSTC-113-2320-B-037-023//National Science and Technology Council, Taiwan/ ; NSTC-112-2320-B-037-012//National Science and Technology Council, Taiwan/ ; NSTC-111-2320-B-037-007//National Science and Technology Council, Taiwan/ ; NSTC-114-2927-I-037-502//National Science and Technology Council, Taiwan/ ; NSTC-113-2811-B-037-011//National Science and Technology Council, Taiwan/ ; NSTC-113-2321-B-037-002//National Science and Technology Council, Taiwan/ ; NSTC-111-2320-B-037-020-MY3//National Science and Technology Council, Taiwan/ ; NSTC-114-2320-B-020-MY3//National Science and Technology Council, Taiwan/ ; NSTC-114-2320-B-037-021-MY3//National Science and Technology Council, Taiwan/ ; NSTC-114-2321-B-037-008//National Science and Technology Council, Taiwan/ ; KMU-TC111A03-3//Drug Development and Value Creation Research Center, Kaohsiung Medical University, Taiwan/ ; KMU-TC112A03-3//Drug Development and Value Creation Research Center, Kaohsiung Medical University, Taiwan/ ; KMU-TC114A203//Drug Development and Value Creation Research Center, Kaohsiung Medical University, Taiwan/ ; KMU-Q113011//Kaohsiung Medical University Research Foundation, Taiwan/ ; NSYSU-KMU-114-P16//NSYSU-KMU joint research project, Taiwan/ ; NSYSU-KMU-115-P15//NSYSU-KMU joint research project, Taiwan/ ; },
mesh = {*Vascular Endothelial Growth Factor Receptor-2/antagonists & inhibitors/metabolism ; *Angiogenesis Inhibitors/pharmacology/chemistry/isolation & purification ; *Leonurus/chemistry/genetics ; Humans ; Molecular Structure ; *Drug Discovery ; Molecular Docking Simulation ; Structure-Activity Relationship ; Tandem Mass Spectrometry ; *Protein Kinase Inhibitors/pharmacology/chemistry/isolation & purification ; Computer Simulation ; Angiogenesis/drug effects ; },
abstract = {Angiogenesis, regulated by vascular endothelial growth factor (VEGF), is crucial in tumor growth, metastasis, and inflammation. Leonurus japonicus Houtt., a traditional Chinese herb, was investigated for its anti-angiogenic potential. DNA sequencing confirmed its identity, distinguishing it from the common morphological misidentification with Leonurus sibiricus by the public. Using UHPLC-MS/MS and GNPS (Global Natural Products Social) molecular networking on the active methanol partition, over 6000 nodes were grouped into 273 clusters. Diterpenoids and flavonoids were targeted. Six compounds were successfully isolated from L. japonicus, including four labdane-type diterpenoids (1-4) and two flavonoids (5, 6) using column chromatography. Compound 1, (-)-8S-acetoxy-15,16-epoxy-8,9-seco-13(16),14-labdadiene, was a new stereoisomer, while Compound 6, nevadensin, was reported for the first time from this species. Compounds were characterized by NMR, ESI-MS, and ECD. At 50 μM, Compounds 1, 4, and 5 exhibited inhibitory effects in endothelial progenitor cell (EPC) tube formation. Molecular docking and dynamics simulations supported this anti-angiogenic activity. Compound 1 showed the highest VEGFR-2 binding affinity (-9.24 kcal/mol), comparable to sunitinib (-9.52 kcal/mol), further verified by an immunoblotting assay. This study demonstrated the successful integration of GNPS and bioactivity-guided isolation for identifying natural VEGFR-2 inhibitors. Our findings highlight Compounds 1 and 4 as promising lead candidates for anti-angiogenic therapy.},
}

*Vascular Endothelial Growth Factor Receptor-2/antagonists & inhibitors/metabolism
*Angiogenesis Inhibitors/pharmacology/chemistry/isolation & purification
*Leonurus/chemistry/genetics
Humans
Molecular Structure
*Drug Discovery
Molecular Docking Simulation
Structure-Activity Relationship
Tandem Mass Spectrometry
*Protein Kinase Inhibitors/pharmacology/chemistry/isolation & purification
Computer Simulation
Angiogenesis/drug effects

@article {pmid42581346,
year = {2026},
author = {Shehata, FA and El-Demerdash, MM and Elsehely, HH and Saad-Allah, KM and Gad, D},
title = {Taxonomic delineation of four Zygophyllum simplex L. (Zygophyllaceae) morphotypes using morphoanatomical, molecular (SCoT) and chemotaxonomic evidence.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42581346},
issn = {1471-2229},
mesh = {Phylogeny ; *Zygophyllum/genetics/classification/anatomy & histology/chemistry ; Egypt ; Plant Leaves/anatomy & histology/chemistry ; },
abstract = {BACKGROUND: This study presents a comprehensive taxonomic adjustment of Zygophyllum simplex (L.) four constituent varieties in Egypt, integrating morphological, anatomical, palynological, molecular, and phytochemical analyses to evaluate their infraspecific differentiation. Samples were collected from the eastern part of Egypt and subjected to detailed morphological, anatomical, and palynological analyses with SCoT molecular genotyping and HPLC phytochemical profiling.

RESULTS: Four distinct morphological groups (informally designated as "cylindrica", "retusa", "orbicularis", and "lanceolata") were distinguished by significant differences in growth habit, leaf and stem anatomy, floral morphology, and fruit architecture. SCoT molecular marker analysis revealed a genetic similarity range of 0.825-0.881, with phylogenetic clustering strongly compatible with the morpho-anatomical groupings. HPLC profiling further identified group-specific accumulation patterns of key phenolic and flavonoid compounds, such as chlorogenic acid and catechin. While palynological analysis showed limited diagnostic value, the collective data from multiple disciplines provide robust evidence for the recognition of these four distinct morphotypes.

CONCLUSIONS: Morphological, anatomical, and fruit architectural traits, together with group-specific phytochemical profiles and SCoT molecular markers, provided robust evidence for the differentiation of four distinct morphotypes within the Z. simplex complex. However, given the moderate resolution of SCoT markers (37.77% polymorphism), formal varietal status is not proposed at this stage. We recommend that future studies employ higher-resolution molecular approaches, such as single nucleotide polymorphism (SNP) analysis and DNA barcoding, to validate whether these morphotypes represent genetically distinct and reproductively coherent varieties. Pending such validation, these taxa should be treated as morphotypes, thereby establishing a preliminary integrative framework for their identification.},
}

Phylogeny
*Zygophyllum/genetics/classification/anatomy & histology/chemistry
Egypt
Plant Leaves/anatomy & histology/chemistry

@article {pmid42581425,
year = {2026},
author = {Hebenstreitová, K and Mahlerová, K and Vaňková, L and Vaněk, D},
title = {Species Determination Within the Felidae Family Using mtDNA Minibarcoding.},
journal = {Animal genetics},
volume = {57},
number = {4},
pages = {e70181},
pmid = {42581425},
issn = {1365-2052},
support = {VJ01010026//Ministerstvo Vnitra České Republiky/ ; },
mesh = {*Felidae/classification/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA Primers ; Electron Transport Complex IV/genetics ; Animals ; },
abstract = {Wildlife forensic analysis frequently deals with highly degraded DNA samples, including those from tanned hides, processed products of traditional Chinese medicine, and specimens stored in preservation fluids. These samples present significant challenges for traditional DNA barcoding due to the difficulty of amplifying sufficiently long DNA fragments. To overcome this limitation, we designed five primer pairs to amplify short mitochondrial DNA (mtDNA) fragments (~100 base pairs). When aligned collectively, these fragments span approximately 500 bp of the cytochrome C oxidase subunit I (COI) gene, which is one of the most common species-barcoding targets. We subjected the primers to a comprehensive validation process, including in silico analysis and experimental verification using various non-degraded and degraded samples of animal tissues. Here, we demonstrate the efficacy and reliability of our DNA minibarcoding method. By addressing the limitations of traditional DNA barcoding, this method improves the accuracy and success of species identification, thereby supporting wildlife conservation, management, and forensic investigations.},
}

*Felidae/classification/genetics
*DNA Barcoding, Taxonomic/methods
DNA Primers
Electron Transport Complex IV/genetics
Animals

@article {pmid42582359,
year = {2026},
author = {Liu, Y and Shen, X and Liang, J and Tian, L and Huang, Y and Tian, W and Zhuge, F and Jiang, D},
title = {Comparative chloroplast genomics clarifies the taxonomic status and supports molecular identification of Viburnum keteleeri 'Sterile' and Viburnum keteleeri.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1908462},
pmid = {42582359},
issn = {1664-462X},
abstract = {Viburnum keteleeri 'Sterile' and V. keteleeri are traditional ornamental plants in China and are highly valued for their large, spherical inflorescences. However, due to long-term artificial selection and morphological similarity, the taxonomic boundary between V. keteleeri 'Sterile' and V. keteleeri has remained controversial. Conventional morphological identification and conventional barcodes have proven insufficient for accurately resolving their taxonomic relationship. In this study, V. keteleeri 'Sterile', V. keteleeri, and their closely related species were investigated using complete chloroplast genome (CPG) data. Comparative genomic analyses were subsequently performed using additional CPGs of Viburnum species retrieved from public databases. The results showed that both CPGs exhibited the typical quadripartite structure of angiosperms, each with a total length of 158,662 bp and containing 133 annotated genes. Simple sequence repeat analysis revealed that T/A-type repeats were the most abundant SSR category, while codon usage analysis indicated a strong preference for synonymous codons ending in A/U. Comparative analyses of 49 Viburnum CPGs demonstrated extremely low genetic divergence between V. keteleeri 'Sterile' and V. keteleeri. Phylogenetic reconstruction consistently placed the two taxa within the same terminal clade, suggesting a very close relationship. Based on the available chloroplast genome evidence, V. keteleeri 'Sterile' is unlikely to represent the nominal species and is more appropriately regarded as a horticultural cultivar or cultivated form derived from V. keteleeri. In addition, 293 lineage-specific single nucleotide polymorphism (SNP) loci were identified, and the ycf1 genes of both V. keteleeri 'Sterile' and V. keteleeri were found to be significantly longer than those of the other examined Viburnum species. These genomic features provide valuable candidate markers for rapid and accurate molecular identification. Overall, this study provides valuable genomic resources for clarifying taxonomic relationships, supporting germplasm conservation, facilitating cultivar authentication, and strengthening plant variety protection and nursery stock quality control in Viburnum.},
}

@article {pmid42584226,
year = {2026},
author = {Liu, Y and Zhao, S and Ren, Z and Li, S},
title = {Photonic fingerprint barcodes mediated by microsphere WGM lasing.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6nr01349j},
pmid = {42584226},
issn = {2040-3372},
abstract = {Optical encoding technologies have emerged as promising tools for biomedical sensing and single-cell tracking, offering unparalleled opportunities for high-precision biological analysis. However, conventional optical barcoding systems suffer from limited coding capacity, poor biocompatibility, and low signal-to-noise ratios. Here, we report a photonic fingerprint barcode platform mediated by biocompatible microsphere lasers, which leverages whispering gallery mode (WGM) lasing to generate unique, fingerprint-like optical signatures. By engineering the structural parameters and excitation conditions of biocompatible polymer microspheres, we generate six distinct photonic fingerprint barcodes, mirroring the arch, tented arch, left loop, right loop, double loop, and whorl patterns of human fingerprints. Each generated barcode is characterized by a unique barcode-like intensity spectrum and waveform profile, enabling high-throughput, label-free biological identification with exceptional specificity. This work establishes a versatile, biocompatible optical encoding strategy, offering a promising tool for precision medicine, single-cell tracking, and multiplexed biosensing.},
}

@article {pmid42586759,
year = {2026},
author = {Su, Q and Zhou, X and Long, Y and Duan, F and Lian, Q},
title = {Pattern-Filter structural validation of single-cell RNA-seq reads reduces artifactual barcodes and improves biological resolution.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281717.125},
pmid = {42586759},
issn = {1549-5469},
abstract = {Single-cell RNA sequencing (scRNA-seq) pipelines rely on the assumption that sequencing reads possess correct structural architecture, a premise we show is incomplete. Standard quantification tools treat errors exclusively as base mismatches, failing to identify structural aberrations arising from off-target priming or nonspecific amplification. We demonstrate that these pervasive artifacts, reads lacking essential anchor motifs like poly(T) tracts, linkers, or template-switching oligos, generate large numbers of spurious barcodes, artificially inflate cell counts, and substantially affect biological interpretation. To resolve this, we developed Pattern-Filter, a universal preprocessing tool that systematically validates read integrity before alignment. It functions by detecting platform-specific anchor sequences and applying strict base-composition filtering to ensure barcodes and UMIs contain only canonical nucleotides. When applied across diverse platforms, including 10x Genomics, Drop-seq, BD Rhapsody, and SPLiT-seq, Pattern-Filter systematically removes 2%-18% of total reads yet reduces spurious barcode diversity by up to 80%. This asymmetric reduction confirms that a small fraction of invalid reads drives the majority of technical noise, compromising cluster stability. Consequently, this targeted removal enhances data reproducibility and recovers biologically relevant cell types, such as dopaminergic neurons in mouse striatum, which were previously obscured by artifact-induced noise. These findings establish structural validation as an essential prerequisite for analysis, positioning Pattern-Filter as a useful standard for ensuring molecular fidelity and reliable biological discovery in single-cell transcriptomics.},
}

@article {pmid42239442,
year = {2026},
author = {Oikonomou, P and Calvary, L and Du, D and Polansky, J and Gattoni, G and Lynch, C and Shi, L and Mayer, C and McFaline-Figueroa, J and Nerurkar, NL},
title = {An endodermal subpopulation gives rise to neuromesodermal progenitors in the posterior chick embryo.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.726401},
pmid = {42239442},
issn = {2692-8205},
abstract = {Embryogenesis occurs through a progressive narrowing of cell fate potential, initiating with the segregation of three distinct germ layers during gastrulation. Although classically, each germ layer contributes to distinct tissue types as development proceeds, this view has been revised with the discovery of neuromesodermal progenitors (NMPs) - a bipotent progenitor population in the posterior embryo that gives rise to traditionally ectodermal and mesodermal tissues after gastrulation has concluded. However, until now the notion of lineage restriction of the endoderm to gastrointestinal, respiratory, and endocrine tissues has largely remained intact. Here, we describe a unique subpopulation in the chick endoderm that initially lines the ventral surface of Hensen's node (the amniote organizer). As posterior regression of the node ends with termination of the primitive streak, these cells undergo an FGF-dependent epithelial-to-mesenchymal transition, erasing their endodermal identity as they invade the tailbud and subsequently differentiate into a remarkably broad range of cell types including paraxial, lateral plate, and intermediate mesoderm, and to a lesser extent, notochord and neural tube. Disrupting ingression of node endoderm reduced embryonic axis elongation - a process attributed to mesoderm - by 50%. Through lineage barcoding, single-cell RNA sequencing, and fate mapping experiments, we conclude that the endodermal compartment of Hensen's node harbors a mixed population of fate restricted and multipotent progenitor cells that give rise to clonal populations spanning traditional germ layer boundaries. These findings illustrate a surprising example of germ layer plasticity and fate convergence across distant progenitor populations during amniote development.},
}

@article {pmid42571322,
year = {2026},
author = {Huang, JF and Liao, YC and Chan, TY and Chen, HM and Smith, DG},
title = {The congrid eel genus Gnathophis in Taiwan (Anguilliformes, Congridae), with descriptions of three new species.},
journal = {ZooKeys},
volume = {1287},
number = {},
pages = {11-46},
pmid = {42571322},
issn = {1313-2989},
abstract = {The genus Gnathophis differs from other genera of Congridae in having a moderately blunt and rounded tail tip and a slightly hardened tail extremity. The fleshy tip of the snout extends distinctly forwards beyond the intermaxillary teeth. A longitudinal fleshy keel is present on the ventral surface of the snout tip. Currently, two species of Gnathophis have been recorded from Taiwan, G. heterognathos and G. asanoi, whereas G. xenica has subsequently been determined to be a misidentification. In this study, three new species of the congrid eel genus Gnathophis Kaup are described from deep-sea waters off northeastern and southwestern Taiwan, based on 130 specimens. Gnathophis kbalanensis sp. nov. is diagnosed by the combination of blackish dorsal, caudal, and anal fins; 34-36 preanal vertebrae, 42-43 precaudal vertebrae, and 134-137 total vertebrae; 32-35 preanal lateral line pores; and elevated lateral line pores above the pectoral fin. Gnathophis melanurum sp. nov. is distinguished from its congeners by having whitish dorsal and anal fins and a blackish caudal fin; 28-32 preanal vertebrae, 37-41 precaudal vertebrae, and 98+-125 total vertebrae; 29-32 preanal lateral line pores; and elevated lateral line pores above the pectoral fin. Gnathophis nanhaiensis sp. nov. is separable from other species of Gnathophis in possessing whitish dorsal, caudal, and anal fins; 40-42 preanal vertebrae, 47-48 precaudal vertebrae, and 139-143 total vertebrae; 37-41 preanal lateral line pores; and lateral line pores above the pectoral fin that are not elevated. The validities of G. kbalanensis sp. nov. and G. melanurum sp. nov. are further supported by DNA barcoding analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Molecular comparisons additionally indicate that specimens of G. heterognathos (Bleeker) from waters off Taiwan exhibit a maximum intraspecific COI sequence divergence of 1.4%.},
}

@article {pmid42571425,
year = {2026},
author = {Pförtner, F and Briem, E and Enard, W and Richter, D},
title = {Increasing usable reads in RNA-seq protocols.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116984},
pmid = {42571425},
issn = {2589-0042},
abstract = {Bulk and single-cell RNA-seq are powerful tools for transcriptomic analysis, providing insights into molecular and cellular phenotypes. Costs constrain the biological insights obtainable within a given budget, and as sequencing prices decline, efficient library protocols have become a decisive factor. In this study, we introduce an approach to systematically optimize the number of usable reads generated by RNA-seq protocols. We applied this "funnel strategy" to prime-seq, an early-barcoding bulk RNA-seq protocol, by systematically testing critical protocol steps totaling 1,256 samples in 65 libraries. This resulted in the optimized prime-seq2 protocol that increases the number of usable reads by 60% and improves one of the most cost-efficient bulk RNA-seq protocols available. Our study also suggests that monitoring usable reads can serve as a valuable quality control for many RNA-seq protocols and sheds light on the complex interplay of experimental conditions that shape RNA-seq library composition and their interpretation.},
}

@article {pmid42573597,
year = {2026},
author = {Laux, M and Jardelino, AC and Vasconcelos, S and Pires, ES and Bernard, E and Oliveira, G and De-Souza, C and Nunes, GL},
title = {The shared performance of different COI regions increases the niche breadth detectable from bat guano eDNA.},
journal = {Genetics and molecular biology},
volume = {49},
number = {3},
pages = {e20250080},
pmid = {42573597},
issn = {1415-4757},
abstract = {The cytochrome c oxidase subunit I (COI), widely adopted as a DNA barcode for Metazoa, exhibits distinct variation levels in different regions within the gene. We investigated the efficacy of combining three arthropod-specific primers to enhance the detection of dietary niches, as opposed to relying on a single primer. This study utilized bat guano collected in bat caves from the Amazon and Caatinga biomes in Brazil. The UEA2-UEA3, UEA3-UEA4, and UEA5-UEA6 primer pairs recovered distinct proportions of Arthropoda (10%, 57%, and 42%, respectively) and exhibited considerable levels of unassigned reads (29%, 33%, and 42%, respectively) and non-target sequences (61%, 10%, and 16%, respectively). The UEA2-UEA3 primarily recovered Chiroptera (57%) but demonstrated the highest taxonomic coverage and richness for Arthropoda. On the other hand, UEA3-UEA4 and UEA5-UEA6 showed the highest α-diversity for Arthropoda; however, UEA5-UEA6 predominantly recovered Lepidoptera (40%) with the highest number of unique Arthropoda genera (45%), while UEA3-UEA4 mostly assigned to Lepidoptera and Diptera. Our results suggest the use of more than one primer pair and show that the analysis of only one primer pair can generate biased outputs. The choice primer is a crucial step in eDNA studies, especially for complex samples such as bat guano.},
}

@article {pmid42575597,
year = {2026},
author = {Rafuna, G and Sherifi, K and Ahmeti, S and Lindhorst, ZTL and Cvetkovikj, A and Kniha, E and Fuehrer, HP and Xhekaj, B},
title = {PCR-based screening for vector-borne pathogens reveals different Mycoplasma species in cats from Kosovo.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {73},
number = {},
pages = {101515},
doi = {10.1016/j.vprsr.2026.101515},
pmid = {42575597},
issn = {2405-9390},
mesh = {Animals ; *Mycoplasma/isolation & purification/genetics/classification ; Cats ; *Cat Diseases/epidemiology/microbiology/parasitology ; Polymerase Chain Reaction/veterinary ; Female ; Kosovo/epidemiology ; *Mycoplasma Infections/veterinary/epidemiology/microbiology ; Prevalence ; Male ; *Vector Borne Diseases/veterinary/epidemiology/microbiology ; },
abstract = {Vector-borne pathogens (VBPs) comprise a diverse range of pathogens, including viruses, bacteria, protozoa, and helminths, that are transmitted to vertebrate hosts by various species of arthropod vectors. The present study aimed to report the first data on the prevalence of VBPs in domestic cats in Kosovo and investigate associations with potential risk factors. Blood samples were collected from 107 domestic cats between April and October 2024 and preserved on filter papers. Samples were screened for VBPs, including Anaplasma spp., Ehrlichia spp., Babesia spp., Hepatozoon spp., Cytauxzoon spp., Bartonella spp., Filarioidea, Mycoplasma spp., Rickettsia spp., and Trypanosoma spp., using polymerase chain reaction (PCR), followed by sequence analysis. Haemotropic mycoplasma DNA was detected in 9 cats (8.4%, 95% CI: 4.2-15.8). Of the sequences obtained, three were identified as Mycoplasma haemofelis and six as Candidatus Mycoplasma haematominutum. The samples resulted negative for the presence of DNA from other VBPs. Significant variations in infection prevalence were associated with age, sex, outdoor access, and health status. This study provides the first molecular detection of Mycoplasma spp. infection in domestic cats from the capital region, Prishtina, and contributes to a better understanding of the epidemiology of this pathogen in the local feline population, which is essential for the development of effective preventive and control strategies.},
}

Animals
*Mycoplasma/isolation & purification/genetics/classification
Cats
*Cat Diseases/epidemiology/microbiology/parasitology
Polymerase Chain Reaction/veterinary
Female
Kosovo/epidemiology
*Mycoplasma Infections/veterinary/epidemiology/microbiology
Prevalence
Male
*Vector Borne Diseases/veterinary/epidemiology/microbiology

@article {pmid42581006,
year = {2026},
author = {Rosen, JD and Vasanthakumari, AD and Salomon, K and de Lange, N and Dash, PM and Keukeleire, P and Hassan, A and Barrera, A and Krupkin, B and Oualline, G and Kircher, M and Love, MI and Schubach, M},
title = {Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.281462.125},
pmid = {42581006},
issn = {1549-5469},
abstract = {As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains challenging. In particular, the study of noncoding genomic variation remains a major challenge because of the lack of accurate functional annotation for activity in a given context and across alleles. Experimental evidence is critical for prioritizing and interpreting functional effects of genetic alterations. Massively parallel reporter assays (MPRAs) have emerged as a powerful high-throughput approach, enabling quantification of regulatory element activity and allelic effects, as well as systematic dissection of gene regulatory logic and variant effects across different contexts. However, the diversity of MPRA designs, lack of standardized formats, and many potential processing parameters hamper data integration, reproducibility, and meta-analyses across studies. To address these challenges, the Impact of Genomic Variation on Function (IGVF) Consortium established an MPRA focus group to develop community standards, including harmonized file formats, and robust analysis pipelines for a wide range of library types and experimental designs. Here, we present these formats and comprehensive computational tools, MPRAlib and MPRAsnakeflow, for uniform processing from raw sequencing reads to counts, processing, and visualization. Using diverse MPRA data sets, we investigated technical variability sources including barcode sequence bias, outlier barcodes, and delivery method (episomal vs. lentiviral). Our results establish best practices for MPRA data generation and analysis, facilitating robust, reproducible research and large-scale integration. The presented tools and standards are publicly available, providing a foundation for future collaborative efforts in regulatory genomics.},
}

@article {pmid42581234,
year = {2026},
author = {Jang, B and Zenhausern, R and Lian, L and Gentry, K and Abbas, AM and Rudden, S and Shin, YJ and Doan, J and Loughrey, D and Curran, EH and Wood, JS and Stammen, RL and Johnson, RP and Kim, H and Dahlman, JE},
title = {Non-invasive nanoparticle barcoding in nonhuman primates.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42581234},
issn = {1546-1696},
abstract = {The clinical relevance of a lipid nanoparticle (LNP)-mRNA drug candidate is often dictated by its behavior in nonhuman primates. Yet, evaluating how chemically distinct LNPs behave in nonhuman primates remains difficult, in part because nanoparticle barcoding assays require euthanasia and difficult downstream tissue processing. Here we report non-invasive nanoparticle barcoding, which quantifies functional mRNA delivery mediated by several LNPs in a single nonhuman primate using 30 µl of serum. This method is enabled by snapCodes, benzylguanine-modified DNA barcodes that covalently bind an mRNA-encoded nanoluciferase-SNAP-tag fusion protein in vivo. The resulting DNA-fusion protein complexes are exported from cells, isolated from serum and sequenced. After validating snapCode and fusion protein activity, we intravenously administer six snapCoded LNPs to mice and nonhuman primates, thereby comparing LNP delivery across species. Measuring mRNA delivery from multiple LNPs using a low-volume blood draw reduces animal use and may help identify promising nanoparticle formulations.},
}

@article {pmid42570715,
year = {2026},
author = {Felizardo, ACC and Catipon, AVT and Fontanilla, IKC and Leonardo, LR and Moendeg-Mamades, K and de Cadiz, AE and Fornillos, RJC and Lv, S and Tabios, IKB},
title = {Molecular identification of Haplorchis taichui and other trematodes infecting thiarid freshwater snails from Southern Philippines.},
journal = {Parasitology international},
volume = {116},
number = {},
pages = {103361},
doi = {10.1016/j.parint.2026.103361},
pmid = {42570715},
issn = {1873-0329},
abstract = {Fish-borne zoonotic trematodiases (FZT) are neglected parasitic infections of global public health significance, persisting in communities where there is a cultural practice of consuming raw or undercooked freshwater fish. In the Philippines, FZT surveillance efforts remain largely focused on human stool-based diagnostics, leaving intermediate host transmission stages poorly characterized. In this study, we provide molecular characterization of the zoonotic trematode cercariae infecting thiarid snails from five FZT-endemic barangays in New Corella, Davao del Norte, Southern Philippines. Of 387 thiarid snails collected in freshwater near human settlements, 26 (6.72%) were infected with three cercarial morphotypes. DNA barcoding and phylogenetic analyses using partial 28S and cox1 sequences identified parapleurolophocercous cercariae from Melanoides tuberculata as Haplorchis taichui, the most prevalent fish-borne zoonotic fluke species reported in the Philippines. The other two morphotypes represented lineages with distinct, non-fishborne transmission routes. Megalurous cercariae confirmed as Philophthalmus gralli, an ocular trematode of birds capable of aberrant human infection, were recovered from Stenomelania sp., representing a putative new first intermediate host record for this species. Virgulate xiphidiocercariae recovered from M. tuberculata were assigned to family Lecithodendriidae, though limited reference sequence coverage precluded genus- or species-level resolution. These findings characterize co-occurring trematode diversity in thiarid snails from Southern Philippines and corroborate active transmission of H. taichui in areas with documented human heterophyid infections. Future work integrating molecular surveillance of both snail and fish intermediate hosts into FZT monitoring may provide a more complete assessment of FZT transmission and human infection risk in these endemic areas.},
}

@article {pmid42566945,
year = {2026},
author = {Wu, Z and Bai, J and Chang, A and Wang, T and Liu, Y and Yu, H},
title = {Intercellular mitochondrial exchange shapes tumor evolution, microenvironment adaptation, and therapeutic vulnerabilities.},
journal = {Translational oncology},
volume = {72},
number = {},
pages = {102913},
doi = {10.1016/j.tranon.2026.102913},
pmid = {42566945},
issn = {1936-5233},
abstract = {Mitochondrial transfer has emerged as a previously underappreciated mode of intercellular communication with major implications for tumor biology. Beyond their cell-autonomous roles in bioenergetics and signalling, mitochondria can be exchanged between cells as intact organelles or as mitochondrial cargo, thereby reshaping the metabolic state, stress tolerance and therapy responsiveness of recipient cells. In tumors, mitochondrial transfer can buffer oxidative stress, compensate for mtDNA damage and restore oxidative phosphorylation, enabling metabolic plasticity and contributing to immune dysfunction within the tumor microenvironment. This review synthesized current evidence for the structural routes and regulatory logic of mitochondrial exchange in cancer, spanning actin-based tunneling nanotubes, extracellular vesicle-mediated export and uptake, and other contact-dependent mechanisms. We highlight actionable "gatekeepers" that constrain transfer efficiency, including conduit biogenesis programs, MIRO1/2-TRAK-motor coupling that licenses mitochondrial trafficking, and EV biogenesis/uptake modules, as well as microenvironmental triggers such as hypoxia and redox stress. We also evaluate emerging methodological standards required to distinguish bona fide organelle transfer from dye leakage or indirect cargo exchange, and discuss how orthogonal validation (genetic reporters, mtDNA barcoding and functional rescue assays) can improve rigor and comparability across studies. By integrating current findings, this article aims to provide a theoretical foundation and strategic guidance for targeting tumor metabolic regulation and improving precision oncology approaches.},
}

@article {pmid42568342,
year = {2026},
author = {Tedersoo, L and Prous, M and Chen, M and Anslan, S and Saar, I and Dubois, B and Mikryukov, V},
title = {Benchmarking Full-Length ITS Metabarcoding Across Illumina 2 × 500, PacBio, and Oxford Nanopore Sequencing Using Mock and Soil Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {6},
pages = {e70189},
pmid = {42568342},
issn = {1755-0998},
support = {101200758//HORIZON EUROPE European Research Council/ ; TK200//Estonian Ministry of Education and Research/ ; 362828//Research Council of Finland/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; *Soil Microbiology ; *Metagenomics/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; DNA, Ribosomal Spacer/genetics/chemistry ; Benchmarking ; Biodiversity ; },
abstract = {Metabarcoding is a powerful tool for biodiversity comparisons, where standard-size DNA barcodes (> 500 bases) offer better taxonomic resolution than shorter ones. Still, the choice of sequencing platforms and bioinformatics pipelines may strongly affect inferred diversity due to various technical biases. We assessed the relative performance of Illumina MiSeq i100 (2 × 500 paired-end), PacBio Revio and Oxford Nanopore MinION sequencing and bioinformatics pipelines, using full-length ITS amplicon sequencing datasets from a 103-species mock community and 45 composite soil samples. Despite numerous low-quality reads, PacBio yielded the lowest overall error rate and highest number of taxa. Illumina revealed the highest proportion of chimeric and index-switched reads, along with a strong bias towards shorter amplicons. MinION data analysed using PRONAME and Minovar-a bioinformatics pipeline presented here-had the largest proportion of low-quality data, and rare taxa were lost during data filtering and read polishing steps. Although Minovar enabled amplicon sequence variant (ASV) level precision for common taxa, we recommend clustering ASVs into OTUs. For PacBio, standard filtering approaches outperformed the ASV approach because they retained rare taxa. For Illumina, a stringent ASV approach or removal of rare OTUs would limit artefacts. Across all platforms, excess PCR cycles promoted chimeric and low-quality reads and lost quantitativity in biodiversity assessments. With moderate differences in effect sizes, all analytical approaches supported the conclusion that sampling design determines how we see soil biodiversity responses to land use. For biodiversity surveys based on the full-length ITS metabarcoding, we recommend using PacBio sequencing with standard, non-ASV pipelines.},
}

*DNA Barcoding, Taxonomic/methods/standards
*Soil Microbiology
*Metagenomics/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
DNA, Ribosomal Spacer/genetics/chemistry
Benchmarking
Biodiversity

@article {pmid42565232,
year = {2026},
author = {Protić, N and Jadrná, I and Škaloud, P and Knotek, P and Čertnerová, D},
title = {Linking variation in genome size to cyst size in chrysophytes.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70217},
pmid = {42565232},
issn = {1529-8817},
support = {23-05546O//Grantová Agentura České Republiky/ ; },
abstract = {Genome size varies tremendously across eukaryotes, which often contain far more DNA than expected from their biological complexity. To explain this paradox, selection-based hypotheses propose that genome size evolves through selection acting on life-history traits correlated with the phenotypic effects, independent of its genic content. To test the association between genome size and resting cyst size-a structure with morphology that may reflect overall body size-we selected chrysophyte algae (Chrysophyceae) producing siliceous stomatocysts as a model. In this study, we obtained and identified 85 chrysophyte strains representing 31 Mallomonas species using nuclear ITS rDNA region barcoding and estimated their genome sizes using propidium iodide flow cytometry. Within this genus, we observed more than a 75-fold variation in genome size (0.15-11.25 pg) and frequent substantial intraspecific variation, in some cases consistent with whole-genome doubling (polyploidization). By summarizing the published genome size records, adding our new measurements and combining them with published cyst sizes, we assembled a data set for 54 chrysophyte species to examine the relationship between genome size and cyst volume. Linear regression on log-transformed data revealed a strong positive correlation (R adj 2 = 0.626, p < 0.001), showing that species with larger genomes tend to produce larger stomatocysts. In chrysophytes, this relationship is considerably stronger than the widely documented genome size-cell size correlation observed across eukaryotes. Our findings suggest that stomatocyst size is a more informative predictor of genome size in this group and highlight the potential for using stomatocyst sizes to infer ancestral genome sizes from the fossil record.},
}

@article {pmid42565653,
year = {2026},
author = {Ugalde, J and Janzen, D and Hallwachs, W and Kohlmann, B and Hebert, P and Brown, B and Whitfield, J and Fernández-Triana, J and Ugalde, R and Rodriguez, E and Zúñiga, R and Smith, M and Steinke, D and Sharkey, M and Quicke, D and Manjunath, R and Puschendorf, R},
title = {Large-scale DNA barcoding reveals highly distinct insect distribution patterns across Costa Rican ecosystems.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-26},
doi = {10.1139/gen-2025-0128},
pmid = {42565653},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Costa Rica ; Biodiversity ; *Ecosystem ; *Insecta/genetics/classification ; Phylogeny ; },
abstract = {Although insects are fundamental to understanding and conserving global biodiversity, they are vastly understudied. Here, we present a national inventory of Costa Rican insects based upon 3.78 million DNA barcodes representing 152 891 Barcode Index Numbers (BINs, proxies for species) from 28 localities sampled from 2017 to 2023 through the national BioAlfa program of Costa Rica. Although only 3.6% of BINs are linked to Linnean species, barcode-based community analyses revealed strong, consistent ecogeographic structure. Clustering of BIN data using bootstrapped Jaccard distances revealed seven distinct mainland assemblages and a distinct island cluster, shaped primarily by Costa Rica's mountain ranges, elevation, and slope orientation. Separate analyses for Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera coupled with analyses focused on some of their largest families (e.g., Braconidae, Cecidomyiidae, Cicadellidae, Erebidae, and Staphylinidae) confirmed these patterns and further revealed extremely high species turnover with most BINs being exclusive to a single region or locality. Our results reveal limited overlap of insect communities across ecosystems, implying that each life zone harbors unique taxonomic assemblages. Large-scale DNA barcoding has detected fine-grained spatial structure, providing a genomic framework for biodiversity monitoring and conservation in diverse tropical regions undergoing rapid environmental change.},
}

Animals
*DNA Barcoding, Taxonomic
Costa Rica
Biodiversity
*Ecosystem
*Insecta/genetics/classification
Phylogeny

@article {pmid42564840,
year = {2026},
author = {Etebari, K and Furlong, MJ},
title = {Interpreting molecular evidence for biosecurity decision-making: Lessons from coconut rhinoceros beetle incursions in the Pacific.},
journal = {Current research in insect science},
volume = {10},
number = {},
pages = {100131},
pmid = {42564840},
issn = {2666-5158},
abstract = {Molecular and genomic tools are increasingly used in biosecurity to support early detection, diagnostics and reconstruction of invasion pathways. However, selecting an appropriate marker for the question being addressed is critical, and translating molecular evidence into operational decisions can be challenging. Over-interpretation of commonly used markers may lead to misleading conclusions about population structure, invasion history and management priorities. DNA barcoding remains valuable for species identification and initial haplotype assignment, but questions concerning invasion pathways, admixture and phenotypic variation require additional molecular and ecological evidence. Here, we use coconut rhinoceros beetle (Oryctes rhinoceros) incursions in the Pacific as a case study to highlight interpretive pitfalls and lessons for applying molecular and genomic tools in biosecurity and biological control. We synthesise evidence on the strengths and limitations of mitochondrial markers, particularly CoxI, for haplotyping and inference of population relationships, and show how incomplete sampling and simplified assays can obscure cryptic diversity and bias interpretation. We then examine factors that complicate interpretation of OrNV-based biocontrol outcomes, including diagnostic sensitivity, study design and environmental modulation of host-pathogen interactions. Overall, these examples show that molecular evidence is most informative when marker choice, biological validation and phenotypic data are aligned with the biosecurity question.},
}

@article {pmid42564887,
year = {2026},
author = {Ngo, NP and Lee, MS and Chiang, P and Huang, JY and Hung, HL and Wu, KC},
title = {Integrated chemical and genetic authentication of Polygoni Multiflori Caulis: Refuting diameter restrictions and exposing market adulteration.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21561},
pmid = {42564887},
issn = {2167-8359},
mesh = {Chromatography, High Pressure Liquid ; Polymorphism, Single Nucleotide ; *Fallopia multiflora/genetics/chemistry/classification ; Emodin/analogs & derivatives/analysis ; *Drug Contamination ; Plant Stems/chemistry/genetics ; Genetic Variation ; *Drugs, Chinese Herbal/chemistry/standards ; Glucosides/analysis ; *Polygonaceae/genetics/chemistry/classification ; },
abstract = {BACKGROUND: Polygoni Multiflori Caulis (PMC), the dried stem of Pleuropterus multiflorus (Thunb.) Turcz. ex Nakai (PM), is a fundamental traditional Chinese medicine utilized for treating sleep disorders. Despite its medicinal importance, species confusion exists due to the taxonomic synonymy of Polygonum multiflorum var. hypoleucum (PMH) and Pleuropterus angulatus (PA) with PM. Furthermore, conventional quality standards often restrict PMC collection to specific stem diameters. This study evaluatedthe chemical and genetic diversity of PMC and its related taxa and assessed the authenticity of commercial PMC products.

METHODS: Authenticated samples of PM, PMH, and PA were analyzed using high-performance liquid chromatography (HPLC) to quantify three key markers, including 2,3,5,4'-tetrahydroxystilbene-2-O-β-D-glucoside (THSG), emodin, and physcion. The ITS2 region was sequenced to evaluate genetic diversity and identify single nucleotide polymorphisms (SNPs). We examined the impact of stem diameter (2.0 to 25.1 mm) on constituent levels in PM and surveyed eleven commercial PMC samples from Taiwanese markets.

RESULTS: Chemical analysis revealed that PMC samples across the entire diameter range (2.0 to 25.1 mm) consistently fulfilled the regulatory standards of the Taiwan Herbal Pharmacopoeia (THP), Chinese Pharmacopoeia (CP), and Hong Kong Chinese Materia Medica Standards (HKCMMS), effectively challenging the previously recommended 4 to 7 mm limit. In contrast, authenticated PMH samples lacked both the characteristic marker THSG and the enlarged tuberous roots typical of PM, and PA stem samples exhibited variable chemical phenotypes, with only a small subset meeting official standards. ITS2 sequencing successfully resolved the three taxa by identifying 13 SNPs and 16 distinct SNP genotypes. Notably, the market survey revealed that 82% of commercial samples were substituted with PA, of which 72% contained undetectable levels of the required analytes.

CONCLUSIONS: The findings demonstrate that PMH and PA represent distinct chemotypic lineages and should not be considered interchangeable botanical sources for PMC. The integration of HPLC quantification and ITS2 SNP barcoding provides a robust, multifaceted framework for quality control. Furthermore, our findings suggest that stems across the 2.0-25.1 mm diameter range can meet current pharmacopoeial requirements, providing preliminary evidence that the traditional 4-7 mm restriction may be unnecessarily narrow.},
}

Chromatography, High Pressure Liquid
Polymorphism, Single Nucleotide
*Fallopia multiflora/genetics/chemistry/classification
Emodin/analogs & derivatives/analysis
*Drug Contamination
Plant Stems/chemistry/genetics
Genetic Variation
*Drugs, Chinese Herbal/chemistry/standards
Glucosides/analysis
*Polygonaceae/genetics/chemistry/classification

@article {pmid42555814,
year = {2026},
author = {Cocchi, S and Talijanovic, M and Høgdall, EV and Lopacinska-Jørgensen, J},
title = {Assessing the Impact of Patient Selection and Analytical Methods on mRNA Biomarker Identification in Ovarian Cancer Using TCGA Data.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261468094},
pmid = {42555814},
issn = {1526-2359},
mesh = {Humans ; Female ; *Ovarian Neoplasms/genetics/drug therapy/pathology ; *Biomarkers, Tumor/genetics ; *Patient Selection ; *RNA, Messenger/genetics ; Retrospective Studies ; Gene Expression Profiling/methods ; Drug Resistance, Neoplasm/genetics ; Gene Expression Regulation, Neoplastic ; },
abstract = {IntroductionThe Cancer Genome Atlas (TCGA) data has been extensively used for differentially expressed genes (DEGs) discovery and validation in high-grade serous ovarian cancer (HGSOC), however platinum-sensitivity biomarkers have not yet reached clinical application. We aimed to propose a robust analytical framework for TCGA platinum sensitivity studies and systematically demonstrate how patient characteristics influence DEG analyses between platinum-sensitive and resistant groups, while also considering experimental platforms and analysis pipelines, as their impact is recognized but not comprehensively evaluated.MethodsThis retrospective TCGA cohort study used publicly available microarray and RNA-seq gene expression data. TCGA-derived datasets were identified through a literature review, including only studies enabling unambiguous patient identification. Three TCGA-based cohorts were assembled-two directly from published studies and one curated through own selection-differing in patient numbers (230, 201 and 142 patients, respectively) and stage distribution. Data were analyzed using DESeq2, edgeR, limma-voom, and Wilcoxon rank-sum test to compare the impact of patient selection and pipeline choice on DEGs outcome. Genes with an adjusted p-value < 0.05 and an |log2 fold change| > 2 were considered differentially expressed.ResultsThe three cohorts showed partial overlap of DEGs across platforms and pipelines. Both patient selection and analytical workflow influenced which genes were identified, highlighting findings variability even when using the same TCGA dataset. We establish a robust analytical framework for TCGA HGSOC biomarker studies, including the provision of patient barcodes and openly shared workflows that enable straightforward replication of our analyses from data download to DEG analysis.ConclusionsReproducibility of TCGA studies is limited by variability in patient selection, platinum sensitivity definitions, data sources, and analysis pipelines. We addressed these factors by providing a robust framework that can serve as a template for data analysis and transparent reporting when identifying and validating predictive signatures of platinum sensitivity in HGSOC patients.},
}

Humans
Female
*Ovarian Neoplasms/genetics/drug therapy/pathology
*Biomarkers, Tumor/genetics
*Patient Selection
*RNA, Messenger/genetics
Retrospective Studies
Gene Expression Profiling/methods
Drug Resistance, Neoplasm/genetics
Gene Expression Regulation, Neoplastic

@article {pmid42558731,
year = {2026},
author = {Chaunzwa, M and McElfresh, GW and Morrow, D and Boggy, GJ and Kaza, M and Benjamin, S and Feltham, S and Ojha, S and Swarbrick, GM and Rott, KH and Gilbride, RM and Labriola, CS and Axthelm, MK and Joag, V and Kain, D and Plessis, ND and Walzl, G and Lewinsohn, DA and Lewinsohn, DM and Hansen, SG and Picker, LJ and Bimber, BN},
title = {T cell antigenic recognition sequencing (TAR-seq) enables precise characterization of vaccine-elicited cellular immunity ex vivo and in vivo.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1823042},
pmid = {42558731},
issn = {1664-3224},
mesh = {Animals ; *Receptors, Antigen, T-Cell/genetics/immunology ; *Immunity, Cellular ; Lymphocyte Activation/immunology ; *Vaccines/immunology ; Macaca mulatta ; *T-Lymphocytes/immunology ; *Simian Immunodeficiency Virus/immunology ; Single-Cell Analysis ; Humans ; Single-Cell Gene Expression Analysis ; },
abstract = {INTRODUCTION: The functional responses of antigen (Ag) specific T cells are complex, clonotype-specific, context-dependent, and incompletely captured by dominant analytic approaches. Here we present T Cell Antigenic Recognition Sequencing (TAR-seq), a two-part process that uses single-cell RNA + T cell receptor sequencing (scRNA/TCR-seq) to provide a precise and comprehensive characterization of the differentiation state and functional response of T cells specific to a given antigen, ex vivo and in vivo.

METHODS: Many approaches use stimulation and activation-induced markers to identify Ag-specific T cells. We extend this by adding an scRNA/TCR-seq readout to identify the responding TCRs for each subject. We performed rigorous validation using tetramer-sorted T cells and developed a reusable probabilistic model to differentiate TCR-stimulated cells from bystander activation. These TCRs provide molecular barcodes to identify Ag-specific cells from unsorted scRNA/TCR-seq data, irrespective of stimulation, enabling a comprehensive view of their activity.

RESULTS: We applied this method to a cohort of SIV-vaccinated rhesus macaques (RMs). We performed SIV-infected cell recognition assays to identify the SIV-specific TCRs for each RM. We used these TCRs to subset SIV-specific cells and perform precise contrasts. Despite identical vaccination, we identified clone- and subject-level variability in their cytotoxic differentiation and cytokine production after incubation with SIV-infected targets. Per clonotype, the percentage of cells that responded after antigen exposure varied widely. Finally, we used TCRs as barcodes to precisely map the in vivo activity of CD8+ T cells 48-120H after SIV challenge. Precise TCR-based identification separated Ag-specific and bystander effects, measuring tissue-specific responses of SIV-specific T cells within 48 hours of infection.

DISCUSSION: Together, our data validate a powerful method to comprehensively understand T cell activity, with relevance to infectious disease, cancer, and autoimmunity, across species.},
}

Animals
*Receptors, Antigen, T-Cell/genetics/immunology
*Immunity, Cellular
Lymphocyte Activation/immunology
*Vaccines/immunology
Macaca mulatta
*T-Lymphocytes/immunology
*Simian Immunodeficiency Virus/immunology
Single-Cell Analysis
Humans
Single-Cell Gene Expression Analysis

@article {pmid42559103,
year = {2026},
author = {Wang, W and Shen, M and Su, Z and Yu, L and Ma, Z},
title = {Comparative plastome analyses and phylogenetic insights of Stellaria (Caryophyllaceae).},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1902479},
pmid = {42559103},
issn = {1664-462X},
abstract = {Stellaria (Caryophyllaceae) comprises approximately 112 species globally, with China serving as a significant center of diversity hosting about 64 species. Despite its taxonomic importance, the genus remains insufficiently studied in China. Previous phylogenetic studies relying on limited DNA barcodes produced weakly supported inferences, while those based on chloroplast genomes are currently lacking. Here, we characterize the chloroplast genome structure and reconstruct its highly resolved infrageneric phylogeny using 60 newly sequenced plastomes. All plastomes displayed a conserved quadripartite structure, with lengths varying from 147,205 bp to 149,409 bp, GC contents ranging from 36.6% to 36.7%, and gene counts spanning 128 to 129 genes. Codon usage patterns were highly conserved with leucine encoded by UUA exhibiting the highest relative synonymous codon usage. A total of 55-74 simple sequence repeats and 42-64 long repeats were detected. Three hypervariable regions-petN-psbM, trnP-rpl33, and ycf1 were identified as promising candidate DNA barcodes. Phylogenomic analysis resolved Stellaria into three strongly supported major clades and 15 well-defined subclades. The results are largely consistent with the established phylogeny of Stellaria. However, we observed certain discrepancies within specific clades. We propose some suggestions for these clades and species based on morphological and molecular evidence. This study provides the first comprehensive phylogenetic framework for Stellaria based on the chloroplast genome, establishing a robust foundation for future taxonomic revisions and evolutionary studies.},
}

@article {pmid42560383,
year = {2026},
author = {Dos Reis, JC and de Melo-Ximenes, AA and Nunes, R and Baptista, LAM and Silva, LCF and de Campos Telles, MP},
title = {DNA barcode markers for birds of the genus Sporophila: advances in species identification.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42560383},
issn = {1573-4978},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; *Birds/genetics/classification ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers/genetics ; Species Specificity ; Male ; NADH Dehydrogenase/genetics ; Haplotypes ; Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Accurate identification of Sporophila is crucial for conservation and combating trafficking. Due to morphological similarity among females, molecular tools are essential. Although cytochrome c oxidase subunit 1 (COI) is the standard animal barcode, its limited resolution in recently diverged species necessitates more informative regions, such as cytochrome b (CYTB) and NADH dehydrogenase 2 (ND2), which are effective for Thraupidae. The aim of this study was to provide molecular mitochondrial markers to support species identification and development of tools that contribute to conservation of Sporophila.

METHODS AND RESULTS: The markers were validated using 62 adult males (13 species) and applied to 47 unidentified females from the Centro de Triagem de Animais Silvestres (CETAS). DNA was amplified via PCR, targeting CYTB and ND2, using genus-specific primers for all samples. COI was amplified exclusively for males, using primers based on literature. Sequences were analyzed using an ABI3500.Maximum likelihood trees and haplotype networks compared each studied region. Nearest-neighbor and barcode gap analyses confirmed marker efficiency for species identification, with CYTB and COI demonstrating the highest reliability. Among the 13 species evaluated, five showed barcode gaps across all markers, while two depended on the marker used. Female samples achieved a 100% amplification rate, with 74.47% showing high identity (> 98%); conclusively, 52.13% were identified with high confidence, whereas the remainder belonged to species falling outside our markers' current discrimination efficiency.

CONCLUSIONS: This study provides efficient tools for future research and conservation initiatives targeting Sporophila species.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Female
Phylogeny
*Birds/genetics/classification
Cytochromes b/genetics
Electron Transport Complex IV/genetics
Genetic Markers/genetics
Species Specificity
Male
NADH Dehydrogenase/genetics
Haplotypes
Polymerase Chain Reaction
Sequence Analysis, DNA/methods

@article {pmid42560944,
year = {2026},
author = {Padhye, SM and Ballesteros-Mejia, L and Agda, J and Agda, J and Hebert, PDN and Ratnasingham, S},
title = {BOLDconnectR: An R package for streamlined retrieval, transformation, and analysis of DNA barcode data on BOLD.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0355496},
pmid = {42560944},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Software ; *Computational Biology/methods ; Biodiversity ; Information Storage and Retrieval ; },
abstract = {DNA barcode data are essential infrastructure for biodiversity science as they enable scalable species identification and integrative analyses that link sequences to specimens, taxonomy, and geography. The Barcode of Life Data System (BOLD) is a centralized bioinformatics workbench that supports the full barcode data lifecycle: including acquisition, storage, validation, analysis, and dataset publication within a secure collaboration model. While BOLD's web interface is optimized for interactive dataset assembly and publication, many researchers require programmatic access to both public data and permissioned private records to build reproducible pipelines for curation and analysis prior to release. We introduce BOLDconnectR, an R package that provides authenticated access to BOLD, returns records in the Barcode Core Data Model (BCDM), performs automated transformation into commonly used R data structures, and enables customizable analytic workflows that generate publication-ready outputs.},
}

*DNA Barcoding, Taxonomic/methods
*Software
*Computational Biology/methods
Biodiversity
Information Storage and Retrieval

@article {pmid42563049,
year = {2026},
author = {David Wegner, K and Resch-Genger, U},
title = {Synthesis of Environmentally Friendly Heavy-Metal-Free AgInS2/ZnS Quantum Dots Using Microwave Heating.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3025},
number = {},
pages = {37-47},
pmid = {42563049},
issn = {1940-6029},
mesh = {*Quantum Dots/chemistry ; *Microwaves ; *Sulfides/chemistry ; *Zinc Compounds/chemistry ; *Indium/chemistry ; *Green Chemistry Technology/methods ; Metals, Heavy/chemistry ; },
abstract = {Luminescent semiconductor nanocrystals, also known as quantum dots (QDs), have had a major impact on applications of optical techniques in the life sciences, such as biosensing and bioimaging. Their unique optical properties, such as broad absorption bands with high molar extinction coefficients, together with their narrow size-dependent photoluminescence (PL) bands, high PL quantum yields (QYs), and a high photostability, are unique advantages for QDs as optical reporters in immunoassays, theranostics, in vitro/in vivo imaging, and flow cytometry. This also laid the foundation for numerous applications of optical multiplexing and barcoding. The most popular QD element compositions are based on heavy-metal elements, such as cadmium or lead, which pose a high toxic risk and are meanwhile restricted in Europe by REACH regulation. Increasing environmental concerns and the growing interest in and need for nanomaterials accessible by sustainable synthesis routes triggered the search for more eco-friendly QDs in the last years. Promising heavy-metal free candidates are ternary AgInS2 QDs, which can be synthesized with high-quality optical properties using aqueous synthesis methods. However, the use of conventional heating mantles or oil baths to heat the reaction mixture to the desired reaction temperature can lead to significant batch to batch variations caused by an inhomogeneous heat diffusion influencing the nucleation and growth of the QDs. A solution to this problem is the use of microwave-assisted heating. This enables a fast and homogeneous heat distribution throughout the entire reaction vessel, resulting in high-quality nanomaterials prepared with high batch-to-batch reproducibility. In this chapter, we will describe the synthesis steps for the preparation of AgInS2/ZnS QDs using microwave-assisted heating. The influence of the stabilizing ligands, variation of precursor concentrations, and the pH of the reaction solution will be detailed in the note section.},
}

*Quantum Dots/chemistry
*Microwaves
*Sulfides/chemistry
*Zinc Compounds/chemistry
*Indium/chemistry
*Green Chemistry Technology/methods
Metals, Heavy/chemistry

@article {pmid42564452,
year = {2026},
author = {Csuzdi, C and Razafindrakoto, M and Hong, Y},
title = {A new and interesting earthworm species from Madagascar (Crassiclitellata, Kynotidae) with an updated key to the Kynotus Michelsen, 1891 species.},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {251-263},
pmid = {42564452},
issn = {1313-2989},
abstract = {A new effort in 2025 to collect earthworms in northern Madagascar resulted in the discovery of a new species of Kynotus, a genus belonging to the endemic family Kynotidae, as well as the rediscovery of K. darwinii, the type species of Kynotus. The latter species had not been collected since its original reports in the late 19[th] century. With the description of the new species, Kynotus insularis sp. nov., the family Kynotidae now has 23 species. New DNA barcode sequences were generated for both species, confirming their distinctness and further demonstrating the high efficiency of the COI barcode region in identifying Kynotus species. An identification key to the currently known kynotid species is also presented.},
}

@article {pmid42564565,
year = {2026},
author = {Gumbau, M and Marteil, C and Groussier, G and Cruaud, A and Nidelet, S and Warot, S and Fernandez-Triana, J and Penet, L and Blazy, JM and Rasplus, JY},
title = {A synopsis of neotropical parasitoid wasps of Diaphania hyalinata (Lepidoptera, Crambidae), with new records from Guadeloupe.},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {293-336},
pmid = {42564565},
issn = {1313-2989},
abstract = {Diaphania hyalinata Linnaeus, 1767 (Lepidoptera, Crambidae), commonly known as the melonworm, is a major pest of cucurbits in the Neotropics. Yet, a comprehensive review of the parasitoid wasps that may act as biocontrol agents of this pest is still lacking. An extensive literature review was conducted to compile the current knowledge on the identity, distribution, and biology of parasitoid wasps associated with D. hyalinata across its range. Eggs, larvae, and pupae of D. hyalinata were collected in Guadeloupe and reared to document the local parasitoid diversity. Among the 37 parasitoids identified in our review, eight were recovered during our field survey, all of which are new records for the island. These parasitoids were photographed and DNA-barcoded to facilitate their potential use in future biological control programs targeting D. hyalinata. The species Trichogramma pretiosa Riley, 1879 (Trichogrammatidae; egg parasitoid) and Schoenlandella montserratensis Kang, 2021 (Braconidae; larval parasitoid) appear to be promising candidates for the biological control of D. hyalinata in Guadeloupe. It may be also worth evaluating the effectiveness of two additional larval parasitoids, Eiphosoma dentator Fabricius, 1804 (Ichneumonidae) and Apanteles impiger Muesebeck, 1958 (Braconidae), while assessing possible non-target effects on local fauna. However, it is important to consider that the presence of the hyperparasitoid Aphanogmus fijiensis Ferrière, 1933 (Ceraphronidae) could undermine biocontrol efforts. Overall, it would be valuable to gain a better understanding of the biological and environmental factors (such as agricultural practices and landscape features) that enhance the natural regulatory activities of this parasitoid community.},
}

@article {pmid42564774,
year = {2026},
author = {Salgado, J and Mariño-Brito, E and Mosquera-Yuqui, F and Ruales Guerra, A and Acebo Arcentales, JJ},
title = {First clinical isolation of Purpureocillium lilacinum in a pediatric oncological patient in Ecuador.},
journal = {Oxford medical case reports},
volume = {2026},
number = {8},
pages = {omag129},
pmid = {42564774},
issn = {2053-8855},
abstract = {BACKGROUND: Purpureocillium lilacinum is a ubiquitous environmental fungus widely utilized as an agricultural biocontrol agent, but it is increasingly recognized as an opportunistic human pathogen. While invasive fungal infections caused by this microorganism have been documented globally, disseminated systemic presentations in pediatric oncology remain exceptionally rare and carry high mortality rates.

CASE DESCRIPTION: We report the case of an 11-year-old female patient with a high-grade osteosarcoma who developed high-risk febrile leukopenia during chemotherapy. Blood cultures from both a subcutaneous port and peripheral blood turned positive for both yeast-like and hyphal structures, which were further identified by DNA barcoding (ITS and EF1a regions) as P. lilacinum. The patient exhibited concurrent multiorgan dissemination, including hyperchromic scaling skin lesions in the perianal region and limbs, as well as diffuse bilateral pulmonary micronodules confirmed via video-thoracoscopy biopsy. Despite initial treatment with amphotericin B and fluconazole, clinical resolution was successfully achieved only after optimizing the antifungal regimen with oral voriconazole. The patient fully recovered and remains stable.

CONCLUSIONS: To our knowledge, this represents the first clinical isolation and reported case of disseminated systemic P. lilacinum infection in a pediatric oncological patient in Ecuador. This case highlights the aggressive nature of this pathogen in immunosuppressed children, the challenge of its diagnosis due to the lack of specialized infrastructure for antifungal susceptibility testing, and the critical importance of a multidisciplinary approach and prompt, targeted first-line therapy with voriconazole to ensure survival.},
}

@article {pmid42553576,
year = {2026},
author = {Schilthuizen, M and Boomsma, R and Faes, S and Jousma, M and Buisman, J and Lankenau, DH and Kountouras, S and van den Broek, M and Hemelaar, EM and Noomen, J and de Vries, R and Lopatriello, G and Limongi, AR and Maestri, S and Kamchev, P and van Manen, S and Khalik, MZ and Delledonne, M and Đokić, J and Mićanović, A and Popović, J and Njunjić, I and Zallot, E},
title = {Two new Cochlostoma species from the Durmitor and Komarnica regions of northern Montenegro (Caenogastropoda, Cochlostomatidae).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e196955},
pmid = {42553576},
issn = {1314-2828},
abstract = {BACKGROUND: Slow-migrating gastropods are key indicators of habitat continuity, i.e. areas of relatively long-term ecological stability. The gastropod genus Cochlostoma (Architaenioglossa, Cochlostomatidae) is a common and widespread component of karst communities throughout the countries surrounding the Mediterranean. Recent work has taken into account genetic and reproductive-anatomical diversity and has revealed that the uniform shell morphology hides surprisingly rich and deep divergences.

NEW INFORMATION: Here, we describe two species of the subgenus Turritus, C. (Turritus) dobrido sp. nov. and C. (Turritus) komarnica sp. nov. They were collected, studied and described as part of citizen-science expeditions to the threatened Komarnica Canyon and to Durmitor National Park, two adjoining regions in Montenegro. The new species were found sympatrically and, in some cases, syntopically with Cochlostoma scalariniforme (A. J. Wagner, 1906), as well as with each other.},
}

@article {pmid42553627,
year = {2026},
author = {Tippery, NP and Larkin, DJ and Bohnen, J and Wendell, DL and Anderson, NO and Galatowitsch, SM and Abbey, M and Smith, AG and Noyszewski, AK},
title = {Molecular methods for differentiating Phragmites australis subspecies and identification of hybrid stands in the Upper Midwestern United States.},
journal = {Applications in plant sciences},
volume = {},
number = {},
pages = {e70073},
pmid = {42553627},
issn = {2168-0450},
abstract = {PREMISE: In North America, Phragmites australis (common reed) has drawn a great deal of research attention. Non-native P. australis subsp. australis is a noxious weed that has locally displaced native P. australis subsp. americanus in some areas. Although morphological features can distinguish the two subspecies, molecular tools often are required to confirm identifications. Additionally, the existence of natural intrasubspecific hybrids presents novel management challenges. Hybrid Phragmites is difficult to detect, and it has become standard practice to apply molecular tools to survey for hybrids.

METHODS: We applied several molecular techniques-microsatellite, DArTseq (a type of genotyping-by-sequencing), restriction fragment length polymorphism (PCR-RFLP), and next-generation sequencing-to characterize P. australis at the landscape scale in Minnesota and Wisconsin and to search for hybrids.

RESULTS: We obtained molecular data for Phragmites plants sampled from 341 stands, ultimately characterizing 98 stands as native and 236 as non-native. Plants from two adjacent stands in Washington County, Minnesota, were confirmed to be hybrids.

DISCUSSION: These are the first confirmed hybrids from the Upper Midwest/western Great Lakes region. We also discuss the relative cost and effectiveness of the various molecular methods and offer recommendations for future studies.},
}

@article {pmid42553711,
year = {2026},
author = {Duong Nguyen Xuan, L and Tran Thi Van, A and Thai Hong, D and Le Thi Tuyet, A and Vo Ngoc Linh, G},
title = {Characterization of the complete plastid genome and 45S nrDNA sequences of Murdannia medica (Lour.) D.Y. Hong (Commelinaceae) and its phylogenetic analysis.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {11},
number = {9},
pages = {1003-1007},
pmid = {42553711},
issn = {2380-2359},
abstract = {Murdannia medica is a Vietnamese traditional medicinal herb. Here, we report DNA super‑barcodes comprising the complete plastid genome (plastome, 177,455 bp) and 45S nuclear ribosomal DNA (45S nrDNA, 5,741 bp) of M. medica. The plastome has a large single‑copy (LSC, 100,132 bp), a small single‑copy (SSC, 21,125 bp), and a pair of inverted repeats (IRs) of 28,099 bp each. It contains 115 annotated genes and has an overall A/T content of 68.2%. Plastome‑based phylogenetic analyses show that M. medica sister with M. edulis. These new genomic resources provide a valuable foundation for future cultivation, conservation, and systematic investigations of M. medica.},
}

@article {pmid42555226,
year = {2026},
author = {Nitta, M and Uchiyama, M and Hayashi, T},
title = {Redescription of the Larval Trematode Taxon Monilicaecum ventricosum (Hemiuroidea: Didymozoidae) from Type Host Cololabis saira, with Inference of the Definitive Host Based on DNA Analysis.},
journal = {Zoological science},
volume = {43},
number = {4},
pages = {417-425},
doi = {10.2108/zs260004},
pmid = {42555226},
issn = {0289-0003},
mesh = {Animals ; *Trematoda/genetics/classification/anatomy & histology ; Larva/classification/genetics ; *Trematode Infections/parasitology/veterinary/epidemiology ; DNA, Helminth/genetics ; Phylogeny ; *Fish Diseases/parasitology ; Host-Parasite Interactions ; Japan ; },
abstract = {The larval trematode taxon Monilicaecum ventricosum Yamaguti, 1942 (Didymozoidae) was redescribed from its type host, the Pacific saury Cololabis saira (Brevoort, 1856), collected from the North Pacific off Eastern Hokkaido, Japan. Because didymozoid larvae and adults differ markedly in morphology, linking these two stages using morphological data alone has traditionally been difficult. Consequently, the monotypic genus Monilicaecum Yamaguti, 1942 is currently regarded as a collective group, similar to genera established solely on larval forms of other trematodes. However, recent advances in molecular studies have enabled researchers to link larval and adult stages, clarify life cycles, and undertake more robust taxonomic evaluations. In this study, newly collected larval specimens were examined morphologically, and DNA barcodes (28S, ITS, and cox1) were generated to confirm their identity as M. ventricosum through morphological comparisons with type materials. These sequences were compared with those available in public databases to determine the corresponding adult stages and definitive hosts. Although no identical adult sequences were detected, M. ventricosum showed a close genetic relationship with four didymozoid species parasitizing the Australian yellowfin tuna, Thunnus albacares (Bonnaterre, 1788), suggesting that its definitive host is likely a species of Thunnus South, 1845. These findings provide essential molecular data for M. ventricosum, contribute to the taxonomic stability of Didymozoidae, and offer a foundation for future studies aimed at elucidating species boundaries and life-cycle connections within this group.},
}

Animals
*Trematoda/genetics/classification/anatomy & histology
Larva/classification/genetics
*Trematode Infections/parasitology/veterinary/epidemiology
DNA, Helminth/genetics
Phylogeny
*Fish Diseases/parasitology
Host-Parasite Interactions
Japan

@article {pmid42546145,
year = {2026},
author = {Ascensao, JA and Yu, Q and Hallatschek, O},
title = {The evolution of genetic drift over 50,000 generations.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyag199},
pmid = {42546145},
issn = {1943-2631},
abstract = {Random variation in reproductive success-genetic drift-profoundly shapes genetic diversity and evolutionary trajectories. The strength of drift depends on the variance in descendant number, σ2d, which governs key evolutionary outcomes: for instance, the establishment probability of a beneficial mutation scales inversely with σ2d. However, whether σ2d itself evolves over long timescales has remained unclear, because allele-frequency fluctuations depend on drift only through the effective population size, Ne = N/σ2d, which blends census population size with descendant-number variance. Here, we disentangle these components by using model-based Bayesian inference combined with joint tracking of (i) frequency fluctuations of neutrally barcoded lineages and (ii) census population sizes across growth cycles in the E. coli Long-Term Evolution Experiment (LTEE). Analyzing 33 clones spanning the ancestor through 50,000 generations in two replicate populations (Ara-2 and Ara+2), we find that the strength of genetic drift evolved markedly-and divergently-between the two replicate populations. Both census size and σ2d changed substantially through time, with most variation in Ne driven by shifts in σ2d rather than census size. After approximately 2,000 generations, the σ2d of the two populations diverged sharply: Ara+2 generally remained close to a bottleneck-only null expectation, whereas Ara-2 exhibited 1.5-5× stronger drift, consistent with an evolved increase in stochasticity during growth. These results imply that mutations can alter both the mean and the variance of the descendant-number distribution, and we show that the joint distribution of mutational effects on fitness and on σ2d can substantially modulate the rate of adaptation. The key parameter governing genetic drift can therefore itself evolve in the LTEE, with direct consequences for adaptation.},
}

@article {pmid42548531,
year = {2026},
author = {Jamdade, R and Al Jasmi, M and Alsallani, M and Al Shaer, K and Al Harthi, E and Gairola, S and Shabana, HA and Mahmoud, T and Mosa, KA and El-Keblawy, A},
title = {An integrative multi-locus DNA barcode library of selected medicinal plants from the United Arab Emirates.},
journal = {3 Biotech},
volume = {16},
number = {8},
pages = {368},
pmid = {42548531},
issn = {2190-572X},
abstract = {UNLABELLED: A multi-locus DNA barcode reference library was developed for 55 medicinal plant species from the 56 collected in the United Arab Emirates using rbcL, matK, and ITS2 markers, generating 397 high-quality sequences from 146 specimens. The rbcL marker showed the highest amplification (82.71%) and sequencing success (94.41%), while ITS2 and matK exhibited greater sequence variability with nucleotide diversities of 20.35 and 27.88, respectively. Genetic divergence analyses revealed minimal within-species variation for rbcL (mean 0.03%) and higher divergence within genera and families for matK (mean up to 10.12%) and ITS2 (mean up to 22.20%), confirming their complementary resolution across taxonomic levels. Barcode-gap assessments identified persistent delimitation challenges within Zygophyllum and Suaeda, where intra- and interspecific distances overlapped across all three markers. Species delimitation using Assemble Species by Automatic Partitioning (ASAP) correctly classified up to 94.9% of specimens with rbcL, while ITS2 and matK achieved 82.2-82.6% accuracy. Support Vector Machine (SVM) classification substantially improved resolution, achieving 96.82% accuracy for rbcL and 100% for both matK and ITS2. Logical consensus evaluation across marker combinations without sequence concatenation further demonstrated that SVM-based pairwise combinations resolved up to 100% of evaluable species, with rbcL+matK, matK+ITS2, and rbcL+matK+ITS2 all achieving perfect resolution, outperforming ASAP-based combinations for identical marker sets. The reference library provides validated DNA barcodes that support molecular identification, herbal-product authentication, biodiversity assessment, and conservation planning, and contributes to the Arabian Barcode of Life initiative.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04946-1.},
}

@article {pmid42548659,
year = {2026},
author = {Du, Q and Zhang, Z and Li, R},
title = {Pan-chloroplast genomes of Hordeum reveal insights into chloroplast evolution in the Poaceae family.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1881945},
pmid = {42548659},
issn = {1664-462X},
abstract = {Chloroplast genomes are widely used in phylogenetic and evolutionary studies due to their conserved structure and maternal inheritance. However, a comprehensive pan-chloroplast analysis across the genus Hordeum remains lacking. In this study, we assembled and annotated 43 chloroplast genomes representing 12 Hordeum species, together with 18 chloroplast genomes from other Poaceae species, to investigate structural variation, repeat sequences, codon usage, RNA editing, selective pressure, and nucleotide diversity. All chloroplast genomes exhibited the typical quadripartite structure with genome sizes ranging from 136,461 bp to 137,149 bp in Hordeum. The lengths of LSC and IR regions showed strong positive correlations with chloroplast genome size (r = 0.853 and 0.857, respectively). IR boundaries were highly conserved within Hordeum, whereas three distinct boundary types were identified across Poaceae. Pentanucleotide simple sequence repeats (SSRs) were universally present in Hordeum but absent in some other Poaceae species, representing a candidate Hordeum-enriched marker pending broader validation. Based on the newly assembled chloroplast genomes of Hordeum, the phylogenetic relationships were reappraised. A total of 66 protein-coding genes contained RNA editing sites, with ndhB harboring the most edits in Hordeum. All examined protein-coding genes showed Ka/Ks values below 1, while ribosomal subunit genes exhibited the highest interspecific variation in Ka/Ks. Hordeum bulbosum displayed the highest intraspecific nucleotide diversity and haplotype diversity, whereas cultivated Hordeum vulgare showed extremely low diversity. Several hypervariable regions were identified as candidate DNA barcodes. This pan-chloroplast genome study provides new insights into the structural and evolutionary dynamics of Hordeum chloroplast genomes and offers valuable genomic resources for phylogeny, germplasm identification, and adaptive evolution in the genus.},
}

@article {pmid42550841,
year = {2026},
author = {Jung, JL and Haderlé, R and Cosnier, K and Al Musallami, M and Al Mehairbi, S and Perumal, P and Al Hammadi, S and Valentini, A and Ung, V and Prazuck, C and Chaveneau, C and Adam, O},
title = {First eDNA-based monitoring of marine vertebrates in the urban marine ecosystem of Abu Dhabi: Mangrove and seagrass beds as biodiversity reservoirs?.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0352249},
pmid = {42550841},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; *DNA, Environmental/genetics/analysis ; *Ecosystem ; *Vertebrates/genetics/classification ; *Environmental Monitoring/methods ; Wetlands ; *Aquatic Organisms/genetics/classification ; United Arab Emirates ; },
abstract = {The Arabian Gulf is a semi-enclosed sea with shallow waters. Its marine fauna must cope with extreme and recurring environmental conditions (high summer temperatures, hypersalinity, hypoxia). In addition, local human activities are very significant and have a marked impact on coastal areas, particularly in urban marine ecosystems (UME). Taken together, the Arabian Gulf's low species richness, its exposure to multiple human-induced stressors, and the proximity of many taxa to their environmental tolerance limits create a particularly concerning situation. Monitoring marine wildlife must be a priority in this context, particularly with respect to marine vertebrates, difficult to study using integrative approaches. The present study aimed to generate relevant data on marine vertebrate biodiversity in the UME of Abu Dhabi, and to provide evidence-based information to inform conservation policy. In addition, investigating marine biodiversity in the world's warmest sea in summer, the Arabian Gulf, will provide us with information of general interest in terms of the adaptation and evolution of marine fauna in the current period of global climate change. We conducted the first environmental DNA (eDNA)-based survey of marine vertebrate diversity in Abu Dhabi's UME. Using a standardized process of water sampling, eDNA metabarcoding using a ~ 97 bp fragment of the mitochondrial 12S rRNA gene as barcode, and taxonomic assignment, we studied vertebrate biodiversity at four urban sites, including a marina, a newly developed area, a seagrass bed, and a protected urban mangrove. We identified 83 distinct taxa, including five birds, two elasmobranchs, one marine mammal, and 75 teleosts. The specific taxonomic richness did not vary significantly between sites. In contrast, phylogenetic diversity metrics revealed lower diversity than expected for the newly developed area, while the mangrove and, to a lesser extent, the seagrass bed exhibited a phylogenetic structure consistent with their species richness. This approach provides a powerful, non-invasive and integrative framework for long-term monitoring and supports evidence-based conservation planning for marine biodiversity in the Arabian Gulf.},
}

Animals
*Biodiversity
*DNA, Environmental/genetics/analysis
*Ecosystem
*Vertebrates/genetics/classification
*Environmental Monitoring/methods
Wetlands
*Aquatic Organisms/genetics/classification
United Arab Emirates

@article {pmid42551976,
year = {2026},
author = {An, SH and Myagmarsuren, T and Heo, GB and Jeong, H and Kang, YM and Dondog, U and Tsogbadrakh, U and Lee, YJ and Tseren-Ochir, EO and Lee, KN},
title = {Clade 2.3.4.4b H5N1 highly pathogenic avian influenza detected in wild bird feces, Eastern Mongolia, 2024.},
journal = {Journal of veterinary science},
volume = {27},
number = {4},
pages = {e38},
doi = {10.4142/jvs.25274},
pmid = {42551976},
issn = {1976-555X},
support = {I-1543418-2021-25-01/QIA/Animal and Plant Quarantine Agency/Korea ; },
mesh = {Animals ; *Influenza A Virus, H5N1 Subtype/isolation & purification/genetics/pathogenicity/classification ; Mongolia/epidemiology ; *Influenza in Birds/virology/epidemiology ; Feces/virology ; Phylogeny ; Birds ; Animals, Wild/virology ; },
abstract = {IMPORTANCE: Despite ongoing intercontinental spread of clade 2.3.4.4b H5N1 highly pathogenic avian influenza (HPAI), surveillance data from Mongolia -- a critical junction between Central and East Asian migratory flyways -- remain scarce, leaving a gap in understanding how viruses move between northern breeding areas and southern wintering grounds.

OBJECTIVE: We aimed to detect and genetically characterize HPAI viruses in wild bird populations in Mongolia and assess their relationship with viruses circulating in East Asia.

METHODS: Active surveillance was conducted at Ganga Lake, Mongolia, in October 2024. A total of 352 wild bird fecal samples were collected and tested for AIVs. Viral isolates were subtyped, whole-genome sequenced, and phylogenetically analyzed. Host species was identified using c oxidase I barcoding.

RESULTS: Sixteen AIVs were isolated, including one clade 2.3.4.4b H5N1 HPAI virus (M9-3) from whooper swan feces. Genomic analysis revealed M9-3 had > 99% similarity with Korean and Japanese H5N1 isolates reported in late 2024 and undergone recent reassortment and disseminated through migratory flyways.

CONCLUSIONS AND RELEVANCE: This is the first detection of clade 2.3.4.4b H5N1 in Eastern Mongolia in a fecal sample during late autumn. These findings underscore Mongolia's importance as a sentinel location for interregional HPAI dissemination.},
}

Animals
*Influenza A Virus, H5N1 Subtype/isolation & purification/genetics/pathogenicity/classification
Mongolia/epidemiology
*Influenza in Birds/virology/epidemiology
Feces/virology
Phylogeny
Birds
Animals, Wild/virology

@article {pmid42552959,
year = {2026},
author = {Spurgeon, BEJ},
title = {Platelet flow cytometry: An evolving platform for clinical hematology.},
journal = {Cytometry. Part B, Clinical cytometry},
volume = {},
number = {},
pages = {},
doi = {10.1002/cyto.b.70060},
pmid = {42552959},
issn = {1552-4957},
abstract = {Flow cytometry has transformed platelet biology and diagnostics through high-resolution, single-cell analysis of surface markers, activation states, and intracellular signaling. This review traces its evolution from early applications in glycoprotein profiling and immune thrombocytopenia to clinical roles in HIT, VITT, and FNAIT. Advances in spectral cytometry, phosphoflow, and fluorescent barcoding have increased analytical depth and supported development of whole blood-compatible platelet function assays. Flow cytometry now enables characterization of platelet subpopulations, assessment of complement deposition, and functional evaluation across immune and thrombotic disorders. These capabilities support applications in diagnostics, bleeding and cardiovascular risk assessment, drug-induced thrombocytopenia, and platelet product quality control. As these technologies mature, flow cytometry is expanding its role in clinical workflows and may enable more biologically informed and individualized approaches in precision hematology.},
}

@article {pmid42553547,
year = {2026},
author = {Schneider, JA and Salden, T and Moser, M and Peters, RS},
title = {kretschmanni's global relatives: The Aphanogmus species with spiny sternite females (Hymenoptera, Ceraphronidae).},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {187-225},
pmid = {42553547},
issn = {1313-2989},
abstract = {The Western Palaearctic Aphanogmus kretschmanni Moser, 2023 is unique among all described species of Ceraphronidae in having two distinct rows of spines on the seventh metasomal sternite of the female. In this study, we examined additional Aphanogmus that share this trait and found at least five additional putative species in an integrative taxonomy approach using morphology and publicly available CO1 barcode data on BOLD. Two new species are described herein: A. manta Schneider, Salden & Peters, sp. nov. and A. liceodosriosi Schneider, Salden & Peters, sp. nov. The diagnosis of A. kretschmanni is updated. The remaining putative species are listed but not formally described as reliable diagnoses require additional material. We also describe males, including male genitalia, of species with spiny sternite females for the first time. Males lack the metasomal sternal spines which implies a sex-specific function of the spines, for example, in oviposition. In our morphological diagnoses, we use characters of the Waterston's evaporatorium (WE) present on the sixth metasomal tergite in both males and females in addition to previously established morphological characters and further highlight the value of the WE in delimiting Ceraphronidae species and morphologically matching males and females. The number of putative species and their distribution literally around the globe (Neotropics, Afrotropics, Palaearctic, Australasia, Orientalis) imply the presence of an unexpectedly large number of relatives of A. kretschmanni. Future investigations are necessary to capture the true diversity within the genus Aphanogmus and to unravel the biological and evolutionary background of the intriguing sternal spines.},
}

@article {pmid42539960,
year = {2026},
author = {Bu, Y and Gao, Y},
title = {New species and new records of Tullbergiidae (Arthropoda, Hexapoda, Collembola, Poduromorpha) from Xizang, Southwest China, with genetic distance analysis within the family.},
journal = {ZooKeys},
volume = {1286},
number = {},
pages = {41-62},
pmid = {42539960},
issn = {1313-2989},
abstract = {The Tullbergiidae of Xizang, Southwest China, are studied based on specimens newly collected in 2024. Metaphorura alticola sp. nov., which was discovered in two localities at extremely high altitudes of 4000-5300 m in Shannan City, is described and illustrated. It can be distinguished from the similar M. motuoensis Bu & Gao, 2017 by the dorsal chaetotaxy, number of vesicles on PAO, and the shape of anal spines on Abd. VI, as well as the large genetic distance of the COI gene. Mesaphorura macrochaeta Rusek, 1976, found from several localities in Xizang, is recorded in China for the first time, and Chinese specimens are described and illustrated. In addition, the distributions for M. hylophila Rusek, 1982, M. krausbaueri (Börner, 1901), M. pacifica Rusek, 1976, and M. yosii (Rusek, 1967) in Xizang are updated according to the newly collected material. DNA barcodes of mitochondrial COI gene for Metaphorura alticola sp. nov., M. macrochaeta, and M. hylophila are newly sequenced and analyzed together with 26 sequences of the family extracted from GenBank. The genetic distances of different levels in the family Tullbergiidae are analysed. A key for all tullbergiid species recorded in Xizang and a map of their distributions are also provided.},
}

@article {pmid42540691,
year = {2026},
author = {Inumaru, M and Noda, R and Itokawa, K and Matsumura, R and Kimura, T and Kuwata, R and Nakao, S and Tsuha, O and Takemura, A and Nishiyama, S and Yamauchi, T and Tamatani, H and Yoshikawa, A and Hattori, M and Sasaki, T and Watanabe, M and Sawabe, K and Aboshi, AR and Kobayashi, D and Yang, C and Yamada, A and Isawa, H and Kasai, S and Higa, Y},
title = {National Distribution of Bisexual and Parthenogenetic Haemaphysalis longicornis of Japan, and a Real-Time PCR-Based Method to Distinguish the Two Reproductive Groups.},
journal = {Journal of parasitology research},
volume = {2026},
number = {},
pages = {9395344},
pmid = {42540691},
issn = {2090-0023},
abstract = {The Asian longhorned tick, Haemaphysalis longicornis, is a well-known vector of several zoonoses including SFTS and Japanese spotted fever. This species consists of two different reproductive forms, bisexual and parthenogenetic, which are suggested to have differential roles in disease transmission. In Japan, the distributions of these forms have been suspected from sex bias in each population. Meanwhile, recent insights about the origin of the parthenogenetic form suggest the possibility of individual-level diagnosis using mitochondrial phylogeny. To reassess the current distribution of those reproductive forms and potential changes over time in Japan, 1750 H. longicornis collected across 23 prefectures of Japan were investigated. The COI barcoding region was used to distinguish the mitochondrial haplogroup of each individual. Additionally, we developed real-time PCR probes to distinguish the two mitochondrial haplogroups representing each reproductive form. As previous studies have suggested, the parthenogenetic mitochondrial haplogroup was present throughout the country, while the bisexual mitochondrial haplogroup was found only in central and western Japan. Interestingly, populations consisting of either one or both haplogroups were found in neighboring areas, highlighting the need for more detailed and fine-scaled investigations in order to fully reveal the distribution of the reproductive groups. The newly developed real-time PCR method successfully differentiated all tested haplotypes. Furthermore, alignment of 173 COI haplotypes revealed that the diagnostic nucleotide selected for the method was consistent across all haplotypes, including those outside of Japan. This suggests that this method can accurately distinguish between the two haplogroups of H. longicornis in both Japan and other countries. This one-step method will serve as a rapid tool to distinguish bisexual and parthenogenetic H. longicornis, making further investigations, particularly into their role in disease transmission and shifts in distributions, possible.},
}

@article {pmid42541285,
year = {2026},
author = {Aupalee, K and Srisuka, W and Takaoka, H and Rodpai, R and Jones, MO and Charoenvilaisiri, K and Saingamsook, J and Pusawang, K and Saeung, A},
title = {Multiplex PCR for the differentiation of Simulium asakoae and molecular detection of pathogens in the S. asakoae species group in Thailand.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {10},
number = {},
pages = {100414},
pmid = {42541285},
issn = {2667-114X},
abstract = {A human-biting black fly, Simulium (Gomphostilbia) asakoae Takaoka & Davies, 1995, together with certain other members of the S. asakoae species group, is of medical and veterinary importance as a vector of various pathogens. However, accurate species identification remains challenging due to the high morphological similarity among related members and the limitations of cox1 barcoding. To address this challenge, this study developed a multiplex PCR assay based on the cox1 gene to differentiate S. asakoae. In addition, diverse pathogens circulating in the S. asakoae species group collected from Chiang Mai Province, northern Thailand, were molecularly detected. The multiplex PCR assay was developed using two allele-specific forward primers combined with universal cox1 primers as an internal control. This assay demonstrated 100% sensitivity and specificity, successfully differentiating S. asakoae from other Thai-related species in the same species group. Pathogen screening of 100 individual specimens and 20 pooled samples of the S. asakoae species group revealed the highest infection rate for Leucocytozoon (14% in individuals and 8.5% minimum infection rate (MIR) in pools), followed by trypanosomatids (10% in individuals and 4% MIR in pools) and filarial nematodes (5% in individuals and 2.5% MIR in pools). Molecular analysis further confirmed the first detection of Leucocytozoon sabrazesi, Trypanosomatidae spp. (including Leptomonas spiculata), Onchocerca sp. Type I, and a possible new Onchocerca sp. in the S. asakoae species group in Thailand. To the best of our knowledge, this study provides the first multiplex PCR assay for the rapid and correct identification of S. asakoae and confirms the circulation of diverse pathogens in the S. asakoae species group, thereby supporting enhanced surveillance and vector control programmes in Thailand.},
}

@article {pmid42542665,
year = {2026},
author = {Kwawukume, S and Kandula, N and Cui, L and Singh, P},
title = {A rapid rhPCR-lateral flow assay for authenticating royal red and Argentine red shrimp in the U.S. seafood supply chain.},
journal = {Food chemistry. Molecular sciences},
volume = {13},
number = {},
pages = {100434},
pmid = {42542665},
issn = {2666-5662},
abstract = {In the United States, approximately one-third of shrimp sold are misrepresented. DNA barcoding requires robust infrastructure and one to three days to generate results, limiting enforcement utility. We hypothesized that RNase H2-dependent PCR (rhPCR) primers targeting cytochrome oxidase subunit I (COI) sequence-specific sites, coupled with lateral flow detection, could enable rapid species authentication of royal red shrimp (Pleoticus robustus) and Argentine red shrimp (Pleoticus muelleri). Species-specific rhPCR primers labeled with FAM and biotin were designed and evaluated using crude DNA extracts from 65 barcoded shrimp specimens representing seven commercially traded species. The assays were further validated using 20 blinded retail samples marketed as royal red shrimp. Both assays demonstrated high specificity comparable to DNA barcoding results, and an analytical sensitivity of 0.01 ng/μL. Analysis of retail samples revealed 60% of samples were not royal red shrimp. Total time-to-results for 20 samples was approximately 150 min, demonstrating a rapid, simpler, and sequencing-free alternative for regulatory enforcement.},
}

@article {pmid42539220,
year = {2026},
author = {McGee, AV and Biar, CG and Martin, BK and Li, T and Lalanne, JB and Kim, H and Shendure, J},
title = {Locus-Scale Massively Parallel Reporter Assays.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42539220},
issn = {2692-8205},
abstract = {Interactions among c is-regulatory elements (CREs) are central to mammalian gene regulation. Long @$$ massively parallel reporter assays (LAMPRAs) integrate combinatorial cloning, molecular barcoding and long- and short-read sequencing, to scalably measure how CRE identities, numbers, spacings, orders, orientations, and interactions shape regulatory output at multi-kilobase length scales. As a proof-of-concept, we assay 36,000 × 5-kb synthetic c is-regulatory loci (sCRLs), each a 5 × 1-kb random combination of enhancers, insulators and spacers, to model how locus composition drives gene expression.},
}

@article {pmid42537001,
year = {2026},
author = {Zolfaghari, A and Fraiture, MA and Vanneste, K and Stuyts, A and Frouin, J and Meunier, AC and Deforce, D and Roosens, NHC and D'aes, J},
title = {RiSpy: a feature selection-based fingerprinting framework for accurate identification of genome-edited rice lines.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
doi = {10.1093/bib/bbag406},
pmid = {42537001},
issn = {1477-4054},
mesh = {*Oryza/genetics ; *Genome, Plant ; *Plants, Genetically Modified/genetics ; *Gene Editing ; *Software ; Computational Biology/methods ; Polymorphism, Single Nucleotide ; Whole Genome Sequencing ; Genomics/methods ; *DNA Fingerprinting/methods ; },
abstract = {The European Union (EU) enforces strict regulations on the traceability and labeling of genetically modified organisms (GMOs), including genome-edited (GE) lines produced through new genomic techniques (NGTs). Identifying GE organisms created by single nucleotide variations (SNVs) is however challenging, as a single SNV alone cannot unambiguously define a GE line. Recently, we introduced the concept of generating a genetic fingerprint to distinguish a specific GE rice line. This proof-of-concept approach integrated whole-genome sequencing (WGS)-based characterization with the Illumina technology, the public 3 K Rice Genomes (3KRG) database, and statistical feature-selection tools, to select and combine key genetic elements, including GE on-target site(s) and cultivar-specific 2-SNV barcodes, into a unique genetic fingerprint. In the present study, we expand this concept into a generalized data-driven framework allowing identification of multiple rice lines. Supported by newly developed bioinformatics and statistical feature-selection-based pipelines, this optimized strategy enables the generation of genetic fingerprints irrespective of a rice cultivar's inclusion in publicly available databases like 3KRG. In addition, this refined strategy can leverage WGS data generated from both Illumina and Oxford Nanopore Technologies (ONT) platforms for fingerprint generation and GE line identification. Using two distinct in-house GE rice lines from different cultivars, along with various publicly available WGS datasets, we demonstrated the robustness, scalability, and specificity of this approach for reliable GE rice line identification. Our findings provide a methodological foundation for data-driven traceability of GE rice lines, reinforcing regulatory compliance, supporting intellectual property (IP) protection, and contributing to the responsible implementation of EU GMO/NGT legislation.},
}

*Oryza/genetics
*Genome, Plant
*Plants, Genetically Modified/genetics
*Gene Editing
*Software
Computational Biology/methods
Polymorphism, Single Nucleotide
Whole Genome Sequencing
Genomics/methods
*DNA Fingerprinting/methods

@article {pmid42533593,
year = {2026},
author = {Świątek, P and Brown, GG and James, S and Urbisz, AZ and Gajda, Ł},
title = {Ovaries of Three Eukerria and Two Kerriona Earthworms (Annelida, Crassiclitellata, Ocnerodrilidae) Are Morphologically Different, but Their Microorganization and Oogenesis Are the Same.},
journal = {Journal of morphology},
volume = {287},
number = {8},
pages = {e70155},
pmid = {42533593},
issn = {1097-4687},
support = {//National Science Center, Poland (2020/37/B/NZ4/00560)/ ; 2020/37/B/NZ4/00560//National Science Center, Poland/ ; },
mesh = {Animals ; Female ; *Oligochaeta/anatomy & histology/ultrastructure/cytology/physiology/genetics ; *Ovary/cytology/ultrastructure/anatomy & histology ; *Oogenesis/physiology ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal/genetics ; Oocytes/cytology/ultrastructure ; RNA, Ribosomal, 18S/genetics ; },
abstract = {The ovaries of five barcoded earthworm species (nuclear 18S rRNA and 28S rRNA, and mitochondrial COI and 12S rRNA gene sequences are provided) from the family Ocnerodrilidae have been analyzed using various microscopic techniques. In both genera studied, ovaries are paired and located in the anterior part of segment XIII. Surprisingly, the ovarian morphology observed in Eukerria differs from that found in Kerriona. Ovaries of Eukerria are flattened, of rectangular or triangular shape, with one or two oocyte rows (egg strings) at the posterior part. Ovaries in Kerriona are fan-shaped, with numerous egg strings. Kerriona's ovaries are of the typical shape found in other representatives of the family Ocnerodrilidae and are similar to the ovaries characteristic of megascolecid earthworms. In contrast, Eukerria ovaries resemble those typical for Lumbricidae. This observation is inconsistent with other reports, which suggested that the ovaries in Ocnerodrilidae are fan-shaped and contain numerous egg strings. Despite the differences in morphology, the internal ovary organization and the course of oogenesis are the same in all studied species and resemble those known from other earthworms. The apical ovary part is composed of a solid mass of germline cells enveloped by thin somatic (follicular) cells. Germline cells are interconnected into syncytial cysts, in which each cell has a single intercellular bridge connecting it to the central cytoplasmic mass, the cytophore. Cysts unite oogonia and early meiotic cells. During diplotene, the future oocyte detaches from the cyst, forms microvilli, and gathers nutrients, whereas the remaining nurse cells do not grow and remain connected to the cytophore. Vitellogenic oocytes finally detach from the ovaries and float freely in the segment lumen. They are 80-90 µm in diameter and are regarded as oligolecithal. Nurse cells probably die within the ovaries; they have never been observed within the coelom.},
}

Animals
Female
*Oligochaeta/anatomy & histology/ultrastructure/cytology/physiology/genetics
*Ovary/cytology/ultrastructure/anatomy & histology
*Oogenesis/physiology
RNA, Ribosomal, 28S/genetics
RNA, Ribosomal/genetics
Oocytes/cytology/ultrastructure
RNA, Ribosomal, 18S/genetics

@article {pmid42534460,
year = {2026},
author = {Zhang, Y and Wu, H and Yang, X and Zeng, Y and Feng, M and Zhang, J and Ye, Y and Liu, P and Wei, J},
title = {Establishment of a two-tiered molecular identification system for Dracaena species - the source plants of dragon's blood.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1851019},
pmid = {42534460},
issn = {1664-462X},
abstract = {BACKGROUND: The unresolved taxonomy of Dracaena species, the botanical sources of the prized traditional medicine Dragon's blood, poses significant challenges to resource conservation, material traceability, and quality control. This study aimed to resolve these taxonomic ambiguities by developing and validating a high-resolution, integrated molecular authentication system. Based on 26 original plant samples from the genus Dracaena, along with relevant DNA barcode loci retrieved from NCBI, five previously reported DNA barcodes were evaluated and assessed. Simple sequence repeat (SSR) sequences from the transcriptome of D. cambodiana were subsequently screened. Finally, the established DNA barcode and SSR molecular marker systems were applied to identify the botanical origin of Dragon's blood.

RESULTS: The trnP-psaJ and psbK-psbI regions were identified as optimal barcodes, effectively distinguishing foreign sources (D. cinnabari and D. draco) from domestic ones. From transcriptomic data, we screened and validated 16 highly polymorphic SSR primers. While DNA barcodes confirmed broad phylogenetic relationships, SSR markers provided superior resolution, clearly delineating the closely related domestic taxa D. cambodiana, D. cochinchinensis, and the "Yanzong" plant into distinct genetic clusters. A key finding was the consistent genetic distinctiveness of Hainan Island populations, supporting the genetic affinity of the Hainan populations with D. cambodiana, indicating that they fall within the genetic variation range of this species based on the available reference samples. Furthermore, cultivation analysis revealed that D. cambodiana is the predominant cultivated species in China; the horticultural variety "Heizhenzhu" was identified as a likely variant of this species, while "Taikongtie" showed ambiguous affinity, possibly involving D. cochinchinensis or Guangxi populations.

CONCLUSIONS: We established a novel, two-tiered molecular identification system that combines the trnP-psaJ barcode for rapid screening with a panel of 16 SSR markers for fine-scale discrimination. This integrated approach successfully clarifies the taxonomy of important Dragon's blood source plants. It provides a reliable, efficient protocol for authenticating Dracaena species and germplasm, offering a critical technical foundation for resource conservation, medicinal material standardization, and targeted breeding programs.},
}

@article {pmid42534551,
year = {2026},
author = {Sterling, MJ and Lees, DC},
title = {A revision of the genus Ptochoryctis Meyrick, 1894 (Lepidoptera, Gelechioidea, Xyloryctidae) with the description of 12 new species.},
journal = {ZooKeys},
volume = {1285},
number = {},
pages = {261-328},
pmid = {42534551},
issn = {1313-2989},
abstract = {The genus Ptochoryctis Meyrick, 1894 is revised and reinstated in the Xyloryctidae (previously treated in Autostichidae) based on molecular and morphological evidence. A fuller description is provided of the morphology of all the species previously described in Ptochoryctis which are not combined elsewhere. The following new species of Ptochoryctis are described: Ptochoryctis blanchella sp. nov., P. caputanatis sp. nov., P. draconella sp. nov., P. flavalbella sp. nov., P. fuscilinea sp. nov., P. kitchingi sp. nov., P. marmorella sp. nov., P. minimella sp. nov., P. persicotincta sp. nov., P. ochraceella sp. nov., P. robinsoni sp. nov. and P. splendidella sp. nov. Deloryctis Meyrick, 1934 is synonymised with Ptochoryctis. The following new combinations are established: Ptochoryctis corticivora (Meyrick, 1934), comb. nov. (which is consequently transferred from Depressariidae to Xyloryctidae), Metathrinca alma (Meyrick, 1908), comb. nov., M. inviolata (Meyrick, 1925), comb. nov., M. ochrograpta (Meyrick, 1923), comb. nov.; and M. perigramma (Meyrick, 1926), comb. nov.},
}

@article {pmid42534578,
year = {2026},
author = {Bhandari, P and Xu, C and Li, BZ and Li, FX and Jiménez-Mejías, P and Zhang, SR and Zhou, SL},
title = {A universal DNA-barcode approach to aid species identification in the family Cyperaceae.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1794327},
pmid = {42534578},
issn = {1664-462X},
abstract = {Cyperaceae, one of the ten largest plant families with a cosmopolitan distribution, presents significant taxonomic challenges due to its highly reduced and complex floral structures. These complexities make species identification through conventional morphology-based methods difficult. To address these limitations, DNA barcoding was employed for accurate species identification. This study evaluates the universality of DNA barcodes across the entire Cyperaceae family using a total of 6739 sequences. The performance of four DNA barcoding regions ITS, matK, rbcL, and rps16, was explored using three analytical approaches, genetic distance, sequence similarity, and phylogenetic tree methods. Among single-locus barcodes, the nuclear region internal transcribed spacer (ITS) showed higher discriminatory power than the chloroplast regions matK, rbcL, and rps16. Among multi-locus combinations, ITS + matK + rps16 was found to be most effective. These findings provide valuable insights for improving the precise identification of Cyperaceae species. Future efforts should focus on sampling species-rich tribes such as Cariceae, Cypereae, Schoeneae, Rhynchosporeae, and Sclerieae, particularly in poorly sampled regions of Asia and Africa. Expanding these efforts is crucial for building a robust and comprehensive GenBank reference database for Cyperaceae.},
}

@article {pmid42530017,
year = {2026},
author = {Quinlan, A and Kuo, LY and Hu, JM and Huang, YM},
title = {Ferns on ferns: gametophyte assemblages on tree ferns reveal associations with accidentally epiphytic ferns.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag232},
pmid = {42530017},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: Tree ferns are substantial hosts for epiphytes, often hosting distinct communities that are considerably different from other hosts. While previous research has highlighted the prevalence of epiphytic ferns growing on tree ferns, studies have yet to explore this host relationship for the gametophyte generation. This study aims to investigate the epiphytic fern gametophyte communities growing on low trunks of Alsophila spinulosa (Cyatheaceae).

METHODS: A high-throughput DNA barcoding approach was used to identify fern gametophytes collected from tree fern trunks and neighboring angiosperm hosts across six established plots. Co-occurring sporophytes were surveyed along the same trunks. Gametophyte identification was achieved by sequencing multiplexed trnL-F amplicons derived from tissue-direct PCR on an Illumina MiSeq platform.

KEY RESULTS: Tree fern trunks harbored a higher abundance and species richness of fern gametophytes than angiosperm trunks, and hosted more cordiform gametophytes, most of which were otherwise terrestrial ferns considered to be accidentally epiphytic. In comparison, angiosperm hosts were associated with non-cordiform, obligately epiphytic ferns. The humid microclimate of tree fern trunks simulate a terrestrial-like environment, offering an indistinct boundary from the forest floor which provides habitat for fern species that typically establish on the ground. Our survey also recovered three species we interpret as independent fern gametophytes Antrophyum henryi., Callistopteris apiifolia, and Haplopteris yakushimensis, given that their sporophyte phases were not present and are not known from nearby localities.

CONCLUSIONS: DNA barcoding techniques provide an opportunity to study the distribution and habit of fern gametophytes, the life history stage of ferns which is often overlooked. Our results demonstrate that gametophyte growth form and habit are correlated with habitat preference and community structure. Our findings support the importance of incorporating gametophytes into broader studies of fern ecology and distribution.},
}

@article {pmid42531124,
year = {2026},
author = {Wu, JW and Xu, Y and Chen, Y and Yang, JM and Huang, CH},
title = {Protocol for multiplexed quantification of fluorescent biosensor FRET efficiency using barcoded cells.},
journal = {STAR protocols},
volume = {7},
number = {3},
pages = {104756},
doi = {10.1016/j.xpro.2026.104756},
pmid = {42531124},
issn = {2666-1667},
abstract = {Genetically encoded fluorescent biosensors frequently use Förster resonance energy transfer (FRET) between donor and acceptor fluorescent proteins (FPs) as readouts for monitoring molecular activities in live cells. Here, we present a protocol for determining FRET efficiency through the simultaneous imaging of multiple FRET biosensors alongside donor and acceptor FPs using spectrally orthogonal fluorescent cell barcodes. We describe steps for culturing and transfecting cells, acquiring and analyzing images, and calculating FRET efficiency. This approach facilitates simultaneous analysis of multiple FRET biosensors. For complete details on the use and execution of this protocol, please refer to Wu et al.[1].},
}