@article {pmid41838382,
year = {2026},
author = {Saini, K and Singh, R},
title = {Regulatory Approaches to Electronic Labelling in the USA, EU, and India: A Comparative Overview.},
journal = {Therapeutic innovation & regulatory science},
volume = {},
number = {},
pages = {},
pmid = {41838382},
issn = {2168-4804},
abstract = {OBJECTIVE: In this era of growth, e-labelling is becoming increasingly important as the labels are important sources of information for patients. However, regulations governing e-labeling for pharmaceuticals and medical equipment varies throughout the countries. This review compares the e-labelling regulation approaches in EU, USA, and India.

SCOPE: The regulations have been initiated by appropriate governments and/or health authorities of EU, USA, and India in collaboration with key stakeholders, including patients, healthcare providers, pharmaceutical companies, environmental and regulatory agencies. EU and USA have established the digital labelling but India still relies on paper instruction manuals with limited digital systems.

METHODOLOGY: The regulatory information and current trends of e-labelling in EU, US, and India were studied and compared for electronic prescribing and electronic decision support systems with health record. Regulatory information was recognized through a structured review of official regulatory agency websites (FDA, EMA, CDSCO), international organizations (WHO, ICH), and peer-reviewed literature accessed through databases such as PubMed and Google Scholar. Eligible sources comprised official regulations, guidance documents, policy reports, and peer-reviewed articles specifically addressing pharmaceutical e-labelling, while draft policies and unrelated documents were excluded. Data were synthesized using qualitative thematic analysis, and cross-jurisdictional comparisons were structured across predefined domains including regulatory scope, legal status, implementation stage, digital infrastructure, and stakeholder accessibility.

KEY FINDINGS: Common challenges include maintaining authenticity, readability, and interoperability of e-labels. Technologies like QR codes, barcoding, and decision support tools increase safety and access. However, digital implementation and regulatory maturity differ generally between the developed and developing nations.},
}

@article {pmid41840192,
year = {2026},
author = {Gülmez, İ and Dönmez, AA and Aydın, ZU},
title = {Comparative chloroplast genome analysis of Polygala species: insights into evolution, phylogeny, and DNA barcoding.},
journal = {Planta},
volume = {263},
number = {4},
pages = {},
pmid = {41840192},
issn = {1432-2048},
support = {118 Z 708//TUBITAK/ ; },
mesh = {*Genome, Chloroplast/genetics ; Phylogeny ; *DNA Barcoding, Taxonomic ; *Polygala/genetics/classification ; Evolution, Molecular ; Genetic Variation ; },
abstract = {Polygala species are rich in saponin molecules and are traditionally used for medical purposes. Research on the chloroplast (cp) genome of Polygala is crucial to understanding its phylogenetics, biogeography, and species identification. In this study, the tetraploid Polygala vulgaris chloroplast genome was reported for the first time via various assembly and annotation tools. By combining these new data with the published cp genomes of 12 Polygala taxa from NCBI, we conducted a comparative analysis of nucleotide diversity, repeat sequences, genome synteny, phylogenetic relationships and DNA barcoding. The final assembled chloroplast genome sizes for the studied Polygala taxa ranged from 165,246 bp to 168,779 bp, with a total of 174 genes annotated, including 102 protein-coding genes, 63 transfer RNA genes, and 13 ribosomal RNA genes in Polygala vulgaris. A total of nine highly divergent genes were identified, including the CDS gene rpl32 as well as the intergenic spacer regions matK-trnK, trnL-trnF, trnH-psbA, trnQ-psbK, ndhI-ndhF, ndhF-rpl32, ccsA-ndhD, and ndhG-ndhI. Phylogenetic relationships were reconstructed based on Bayesian inference and maximum likelihood analyses using ortholog-based and concatenated datasets derived from the identified hypervariable regions separately. The topological structure of the constructed phylogenetic tree showed biogeographic disjunction, and the most similar relative of Polygala vulgaris was one of the European taxa, P. amerella, based on high support values. The analysis of relative synonymous codon usage revealed that a codon usage pattern largely consistent with that observed across other Polygala species. A total of three types of repeat sequences, forward, palindromic, and reverse, were identified across the chloroplast genomes of the analyzed species. These findings provide a valuable reference for phylogenomic and evolution of Polygala taxa as well as to develope molecular markers for DNA barcoding.},
}

*Genome, Chloroplast/genetics
Phylogeny
*DNA Barcoding, Taxonomic
*Polygala/genetics/classification
Evolution, Molecular
Genetic Variation

@article {pmid41835227,
year = {2026},
author = {Sun, L and Zheng, H and Huang, Y and Huang, X and Yan, K and Wang, Z and Yang, L and Yue, Y and Gou, X and Du, G and Wang, Y and Wu, X and Liu, H and Chen, H and Ma, D and Han, Y and Dai, J and Cao, G},
title = {Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq.},
journal = {National science review},
volume = {13},
number = {5},
pages = {nwag004},
pmid = {41835227},
issn = {2053-714X},
abstract = {Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and its underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate an integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of the mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated the projectomic atlas with its distinct spectrum of neurotransmitters/neuropeptides with their receptor-related gene profiles in order to demonstrate the PFC neural signal transmission network, by which means we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information. As a proof of concept, we used this model to predict projections of fear recall engram neurons. This study facilitates our understanding of the brain multi-modal network and neural computation.},
}

@article {pmid41835454,
year = {2026},
author = {Walterspiel, F and Ugarte-Uribe, B and Terjung, S and Cabrera, A and Khan, AUM and Deo, C},
title = {Photoclickable Halotag ligands for spatiotemporal multiplexed protein labeling on living cells.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41835454},
issn = {2633-0679},
abstract = {Precise spatiotemporal control over fluorescence labeling is a powerful approach for selective marking and tracking of proteins of interest within living systems. Here, we report a photoclickable labeling platform based on the 2,3-diaryl-indanone epoxide (DIO) photoswitch scaffold and the self-labeling protein HaloTag. Upon illumination, the protein-bound DIO undergoes reversible photoisomerization to form a metastable oxidopyrylium ylide (PY) that reacts with ring-strained dipolarophiles via [5 + 2] cycloaddition, enabling covalent spatiotemporal labeling. We synthesize and characterize a library of DIO-HaloTag and DIO-SNAP-tag ligands, systematically examining the effects of linker architecture and scaffold substitution on the photoswitching and photoclick reactivity in vitro and on living cells. We identify a naphthyl-substituted DIO ligand exhibiting superior photoswitching and photoclick efficiency, allowing fast, selective labeling of HaloTagged proteins on the surface of living cells using visible light activation (405 nm). Using this system, we achieve two- and three-color labeling of defined cell surface regions with excellent spatial and temporal precision, additionally allowing combinatorial labeling. Together, this work establishes a versatile framework for multiplexed, light-directed protein labeling compatible with living systems, with promising future applications including multiplexed long-term tracking and cellular barcoding.},
}

@article {pmid41836496,
year = {2024},
author = {Miller, DR and Jacobs, JT and Rockefeller, A and Singer, H and Bollinger, IM and Conway, J and Slot, JC and Cliffel, DE},
title = {Cultivation, chemistry, and genome of Psilocybe zapotecorum.},
journal = {Journal of psychedelic studies},
volume = {8},
number = {1},
pages = {63-81},
pmid = {41836496},
issn = {2559-9283},
abstract = {Psilocybe zapotecorum is a strongly blue-bruising psilocybin mushroom used by indigenous groups in southeastern Mexico and beyond. While this species has a rich history of ceremonial use, research into its chemistry and genetics has been limited. Herein, we report on mushroom morphology, cultivation parameters, chemical profile, and the full genome sequence of P. zapotecorum. First, we detail growth and cloning methods that are simple, and reproducible. In combination with high resolution microscopic analysis, the strain was identified by DNA barcoding, confirming the field identification. Full genome sequencing reveals the architecture of the psilocybin gene cluster in P. zapotecorum, and can serve as a reference genome for Psilocybe clade I. Characterization of the tryptamine profile revealed a psilocybin concentration of 17.9 ± 1.7 mg/g, with a range of 10.6-25.7 mg/g (n = 7), and similar tryptamines (psilocin, baeocystin, norbaeocystin, norpsilocin, aeruginascin, and 4-HO-tryptamine) in lesser concentrations for a combined tryptamine concentration of 22.5 ± 3.2 mg/g. These results show P. zapotecorum to be a potent and chemically variable Psilocybe mushroom. Chemical profiling, genetic analysis, and cultivation assist in demystifying these mushrooms. As clinical studies with psilocybin gain traction, understanding the diversity of Psilocybe expands the conversation beyond the molecule.},
}

@article {pmid41837206,
year = {2026},
author = {Kočárek, P and Fontana, P and Kočárková, I and Bonczek, V},
title = {A new cryptic species of Chelidurella Verhoeff, 1902 (Dermaptera, Forficulidae) from the Italian Alps: molecular evidence reveals hidden diversity in a high-altitude refugium.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {173-188},
pmid = {41837206},
issn = {1313-2989},
abstract = {The cryptic diversity within the earwig genus Chelidurella Verhoeff, 1902 remains underestimated despite growing evidence from molecular phylogenetic studies. During recent collecting efforts in the Adamello-Presanella Alps, a population of Chelidurella specimens that morphologically resemble C. mutica (Krauss, 1886) but exhibit distinct molecular divergence was discovered. Based on integrative taxonomic analysis combining molecular evidence with detailed morphological examination, Chelidurella maccagnoae Kočárek & Fontana, sp. nov. is described. Despite sharing the diagnostic shortened pygidium with C. mutica, phylogenetic analysis reveals that C. maccagnoae Kočárek & Fontana, sp. nov. is more closely related to the C. vignai / C. pseudovignai species complex, indicating convergent evolution of this character rather than shared ancestry. An updated identification key to Chelidurella males is provided and the biogeographic implications for understanding Quaternary diversification patterns in flightless Alpine arthropods discussed.},
}

@article {pmid41837210,
year = {2026},
author = {Ponce, P and Cevallos, V and Carrazco-Montalvo, A and Gallardo-Cóndor, J and Arévalo, V and Galarza, X and Coloma, J},
title = {An updated checklist of mosquitoes (Diptera, Culicidae) of Ecuador: new records and public health significance.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {67-136},
pmid = {41837210},
issn = {1313-2989},
abstract = {Mosquitoes are major vectors of human and animal diseases, making their accurate identification essential for vector surveillance and control. However, morphological identification has often been challenging, requiring taxonomic expertise and well-preserved specimens. Molecular markers, particularly DNA barcoding, offer an effective alternative for identifying both adult and immature stages. Ecuador is one of the most biodiverse countries in the world, a diversity that is also evident in its Culicidae fauna. This study provides a comprehensive revision of Ecuadorian mosquitoes, updating the national checklist and emphasizing species of public health importance. For species identification, an integrative approach was used combining morphology and DNA barcoding (COI and ITS2 regions). We list 266 species in 22 genera, of which 17 species are new national records, and 33 species are validated through molecular analysis. The updated checklist highlights Ecuador's Culicidae diversity across its biogeographic regions, which represent 7% of the world's mosquito diversity. These findings provide a critical foundation for future entomological research and vector control in the country.},
}

@article {pmid41822874,
year = {2026},
author = {van der Nol, E and Luo, Z and Gao, QQ and Haupt, NA and Böcker, S and Pomplun, S},
title = {Integration of palladium-catalyzed C-N coupling into self-encoded libraries for accelerated hit discovery.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {41822874},
issn = {2633-0679},
abstract = {Affinity screenings with encoded libraries are transformative tools for rapid hit discovery from vast compound collections. Yet the adaptation of established chemical reactions to DNA-encoded libraries (DELs) remains challenging due to DNA-compatibility constraints and mismatches between barcode and chemical structure in case of incomplete reactions or side product formation. Recently, we introduced self-encoded libraries (SELs) as a barcode-free alternative to DELs. The SEL platform offers unmatched flexibility in reaction conditions and decodes screening hits directly from their chemical structure, avoiding the problem of mismatched barcode-compound pairs. Here, we expand the SEL platform to Buchwald-Hartwig aminations, enabling the construction of new high diversity SELs. We performed a thorough reaction condition optimization and tested a scope of >170 different building blocks. We adapted our automated MS/MS-based decoding methodology SIRIUS-COMET to the resulting scaffolds, enabling accurate compound decoding from complex mixtures. A 25 725-member library was synthesized and screened all at once against carbonic anhydrase IX (CAIX), resulting in robust enrichment of hits with specific building block patterns and yielding several nanomolar-affinity binders. This work showcases the seamless integration of palladium-catalyzed cross-couplings into SELs, expanding the chemical space of this technology and accelerating hit discovery with high synthetic versatility.},
}

@article {pmid41823389,
year = {2026},
author = {Ogola, EO and Slothouwer, I and Rotich, G and Kopp, A and Bastos, ADS and Getugi, C and Melchert, J and Jones, TC and Omoga, DCA and Sang, R and Torto, B and Tchouassi, DP and Junglen, S},
title = {Identification and full genome sequencing of previously unknown sandfly-borne phleboviruses using a newly established capture-based next-generation sequencing approach.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0108225},
doi = {10.1128/jcm.01082-25},
pmid = {41823389},
issn = {1098-660X},
abstract = {Sandfly-borne phleboviruses cause febrile illness and neuroinvasive disease in humans. While infections are reported in the Mediterranean region, the discovery of previously unknown phleboviruses in sandflies from Kenya suggests a wider geographic distribution. Detection and characterization of novel phleboviruses are often hindered by low-quality and low-viral-load samples. We developed a capture-based target enrichment next-generation sequencing approach that showed a 99%-100% fold enrichment of viral genomes from primary material and provides a robust tool for generating complete genomes of both known and previously unknown viruses. From a collection of 15,652 sandflies in Kenya, we recovered seven complete coding sequences of Embossos, Bogoria, and Kiborgoch viruses, and of two previously unknown phleboviruses, which were named Sosoik and Shable viruses. Sosoik virus shared 83% amino acid identity in its RdRp gene with that of Bogoria virus, while Shable virus shared ca. 88% amino acid identity with viruses of the Salehabad serocomplex. Additionally, a reassortant of Shable virus was detected that possessed an M segment from an undescribed Ponticelli-like virus. DNA barcoding of blood-fed sandflies revealed several potentially novel Sergentomyia species and evidence of host-feeding on humans, livestock, and reptiles, suggesting possibilities for zoonotic transmission. Overall, our findings increase the known genetic diversity of Old World sandfly-borne phlebovirus species from 18 to 25 (by 38.9%), including the detection of viruses from all pathogenic sandfly-borne phlebovirus serocomplexes in East Africa, opening new horizons in disease ecology research.IMPORTANCEKnowledge of the genetic diversity of circulating pathogens is crucial for providing appropriate diagnostics and disease management. This study established a novel capture-based target enrichment next-generation sequencing approach that enabled the near-complete viral genome recovery from primary samples, while native NGS yielded negative or poor-quality results. In addition to the five recently discovered sandfly-borne phleboviruses in Kenya, two previously unknown phleboviruses were detected in sandflies from the same region. The viruses were detected in several sandfly species, which showed diverse host-feeding behaviors, including mixed feeding on humans and chickens. The study significantly advances the understanding of sandfly-borne phleboviruses by uncovering their broader geographic distribution and genetic diversity, particularly in East Africa, highlighting the importance of expanding surveillance efforts beyond traditionally studied regions.},
}

@article {pmid41823847,
year = {2026},
author = {Bunchom, N and Kongim, B and Manphae, A and Pilap, W and Andrews, RH and Tantrawatpan, C and Saijuntha, W},
title = {Morphological Differentiation Among Three Mitochondrial Lineages of Hydrobioides nassa Theobald, 1865 (Gastropoda: Bithyniidae) from Thailand.},
journal = {Biology},
volume = {15},
number = {5},
pages = {},
pmid = {41823847},
issn = {2079-7737},
support = {//Mahasarakham University/ ; },
abstract = {The identification of species complexes in freshwater snails remains challenging due to limited diagnostic morphological characters and incomplete taxonomic knowledge in many taxa. Within the family Bithyniidae, species have traditionally been classified using shell morphology and genital anatomy to distinguish intraspecific variation from interspecific differences. However, extensive morphological plasticity has hindered reliable species delimitation, and the presence of cryptic diversity further complicates taxonomy. Recent DNA barcoding studies of Hydrobioides have provided evidence of such cryptic diversity, highlighting the need for taxonomic reassessment within the genus. In the present study, we examined morphological variation in Hydrobioides nassa from Thailand in conjunction with mitochondrial DNA sequence data. Molecular phylogenetic analyses based on cytochrome c oxidase subunit I (cox1) sequences revealed three well-supported genetic lineages within H. nassa, accompanied by high levels of pairwise genetic divergence. Morphological comparisons of shell, operculum, and radular characters further supported differentiation among these lineages, although some characters showed overlap. While Hydrobioides has previously been regarded as comprising a single morphologically defined species, our results demonstrate that H. nassa represents a complex of genetically distinct lineages with subtle but consistent morphological differences. This study highlights the importance of integrating molecular approaches with traditional morphological analyses to improve taxonomic resolution and to better understand biodiversity within freshwater snail groups exhibiting cryptic diversity.},
}

@article {pmid41823851,
year = {2026},
author = {Lee, SJ and Lee, EY and Kim, BY and Lee, SR},
title = {DNA Barcoding for Herbarium Specimens of the Red Alga Meristotheca pilulaora and Molecular Marker Development for Species Identification.},
journal = {Biology},
volume = {15},
number = {5},
pages = {},
pmid = {41823851},
issn = {2079-7737},
support = {NFQS2026001//National Fishery Products Quality Management Service (Development and Management of Dis-ease Control Program for Aquatic Life)/ ; NIBR202602103//National Institute of Biological Resources (NIBR)/ ; },
abstract = {The genus Meristotheca (Gigartinales, Solieriaceae) comprises edible red algae that are economically important food ingredients in Korea, Japan, and China. In Korea, two species, Meristotheca coacta and Meristotheca papulosa, have been identified, with the latter being predominantly reported. Recently, molecular phylogenetic analysis enabled the identification of Meristotheca pilulaora (Gigartinales; Solieriaceae) on Jeju Island (Korea). In this study, we used a DNA barcoding method to re-examine M. papulosa herbarium specimens deposited at the National Institute of Biological Resources (Incheon, Korea). Specimens were collected from Korean coastal regions between 2009 and 2019. Molecular analyses based on the rbcL and cox1 sequences of the "M. papulosa" herbarium specimens revealed that the specimens were of two other species, M. pilulaora and Gracilaria textorii (Gracilariales; Gracilariaceae). Our work represents a case study for establishing a misidentification at the inter-ordinal level among herbarium specimens without DNA sequence verification. Moreover, we developed a molecular marker for the effective species-level identification of M. pilulaora and G. textorii specimens. The DNA barcoding method provides useful information regarding M. pilulaora distribution and taxonomy.},
}

@article {pmid41826340,
year = {2026},
author = {Lin, BA and Leung, KT and Han, W and Liu, M and Lam, VYY and Seymour, M},
title = {Biodiversity of Hong Kong purse seine fisheries: An integrated DNA barcode reference library.},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06981-2},
pmid = {41826340},
issn = {2052-4463},
abstract = {Here we present a multi-marker DNA barcoding library for Hong Kong marine fishes (Teleostei), cephalopods (Mollusca), and crustaceans (Arthropoda) frequently captured by purse seine fisheries. In total, 605 specimens were morphologically identified with 562 specimens sequenced and assigned to 185 fish species from 146 genera, 64 families, and 26 orders; 8 cephalopod species from 6 genera, 4 families and 4 orders (24 specimens); and 13 crustacean species from 10 genera, 5 families and 1 order (19 specimens). The barcode library includes mitochondrial cytochrome c oxidase subunit I (COI) and mitochondrial 12S ribosomal RNA (12S) barcodes for fishes, and COI and mitochondrial 16S ribosomal RNA (16S) barcodes for cephalopods and crustaceans. Specimens were assigned to species-level using integrated morphological and genetic assessment. The library represents the first barcode reference dataset for marine fishes, cephalopods and crustaceans from Hong Kong, increasing our knowledge of species diversity, enabling accurate identification of the three nekton groups and improving species identification reliability for eDNA metabarcoding studies in Hong Kong waters and the northern South China Sea.},
}

@article {pmid41832919,
year = {2026},
author = {Chai, MJ and Bogutskaya, NG and Reier, S and Friedrich, R and Rund, H and Wanzenböck, S and Wanzenböck, J and Glaser, F and Marcante, S and Prowatke, I and Jung, M and Mikschi, E and Palandačić, A},
title = {Data collected in a citizen scientist study uncover a new species record of Phoxinus minnow for Austria.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41832919},
issn = {1573-2959},
support = {SPSC_01_021//Federal Ministry of Women, Science and Research; Austria's Agency for Education and Internationalisation (OeAD); Sparkling Science 2.0/ ; SPSC_01_021//Federal Ministry of Women, Science and Research; Austria's Agency for Education and Internationalisation (OeAD)/ ; },
mesh = {Austria ; *Biodiversity ; *Environmental Monitoring/methods ; *Cyprinidae/classification/genetics ; Animals ; Citizen Science ; DNA Barcoding, Taxonomic ; Ecosystem ; },
abstract = {Freshwaters are among the most vulnerable ecosystems, yet the scarcity of biodiversity assessments prevents the detection of changes incurred by neobiota. Minnows of the genus Phoxinus were long thought to be represented by a single species in Eurasia, the common minnow P. phoxinus, but the genus now includes more than 25 valid species. However, their distributions do not follow drainage boundaries, there are known cases of human translocations, and morphological species assignation is difficult due to intra- and interpopulation phenotypic diversity. Hence, the species were delimited and are now determined mostly using molecular methods. In Austria, recent studies have identified at least four different species of Phoxinus, three of which are considered native and one introduced. However, more data were needed; thus, extensive collecting and DNA barcoding of minnow populations was undertaken with the help of recreational fishers, school pupils, and field biologists. DNA barcodes of museum specimens and environmental DNA collected from water samples were also included. Altogether, the genetic lineage of 258 new Phoxinus specimens was determined. The results confirmed the distribution of P. marsilii in eastern Austria, P. lumaireul in southern Austria and P. csikii in central and western Austria. Additional populations of the introduced P. phoxinus were identified. Most importantly, a new species record for Austria, P. cf. morella, was discovered, yet it is unclear whether its distribution in Austria is natural. This study also confirmed the potential of citizen science for biodiversity monitoring, with the number of specimens analyzed increasing fourfold in just two years.},
}

Austria
*Biodiversity
*Environmental Monitoring/methods
*Cyprinidae/classification/genetics
Animals
Citizen Science
DNA Barcoding, Taxonomic
Ecosystem

@article {pmid41820665,
year = {2026},
author = {Chen, D and Isakova, A and Wan, Z and Wagner, MJ and Wu, Y and Zhao, BS},
title = {Connectome-seq: high-throughput mapping of neuronal connectivity at single-synapse resolution via barcode sequencing.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41820665},
issn = {1548-7105},
abstract = {Understanding neuronal connectivity at single-cell resolution remains a fundamental challenge in neuroscience, with current methods particularly limited in mapping long-distance circuits and preserving cell type information. Here we present Connectome-seq, a high-throughput method that combines engineered synaptic proteins, RNA barcoding and parallel single-nucleus and single-synaptosome sequencing to map neuronal connectivity at single-synapse resolution. This adeno-associated virus-based approach enables simultaneous capture of both synaptic connections and molecular identities of connected neurons. We validated this approach in the mouse pontocerebellar circuit, identifying both established and potentially uncharacterized synaptic connections. Through integrated analysis of connectivity and gene expression, we identified molecular markers enriched in connected neurons, suggesting potential molecular determinants of circuit-specific connectivity. By enabling systematic mapping of neuronal connectivity across brain regions with single-cell precision and gene expression information, Connectome-seq provides a scalable platform for comprehensive circuit analysis across different experimental conditions and biological states.},
}

@article {pmid41819881,
year = {2026},
author = {Bhowmik, D and Rickard, JJS and Goldberg Oppenheimer, P},
title = {Advanced Real-Time, Non-Destructive Spectral Fingerprinting for Early microbial Spoilage Detection: AI-Integrated Raman Biosensing Platform for Scalable Food Safety and Quality.},
journal = {Food research international (Ottawa, Ont.)},
volume = {231},
number = {Pt 2},
pages = {118745},
doi = {10.1016/j.foodres.2026.118745},
pmid = {41819881},
issn = {1873-7145},
mesh = {*Food Safety/methods ; *Biosensing Techniques/methods ; *Food Microbiology/methods ; *Spectrum Analysis, Raman/methods ; Animals ; *Food Contamination/analysis ; Meat/analysis/microbiology ; Neural Networks, Computer ; Milk/microbiology/chemistry ; Food Quality ; },
abstract = {Food spoilage poses a global challenge, contributing to economic losses, food insecurity, and health risks from microbial contamination. Conventional detection methods are often destructive, time-consuming and ineffective at identifying early biochemical changes or stereospecific microbial by-products. We developed SkiNET-FoodSpec, a novel, non-invasive biosensor platform integrating biomolecular spectroscopy with an advanced self-organising map-based neural network (SkiNET) for rapid, real-time spoilage detection. The system achieves >93% classification accuracy across a range of food matrices, including meat, milk and leafy greens. It detects key spoilage markers, such as cadaverine in meat (LoD: 0.06875 mg/kg), D-/L-lactic acid enantiomers in milk (LoD:3 mmol/mL) and carotenoid and cellulose degradation in greens (LoD: 0.071 mg/kg). By generating matrix-specific spectral barcodes, SkiNET-FoodSpec identifies early spoilage prior to visible or olfactory cues. This advance in biotechnology enables intelligent, point-of-need diagnostics for food quality assurance, offering a powerful tool to enhance food safety, reduce waste and support resilient, sustainable food systems.},
}

*Food Safety/methods
*Biosensing Techniques/methods
*Food Microbiology/methods
*Spectrum Analysis, Raman/methods
Animals
*Food Contamination/analysis
Meat/analysis/microbiology
Neural Networks, Computer
Milk/microbiology/chemistry
Food Quality

@article {pmid41816200,
year = {2026},
author = {Srinivasan, P and Xian, PTZ and Tan Shu Ya, E and Ang, Y},
title = {A new species of Oriental-endemic Thalerosphyrus Eaton, 1881 (Ephemeroptera, Heptageniidae) from the Chinese Yunnan Oriental-Palaearctic transition zone and insights into cryptic diversity in the T. flowersi complex.},
journal = {ZooKeys},
volume = {1272},
number = {},
pages = {33-45},
pmid = {41816200},
issn = {1313-2989},
abstract = {The Ephemeropteran genus Thalerosphyrus Eaton, 1881 (Heptageniidae: Ecdyonurinae) is an Oriental-endemic genus hitherto comprising ten species, distributed from Sundaland to the Western Ghats of India and northeastern Indochina. Here, Thalerosphyrus lannaae sp. nov., belonging to the T. sinuosus group, is described from Yunnan Province (China), marking the northernmost record of the genus and extending its distribution into the Oriental-Palaearctic transitional zone. We also examined existing molecular data for T. flowersi, which revealed multiple deeply divergent lineages across India and Thailand, with the new species genetically closest to one of the Thai lineages. These findings highlight unrecognised cryptic diversity within the genus and underscore the need for taxonomic revision. An updated species key to Thalerosphyrus is provided. We discuss how larval preference for moderately cool, fast-flowing streams may explain the discovery of this tropically adapted Oriental-endemic genus in such high latitudes, and we explore the importance of transitional zones for aquatic insect diversity.},
}

@article {pmid41815967,
year = {2026},
author = {Thornval, NR and Lacy-Roberts, N and Rebelo, AR and Nilsson, P and Mourão, J and Gibson, C and Hasman, H and Hendriksen, RS},
title = {Optimization of nanopore sequencing for surveillance of antimicrobial resistance in low-resource settings.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1755877},
pmid = {41815967},
issn = {2296-2565},
mesh = {*Nanopore Sequencing/methods/economics ; Humans ; *Whole Genome Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Whole-genome sequencing (WGS) is emerging as a valuable tool for antimicrobial resistance (AMR) surveillance, yet implementation in low-resource settings remains limited by prohibitory costs and infrastructure constraints. Oxford Nanopore Technologies (ONT) offers portable sequencing platforms that can overcome these barriers, but optimal workflows for bacterial WGS are not fully standardized. We evaluated the impact of multiplexing level (12-, 24-, and 36-plex) and input DNA amounts (50 ng, 100 ng, and 200 ng) on sequencing performance using ONT's Rapid Barcoding Kit v14 and R10.4.1 flow cells. Sequencing success was defined as assemblies with ≥30 × depth of coverage, complete MLST assignment, and full AMR gene detection. Across nine run configurations, sequencing success was highest for 12-plex runs (92-100% success) and 24-plex runs (79-82% success) when using ≤100 ng DNA input. 36-plex configurations and high DNA input markedly reduced performance (as low as 2.8% success). Lower DNA input (50 ng) did not compromise outcomes and mitigated negative effects of multiplexing. Cost analysis showed per-sample costs decreased with higher multiplexing, but excessive batching compromised data quality. These findings support practical ONT workflows for decentralized AMR surveillance, recommending ≤24 samples per flow cell and ≤100 ng DNA input to balance cost-effectiveness and sequencing success in low-resource laboratory settings.},
}

*Nanopore Sequencing/methods/economics
Humans
*Whole Genome Sequencing/methods
*Drug Resistance, Bacterial/genetics

@article {pmid41815890,
year = {2026},
author = {Song, P and Su, J and Kristine Vraa, CL and Gockert, M and Fjelstrup, S and Hager, H and Kjems, J},
title = {Optimizing C14120-based LNPs for in vitro and in vivo mRNA delivery.},
journal = {Molecular therapy. Nucleic acids},
volume = {37},
number = {1},
pages = {102866},
pmid = {41815890},
issn = {2162-2531},
abstract = {Lipid nanoparticles (LNPs) have proven to be an effective delivery system for RNA therapeutics. The chemical composition of LNPs determines their functional delivery efficiency and targeting properties, which vary between in vitro and in vivo contexts. Here, we have systematically characterized and compared 25 novel C14120-based LNP formulations for mRNA delivery in vitro and assessed in vivo mRNA expression and biodistribution using deep sequencing of DNA barcodes in a pooled LNP-mRNA library. In vitro experiments showed correlations of lipid composition with particle size and mRNA transfection efficiency in 4 different cell lines of distinct tissue and species origin. In vivo experiments employed a pooled LNP delivery of luciferase mRNA in combination with a multiplexed barcode system and identified LNP compositions with organ-specific targeting properties. Individual validation of three selected LNP candidates based on mRNA expression analysis confirmed high specificity for the lung-targeting candidate, lower specificity for the liver-targeting candidate, and inconclusive results for the spleen-targeting candidate. These findings identify LNP formulations with promising potential for in vitro and in vivo organ-targeted delivery.},
}

@article {pmid41814093,
year = {2026},
author = {Jozić, A and Le Roux, C and Kim, J and Berchel, M and Sahel, DK and Bodi, EK and Palumbo, M and Vasudevan, A and Murthy, NTV and Eygeris, Y and Gautam, M and Bloom, E and Barnes, AP and Jaffrès, PA and Sahay, G},
title = {In vivo endosomal escape assay identifies mechanisms for efficient hepatic LNP delivery.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41814093},
issn = {1546-1696},
support = {HR0011-25-9-0008//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; R01EY033423//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; R01CA270783//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 2R01HL146736-06A1//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Endosomal escape is a central barrier to efficient nucleic acid delivery by lipid nanoparticles (LNPs) and remains challenging to quantify in vivo. We report a library of branched ionizable phospholipids that markedly enhance messenger RNA delivery to the liver. The lead candidate BiP-20 outperformed the clinical benchmark LP01 by eightfold for CRISPR-Cas9 editing of the TTR gene at low dose with rapid pharmacokinetics. To quantify the endosomal escape kinetics of BiP-20, we used LysoTag mice, which allow immunoisolation of liver lysosomes, and our Lysosomal Barcoding method, finding that ~8% of BiP-20 LNPs reach the cytosol within 30 min of administration. Lysosomal proteomics revealed mechanistic regulators of escape and BiP-20-induced alterations in endosomal maturation and recycling pathways. Loss of Rab7, a mediator of late endosomal maturation, increased LNP escape. These findings provide a potent class of ionizable lipids for RNA delivery, a method to quantify endosomal escape in vivo, and mechanistic insight into the endolysosomal determinants of LNP trafficking.},
}

@article {pmid41809908,
year = {2026},
author = {Ngo, DM and Vu, LT and Nguyen, HD and Vu, TTT and Chu, MH},
title = {Dataset of chloroplast DNA sequences, ndhC-trnV, rpoA, trnK-matK, and trnK-rps16 regions of Platycodon grandiflorus (Jacq.) A.DC. from Vietnam.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112627},
pmid = {41809908},
issn = {2352-3409},
abstract = {Platycodon grandiflorus (Jacq.) A.DC., a member of the Campanulaceae family, is a well-known medicinal herb traditionally used to relieve coughs, promote expectoration, reduce inflammation, and protect the respiratory system. In recent years, numerous commercial products containing Platycodon extracts have been introduced to the market. However, during processing and distribution, the morphological and anatomical features of the raw material are often lost or altered, increasing the risk of misidentification or adulteration with morphologically similar species, thereby compromising product quality and therapeutic efficacy. Therefore, the application of DNA barcode markers is essential for accurate species identification and quality control of raw materials. This study presents a dataset of P. grandiflorus samples collected from natural populations and analyzes four chloroplast DNA regions (ndhC-trnV, rpoA, trnK-matK, and trnK-rps16) to support species identification. Phylogenetic analysis based on these sequences revealed that P. grandiflorus is closely related to, and clusters within, the Campanulaceae family, with high bootstrap support values (96-100%). These four chloroplast regions are proposed as potential DNA barcodes for the reliable identification and differentiation of P. grandiflorus from related species.},
}

@article {pmid41808340,
year = {2026},
author = {Senjarini, K and Hasanah, LNU and Wathon, S and Oktarianti, R and Labes, A},
title = {Malaria Vector Surveillance in Indonesia: COX1 Phylogenetic Reveals Monophyletic Clades and Cryptic Diversity in Anopheles Mosquitoes.},
journal = {Journal of vector borne diseases},
volume = {},
number = {},
pages = {},
doi = {10.4103/jvbd.jvbd_331_25},
pmid = {41808340},
issn = {0972-9062},
abstract = {BACKGROUND OBJECTIVES: Anopheles mosquitoes are key malaria vectors, their high diversity influences transmission competence. Accurate species identification is crucial for understanding malaria epidemiology and implementing effective vector control strategies. The COX1 gene is a widely used DNA barcoding marker for Anopheles due to its high mutation rate and species-specific variations. This study evaluates the consistency of morphological and molecular identification using COX1, analyzes phylogenetic relationships, and explores the implications of these findings for malaria vector control strategies.

METHODS: Anopheles mosquitoes were collected from Bangsring, Banyuwangi, and Hargowilis, Kulonprogo, Indonesia, two geographically distinct sites with a history of malaria outbreaks. Mosquitoes were collected using human landing catches. Identification was performed morphologically and confirmed by molecular analysis based on COX1 sequences. Phylogenetic tree and genetic distances were analyzed in MEGA11 using the Neighbor-Joining method with the Kimura-2 Parameter model.

RESULTS: Morphological and COX1-based identification were mostly consistent; however, specimens identified as Anopheles (An.) aconitus and An. minimus from Hargowilis were molecularly confirmed as An. flavirostris. Phylogenetic analysis revealed eight monophyletic clades with strong bootstrap support (≥99% for six), confirming species groupings. Genetic distance analysis showed An. minimus from Hargowilis clustering more closely with An. flavirostris than with An. minimus from other Asian regions. The dominance of An. sundaicus (68%) in Bangsring and An. flavirostris (13%) in Hargowilis highlights the need for targeted vector control strategies.

INTERPRETATION CONCLUSION: Misidentification of cryptic Anopheles species may lead to ineffective vector control in specific epidemiological settings. Integrating molecular tools into malaria surveillance can support more accurate species identification and contribute to informed disease prevention strategies.},
}

@article {pmid41806682,
year = {2026},
author = {Park, SH and Na, JY and Kim, YR and Lee, H and Lee, JH and Yoon, JH and Jang, JW and Kim, MJ},
title = {Validating the Efficacy of archival microclimate proxies for indoor postmortem interval Estimation: A case study using Boettcherisca peregrina (Robineau-Desvoidy, 1830).},
journal = {Legal medicine (Tokyo, Japan)},
volume = {82},
number = {},
pages = {102831},
doi = {10.1016/j.legalmed.2026.102831},
pmid = {41806682},
issn = {1873-4162},
abstract = {Indoor death scenes challenge defensible estimation of the minimum postmortem interval (PMImin) because colonization delay, refrigeration, and poorly characterized microclimates often undermine transparency and reproducibility in medicolegal contexts. We report an indoor death investigation from Busan, Republic of Korea, in which post-feeding third-instar larvae of Boettcherisca peregrina (Diptera: Sarcophagidae) provided the principal entomological evidence. Species identity was confirmed by morphology and COI barcoding. Developmental age was estimated using an accumulated degree-hours (ADH)-only framework parameterized with species-specific constants (developmental zero, D0 = 10.87 °C). Larval thermal exposure was reconstructed using an archival indoor May temperature proxy (mean = 23.2 °C), with a ± 1 °C sensitivity envelope propagated across all calculations to reflect plausible room-scale variability. The body was removed from the scene on 16 May 2025 (∼15:00) and stored at ≤ 4 °C until autopsy on 19 May 2025 (09:00), arresting further development; thus, larval age refers exclusively to the pre-removal interval. Back-calculation from wandering-phase thresholds yielded a PMImin of 3.1-8.3 days across the ± 1 °C range. Expressed as calendar bounds, larviposition was estimated between 08 May 2025 (∼21:00) and 13 May 2025 (∼03:00 KST), with a nominal estimate of 09 May (∼12:00) to 11 May (∼01:00 KST) at 23.2 °C. These estimates are coherent with independent administrative anchors and the documented discovery-transfer-autopsy timeline. This report provides a reproducible workflow for indoor PMImin estimation that explicitly separates pre-removal development from refrigeration arrest and propagates indoor thermal uncertainty, thereby improving transparency and courtroom defensibility in constrained indoor scenes.},
}

@article {pmid41806198,
year = {2026},
author = {Iwahashi, N and Noguchi, T and Sakai, K and Yahata, T and Nishioka, K and Fujino, M and Takeda, S and Suzuki, N and Nishio, K and Ino, K},
title = {Comprehensive circulating tumor DNA mutation profiling via CAPP-Seq liquid biopsy for cervical cancer.},
journal = {International journal of clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {41806198},
issn = {1437-7772},
support = {20K18228//Japan Society for the Promotion of Science/ ; 23K08894//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Liquid biopsy using circulating tumor DNA (ctDNA) is a minimally invasive approach for detecting tumor-associated genomic alterations. Although ctDNA analysis has been widely explored in solid tumors, its application to cervical cancer remains limited. Cancer personalized profiling by deep sequencing (CAPP-Seq) enables sensitive ctDNA profiling via molecular barcoding and digital error suppression.

METHODS: We evaluated the feasibility of ctDNA-based mutation profiling in cervical cancer using the CAPP-Seq platform by analyzing plasma samples from 38 patients.

RESULTS: The cohort included three patients with stage I disease, nine with stage II, 19 with stage III, and seven with stage IV. Somatic gene alterations were detected in 33 of the 38 cases (87%), including squamous cell carcinoma (27/29 [93%]) and adenocarcinoma (6/9 [67%]). Non-synonymous mutations were identified in 23 patients (59%), with PIK3CA being the most frequently mutated gene [13/38 (34%)]. Copy number gains of EGFR, MET, and ERBB2 were observed in 24%, 11%, and 5% of cases, respectively. The median blood tumor mutational burden was 17.7 mutations/Mb, and 50% of the patients exhibited a hypermutated phenotype. In a subset of four patients who received concurrent chemoradiotherapy, longitudinal changes in ctDNA mutation profiles between pre- and post-treatment samples were associated with treatment response.

CONCLUSIONS: This study demonstrates the feasibility of ctDNA-based mutation profiling using CAPP-Seq in cervical cancer, with a high detection rate of tumor-associated genomic alterations across histological subtypes. ctDNA analysis may represent a minimally invasive approach for the molecular characterization and disease monitoring of cervical cancer.},
}

@article {pmid41806065,
year = {2026},
author = {Guerretti, V and Abd-Ellatif, MAA and Vangone, R and Cucolo, C and De Vivo, MM and Moustafa, AA and Guerriero, G and Mansour, SR},
title = {Bird diversity and health status of bioindicator species (Coturnix coturnix, Horsfield, 1821) in Egypt's Manzala Lagoon: seasonal resilience monitoring.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {4},
pages = {},
pmid = {41806065},
issn = {1573-2959},
mesh = {Animals ; Egypt ; *Biodiversity ; *Environmental Monitoring ; Wetlands ; Seasons ; *Birds/physiology ; DNA Damage ; },
abstract = {Manzala Lagoon, the largest coastal wetland of Egypt, lies within the Nile Delta and serves as an essential sanctuary for both resident and migratory birds. Despite its importance for regional biodiversity, the ecosystem faces significant anthropogenic pressures, with recent dredging activities constituting a major disturbance. This study aimed to evaluate dredging impacts on bird diversity and environmental health in the Ashtoum El-Gamil Protected Area. Seasonal monitoring in 2024, combining camera-based morphological identification with molecular barcoding of feathers (n = 13; cytochrome oxidase 1 gene), documented 123 species across 11 orders and 23 families, with 51 species consistently observed year-round. Health assessments in the endemic Coturnix coturnix (common quail) were conducted by measuring genotoxic damage, DNA repair capacity (via poly(ADP)-ribosylation), and total antioxidant capacity (TAC) in the gut, liver, and gonads. Results revealed reduced DNA recovery, elevated antioxidant capacity, and a prominent 40 kDa PARP immunoreactive band, particularly in gut and gonads. These oxidative stress indicators were independent of low heavy metal loads, implicating factors like rising temperatures may be the primary drivers. These findings highlight dredging's limited immediate effects on species diversity but underscore subtle health risks, advocating sustained, long-term monitoring and targeted management to safeguard wetland biodiversity.},
}

Animals
Egypt
*Biodiversity
*Environmental Monitoring
Wetlands
Seasons
*Birds/physiology
DNA Damage

@article {pmid41805294,
year = {2026},
author = {Anfang, M and Yahya, RH and Caldararu, O and Ben Yaakov, S and Landau, U and Berman, A and Hu, Y and Belew, ZM and Crocoll, C and Xu, D and Nour-Eldin, HH and Mayrose, I and Shani, E},
title = {Targeting redundant gene families: A multiplexed, tissue-specific CRISPR toolbox for Arabidopsis genetic screens.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117055},
doi = {10.1016/j.celrep.2026.117055},
pmid = {41805294},
issn = {2211-1247},
abstract = {Genome-scale targeted CRISPR libraries for forward genetic screens in plants are powerful tools for functional analysis, but they suffer from limited spatial control, single sgRNA design, and poor handling of genetic redundancy. We develop multiplexed CRISPR libraries in which each construct contains two sgRNAs that simultaneously target multiple members of a gene family. The libraries can also function at the cell-type-specific and tissue levels. A double-barcoding strategy enables efficient tracking and identification of sgRNA combinations at the plant level without individually sequencing each line. Using this platform, we generate over 1,000 Arabidopsis lines that express sgRNAs targeting 707 transporter genes across 114 gene families involved in nutrient uptake. The multiplexed design increases gene coverage and editing efficiency, underscoring its improved targeting capability to reveal hidden phenotypes. This toolbox provides a scalable resource for multi-targeted genome editing and spatially precise forward genetic screens in plants.},
}

@article {pmid41688672,
year = {2026},
author = {Di Batista Borko, Š and Grimm, J and Hahn, C and Takács, P and Greilberger, AM and Koblmüller, S and Sefc, KM},
title = {Habitat preferences and genetic diversity of the amphipod Gammarus roeselii across the Eastern Alps and western Pannonian Basin.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41688672},
issn = {2045-2322},
support = {FFT NP FTA, NP2022-II3/2022//Sustainable Development and Technologies National Program of the Hungarian Academy of Sciences/ ; C321069//Austrian Biodiversity Fund of the Federal Ministry of Agriculture and Forestry, Climate and Environmental Protection, Regions and Water Management of the Republic of Austria/ ; },
abstract = {UNLABELLED: Freshwater amphipods often exhibit cryptic diversity and are undergoing range shifts driven by environmental changes. Gammarus roeselii, a species inhabiting streams, rivers and lakes across Europe, diversified into ancient genetic lineages in the Balkan Peninsula and the Pannonian Basin, with only one lineage colonizing Central and Western Europe after the ice ages. We investigated the distribution and genetic diversity of G. roeselii by sampling over 1,000 sites across the eastern Alpine region and the Western Pannonian Basin. Cytochrome oxidase I barcoding assigned all sequenced G. roeselii (528 individuals from 174 sites) to the Central-Western European lineage. The occurrence of G. roeselii was associated with low elevation, high summer temperature and gentle stream and river slopes and was biased towards downstream reaches and rivers with large drainage sizes. Its distribution partially overlapped with G. fossarum, which predominates in cooler, faster-flowing streams. Species distribution modelling under future climate scenarios predicted a range expansion of G. roeselii into current G. fossarum habitat. Genetic diversity patterns are consistent with longstanding stable populations in the Southwestern Pannonian Basin, a post-glacial range expansion across alpine forelands, and recent colonization of some alpine valleys.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-39958-7.},
}

@article {pmid41805176,
year = {2026},
author = {Helsmoortel, M and Sentausa, E and Villain, A and Tran, V-D and Santiago-Allexant, E and Beaulieu, C and Hesketh, A and Abi-Ghanem, J and Leissner, P and Saliou, A},
title = {Oxford Nanopore enhanced accuracy of long-read amplicons applied to microbial whole-genome sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0285625},
doi = {10.1128/spectrum.02856-25},
pmid = {41805176},
issn = {2165-0497},
abstract = {The development of long-read sequencing technologies has enabled the analysis of extended nucleic acid sequences. These methods have proven their strength through their capacity to generate long reads, facilitating the analysis of complex genomic regions and rearrangements. Oxford Nanopore Technologies (ONT) offers a rapid and portable system that brings sequencing to the field. Although this is a great advantage for clinical settings, applications of long-read sequencing in this context have been limited by the high error rates reported for these methods. Here, we report an adaptation of an amplicon sequencing approach combined with unique molecular identifiers. We applied this method to whole-genome sequencing using mock community samples and human blood cultures spiked with common bloodstream infection pathogens. Our results showed a total error rate of <0.1% with V9 chemistry, which was further reduced by <0.05% when using the V14 chemistry. Our results also highlight the improvements of the V14 chemistry on the standard ONT ligation protocol and the importance of the basecalling tool for sequencing accuracy.IMPORTANCERecent advances in genome sequencing have greatly improved our ability to study microbes and detect infections. One such technology, Oxford Nanopore Technologies (ONT), can read long stretches of nucleic acids. ONT is also portable and can sequence in real time, making it useful in clinical settings. However, ONT accuracy is known to be lower than traditional short-read methods, limiting its widespread use. Fortunately, many strategies have emerged to overcome this limitation: better ONT chemistry, better basecaller, and hybrid approaches combining ONT with highly accurate short reads. Another promising method uses molecular barcodes or "Unique Molecular Identifiers" (UMIs) to make long reads at high accuracy, reaching accuracy levels similar to the existing short-read technologies. In our study, we optimized this UMI-based method and successfully applied it to human blood samples spiked with common infection-causing bacteria. The results showed a significant drop in ONT error rate, suggesting that this approach could make ONT a reliable tool for diagnosing infections and analyzing microbial DNA in clinical samples.},
}

@article {pmid41803893,
year = {2026},
author = {Andrus, PS and Han, QC and Yang, LM and Wade, CM and Qin, ZQ and Kassegne, K and Wu, XN and Guo, YH and Zhou, XN},
title = {Population genetic diversity of invasive Pomacea snails and surveillance of Angiostrongylus cantonensis in Shanghai, East China.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07224-w},
pmid = {41803893},
issn = {1756-3305},
support = {No. W2533202//National Natural Science Foundation of China/ ; TF2024012//Technology Innovation Support Program, NIPD, China CDC/ ; WSJK2024MS226//Hainan Province Health Technology Innovation Joint Project/ ; 2021YFC2300800//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Golden apple snails (Gastropoda: Ampullariidae: Pomacea) were introduced into China in the 1980s for aquaculture and have since become widespread agricultural pests across East Asia. In addition to their invasive impact, they are a key intermediate host of the rat lungworm Angiostrongylus cantonensis (Secernentea: Angiostrongylidae) in China, the causative agent of eosinophilic meningitis in humans.

METHODS: We conducted a malacological survey of 55 freshwater sites across Shanghai and neighboring East China provinces to assess Pomacea distribution, genetic diversity, and A. cantonensis infection status. A total of 700 Pomacea snails were examined for A. cantonensis using traditional lung microscopy and molecular xenomonitoring (PCR and LAMP). Mitochondrial COI barcoding was performed on 200 individuals from 20 high-density sites to assess species composition and genetic diversity.

RESULTS: Pomacea snails were found at 81.8% (45/55) of sites surveyed. No A. cantonensis infections were detected by microscopy or molecular assays. Genetic analyzes revealed three Pomacea species (P. canaliculata, P. maculata, and P. occulta) and nine distinct COI haplotypes. Pomacea canaliculata was the most common and genetically diverse species, with four unique haplotypes (H5-H8) occurring only in Shanghai, indicative of recent introductions. Overall, populations showed moderate haplotype diversity (Hd = 0.73) and population structure (FST = 0.24).

CONCLUSIONS: Although no A. cantonensis infections were detected in the snails examined in this survey, these negative findings do not preclude the possibility of low-prevalence or newly emerging infections. The wide distribution and high genetic diversity of Pomacea populations across Shanghai and East China highlight that suitable hosts are already well-established, emphasizing the ongoing risk of parasite introduction and spread into currently nonendemic regions. Continued molecular surveillance, public awareness, and strengthened biosecurity measures remain essential to effectively manage invasive snail populations and mitigate future public health threats.},
}

@article {pmid41801891,
year = {2026},
author = {Schoenefuss, P and Whatmore, P and Windell, C and Baker, AM and Hurwood, DA},
title = {Non-destructive environmental DNA extracted from owl pellet contents: A valuable tool for monitoring mammalian species richness.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344097},
pmid = {41801891},
issn = {1932-6203},
mesh = {Animals ; *Strigiformes/genetics ; *Biodiversity ; *DNA, Environmental/isolation & purification/genetics ; DNA Barcoding, Taxonomic ; *Mammals/genetics/classification ; Queensland ; },
abstract = {Environmental DNA (eDNA) offers valuable presence/absence data for populations and has been widely used in comprehensive biodiversity assessments. However, applying eDNA in terrestrial environments poses unique challenges, particularly in obtaining samples that are representative of ecological communities. eDNA extracted from top-predator dietary samples can be an effective sampling source in monitoring prey populations. In this study, we tested a novel, non-destructive protocol to assess the efficacy of eDNA from barn owl (Tyto javanica delicatula) pellets as a tool for monitoring small mammal communities in an arid environment. We assessed the species composition and abundance of small mammals from owl pellets collected in the Simpson Desert in far western Queensland, Australia, using a three-tiered approach. We extracted DNA from 50 owl pellets and targeted a 16S mini-barcode for metabarcoding. We compared species detection via genetic analysis with that of morphological analysis, and finally with historical small mammal trapping data. The DNA extraction method presented here resulted in full preservation of prey bones and fur material for museum archival. eDNA detected four mammal species that were not detected via morphological pellet analysis, three of which are significant detections that had not been observed at this location before but were expected to occur based on likely distribution ranges. However, a key limitation of the eDNA approach demonstrated in this study, is that taxonomic identification was constrained by the completeness of reference databases, which can result in false negatives or ambiguous assignments. The results of the present study demonstrate that the specificity of an eDNA approach can offer advantages compared with morphological identification of mammalian remains from owl pellets, and that genetic owl pellet analysis may be particularly useful in full vertebrate diversity assessments that include reptiles, birds and amphibians that are unidentifiable from skeletal remains.},
}

Animals
*Strigiformes/genetics
*Biodiversity
*DNA, Environmental/isolation & purification/genetics
DNA Barcoding, Taxonomic
*Mammals/genetics/classification
Queensland

@article {pmid41800390,
year = {2026},
author = {Pho, HTT and Nguyen, NTT and Sy, TD and Nguyen, QH and Chu, MH},
title = {Dataset on intergenic spacer sequences of the chloroplast genome and potential DNA barcodes of Adinandra glischroloma Hand.-Mazz. from Vietnam.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112606},
pmid = {41800390},
issn = {2352-3409},
abstract = {Adinandra glischroloma Hand.-Mazz. is a woody species of the genus Adinandra (Pentaphylacaceae), a taxonomic group in which species delimitation is often complicated by high morphological similarity. Moreover, genetic information for A. glischroloma is still scarce, limiting molecular identification and comparative studies. This article reports a dataset of nucleotide sequences from five chloroplast intergenic regions, namely rps15-ycf1, ndhF-rpl32, rpl32-trnL, accD-psaI, and petA-psbJ. These sequences were extracted from the chloroplast genome of A. glischroloma collected in Y Ty commune, Bat Xat district, Lao Cai province, Vietnam. The dataset includes voucher specimen images (AGYT03), the nucleotide sequences, fragment lengths, sampling metadata, and phylogenetic trees reconstructed separately for each intergenic region to facilitate phylogenetic interpretation within the order Ericales. These data provide a useful molecular resource for species identification, phylogenetic inference, and the evaluation of candidate DNA barcodes in Adinandra and related taxa.},
}

@article {pmid41800269,
year = {2026},
author = {Cohen, OR and Orange Kedem, R and Leites, L and Parizat, A and Jeffet, J and Laufer, L and Stern, S and Ebenstein, Y and Shechtman, Y},
title = {Compact Spectral Encoding Microscopy by Terrace Grating Optics.},
journal = {ACS photonics},
volume = {13},
number = {5},
pages = {1407-1416},
pmid = {41800269},
issn = {2330-4022},
abstract = {Spectral information is essential in microscopy, yet many multispectral imaging solutions require increased optical complexity or restrict the spectrum to a few discrete bands. In this work we introduce the Terrace grating optics family: flat, 3D-printable elements that provide continuous spectral encoding, as a plug-and-play add-on component to standard microscopes. The Terrace design preserves the illumination path in widefield operation and integrates trivially with other microscopy phase masks. We introduce two variants: a Single-order Terrace that concentrates energy into one diffraction order for high signal-to-noise ratio, and a Dual-order Terrace that adds a wavelength-independent reference spot, enabling robust color decoding. Using a Fourier-optics model, we show that the wavelength displacement is linearly controlled by the Terrace step-width and refractive-index mismatch. We validate the approach in two settings: snapshot decoding of four-color mRNA barcodes and multicolor NeuroPAL worm imaging with a single camera exposure and instantaneous color readout. Furthermore, we demonstrate continuous spectral and depth encoding masks yielding simultaneous depth and color readout via PSF shape, which remains compact and efficient. Terrace gratings thus offer a practical alternative to prisms and blazed gratings, enabling continuous multispectral encoding and straightforward integration with conventional microscopes.},
}

@article {pmid41800140,
year = {2026},
author = {Kasymova, U and Ulug, A},
title = {Genetic differentiation of morphologically similar polyploid wheat species.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20723},
pmid = {41800140},
issn = {2167-8359},
mesh = {*Triticum/genetics/classification ; *Polyploidy ; DNA, Plant/genetics ; Genetic Markers ; },
abstract = {BACKGROUND: Wheat is a globally important polyploid crop, with hexaploid bread wheat (Triticum aestivum L.) and tetraploid durum wheat (T. turgidum subsp. durum (Desf.) Husn.) as its main cultivated forms. Despite distinct end-use properties, these species are morphologically similar, making their identification difficult. Traditional phenotypic approaches often fail to resolve closely related polyploid wheats, emphasizing the need for a reliable molecular diagnostic and wheat barcoding strategy.

METHOD: This study developed and validated a multilocus molecular diagnostic framework for the discrimination of polyploid wheat species. The approach integrates plastid (rbcL, matK), nuclear ribosomal (ITS2, IGS), and nuclear-coding markers (Glu-1 and XDuPw167), all amplified using the Polymerase Chain Reaction. Validation was performed using ten experimental samples and 203 reference sequences retrieved from the NCBI GenBank database. We developed and validated a multilocus molecular diagnostic method for the reliable discrimination of wheat species.

RESULTS: Plastid loci showed limited variation, whereas the IGS region contained a diagnostic 71 bp insertion linked to the D genome, clearly distinguishing hexaploids from tetraploids. The Glu-1 and XDuPw167 loci exhibited genome-specific polymorphisms that further differentiated the two species. The multilocus diagnostic method achieved over 95% amplification success and consistent sequence profiles across replicates, confirming its accuracy and reproducibility.

CONCLUSIONS: The proposed molecular diagnostic method provides a reproducible, cost-effective, and high-resolution molecular diagnostic tool for reliable wheat species identification. By combining genome-specific nuclear and expressed sequence tag-simple sequence repeat (EST-SSR) markers, this approach establishes a robust and scalable system applicable to species authentication, seed purity testing, germplasm characterization, and genetic resource management.},
}

*Triticum/genetics/classification
*Polyploidy
DNA, Plant/genetics
Genetic Markers

@article {pmid41798179,
year = {2026},
author = {Shinoda, H and Fujita, H and Toyota, K and Nakano, T and Shimomura, M},
title = {A new species of Athelges (Crustacea, Isopoda, Epicaridea, Bopyridae) from Japan, with morphological and DNA barcode data.},
journal = {ZooKeys},
volume = {1270},
number = {},
pages = {207-222},
pmid = {41798179},
issn = {1313-2989},
abstract = {Athelges pileus sp. nov. is described as an abdominal bopyrid of the hermit crab Diogenes edwardsii collected from the Noto Peninsula, Japan. Athelges pileus sp. nov. is distinguished from its congeners by the following combination of characters. Female: head deeply sunk in thorax, anterolateral margin of head with pair of notches; anterior margin of frontal lamina concave; merus of pereopod 1 with broad and long projection ventrally; pereopods 5 and 6 with large gap between them; pleomeres 1-4 each with subovate biramous pleopods; each pleopod with peduncle, becoming smaller posteriorly; pleotelson with mushroom-shaped end. Male: pleon subovate with anal cone distally. The present species is the 14[th] member of the genus Athelges, and the second species from Asia. This is the second species of Athelges infesting Diogenes edwardsii. We also provide a partial sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene (658 bp), mitochondrial 16S rRNA gene (482 bp), and nuclear 18S rRNA (724 bp) as a DNA barcode for the species. We show by molecular phylogenetic analysis that the present species is distinct from A. takanoshimensis.},
}

@article {pmid41798178,
year = {2026},
author = {Estivals, G and Delgado-Barboza, R and Ruiz-Tafur, M and Chuctaya, J and Caminade, P and Garcia-Davila, C and Hubert, N},
title = {Assessing fish diversity in small streams and ponds of the Peruvian Amazon using environmental DNA metabarcoding.},
journal = {ZooKeys},
volume = {1270},
number = {},
pages = {349-365},
pmid = {41798178},
issn = {1313-2989},
abstract = {The Amazon basin harbors exceptional fish diversity, with more than 3,500 species reported. However, this biodiversity is increasingly threatened by anthropogenic activities and climate change. The Peruvian Amazon alone is home to nearly 1,000 freshwater fish species - approximately one-third of the entire Amazon - yet significant gaps remain in our understanding of their distribution, ecology, and conservation status. Molecular approaches, particularly environmental DNA (eDNA) metabarcoding, have emerged as promising alternatives for rapid and accurate biodiversity assessment. In this study, a metabarcoding workflow targeting a fragment of the 12S gene to eDNA samples collected from small streams and ponds near Iquitos, Peru, was applied to evaluate the applicability of this approach for local fish community inventories. Water from 12 sites was filtered, and DNA was extracted, amplified, and sequenced using high-throughput Illumina technology. Bioinformatic analyses included MOTU clustering, haplotype identification, and taxonomic assignment using the Lowest Common Ancestor (LCA) algorithm. A total of 226 amplicon sequence variants (ASVs) were identified, 95 of which were assigned to fish taxa and clustered into 44 MOTUs across four orders: Characiformes, Gymnotiformes, Siluriformes, and Cichliformes. The study highlights the effectiveness of eDNA metabarcoding in detecting both common and elusive species, while also highlighting current limitations due to incomplete DNA barcode reference libraries. These findings underscore the need to expand barcode databases to fully harness the potential of eDNA for monitoring Amazonian fish biodiversity and support its use as a valuable tool for inventorying fish communities in sensitive and understudied environments.},
}

@article {pmid41794966,
year = {2026},
author = {Moraes, SS and Machado, PA and Stanton, MA and Ancajima, GP and Yamaguchi, LF and Magaldi, LM and Kato, MJ and Freitas, AVL},
title = {Unveiling cryptic diversity: integrative taxonomy discovers eight new species of moths and exposes biodiversity shortfalls in a Neotropical region.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41222-x},
pmid = {41794966},
issn = {2045-2322},
support = {2021/02524-3, 2023/13856-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2021/13396-6; 2024/18838-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2024/01515-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/50316-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
}

@article {pmid41793313,
year = {2026},
author = {Yang, H and Shi, M and Cheng, Y and Zhang, W and Gui, B and Huang, R and Wang, Y and Xia, XQ},
title = {A Survey of the Species Origins of Common Fish Cell Lines-With a Particular Focus on the Grass Carp Ovarian Cell Line (GCO).},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70153},
doi = {10.1111/jfd.70153},
pmid = {41793313},
issn = {1365-2761},
support = {32473146//National Natural Science Foundation of China/ ; 2023YFD2401603//National Key R&D Program of China/ ; BRESG202306//Foundation of State Key Laboratory of Mariculture Biobreeding and Sustainable Goods/ ; 2023LZGC020//Key R&D Program of Shandong Province China/ ; 2024BBSA01//project of cross-disciplinary research team of the State Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture/ ; },
abstract = {Cell line misidentification or contamination undermines the reliability of research outcomes. In this study, we verified the species origin of commonly used fish cell lines, with a particular focus on the grass carp ovarian cell line (GCO). RNA-seq data from 146 samples of 11 widely used fish cell lines were collected from public databases (NCBI-SRA) and were mapped to the reference genomes of eight species. GCO RNA-seq samples from three Chinese laboratories showed a mapping rate of 21.64% ± 3.61% to the grass carp genome, but 89.81% ± 4.83% to the fathead minnow genome. Further transcriptomic similarity analysis revealed that these GCO RNA-seq samples clustered more closely with cell lines originating from fathead minnow. Targeted analysis of the COI gene amplification region confirmed that nearly all reads from GCO RNA-seq samples mapped exclusively to the fathead minnow COI amplicon. Collectively, these results indicate that GCO may have undergone cross-contamination or species misidentification. This study raises doubts about the true species origin of the GCO cell line and proposes that COI DNA barcoding can be used to discriminate the species origin of fish cell lines.},
}

@article {pmid41793301,
year = {2026},
author = {Li, H and Zhang, HY and Liu, S and Ye, HJ and Xu, CQ and Qiao, HL and Lu, PF},
title = {Sex pheromone of Carposina coreana (Lepidoptera: Carposinidae), a key pest of traditional Chinese medicinal plant Cornus officinalis: identification, field evaluation, and trap optimization.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70718},
pmid = {41793301},
issn = {1526-4998},
support = {//Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources (2060302)/ ; //The National Key R&D Program of China (2023YFC2604802)/ ; //The National Key Research and Development Program of China (2022YFC3501502)/ ; },
abstract = {BACKGROUND: Cornus officinalis is an important Chinese medicinal herb with high economic value. Carposina coreana Kim (Lepidoptera: Carposinidae) is a severe fruit-boring pest that inflicts devastating damage on C. officinalis. There is an urgent need to develop attractants to monitor and control this pest.

RESULTS: Using gas chromatography-mass spectrometry (GC-MS) and gas chromatography-electroantennogram detection (GC-EAD), we identified (Z)-7-eicosen-11-one and (Z)-7-tricosene as the female-produced sex pheromone components of C. coreana to attract its conspecific males. Field experiments showed that rubber septa dispenser baited with a blend of 1000 μg (Z)-7-eicosen-11-one and 500 μg (Z)-7-tricosene is the optimal lure formulation for attracting the male moths. Further experiments revealed that the most efficient traps are green Delta sticky traps, hung at 1.5-2.0 m aboveground from tree branches and ≈15-20 m from the forest edge. Finally, we validated the trap effectiveness in a 2-month monitoring survey conducted in three major C. officinalis production regions, and the identity of the captured insects was confirmed by DNA barcoding.

CONCLUSION: We identified the sex pheromone components of C. coreana, which provide technical support for the monitoring and control of this pest. Our findings establish a foundation for developing sustainable pest management strategies to improve C. officinalis production. © 2026 Society of Chemical Industry.},
}

@article {pmid41790309,
year = {2026},
author = {Habib, Z and Ijaz, S and Haq, IU and Afzal, I and Ali, GM},
title = {Identification of plastome-derived mini barcodes by DNA metabarcoding and comparative effectiveness to decipher their strength and resolving power for taxonomic topology-based phylogenetic determination of Chenopodium quinoa.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41790309},
issn = {1573-4978},
}

@article {pmid41788591,
year = {2026},
author = {Yang, Y and Yang, D and Shi, M and Huang, Z and Zhang, X and Zheng, D and Chu, T and Ma, W},
title = {Development of a MIRA-CRISPR/Cas12a-based nucleic acid detection system for the discrimination of Panax ginseng and Panax quinquefolium.},
journal = {Journal of ginseng research},
volume = {50},
number = {2},
pages = {100923},
pmid = {41788591},
issn = {1226-8453},
abstract = {BACKGROUND: Accurate identification of closely related herbal species is essential for ensuring the safety, efficacy, and authenticity of traditional Chinese medicine (TCM) products. Panax ginseng (PG) and Panax quinquefolium (PQ) are two widely used ginseng species with similar morphological characteristics but distinct pharmacological profiles and market values.

METHODS: We developed a nucleic acid detection platform that integrates multienzyme isothermal rapid amplification (MIRA) with CRISPR/Cas12a-based fluorescence or lateral flow assay (LFA) for the rapid discrimination of PG and PQ. By targeting highly divergent mitochondrial gene regions, we designed species-specific crRNAs that enabled precise identification of PG and PQ with high sensitivity and specificity.

RESULTS: By optimizing the conditions, the system can effectively distinguish PG and PQ, with a fluorescence detection limit of 10[-4] ng/μL and a LFA detection limit of 10[-3] ng/μL. It was also validated using 29 commercial samples including complex Chinese medicines. Compared with traditional DNA barcoding, the MIRA-CRISPR/Cas12a system demonstrated superior performance in detecting mixed or processed herbal products.

CONCLUSION: This method offers a promising solution for point-of-care testing (POCT) in TCM quality control and provides a foundation for broader applications of CRISPR-based molecular authentication in herbal medicine.},
}

@article {pmid41787016,
year = {2026},
author = {Zhanybekova, Z and Bayanbay, S and Danilova, A and Imanbayeva, A and Kakimzhanova, А},
title = {Micropropagation and ex vitro acclimatization of Lonicera caerulea var. altaica: molecular identification and protocol optimization.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-43068-9},
pmid = {41787016},
issn = {2045-2322},
support = {No. BR21882166//Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
}

@article {pmid41785259,
year = {2026},
author = {Mahjabin, M and Datta, SK and Labib, AF and Akhter, S and Antu, DR and Ahmed, MS},
title = {DNA-based characterization of rays (Elasmobranchii: Batoidea) from Bangladesh using mitochondrial markers: Implications for conservation and management.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344352},
pmid = {41785259},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Skates, Fish/genetics/classification ; *Conservation of Natural Resources ; *DNA Barcoding, Taxonomic/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *DNA, Mitochondrial/genetics ; Genetic Markers ; Electron Transport Complex IV/genetics ; },
abstract = {Rays are an iconic group of chondrichthyan fishes, with many species currently threatened with extinction. Although conservation laws exist in Bangladesh to protect their population, lack of comprehensive law enforcement strategies together with commercial exploitation and habitat destruction resulted in population decline of many species nonetheless. One significant challenge to this conservation effort is a rapid and authentic species identification strategy, as traditional morphological diagnosis is hindered by frequent misidentification, especially when species are morphologically similar or when specimens are damaged or missing key features. The emergence of DNA barcoding technique can overcome this barrier, requiring only a small tissue sample for authentic identification. In the present study, this state-of-the-art technique has been employed for species identification of rays using three different mitochondrial marker gene, namely 16s rRNA, COI, and NADH2. A total of 94 new barcode sequences were generated, including 43 COI, 31 16S rRNA, and 20 NADH2 sequences, representing 23 ray species across 15 genera, 9 families, and 3 orders. Mean genetic distances varied across markers: for COI, 0.23 within species, 7.60 within genera, and 17.34 within families; for 16S rRNA, 0.04, 5.49, and 8.72, respectively; and for NADH2, 0.22, 13.52, and 20.72, respectively. Based on genetic divergence, barcode gap, and phylogenetic resolution, NADH2 proved to be a valuable alternative marker to COI for species-level identification. In contrast, 16s rRNA displayed the lowest divergence limiting its discriminatory power for species-level identification. Approximately 82.61% of our recorded species are categorized as different threatened categories (CR, EN, VU, NT) under the IUCN Global Red List. However, only 4 species are listed in CITES Appendix II for protection, leaving the majority of the ray species vulnerable for exploitation. Furthermore, several Schedule I and II species under Bangladesh Wildlife Act are openly traded in domestic market despite their supposed protection. This study highlights the urgent need to raise awareness among fishing communities and to strengthen measures against this illegal trade of ray species listed under national wildlife protection schedules.},
}

Animals
Bangladesh
*Skates, Fish/genetics/classification
*Conservation of Natural Resources
*DNA Barcoding, Taxonomic/methods
Phylogeny
RNA, Ribosomal, 16S/genetics
*DNA, Mitochondrial/genetics
Genetic Markers
Electron Transport Complex IV/genetics

@article {pmid41783569,
year = {2026},
author = {Kim, IH and Hwang, UW},
title = {Morphology and mitochondrial genome-based analysis of the systematics and evolution of Acanthochitona species (Polyplacophora: Acanthochitonidae).},
journal = {Marine life science & technology},
volume = {8},
number = {1},
pages = {49-67},
pmid = {41783569},
issn = {2662-1746},
abstract = {Chitons, known as marine living fossils, have retained their ancestral traits for approximately 300 million years. The genus Acanthochitona (Polyplacophora: Acanthochitonidae), characterized by the presence of 9 pairs of sutural tufts on a well-expanded girdle, is distributed across the intertidal zones of South Korea, Japan, China, and the Indo-Pacific. This study examined five Acanthochitona species from South Korea: A. achates, A. circellata, A. defilippii, A. rubrolineata, and A. feroxa sp. nov. Their mitochondrial genome sequences ranged from 14,986 to 15,006 bp in length and with a gene content typical for Polyplacophora. Genetic (including a transitive consistency score [TCS] genetic network), principal coordinate, phylogenetic network, and CO1-based barcoding gap analyses confirmed a new species, A. feroxa sp. nov., which exhibited morphologically distinct dorsal spicules and radulae. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed based on the CO1 sequences of 28 polyplacophoran species belonging to 9 families, which placed these five Acanthochitona species within a monophyletic family, Acanthochitonidae. The analyses also indicated the polyphyletic nature of Mopaliidae, recommending a reclassification. Divergence time estimation revealed that Acanthochitona deviated during the Late Cretaceous (ca. 83.94 mya), with continued speciation occurring in the Paleogene and Neogene periods. Additionally, we constructed a pictorial key based on the ML tree for morphologically identifying the five Acanthochitona species. This study contributes to the understanding of speciation and phylogenetic relationships within the Acanthochitonidae, offering valuable insights into the classification scheme and mitochondrial genome evolution of chitons in the western Pacific.},
}

@article {pmid41779816,
year = {2026},
author = {Golchini, MM and Soorni, A},
title = {Structural and phylogenetic insights from complete chloroplast genomes of seven Vicia species.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0340630},
pmid = {41779816},
issn = {1932-6203},
mesh = {*Genome, Chloroplast ; *Phylogeny ; Evolution, Molecular ; Genomics ; High-Throughput Nucleotide Sequencing ; },
abstract = {The legume genus Vicia L. (Fabaceae) is of significant ecological and agronomic importance, comprising species widely utilized as forage crops, green manure, and sources of valuable phytochemicals. Despite this, a comprehensive genomic understanding of many species, particularly those endemic to underrepresented regions like Iran, remains limited. To address this, we employed a high-throughput sequencing and comparative genomics approach to elucidate the chloroplast (cp) genome architecture and evolutionary relationships of seven previously uncharacterized Iranian Vicia species including V. hirsuta, V. hybrida, V. lathyroides, V. lutea, V. narbonensis, V. peregrina, and V. villosa. Total genomic DNA was sequenced on an Illumina HiSeq 2000 platform, and the cp genomes were assembled de novo using GetOrganelle, followed by comprehensive annotation with a suite of bioinformatic tools. The analysis revealed considerable size variation, ranging from 118,660-130,223 bp, and a key structural divergence involving the loss of one inverted repeat (IR) region in six species, consolidating their placement within the IR-lacking clade (IRLC), while V. villosa retained the ancestral quadripartite structure. Lineage-specific gene losses were documented, including accD in V. lathyroides and ycf2 in V. narbonensis. Microsatellite analysis identified a predominance of A/T-rich mononucleotide simple sequence repeats (SSRs), with V. hybrida exhibiting the highest SSR density. Nucleotide diversity (Pi) analysis across coding regions identified clpP (Pi = 0.19772) and ycf1 (Pi = 0.16964) as hypervariable loci, while the ribosomal protein genes rps7 and rpl20 were validated as highly effective phylogenetic barcodes. Maximum likelihood phylogenetic reconstruction, based on a concatenated alignment of 86 shared protein-coding genes, resolved the species into well-supported clades, providing a robust evolutionary framework. This study delivers essential genomic resources that deepen the understanding of cp genome evolution in the IRLC and provides powerful molecular tools for future research in Vicia systematics, conservation genetics, and precision breeding.},
}

*Genome, Chloroplast
*Phylogeny
Evolution, Molecular
Genomics
High-Throughput Nucleotide Sequencing

@article {pmid41779717,
year = {2026},
author = {Sarkar, I and Sarkar, KR},
title = {Pre-analytical errors in a high-volume Bangladeshi diagnostic centre: Prevalence, workload impact, and mitigation strategies.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0341908},
pmid = {41779717},
issn = {1932-6203},
mesh = {Bangladesh/epidemiology ; Humans ; *Workload/statistics & numerical data ; Cross-Sectional Studies ; Prevalence ; *Diagnostic Errors/statistics & numerical data/prevention & control ; *Laboratories, Clinical/standards ; },
abstract = {BACKGROUND: Pre-analytical errors are the most frequent cause of laboratory mistakes, accounting for nearly half of all diagnostic inaccuracies worldwide. These errors can invalidate test results, delay clinical decisions, and waste valuable healthcare resources, particularly in resource-limited, high-volume diagnostic laboratories. This study aimed to assess the prevalence, contributing factors, and severity of pre-analytical errors in a large diagnostic centre in Bangladesh.

METHODS: An observational, cross-sectional study was conducted over two months in the Biochemistry and Immunology Laboratories of a high-volume diagnostic centre in Dhaka, Bangladesh. Data from 195 documented pre-analytical errors and a structured survey of 27 laboratory staff were analysed. Errors were classified into minor, moderate, or major using definitions adapted from ISO 15189:2022 and WHO guidelines. Descriptive statistics and Chi-square tests were performed to explore associations between workload level (≥ 931 samples/day) and error frequency, with p < 0.05 considered statistically significant.

RESULTS: The most frequent errors were sample misplacement (38.5%) and incorrect labelling (17.9%). The sample collection (42.6%) and pick-and-drop (38.5%) units contributed the majority of errors. Morning shifts (65.1%) and high-workload days (70.8%) showed higher error frequencies, with a statistically significant association between workload and error occurrence (χ² = 121.093, p < 0.001). Major errors accounted for 37.4% of incidents.

CONCLUSION: Pre-analytical errors remain a critical threat to diagnostic accuracy in resource-limited laboratories. Improving workflow organization, implementing barcoding and automation, and strengthening staff training and workload management can substantially reduce error rates and enhance patient safety in high-throughput clinical settings.},
}

Bangladesh/epidemiology
Humans
*Workload/statistics & numerical data
Cross-Sectional Studies
Prevalence
*Diagnostic Errors/statistics & numerical data/prevention & control
*Laboratories, Clinical/standards

@article {pmid41778278,
year = {2026},
author = {Akhlaghi, AA and Sakib, S and MacLachlan, R and Manek, J and Osman, E and Saxena, S and Heydarian Dolatabadi, E and Gu, J and Li, Y and Soleymani, L},
title = {Motorized DNAzymes Drive Enhanced Electrochemical Biosensing for Rapid Bacterial Detection.},
journal = {Small methods},
volume = {},
number = {},
pages = {e01072},
doi = {10.1002/smtd.202501072},
pmid = {41778278},
issn = {2366-9608},
support = {//Canada Research Chairs/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Self-propelled micromotors hold great promise for improving the performance of electrochemical biosensors by overcoming mass transport limitations inherent to target recognition on electrode surfaces. However, the successful integration of micromotors in electrochemical biosensors for the analysis of crude biological samples has remained elusive. In this study, we introduce the Motolyzer, a micromotor-based assay that utilizes DNAzymes for the identification and detection of bacterial targets in crude biological samples. In this system, immobilized DNAzymes are propelled by magnetic-layered micromotors within biological samples. Upon encountering their specific targets, these DNAzymes release redox DNA barcodes, which are subsequently analyzed using electrochemical chips. The Motolyzer significantly enhances the target-to-blank ratio of the biosensor (4.5 times) and achieves a limit-of-detection of 2 × 10[4] CFU mL[-1] for Legionella pneumophila, a slow-growing bacterium, within 1 h, thereby eliminating the need for bacterial culture. Notably, the Motolyzer exhibits high specificity against non-target bacterial strains as well as non-bacterial metabolites, establishing it as a reliable, rapid assay for the identification of specific bacteria in crude biological samples. The versatility of this approach opens promising avenues for the rapid detection of various pathogens and biomarkers in both clinical and environmental settings.},
}

@article {pmid41777690,
year = {2026},
author = {Ivanova, NV and Watson, LC and Comte, J and Bessonov, K and Abrahamyan, A and Crevecoeur, S and Watson, SB},
title = {Rapid assessment of phytoplankton assemblages using Next Generation Sequencing and Barcode of Life Data System: a widely applicable HAB-ID toolkit for detecting and monitoring biodiversity loss and harmful algal blooms.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20747},
pmid = {41777690},
issn = {2167-8359},
mesh = {*Harmful Algal Bloom ; *Phytoplankton/genetics/classification ; *High-Throughput Nucleotide Sequencing/methods ; *Cyanobacteria/genetics/classification ; *Biodiversity ; *DNA Barcoding, Taxonomic/methods ; *Environmental Monitoring/methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Harmful algal blooms have important implications for the health, functioning, and services of aquatic ecosystems. Our ability to detect and monitor these events is often challenged by the lack of rapid and cost-effective methods to identify bloom-forming organisms and their potential for toxin production. Here, we developed and applied a combination of DNA barcoding and Next Generation Sequencing (NGS) for the rapid assessment of phytoplankton community composition with a focus on two important indicators of ecosystem health: toxigenic bloom-forming cyanobacteria and impaired planktonic biodiversity. To develop this molecular toolset for identification of cyanobacterial and algal species present in HABs (harmful algal blooms), hereafter called HAB-ID, we achieved three goals: creating a validated reference database, optimizing molecular protocols, and developing original bioinformatics pipeline tailored to uncertainty of algal taxonomy. The BOLD (Barcode of Life Data System) 16S reference database from cultures of 211 cyanobacterial and algal strains representing 102 species with particular focus on bloom and toxin producing taxa was constructed with Sanger sequencing and further refined using Single Molecule Real Time Sequencing (SMRT-sequencing). Using the new reference database of 16S rDNA sequences and constructed mock communities of mixed strains for protocol validation, we developed new NGS primer sets which can recover 16S from both cyanobacteria and eukaryotic algal chloroplasts. We also developed DNA extraction protocols for cultured algal strains and environmental samples, which match commercial kit performance and offer a cost-efficient solution for large scale ecological assessments of harmful blooms while giving benefits of reproducibility and increased accessibility. Our innovative bioinformatics pipeline was designed to handle low taxonomic resolution for problematic genera of cyanobacteria such as the Anabaena-Aphanizomenon-Dolichospermum complex, two clusters of Anabaena (I and II), Planktothrix and Microcystis. This newly developed HAB-ID toolset was further validated by applying it to assess cyanobacterial and algal composition in field samples from waterbodies with recurrent HABs events.},
}

*Harmful Algal Bloom
*Phytoplankton/genetics/classification
*High-Throughput Nucleotide Sequencing/methods
*Cyanobacteria/genetics/classification
*Biodiversity
*DNA Barcoding, Taxonomic/methods
*Environmental Monitoring/methods
RNA, Ribosomal, 16S/genetics

@article {pmid41777528,
year = {2025},
author = {Fola, AA and Mehra, S and Razook, Z and Lautu-Gumal, D and Nate, E and Lee, S and Kattenberg, JH and Koepfli, C and Kazura, J and Ome-Kaius, M and Laman, M and Robinson, LJ and Mueller, I and Barry, AE},
title = {Population genetics of Plasmodium vivax with transmission decline and rebound in two endemic areas of Papua New Guinea.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1621920},
pmid = {41777528},
issn = {1664-8021},
abstract = {BACKGROUND: Global efforts to control and eventually eliminate malaria have been less effective for Plasmodium vivax relative to Plasmodium falciparum due to its unique biology, including dormant liver stages that cause later relapse, and earlier commitment to transmission stages. After the nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG), P. vivax initially reduced to low prevalence, but again resurged to levels similar to those before LLIN distributions.

METHOD: To explore changes in P. vivax population structure and identify sources of resurgence over this period, we applied a previously validated genome-wide SNP barcode to genotype 336 P. vivax isolates obtained from serial cross-sectional surveys conducted over a decade in East Sepik (2005, 2012, 2016) and Madang Province (2006, 2010, 2014).

RESULTS: Population genetic analyses of the resulting parasite genotypes revealed contrasting spatiotemporal patterns between the two provinces. In Madang, the complexity of infection, genetic diversity, and population structure varied with prevalence, with a possible population bottleneck and early clonal expansion at low transmission, and rapid recovery of the population with resurgence. In East Sepik, there was a less dramatic impact on the parasite population after prevalence decline, and ongoing transmission of multiple residual lineages throughout the study period. P. vivax decline was also accompanied by an increase in genetic differentiation between the two areas, which reduced with resurgence suggesting changes in parasite migration between areas associated with prevalence.

CONCLUSION: The earlier implementation of LLIN in East Sepik, smaller rebound, heterogeneity in transmission and relative isolation, compared to Madang may have contributed to these differing patterns. The results demonstrate that long term sustained control efforts are essential to make a lasting impact on the P. vivax population, and that SNP barcodes can provide valuable insights into parasite transmission dynamics as a result of control efforts.},
}

@article {pmid41776385,
year = {2026},
author = {Malamon, JS},
title = {DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41776385},
issn = {1471-2105},
abstract = {DNA N-gram analysis methodologies have been successfully deployed to provide a wide range of elegant solutions to a variety of complex problems in bioinformatics, such as sequence alignment, DNA barcoding, the identification of functional gene elements, the analysis of microbial genomes, the characterization of protein structures, and the detection of DNA sequence artifacts. Because biological DNA contamination is ubiquitous and therefore unavoidable, it has a significant impact on genomics and genetics research, posing substantial challenges in population genotype calling quality, model organism research, proteomics, and clinical gene therapies such as recombinant adeno-associated viral vector preparations. To this end, I present DNASCAN, DNA Sequence Contamination Analyzer, a scalable and efficient algorithm designed for the high-resolution detection of biological contaminants within source DNA sequences. DNASCAN leverages N-gram analysis, supervised random forest classification, and Bayesian change-point detection to provide precise breakpoints and highly accurate impurity estimates. In summary, DNASCAN yielded 100% purity estimates and breakpoint detection accuracy rates at bacterial contamination levels above 0.1%. Using long-read sequencing data, DNASCAN detected all impurity levels above 0.025%, making it ideal for the removal and reconstitution of contaminated DNA sequences. The software, documentation, and vignettes with detailed code demonstrations are available at https://github.com/jmal0403/DNASCAN/wiki.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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