@article {pmid40472750,
year = {2025},
author = {Fogt-Wyrwas, R and Dabert, M and Jarosz, W},
title = {DNA barcoding shows that Toxocara cati infecting domestic and wild felids is a species complex.},
journal = {Veterinary parasitology},
volume = {338},
number = {},
pages = {110514},
doi = {10.1016/j.vetpar.2025.110514},
pmid = {40472750},
issn = {1873-2550},
abstract = {The insufficient attention paid to the importance of Toxocara cati in the epidemiology of toxocariasis has resulted in significant gaps in the understanding of the true zoonotic potential of this parasite. Therefore, further research is necessary to understand its biology and epidemiology. In this article, the hypothesis of possible speciation in the T. cati complex was tested using cox1 sequences from T. cati individuals infecting domestic and wild felids from different parts of the world. Using DNA barcoding, a phylogenetic analysis was performed that grouped T. cati representatives into five clades according to the host species. The differences in cox1 sequences between T. cati from domestic cats and T. cati from wild felids were substantial (6.68 %-10.84 %). The results of the Assemble Species by Automatic Partitioning analysis supported the species status of the clades. However, the determination of the actual species diversity of the T. cati complex would necessitate an analysis of a wider range of wild hosts. A detailed understanding of the genetic diversity and phylogenetic relationships between species in the T. cati complex will contribute to more accurate identification, diagnosis and better control of these parasites.},
}

@article {pmid40472314,
year = {2025},
author = {, },
title = {Correction: DNA Barcode, chemical analysis, and antioxidant activity of Psidium guineense from Ecuador.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0326074},
doi = {10.1371/journal.pone.0326074},
pmid = {40472314},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0319524.].},
}

@article {pmid40465191,
year = {2025},
author = {Tenge, BN and Muiru, WM and Kimenju, JW and Linguya, SK and Schwake-Anduschus, C and Amata, RL and Onyango, LO},
title = {Cultural and molecular identification of fungal genera and species occurring in maize : Fungi genera and species found in maize.},
journal = {Mycotoxin research},
volume = {},
number = {},
pages = {},
pmid = {40465191},
issn = {1867-1632},
support = {323-06.01-03-2816PROC11//German Federal Ministry of Food and Agriculture (BMEL)/ ; 323-06.01-03-2816PROC11//German Federal Ministry of Food and Agriculture (BMEL)/ ; 323-06.01-03-2816PROC11//German Federal Ministry of Food and Agriculture (BMEL)/ ; 323-06.01-03-2816PROC11//German Federal Ministry of Food and Agriculture (BMEL)/ ; },
abstract = {Mycotoxins contribute to a substantial loss of global maize grain yields in terms of tonnes. However, in sub-Saharan Africa, screening of mycotoxin-producing fungi predominantly relies on culture-based methods, which are both time-consuming and labour-intensive. This study examined the major fungal species responsible for aflatoxin production in major maize-producing regions of Kenya using molecular techniques. Maize samples were collected from Kilifi, Makueni, and Kisumu counties. For fungal isolation followed by molecular identification targeting the internal transcribed spacer region (ITS) for Fusarium and calmodulin (CaM) genes for Aspergillus, Penicillium, and Trichoderma, this was followed by basic local alignment search tool (BLAST) analysis. The study revealed 14 fungal species belonging to four genera namely Aspergillus, Penicillium, Fusarium, and Trichoderma. Kisumu County had the highest diversity of fungal species, representing 47.8% of the total identified. Within Kisumu, Penicillium species were the most prevalent, with an incidence rate of 72.9%. In contrast, Aspergillus species were most common in Kilifi County (54.5% incidence). The application of DNA barcoding techniques significantly enhanced the precision of identifying aflatoxin-producing fungi compared to conventional identification methods. This study confirms the presence of multiple fungal species responsible for aflatoxin production in Kenya's maize-growing regions.},
}

@article {pmid40464340,
year = {2025},
author = {Wang, Q and Wang, C and Fang, Z and Zhang, Z and Zhao, Y and Ma, T and Shang, L},
title = {Hydroxypropyl Cellulose Assembled Microspheres as Structural Color Barcodes from Revolving Microfluidics.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e06556},
doi = {10.1002/advs.202506556},
pmid = {40464340},
issn = {2198-3844},
support = {2024YFA0919100//National Key Research and Development Program of China/ ; 32271383//National Natural Science Foundation of China/ ; },
abstract = {Optical barcodes are versatile information carriers widely applied for encryption, commercial anti-counterfeiting, and biomedical fields. Hydroxypropyl cellulose (HPC), as a natural derivative, exhibits excellent biocompatibility and can self-assemble into cholesteric liquid crystals (CLCs) with structure color. However, the high viscosity of HPC CLCs is a huge hurdle for material processing and thus limits their applications. In this study, a high-speed revolving microfluidic platform is developed for emulsifying high-viscosity methacrylate functionalized HPC (HPC-MA) solution to form droplets. HPC-MA molecules in the droplets can self-assemble into CLCs by water evaporation, and the resultant CLCs droplets can be cross-linked to form structural color barcode particles. The prepared HPC-MA CLCs barcoded particles exhibit well-defined and adjustable encoding information while maintaining excellent biocompatibility. Furthermore, the prepared barcode particles also demonstrate great potential in 3D cell culture and multiplex immunoassays. This work introduces an efficient way to continuously produce HPC-MA CLCs barcode particles with finely tunable size and uniformity. Such barcode particles are promising for widespread applications in bioanalysis and biodiagnostics.},
}

@article {pmid40461651,
year = {2025},
author = {Soares, RRG and García-Soriano, DA and Larsson, J and Fange, D and Schirman, D and Grillo, M and Knöppel, A and Sen, BC and Svahn, F and Zikrin, S and Ratz, M and Nilsson, M and Elf, J},
title = {Pooled optical screening in bacteria using chromosomally expressed barcodes.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {851},
pmid = {40461651},
issn = {2399-3642},
support = {2016-0621//Vetenskapsrådet (Swedish Research Council)/ ; 2018-03958//Vetenskapsrådet (Swedish Research Council)/ ; 2019-01238//Vetenskapsrådet (Swedish Research Council)/ ; 885360//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2016.0077//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2017.0291//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2019.0439//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; Luminescent Proteins/genetics/metabolism ; Red Fluorescent Protein ; *Chromosomes, Bacterial/genetics ; *DNA Barcoding, Taxonomic/methods ; Gene Library ; },
abstract = {Optical pooled screening is an important tool to study dynamic phenotypes for libraries of genetically engineered cells. However, the desired engineering often requires that the barcodes used for in situ genotyping are expressed from the chromosome. This has not previously been achieved in bacteria. Here we describe a method for in situ genotyping of libraries with genomic barcodes in Escherichia coli. The method is applied to measure the intracellular maturation time of 84 red fluorescent proteins.},
}

*Escherichia coli/genetics/metabolism
Luminescent Proteins/genetics/metabolism
Red Fluorescent Protein
*Chromosomes, Bacterial/genetics
*DNA Barcoding, Taxonomic/methods
Gene Library

@article {pmid40459854,
year = {2025},
author = {Devitt, G and Hanrahan, N and Ramírez Moreno, M and Mudher, A and Mahajan, S},
title = {A Novel Spectral Barcoding and Classification Approach for Complex Biological Samples Using Multiexcitation Raman Spectroscopy (MX-Raman).},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c00776},
pmid = {40459854},
issn = {1520-6882},
abstract = {We report the development and application of a novel spectral barcoding approach that exploits our multiexcitation (MX) Raman spectroscopy-based methodology for improved label-free detection and classification of complex biological samples. To develop our improved MX-Raman methodology, we utilized post-mortem brain tissue from several neurodegenerative diseases (NDDs) that have considerable clinical overlap. For improving our methodology we used three sources of spectral information arising from distinct physical phenomena to assess which was most important for NDD classification. Spectral measurements utilized combinations of data from multiple, distinct excitation laser wavelengths and polarization states to differentially probe molecular vibrations and autofluorescence signals. We demonstrate that the more informative MX-Raman (532 nm-785 nm) spectra are classified with 96.7% accuracy on average, compared to conventional single-excitation Raman spectroscopy that resulted in 78.5% accuracy (532 nm) or 85.6% accuracy (785 nm) using linear discriminant analysis (LDA) on 5 NDD classes. By combining information from distinct laser polarizations we observed a nonsignificant increase in classification accuracy without the need of a second laser (785 nm-785 nm polarized), whereas combining Raman spectra with autofluorescence signals did not increase classification accuracy. Finally, by filtering out spectral features that were redundant for classification or not descriptive of disease class, we engineered spectral barcodes consisting of a minimal subset of highly disease-specific MX-Raman features that improved the unsupervised and cross-validated clustering of MX-Raman spectra. The results demonstrate that increasing spectral information content using our optical MX-Raman methodology enables enhanced identification and distinction of complex biological samples but only when that information is independent and descriptive of class. The future translation of such technology to biofluids could support diagnosis and stratification of patients living with dementia and potentially other clinical conditions such as cancer and infectious disease.},
}

@article {pmid40458985,
year = {2025},
author = {Carné, A and Vieites, DR and van den Burg, MP},
title = {In Vouchers We (Hope to) Trust: Unveiling Hidden Errors in GenBank's Tetrapod Taxonomic Foundations.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17812},
doi = {10.1111/mec.17812},
pmid = {40458985},
issn = {1365-294X},
support = {10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades, Agencia Estatal de Investigación./ ; },
abstract = {Genetic repositories are invaluable resources foundational to various biological disciplines. While their data and metadata reliability are essential for robust research outcomes, numerous studies have highlighted data quality and consistency issues. Here, we detect and quantify errors at the most fundamental level by analysing the congruence of sequences derived from the same genetic marker and specimen voucher across tetrapods. Our analysis reveals that 32% of re-sequenced vouchers (with identical field or museum numbers) yield unequal sequences, ranging from a few mutations to significant divergences (0.06%-33.95%). These divergences may result from sample misidentification, labelling errors, fidelity disparities between sequencing methods, or contamination at various stages of the research process. Our findings demonstrate errors within GenBank at its most basal level and suggest that, although undetectable, a similar error rate likely exists in non-re-sequenced data. These previously overlooked errors are concerning because they arise from replicated experiments, which are uncommon, and raise serious questions about the reliability of non-re-sequenced specimens. Such errors can compromise the accuracy of biodiversity assessments (e.g., taxonomic assessment, eDNA and barcoding), phylogenetic analyses and conservation planning by artificially inflating the intraspecific divergence or misidentifying (to-be-described) species. Additionally, the accuracy of large-scale biological studies that rely on such data can be compromised. Our concerning results call for protocols ensuring sample traceability to the specimens or tissues during the whole process of data generation, analysis and deposition in a database. We propose a third-party annotation system for individual GenBank records that would allow flagging common errors and alert both the original submitter and all users to potential problems without modifying the original records.},
}

@article {pmid40457637,
year = {2025},
author = {Buchan, E and Rickard, JJS and Thomas, MR and Oppenheimer, PG},
title = {Advanced Multipurpose Spectroscopic Nanobio-Device for Concurrent Lab-on-a-Chip Label-Free Separation and Detection of Extracellular Vesicles as Key-Biomarkers for Point-of-Care Cardiovascular Disease Diagnostics.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2500122},
doi = {10.1002/adhm.202500122},
pmid = {40457637},
issn = {2192-2659},
support = {//National Institute for Health Research/ ; EP/Y030206/1/ERC_/European Research Council/International ; EP/V029983/1//Engineering and Physical Sciences Research Council/ ; EP/L016346/1//Engineering and Physical Sciences Research Council/ ; 174ISSFPP/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The global aging population presents a major public health challenge, with cardiovascular diseases (CVDs) remaining the leading cause of death worldwide. Often asymptomatic in early-stages, CVDs are frequently undiagnosed until critical events like myocardial infarction or stroke occur. To address this gap, an advanced integrated multipurpose spectroscopic lab-on-a-chip bionano-device has been developed for early CVD detection through extracellular vesicle (EV). EVs, which reflect the molecular state of their originating cells, are separated and analyzed using the combined Raman spectroscopy's molecular specificity with AI-driven classification from clinical CVD biofluids. AIMSpec-LoC unprecedently achieves rapid, label-free, size-based separation of EV subtypes, including small, mid and large EVs from biofluids, whilst preserving EV integrity and eliminating extensive preprocessing. The device enables real-time, multiplexed molecular profiling of EV cargo, identifying CVD-specific biomarkers with sensitivity and specificity >96% and linking these to CVD progression, achieving >97% accuracy in identifying disease-specific molecular fingerprints. This bionanotechnological device generates quantitative barcodes to support prognostic modeling and therapeutic evaluation, providing clinicians with actionable insights for timely-diagnosis and personalized treatment. AIMSpec-LoC platform offers a transformative solution for point-of-care CVD diagnostics, addressing critical unmet needs in cardiovascular medicine, enhancing clinical decision-making, improving patient health and reducing the global burden of CVDs.},
}

@article {pmid40456603,
year = {2025},
author = {Zidane, N and Rodrigues, C and Bouchez, V and Rethoret-Pasty, M and Passet, V and Brisse, S and Crestani, C},
title = {Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279829.124},
pmid = {40456603},
issn = {1549-5469},
abstract = {High-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with complete genome reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents an alternative that offers benefits including real-time sequencing and cost-efficiency, particularly useful in resource-limited settings. However, the historically higher error rates of ONT data have so far limited its application in high-precision genomic typing. The recent release of ONT's R10.4.1 chemistry, with significantly improved raw read accuracy (Q20+), offers a potential solution to this problem. The aim of this study was to evaluate the performance of ONT's latest chemistry for bacterial genomic typing against the gold standard Illumina technology, focusing on three respiratory pathogens of public health importance, Klebsiella pneumoniae, Bordetella pertussis, and Corynebacterium diphtheriae, and their related species. Using the Rapid Barcoding Kit V14, we generated and analyzed genome assemblies with different basecalling models, at different simulated depths of coverage. ONT assemblies were compared to the Illumina reference for completeness and core genome multilocus sequence typing (cgMLST) accuracy (number of allelic mismatches). Our results show that genomes obtained from raw ONT data basecalled with Dorado SUP v0.9.0, assembled with Flye, and with a minimum coverage depth of 35×, optimized accuracy for all bacterial species tested. Error rates were consistently below 0.5% for each cgMLST scheme, indicating that ONT R10.4.1 data is suitable for high-resolution genomic typing applied to outbreak investigations and public health surveillance.},
}

@article {pmid40454788,
year = {2025},
author = {Bringloe, TT and Grant, WS and Zaparenkov, D and Starko, S and Fort, A and Inaba, M and Sulpice, R and Saunders, GW and Verbruggen, H},
title = {Revisiting the species problem in Northeast Pacific ribbon kelp lineages (genus Alaria): Lessons learned using whole genome data.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70040},
pmid = {40454788},
issn = {1529-8817},
support = {//University of Melbourne McKenzie Postdoctoral Fellowship/ ; //Phychological Society of America Norma J. Lang Early Career Fellowship/ ; //European Union Northern Periphery and Arctic Program/ ; 19/FFP/6841//SFI Frontiers for the Future project Pristine Coasts/ ; //Forrest Research Foundation/ ; 1618//North Pacific Research Board/ ; CEECIND:2023.06155//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {The transition from interbreeding populations to species continues to represent difficult terrain for phylogenetic investigations. Genotyping entire genomes holds promise for enhancing insights into the process of speciation and evolutionary relationships among recently speciated taxa. Northeast Pacific ribbon kelp was once recognized as four species before they were folded into Alaria marginata based on DNA barcodes, although several lineages continue to be recognized. We used whole genome sequencing to determine whether these lineages represente species. Whole genomes of 69 individuals from five genetically distinctive lineages in the Gulf of Alaska (United States) and Salish Sea (Canada) were analyzed, along with 63 genomes from three other species of Alaria. Our analysis of >3.4 million single nucleotide polymorphisms reaffirmed that organellar and nuclear phylogenetic signals are incongruent in Alaria, producing different topologies among five organellar and six nuclear A. marginata lineages. Lineages appeared to be reproductively isolated, as evidenced by strong clustering and lack of recent admixture across nuclear genomes. Genetic divergence between A. marginata lineages also exceeded intra-lineage divergence, proxied by A. esculenta populations, but fell short of distances observed across other species of Alaria. Despite the genomic data supporting predictions of the biological and genetic species concepts, we encountered inherent limitations in declaring species status. While our work shifts taxonomic conversations toward a genome-scale framework that provides a more comprehensive picture of divergence and connectivity, our work also highlights that philosophical challenges inherent to defining species persist and that integrative approaches continue to be necessary in the genomic era.},
}

@article {pmid40454326,
year = {2025},
author = {Baban, NS and Bhattacharjee, S and Song, YA and Chakrabarty, K and Karri, R},
title = {Cyber-physical security of biochips: A perspective.},
journal = {Biomicrofluidics},
volume = {19},
number = {3},
pages = {031304},
pmid = {40454326},
issn = {1932-1058},
abstract = {Microfluidic biochips (MBs) are transforming diagnostics, healthcare, and biomedical research. However, their rapid deployment has exposed them to diverse security threats, including structural tampering, material degradation, sample-level interference, and intellectual property (IP) theft, such as counterfeiting, overbuilding, and piracy. This perspective highlights emerging attack vectors and countermeasures aimed at mitigating these risks. Structural attacks, such as stealthy design code modifications, can result in faulty diagnostics. To address this, deep learning -based anomaly detection leverages microstructural changes, including optical changes such as shadows or reflections, to identify and resolve faults. Material-level countermeasures, including mechano-responsive dyes and spectrometric watermarking, safeguard against subtle chemical alterations during fabrication. Sample-level protections, such as molecular barcoding, ensure bio-sample integrity by embedding unique DNA sequences for authentication. At the IP level, techniques like watermarking, physically unclonable functions, fingerprinting, and obfuscation schemes provide robust defenses against reverse engineering and counterfeiting. Together, these approaches offer a multi-layered security framework to protect MBs, ensuring their reliability, safety, and trustworthiness in critical applications.},
}

@article {pmid40453775,
year = {2025},
author = {Kubátová, A and Kunz, B and Hubka, V},
title = {Reintroducing Akanthomyces ampullifer: providing genetic barcodes, culture, and updated description for the dipteran pathogen rediscovered in Germany.},
journal = {Mycoscience},
volume = {65},
number = {6},
pages = {260-269},
pmid = {40453775},
issn = {1618-2545},
abstract = {The genus Akanthomyces (Ascomycota, Hypocreales) includes entomopathogenic species known to infect a variety of insects and spiders. In this study, we present the first isolate of A. ampullifer characterized by molecular methods, found on dead bodies of the common cave limoniid Limonia nubeculosa (Diptera) in the subterranean spaces of southwestern Germany. In total, seven specimens exhibited distinctive morphological traits that, when compared with historical records, confirm their identification as A. ampullifer-particularly noted for its affinity to dipteran hosts. Absent from culture collections and molecular repositories, this species has eluded detailed scientific documentation using modern methods. Our research bridges this knowledge gap, providing the first genetic identification barcodes of five genes, living culture, cultivation requirements, and an updated description. This overlooked fungus is phylogenetically most closely related to the species A. pyralidarum, A. laosensis, and some other species mostly associated with adult moths. It demonstrates a unique morphological signature with monoblastic phialides forming a layer on the surface of synnemata and produces long, cylindrical, chain-forming conidia. It prefers lower temperatures, exhibiting an inability to grow at 25 °C, coupled with notably slow growth in culture.},
}

@article {pmid40453413,
year = {2025},
author = {Martoni, F and Tweed, JMH and Blacket, MJ and Percy, DM},
title = {An annotated checklist of the psyllids (Hemiptera, Psylloidea) of Norfolk Island with keys to species, new records, and descriptions of two new endemic species.},
journal = {ZooKeys},
volume = {1238},
number = {},
pages = {297-348},
pmid = {40453413},
issn = {1313-2989},
abstract = {Norfolk Island is a small, isolated archipelago in the Pacific Ocean, 1400 km east of the Australian mainland. The history of human colonisation and land use on the island has resulted in a substantial reduction in the extent and quality of indigenous habitat. A quarantine survey of Norfolk Island in 2012-2014 provided the first records of psyllid species, reporting six taxa from the island. Additional collection records are provided that increase the number to 14 species, of which nine are regarded as adventive, four as native of which two are endemic, and one whose additional distribution is unknown. Two species are formally described here and are the first psyllid species to be described from Norfolk Island. These new species, Pseudophacopteronaewagriini Percy & Martoni, sp. nov. (Aphalaridae) and Acizziaaliceae Percy & Martoni, sp. nov. (Psyllidae) are both considered endemic to Norfolk Island and are associated with native plants, the endemic Alyxiagynopogon (Apocynaceae) and the native Dodonaeaviscosa (Sapindaceae), respectively. In addition to an updated checklist, identification keys to adults and immatures of the psyllids found on Norfolk Island and DNA barcodes for all species are provided. Both new species have had complete mitochondrial genomes sequenced in a previous study and here a full annotation of the mitochondrial genome of Acizziaaliceae Percy & Martoni, sp. nov. is supplied. Lastly, the barcode data was analysed in a maximum likelihood constraint framework with previous genome data to investigate the phylogenetic origins of the Norfolk Island taxa.},
}

@article {pmid40452930,
year = {2025},
author = {Maslakova, S and Cherneva, I and Kahn, E and Wong, A and Paulay, G},
title = {A hundred species, mostly new-first assessment of ribbon worm diversity and distribution in Oman.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19438},
pmid = {40452930},
issn = {2167-8359},
mesh = {Animals ; Oman ; *Biodiversity ; *Invertebrates/classification/genetics ; Phylogeny ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Ecosystem ; },
abstract = {BACKGROUND: Biodiversity is a key characteristic of any ecosystem but remains largely undescribed for most marine animals. Ribbon worms (phylum Nemertea), a diverse but poorly sampled phylum ubiquitous in the world's oceans, are a case in point. Aside from their function as predators in marine communities, nemerteans are biomedically relevant because they produce diverse toxins, and some impact bivalve, decapod, and glass eel fisheries. Identification of nemerteans is challenging because many species look alike. The task is further complicated by many descriptions being based on preserved specimens, and therefore lacking characters of external appearance of live specimens. Characters of internal anatomy form the basis of traditional systematics but are more recently shown to be of little use in distinguishing between closely related species. This makes DNA data essential in species descriptions, and assessments of diversity and distribution.

METHODS: In a first modern survey of the phylum in Arabian waters, we collected nemerteans from a variety of habitats, focusing sampling on hard-bottom substrata, especially coral reefs. Specimens were triple-documented with photos, morphological vouchers, and DNA barcodes. Species delineation was based on morphology and Cytochrome Oxidase I sequences. Sequences and associated data are deposited in public databases, and vouchers at the Florida Museum of Natural History.

RESULTS: We documented 107 nemertean species in Oman, where none were previously known. This doubles the number of genetically characterized nemertean species for the entire Indo-West Pacific-a testament to how poorly sampled the phylum is in the most biodiverse marine region of the world. As many as 98% of the species were undescribed, and 93% are not documented outside Arabia. Half of the species were rare, and most-cryptic. Undescribed species were assigned unique alphanumeric temporary names for tracking in the literature and public databases. Estimates of source diversity suggest that future surveys might uncover an additional ∼200 species by including other locations and types of habitats, particularly soft bottoms, and the water column. Little overlap was observed between species found in the northern (Gulf of Oman) and southern (Sea of Arabia) regions, and many that occurred in both areas showed evidence of genetic differentiation corresponding to the major biogeographic break at R'as-al-Hadd.

CONCLUSIONS: The high diversity, novelty, and distinctiveness of this fauna underscore the importance of sampling the most biodiverse and least studied tropical marine regions of the world. The large amount of cryptic and undescribed diversity highlights the critical role of DNA barcodes and rapid approaches to species descriptions.},
}

Animals
Oman
*Biodiversity
*Invertebrates/classification/genetics
Phylogeny
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic
Ecosystem

@article {pmid40451908,
year = {2025},
author = {Gusmao, ACB and van Dijk, RL and Girard, EB and Peijnenburg, KTCA and Macher, J and Kucera, M and Morard, R},
title = {Exploring the potential of the COI gene marker for DNA barcoding of planktonic foraminifera.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19205},
pmid = {40451908},
issn = {2045-2322},
mesh = {*Foraminifera/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; *Plankton/genetics/classification ; Genetic Markers ; Phylogeny ; },
abstract = {Metabarcoding is a cornerstone of modern ecology, but its accuracy is dependent on the chosen gene marker. While the small subunit ribosomal DNA (SSU) is a powerful tool to describe protist diversity, its reliability in retrieving the composition of communities is less obvious. It is particularly challenging to obtain quantitative estimates of abundance in planktonic foraminifera, where the variability of the SSU gene copy number can span three orders of magnitude. As an alternative, we explored the potential of the mitochondrial cytochrome c oxidase subunit I (COI) marker. We developed a reference barcode library of 130 sequences of a 1200 bp long COI fragment belonging to 26 morphospecies of foraminifera and performed 201 single-cell qPCR quantifications to evaluate the relationship between the number of COI copies, and the size of individual foraminifera. We found that the COI evolves between 25 and 1000 times slower than the SSU and therefore has a poor taxonomic resolution. However, we observed a significant relationship between COI copy number and foraminifera size. These results suggest that SSU and COI can play complementary roles: the SSU is well-suited for capturing taxonomic diversity, while the COI is useful to retrieve crude information on the community composition.},
}

*Foraminifera/genetics/classification
*DNA Barcoding, Taxonomic/methods
*Electron Transport Complex IV/genetics
*Plankton/genetics/classification
Genetic Markers
Phylogeny

@article {pmid40450781,
year = {2025},
author = {Guidoni, L and Drais, MI and Turco, S and Mazzaglia, A and Vannini, A and Morales-Rodríguez, C},
title = {Survival of plant pathogens during composting of bio-waste: a case study for oomycetes and fungi.},
journal = {The Science of the total environment},
volume = {986},
number = {},
pages = {179767},
doi = {10.1016/j.scitotenv.2025.179767},
pmid = {40450781},
issn = {1879-1026},
abstract = {European countries have implemented national strategies to reduce the use of peat in horticulture due to its environmental impact. Studies demonstrated the possibility of reducing peat consumption by using compost as a substitute without affecting the growth and development of potted horticulture plants. However, any substitute must be produced considering quality standards and requirements that are adopted for peat. Among others, the risk of contamination of compost with plant pathogens is particularly high. Furthermore, the assessment of the survival of specific plant pathogens during the composting process requires proper detection methods. This study evaluated the survival/presence of the oomycete Phytophthora cinnamomi, as a model plant pathogen, in woody chips of artificially inoculated Castanea sativa saplings used as a bulking agent in composting processes. Detection techniques for assessment included isolation in pure culture, quantitative PCR (qPCR) and High Throughput Sequencing (HTS). The pathogen was easily detected in woody chips at the beginning of the composting process with baiting and molecular barcoding. By the end of the maturation phase, no P. cinnamomi was detectable by any diagnostic method including baiting, confirming the efficacy of a proper composting process in eradicating the pathogen. HTS approach was also able to detect throughout the process the DNA of plant pathogenic fungal genera naturally present in the green residues and bulk agents. These findings are crucial for developing diagnostic pipelines to be included in protocols for compost biosafety certification. Finally, the present study demonstrated the possibility of processing recycled horticulture biowaste to obtain high-quality and safe compost without the need for complex and expensive composting plants.},
}

@article {pmid40448040,
year = {2025},
author = {Akrami, AM and Meratian Esfahani, S and Soorni, A},
title = {Decoding the chloroplast genomes of five Iranian Salvia species: insights into genomic structure, phylogenetic relationships, and molecular marker development.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {545},
pmid = {40448040},
issn = {1471-2164},
abstract = {BACKGROUND: The genus Salvia, a prominent member of the Lamiaceae family, is renowned for its ecological, medicinal, and economic significance. Despite its importance, molecular data, particularly chloroplast (cp.) genome information, remain scarce for many native Iranian Salvia species. In this study, we sequenced and analyzed the complete cp. genomes of five Iranian Salvia species (S. aethiopis, S. sclarea, S. glutinosa, S. verticillata, and S. officinalis) to elucidate their genomic structure, evolutionary relationships, and potential for biotechnological applications.

RESULTS: The cp. genomes of the five Salvia species exhibited a conserved quadripartite structure, with sizes ranging from 151,163 to 151,662 bp, and a GC content of 38%. Each genome contained 132 or 131 genes, comprising 86 or 87 protein-coding, 8 rRNA, and 37 tRNA genes, with duplications in rpl2, rpl23, and rps12. Minor variations in gene content were observed, such as the absence of trnS-CGA in S. glutinosa. Comparative analysis of IR boundaries showed subtle expansions in S. officinalis and S. sclarea, while S. glutinosa remained stable. Trans-splicing of the rps12 gene was observed in all species, with complex structures in S. glutinosa and S. sclarea. Codon usage analysis revealed a preference for A/U-ending codons, with S. verticillata displaying unique patterns. Nucleotide diversity (Pi) identified highly variable regions, such as rpl14-rpl16 and psbK-psbI, as potential molecular markers. Phylogenetic analysis resolved distinct clades, with S. aethiopis and S. sclarea forming a close group, S. glutinosa clustering with S. chanryoenica, and S. officinalis showing genetic homogeneity with Mediterranean species. S. verticillata exhibited an earlier divergence, highlighting the genus's evolutionary complexity.

CONCLUSIONS: This study provides critical genomic resources for species identification, phylogenetic studies, and the development of molecular markers, facilitating the conservation of native Salvia species and their utilization in breeding programs for medicinal and aromatic traits.},
}

@article {pmid40447760,
year = {2025},
author = {Hebert, JD and Xu, H and Tang, YJ and Ruiz, PA and Detrick, CR and Wang, J and Hughes, NW and Donosa, O and Siah, VP and Andrejka, L and Karmakar, S and Aboiralor, I and Tang, R and Sotillo, R and Sage, J and Cong, L and Petrov, DA and Winslow, MM},
title = {Efficient and multiplexed somatic genome editing with Cas12a mice.},
journal = {Nature biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {40447760},
issn = {2157-846X},
support = {P01-CA244114//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01-CA231253//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01-CA234349//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30-CA124435//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35-CA231997//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35-HG011316//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01-GM141627//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01-CA231253//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01-CA234349//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; PF-21-112-01-MM//American Cancer Society (American Cancer Society, Inc.)/ ; T34FT8013//Tobacco-Related Disease Research Program (TRDRP)/ ; T34FT8013//Tobacco-Related Disease Research Program (TRDRP)/ ; DGE-2146755//National Science Foundation (NSF)/ ; K00CA234962//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations. However, existing models have a limited ability to create multiple targeted edits, hindering our understanding of complex genetic interactions. Here we generate transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a), which robustly generates compound genotypes, including diverse cancers driven by inactivation of trios of tumour suppressor genes or an oncogenic translocation. We integrate these modular CRISPR RNA (crRNA) arrays with clonal barcoding to quantify the size and number of tumours with each array, as well as the impact of varying the guide number and position within a four-guide array. Finally, we generate tumours with inactivation of all combinations of nine tumour suppressor genes and find that the fitness of triple-knockout genotypes is largely explainable by one- and two-gene effects. These Cas12a alleles will enable further rapid creation of disease models and high-throughput investigation of coincident genomic alterations in vivo.},
}

@article {pmid40447231,
year = {2025},
author = {Rochwarger, A and Kaufmann, L and Zhao, J and Makky, A and Nguyen, NA and Lehmann, N and Samusik, N and Beschorner, C and Manmadhan, SS and Greif, K and Schürch, CM},
title = {A validation workflow for novel oligonucleotide sequences to expand the multiplexing capacity of the CODEX platform.},
journal = {Laboratory investigation; a journal of technical methods and pathology},
volume = {},
number = {},
pages = {104200},
doi = {10.1016/j.labinv.2025.104200},
pmid = {40447231},
issn = {1530-0307},
abstract = {Antibody-based multiplexed tissue imaging has the potential to provide critical advances in biological discoveries and their translation for clinical applications. With the increasing introduction of markers and modalities for spatial analysis, there is an according demand for the expansion of multiplexing capacities of such imaging platforms. CO-Detection by indEXing (CODEX) is a widely used multiplexed tissue imaging platform that utilizes DNA-conjugated antibodies for imaging. The multiplexing capacity of CODEX is limited by the availability of unique DNA oligonucleotide sequences for antibody barcoding. In this study, we demonstrate a workflow for the validation and the introduction of novel sets of candidate DNA oligonucleotide sequences for CODEX. Through cross-validation multicycle experiments with the already published library of DNA barcodes, we here present a set of 27 novel oligonucleotide sequences for CODEX, increasing the potential multiplexing capacity to 85+ markers. We confirmed the utility of the new barcodes by using a 74-plex antibody panel on a multi-tumor tissue microarray of paraffin-embedded tissues. The workflow presented here provides a reproducible method for extending the plexity of the CODEX platform, facilitating a deeper understanding of tissue microenvironments.},
}

@article {pmid40445869,
year = {2025},
author = {Moisseyev, R and Kostyukova, VS and Pozharskiy, AS and Mendybayeva, A and Gritsenko, D},
title = {First Report of Grapevine Yellow Speckle Viroids and Hop Stunt Viroid in Vitis vinifera in Kazakhstan.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-04-25-0798-PDN},
pmid = {40445869},
issn = {0191-2917},
abstract = {Grapevine viroids are the smallest pathogens affecting viticulture. Infected grapevines may show symptoms such as leaf yellowing, mottling, stunted growth, reduced fruit quality, and overall vine decline. Asymptomatic viroid infections in grapevines can still decrease grapevine productivity, thereby posing a hidden economic threat to viticulture (Wolpert et al., 1996; Wu et al., 2023). This study aimed to detect three widely distributed viroid species of the Pospiviroidae family: Grapevine yellow speckle viroid 1 (GYSVd-1), Grapevine yellow speckle viroid 2 (GYSVd-2), and Hop stunt viroid (HSVd). The study focused on grapevine (Vitis vinifera) cultivars 'Saperavi' and 'Rkatsiteli' cultivated in Kazakhstan. Three fields in Shirin village and one field in Tyulkubas village (each about 600 ha) in Almaty region were tested for the presence of viroids due to a decline in yield observed despite the negative tests for common viruses (past 3 years). Symptoms typical for viral infections were observed sporadically without a consistent pattern of infection. Total 17 samples from Shirin (July 2023) and 14 from Tyulkubas (June 2024) with visible symptoms were collected randomly. Validated primers were used to identify GYSVd-1 (mF/mR1, 250 bp) (Hajizadeh et al. 2012) GYSVd-2 (P1/P2, 375 bp) (Jiang et al. 2009) and HSVd (78P/83M, 312 bp) (Sano et al. 2001) using conventional RT-PCR. Among the analyzed samples, in Shirin village, 6 samples tested positive for GYSVd-1, 15 for GYSVd-2, and 15 for HSVd, including 2 positive for both HSVd and GYSVd-1. In Tyulkubas village, 2 samples were positive for GYSVd-1 and 12 for HSVd; GYSVd-1 positive samples als were positive for HSVd, including 8 positive for both HSVd and GYSVd-2 and 6 positive for three viroids. Amplicons for each viroid were further sequenced using the Sanger's method on ABI 3500 Genetic Analyser with BigDye v.3.1 kit and using MinION sequencer with the Rapid Barcoding Kit 96 V14 (Oxford Nanopore Technologies) according to the manufacturer's protocol. The obtained reads were mapped to reference sequences from GenBank-GYSVd-1 NC_001920.1, HSVd NC_001351.1, and GYSVd-2 MG780425.1-using Minimap v.2.2.0 with default parameters in Geneious software. Sequencing produced total 2253 reads for GYSVd-1 (average length 159 bp, range 42-296), 2095 for GYSVd-2 (203.6 bp, 49-578), and 1235 for HSVd (218.5 bp, 53-440). Of these, 947 (42.0%) were been mapped to GYSVd-1, 1778 (84.9%) to GYSVd-2, and 678 (54.9%) to HSVd. Genome coverage was 62.3% (GYSVd-1), 98.1% (GYSVd-2), and 73.8% (HSVd), with mean depths of 889X, 1282X, and 659X, respectively. Each viroid resulted a single contig corresponding to the target amplicon. No reads corresponding to other viral or bacterial agents have been identified. NCBI BLASTn search resulted total 141 hits with coverage 59-68% and identity 98.69-99.35% for GYSVd-1; 128 hits with coverage 82-100% and identity 97.59-100% for GYSVd-2; 157 hits with coverage 99-100% and identity 95.49-97.29%; no not-specific matches were identified for three viroids. The assembled viroid sequences obtained using nanopore sequencing have been uploaded into NCBI database (accessions PV341024-PV341026). Viroids GYSVd-1,2 and HSVd have been detected for the first time in Kazakhstan. The results indicate the need for further studies to estimate impact of these viroids on viticulture and lay a basis for their monitoring in the country.},
}

@article {pmid40444175,
year = {2025},
author = {Bhuvaneshwaran, S and Padmanaban, VS and Radja, RD and Anandan, G and Venkatesan, S and Semalaiyappan, J and Kumar, A and Kuttiatt, VS},
title = {Molecular identification of immature stages of medically important fly species, Puducherry, South India: a preliminary study.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1551807},
pmid = {40444175},
issn = {2673-8600},
abstract = {Flies and maggots are of medical importance, and it is often necessary to identify them at species level. Conventionally, this is carried out based on morphological features using taxonomic keys. However, identification of maggots based on morphology is difficult and required entomological expertise is often lacking in clinical settings. Molecular methods can be an alternative to morphology-based identification and find special application when only tiny pieces of specimens are available especially in cases of human myiasis. In this preliminary study, we explored the utility of mitochondrial COI gene based molecular method, for identifying immature stages of certain medically important flies captured from the field in Puducherry, India. Maggots were captured from different locations in Puducherry using rotten fish and kitchen waste as baits and a 700 bp segment of the COI gene was amplified and genetic relationship was assessed by performing haplotype network analysis. High quality sequences were available for 11 specimens and were subjected to BLAST analysis to identify matches from the database for identification of the species. The identified maggots belonged to Sarcophaga peregrina (Robineau-Desvoidy, 1830), Hemipyrellia ligurriens (Wiedemann, 1830) and Chrysomya megacephala (Fabricius, 1794). This study generated representative molecular sequence data for two less studied fly species of medical importance, S. peregrina and H. ligurriens from South India. In future, there is a need for further detailed molecular studies on flies in the diverse epidemiological and geographic settings in India with a view to identify cryptic species and new haplotypes.},
}

@article {pmid40444067,
year = {2025},
author = {Yela, JL and Molina, D and Ortiz, AS},
title = {Agrotisvillenensis-a new species of Noctuinae (Lepidoptera, Noctuidae) from the southeastern Iberian Peninsula.},
journal = {ZooKeys},
volume = {1239},
number = {},
pages = {21-32},
pmid = {40444067},
issn = {1313-2989},
abstract = {Agrotisvillenensis sp. nov. is described from the Iberian Peninsula. Differential superficial, genital and genetic (barcode) characters from its closest Iberian and European relative species, Agrotisvestigialis (Hufnagel, 1766), are presented. Morphologically, the new species is best characterized in the male genitalia by the shape of the basal vesica and the presence of a median diverticulum and in the female genitalia by its comparatively long appendix bursae. The barcode of A.villenensis differs from those of related species and is assigned a unique BIN.},
}

@article {pmid40443187,
year = {2025},
author = {Jiang, C and Wang, Q and Shi, Z and Liu, S and Chen, G and Liang, B and Li, D and Ye, X},
title = {Controlled fabrication of novel magneto-fluorescent encoded microspheres with host-guest structures for simultaneous detection of thyroxine and thyroid stimulating hormone.},
journal = {Analytical methods : advancing methods and applications},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5ay00554j},
pmid = {40443187},
issn = {1759-9679},
abstract = {Simultaneous detection of serum thyroxine (T4) and thyroid stimulating hormone (TSH) is essential for diagnosis and monitoring of congenital hypothyroidism (CH). Here, we reported a novel suspension array platform based on host-guest-structured magneto-fluorescent encoded beads (HGBs) for concurrent T4 and TSH detection. The foundation of HGBs lays in low-density polystyrene microsphere templates, ingeniously transformed into micron-scale host beads through the sequential deposition of iron oxide nanoparticles, quantum dots, and silica layers, resulting in good magnetism, satisfactory suspension ability and fluorescence stability. By combining micron-scale host beads exhibiting distinct red fluorescence intensities with nano-scale guest beads displaying varying green fluorescence intensities, we could repeatedly and accurately prepare 24 discriminable HGBs easily. Then, two representative HGBs were selected to construct a suspension arrays system for concurrent T4 and TSH detection. Under the optimal detection conditions, the suspension arrays we tested on T4 and TSH could be assayed in the ranges of 4 to 400 ng mL[-1], and 0.032 to 100 mIU L[-1] with limits of detection of 1.2 ng mL[-1], and 0.014 mIU L[-1], respectively. This innovative methodology not only exhibits commendable accuracy and precision but also demonstrates strong concordance with established chemiluminescence immunoassay results. Consequently, the suspension arrays based on HGB barcodes hold immense promise for enhancing the diagnostic efficiency in the realm of CH management.},
}

@article {pmid40443169,
year = {2025},
author = {Tang, CN and Lai, NW and Ho, HC},
title = {Description of a new liopropomine basslet, Liopropoma terecaudum, from northern Taiwan (Perciformes: Epinephelidae).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70086},
pmid = {40443169},
issn = {1095-8649},
support = {//National Museum of Marine Biology and Aquarium/ ; //National Kaohsiung University of Science and Technology/ ; },
abstract = {Liopropoma terecaudum sp. nov. is described based on 12 specimens collected off northern Taiwan. The new species most closely resembles two sympatric species, L. japonicum and L. dorsoluteum, but differs from both species and all other congeneric species of Liopropoma based on the following combination of morphological and colouration characters: caudal fin round; dorsal-fin elements VIII, 13 and lacking a distinct notch; lateral side of body with a broad red stripe; base of caudal fin with a large red blotch. Phylogenetic analysis of mitochondrial DNA barcode sequences places L. terecaudum in a clade with L. dorsolutum and L. japonicum. The average genetic divergences between L. terecaudum and L. dorsoluteum, and between L. terecaudum and L. japonicum, are measured to be 11.8% and 11.9%, respectively. The description of L. terecaudum brings the total number of Liopropoma in Taiwanese waters to 11.},
}

@article {pmid40442801,
year = {2025},
author = {Tepboonrueng, P and Pataradool, T and Boonserm, R and Rimmer, LW and Preativatanyou, K and Sunantaraporn, S and Siriyasatien, P},
title = {DNA barcoding of Culicoides biting midges (Diptera: Ceratopogonidae) and detection of Leishmania and other trypanosomatids in southern Thailand.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {194},
pmid = {40442801},
issn = {1756-3305},
abstract = {BACKGROUND: Biting midges of the genus Culicoides play an important role in the transmission of pathogenic arboviruses and parasites. Thailand has documented more than 100 species of Culicoides; however, several cryptic species complexes remain to be clarified. Recent studies in areas with leishmaniasis indicate that several species of Culicoides might be potential vectors of Leishmania in the subgenus Mundinia, but evidence supporting the hypothesis is still lacking. Therefore, the diversity of Culicoides biting midges and their potential role as vectors of leishmaniasis in southern Thailand remains uncertain.

METHODS: Female Culicoides biting midges were collected using Centers for Disease Control and Prevention (CDC) ultraviolet (UV) light traps from four locations within leishmaniasis-affected areas in three provinces of southern Thailand, including Nakhon Si Thammarat, Krabi, and Surat Thani. Culicoides species were identified based on the morphology of wing spot patterns and subsequently confirmed by cytochrome c oxidase subunit I (COI) Sanger sequencing. A potential cryptic species was classified using an integrative taxonomic approach associated with DNA barcoding identification by Barcode of Life Database (BOLD) and Basic Local Alignment Search Tool (BLAST) searches. Furthermore, three different methods of species delimitation, namely ASAP [Assemble Species by Automatic Partitioning], TCS [Templeton, Crandall, and Sing], and PTP [Poisson Tree Processes], were employed to verify the sequences into the molecular operational taxonomic unit (MOTU). Detection of Leishmania and other trypanosomatid parasites was performed by polymerase chain reaction (PCR) based on the ITS1 region and small subunit SSU ribosomal RNA (rRNA) gene, followed by Sanger sequencing and haplotype diversity analysis. The identification of host blood sources was carried out using host-specific multiplex PCR.

RESULTS: A total of 716 unfed midges and 159 blood-fed specimens were morphologically identified into 25 species belonging to five subgenera (Avaritia, Hoffmania, Meijerehelea, Remmia, and Trithecoides) and four species groups (Clavipalpis, Ornatus, Shermani, and Shortti). Two unidentified specimens were classified into two subgenera (Trithecoides and Avaritia). The DNA barcoding identification exhibited an 82.20% success rate. Species delimitation analyses demonstrated the presence of cryptic species complexes, categorized into six species: Culicoides actoni, C. orientalis, C. huffi, C. palpifer, C. clavipalpis, and C. jacobsoni. Furthermore, 6.42% of the Culicoides biting midges tested positive for Leishmania DNA in three sampling sites in Nakhon Si Thammarat and Surat Thani provinces (with no positive results in Krabi province). Furthermore, the sympatric infection of Leishmania martiniquensis and Leishmania orientalis was identified in several Culicoides species in Ron Phibun and Phunphin districts in Nakhon Si Thammarat and Surat Thani, respectively. In contrast, L. orientalis was detected in Sichon district, Nakhon Si Thammarat province. A genetic diversity analysis revealed high haplotype diversity and relatively low nucleotide diversity in both parasite populations. Additionally, Crithidia sp. and Crithidia brevicula were detected in Culicoides peregrinus and Culicoides subgenus Trithecoides. The analysis of the host blood meal from Ron Phibun also demonstrated that Culicoides had fed on cows, dogs, and chickens, and mixed blood preferences for humans and cows or chickens and cows were detected.

CONCLUSIONS: The findings of the present study demonstrate the presence of mixed blood hosts and co-circulation of L. martiniquensis and L. orientalis in Culicoides in areas of leishmaniasis, as well as cryptic species of Culicoides biting midges, through an integrative taxonomic approach. These findings support the hypothesis that Culicoides biting midges may serve as potential vectors in southern Thailand, and vector diversity is a contributing factor to the risk of zoonotic transmission.},
}

@article {pmid40442452,
year = {2025},
author = {Ohtani, H and Ichikawa, R and Mori, K and Kato, T and Nishioka, M},
title = {Single-molecule DNA analysis implicates brain mitochondria pathology in bipolar disorder.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40442452},
issn = {1476-5578},
support = {JP24tm0424229//Japan Agency for Medical Research and Development (AMED)/ ; JP24tm0424224//Japan Agency for Medical Research and Development (AMED)/ ; },
abstract = {Bipolar disorder (BD), characterized by recurrent manic and depressive episodes, is a global medical challenge. Based on its high heritability, various genomic studies have elucidated the genetic architecture of BD. Nonetheless, the specific genomic mechanisms underpinning BD pathogenesis remain elusive. Among under-investigated genomic factors, mitochondrial variants-particularly brain heteroplasmic variants-are of particular interest, given the critical role of mitochondria in neural function and the frequent psychiatric symptoms observed in mitochondrial diseases. In this study, we analyzed 163 brain DNA samples from 54 BD patients, 54 controls, and 55 schizophrenia patients to investigate the association between BD and mitochondrial heteroplasmic variants. Duplex molecular barcoding sequencing was employed for single-molecule resolution. We found an enrichment of ultra-rare heteroplasmic variants with allele fractions exceeding 1% in BD. Among them, potentially pathogenic variants, including m.3243A>G, loss-of-function variants, and rRNA variants, were particularly enriched in BD. In contrast, single-molecule analysis did not reveal a general trend of increases in low-level heteroplasmic variants in BD, in terms of per-base mutation frequency and heteroplasmic fractions. Thus, a subset of BD patients may be stratified according to the presence of ultra-rare mitochondrial variants. Our findings provide a foundation for future research into targeted therapeutic strategies for BD, grounded in genomic stratification by mitochondrial variants.},
}

@article {pmid40439147,
year = {2025},
author = {Kipen, J and Jaldén, J},
title = {Brownian motion data augmentation: a method to push neural network performance on nanopore sensors.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf323},
pmid = {40439147},
issn = {1367-4811},
abstract = {MOTIVATION: Nanopores are highly sensitive sensors that have achieved commercial success in DNA/RNA sequencing, with potential applications in protein sequencing and biomarker identification. Solid-state nanopores, in particular, face challenges such as instability and low signal-to-noise ratios (SNRs), which lead scientists to adopt data-driven methods for nanopore signal analysis, although data acquisition remains restrictive.

RESULTS: We address this data scarcity by augmenting the training samples with traces that emulate Brownian motion effects, based on dynamic models in the literature. We apply this method to a publicly available dataset of a classification task containing nanopore reads of DNA with encoded barcodes. A neural network named QuipuNet was previously published for this dataset, and we demonstrate that our augmentation method produces a noticeable increase in QuipuNet's accuracy. Furthermore, we introduce a novel neural network named YupanaNet, which achieves greater accuracy (95.8%) than QuipuNet (94.6%) on the same dataset. YupanaNet benefits from both the enhanced generalization provided by Brownian motion data augmentation and the incorporation of novel architectures, including skip connections and a soft attention mask.

The source code and data are available at: https://github.com/JavierKipen/browDataAug.

SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.},
}

@article {pmid40437799,
year = {2025},
author = {Krawczyk, K and Maździarz, M and Paukszto, Ł and Nobis, M and Sawicki, J},
title = {Phylogenetic reconstruction and species delimitation in Stipeae with special reference to Stipa (Poaceae, Pooideae) using mitochondrial genomes.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/cla.12618},
pmid = {40437799},
issn = {1096-0031},
support = {2023/51/B/NZ8/01179//the National Science Centre, Poland/ ; },
abstract = {Compared to plastid genomes, plant mitochondrial genomes have been less frequently used for species discrimination and phylogenetic studies due to assembly challenges, lower substitution rates and rapid structural evolution. However, this study demonstrates that mitochondrial genome fragments can be valuable for both molecular species identification and phylogenetic analysis in grasses of the tribe Stipeae. To explore this potential, we first assembled the complete mitochondrial genome of Nassella tenuissima-the first fully described mitogenome in Stipeae-which served as a reference for selecting 29 aligned mitochondrial genome fragments totalling 139 680 bp. These fragments were then analysed across 49 representatives of the tribe, including 43 Stipa species and six other taxa. The mitochondrial fragments achieved a species discrimination efficiency of 75%, slightly exceeding the 71% efficiency observed for plastid super-barcodes. Additionally, comparative phylogenetic analyses using plastid and mitochondrial genomes underscored the utility of mitochondrial data in resolving phylogenetic relationships within Stipeae. Our findings provide a valuable resource for future research in transcriptomics, comparative genomics, phylogenomics and phylogeography of grasses.},
}

@article {pmid40436818,
year = {2025},
author = {Cao, SH and Wan, Z and Johansen, E and Ma, G and Desai, P and Zhu, H and Wang, S},
title = {Plasmonic DNA-Barcoded Virion Nano-Oscillators for Multiplexed Quantification of Small-Molecule Binding Kinetics to Membrane Proteins.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202506464},
doi = {10.1002/anie.202506464},
pmid = {40436818},
issn = {1521-3773},
support = {R33CA235294/NH/NIH HHS/United States ; R42GM157918/NH/NIH HHS/United States ; },
abstract = {A high-density nano-oscillator platform using self-assembled DNA-barcoded virion sensors is developed to address the critical need for high-throughput label-free measurement of small-molecule binding to membrane proteins. By integrating virion display technology with charge-sensitive plasmonic detection, our platform enables robust, label-free quantification of small-molecule binding kinetics to membrane proteins. Gold nanoparticle-virion conjugates are self-assembled onto a plasmonic sensor chip via a flexible molecular linker to form high-density nano-oscillators. Driven by an alternating electric field, the oscillation amplitudes of the nano-oscillators are precisely measured via widefield plasmonic imaging. This charge-sensitive mechanism can sensitively detect the binding of small-molecule ligands to the membrane proteins displayed on the virions at single-nanosensor resolution, overcoming the sensitivity limit of conventional mass-sensitive techniques. More importantly, the platform employs novel affinity-discriminated DNA barcodes for multistate decoding with exponential multiplexing capacity, enabling high-throughput screening of a library of membrane proteins. For a proof-of-concept demonstration, binding kinetics of five pairs of G-protein-coupled receptors and their corresponding small molecule ligands are measured on a single sensor chip, with all individual nano-oscillators identified by just two affinity-discriminated, quadra-state DNA decoders. This technology advances membrane protein research and drug screening capabilities, offering a practical solution for biomolecular interaction studies and biosensing applications.},
}

@article {pmid40434228,
year = {2025},
author = {Cho, S and Moon, W and Martino, N and Yun, SH},
title = {Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e2418710},
doi = {10.1002/adma.202418710},
pmid = {40434228},
issn = {1521-4095},
support = {1541959//National Science Foundation/ ; R01-EB033155/NH/NIH HHS/United States ; R01-EB034687/NH/NIH HHS/United States ; },
abstract = {Laser particles (LPs) emitting narrowband spectra across wide spectral ranges are highly promising for high-multiplex optical barcoding of biological cells. Here, LPs based on indium phosphide (InP) nanodisks are presented, operating in the near-infrared wavelength range of 740-970 nm. Utilizing low-order whispering gallery resonance modes in size-tuned nanodisks, an ultrawide color palette with 25% spectral utilization and nanometer-scale linewidth is achieved. A simple theoretical model accurately predicts spectral ranges based on particle size. The minimum laser size is 430 nm in air and 560 nm within cells, operating at mode orders of 4 or 5. The high brightness and narrow linewidths of polymer-silica-protected InP LPs, combined with a silicon-detector spectrometer, enable spectral detection of laser peaks with high signal-to-background ratios in highly-scattering media, including 1-cm-thick chicken breast tissue and blood vessels in live mice.},
}

@article {pmid40433188,
year = {2024},
author = {Mahmud, BU and Hong, GY and Sharmin, A and Asher, ZD and Hoyle, JD},
title = {Accurate Medical Vial Identification Through Mixed Reality: A HoloLens 2 Implementation.},
journal = {Electronics},
volume = {13},
number = {22},
pages = {4420},
pmid = {40433188},
issn = {2079-9292},
abstract = {The accurate identification of medicine vials is crucial for emergency medical services, especially for vials that resemble one another but have different labels, volumes, and concentrations. This study introduces a method to detect vials in real-time using mixed reality technology through Microsoft HoloLens 2. The system is also equipped with an SQL server to manage barcode and vial information. We conducted a comparative analysis of the barcode detection capabilities of the HoloLens 2 camera and an external scanner. The HoloLens 2 effectively identified larger barcodes when they were 20-25 cm away in normal lighting conditions. However, it faced difficulties in detecting smaller barcodes that were consistently detected by the external scanner. The frame rate investigation revealed performance fluctuations: an average of 10.54 frames per second (fps) under standard lighting conditions, decreasing to 10.10 fps in low light and further reducing to 10.05 fps when faced with high barcode density. Resolution tests demonstrated that a screen resolution of 1920 × 1080 yielded the best level of accuracy, with a precision rate of 98%. On the other hand, a resolution of 1280 × 720 achieved a good balance between accuracy 93% and speed. The HoloLens 2 demonstrates satisfactory performance under ideal circumstances; however, enhancements in detecting algorithms and camera resolution are required to accommodate diverse surroundings. This approach seeks to help paramedics make quick and accurate decisions during critical situations and tackle common obstacles such as reliance on networks and human mistakes. Our new approach of a hybrid method that integrates an external Bluetooth scanner with the MR device gives optimal results compared to the scanner-only approach.},
}

@article {pmid40431228,
year = {2025},
author = {Hoxha, I and Dervović, J and Ruivo, M and Wijnveld, M and Obwaller, AG and Jäger, B and Weiler, M and Walochnik, J and Kniha, E and Alić, A},
title = {Molecular Typing of Tick-Borne Pathogens in Ixodids of Bosnia and Herzegovina.},
journal = {Microorganisms},
volume = {13},
number = {5},
pages = {},
doi = {10.3390/microorganisms13051054},
pmid = {40431228},
issn = {2076-2607},
support = {P33867//FWF Austrian Science Fund/ ; 886318//Austrian defense research program FORTE of the Federal Ministry of Finance (BMF)/ ; },
abstract = {Ticks are key vectors of zoonotic pathogens, and their expanding distribution in Europe heightens public health concerns. In Bosnia and Herzegovina, while tick distribution is well documented, molecular data on tick-borne pathogens remain limited. This study aimed to illustrate the presence and diversity of these pathogens, focusing on areas with high human activity. Ticks (n = 556) were collected in April 2022 from eight diverse locations, including urban parks, private properties, and rural sites. PCR-based screening was employed to detect Anaplasmataceae, Borrelia, Francisella, Piroplasmida, Rickettsia, and tick-borne encephalitis virus (TBEV), with subsequent sequencing to confirm results. Further characterization of Borrelia burgdorferi sensu lato was achieved via reverse line blotting (RLB) hybridization and sequencing. Ixodes ricinus was the most prevalent species, followed by Dermacentor marginatus and D. reticulatus. Our analysis revealed an overall infection rate of 22.1% in questing ticks, with Rickettsia spp. and Borrelia spp. predominating. Notably, seven Borrelia species were identified in I. ricinus, alongside Anaplasma phagocytophilum, Rickettsia helvetica, and R. monacensis, with co-infections mainly observed in peri-urban areas. This study provides the first molecular evidence of multiple tick-borne pathogens in the region, underscoring the need for further surveillance and risk assessment of tick-borne diseases in the region.},
}

@article {pmid40431057,
year = {2025},
author = {Wolella, EK and Cheng, Z and Li, M and Xia, D and Zhang, J and Duan, L and Liu, L and Li, Z and Zhang, J},
title = {Large-Scale Rice Mutant Establishment and High-Throughput Mutant Manipulation Help Advance Rice Functional Genomics.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/plants14101492},
pmid = {40431057},
issn = {2223-7747},
support = {YBXM2435//Nanfan special project of CAAS/ ; },
abstract = {Rice (Oryza sativa L.) is a stable food for over half of the world population, contributing 50-80% of the daily calorie intake. The completion of rice genome sequencing marks a significant milestone in understanding functional genomics, yet the systematic identification of gene functions remains a bottleneck for rice improvement. Large-scale mutant libraries in which the functions of genes are lost or gained (e.g., through chemical/physical treatments, T-DNA, transposons, RNAi, CRISPR/Cas9) have proven to be powerful tools for the systematic linking of genotypes to phenotypes. So far, using different mutagenesis approaches, a million mutant lines have been established and about 5-10% of the predicted rice gene functions have been identified due to the high demands of labor and low-throughput utilization. DNA-barcoding-based large-scale mutagenesis offers unprecedented precision and scalability in functional genomics. This review summarizes large-scale loss-of-function and gain-of-function mutant library development approaches and emphasizes the integration of DNA barcoding for pooled analysis. Unique DNA barcodes can be tagged to transposons/retrotransposons, DNA constructs, miRNA/siRNA, gRNA, and cDNA, allowing for pooling analysis and the assignment of functions to genes that cause phenotype alterations. In addition, the integration of high-throughput phenotyping and OMICS technologies can accelerate the identification of gene functions.},
}

@article {pmid40429242,
year = {2025},
author = {Ma, Y and Niu, L and Wang, B and Li, D and Gao, Y and Ha, S and Fan, B and Xiong, Y and Cong, B and Chen, J and Deng, J},
title = {Preliminary Development of Global-Local Balanced Vision Transformer Deep Learning with DNA Barcoding for Automated Identification and Validation of Forensic Sarcosaphagous Flies.},
journal = {Insects},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/insects16050529},
pmid = {40429242},
issn = {2075-4450},
support = {82060341//the National Natural Science Foundation of China/ ; YSPTZX202134//Innovation Platform for Academicians of Hainan Province/ ; Grant Number: Qhys2024-464//Innovative Research Projects for Postgraduates in Hainan Province/ ; },
abstract = {Morphological classification is the gold standard for identifying necrophilous flies, but its complexity and the scarcity of experts make accurate classification challenging. The development of artificial intelligence for autonomous recognition holds promise as a new approach to improve the efficiency and accuracy of fly morphology identification. In our previous study, we developed a GLB-ViT (Global-Local Balanced Vision Transformer)-based deep learning model for fly species identification, which demonstrated improved identification capabilities. To expand the model's application scope to meet the practical needs of forensic science, we extended the model based on the forensic science practice scenarios, increased the database of identifiable sarcosaphagous fly species, and successfully developed a WeChat Mini Program based on the model. The results show that the model can achieve fast and effective identification of ten common sarcosaphagous flies in Hainan, and the overall correct rate reaches 94.00%. For the few cases of identification difficulties and suspicious results, we have also constructed a rapid molecular species identification system based on DNA Barcoding technology to achieve accurate species identification of the flies under study. As the local fly database continues to be improved, the model is expected to be applicable to local forensic practice.},
}

@article {pmid40429233,
year = {2025},
author = {Huo, QB and Fan, SX and Zhu, YF and Du, YZ},
title = {Diversity and the Origin of Perlodinella Klapálek 1912 (Plecoptera: Perlodidae) in Qinghai Province, China.},
journal = {Insects},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/insects16050520},
pmid = {40429233},
issn = {2075-4450},
support = {32170459; 32370480//the National Natural Science Foundation of China/ ; },
abstract = {The article presents integrative research of the perlodid genus Perlodinella in Qinghai Province, northwestern China. P. tatunga Wu, 1973 is considered a junior synonym of P. kozlovi Klapálek, 1912, with a further description of intraspecific morphological variability, while P. unimacula Klapálek, 1912 is considered to be nomen dubium. The COI barcodes of the three valid species in Qinghai, P. epiproctalis (Zwick, 1997), P. kozlovi Klapálek, 1912, and P. microlobata Wu, 1938 are firstly sequenced, enabling adult-larva matching and the analysis of genetic diversity. The larval morphology of P. kozlovi and P. microlobata is described for the first time. Additionally, the biology, ecological adaptability, and fungal infections of Perlodinella are firstly recorded with an environment-related comparison. The discussion of the origin and immigration of the genus is also provided.},
}

@article {pmid40429198,
year = {2025},
author = {Jia, N and Niu, F and Wang, X and Chi, D and Yu, J},
title = {A New Threat to Conifer Cones: Cydia kamijoi (Oku, 1968) (Lepidoptera, Tortricidae), a New Record for China, Based on Morphological and DNA Barcoding Analyses.},
journal = {Insects},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/insects16050485},
pmid = {40429198},
issn = {2075-4450},
support = {No. 2022YFD1401004//National Key R & D Program of China/ ; No. 2572018BA06//Central University Basic Research Business Expenses Special Fund Project/ ; },
abstract = {Cydia kamijoi (Oku, 1968) (Lepidoptera, Tortricidae) is a pest of conifer cones. It was first found in Hokkaido, Japan and was considered to be an endemic species of Hokkaido, which was rarely reported. Here, we report C. kamijoi in China for the first time, whose larvae feed on Pinus koraiensis pine cones. Descriptions of the larval and adult morphology of C. kamijoi, along with the COI DNA barcoding data available and the phylogenetic analysis are provided for this species for the first time. The emergence of C. kamijoi has severely threatened the health of P. koraiensis cones. This work may have important implications for the pest control of P. koraiensis cones in Northeast China.},
}

@article {pmid40429151,
year = {2025},
author = {Huemer, P and Berggren, K and Aarvik, L and Rennwald, E and Hausmann, A and Segerer, A and Staffoni, G and Aspaas, AM and Trichas, A and Hebert, PDN},
title = {Extensive DNA Barcoding of Lepidoptera of Crete (Greece) Reveals Significant Taxonomic and Faunistic Gaps and Supports the First Comprehensive Checklist of the Island's Fauna.},
journal = {Insects},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/insects16050438},
pmid = {40429151},
issn = {2075-4450},
abstract = {Comprehensive genetic surveys of Lepidoptera are still largely lacking across most of the eastern Mediterranean. Consequently, there is a lack of modern, taxonomically validated checklists that meet current scientific standards. In this study, we analyze the butterfly and moth fauna of Crete (Greece) for the first time, based on 3110 DNA barcode sequences, primarily obtained from specimens based on our own sampling program. Building on these data, and incorporating previously published records from print sources and online forums, we establish the first comprehensive checklist of the island's fauna. In total, the occurrence of 1230 species from 62 families is confirmed, with 724 of them genetically verified. Among them, 75 species appear to be island endemics. The checklist includes 125 newly recorded species for Crete, validated by DNA barcoding (with 36 also being new for Greece), along with 23 species confirmed solely through morphological study, and another 16 only documented by photographs. Conversely, 212 previously reported species had to be removed as likely invalid. Furthermore, 112 unidentified sequence clusters (BINs-Barcode Index Numbers) were documented, taxonomic uncertainties that will require future integrative resolution.},
}

@article {pmid40426188,
year = {2025},
author = {Bourquia, M and Zahri, A and Ahlamine, M and Balenghien, T and Meyer, P and Sauer, FG and Lühken, R},
title = {First molecular confirmation of the presence of Hippobosca longipennis (Diptera: Hippoboscidae) and infestation of sheltered dogs in Morocco.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {193},
pmid = {40426188},
issn = {1756-3305},
support = {01Kl2022//Federal Ministry of Education and Research of Germany/ ; 01Kl2022//Federal Ministry of Education and Research of Germany/ ; 01Kl2022//Federal Ministry of Education and Research of Germany/ ; },
abstract = {BACKGROUND: Hippobosca longipennis (Diptera: Hippoboscidae) is an obligate hematophagous ectoparasite that infests a wide range of vertebrate hosts across Africa, Southern Europe, the Middle East, and Asia. It is a potential vector of Acanthocheilonema dracunculoides (Filarioidea: Onchocercidae) and serves as a phoretic host for Cheyletiella yasguri (Acari: Cheyletiellidae), a known causative agent of dermatitis in both dogs and humans. Due to the lack of data on hippoboscids in Morocco, this study aimed to investigate the louse fly fauna of sheltered dogs in the country as well as the filarial nematodes they may harbor.

METHODS: Between April and November 2022, 230 sheltered dogs from four cities in Central Morocco were randomly examined as part of an entomological and epidemiological study on arthropod vectors and canine vector-borne pathogens. All visible louse flies on the domestic dogs were randomly collected and then morphologically and molecularly identified. DNA was subsequently extracted for screening of filarial nematodes.

RESULTS: A total of 30 dogs (13.1%) were infested with 35 H. longipennis louse flies, consisting of 33 adults (10 males, 19 non-gravid females, and four gravid females) and two larvae. Two representative specimens were confirmed through DNA barcoding of the cytochrome oxidase subunit I gene. All fly pools (gravid females, non-gravid females, males, and larvae) tested negative for filarial nematodes in the 12S rRNA PCR.

CONCLUSIONS: This study represents the first morphological and molecular characterization of H. longipennis flies in Morocco. Further national-scale investigations are needed to address gaps in the knowledge of unrecorded hippoboscid species and the pathogens of medical and veterinary importance that they may carry.},
}

@article {pmid40424257,
year = {2025},
author = {He, Q and Lu, Q and Xie, N and Liu, X and Wang, X and Pan, J and Litchev, S and Hu, Y and Li, X and Zheng, B and Lin, J and Chen, E and Chen, XG and Zhou, X and Kong, Q and Lu, S},
title = {Real-time dynamic monitoring and multiplex PCR identification of vector mosquitoes in Zhejiang, China.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {5},
pages = {e0013129},
doi = {10.1371/journal.pntd.0013129},
pmid = {40424257},
issn = {1935-2735},
abstract = {The monitoring and identification of mosquito vectors are crucial for controlling the transmission of mosquito-borne diseases. Traditional mosquito morphological identification and surveillance methods, such as human landing catches, human-baited double net traps and BG-Sentinel mosquito traps, require a large amount of manpower but can only provide fragmented data. We utilized the MS-300, an internet-based vector mosquito monitor, to continuously capture and upload real-time data to cloud services across ten monitoring sites located in seven cities in Zhejiang Province, China from May to December 2023. A new multiplex PCR system was developed for amplifying the internal transcribed spacer 2 region, followed by employing both multiplex PCR and DNA barcoding techniques for detecting wild mosquitoes. A comprehensive monitoring of 9749 mosquitoes was conducted. The mosquito density gradually increased from May 2023, peaked around June 22nd, and then declined in a wave-like pattern. The mosquitoes have two peak activity times, the peak times may vary depending on different locations and seasons. The study showed the high specificity of a multiplex PCR system in distinguishing six mosquito species: Aedes albopictus, Aedes aegypti, Culex pipiens pallens, Armigeres subalbatus, Anopheles sinensis and Anopheles anthropophagus. Notably, the sensitivity of detecting An. anthropophagus reached an impressive 0.1fg/µL. With the exception of Ae. aegypti and An. anthropophagus, all four other mosquito species have been identified in Zhejiang Province, with Cx. p. pallens being the predominant population. The results were highly consistent with DNA barcoding technology. The MS-300 continuously and automatically monitors mosquito population density and activity, providing effective guidance for mosquito control based on the environment and reducing labor costs. Our newly established multiple PCR system enables precise identification of crucial vector mosquitoes, facilitating a comprehensive understanding of population structures across diverse regions for selecting effective control measures.},
}

@article {pmid40424190,
year = {2025},
author = {Guery, MA and Ceesay, S and Drammeh, S and Jaiteh, FK and D'Alessandro, U and Bousema, T and Conway, DJ and Claessens, A},
title = {Household clustering and seasonal genetic variation of Plasmodium falciparum at the community-level in The Gambia.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.103047},
pmid = {40424190},
issn = {2050-084X},
support = {NWO 016.158.306//Netherlands Organisation for Scientific Research/ ; INDIE OPP1173572//Bill and Melinda Gates Foundation/ ; MRC/LSHTM fellowship/MRC_/Medical Research Council/United Kingdom ; MRC/LSHTM fellowship//London School of Hygiene and Tropical Medicine/ ; Transversales//Centre National de la Recherche Scientifique/ ; ANR 18-CE15-0009-01//Agence Nationale de la Recherche/ ; EQU202303016290//Fondation pour la Recherche Médicale/ ; },
mesh = {Gambia/epidemiology ; *Plasmodium falciparum/genetics/isolation & purification/classification ; Humans ; *Seasons ; *Genetic Variation ; *Malaria, Falciparum/epidemiology/parasitology/transmission ; Longitudinal Studies ; Male ; Female ; Adolescent ; Adult ; *Family Characteristics ; Child ; Young Adult ; Genotype ; Child, Preschool ; Middle Aged ; Cluster Analysis ; Infant ; },
abstract = {Understanding the genetic diversity and transmission dynamics of Plasmodium falciparum, the causative agent of malaria, is crucial for effective control and elimination efforts. In some endemic regions, malaria is highly seasonal with no or little transmission during up to 8 mo, yet little is known about how seasonality affects the parasite population genetics. Here, we conducted a longitudinal study over 2.5 y on 1516 participants in the Upper River Region of The Gambia. With 425 P. falciparum genetic barcodes genotyped from asymptomatic infections, we developed an identity by descent (IBD) based pipeline and validated its accuracy against 199 parasite genomes sequenced from the same isolates. Genetic relatedness between isolates revealed a very low inbreeding level, suggesting continuous recombination among parasites rather than the dominance of specific strains. However, isolates from the same household were sixfold more likely to be genetically related compared to those from other villages, suggesting close transmission links within households. Seasonal variation also influenced parasite genetics, with most differentiation occurring during the transition from the low transmission season to the subsequent high transmission season. Yet chronic infections presented exceptions, including one individual who had a continuous infection by the same parasite genotype for at least 18 mo. Our findings highlight the burden of asymptomatic chronic malaria carriers and the importance of characterizing the parasite genetic population at the community-level. Most importantly, 'reactive' approaches for malaria elimination should not be limited to acute malaria cases but be broadened to households of asymptomatic carriers.},
}

Gambia/epidemiology
*Plasmodium falciparum/genetics/isolation & purification/classification
Humans
*Seasons
*Genetic Variation
*Malaria, Falciparum/epidemiology/parasitology/transmission
Longitudinal Studies
Male
Female
Adolescent
Adult
*Family Characteristics
Child
Young Adult
Genotype
Child, Preschool
Middle Aged
Cluster Analysis
Infant

@article {pmid40423701,
year = {2025},
author = {Krivina, E and Sinetova, M and Starikov, A and Anissimova, O and Temraleeva, A},
title = {Testing the Effectiveness of DNA Barcoding Markers and Species Delimitation Methods Within the Genus Coelastrella (Sphaeropleales, Chlorophyta), With a Description of Coelastrella polaris sp. nov. Isolated from Arctic Soils.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {311},
pmid = {40423701},
issn = {1432-0991},
support = {FMRM-2022-0019//Ministry of Science and Higher Education of the Russian Federation/ ; 21-74-30003//Russian Science Foundation/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Phylogeny ; *Soil Microbiology ; Arctic Regions ; *Chlorophyta/genetics/classification ; Russia ; DNA, Ribosomal Spacer/genetics ; Fatty Acids/analysis ; },
abstract = {The species diversity in the genus Coelastrella is not yet fully unclarified, particularly with regard to algal communities in ecosystems characterized by extreme climatic conditions, such as those found in polar regions. The study objects were strains VKM Al-421, VKM Al-488, and VKM Al-489 isolated from the soils of the Far North, Russian Federation. The analysis of the 18S-ITS1-5.8S-ITS2 fragment revealed that these strains represent a unique phylogenetic lineage outside the 'core Coelastrella' group. The species status is also confirmed by morphological differences between the studied species and its sister species (absence of edges) (lack of ribs), interspecific genetic distances, the presence of compensatory base changes in the internal transcribed spacers ITS1 and ITS2, as well as the results of delimitation using various algorithms applied to both the full-length fragment and shorter barcodes. The strain VKM Al-421 of the new species exhibits a fatty acid profile characteristic of the genus Coelastrella; however, it differs from closely related strains due to the presence of Δ7,10,13-hexadecatrienoic acid and a notably high concentration of α-linolenic acid. These features may indicate an adaptation to polar regions. In addition, the studied strain has the potential to be used as a producer of α-linolenic acid, which is essential for human health. A detailed comparative analysis of the effectiveness of different DNA barcodes showed that ITS2 is the most promising for distinguishing species within Coelastrella. Among all species delimitation algorithms, GMYC is the most accurate when working with variable barcodes. At the same time, the less laborious KoT algorithm demonstrated a similar level of accuracy for ITS1.},
}

*DNA Barcoding, Taxonomic/methods
Phylogeny
*Soil Microbiology
Arctic Regions
*Chlorophyta/genetics/classification
Russia
DNA, Ribosomal Spacer/genetics
Fatty Acids/analysis

@article {pmid40415972,
year = {2025},
author = {Awad, J and Reinisch, R and Moser, M and Vasilița, C and Krogmann, L},
title = {Untangling host specialization in a "double dark taxa" system.},
journal = {Annals of the Entomological Society of America},
volume = {118},
number = {3},
pages = {206-219},
pmid = {40415972},
issn = {0013-8746},
abstract = {Platygastrine wasps (Hymenoptera: Platygastridae) are parasitoids of gall midges (Diptera: Cecidomyiidae). They and their hosts are exceptionally abundant and speciose, with great relevance to agriculture and biodiversity research. Both groups are also "dark taxa," whose species identification and ecological associations are obscured by a history of taxonomic confusion and neglect. Verified host records are few in number and limited in scope. In order to understand host specialization, more records are needed. However, rearing Cecidomyiidae is challenging, as many species require living host tissue to complete development. There is no universal rearing method for Cecidomyiidae and their parasitoids. The present work applies an exploratory approach to rearing gall midges, with the aim of obtaining accurate host associations and parasitoid identifications. We obtained 5 species of Platygastrinae from reared material, 3 of which are identified and diagnosed. Platygaster demades Walker (= Platygaster marchali Kieffer, syn. nov. = Platygaster ornata Kieffer, syn. nov.) is not host-specific, attacking Cecidomyiidae on Rosaceae worldwide, including Filipendula ulmaria. Synopeas gibberosum Buhl apparently specializes on Dasineura ulmaria (Bremi) on F. ulmaria. Synopeas rhanis (Walker) is known only from galls of D. urticae (Perris), but may attack other midge species on Urtica dioica. Amblyaspis sp. emerged from Hartigiola annulipes (Hartig) galls on Fagus sylvatica, and Synopeas sp. was associated with Mycodiplosis sp. on Rubus sp. Illustrations, DNA barcodes, and distributions are provided. We discuss challenges to understanding "double dark taxa" interactions, implications for biological control, and possible solutions for future research on these important but neglected systems.},
}

@article {pmid40413466,
year = {2025},
author = {Novianto, D and Tuangpermsub, S and Ngamprasertwong, T and Kaewthamasorn, M},
title = {Host associations and genetic diversity of bat flies (Diptera: Nycteribiidae and Streblidae) in bats from Thailand.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {188},
pmid = {40413466},
issn = {1756-3305},
mesh = {Animals ; Thailand/epidemiology ; *Diptera/genetics/classification/physiology ; *Genetic Variation ; Phylogeny ; *Chiroptera/parasitology ; *Host-Parasite Interactions ; Male ; Female ; DNA Barcoding, Taxonomic ; Haplotypes ; *Ectoparasitic Infestations/veterinary/parasitology/epidemiology ; RNA, Ribosomal, 28S/genetics ; },
abstract = {BACKGROUND: Bat flies belong to the order Diptera and superfamily Hippoboscoidea. They can be divided into two families, Streblidae and Nycteribiidae, which collectively encompass 239 and 280 species worldwide, respectively. In Thailand, 43 species of Nycteribiidae and 16 species of Streblidae have been documented. Despite their diversity, the molecular characteristics and host-parasite interactions of these ectoparasites remain poorly understood.

METHODS: During a bat survey conducted between 2019 and 2022, bat flies were collected across eight sites in three provinces of Thailand. Morphological identification was performed using identification keys and a bat fly checklist endemic to Thailand. DNA barcoding targeted to the mitochondrial Cox1 and nuclear 28S rRNA genes was utilized. Infestation patterns were analyzed in relation to host sex, sampling site, and physiological status. Species identification was confirmed via BLASTN searches, and species delimitation was conducted using the ASAP algorithm under three substitution models. Phylogenetic relationships were inferred using Maximum Likelihood methods, while genetic variation was assessed through TCS haplotype network analysis. Tripartite network analysis was employed to examine site-host-parasite associations.

RESULTS: A total of 1,042 bats, representing 28 species, were captured during the study, of which 298 individuals (28.59%) were infested with bat flies. In total, 773 bat flies were collected, comprising 737 from the family Streblidae and 36 from Nycteribiidae. Morphological and molecular analyses identified three genera-Raymondia, Brachytarsina, and Nycteribia-along with seven hypothetical species. Phylogenetic reconstruction using mitochondrial (Cox1) and nuclear (28S rRNA) gene markers revealed distinct clades within each genus, underscoring substantial genetic diversity. Haplotype analyses identified 18 haplotypes in Raymondia, six in Brachytarsina, and two in Nycteribia, with evidence of site-specific host-parasite associations. Infestation rates varied by host species, sex, and location, with larger bat populations demonstrating higher infestation intensities. Raymondia sp. 1 is the most frequently encountred species an predominantly infested Hipposideros gentilis.

CONCLUSIONS: This study provides the first molecular characterization of bat fly diversity in Thailand, revealing their genetic complexity, taxonomy, host specificity, and ecological interactions. The findings establish a crucial foundation for further research concerning the biodiversity, host-parasite dynamics, and zoonotic risks associated with bat flies.},
}

Animals
Thailand/epidemiology
*Diptera/genetics/classification/physiology
*Genetic Variation
Phylogeny
*Chiroptera/parasitology
*Host-Parasite Interactions
Male
Female
DNA Barcoding, Taxonomic
Haplotypes
*Ectoparasitic Infestations/veterinary/parasitology/epidemiology
RNA, Ribosomal, 28S/genetics

@article {pmid40413247,
year = {2025},
author = {Ferreira, C and Martins, T and Melo, L and Veneza, I and Santana, P and Miranda, J and Lutz, Í and Sousa, J and Cardoso, B and Miranda, A and da Costa, JL and Matos, S and Holanda, FC and Vallinoto, M and Sampaio, I and Evangelista-Gomes, G},
title = {DNA reveal new invasive species of tiger shrimp Penaeus monodon (Penaeidae) along the world's largest mangrove region in the Brazilian Blue Amazon.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {18058},
pmid = {40413247},
issn = {2045-2322},
support = {CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; CNPq (407536/2021-3).//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Penaeidae/genetics/classification ; Brazil ; DNA Barcoding, Taxonomic ; *Introduced Species ; Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Wetlands ; Biodiversity ; Haplotypes ; Ecosystem ; *DNA/genetics ; },
abstract = {Bioinvasions represent a major environmental issue, particularly when they take place in biodiversity hotspots, such as mangrove ecosystems that serve as shelter for many marine species and fisheries resources. In this work, we used an integrative approach based on DNA and morphological analyses to identify individuals and the putative presence of cryptic diversity in the invasive tiger prawn (Penaeus monodon) along a mangrove area on the northern coast of Brazil, referred to as "Blue Amazon". A fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was selected for DNA Barcode and associated with distance-based (ABGD-Automatic Barcode Gap Discovery) and probabilistic (GMYC-Generalized Mixed Yule Coalescent and bPTP-Bayesian Poisson tree processes) species delimitation methods. Furthermore, the maternal origin of collected specimens was tracked. The molecular analyses recovered two genetically divergent lineages (7.7%) within the tiger prawn, indicating the occurrence of two species of this bioinvader on the northern coast of Brazil. Even though no differences in external morphology were detected, both lineages could be differentiated by their internal structures. The molecular traceability of the origin of samples showed that lineages I and II shared haplotypes with specimens from 11 and nine countries, respectively, including a shrimp breeding center in Vietnam. This is the first record of two species of tiger prawn along the Brazilian continental shelf. These findings are useful to the development of effective management policies in a region of particular biological relevance.},
}

Animals
*Penaeidae/genetics/classification
Brazil
DNA Barcoding, Taxonomic
*Introduced Species
Phylogeny
Electron Transport Complex IV/genetics
Genetic Variation
Wetlands
Biodiversity
Haplotypes
Ecosystem
*DNA/genetics

@article {pmid40411728,
year = {2025},
author = {Laskar, BA and Adimalla, H and Banerjee, D and Song, SH and Kang, HE and Kim, HW and Kundu, S},
title = {Integrative morphometric and phylogenetic insights into Eastern Ghats channids (Teleostei: Channidae) unveil the transboundary dispersal of the Dwarf Snakehead (Channa kelaartii) across India and Sri Lanka.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {499},
pmid = {40411728},
issn = {1573-4978},
support = {This work was supported by a Research Grant of Pukyong National University (2024)//Pukyong National University, South Korea/ ; },
mesh = {Sri Lanka ; India ; Animals ; Phylogeny ; Genetic Variation/genetics ; *Fishes/genetics/classification/anatomy & histology ; Haplotypes/genetics ; Bayes Theorem ; Phylogeography ; Genetics, Population ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: The biogeography of Eastern Ghats channids, including the Dwarf Snakehead Channa kelaartii, poses a complex challenge, especially with recent evidence confirming its presence in both India and Sri Lanka. While the Sri Lankan population is well- documented through integrative approach, the Indian population remains unexplored, requiring further research to elucidate its genetic structure and phylogenetic relationships.

METHODS: This study examines the morphology and mtCOI-based genetic diversity of 10 channid species, including seven from the Gachua complex. An integrative approach is also applied to assess population-level variation in C. kelaartii, aiming to clarify its genetic diversity with geographically isolated Sri Lankan populations.

RESULTS: Morphological analysis distinctly identified all Channa species and indicated a close resemblance between Indian and Sri Lankan C. kelaartii populations. Genetic analysis revealed considerable divergence between C. kelaartii and other members of the Gachua group, ranging from 6.15 to 21.31%. Bayesian phylogenetic reconstruction robustly resolved all species, including C. kelaartii. Combined mitochondrial data from India and Sri Lanka revealed 13 haplotypes, with mean intra-regional genetic distances of 0.5% (Sri Lanka) and 0.7% (India), and maximum divergences of 1.24% and 2.29%, respectively. A haplotype from the Western Ghats exhibited only 0.17% divergence from Sri Lankan populations, indicating potential historical gene flow between the two regions.

CONCLUSIONS: Overall, this study provides a comprehensive assessment of Channa diversity in the Eastern Ghats and confirms the presence of C. kelaartii in both peninsular India and Sri Lanka, likely shaped by historical land connections and freshwater dispersal across the Palk Isthmus during the Plio-Pleistocene.},
}

Sri Lanka
India
Animals
Phylogeny
Genetic Variation/genetics
*Fishes/genetics/classification/anatomy & histology
Haplotypes/genetics
Bayes Theorem
Phylogeography
Genetics, Population
DNA, Mitochondrial/genetics

@article {pmid40410279,
year = {2025},
author = {Liao, H and Chen, H and Liu, S},
title = {The complete chloroplast genomes of four Aspidopterys species and a comparison with other Malpighiaceae species.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17893},
pmid = {40410279},
issn = {2045-2322},
mesh = {*Genome, Chloroplast ; Phylogeny ; Base Composition ; Microsatellite Repeats ; },
abstract = {The genus Aspidopterys has multiple functions in medicine, food and ecological restoration. Due to the similar morphological characteristics of some species and the limited genomic information hinder the studies on germplasm identification and molecular phylogeny analysis. In this study, we compared and explored the six complete chloroplast (cp) genomes including four Aspidopterys species (A. glabriuscula, A. concava, A. cavaleriei, A. obcordata), Banisteriopsis caapi and Bunchosia argentea. Their cp genomes in length were 158,473 to 161,091 bp, displaying the high conserved degree in the structure, gene arrangement and GC content. Moreover, 57-80 long repeats and 61-92 SSRs were identified, most of which were forward or palindromic repeats and mononucleotides, respectively. Eleven non-coding regions and 12 coding regions, especially ndhH_ndhA, rpl32_ndhF and ycf1, had the higher nucleotide diversity values that could can be regarded as DNA barcodes of Malpighiaceae species. In addition, the 9 genes (like accD, atpE, atpF, clpP) were conducted positive selection (Ka/Ks > 1). As indicated by phylogenetic analysis, those four Aspidopterys were clustered into single clade with other Malpighiaceae species and were closely related to B. caapi and B. argentea. This study sheds more lights on further phylogenetic, evolutionary and genetic diversity studies on the genus Aspidopterys and even the Malpighiaceae species.},
}

*Genome, Chloroplast
Phylogeny
Base Composition
Microsatellite Repeats

@article {pmid40409527,
year = {2025},
author = {Schols, R and Henrard, A and Brecko, J and Mudavanhu, A and Goossens, E and Steffanie, N and Clegg, S and Vanhove, MPM and Huyse, T},
title = {Innovating stomach fluke identification: An integrative approach combining Micro-CT imaging and molecular tools.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.05.002},
pmid = {40409527},
issn = {1879-0135},
abstract = {The rapid loss of biodiversity driven by anthropogenic pressures highlights the urgent need for improved species identification methods. Parasites, vital ecosystem regulators, are being lost at disproportionate rates, with amphistomes-a broadly distributed group of trematode parasites, infecting all major vertebrate groups-facing significant challenges. Many amphistome species remain undescribed, and reference sequences for known species are scarce, partly due to the reliance on labour-intensive identification methods, such as Scanning Electron Microscopy (SEM) and median sagittal sections. While sagittal sectioning is particularly informative for diagnostic traits, it is destructive, requires toxic chemicals, and demands specialized personnel. In this study, we evaluated micro-computed tomography (micro-CT) imaging as a non-destructive alternative for identifying three amphistome species, Gigantocotyle gigantocotyle (Brandes in Otto, 1896); Carmyerius aff. chabaudi van Strydonck, 1970; and Carmyerius aff. endopapillatus Dollfus, 1962, isolated from the common hippopotamus, Hippopotamus amphibius Linnaeus, 1758. By comparing micro-CT imaging with traditional sectioning, SEM and incorporating molecular barcoding, we reveal the need for a taxonomic revision of Carmyerius, focussed on identifying new diagnostic characters, to better reflect species boundaries. Moreover, the integrated taxonomic effort represented in this work uncovered evidence that C. aff. chabaudi is a new species record from the common hippopotamus. Additionally, we provide high-resolution images of the original type specimens of Carmyerius cruciformis (Leiper, 1910) and G. gigantocotyle and designate new lectotypes and paralectotypes. Our findings demonstrate that micro-CT imaging is a powerful, non-invasive tool for amphistome identification, facilitating access to fragile natural history collections and advancing integrative taxonomy.},
}

@article {pmid40408506,
year = {2025},
author = {Blois, S and Goetz, BM and Mojumder, A and Sullivan, CS},
title = {Shedding dynamics of a DNA virus population during acute and long-term persistent infection.},
journal = {PLoS pathogens},
volume = {21},
number = {5},
pages = {e1013083},
doi = {10.1371/journal.ppat.1013083},
pmid = {40408506},
issn = {1553-7374},
abstract = {Although much is known of the molecular mechanisms of virus infection within cells, substantially less is understood about within-host infection. Such knowledge is key to understanding how viruses take up residence and transmit infectious virus, in some cases throughout the life of the host. Here, using murine polyomavirus (muPyV) as a tractable model, we monitor parallel infections of thousands of differentially barcoded viruses within a single host. In individual mice, we show that numerous viruses (>2600) establish infection and are maintained for long periods post-infection. Strikingly, a low level of many different barcodes is shed in urine at all times post-infection, with a minimum of at least 80 different barcodes present in every sample throughout months of infection. During the early acute phase, bulk shed virus genomes derive from numerous different barcodes. This is followed by long term persistent infection detectable in diverse organs. Consistent with limited productive exchange of virus genomes between organs, each displays a unique pattern of relative barcode abundance. During the persistent phase, constant low-level shedding of typically hundreds of barcodes is maintained but is overlapped with rare, punctuated shedding of high amounts of one or a few individual barcodes. In contrast to the early acute phase, these few infrequent highly shed barcodes comprise the majority of bulk shed genomes observed during late times of persistent infection, contributing to a stark decrease in bulk barcode diversity that is shed over time. These temporally shifting patterns, which are conserved across hosts, suggest that polyomaviruses balance continuous transmission potential with reservoir-driven high-level reactivation. This offers a mechanistic basis for polyomavirus ubiquity and long-term persistence, which are typical of many DNA viruses.},
}

@article {pmid40405610,
year = {2025},
author = {Liu, L and Ju, P and Yang, K and Li, X and Duan, K and Xie, J and Liu, M and Chen, J and Luo, R},
title = {Extended Linear Confined Zipper Cascaded Reaction for Highly Efficient Intracellular Imaging and Assisting Diagnosis of Thyroid Cancer.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2500202},
doi = {10.1002/smll.202500202},
pmid = {40405610},
issn = {1613-6829},
support = {82302621//National Natural Science Foundation of China/ ; KJQN202300435//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0183//Future Medical Youth Innovation Team Development Support Program Project of Chongqing Medical University/ ; CSTB2023TIAD-STX0040//Technological Innovation and Application Development/ ; },
abstract = {Highly sensitive detection and in situ tracing analysis of small-molecule biomarkers are particularly indispensable to deciphering the pathogenesis and pathological process. Despite DNA assembly-based barcoding and amplification strategies across the breadth of molecular in situ analysis, an easy-to-design, nonenzymatic, highly efficient, background leakage-avoided, highly specific, and sensitive system is highly required yet is still in its infancy. Spatial confinement nano-assembly can increase the reaction efficiency in a localized isothermal autonomous manner. Here in this work, the DNA assembly that originally relies on random collisions between freely diffusing probes is constructed between two extended linear confined probes, by which a novel confined reaction model named as extended linear confined zipper hybridization chain reaction (ZHCR) is proposed. ZHCR can significantly improve the efficiency of probe assembly and enable stable assembly within live cells, providing precise in situ target information. ZHCR system is employed to analyze two thyroid cancer-specific miRNAs, achieving in situ tracing and serum content detection. By integrating machine learning algorithms, ZHCR demonstrates significant potential in thyroid cancer auxiliary diagnosis, establishing a versatile platform that enables both highly sensitive homogeneous detection and in situ analysis of low-abundance nucleic acid fragments.},
}

@article {pmid40404925,
year = {2025},
author = {Xu, Z and Wang, Y and Cai, W and Chen, Y and Wang, Y},
title = {Single microorganism RNA sequencing of microbiomes using smRandom-Seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40404925},
issn = {1750-2799},
support = {32200073//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32250710678//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82200977//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Bacteria colonize nearly every part of the human body and various environments, displaying remarkable diversity. Traditional population-level transcriptomics measurements provide only average population behaviors, often overlooking the heterogeneity within bacterial communities. To address this limitation, we have developed a droplet-based, high-throughput single-microorganism RNA sequencing method (smRandom-seq) that offers highly species specific and sensitive gene detection. Here we detail procedures for microbial sample preprocessing, in situ preindexed cDNA synthesis, in situ poly(dA) tailing, droplet barcoding, ribosomal RNA depletion and library preparation. The main smRandom-seq workflow, including sample processing, in situ reactions and library construction, takes ~2 days. This method features enhanced RNA coverage, reduced doublet rates and minimized ribosomal RNA contamination, thus enabling in-depth analysis of microbial heterogeneity. smRandom-seq is compatible with microorganisms from both laboratory cultures and complex microbial community samples, making it well suited for constructing single-microorganism transcriptomic atlases of bacterial strains and diverse microbial communities. This Protocol requires experience in molecular biology and RNA sequencing techniques, and it holds promising potential for researchers investigating bacterial resistance, microbiome heterogeneity and host-microorganism interactions.},
}

@article {pmid40401933,
year = {2025},
author = {Das, J and Pal, S and Negi, A and Sundharam, SS and Yadav, A and Subramanian, S and Sinha, SK and Samanta, J and Krishnamurthi, S},
title = {Genomic insights into novel predatory myxobacteria isolated from human feces.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0214724},
doi = {10.1128/spectrum.02147-24},
pmid = {40401933},
issn = {2165-0497},
abstract = {Myxobacteria are Gram-negative, spore-forming predatory bacteria isolated from diverse environmental samples that feed on other microbes for their survival and growth. However, no reports of cultured representatives from the human gut have been published to date, although previous investigations have revealed the presence of myxobacterial operational taxonomic units (OTUs) in skin and fecal samples. In this study, three myxobacterial strains designated as O35, O15, and Y35 were isolated and purified from fecal samples of two inflammatory bowel disease (IBD) patients. The 16S rRNA gene sequence analysis and phylogeny identified the strains as Myxococcus spp. belonging to two different clades. Genome-based phylogeny and overall genome-related indices, i.e., average amino acid identity and percentage of conserved proteins, confirmed the heterogeneity within the genus and placed the three strains within two different clades separated at the level of different genera. Digital DNA-DNA hybridization and average nucleotide identity values indicated that they belonged to two novel Myxococcus spp. The analysis of meta-barcoding data from IBD and control cohorts detected OTU lineages closely affiliated to the three novel strains. Based on evidence from detailed structural and functional genomics, we propose the novel species Myxococcus faecalis sp. nov. O35[T] and a new genus Pseudomyxococcus gen. nov. to accommodate the novel species Pseudomyxococcus flavus sp. nov. Y35[T]. Overall, these findings provide new information about the occurrence of myxobacteria in the human gut and lay the foundations for a new classification scheme for myxobacterial taxa.IMPORTANCEMyxobacteria have been described from a variety of niches ranging from terrestrial to marine habitats and are known to harbor a diverse portfolio of bioactive molecules. However, to date, there has been no report of isolating culturable representatives from the human gut. This study describes novel myxobacteria from the human gut based on phylogenomics and phenotypic description. The findings are complemented by sequence-based data, wherein operational taxonomic unit (OTU) lineages closely affiliated with the isolated strains have been identified, thus opening a Pandora's box of opportunities for research into the microbial ecology and functional potential of these taxa in the gut ecosystem. Additionally, the study also seeks to establish a new systematic framework, expanding our understanding of myxobacterial taxonomy.},
}

@article {pmid40401310,
year = {2025},
author = {Wang, Y and Liu, D and Wang, R and Chen, A and Fang, X},
title = {An orthogonal barcoding enabled smart nanodevice for highly efficient isolation and proteomic profiling of tumor-derived extracellular vesicles.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5an00348b},
pmid = {40401310},
issn = {1364-5528},
abstract = {Tumor-derived extracellular vesicles (T-EVs) are small, membrane-bound particles secreted by cancer cells into the extracellular environment. These vesicles carry tumor-specific molecules, making them promising candidates as biomarkers for cancer diagnosis and monitoring. Among the various molecular components of T-EVs, such as nucleic acids and lipids, proteins stand out due to their unique characteristics and functional significance in cancer progression, diagnosis, and therapy. However, the heterogeneity of T-EVs poses a significant challenge to their effective utilization. Herein, we developed an orthogonal barcoding enabled smart nanodevice for the isolation of T-EVs and proteomic profiling. The T-EVs subpopulations were recognized from complex clinical samples, specifically through an orthogonal labeling barcode, which was created using two allosteric aptamers against the exosomal marker CD63 and the tumor marker EpCAM. Simultaneously, the labeled barcode on T-EVs initiated targeted binding with the DNA complementary tag modified mesoporous silica foam (MOSF-tag), achieving in situ exosomal protein extraction and digestion within the nanopores of the MOSF-tag. This integrated strategy not only streamlines the process by eliminating complex steps and minimizing sample loss but also significantly enhances protein identification efficiency. Compared to traditional methods for T-EVs isolation and protein digestion, the smart nanodevice has demonstrated a remarkable improvement in the detection of exosomal proteins and specific proteins from the cell culture medium. As a proof of concept, we applied this strategy to serum samples from prostate cancer (PCa) patients, confirming its efficacy. A total of 832 proteins were identified, with 211 showing differential expression between patients and healthy controls. Among these, 113 proteins were significantly upregulated in the PCa group. These uniquely expressed proteins are likely associated with PCa development, invasion, and metastasis, highlighting their potential as biomarkers for the early diagnosis and prognosis of PCa in the future. This innovative approach not only advances the field of T-EVs research but also opens new avenues for the discovery of clinically relevant biomarkers in cancer.},
}

@article {pmid40400687,
year = {2025},
author = {Guerrero-Flores, S and Contreras-Peruyero, H and Ibarra-Rodríguez, JM and Lovaco-Flores, JA and Nieto-de la Rosa, FS and Fontove-Herrera, F and Sélem-Mojica, N},
title = {Topological data analysis captures horizontal gene transfer in antimicrobial resistance gene families among clinically relevant bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1461293},
pmid = {40400687},
issn = {1664-302X},
abstract = {Antibiotic resistance, projected to cause 10 million deaths annually by 2050, remains a critical health threat. Hospitals drive multidrug resistance via horizontal gene transfer. The 2023 Critical Assessment of Massive Data Analysis challenge presents resistance markers from 146 Johns Hopkins bacterial isolates, aiming to analyze resistomes without metadata or genomic sequences. Persistent homology, a topological data analysis method, effectively captures processes beyond vertical inheritance. A 1-hole is a topological feature representing a loop or gap in the data, where relationships form a circular structure rather than a linear one. Unlike vertical inheritance, which lacks topological 1-holes, horizontal gene transfer generates distinct patterns. Since antimicrobial resistance genes often spread via horizontal gene transfer, we simulated vertical and horizontal inheritance in bacterial resistomes. The number of 1-holes from simulations and a documented horizontal gene transfer case was analyzed using persistence barcodes. In a simulated population of binary sequences, we observed that, on average, two 1-holes form for every three genomes undergoing horizontal gene transfer. Using a presence-absence gene table, we confirmed the existence of 1-holes in a documented case of horizontal gene transfer between two bacterial genera in a Pittsburgh hospital. Notably, the Critical Assessment of Massive Data Analysis resistomes of Klebsiella and Escherichia exhibit 1-holes, while Enterobacter shows none. Lastly, we provide a mathematical example of a non-tree-like space that contains no 1-holes. Persistent homology provides a framework for uncovering complex clinical patterns, offering an alternative to understanding resistance mobility using presence-absence data, which could be obtained through methods beyond genomic sequencing.},
}

@article {pmid40399693,
year = {2025},
author = {Ishiguro, S and Ishida, K and Sakata, RC and Ichiraku, M and Takimoto, R and Yogo, R and Kijima, Y and Mori, H and Tanaka, M and King, S and Tarumoto, S and Tsujimura, T and Bashth, O and Masuyama, N and Adel, A and Toyoshima, H and Seki, M and Oh, JH and Archambault, AS and Nishida, K and Kondo, A and Kuhara, S and Aburatani, H and Klein Geltink, RI and Yamamoto, T and Shakiba, N and Takashima, Y and Yachie, N},
title = {A multi-kingdom genetic barcoding system for precise clone isolation.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40399693},
issn = {1546-1696},
abstract = {Cell-tagging strategies with DNA barcodes have enabled the analysis of clone size dynamics and clone-restricted transcriptomic landscapes in heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here we present a multi-kingdom genetic barcoding system, CloneSelect, which enables a target cell clone to be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first stably tagged with DNA barcodes and propagated so that their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored during the experiment using CRISPR base editing. CloneSelect is scalable and compatible with single-cell RNA sequencing. We demonstrate the versatility of CloneSelect in human embryonic kidney 293T cells, mouse embryonic stem cells, human pluripotent stem cells, yeast cells and bacterial cells.},
}

@article {pmid40399676,
year = {2025},
author = {Chen, Q and Schafer, CT and Mukherjee, S and Wang, K and Gustavsson, M and Fuller, JR and Tepper, K and Lamme, TD and Aydin, Y and Agrawal, P and Terashi, G and Yao, XQ and Kihara, D and Kossiakoff, AA and Handel, TM and Tesmer, JJG},
title = {Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40399676},
issn = {1476-4687},
abstract = {Unique phosphorylation 'barcodes' installed in different regions of an active seven-transmembrane receptor by different G-protein-coupled receptor (GPCR) kinases (GRKs) have been proposed to promote distinct cellular outcomes[1], but it is unclear whether or how arrestins differentially engage these barcodes. Here, to address this, we developed an antigen-binding fragment (Fab7) that recognizes both active arrestin2 (β-arrestin1) and arrestin3 (β-arrestin2) without interacting with bound receptor polypeptides. We used Fab7 to determine the structures of both arrestins in complex with atypical chemokine receptor 3 (ACKR3) phosphorylated in different regions of its C-terminal tail by either GRK2 or GRK5 (ref. [2]). The GRK2-phosphorylated ACKR3 resulted in more heterogeneous 'tail-mode' assemblies, whereas phosphorylation by GRK5 resulted in more rigid 'ACKR3-adjacent' assemblies. Unexpectedly, the finger loops of both arrestins engaged the micelle surface rather than the receptor intracellular pocket, with arrestin3 being more dynamic, partly because of its lack of a membrane-anchoring motif. Thus, both the region of the barcode and the arrestin isoform involved can alter the structure and dynamics of GPCR-arrestin complexes, providing a possible mechanistic basis for unique downstream cellular effects, such as the efficiency of chemokine scavenging and the robustness of arrestin binding in ACKR3.},
}

@article {pmid40399669,
year = {2025},
author = {Scherer, M and Singh, I and Braun, MM and Szu-Tu, C and Sanchez Sanchez, P and Lindenhofer, D and Jakobsen, NA and Körber, V and Kardorff, M and Nitsch, L and Kautz, P and Rühle, J and Bianchi, A and Cozzuto, L and Frömel, R and Beneyto-Calabuig, S and Lareau, C and Satpathy, AT and Beekman, R and Steinmetz, LM and Raffel, S and Ludwig, LS and Vyas, P and Rodriguez-Fraticelli, A and Velten, L},
title = {Clonal tracing with somatic epimutations reveals dynamics of blood ageing.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40399669},
issn = {1476-4687},
abstract = {Current approaches used to track stem cell clones through differentiation require genetic engineering[1,2] or rely on sparse somatic DNA variants[3,4], which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity. We demonstrate that targeted single-cell profiling of DNA methylation[5] at single-CpG resolution can accurately extract both layers of information. To that end, we develop EPI-Clone, a method for transgene-free lineage tracing at scale. Applied to mouse and human haematopoiesis, we capture hundreds of clonal differentiation trajectories across tens of individuals and 230,358 single cells. In mouse ageing, we demonstrate that myeloid bias and low output of old haematopoietic stem cells[6] are restricted to a small number of expanded clones, whereas many functionally young-like clones persist in old age. In human ageing, clones with and without known driver mutations of clonal haematopoieis[7] are part of a spectrum of age-related clonal expansions that display similar lineage biases. EPI-Clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.},
}

@article {pmid40399518,
year = {2025},
author = {},
title = {Patterns of DNA modifications provide a 'barcode' for cell-lineage tracing.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40399518},
issn = {1476-4687},
}

@article {pmid40396603,
year = {2025},
author = {Verneau, O and Quinn, D and Smith, KG and Malone, JH and du Preez, L},
title = {Role of Trachemys scripta elegans in polystome (Platyhelminthes, Monogenea, Polystomatidae) spillover and spillback following the trade of freshwater turtles in southern Europe and North America.},
journal = {Parasite (Paris, France)},
volume = {32},
number = {},
pages = {30},
doi = {10.1051/parasite/2025022},
pmid = {40396603},
issn = {1776-1042},
mesh = {Animals ; *Turtles/parasitology ; *Introduced Species ; Fresh Water ; North America ; Europe ; Phylogeny ; Ecosystem ; Commerce ; *Trematode Infections/veterinary/parasitology/transmission/epidemiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Trematoda/genetics/classification ; },
abstract = {The red-eared slider, Trachemys scripta elegans (Wied, 1938), has been introduced worldwide, partly because of the exotic pet trade in the 1980s and 1990s. When T. s. elegans is released or escapes into natural environments, it often establishes new feral populations due to its tolerance for a variety of aquatic ecosystems. Therefore, it is now considered one of the most invasive species in the world because it can compete with native turtle species. In the present study, our objectives were to identify the potential for polystome spillover and spillback resulting from the introduction of the red-eared slider into new environments in North America. Fieldwork investigations were thus conducted mainly in aquatic habitats in Florida and North Carolina, United States, but also in Connecticut, Indiana, Kansas, Maine, Nebraska and New York. Using DNA barcoding based on cytochrome c oxidase I (COI) sequences, we surveyed the species diversity of polystome within American freshwater turtles. These included T. s. elegans but also Apalone ferox, Apalone spinifera, Chelydra serpentina, Chrysemys picta, Kinosternon baurii, Pseudemys spp., Sternotherus minor and Sternotherus odoratus. Genetic evidence confirmed that invasive populations of T. s. elegans in southern Europe have transmitted their own polystomes to native host species following spillover effects, and revealed here that T. s. elegans in non-indigenous habitats in the United States acts as a new reservoir of infection for native polystomes following spillback effects, thus increasing indigenous parasite transmission in the wild. Together, these findings raise further concern about the spread of non-native turtles and their impact on parasite transmission.},
}

Animals
*Turtles/parasitology
*Introduced Species
Fresh Water
North America
Europe
Phylogeny
Ecosystem
Commerce
*Trematode Infections/veterinary/parasitology/transmission/epidemiology
DNA Barcoding, Taxonomic
Electron Transport Complex IV/genetics
*Trematoda/genetics/classification

@article {pmid40394107,
year = {2025},
author = {Wasakul, V and Verschuuren, TD and Thuy-Nhien, N and Booth, E and Quang, HH and Thang, ND and Chindavongsa, K and Sovannaroth, S and Banouvong, V and Sengsavath, V and Mayxay, M and Tuyen, NTK and Phuong, VNL and Duc Trung, P and Gonçalves, S and Chen, S and Phalivong, S and Xayvanghang, S and Mahaphontrakoon, S and Pearson, RD and Newton, PN and Maude, RJ and Ashley, EA and Ariani, CV and Simpson, VJ and Day, NP and Dondorp, AM and Miotto, O},
title = {Genetic surveillance of Plasmodium falciparum populations following treatment policy revisions in the Greater Mekong Subregion.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4689},
pmid = {40394107},
issn = {2041-1723},
support = {OPP11188166, OPP1204628, INV-001927//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; QSE-M-UNOPS-MORU-20864-007-44//Global Fund to Fight AIDS, Tuberculosis and Malaria (Global Fund)/ ; },
abstract = {Genetic surveillance of Plasmodium falciparum (Pf) can track antimalarial-resistant strains, to inform decision-making by National Malaria Control Programmes (NMCPs). The GenRe-Mekong project prospectively collected 5982 samples in the Greater Mekong Subregion (GMS) between 2017 and 2022, genotyping drug resistance markers, and barcodes that recapitulate genetic variation. Genotypes were analyzed with the grcMalaria R package, first described in this paper, to translate genetic epidemiology data into actionable visual information. Since 2020, Pf incidences decreased rapidly, accompanied by a decline of dihydroartemisinin-piperaquine (DHA-PPQ) resistant lineages, previously dominant in the eastern GMS. The frequency of plasmepsin2/3 amplifications, conferring piperaquine resistance, dropped from 62% in 2017-2019 to 2% in 2022, coinciding with a switch in frontline therapy in Cambodia, Thailand, and Vietnam. While regional artemisinin resistance levels remained high, no evidence of emerging mefloquine resistance was found. Routine genetic surveillance proved valuable in monitoring rapid parasite population changes in response to public health interventions, providing actionable information for NMCPs.},
}

@article {pmid40392669,
year = {2025},
author = {Letsch, H and Greve, C and Hundsdoerfer, AK and Irisarri, I and Moore, JM and Espeland, M and Wanke, S and Arifin, U and Blom, MPK and Corrales, C and Donath, A and Fritz, U and Köhler, G and Kück, P and Lemer, S and Mengual, X and Salas, NM and Meusemann, K and Palandačić, A and Printzen, C and Sigwart, JD and Silva-Brandão, KL and Simões, M and Stange, M and Suh, A and Szucsich, N and Tilic, E and Töpfer, T and Böhne, A and Janke, A and Pauls, S},
title = {Type genomics: a Framework for integrating Genomic Data into Biodiversity and Taxonomic research.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syaf040},
pmid = {40392669},
issn = {1076-836X},
abstract = {Name-bearing type specimens have a fundamental role in characterising biodiversity, as these objects represent the physical link between a scientific name and the biological organism. Type specimens are usually deposited in natural history collections, which provide key infrastructure for research on essential biological structures and processes, while preserving records of biodiversity for future generations. Modern systematics increasingly depends on genetic and genomic data to differentiate and characterise species. While the results of genome sequencing are often connected to a physical voucher specimen, they are rarely derived from the ultimate taxonomic reference for a species, i.e., the name-bearing type specimens. This is a known but under-appreciated problem for ensuring the replicability of findings, especially those that affect the interpretation of biodiversity distributions and phylogenetic relationships. Destructive sampling of museum specimens, particularly of type material, often carries a high risk of sequencing failure, and thus the cost of damage to the specimen may outweigh the resulting benefit. Both taxonomic work and genome sequencing require specialist skills and there are often communication gaps between the respective experts. A new, harmonised approach, maximising information extraction while minimising risk to type specimens, is a critical step forward toward linking disciplines across biodiversity research and promoting a better taxonomic and systematic understanding of eukaryotic diversity. The genetic make-up of a type specimen is a fundamental part of its biological information, which can and should be made freely and digitally available through type genomics. Here we describe guidelines for the use of nomenclatural types in genome sequencing approaches considering different kinds of types in different stages of preservation and different data types.},
}

@article {pmid40391818,
year = {2025},
author = {Sarsaiya, S and Jain, A and Chen, J and Shi, J},
title = {A comprehensive review on the quality and quantity assessment of the Narmada River of India: Current status, technological advancement, efforts and initiatives, challenges, and future outlook.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {97},
number = {5},
pages = {e70090},
doi = {10.1002/wer.70090},
pmid = {40391818},
issn = {1554-7531},
support = {[2017]5733-001//Guizhou Science and Technology Corporation Platform Talents Fund/ ; CK-1130-002//Guizhou Science and Technology Corporation Platform Talents Fund/ ; U1812403//National Natural Science Foundation of China/ ; 82373981//National Natural Science Foundation of China/ ; 82060750//National Natural Science Foundation of China/ ; [2022]026//2011 Collaborative Innovation Centre of Traditional Chinese Medicine in Guizhou Province/ ; },
mesh = {India ; *Rivers/chemistry ; *Water Quality ; *Environmental Monitoring/methods ; },
abstract = {This comprehensive review examines the current status of the Narmada River in India, focusing on the quality and quantity of its water resources. The primary objectives are to assess existing technological advancements, ongoing efforts and initiatives, and challenges, and provide a future outlook for sustainable river management. The Narmada River faces significant water quality and quantity challenges, primarily because of pollution from various sources and increasing water demand. The status of the river is a cause of concern, and monitoring is essential for informed decision-making. Various technical options are available for monitoring, analysis, and data evaluation, ranging from conventional methods to cutting-edge technologies. These include DNA barcoding and sequencing, geographic assessment tools, data mining software, geoinformatics, and statistical modeling instruments. This review underscores the alarming levels of environmental pollution in the Narmada River, highlights the feasibility of using advanced techniques to assess water quality, identify pollutants, and develop mitigation strategies. This review identifies research gaps related to the integration of advanced technologies, comprehensive water quality modeling, and the development of holistic management strategies. The review concludes with recommendations for integrating advanced monitoring technologies, policy reforms, and increasing public awareness. In conclusion, the Narmada River faces significant challenges in terms of water quality and quantity. While efforts are being made to address these challenges, a multidisciplinary and integrated approach, along with the adoption of advanced technologies, is crucial for the river's long-term health and the well-being of the communities that depend on it. PRACTITIONER POINTS: Highlight the challenges faced by the Narmada River in India concerning both water quality and quantity; Provided insights into the wide range of technological advancements available for monitoring and assessment; Emphasized the alarming levels of pollution and explores the feasibility of using advanced techniques; Discussed various efforts and initiatives aimed at improving the quality and quantity of water resources; Provided recommendations for integrating advanced technologies, policy reforms, and increasing public awareness.},
}

India
*Rivers/chemistry
*Water Quality
*Environmental Monitoring/methods

@article {pmid40391427,
year = {2025},
author = {Oh, N and Kim, JY},
title = {Ionizable Lipids Drive Subcellular Localization and Immune Cell Targeting of Barcoded Nanoparticles in Lung Cancer.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c02283},
pmid = {40391427},
issn = {1936-086X},
abstract = {To accurately predict the effect of a drug and enhance its potency, it is essential to examine not only the arrival of the carrier and its payload at the target cell but also the final destination of the subcellular organelle because a considerable number of diseases are associated with the malfunctioning of cellular organelles. Here, we present nanoparticle (NP) microscopy via signal amplification of DNA barcodes combined with the multiplexed cyclic immunofluorescence technique for quantifying multiple NP types simultaneously. This technique enhanced the fluorescence signal-to-noise by 15-fold compared to standard fluorescence in situ hybridization, thereby providing a more precise means of analyzing the intra- and interdistribution of three core-shell NPs (G0-P5, 7C1-F5, and C12-D) in vitro and in vivo. The in vitro results demonstrated that in macrophages, nucleic acids condensed with G0-C14 cationic lipids were often located in lysosomes, whereas in tumor cells, nucleic acids were mainly located in mitochondria, regardless of the type of cationic lipid. Together, the in vivo results reveal that nucleic acids condensed with G0-C14 cationic lipids demonstrated the greatest uptake by CD206+ immune cells, whereas nucleic acids condensed with 7C1 and C12-200 cationic lipids exhibited the highest level of uptake by CD206+CD11c+Arg1+ immune cells.},
}

@article {pmid40390141,
year = {2025},
author = {Mittelstrass, J and Heinzelmann, R and Eschen, R and Hartmann, M and Kupper, Q and Schneider, S and Prospero, S and Franić, I},
title = {Metabarcoding with Illumina and Oxford Nanopore Technologies provides complementary insights into tree seed mycobiota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {53},
pmid = {40390141},
issn = {2524-6372},
support = {00.0482.PZ/B4387AFF4//Swiss Federal Office for the Environment (FOEN)/ ; 174644//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {BACKGROUND: Culturing of fungi is labor-intensive and reveals limited diversity, while high-throughput sequencing of barcodes (i.e., metabarcoding) enables a simultaneous detection of fungi from multiple environmental samples. Metabarcoding using short-read sequencers, such as Illumina platforms, provides high sequencing depths but results in many unidentified taxa. Long-read sequencing can improve species and genus assignments but might encompass lower sequencing depth and limit diversity coverage. In this study, fungi in seeds of eleven angiosperm and gymnosperm tree species were assessed using traditional culturing, Illumina short-read metabarcoding, and Oxford Nanopore Technologies long-read metabarcoding. We focused on seed-borne fungi as understanding their diversity and potential impacts on seedlings is crucial for securing plant health. We compared (1) the number and identity of fungal genera and species between metabarcoding approaches and traditional culturing and (2) fungal alpha- and beta-diversity between metabarcoding methods, considering different hosts and fungal lifestyles.

RESULTS: In both short- and long-read metabarcoding datasets, similar numbers of fungal reads and operational taxonomic units were assigned to comparable numbers of fungal genera and species. About one-third of the identified genera were plant pathogens, followed by saprotrophs and endophytes. Culturing overall revealed fewer fungal genera, while most of the fungal reads in short-read metabarcoding datasets stemmed from cultured taxa. Long-read metabarcoding revealed lower per-sample diversity than short-read metabarcoding and distinct fungal communities compared to those from the short-read datasets. Host-dependent patterns in alpha- and beta-diversity were observed across methods, with angiosperms harboring more fungal taxa than gymnosperms, and distinct community structuring across host tree groups and species, although the differences were stronger in short-read than long-read metabarcoding datasets.

CONCLUSIONS: Illumina and Oxford Nanopore Technologies metabarcoding captured similar host-dependent diversity patterns despite observed differences in numbers and composition of fungi. Short-read metabarcoding might be optimal for fungal biodiversity studies due to higher sequencing depths and resultant breadth of diversity. As error rates are continuing to decrease, reference databases expand, and throughput improves, long-read metabarcoding is becoming a strong candidate for future diagnostic studies of fungi. Traditional culturing captures most of the fungi from short-read metabarcoding and remains valuable for obtaining isolates for further research.},
}

@article {pmid40387751,
year = {2025},
author = {Xu, ZY and Huang, SD and Zou, J and Zeng, WH and Guo, YC and Jiang, JH},
title = {An Integrated Solution for Application of Next-Generation Sequencing in Newborn Screening.},
journal = {Clinical laboratory},
volume = {71},
number = {5},
pages = {},
doi = {10.7754/Clin.Lab.2024.241006},
pmid = {40387751},
issn = {1433-6510},
mesh = {Humans ; *Neonatal Screening/methods ; *High-Throughput Nucleotide Sequencing/methods ; Infant, Newborn ; Computational Biology ; *Genetic Testing/methods ; *Genetic Diseases, Inborn/diagnosis/genetics ; Multiplex Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Next-generation sequencing (NGS) has greatly improved the diagnostic process for hereditary diseases, and incorporation of NGS into newborn screening (NBS) programs for more actionable diseases has been widely discussed. The aim of this study was to evaluate an integrated solution for application of NGS in newborn screening.

METHODS: An NGS panel targeting 155 genes related to inborn errors of metabolism, hearing loss, severe combined immunodeficiency, congenital hypothyroidism, and other actionable genetic diseases, was designed. An all-in-one library preparation strategy was developed to combine multiplex PCR target enrichment and sample barcoding. A clinical genetic analysis system was assembled to facilitate bioinformatics analysis and reporting. The integrated solution was validated using 160 samples with known variants.

RESULTS: The end-to-end time from DNA isolation to sequencing was approximately 34 hours, and bioinformatics analysis pipeline took 4 hours for 160 samples in parallel. This allowed reporting of results on day 3. All known variants were confirmed by the NGS workflow, and two large insertion/deletions were additionally detected in two cases with previously clinically but not genetically confirmed diseases.

CONCLUSIONS: The integrated solution for application of NGS in NBS provided reasonable turnaround time to meet the NBS timeframe and could be implemented at scale.},
}

Humans
*Neonatal Screening/methods
*High-Throughput Nucleotide Sequencing/methods
Infant, Newborn
Computational Biology
*Genetic Testing/methods
*Genetic Diseases, Inborn/diagnosis/genetics
Multiplex Polymerase Chain Reaction
Sequence Analysis, DNA/methods

@article {pmid40387421,
year = {2025},
author = {Aggarwal, SD and Toussaint, J and Lees, JA and Weiser, JN},
title = {Colonization dynamics of Streptococcus pneumoniae are determined by polymorphisms in the BlpAB transporter.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0006125},
doi = {10.1128/iai.00061-25},
pmid = {40387421},
issn = {1098-5522},
abstract = {Colonization of the human airways, the first step in the pathogenesis of Streptococcus pneumoniae (Spn), is the determining factor in the ecological spread of the bacterium. Since co-colonization by multiple strains is common, within-host bacterial competition contributes to the success of Spn strains. Competition both between and within strains is mediated by bacteriocin gene clusters, notably the quorum sensing-regulated bacteriocin-like peptide (blp) locus. A key component of this system is the BlpAB transporter that exports pheromones and bacteriocins expressed by the blp locus. However, ~75% of Spn strains lack a functional BlpAB transporter and instead rely on the paralogous ComAB transporter for this export, raising questions about the evolutionary persistence of BlpAB(+) strains. Using molecular barcoding, we demonstrate that BlpAB(+) and BlpAB(-) strains show major differences in population dynamics during colonization modeled in mice. The BlpAB(+) strains exhibit slower loss of clonal diversity as a consequence of intrastrain competition relative to their isogenic BlpAB(-). The contribution of a functional BlpAB transporter was then examined in an association study of >2,000 human carriage isolates from a highly colonized population. The median carriage duration was ~177 days longer for BlpAB(+) relative to BlpAB(-) strains. This increased duration of natural carriage correlates with a competitive advantage for BlpAB(+) strains when tested in the murine model. Thus, our work provides insight into how differences in the population dynamics of Spn mediated by bacterial competition impact host colonization.IMPORTANCESpn is a frequent colonizer of the human upper respiratory tract. Success during colonization is dictated by the arsenal of weapons these bacteria possess, which provides them with an advantage over their competitors. A key example includes the blp bacteriocins that are exported by the cell through both BlpAB and ComAB transporters. While most Spn strains lack a functional BlpAB, a subset of the strains retains it. Given this redundancy in export systems, our study questioned the evolutionary advantage of retaining BlpAB. Herein, we show that a functional BlpAB transporter causes a slower loss of clonal diversity in vivo. This correlates with longer Spn carriage duration in the human population and a competitive advantage during experimental co-colonization. Our work highlights the reasons behind the persistence of Spn with a functional BlpAB. These findings reveal how genetic variability in the blp locus shapes Spn colonization and evolutionary success.},
}

@article {pmid40386686,
year = {2025},
author = {Fernandez-Triana, JL and Boudreault, C and Whitfield, JB and Höcherl, A and Smith, MA and Hallwachs, W and Janzen, DH},
title = {A revision of the parasitoid wasp genus Dolichogenidea Viereck (Hymenoptera, Braconidae) in the Neotropical region, with the description of 102 new species.},
journal = {ZooKeys},
volume = {1237},
number = {},
pages = {1-250},
pmid = {40386686},
issn = {1313-2989},
abstract = {The parasitoid wasp genus Dolichogenidea is currently the second most speciose within the subfamily Microgastrinae (Hymenoptera: Braconidae), with 366 world species known so far, but with hundreds awaiting to be described. Here, the fauna of the Neotropical region is revised, with an emphasis in the Area de Conservación Guanacaste (ACG), Costa Rica. In addition to 23 species previously recorded from the Neotropics, 102 additional species are described as new, increasing the regional and world richness to 125 and 468 species, respectively. All species are diagnosed and described by using a combination of basic morphology (dichotomous key and brief diagnostic descriptions) and, when available DNA COI barcodes, biology (host data and wasp cocoon strategy), and distribution data. Neither morphology, biology, nor molecular data alone were sufficient to unambiguously separate all taxa, as all approaches were found to have limitations, but the combination of all three approaches provided stronger support to species delimitation. Morphology allowed the inclusion of all known species, therefore building a foundation upon which to improve as more molecular and biological data become available and new species are discovered; however, it was not sufficient (or it was very difficult to use) to separate at least 15% of all species keyed out in the dichotomous key. DNA barcoding was better able to separate species, and it is likely to become the most efficient way to identify species in the near future; however, DNA failed to identify 8.3% of the species with molecular data available, in addition to one third of the described species currently lacking molecular data. Biological data is currently the most incomplete, with only 42% of the species having associated host information, with a strong data availability bias towards ACG specimens. A total of 11 Lepidoptera families are here recorded to be parasitized by Neotropical Dolichogenidea, mainly Depressariidae (34% of all host data available), Gelechiidae (17%), Crambidae (14%), Tortricidae (10%), Thyrididae (8%) and Pyralidae (7%). Most of the wasps seem to be monophagous or at most oligophagous, as 56% are known to only parasitize a single host species, whereas 23% parasitize two host species and 10% parasitize three hosts; in almost all cases, the hosts species belong to one genus (or related genera) in the same Lepidoptera family. Most species of Dolichogenidea are found between 400-1,500 m, but a few have been found at higher elevations, including a few examples higher than 3,000 m (Costa Rica) and 4,000-4,100 m in the Andes (South America). The following nomenclatural acts are proposed: 1) the genus Exoryza is synonymized under Dolichogenidea, syn. nov.; 2) a total of 16 species are transferred to Dolichogenidea as comb. nov., one species formerly in the genus Apanteles: Dolichogenideacroceicornis (Muesebeck, 1958) and all 15 species formerly placed within Exoryza (six of them from the Neotropics): Dolichogenideaasotae (Watanabe, 1932), Dolichogenideabelippicola (Liu & You, 1988), Dolichogenideahylas (Wilkinson, 1932), Dolichogenideamariabustosae (Fernandez-Triana, 2016), Dolichogenideamegagaster (de Saeger, 1944), Dolichogenideaminnesota (Mason, 1981), Dolichogenideamonocavus (Valerio & Whitfield, 2004), Dolichogenideaoryzae Walker, 1994, Dolichogenideareticarina (Song & Chen, 2003), Dolichogenidearichardashleyi (Fernandez-Triana, 2016), Dolichogenidearitaashleyae (Fernandez-Triana, 2016), Dolichogenidearosamatarritae (Fernandez-Triana, 2016), Dolichogenideasafranum (Rousse & Gupta, 2013), Dolichogenideaschoenobii (Wilkinson, 1932) and Dolichogenideayeimycedenoae (Fernandez-Triana, 2016); 3) Dolichogenideayeimycedenoae (Fernandez-Triana, 2016) becomes a senior secondary homonym of Dolichogenideayeimycedenoae Fernandez-Triana & Boudreault, 2019; therefore, Dolichogenideacedenoae Fernandez-Triana & Boudreault, 2025 is a replacement name for Dolichogenideayeimycedenoae Fernandez-Triana & Boudreault, 2019; 4) the following 102 species, all authored by Fernandez-Triana & Boudreault, are described as sp. nov.: D.aceituno, D.alanflemingi, D.alejandromarini, D.alerce, D.alexamasisae, D.alexandrei, D.alixhamiltonae, D.amazonas, D.anacamposae, D.andreamezae, D.angelsolisi, D.anikenpalolae, D.anniapicadoae, D.annlisterudae, D.annychaverae, D.antioquia, D.antjevirkusae, D.arenal, D.bernardoespinozai, D.beryllacosteae, D.bradzlotnicki, D.caldas, D.carlosalvaradoi, D.carlosviquezi, D.chichicastenango, D.christinaagapakisae, D.claudiadoblesae, D.dole, D.encruzilhada, D.ericpalolai, D.ericsimoni, D.escobarae, D.felipechavarriai, D.frankjoycei, D.fredhicksi, D.helenedumasae, D.heredia, D.ingredolsonae, D.isabelleae, D.isidrochaconi, D.jaimelewisi, D.jasonkelleyi, D.jennyphillipsae, D.jessiehillae, D.johnrobinsoni, D.jorgecarvajali, D.jorgecortesi, D.josephfridmani, D.joshdarfleri, D.juanmatai, D.junhyongkimi, D.kasiiya, D.katiemccluskeyae, D.kenzabaddouae, D.lacochaparamo, D.leahdennisae, D.limoncocha, D.luishamiltoni, D.luzmariaromeroae, D.machupichu, D.mehdirheljari, D.moniqueae, D.moniquegilbertae, D.ninamasisae, D.nothofagus, D.oiketicus, D.palenque, D.papallacta, D.paulfryi, D.pedroleoni, D.puschendorfi, D.putumayo, D.puyo, D.rexhamiltoni, D.robertofernandezi, D.robinsherwoodae, D.robmacewani, D.robpringlei, D.rociocordobae, D.rodrigogamezi, D.ronaldzunigai, D.rubymacpearsae, D.rudyamadori, D.sallydaleyae, D.sarahoconnorae, D.scottmilleri, D.shelleymcsweeneyae, D.sigifredomarini, D.stephmae, D.stevestroudi, D.susanabramsae, D.teremariae, D.tiboshartae, D.timrichi, D.tomdaleyi, D.tristanpalolai, D.tucuman, D.verobrondexae, D.virgendelparamo, D.weaversway, D.yungas, D.yvesbraeti.},
}

@article {pmid40385613,
year = {2025},
author = {Yu, CJ and Du, XC},
title = {Revision of the genus Hemopsis Kirti & Rose, 1987 (Lepidoptera, Crambidae), with descriptions of three new species from China.},
journal = {ZooKeys},
volume = {1238},
number = {},
pages = {17-31},
pmid = {40385613},
issn = {1313-2989},
abstract = {The genus Hemopsis is revised based on adult morphological characteristics and DNA barcodes. Hemopsisabstracta sp. nov., H.coalita sp. nov., and H.heteroidea sp. nov. are described as new to science, and Hemopsisdissipatalis (Lederer, 1863) is DNA barcoded and redescribed based on new material from southern China. A key to Hemopsis species is given based on external morphology of adults and their genitalia characteristics. Images of adults and genitalia are provided.},
}

@article {pmid40385519,
year = {2025},
author = {Haro, M and Ramos, S and Magalhães, T},
title = {Electronic Transfusion Safety System: Characterization of Patient Safety Incidents.},
journal = {Portuguese journal of public health},
volume = {},
number = {},
pages = {1-17},
pmid = {40385519},
issn = {2504-3145},
abstract = {INTRODUCTION: The healthcare system is complex and dynamic, and the implementation of information technology is seen as an important aid to patient safety. Data reveal that 1 in every 10 patients in developed countries is affected by a clinical error. The transfusion process involves several stakeholders and multiple stages with various critical points within the hospital. This study aims to understand patient safety incidents caused by failures in the Electronic Transfusion Safety System (ETSS) based on barcode technology in a hospital setting, from storage to the administration of blood components to the patient.

METHODS: A retrospective study spanning 3 years (2021-2023) with a mixed-methods approach was chosen. A Focus Group with six experts was conducted, and 136 reports from the anonymized incident reporting database with the typology "Blood and Blood Products" from a hospital in Lisbon were analyzed.

RESULTS: The ETSS diagram using barcodes allowed for the identification and description of all stages and their stakeholders. The critical points identified were patient identification, multiple relabeling, and transportation. A higher incidence rate of near-miss events was observed during sample collection and prescription.

DISCUSSION: This ETSS is hybrid, meaning that it has both human and technological components. Since 96% of the incidents did not cause harm to the patient, error detection and prevention mechanisms are being activated. This study has demonstrated the importance of IT in the transfusion process, as well as the relevance of continuous investment and the involvement of all stakeholders for a better patient safety environment.},
}

@article {pmid40385223,
year = {2025},
author = {Alsanie, SI and Abd-Elgawad, ME},
title = {Influence of Soil Salinity on Genetic Diversity and Phylogenetic Relationships in Tetraena Species: Insights from Electrical Conductivity Analysis, Inter-retrotransposon Amplified Polymorphism Markers, and DNA Barcoding.},
journal = {ACS omega},
volume = {10},
number = {18},
pages = {18629-18640},
pmid = {40385223},
issn = {2470-1343},
abstract = {Soil salinity is a significant environmental stressor that impacts species distribution, plant development, and genetic diversity. Conservation and ecological management depend on an understanding of how Tetraena species respond to salinity. The genus Tetraena, which includes several species of succulent shrubs native to arid regions, is of significant interest for studying plant adaptation mechanisms. The study aims to evaluate the genetic diversity and ecological characteristics of eight groups of Tetraena species in Saudi Arabia using inter-retrotransposon amplified polymorphism (IRAP) markers, ycf5 and trnH gene sequences, as well as soil pH and electrical conductivity (EC). Soil pH indicated slightly alkaline conditions, while electrical conductivity (EC) ranged from 822 μS/cm in the T. propinqua population at Al Thumama Road (population 8) to 23,800 μS/cm in the T. hamiensis population at Al Jawhara-Dammam Road (population 2). The genetic relationships were determined by analyzing IRAP marker polymorphism, generated using 10 primers. Clustering through principal component analysis and biostatistical methods distinguished the populations of T. propinqua subsp. Migahidii (6, 7, and 8) from the populations of T. hamiensis var. qatarensis (1, 3), (4, 5), and (2). Ten primers had high polymorphism (60.5%) according to IRAP analysis between T. hamiensis and T. propinqua. The evolutionary trees of T. propinqua and T. hamiensis cluster together. Analysis of conserved motifs revealed common motifs that support the use of ycf5 and trnH as barcodes. The genetic diversity and population clustering of T. hamiensis and T. propinqua are influenced by environmental salinity and species-specific genetic adaptations. While T. hamiensis has more differentiation, maybe as a result of historical separation or localized adaptations, T. propinqua exhibits strong genetic similarities. These results demonstrate that common environmental stresses and species-specific characteristics are the main drivers of genetic diversity. Future studies should explore adaptive genetic mechanisms at the molecular level and assess the functional roles of salinity-responsive genes in support conservation efforts.},
}

@article {pmid40382734,
year = {2025},
author = {Swaraj, P and Reshmi, MVN and Rijin, K and Drisya, OK and Priya, TAJ and Kappalli, S},
title = {Bomolochidae Claus, 1875 (Cyclopoida: Copepoda) Parasitizing the Marine Fishes of Kerala Coast (India): Host-Parasite Interaction and Species Diversity.},
journal = {Acta parasitologica},
volume = {70},
number = {3},
pages = {111},
pmid = {40382734},
issn = {1896-1851},
support = {No. DST/INSPIRE Fellowship/2017/IF170696, 04.07.2018//DST INSPIRE/ ; SR/WOS-A/LS/78/2018(G, 28.06.2019)//DST-WOS-A/ ; No. INT/RUS/RFBR/P-330, 10.01.2019//DST-RFBR collaborative research project/ ; No. DST INT JSPS P-316 2020, dated 30.07.2021//DST-JSPS collaborative research project/ ; No. EMR/2016/001163/ AS, 28 August 2017//DST-SERB research project/ ; No. KSCSTE/5224/2017-SRSLS, dated: 03/04/2018//KSCSTE/ ; },
mesh = {Animals ; *Copepoda/classification/genetics/physiology ; India/epidemiology ; *Fish Diseases/parasitology/epidemiology ; Phylogeny ; *Fishes/parasitology ; *Host-Parasite Interactions ; Biodiversity ; *Ectoparasitic Infestations/veterinary/parasitology/epidemiology ; Electron Transport Complex IV/genetics ; Host Specificity ; Prevalence ; },
abstract = {PURPOSE: This study aims to assess region-wise host-parasite interaction and diversity indices of bomolochid species infecting marine fishes along the Kerala coast. Also, it aims to generate COI barcodes and analyse the phylogenetics.

METHODS: Marine fish species along the Kerala coast were sampled for the period 2016-2023 and examined for parasitization by bomolochid copepods. Host preference, prevalence, site-specificity, mean intensity, and biodiversity indices of recovered parasite species were assessed specifically in northern and southern regions of this coast. Mitochondrial COI sequences from bomolochid species were also generated, and their phylogenetic relationships were assessed with those of their counterparts found in the NCBI database.

RESULTS: Among the sampled fishes, 21 species from 20 genera and 14 families showed parasitization with 20 species of bomolochids. Four host families: Sciaenidae, Acanthuridae, Engraulidae, and Sillaginidae were recorded as new to the bomolochid infection along the Indian coast. Recovered bomolochid species, including nine Bomolochus species, six Nothobomolochus species, two Pumiliopes species, and one each of Pseudorbitacolax, Ceratocolax, and Orbitacolax species, with overall prevalence ranging from 0.28% to 57%. 65% of species prefer single-host, and 35% rely on two or three host species. The northern region encompassed all 20 bomolochid species, whereas only 10 species represented the southern region. Six species showed no region-specific host preference, but their prevalence showed marked differences (4.8-73.8%). The host preference of some bomolochid species spans multiple fish species within the same genus or family, as well as across different genera and families, with a varying degree of prevalence, either region-dependent or independent. The northern region displayed the highest species richness and diversity index compared to the southern region. However, the evenness values from both regions were found to be similar. The mitochondrial COI sequences from five bomolochid species signify the reliability of COI DNA barcoding for the identification of bomolochids at the species level. The analysis of phylogenetic relationships with those of its counterparts found in the NCBI database revealed that Bomolochidae constituted a biphyly topology that is distinct from that of the outgroup, i.e., Harpacticoida.

CONCLUSION: The generated information on bomolochid new host record, host preference, prevalence, site specificity, seasonality, diversity and genetic divergence forms the basis not only for further exploration of the species diversity and genetic variation of bomolochids but for analyzing the ecological and evolutionary aspects of species diversity and genetic variation of bomolochids and new host record along the Indian coasts and Indo-pacific region as well.},
}

Animals
*Copepoda/classification/genetics/physiology
India/epidemiology
*Fish Diseases/parasitology/epidemiology
Phylogeny
*Fishes/parasitology
*Host-Parasite Interactions
Biodiversity
*Ectoparasitic Infestations/veterinary/parasitology/epidemiology
Electron Transport Complex IV/genetics
Host Specificity
Prevalence

@article {pmid40378848,
year = {2025},
author = {Weber, TS and Biben, C and Miles, DC and Glaser, SP and Tomei, S and Lin, CY and Kueh, A and Pal, M and Zhang, S and Tam, PPL and Taoudi, S and Naik, SH},
title = {LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.026},
pmid = {40378848},
issn = {1097-4172},
abstract = {Much remains to be learned about the clonal fate of mammalian epiblast cells. Here, we develop high-diversity Cre recombinase-driven LoxCode barcoding for in vivo clonal lineage tracing for bulk tissue and single-cell readout. Embryonic day (E) 5.5 pre-gastrulation embryos were barcoded in utero, and epiblast clones were assessed for their contribution to a wide range of tissues in E12.5 embryos. Some epiblast clones contributed broadly across germ layers, while many were biased toward either blood, ectoderm, mesenchyme, or limbs, across tissue compartments and body axes. Using a stochastic agent-based model of embryogenesis and LoxCode barcoding, we inferred and experimentally validated cell fate biases across tissues in line with shared and segregating differentiation trajectories. Single-cell readout revealed numerous instances of asymmetry in epiblast contribution, including left-versus-right and kidney-versus-gonad fate. LoxCode barcoding enables clonal fate analysis for the study of development and broader questions of clonality in murine biology.},
}

@article {pmid40376947,
year = {2025},
author = {Sun, Y and Fan, J and Zong, Y and Jin, B and Yao, W and Wang, Z and Fu, T and Fang, L and Liu, Y and Tan, W},
title = {Aptamer-Signatured Nanoparticle Protein Corona for Size-Dependent Fluorescent Barcoding Diagnosis.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2410434},
doi = {10.1002/smll.202410434},
pmid = {40376947},
issn = {1613-6829},
support = {2022YFC3401002//National Key Research and Development Program of China/ ; 2023SDYXS0001//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; YXD24B0402//Zhejiang Provincial Natural Science Foundation of China/ ; 22204144//National Natural Science Foundation of China/ ; 21CAA02059//National Natural Science Foundation of China/ ; },
abstract = {Cancer-specific nanoparticl protein corona (NPC) opens a new avenue for biomarker discovery and diagnosis. However, the simultaneous detection of multiplex protein biomarkers from NPC is very challenging owing to ultra-low abundance and limited detection probes. Here, an aptamer-signatured NPC (ASNC)-based size-dependent fluorescence barcode is developed for flow cytometry profiling (FBFC) sensing platform to diagnose hepatocellular carcinoma (HCC). First, HCC-specific NPC is obtained from incubating magnetic nanoparticles with clinical serum samples. A 12-aptamer panel is incubated with NPC for the assembly of ASNC. Six aptamers are selected from the preliminary profiling of 30 HCC and healthy controls, resulting in ASNC for subsequent multiplex detection. To achieve simultaneous and orthogonal detection in one pot, advantage of the size-dependent fluorescent microbeads are taken to profile the signature aptamers eluted from NPC via flow cytometry-distinguishable barcodes. With 84 clinical HCC and healthy serum samples, a diagnostic accuracy of 94.12%, have attained which is higher than other single biomarkers or any combinations. Overall, by transferring protein biomarkers to ASNC, a simultaneous and multiplex ASNC-based FBFC platform have developed which holds immense potential in facile and precise cancer diagnosis.},
}

@article {pmid40376620,
year = {2025},
author = {Merchán Mayorga, JI and Quiroga, SY and Posada-Restrepo, I and García-Ramos, KA},
title = {Free-living clinging flatworms (Rhabditophora, Polycladida) associated with Sargassum from the Caribbean Coast of Colombia.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e150699},
pmid = {40376620},
issn = {1314-2828},
abstract = {BACKGROUND: Polyclads are a diverse group of marine free-living flatworms, with some species adapted to life in floating Sargassum mats. Recent studies suggest that, rather than being inherently pelagic, these flatworms should be classified as "clinging fauna", as they rely on floating substrates for habitat.

NEW INFORMATION: This study documents, for the first time, the occurrence of Gnesiocerossargassicola and Chatziplanagrubei in Sargassum along the Caribbean coast of Colombia. High-definition photographs of whole mounts and histological sections are provided for both species, along with detailed observations of their reproductive structures and 28S rDNA barcodes. These findings underscore the importance of exploring the fauna associated with Sargassum, contributing to a better understanding of polyclad distribution and raising the number of recorded species for Colombia to 26.},
}

@article {pmid40376046,
year = {2025},
author = {Kang, X and Wang, Y and Zheng, R and Mamy Jayne Nelly, R and Liu, L and Li, S and Sun, X and Kang, L and Zhang, N and Zou, Z and Xia, Q},
title = {Variations in the Bacterial Ecosystems of Mosquito Populations - Haikou and Sanya Cities, Hainan Province, China, 2019.},
journal = {China CDC weekly},
volume = {7},
number = {16},
pages = {523-530},
pmid = {40376046},
issn = {2096-7071},
abstract = {INTRODUCTION: This study explores the midgut microbiota of mosquitoes in Haikou and Sanya cities, regions critical for understanding vector-borne disease dynamics in Hainan Province, China. It provides baseline data on microbial composition and examines their potential role in influencing mosquito biology and vector competence, while highlighting the need for further research into their association with vector-borne viral infections.

METHODS: Adult mosquitoes were collected using light traps and human bait methods. Species identification was conducted through morphological examination and DNA barcoding using the cytochrome c oxidase subunit 1 gene (cox1). The V3-V4 hypervariable regions of the microbial 16S ribosomal RNA (rRNA) gene were sequenced using high-throughput methods to investigate the midgut microbiota. Statistical analyses, including Alpha and Beta diversity assessments of the sequencing results, were performed using SPSS 21.0 and R version 3.11.

RESULTS: The predominant mosquito species identified were Aedes albopictus, Armigeres subalbatus, and Culex pipiens. Microbiota analysis of 281 midguts revealed that Proteobacteria dominated (85.28%), with significant fractions being Alphaproteobacteria (52.14%), Gammaproteobacteria (29.90%), and Betaproteobacteria (3.22%). Other notable phyla included Firmicutes (6.24%), Actinobacteria (3.81%), and lesser quantities of Thermi, Cyanobacteria, and Bacteroidetes. Significant geographic variation in bacterial communities was observed between Haikou and Sanya (P<0.05), with unique taxa like Thermi and Cyanobacteria identified only in Haikou and Chlamydiae found solely in Sanya. The analysis revealed 204 overlapping species, with 473 unique to Haikou and 64 to Sanya.

CONCLUSIONS: This study revealed significant geographic differences in the midgut microbiota of mosquitoes from Haikou and Sanya, providing foundational data for understanding their potential impact on mosquito biology and disease transmission. While the direct relationship between these microbial variations and vector-borne disease dynamics requires further investigation, these findings underscore the importance of mosquito microbiota research as part of broader strategies to mitigate vector-borne disease risks.},
}

@article {pmid40375325,
year = {2025},
author = {Chong, SQY and Yeo, D and Arceo, AVV and Ong, JLY and Lee, CHE and Yeak, RJY and Wee, ASZ and Teo, PYZ and Tay, MKJ and Chan, AHJ and Fernandez, CJ and Xie, R and Wong, AMS and How, CB and Chang, SF},
title = {Cytauxzoon paradoxurus n. sp., a novel Cytauxzoon species identified in common palm civets in Singapore.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {175},
pmid = {40375325},
issn = {1756-3305},
mesh = {Animals ; Singapore/epidemiology ; *Viverridae/parasitology ; Phylogeny ; *Protozoan Infections, Animal/parasitology/epidemiology ; Male ; Female ; RNA, Ribosomal, 18S/genetics ; *Piroplasmida/isolation & purification/genetics/classification ; DNA, Protozoan/genetics ; },
abstract = {BACKGROUND: The common palm civet (Paradoxurus musangus) is a species native to Southeast Asia. Highly adapted to urbanised environments, these civets can often be found in proximity to humans and companion animals, raising the concern of pathogen transmission at the human-wildlife and wildlife-domestic animal interface. Whilst there have been reports of various bacteria and viruses detected in civets, little is known about the protozoa that they may harbour. In this study, we screened the common palm civets in Singapore for tick-borne protozoan parasites known as piroplasms.

METHODS: Over a 2-year period, blood samples were opportunistically collected from 135 wild common palm civets following a physical examination. The sex and weight of each civet were recorded, and any ectoparasites detected were identified through DNA barcoding. DNA extracts of blood samples were screened using a PCR assay targeting the 18S rRNA gene of piroplasmids.

RESULTS: A novel Cytauxzoon species was detected in 29 civets (21.5%), and a statistically significant association was found between infection and the civet's weight. Two cat flea (Ctenocephalides felis) specimens were discovered on two sampled civets; however, Cytauxzoon DNA was not detected in either the flea or the sampled civet. Phylogenetic analysis of the Cytauxzoon 18S rRNA gene sequences from 29 civets revealed that this piroplasmid is most closely related to a Cytauxzoon sp. detected in meerkats in South Africa but molecularly distinct from the six currently described Cytauxzoon species.

CONCLUSIONS: This detection documents the first molecular confirmation of Cytauxzoon sp. infection in Southeast Asia and the first report of Cytauxzoon sp. in a viverrid host. Further studies are required to determine the vector involved in the transmission of this novel Cytauxzoon species, as no ticks were found on the sampled civets. The discovery of Cytauxzoon paradoxurus n. sp. highlights the importance of expanded biosurveillance to better understand the diversity of piroplasms harboured by wildlife in the region and its potential for cross-species transmission.},
}

Animals
Singapore/epidemiology
*Viverridae/parasitology
Phylogeny
*Protozoan Infections, Animal/parasitology/epidemiology
Male
Female
RNA, Ribosomal, 18S/genetics
*Piroplasmida/isolation & purification/genetics/classification
DNA, Protozoan/genetics

@article {pmid40374562,
year = {2025},
author = {Zhang, F and Dai, W and Zhang, M and Dong, H and Zhang, X},
title = {Programmed Fluorescence-Encoding DNA Nanoflowers for Cell-Specific-Target Multiplexed MicroRNA Imaging.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c06960},
pmid = {40374562},
issn = {1520-6882},
abstract = {The precise identification and differentiation of multiple microRNAs (miRNAs) with high spatial resolution in specific cells remain a significant challenge, primarily due to the limited availability of spectrally distinguishable fluorophores and the absence of cell-specific recognition capabilities. In this study, we introduce a programmed fluorescence-encoding DNA nanoflower (CNFs) system based on the self-assembly of rolling circle amplification (RCA), enabling multiplexed miRNA imaging in living cells. The CNFs system is rationally designed to consist of three key components: a CD63 aptamer region, dual fluorophore encoding regions, and an miRNA recognition region. The polyvalent tandem CD63 aptamer enhances the cellular targeting specificity and endocytic uptake efficiency. By controlling dual fluorophores and three levels of intensity within encoding regions, it generates 9 distinct barcodes for labeling multiple targets. Additionally, when conjugated with molecular beacons (MBs), CNFs facilitate the simultaneous detection of multiplexed intracellular miRNAs. Using this CNFs system, we successfully evaluated the expression profiles of nine miRNAs in breast cancer. Overall, we expect that this CNFs system will be a valuable tool for disease-related multiplex miRNAs biomarker imaging in specific cells and the exploration of miRNAs' molecular regulation mechanisms.},
}

@article {pmid40370916,
year = {2025},
author = {Hammond, A and Mankad, A},
title = {Retrospective Lineage Tracing: An Optimal Approach for the Study of Intrinsic Cellular Development.},
journal = {Cureus},
volume = {17},
number = {4},
pages = {e82241},
pmid = {40370916},
issn = {2168-8184},
abstract = {Lineage tracing is an essential tool for understanding cellular development and tissue dynamics. This review examines retrospective lineage tracing as an optimal approach for studying cellular development and contrasts retrospective with prospective lineage tracing methods. Retrospective lineage tracing approaches leverage naturally occurring genetic barcodes, such as single nucleotide polymorphisms (SNPs), copy number variants (CNVs), and mitochondrial DNA mutations, which enables the detailed reconstruction of cell lineages without prior genetic manipulation. Researchers can ultimately infer developmental trajectories and clonal relationships across hematopoiesis and tumorigenesis by analyzing these endogenous markers. This paper considers how retrospective lineage tracing methods circumvent the limitations of prospective approaches, such as the need for exogenous labeling, and is valuable for studying human hematopoiesis.},
}

@article {pmid40370429,
year = {2025},
author = {Firouzi, S and Solouki, M and Fazeli-Nasab, B and Salehi-Sardoei, A and Hatami, M and Ghorbanpour, M and Zhang, B},
title = {Ability to use ITS and rbcL sequencing for determination of the genetic diversity and relationships among olive (Olea europaea L.) genotypes.},
journal = {3 Biotech},
volume = {15},
number = {6},
pages = {161},
pmid = {40370429},
issn = {2190-572X},
abstract = {UNLABELLED: Olives are of considerable economic and commercial importance and are mostly used in both daily life and industries. The DNA barcode method has a lot of potential for reviving the science of arithmetics and traditional biodiversity studies, so it has been widely used on plants and for classification and arithmetic purposes. In this study, we sequenced seven different olive genotypes (Olea europaea cv. Olive yellow, O. europaea cv. Oliy, O. europaea cv. Roodbar Oily, O. europaea cv. Mari, O. europaea cv. Fishemi, O. europaea cv. Manzanila, O. europaea cv. Koroneiki) to study their diversity and evolution. The data were analyzed using Clustalw2 and BioEdit software. The homology rate of rbcL and ITS sequences was all in the range of 97-100%. It was identified, for ITS, 1,059 genetic luci (580 luci without deletion and addition and 479 luci with deletion and addition (328 luci polymorphs, 151 monomorphs), 217 singletons, and for rbcL, 565 genetic luci with (60 luci without deletion and addition and 505 luci with deletion and addition (2 luci with polymorphs, 503 monomorphs), 1 singleton. It was determined that the number of four haplotypes (haplotype diversity index = 0.80) was determined for ITS and three haplotypes (haplotype diversity index = 0.71) for RBCL. The results indicated that in the nucleotide sequence of the ITS gene among olive varieties, guanine was the most abundant base at 28.7%, while adenine had the lowest abundance at 5%. In contrast, the rbcL gene showed that thymine was the most abundant base at 29.8%, with cytosine being the least abundant at 20.6%. Estimates of nucleotide transitions in the ITS gene revealed a high frequency of pyrimidine transitions, with a thymine-to-cytosine transition rate of 16.84% and a cytosine-to-thymine transition rate of 11.63%. The ITS primer successfully identified and separated only six genotypes, whereas rbcL identified all seven genotypes. Although the success rates of 60-70% for both ITS and rbcL may not seem particularly high, they still significantly contribute to large-scale biodiversity inventories, especially for olive species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04336-z.},
}

@article {pmid40370263,
year = {2025},
author = {Cui, X and Liu, Y and Wu, T and Tay, MZ and Cheow, LF},
title = {Microfluidic-Enabled Production of DNA Barcoded APC Library (MEDAL) for High Throughput T Cell Epitope Screening.},
journal = {Small methods},
volume = {},
number = {},
pages = {e2500150},
doi = {10.1002/smtd.202500150},
pmid = {40370263},
issn = {2366-9608},
support = {MOE-T2EP30224-0047//Ministry of Education of Singapore/ ; NRF-F-CRP-2024-0003//National Research Foundation Frontier Competitive Research Programme/ ; },
abstract = {Screening for peptide fragments that can be displayed on antigen-presenting cells is an essential step in vaccine development. The current approach for this process is slow and costly as it involves separately pulsing cells with chemically synthesized peptides. This study presents Microfluidic-Enabled production of DNA-barcoded APC Library (MEDAL), a high throughput microfluidic droplet platform for parallel production of DNA-barcoded Antigen Presenting Cells (APCs) loaded with enzymatically synthesized peptides. Droplets containing peptides and their encoding DNA are produced from microfluidic PCR-IVTT reaction. APCs presenting both peptides and DNA barcodes are obtained by injecting cells into these droplets. Up to 9000 different APCs can be produced and screened within a 10-h workflow. This approach allows to identify peptide sequences that bind to APCs expressing H-2Kb MHC class I molecule with next-generation sequencing of DNA barcodes. Finally, co-culture of T cells and APC libraries prepared with MEDAL identified specific epitopes recognized by T cells.},
}

@article {pmid40370414,
year = {2016},
author = {Dellinger, TA and Wong, V and Marek, PE},
title = {Makelabels: a Bash script for generating data matrix codes for collection management.},
journal = {Biodiversity data journal},
volume = {4},
number = {},
pages = {e9583},
pmid = {40370414},
issn = {1314-2828},
abstract = {BACKGROUND: Digitization of natural history collections allows easy access and reuse of the invaluable biodiversity data held within a collection by providing access to specimen level data through the Internet. Each digitized specimen in a database requires a unique catalog number to distinguish it from the many other biologically unique specimens within the collection. However, there are few open source barcode generators available, and of these even fewer platforms exist to enable the mass production of barcode labels required by natural history collections. We developed a low-cost, open source solution to generating data matrix barcodes with unique catalog numbers for use in the Virginia Tech Insect Collection.

NEW INFORMATION: Here we describe the makelabels script, which uses the open source Unix packages libdmtx and ImageMagick to generate unique specimen labels containing both a human-readable catalog number and a machine-readable data matrix barcode. The mass production of labels and use of both types of catalog symbology provides flexibility in specimen management and increased efficiency in digitization and specimen processing workflows.},
}

@article {pmid40367034,
year = {2025},
author = {Ocaña-Cabrera, JS and Martin-Solano, S and Ron-Román, J and Rivas, J and Garigliany, MM and Saegerman, C},
title = {Pot-pollen DNA barcoding as a tool to determine the diversity of plant species visited by Ecuadorian stingless bees.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323306},
doi = {10.1371/journal.pone.0323306},
pmid = {40367034},
issn = {1932-6203},
abstract = {Identifying the main species of plants from where Ecuadorian stingless bees collect pollen is one of the key objectives of management and conservation improvement for these insects. This study aims to determine the botanical origin of pot-pollen using two barcodes, comparing two methodologies (DNA barcoding versus electron microscopy and morphometric tools) and determine the genus and species of pollen source plants of the main honey-producing stingless bees in Ecuador. As main results, Prockia crucis, Coffea canephora, Miconia nervosa, Miconia notabilis, Laurus nobilis, Cecropia ficifolia, Theobroma sp., Artocarpus sp., Croton sp., Euphorbia sp., Mikania sp., and Ophryosporus sp., were the genera and species with the highest presence in the nests (n = 35) of three genera of stingless bees of two provinces located in different climatic regions inside the continental Ecuador. Plant species richness in both areas was statistically similar (p-value = 0.21). We concluded that floral sources' molecular identification with the ITS2 region had a higher number of genera and species detected, than the rbcL gene and microscopy tools, for the Ecuadorian landscapes. We confirmed that the foraging behavior of Melipona sp., Scaptotrigona sp., and Tetragonisca sp., could include non-native flora (27%, 12/44 identifications) that provide a rich source of pollen. Stingless beekeepers could use this information to create flower calendars and establish a schedule for better management of stingless bees in secondary and modified environments.},
}

@article {pmid40364976,
year = {2025},
author = {Meadow, ME and Broas, S and Hoare, M and Ahmed, M and Alimohammadi, F and Welle, KA and Swovick, K and Hryhorenko, JR and Jain, A and Martinez, JC and Seluanov, A and Gorbunova, V and Buchwalter, A and Ghaemmaghami, S},
title = {Proteome Birthdating: A Single-Sample Approach for Measuring Global Turnover Dynamics and "Protein Age".},
journal = {Bio-protocol},
volume = {15},
number = {9},
pages = {e5296},
pmid = {40364976},
issn = {2331-8325},
abstract = {Within a cell, proteins have distinct and highly variable half-lives. As a result, the molecular ages of proteins can range from seconds to years. How the age of a protein influences its environmental interactions is a largely unexplored area of biology. To facilitate such studies, we recently developed a technique termed "proteome birthdating" that differentially labels proteins based on their time of synthesis. Proteome birthdating enables analyses of age distributions of the proteome by tandem mass spectrometry (LC-MS/MS) and provides a methodology for investigating the protein age selectivity of diverse cellular pathways. Proteome birthdating can also provide measurements of protein turnover kinetics from single, sequentially labeled samples. Here, we provide a practical guide for conducting proteome birthdating in in vitro model systems. The outlined workflow covers cell culture, isotopic labeling, protein extraction, enzymatic digestion, peptide cleanup, mass spectrometry, data processing, and theoretical considerations for interpretation of the resulting data. Key features • Proteome birthdating barcodes the proteome with isotopically labeled precursors based on time of synthesis or "age." • Global protein turnover kinetics can be analyzed from single, sequentially labeled biological samples. • Protein age distributions of subsets of the proteome can be analyzed (e.g., ubiquitinated proteins). • Age selectivity of protein properties, cellular pathways, or disease states can be investigated.},
}

@article {pmid40364432,
year = {2025},
author = {Chedao, N and Pandey, AC and Suraninpong, P},
title = {Identification of Indigenous Thai Phlegmariurus Genotypic Population by Integrating Morphological and Molecular Studies.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/plants14091400},
pmid = {40364432},
issn = {2223-7747},
support = {0000//Walailak University/ ; },
abstract = {Phlegmariurus, a diverse genus within the Lycopodiaceae family, has wide diversity in tropical regions, including Thailand. Accurate species delimitation in the tropical clubmoss genus Phlegmariurus is challenged by high morphological plasticity and genetic complexity. This study applied an integrative multilocus approach combining morphometric analysis of 27 complete specimens, 35 Phlegmariurus and one Lycopodiella accessions for AFLP genotyping (926 loci; PIC 0.32), SSR profiling (44 loci; PIC 0.57; expected heterozygosity 0.35), and chloroplast barcoding using rbcL (1308 bp; bootstrap 89-99%) and the psbA-trnH intergenic spacer (308 bp; bootstrap ≥ 94%). A total of 13 were identified as belonging to seven known species, including P. nummulariifolius (NST01, NST15, NST36), P. goebelii (JP04), P. phlegmaria (NST13), P. verticillatus (PHI16), P. squarrosus (NST21, NST22, MY31), P. tetrastichus (NST30), and P. carinatus (MY32, MY33, NST34). Morphological clustering and molecular markers consistently distinguished Phlegmariurus accessions from the Lycopodiella outgroup. Additionally, 19 previously unclassified Phlegmariurus accessions were successfully identified as belonging to the species P. nummulariifolius (NST23), P. goebelii (NST03, JP05, STN12, PNA14, SKA25, CPN26, KRB27, PNA28), P. phlegmaria (NWT07, STN08, NST09, NST10, PHI29), P. squarrosus (NST17), and P. carinatus (PNA06, STN18, CPN19, JP24). Moreover, this study identified three novel lineages (NST02, STN11, NST20) with strong support across datasets. The combination of broad genomic coverage (AFLP), fine-scale allelic resolution (SSR), deep-branch backbone (rbcL), and terminal-branch discrimination (psbA-trnH) yields a robust framework for species identification. These results define clear operational units for conservation prioritization and establish a foundation for marker-assisted development of ornamental Phlegmariurus cultivars.},
}

@article {pmid40362097,
year = {2025},
author = {Zhang, J and Cui, X and Lin, L and Liu, Y and Ye, J and Zhang, W and Li, H},
title = {Unraveling Fish Community Diversity and Structure in the Yellow Sea: Evidence from Environmental DNA Metabarcoding and Bottom Trawling.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ani15091283},
pmid = {40362097},
issn = {2076-2615},
support = {2024YFF0808802; FREU2020-03; 2020-A-06//National Key Research and Development Program of China; the Fund of Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, P. R. China; Doctoral Research Initiation of Foundation of Nat/ ; },
abstract = {The use of environmental DNA (eDNA) metabarcoding to analyze fish species diversity across different aquatic ecosystems is well documented. Nonetheless, there is a gap in validating eDNA metabarcoding studies on the diversity and structure of fish communities in coastal ecosystems, particularly in comparing these findings with bottom trawl catch data. In this study, we employed eDNA metabarcoding to explore species composition and relative abundance in fish communities, taxonomic-level diversity variations, and the interplay between community structures and environmental factors in the Yellow Sea and compared these results with those obtained from bottom trawl catches. In addition, we compared the various methods used to estimate the distributions of taxonomic, phylogenetic, and functional diversity factors. We found that eDNA metabarcoding detected a greater number of species (86 vs. 41), genera (73 vs. 37), and families (42 vs. 25) than bottom trawl results at each sampling station. eDNA metabarcoding provided higher Shannon, Simpson, and Chao1 alpha diversity indices than the bottom trawl results. The PCoA results showed that eDNA metabarcoding samples could be more clearly separated at the sampling sites in the Zhuanghe (ZH) and Lianyungang (LYG) areas than bottom trawling samples. The RDA analysis indicated that temperature, along with NO3- and NH4[+] concentrations, were pivotal in shaping the geographical patterns of fish communities, as identified through eDNA metabarcoding, echoing findings from bottom trawling studies. Furthermore, our findings suggest that eDNA barcoding surpasses bottom trawling in detecting taxonomic and phylogenetic diversity, as well as in uncovering greater functional diversity at the local level. Conclusively, eDNA metabarcoding emerges as a valuable complement to bottom trawling, offering a multifaceted approach to biodiversity monitoring that not only boosts efficiency but also reduces environmental impact on coastal ecosystems.},
}

@article {pmid40362082,
year = {2025},
author = {Wang, D and Li, Q and Gao, J and Hou, L and Zou, Y and Lian, X},
title = {Dietary Differentiation Mitigates Interspecific Interference Competition Between Sympatric Pallas's Cats (Otocolobus manul) and Red Foxes (Vulpes vulpes).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ani15091267},
pmid = {40362082},
issn = {2076-2615},
abstract = {The comparative analysis of the feeding ecology among sympatric small carnivores reveals both differentiation and overlap in resource utilization patterns, which serves as a critical pathway for understanding interspecific interactions and maintaining ecosystem stability. In this study, we collected fecal samples from sympatric Pallas's cats (Otocolobus manul, n = 26) and red foxes (Vulpes vulpes, n = 13) within the Sanjiangyuan National Park (SNP) in China. Subsequently, DNA barcoding technology was employed to analyze the dietary composition and interspecific differences of these two small carnivores. The results demonstrated that both species primarily prey on plateau pikas (Ochotona curzoniae) and small rodents. Despite a high trophic niche overlap between Pallas's cats and red foxes (Ojk = 0.81), interspecific competition is mitigated through differentiate feeding proportions of shared prey species. Furthermore, the trophic niche breadth of red foxes (B = 267.89) exceeds that of Pallas's cats (B = 162.94), reflecting a greater diversity of prey resources utilized by red foxes. Consequently, the two small carnivores achieve sympatric coexistence via differentiated resource utilization. These findings enhance our understanding of the coexistence mechanisms within carnivore communities and provide a scientific basis for the conservation of wildlife in the SNP.},
}

@article {pmid40362051,
year = {2025},
author = {Chetverikov, PE and Peralta Alba, LE},
title = {First Bisexually Dimorphic Phytoptid Taxon (Eriophyoidea, Phytoptidae) from Gondwanian Angiosperm Host.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/ani15091236},
pmid = {40362051},
issn = {2076-2615},
support = {125013001089-0//Zoological Institute of Russian Academy of Sciences/ ; },
abstract = {Acariform mites of the superfamily Eriophyoidea are permanent parasites of higher vascular plants. Seasonal morphological dimorphism in females has been documented across various eriophyoid taxa, while male dimorphism remains poorly understood. In this study, we analyzed morphological, molecular, and biological data from the genus Austracus Keifer 1944, with a particular focus on the type species, A. havrylenkonis Keifer 1944, associated with Nothofagus. Using new material collected from Chile and Argentina, we demonstrated that this species exhibits two distinct forms of both males and females, making it the first known bisexually dimorphic taxon within the family Phytoptidae. The summer form of A. havrylenkonis displays the unstable annulation of the dorsal opisthosoma, characterized by a significant variation in the number of thin, microtuberculated dorsal annuli interspersed among the broader, plate-like annuli typical of the winter form. This finding aligns with the previous observations of atypical deuterogyny in Eriophyoidea and leads us to hypothesize that gall mites employ diverse adaptive strategies-manifesting as either gradual or discrete morphological changes-to cope with seasonal environmental fluctuations. Investigating the genetic mechanisms underlying these adaptive strategies, along with further studies of eriophyoids associated with Nothofagus in the Southern Hemisphere, represents a promising direction for future research.},
}

@article {pmid40361631,
year = {2025},
author = {Andronache, J and Cichna-Markl, M and Dobrovolny, S and Hochegger, R},
title = {Development of a DNA Metabarcoding Method for the Identification of Crustaceans (Malacostraca) and Cephalopods (Coleoidea) in Processed Foods.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/foods14091549},
pmid = {40361631},
issn = {2304-8158},
abstract = {Seafood is a valuable commodity with increasing demand, traded for billions of USD each year. The volatility in supply chains and fluctuating prices contribute to the susceptibility of the seafood market to food fraud. Analytical methods are required to identify seafood in processed foods to ensure food authenticity and compliance with European laws. To address this need, we developed and validated a DNA metabarcoding method for the authentication of crustaceans and cephalopods in processed food samples, as both are prone to food fraud, especially in mixed products. A ~200 bp barcode of the mitochondrial 16S rDNA was selected as the marker for identification and sequenced on Illumina platforms. The DNA metabarcoding method utilizes two primer systems, one for the amplification of crustacean DNA and another for cephalopods. The crustacean primer system comprises two forward and two reverse primers, while the cephalopod primer system includes three forward and one reverse primer. DNA extracts from reference materials, model foods, processed foodstuffs, and DNA extract mixtures were investigated. Even species with a close phylogenetic relationship were successfully identified and differentiated in commercial samples, while single species were detected at amounts as low as 0.003% in model foods. However, false-negative results were obtained for certain species in DNA extract mixtures, which are most likely due to degraded or low-quality DNA and can best be prevented by optimized DNA extraction procedures. Our DNA metabarcoding method demonstrates strong potential as a qualitative screening tool in combination with other in-house DNA metabarcoding methods for food authentication in routine analysis.},
}

@article {pmid40359979,
year = {2025},
author = {Iwaszkiewicz-Eggebrecht, E and Goodsell, RM and Bengsson, BÅ and Mutanen, M and Klinth, M and van Dijk, LJA and Łukasik, P and Miraldo, A and Andersson, A and Tack, AJM and Roslin, T and Ronquist, F},
title = {High-throughput biodiversity surveying sheds new light on the brightest of insect taxa.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2046},
pages = {20242974},
doi = {10.1098/rspb.2024.2974},
pmid = {40359979},
issn = {1471-2954},
support = {Career Support grant to TR//Swedish University of Agricultural Sciences/ ; 2017.088//Knut and Alice Wallenberg Foundation/ ; //Uppsala Multidisciplinary Center for Advanced Computational Science/ ; 2018/31/B/NZ8/01158//Polish National Science Centre/ ; Synergy Grant 856506/ERC_/European Research Council/International ; PPN/PPO/2018/1/00015//Polish National Agency for Academic Exchange/ ; 2018-04620, 2021-03784, 2021-05563//Swedish Research Council/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Sweden ; *Lepidoptera/genetics/classification ; },
abstract = {DNA metabarcoding of species-rich taxa is becoming a popular high-throughput method for biodiversity inventories. Unfortunately, its accuracy and efficiency remain unclear, as results mostly pertain to poorly known taxa in underexplored regions. This study evaluates what an extensive sampling effort combined with metabarcoding can tell us about the lepidopteran fauna of Sweden-one of the best-understood insect taxa in one of the most-surveyed countries of the world. We deployed 197 Malaise traps across Sweden for a year, generating 4749 bulk samples for metabarcoding, and compared the results to existing data sources. We detected more than half (1535) of the 2990 known Swedish lepidopteran species and 323 species not reported during the sampling period by other data providers. Full-length barcoding confirmed three new species for the country, substantial range extensions for two species and eight genetically distinct barcode variants potentially representing new species, one of which has since been described. Most new records represented small, inconspicuous species from poorly surveyed regions, highlighting components of the fauna overlooked by traditional surveying. These findings demonstrate that DNA metabarcoding is a highly efficient and accurate biodiversity sampling method, capable of yielding significant new discoveries even for the most well known of insect faunas.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Biodiversity
Sweden
*Lepidoptera/genetics/classification

@article {pmid40359875,
year = {2025},
author = {Morán Torres, JP and Lyu, J and Chen, X and Klaas, AM and Vonk, PJ and Lugones, LG and de Cock, H and Wösten, HAB},
title = {Single and combinatorial gene inactivation in Aspergillus niger using selected as well as genome-wide gRNA library pools.},
journal = {Microbiological research},
volume = {298},
number = {},
pages = {128204},
doi = {10.1016/j.micres.2025.128204},
pmid = {40359875},
issn = {1618-0623},
abstract = {Aspergillus niger is a saprotroph, a pathogen, an endophyte, a food spoiler and an important cell factory. Only a minor fraction of its genes has been experimentally characterized. We here set up a CRISPR/Cas9 mutagenesis screen for functional gene analysis using co-transformation of a pool of gene editing plasmids that are maintained under selection pressure and that each contain a gRNA. First, a pool of gRNA vectors was introduced in A. niger targeting five genes with easy selectable phenotypes. Transformants were obtained with all possible single, double, triple, quadruple and quintuple gene inactivation phenotypes. Their genotypes were confirmed using the gRNA sequences in the transforming vector as barcodes. Next, a gRNA library was introduced in A. niger targeting > 9600 genes. Gene nsdC was identified as a sporulation gene using co-transformation conditions that favored uptake of one or two gRNA construct(s) from the genome-wide vector pool. Together, CRISPR/Cas9 vectors with a (genome-wide) pool of gRNAs can be used for functional analysis of genes in A. niger with phenotypes that are the result of the inactivation of a single or multiple genes.},
}

@article {pmid40359386,
year = {2025},
author = {Rodriguez, LG and Lombard-Banek, C and Quach, VM and Choi, SB and Manzini, MC and Nemes, P},
title = {A Multipoint Validation of Quantification in Capillary Electrophoresis Mass Spectrometry Proteomics: Isobaric Multiplexing with Tandem Mass Tags.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c01832},
pmid = {40359386},
issn = {1520-6882},
abstract = {Multiplexing quantification using isobaric barcoding has gained traction in trace-sensitive and single-cell mass spectrometry (MS), both in nanoflow liquid chromatography (nanoLC) and capillary electrophoresis (CE). In nanoLC-MS, ratio compression from isobaric interferences is known to challenge quantification accuracy during tandem MS (MS[2]), which is effectively remedied using simultaneous precursor selection (SPS) MS[3]. Despite mounting interest in CE-MS for trace-sensitive bottom-up proteomics, the fidelity of multiplexed quantification is unknown using this technology. Here, we address this fundamental knowledge gap by holistically investigating quantification depth, reproducibility, and accuracy using a validated mouse-yeast two-proteome model. CE-based quantification via the MS[2] and SPS-MS[3] strategies were benchmarked against the nanoLC SPS-MS[3] gold standard. We found electrophoresis-correlative (Eco) ion sorting to order peptides into high-flux transients of nominally isobaric m/z values (Δm/z < 1-2 Th). While the MS[2] approach struggled with ratio distortion, the SPS-MS[3] robustly eliminated them for both separations. The reproducibility and accuracy proved indistinguishable between CE and nanoLC using MS[2] or SPS-MS[3] quantification. CE enhanced the depth of quantification by ∼12-fold. These analytical insights can be used to design trace CE-MS studies with high scientific rigor.},
}

@article {pmid40359107,
year = {2025},
author = {Nguyen, LV and Eyal-Lubling, Y and Guerrero-Romero, D and Kronheim, S and Chin, SF and Manzano Garcia, R and Sammut, SJ and Lerda, G and Lui, AJW and Bardwell, HA and Greenwood, W and Shin, HJ and Masina, R and Kania, K and Bruna, A and Esmaeilishirazifard, E and Kolyvas, EA and Aparicio, S and Rueda, OM and Caldas, C},
title = {Fitness and transcriptional plasticity of human breast cancer single-cell-derived clones.},
journal = {Cell reports},
volume = {44},
number = {5},
pages = {115699},
doi = {10.1016/j.celrep.2025.115699},
pmid = {40359107},
issn = {2211-1247},
abstract = {Clonal fitness and plasticity drive cancer heterogeneity. We used expressed lentiviral-based cellular barcodes combined with single-cell RNA sequencing to associate single-cell profiles with in vivo clonal growth. This generated a significant resource of growth measurements from over 20,000 single-cell-derived clones in 110 xenografts from 26 patient-derived breast cancer xenograft models. 167,375 single-cell RNA profiles were obtained from 5 models and revealed that rare propagating clones display a highly conserved model-specific differentiation program with reproducible regeneration of the entire transcriptomic landscape of the original xenograft. In 2 models of basal breast cancer, propagating clones demonstrated remarkable transcriptional plasticity at single-cell resolution. Dichotomous cell populations with different clonal growth properties, signaling pathways, and metabolic programs were characterized. By directly linking clonal growth with single-cell transcriptomes, these findings provide a profound understanding of clonal fitness and plasticity with implications for cancer biology and therapy.},
}

@article {pmid40352821,
year = {2025},
author = {Jin, D and Kim, SS and Shin, B and Choi, SW},
title = {An updated list of the genus Hypena Schrank (Lepidoptera, Erebidae) from Korea with five additional records to the fauna.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e155581},
doi = {10.3897/BDJ.13.e155581},
pmid = {40352821},
issn = {1314-2828},
abstract = {BACKGROUND: The paper provides the updated checklist of the genus Hypena Schrank from Korea. This genus is one of the largest genera within the Noctuoidea comprising more than 680 species worldwide and the genus is the monophyletic group based on the morphological characters. The external examination along with the genitalia examination and DNA barcoding could reveal the diversity of the genus in Korea.

NEW INFORMATION: In this study, we examined a total of 192 specimens and barcoded 16 species and listed a total of 29 species of Hypena including five new additions, Hypenatamsi Filipjev (1927), Hypenaobacerralis Walker (1859), Hypenapulverulenta Wileman (1911), Hypenaperspicua Leech (1900) and Hypenamandarina Leech (1900) to the Korean fauna. We provided the detailed distribution of each species of the genus across South Korea and the photographs of adults and genitalia. In addition, the monophyly of the genus was also confirmed using two outgroup species of Herminiinae. This study significantly contributes to the knowledge of erebid fauna in Korea and the phylogenetic relationship amongst the species of the genus.},
}

@article {pmid40352767,
year = {2025},
author = {Vasu, AC and Ravidas, VA and Tharakan, ST and Kadunganattil, S},
title = {Toxicity profiling and HR-LCMS analysis of Indigofera longiracemosa leaf methanolic extract exhibiting anti-inflammatory activity.},
journal = {3 Biotech},
volume = {15},
number = {6},
pages = {160},
doi = {10.1007/s13205-025-04320-7},
pmid = {40352767},
issn = {2190-572X},
abstract = {Indigofera longiracemosa, a member of the Fabaceae family documented in traditional medicine for its therapeutic potential, holds promise as a viable natural indigo source. The dearth of reliable and coherent research on the safety and medicinal advantages of phytochemicals obtained from this specific plant species prompted us to examine therapeutic potential of extracts prepared from the leaf and stem of this dye yielding plant. The aerial parts (leaf and stem) of I. longiracemosa were extracted separately using solvents of increasing polarity. In vitro anti-inflammatory studies such as lipoxygenase inhibition, albumin denaturation, and protease inhibitory activity revealed leaf methanolic extract (LME) to show the best anti-inflammatory property. Furthermore, short term toxicity studies (acute and sub-acute) were done in Balb/c mice to evaluate LME's toxicity. In acute toxicity study, LME administered at 2000 mg/kg body weight was found to be non-toxic. Consequently, sub-acute toxicity study was done in both male and female Balb/c mice at three doses (100, 200 and 400 mg/kg body weight, respectively). Following sub-acute toxicity study for 28 days, serum analysis and histological evaluation of tissues did not reveal any signs of toxicity at the administered doses, thereby indicating non-toxic nature of LME. Furthermore, to identify phytochemicals associated with LME, HRLCMS-QTOF untargeted metabolomics was done, and the predominant phytochemicals identified were phenols. The enhanced anti-inflammatory property observed in LME may be attributed to the predominance of phenols. Our studies have, therefore, illustrated the non-toxic nature and therapeutic potential of LME, an extract prepared from I. longiracemosa.},
}

@article {pmid40350868,
year = {2025},
author = {Li, H and Zeng, YJ and Li, XY and Abdullah, and Huang, YH and Yan, RS and Shao, R and Wang, Y and Tian, XX},
title = {[Mini-barcode development based on chloroplast genome of Descurainiae Semen Lepidii Semen and its adulterants and its application in Chinese patent medicine].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {7},
pages = {1758-1769},
doi = {10.19540/j.cnki.cjcmm.20250113.101},
pmid = {40350868},
issn = {1001-5302},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Drugs, Chinese Herbal/chemistry ; *Drug Contamination ; *Genome, Chloroplast ; Medicine, Chinese Traditional ; },
abstract = {Descurainiae Semen Lepidii Semen, also known as Tinglizi, originates from Brassicaceae plants Descurainia sophia or Lepidium apetalum. The former is commonly referred to as "Southern Tinglizi(Descurainiae Semen)", while the latter is known as "Northern Tinglizi(Lepidii Semen)". To scientifically and accurately identify the origin of Tinglizi medicinal materials and traditional Chinese medicine products, this study developed a specific DNA mini-barcode based on chloroplast genome sequences. By combining the DNA mini-barcode with DNA metabarcoding technology, a method for the qualitative and quantitative identification of Tinglizi medicinal materials and Chinese patent medicines was established. In this study, chloroplast genomes of Southern Tinglizi and Northern Tinglizi and seven commonly encountered counterfeit products were downloaded from the GenBank database. Suitable polymorphic regions were identified to differentiate these species, enabling the development of the DNA mini-barcode. Using DNA metabarcoding technology, medicinal material mixtures of Southern and Northern Tinglizi, as well as the most common counterfeit product, Capsella bursa-pastoris seeds, were analyzed to validate the qualitative and quantitative capabilities of the mini-barcode and determine its minimum detection limit. Additionally, the mini-barcode was applied to Chinese patent medicines containing Tinglizi to authenticate their botanical origin. The results showed that the developed mini-barcode(psbB) exhibited high accuracy and specificity, effectively distinguishing between the two authentic origins of Tinglizi and commonly encountered counterfeit products. The analysis of mixtures demonstrated that the mini-barcode had excellent qualitative and quantitative capabilities, accurately identifying the composition of Chinese medicinal materials in mixed samples with varying proportions. Furthermore, the analysis of Chinese patent medicines revealed the presence of the adulterant species(Capsella bursa-pastoris) in addition to the authentic species(Southern and Northern Tinglizi), indicating the occurrence of adulteration in commercially available Tinglizi-containing products. This study developed a method for the qualitative and quantitative identification of multi-origin Chinese medicinal materials and related products, providing a model for research on other multi-origin Chinese medicinal materials.},
}

*DNA Barcoding, Taxonomic/methods
*Drugs, Chinese Herbal/chemistry
*Drug Contamination
*Genome, Chloroplast
Medicine, Chinese Traditional

@article {pmid40349990,
year = {2025},
author = {Yuda, A and Nakamura, T and Momose, S and Ishii, S and Tanaka, H and Yamamoto-Hanada, K and Fukuie, T and Ohya, Y and Nomura, T and Noguchi, E},
title = {A comprehensive approach for identifying filaggrin mutations and copy number variants by long-read sequencing.},
journal = {Genomics},
volume = {},
number = {},
pages = {111055},
doi = {10.1016/j.ygeno.2025.111055},
pmid = {40349990},
issn = {1089-8646},
abstract = {Filaggrin (FLG) is essential for skin barrier function, but has highly diverse and complex mutations linked to various allergic and dermatological diseases. Current genotyping methods often fail to capture the full range of FLG variants, especially in regions with high sequence homology. To overcome this limitation, we developed a singleplex PCR method that amplifies FLG exon 3 using FLG-specific primers tailed with barcodes for sample identification, followed by long-read sequencing on the PacBio Sequel IIe system. After demultiplexing with the barcode sequences, pbmm2 and GATK HaplotypeCaller were used for alignment and variant calling, respectively. This method successfully identified single nucleotide variants, insertion-deletion variants, and copy number variations (CNVs), including several loss-of-function mutations. We also determined the FLG copy number in each allele, which ranged from 7 to 20 repeats. This comprehensive, convenient genotyping approach could significantly enhance diagnostic accuracy and personalized treatment strategies for allergy- and skin-related conditions.},
}

@article {pmid40348924,
year = {2025},
author = {Brunet, S and Grankvist, A and Jaen-Luchoro, D and Bergdahl, M and Tison, JL and Wester, A and Elfving, K and Brandenburg, J and Gullsby, K and Lindsten, C and Arvidsson, LO and Larsson, H and Eilers, H and Strand, AS and Lannefors, M and Keskitalo, J and Rylander, F and Welander, J and Jungestrom, MB and Geörg, M and Kaden, R and Karlsson, I and Linde, AM and Mernelius, S and Berglind, L and Feuk, L and Kerje, S and Karlsson, L and Sjödin, A and Guerra-Blomqvist, L and Wallin, F and Fagerström, A and Vondracek, M and Mölling, P and Hallbäck, ET},
title = {Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40348924},
issn = {1435-4373},
abstract = {PURPOSE: Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.

METHODS: Thirteen mock samples comprised of various bacterial strains and an External Quality Assessment (EQA) panel from QCMD (Quality Control for Molecular Diagnostics) were analysed by 20 microbiological laboratories across Sweden, using the recent v14 chemistry. Most laboratories generated full-length 16S rRNA sequencing libraries using an optimized protocol for the 16S Barcoding Kit 24, while two laboratories employed in-house PCR coupled with the Ligation Sequencing Kit. The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).

RESULTS: Seventeen out of 20 laboratories successfully sequenced and analysed the samples. Laboratories that used sodium acetate-containing elution buffers faced compatibility issues during library construction, resulting in reduced read count. High bacterial load samples were generally well-characterized, whereas hard-to-lyse bacteria such as Gram-positive strains were detected at lower abundance. The GMS-16S tool provided improved species-level identification compared to the 1928-16S pipeline, particularly for closely related taxa within the Streptococcus and Staphylococcus genera.

CONCLUSION: Nanopore sequencing demonstrated promising potential for bacterial identification in a clinical setting. The results prompt further optimization of the protocol to improve detection of a broader range of species. This multicentre study highlights the feasibility of implementing Nanopore sequencing into clinical microbiological laboratories, for improved national precision diagnostics.},
}

@article {pmid40343328,
year = {2025},
author = {McLamb, F and Vazquez, A and Olander, N and Vasquez, MF and Feng, Z and Malhotra, N and Bozinovic, L and Najera Ruiz, K and O'Connell, K and Stagg, J and Bozinovic, G},
title = {Comparative Three-Barcode Phylogenetics and Soil Microbiomes of Planted and Wild Arbutus Strawberry Trees.},
journal = {Plant direct},
volume = {9},
number = {5},
pages = {e70078},
doi = {10.1002/pld3.70078},
pmid = {40343328},
issn = {2475-4455},
abstract = {Taxonomic identification of closely related plants can be challenging due to convergent evolution, hybridization, and overlapping geographic distribution. To derive taxonomic relationships among planted and wild Arbutus plants across a large geographic range, we complemented three standard plastid barcodes rbcL, matK, and trnH-psbA with soil and fruit chemistry, soil microbiome, and plant morphology analyses. Soil and plant sampling included planted Arbutus from manicured sites in Southern California, USA, wild plants from Southern and Northern California, and wild populations from Mediterranean island of Hvar, Croatia. We hypothesized that phenotypic variation within and between sites correlates with plants' genotype and geographic distribution. Similar fruit chemistry corresponds to geographical proximity and morphological resemblance, while bulk soil bacterial content defines three distinct clusters distinguishing planted versus wild trees and continent of origin. The soil microbiome of wild California Arbutus was characterized by an abundance of Nitrobacter, while the presence of Candidatus Xiphinematobacter was high in wild Hvar samples and most planted samples, but low in all wild California samples. Although all three barcodes resolved four main groups, the position of samples varies across barcodes. The rbcL phylogram is relatively unbalanced, suggesting slower diversification among wild California populations and exhibiting greater resolution than other barcodes among planted individuals. While our data demonstrate an overall agreement among standard plant barcodes relative to geo-distribution and plant morphology, sustained efforts on cost-effective global plant DNA barcode library standardization for closely related and geographically overlapping plants is recommended.},
}

@article {pmid40342730,
year = {2025},
author = {Cometti, V and Cecchetto, M and Guzzi, A and Grillo, M and Noli, NF and Corsolini, S and Schiaparelli, S},
title = {Checklist of pioneer benthic taxa found on Autonomous Reef Monitoring Structures (ARMS) in Terra Nova Bay (Ross Sea, Antarctica).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e148863},
doi = {10.3897/BDJ.13.e148863},
pmid = {40342730},
issn = {1314-2828},
abstract = {BACKGROUND: Benthic communities studies in the Southern Ocean highlight their potential for assessing climate and anthropogenic impacts. However, the lack of standardised methods limits result reliability and interpretation. This dataset presents the first checklist focus on the Antarctic pioneer benthic communities collected using a standardised approach such as Autonomous Reef Monitoring Structures (ARMS) located at 25 m depth in the surroundings of the Italian research station "Mario Zucchelli" (MZS) in the Terra Nova Bay (TNB) area of the Ross Sea, Antarctica. The data encompass ARMS time series corresponding to deployments of 1, 2, 3 and 5 years, from which 277 occurrence data corresponding to 12 phyla, 43 families, 49 genera and 39 species were obtained. All retrieved specimens are curated by the Italian National Antarctic Museum (MNA, section of Genoa). This dataset is a contribution to the Antarctic Biodiversity Portal, the thematic Antarctic node for both the Ocean Biogeographic Information System (AntOBIS) and the Global Biodiversity Information Facility Antarctic Biodiversity Information Facility (ANTABIF). The dataset was uploaded and integrated with the SCAR-AntOBIS database under the licence CC-BY 4.0. Please follow the guidelines from the SCAR Data Policy (ISSN 1998-0337) when using the data. If you have any questions regarding this dataset, please contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at the biodiversity-aq GitHub project.

NEW INFORMATION: We describe the biodiversity of the Antarctic pioneer benthic communities of TNB sampled using the ARMS installed at the Italian research station "Mario Zucchelli". ARMS is a standardised, reproducible and comparable method for quantifying biodiversity. This dataset provides essential baseline data on the occurrence and abundance of pioneer benthic communities in this study area, representing an important contribution for understanding the dynamics of benthic pioneer communities in an area where these structures have never been deployed and, in general, for an exposure time that largely exceed the standard one, which is usually of one year only.The 277 occurrences reported here have been classified at the lowest possible taxonomic level and comprise 39 recognised species, 49 genera and 43 families. Approximately 98% of the samples are stored in 96% ethanol, while the others at -20°C, representing a potential resource for future genetic studies. To date, the entire ARMS collection has not been DNA barcoded, although preliminary metabarcoding analyses have already been published in Cecchetto et al. (2024). Outcomes of the barcoding activity will be the target of another future publication (Cometti et al., in prep). The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the framework of EU-Lifewatch as a contribution to the SCAR Antarctic Biodiversity Portal (bio diversity.aq).},
}

@article {pmid40342375,
year = {2025},
author = {Klaiklueng, N and Kumlert, R and Moonmake, S and Ruang-Areerate, T and Siriyasatien, P and Sunantaraporn, S and Wanachiwanawin, D and Ruenchit, P and Wongkamchai, S},
title = {Species distribution and screening of Trypanosoma DNA in phlebotomine sand flies from four southern provinces of Thailand.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {7},
number = {},
pages = {100263},
doi = {10.1016/j.crpvbd.2025.100263},
pmid = {40342375},
issn = {2667-114X},
abstract = {Sand flies are principal vectors of Leishmania spp. and Trypanosoma spp. Identifying precise vector species is crucial for effective control. We conducted a study on the species distribution of phlebotomine sand flies in cave-dwelling and non-cave-dwelling in four southern provinces of Thailand. In this study, we collected 621 sand flies (346 females and 275 males) and identified all specimens based on morphology and DNA barcoding, employing cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes. In female specimens, we also screened the small subunit 18S ribosomal RNA (18S rRNA) gene for Leishmania spp. and Trypanosoma spp. Morphologically, 467 (75.2%) sand flies were identified to species level, 47 (7.57%) to subgenus level, and 107 (17.23%) to genus level. These included Idiophlebotomus asperulus (43.48%), Sergentomyia khawi (26.73%), S. anodontis (2.25%), S. brevicaulis (2.25%), Grassomyia indica (0.48%), Phlebotomus (Euphlebotomus) spp. (4.83%), Phlebotomus (Lewisius) spp. (2.74%), Sergentomyia spp. (9.18%), and Phlebotomus spp. (8.05%). Among the 107 specimens identified to genus level, DNA barcoding further identified 49 (45.79%) as Sergentomyia barraudi (1.61%), S. bailyi (0.16%), Phlebotomus kiangsuensis (2.9%), and Ph. stantoni (1.61%). No Leishmania DNA was detected, but Trypanosoma DNA was found in females of S. khawi from Narathiwat Province. Expanding genetic reference databases of sand flies located in four provinces of southern Thailand will improve barcoding accuracy. Understanding sand fly species composition and distribution is imperative for vector control and disease prevention in Thailand.},
}

@article {pmid40339340,
year = {2025},
author = {Wang, Q and Wu, Y and Wang, Y and Mei, R and Zhao, R and Wang, X and Chen, L},
title = {Surface enhanced Raman scattering tag enabled ultrasensitive molecular identification of Hippocampus trimaculatus based on DNA barcoding.},
journal = {Talanta},
volume = {294},
number = {},
pages = {128289},
doi = {10.1016/j.talanta.2025.128289},
pmid = {40339340},
issn = {1873-3573},
abstract = {Rapid and precise DNA barcode-based identification of biological species holds significant potential for pharmaceutical authentication and biomedical diagnostics. Herein, we present a polymerase chain reaction (PCR)-surface-enhanced Raman scattering (SERS) platform that integrates SERS tags for ultrasensitive and fast authentication of Hippocampus trimaculatus, a high-value traditional Chinese medicine (TCM). The SERS tags are composed of gold nanostars, near-infrared cyanine7 Raman reporters and carboxylated polystyrene shells, which achieve single-particle detection sensitivity under 780 nm irradiation. The tags also show excellent colloidal and SERS stability under physiologically relevant conditions (e.g., phosphate buffer saline, serum, 1 mM NaCl, and pH 1-12), with signal variations less than 5 %. The carboxylated polystyrene shells enable efficient DNA functionalization. Leveraging these advancements, the PCR-SERS assay detects genomic DNA (gDNA) at concentrations as low as 10 copies/μL within 20 thermal cycles, with remarkable specificity for Hippocampus trimaculatus over four common adulterant species. Notably, the method reduces amplification requirements to 5 thermal cycles (detection limit of 10[6] copies/μL) while completing the entire workflow in less than 30 min (conventional qPCR, 20-30 cycles, 1-2 h). Beyond TCM verification, this PCR-SERS platform holds broad applicability for rapid nucleic acid detection in fields ranging from environmental eDNA monitoring to point-of-care diagnostics.},
}