@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.},
}

@article {pmid40338382,
year = {2025},
author = {Gil-Fernández, M and Carthey, AJR and Mendoza, E and Godínez-Gómez, O and G, MCM and Blanco-García, A and Delfín-Alfonso, CA and Le Roux, JJ},
title = {The impact of land use change on mycorrhizal fungi and their associations with rodents: insights from a temperate forest in Mexico.},
journal = {Mycorrhiza},
volume = {35},
number = {3},
pages = {36},
pmid = {40338382},
issn = {1432-1890},
support = {20224755//Macquarie University/ ; OSP Fellowship//Macquarie University/ ; },
abstract = {Ecosystem functioning is influenced by biological diversity, ecological interactions, and abiotic conditions. Human interactions with ecosystems can cause major changes in how they function when involving changes in the vegetation cover and structure (i.e., land use change). This study examines how land use change affects the diversity of arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) in soil and rodent scats in temperate forest sites. We collected soil and rodent scat samples at five paired sites (i.e., disturbed vs. undisturbed) in Michoacan, Mexico. We identified 112 putative mycorrhizal fungi species using DNA barcoding based on partial internal transcribed region 1 (ITS) sequences. We found a higher richness of EMF in undisturbed soil samples compared to disturbed soil samples and a higher AMF diversity in rodent scat samples from disturbed than undisturbed sites. Scat samples had a high incidence of both AMF (75%) and EMF (100%). We found significant differences in the diversity of both AMF and EMF depending on the rodent species associated with them. We also found a higher diversity of EMF in scats in the wet season than in the dry season. We also report, for the first time, associations between Sigmodon hispidus and numerous AMF and EMF species. Overall, our study highlights the role of rodents as important dispersal vectors of mycorrhizal fungi, particularly for EMF that could be essential to build up mycorrhizal fungi spore banks in disturbed forests.},
}

@article {pmid40337478,
year = {2025},
author = {Abele, S and Alanis-Lobato, G and Oti, M and Rust, W and Blazevic, D and Danner-Liskus, J and Mayer, C and Zimmermann, G and Zuckschwerdt, K and Schönberger, T and Gross, P and Lempp, C and Michelfelder, S and Strobel, B},
title = {Mapping administration route-dependent transduction profiles of commonly used AAV variants in mice by barcode amplicon sequencing.},
journal = {Molecular therapy. Methods & clinical development},
volume = {33},
number = {2},
pages = {101468},
doi = {10.1016/j.omtm.2025.101468},
pmid = {40337478},
issn = {2329-0501},
abstract = {The tissue transduction profiles and transgene expression efficiencies of adeno-associated viruses (AAVs) depend not only on the utilized capsid and dose but also on the administration route. Yet, despite the plethora of available natural and capsid-engineered variants, a comprehensive evaluation of the administration route dependency of AAV tropism has been lacking so far. Therefore, we here compared transduction and transgene expression profiles for 34 well-known AAV capsids following intravenous (i.v.) and intraperitoneal (i.p.) injection in male C57BL/6 mice by multiplexed biodistribution analyses based on AAV genome-barcoding. Readout on viral genome and transcript level confirmed pronounced liver targeting by most AAV variants after i.v. administration, as well as known tissue tropism for benchmark capsids (e.g., AAV-PHP.eB: brain and AAV2-ESGHGYF: lung). In contrast, i.p. administration generally decreased liver targeting, while concurrently increasing expression in other abdominal organs in a capsid-specific fashion. For example, AAV6.2 and AAV-DJ, which showed almost exclusive liver transduction after i.v. administration, displayed differential biodistribution profiles with enhanced expression in the diaphragm, adipose tissue, and pancreas when administered intraperitoneally. In summary, our data guide study design by enabling the selection of optimal vector and administration route combinations for refined tissue targeting approaches in preclinical in vivo experiments.},
}

@article {pmid40336863,
year = {2025},
author = {Zhang, H and Hoang, QD and Lei, S},
title = {Description of two new huntsman spiders from Vietnam (Araneae, Sparassidae).},
journal = {ZooKeys},
volume = {1236},
number = {},
pages = {129-140},
doi = {10.3897/zookeys.1236.145146},
pmid = {40336863},
issn = {1313-2989},
abstract = {Two new species of the sparassid genera Heteropoda Latreille, 1804 and Pseudopoda Jäger, 2000 are described from Vietnam: Heteropodataygiangensis sp. nov. (♂) from Quang Nam Province and Pseudopodatadungensis sp. nov. (♀) from Dak Nong Province. The new Pseudopoda species is described and diagnosed based on both morphological characteristics and DNA barcoding. DNA barcode data (COI) are provided for both new species.},
}

@article {pmid40334225,
year = {2025},
author = {Ngai, HL and Cheng, SW and Tse, TS and Lee, HK and Shaw, PC},
title = {Quality assessment of medicinal material Daqingye and Banlangen from Isatis tinctoria Fort. reveals widespread substitution with Strobilanthes species.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323084},
doi = {10.1371/journal.pone.0323084},
pmid = {40334225},
issn = {1932-6203},
mesh = {*Isatis/chemistry/genetics ; Chromatography, High Pressure Liquid ; *Drugs, Chinese Herbal/chemistry/standards ; *Plants, Medicinal/chemistry/genetics ; Drug Contamination ; DNA Barcoding, Taxonomic ; Plant Leaves/chemistry ; Plant Roots/chemistry ; Hong Kong ; Quality Control ; },
abstract = {BACKGROUND: Isatidis Folium (Daqingye, DQY) and Isatidis Radix (Banlangen, BLG) are the leaf and root of the plant Isatis tinctoria Fort. (syn. Isatis indigotica Fort.), commonly prescribed for detoxification, and the inhibition of viral and oxidative activities. Given their widespread use, we set forth to investigate the authenticity and chemical composition of DQY and BLG samples obtained from eighteen administrative districts in the Hong Kong market.

METHODS: The present study screened the identities and chemical composition of DQY and BLG through molecular authentication and HPLC methods, respectively. Molecular authentication utilized DNA barcoding, focusing on nuclear ribosomal and chloroplast regions. The HPLC methods were conducted in accordance with the Hong Kong Chinese Materia Medica Standards (HKCMMS).

RESULTS: We found that only one sample was genuine according to the species definition in the Chinese Pharmacopoeia and HKCMMS for both herbs. The chemical composition of the adulterated and the genuine samples were completely different, that the adulterant samples did not have the standard chemical markers epigoitrin and indirubin of Banlangen and Daqingye as listed in the Chinese Pharmacopoeia.

CONCLUSION: Our investigation underscores the widespread substitution by Strobilanthes (Nanbanlangen and Nandaqingye) species, mainly due to the preference of use of this herb in southern China. The adulteration of Daqingye by Blumea balsamifera (Ainaxiang) was probably due to mislabeling in the herb shop, though the error might have originated from the supplying sources. We recommend providing education on the necessity of using authentic Daqingye and Banlangen, especially in combined regimens, to standardize treatment effects. More education is also needed on the morphological differentiation of Banlangen from Nanbanlangen and Daqingye from Nandaqingye. The implementation of a track-and-trace system is strongly recommended to prevent and deter incorrect supply chain practices that lead to substitution or adulteration.},
}

*Isatis/chemistry/genetics
Chromatography, High Pressure Liquid
*Drugs, Chinese Herbal/chemistry/standards
*Plants, Medicinal/chemistry/genetics
Drug Contamination
DNA Barcoding, Taxonomic
Plant Leaves/chemistry
Plant Roots/chemistry
Hong Kong
Quality Control

@article {pmid40332883,
year = {2025},
author = {Yao, Y and Chen, JY and Gong, XL and Li, CH and Liu, Z and Lin, XL},
title = {Species Delimitation and Cryptic Diversity in Rheotanytarsus Thienemann & Bause, 1913 (Diptera: Chironomidae) Based on DNA Barcoding.},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040370},
pmid = {40332883},
issn = {2075-4450},
support = {A2-2006-23-200303//Shanghai Ocean University/ ; 31900344//National Natural Science Foundation of China/ ; },
abstract = {The genus Rheotanytarsus Thienemann & Bause, 1913 (Diptera: Chironomidae) currently includes more than 120 recognized species worldwide, but precise species-level identification based solely on morphology remains challenging. Pronounced morphological differences among life stages and the time-consuming inefficiency of rearing larvae further complicate life-stage matching in this genus. In this study, we assessed species diversity by integrating morphological examination and DNA barcoding, analyzing 911 DNA barcodes from newly collected samples and a public database. Based on these results, we further constructed a relatively complete life-history framework. Our results show that 911 Rheotanytarsus DNA barcodes belong to 69 putative species. The maximum intraspecific divergence reached 7.35% in R. pentapoda, and the average minimal interspecific distance was 11.44%. Substantial intraspecific divergence in certain species complexes suggests the presence of cryptic species. Therefore, to resolve these potential cryptic species issues, more extensive sampling and morphological examination of specimens from geographically distant regions-supplemented by nuclear and ecological data-are required.},
}

@article {pmid40332868,
year = {2025},
author = {Adnan, A and Mona, S and Rakha, A and Nazir, S and Wang, H and Ren, F},
title = {Molecular Diversity of Three Forensically Relevant Dipterans from Cadavers in Lahore, Pakistan.},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040381},
pmid = {40332868},
issn = {2075-4450},
support = {(2024021179-JH2/1019)//Department of Science and Technology of Liaoning province PR China/ ; },
abstract = {Molecular diversity, which reflects variation in species abundance and genetic structure, plays a pivotal role in forensic entomology by enabling the accurate identification of insect evidence through tools such as DNA barcoding. In Pakistan, the absence of trained forensic entomologists and limited research on insect biodiversity hinder the effective use of entomological evidence in criminal investigations. Traditional morphological identification methods are insufficient for resolving complex forensic cases, particularly when dealing with immature insect stages. This highlights the urgent need for molecular approaches, such as DNA barcoding, to enhance species identification and genetic analysis of forensically relevant insects. This study uniquely focuses on evaluating the utility of a 658 bp fragment of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene for identifying dipteran species collected from cadavers in Lahore, Pakistan. The primary goal was to identify forensically relevant insect species, assess their genetic diversity and population structure, and compare these findings with global data to contextualize the results within forensic entomology. Three blow fly species were identified: Chrysomya megacephala (Fabricius, 1794), Chrysomya saffranea (Bigot, 1877), and Chrysomya rufifacies (Macquart, 1843). Low genetic diversity was observed within populations, while significant genetic differentiation among populations was indicated by a high fixation index (FST = 0.83992). These findings suggest unique genetic signatures for blow fly populations in Lahore. This study underscores the importance of molecular tools like DNA barcoding for species identification and highlights the need for further research to establish a comprehensive database of forensically relevant insects in Pakistan, given the limited species diversity and unique genetic profiles observed. By laying the groundwork for future research, this study contributes to advancing forensic entomology in Pakistan by improving species identification, which, when combined with future thermobiological data, can enhance postmortem interval (PMI) estimation and forensic investigations.},
}

@article {pmid40332859,
year = {2025},
author = {Lesieur, V and Thomann, T and Jourdan, M and Kashefi, J and Bon, MC},
title = {Fly in the Ointment: Host-Specificity Challenges for Botanophila turcica, a Candidate Agent for the Biological Control of Saffron Thistle in Australia.},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040357},
pmid = {40332859},
issn = {2075-4450},
support = {PRJ--010527//AgriFutures Australia/ ; },
abstract = {In classical biological control of weeds, the risk posed by a candidate agent to close relatives of the target weed in the intended area of release is a key criterion (i.e., candidate agents that demonstrate a high degree of host specificity). In this study, we investigated if the rosette crown-feeding fly Botanophila turcica Hennig (Diptera: Anthomyiidae) could meet this criterion and thus be considered a good candidate to control saffron thistle Carthamus lanatus L. (Asteraceae: Cardueae) in Australia. Previous studies indicated that B. turcica is specific to Ca. lanatus and did not infest the closely related crop, safflower (Carthamus tinctorius L.). However, more recent field observations made in Greece reported that B. turcica infested safflower in cultivated fields. To determine if B. turcica is safe for release as a biocontrol agent, we re-examined the host range of B. turcica by performing new host-specificity testing combined with field surveys carried out in the south of France during two consecutive years. We also investigated the species identity of the flies by comparing DNA sequences (COI barcode region) of specimens collected in France from Ca. lanatus and Centaurea solstitialis L. with those from Greece collected from Ce. solstitialis and Centaurea diffusa Lam. Our COI analyses confirmed that French and Greek samples identified as B. turcica belonged to the same species, while a second group of Greek samples matched B. brunneilinea, indicating two distinct species. Our results also demonstrated that B. turcica has a wider host range than previously suggested. Laboratory testing indicated that Ca. lanatus, Ca. tinctorius, and Ce. solstitialis are suitable for the development of B. turcica. Field surveys also revealed that Ce. diffusa is part of the host range of the fly. Based on the results reported here, B. turcica may have the potential to control both the target weed, Ca. lanatus, and Ce. Solstitialis, but it may also be a threat to safflower, Ca. tinctorius. Further investigations to assess under what conditions B. turcica attacks Ca. tinctorius may help clarify the level of risk to Australian growers.},
}

@article {pmid40332619,
year = {2025},
author = {Rai, M and Dhanker, R and Sharma, N and Kamakshi, and Kamble, SS and Tiwari, A and Du, ZY and Mohamed, HI},
title = {Responses of natural plastisphere community and zooplankton to microplastic pollution: a review on novel remediation strategies.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {136},
pmid = {40332619},
issn = {1432-072X},
mesh = {*Microplastics/metabolism/toxicity/analysis ; Animals ; *Zooplankton/drug effects/metabolism ; *Water Pollutants, Chemical/metabolism/analysis ; Ecosystem ; *Environmental Restoration and Remediation/methods ; Microbiota ; Biodegradation, Environmental ; },
abstract = {The ubiquitous presence of microplastics (MP) in different environments has been well documented. Microplastic contamination has rapidly become a serious environmental issue, threatening marine ecosystems and human health. MP has been reported to accumulate organic pollutants associated with various microbial communities. The MP hazard is specifically serious in urban lakes, near-shore beaches, and benthic sediments. To prevent the further spread of MP and mitigate the increasing level of MP contamination, along with its associated environmental and economic concerns, it is essential to address mitigation strategies and their negative impacts. Contributed by low degradability, hydrophobicity, and sorption potential, the plastic surface acts as an important substrate colonized by several microorganisms known as the plastisphere community. Adaptive responses of the plastisphere community, MP ingestion, and surface modifications by the zooplankton provide insight into novel remediation strategies based on integrated natural community-level approaches. Zooplankton studies are extensive and encompass assessments of their abundance, biomass, distribution, and DNA meta-barcoding. Additionally, zooplankton has been utilized as an indicator in various freshwater environmental policies. Overall, employing zooplankton as an indicator in environmental policies is a vital tool for assessing the health of aquatic ecosystems and can assist in guiding management and conservation efforts. This review summarizes (i) the current literature on the estimation of MP distribution in aquatic environments, (ii) the effects of MP accumulation on the environment and its inhabitants, i.e., the interactions with marine microbiota,, (iii) addresses the bioremediation strategies with an emphasis on microbial degradation, ecological functioning and adaptive responses of marine microbes and finally, (iv) the directions of further research aiming to in situ mitigation of MP pollution. Recent advancements have focused on innovative methods such as membrane bioreactors, synthetic biology, organosilane-based techniques, biofilm-mediated remediation, and nanomaterial-enabled strategies. Nano-enabled technologies show substantial potential to enhance microplastic removal efficiency. Further investigation is necessary to develop advanced treatment technologies that can enhance the removal efficiency of microplastics (MPs) in drinking water. Additionally, more research is needed to understand the toxic impacts of MPs on marine ecosystems, including coral reefs, seagrass beds, mangroves, and other important habitats.},
}

*Microplastics/metabolism/toxicity/analysis
Animals
*Zooplankton/drug effects/metabolism
*Water Pollutants, Chemical/metabolism/analysis
Ecosystem
*Environmental Restoration and Remediation/methods
Microbiota
Biodegradation, Environmental

@article {pmid40331605,
year = {2025},
author = {Bu, AX and Wu, GY and Hu, LH},
title = {[Progress and prospect of separation and analysis of single-cell and single-particle exosomes].},
journal = {Se pu = Chinese journal of chromatography},
volume = {43},
number = {5},
pages = {399-412},
doi = {10.3724/SP.J.1123.2024.11001},
pmid = {40331605},
issn = {1872-2059},
mesh = {*Exosomes/chemistry ; *Single-Cell Analysis/methods ; Humans ; Animals ; },
abstract = {Exosomes are nanoscale vesicles secreted by cells and are encapsulated in lipid bilayers. They play crucial roles in cell communication and are involved in a variety of physiological and pathological processes, including immune regulation, angiogenesis, and tumor initiation and metastasis. Exosomes carry a variety of biomolecules from maternal cells and are therefore important vehicles for discovering disease markers. Traditional detection methods only provide average cell-population information for a given sample and cannot establish clear relationships between the biological functions of exosomes and subtype owing to the significant heterogeneity associated with exosomes from different cell subsets. Therefore, characterizing exosomes at the single-cell and single-particle levels requires exosome specificities to be further explored and the characteristics of various exosome subtypes to be distinguished. Commonly used single-particle exosome characterization technologies include flow cytometry, super-resolution microscopy, atomic force microscopy, surface-enhanced Raman spectroscopy, proximity barcoding assay and MS. In this paper, we summarize recent advances in the separation and characterization of single-cell exosomes based on microfluidics and provide future applications prospects for emerging technologies (such as Olink proteomics, click chemistry, and molecular imprinting) for studying single-cell and single-particle exosomes.},
}

*Exosomes/chemistry
*Single-Cell Analysis/methods
Humans
Animals

@article {pmid40330878,
year = {2025},
author = {Baglamis, S and Sheraton, VM and van Neerven, SM and Logiantara, A and Nijman, LE and Hageman, LA and Léveillé, N and Elbers, CC and Bijlsma, MF and Vermeulen, L and Krawczyk, PM and Lenos, KJ},
title = {Clonal dispersal is associated with tumor heterogeneity and poor prognosis in colorectal cancer.},
journal = {iScience},
volume = {28},
number = {5},
pages = {112403},
pmid = {40330878},
issn = {2589-0042},
abstract = {Clonal dispersal, resulting from the intermingling of tumor cell subpopulations, is thought to be a key driver of tumor heterogeneity. Despite advances in spatial modeling of cancer biology, quantification of clonal dispersal has been challenging. This study introduces a straightforward method, relying on fluorescent cell barcoding, to quantify clonal dispersal in various in vitro and in vivo models of colorectal cancer (CRC). Our approach allows for precise localization of clones and uncovering the degree of clonal mixing across different CRC models. Our findings suggest that clonal dispersal is correlated with the expression of genes involved in epithelial-mesenchymal transition and CMS4-related signaling pathways. We further identify a dispersal gene signature, associated with intratumor heterogeneity, which is a robust clinical predictor of poor prognosis and recurrence in CRC, highlighting its potential as a prognostic marker and a putative direction for therapeutic targeting.},
}

@article {pmid40330101,
year = {2025},
author = {Nolan, JM and Skujina, I and Hurpy, G and Tighe, AJ and Whelan, C and Teeling, EC},
title = {Evaluation of Oxford Nanopore Technologies MinION Sequencer as a Novel Short Amplicon Metabarcoding Tool Using Arthropod Mock Sample and Irish Bat Diet Characterisation.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71333},
pmid = {40330101},
issn = {2045-7758},
abstract = {Biodiversity monitoring using metabarcoding is now widely used as a routine environmental management tool. However, despite the rapid advancement of third-generation high-throughput sequencing platforms, there are limited studies assessing the most suitable tools and approaches for environmental metabarcoding studies. We tested the utility of Oxford Nanopore Technologies MinION sequencing for short-read amplicon sequencing of mitochondrial COI mini-barcodes from a known composition of arthropod species and compared its performance with more commonly used Illumina NovaSeq sequencing. The mock arthropod species assemblage allowed us to optimise a bioinformatic filtering pipeline to identify arthropod species using MinION long reads. Using this pipeline, we identified host species and diet composition by sequencing droppings collected from five individual Irish brown long-eared bats (Plecotus auritus) roosts. We showed that MinION data provided a similar taxonomic assignment to NovaSeq but only if the reference species barcode database was accurate and comprehensive. The P. auritus diet inferred was as expected based on previous morphological and Illumina metabarcoding studies. We showed that less sequencing depth, but a higher number of biological samples were necessary for complete species composition detection by MinION. A relatively simple bioinformatic filtering tool such as NanoPipe could adequately retrieve both host species and diet composition. The biggest standing challenge was the reference database format transferability and comprehensiveness. This pipeline can be used to guide future metabarcoding studies using nanopore sequencing to minimise the cost and effort while optimising results.},
}

@article {pmid40329956,
year = {2024},
author = {Frank, LE and Lindsey, LL and Kipp, EJ and Faulk, C and Stone, S and Roerick, TM and Moore, SA and Wolf, TM and Larsen, PA},
title = {Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling.},
journal = {Journal of mammalogy},
volume = {105},
number = {5},
pages = {965-975},
pmid = {40329956},
issn = {0022-2372},
abstract = {Accurate taxonomic species identification is essential to the study of mammals. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for noninvasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a polymerase chain reaction (PCR)-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from 9 mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS barcoding of noninvasive samples. By mapping to the entire National Center for Biotechnology Information mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all fecal samples. Eight of 9 species identifications matched previous PCR or animal/fecal appearance-based identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications-particularly in field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts cause changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies.},
}

@article {pmid40328385,
year = {2025},
author = {Ahmad, H and Rahman, S and Ali, M},
title = {Molecular identification and genetic diversity of Pteropus giganteus and Pipistrellus javanicus from Pakistan: A non-invasive approach.},
journal = {Gene},
volume = {},
number = {},
pages = {149540},
doi = {10.1016/j.gene.2025.149540},
pmid = {40328385},
issn = {1879-0038},
abstract = {The scarcity of genetic data hinders bat species identification in Pakistan. Despite more than 1480 bat species worldwide, morphology-based identification remains challenging due to the similarity in physical characteristics and the lack of distinct morphological features among many species. This study addresses this gap by employing DNA barcoding (cytochrome b) to identify bat species non-invasively from fecal samples, collected samples without harming the bats, across various regions of Pakistan and identified two bat species, Pteropus giganteus and Pipistrellus javanicus. Phylogenetic analysis of Pipistrellus javanicus sequences clustered with a sequence previously reported sequences from India and China while Pteropus giganteus was made and clustered with previously reported sequences from Bangladesh indicating possible gene flow. We investigated haplotype diversity and nucleotide diversity that revealed P. giganteus displayed moderate genetic diversity (h = 0.714, π = 0.003 respectively) and P. javanicus showed high genetic diversity (h = 1.000, π = 0.020). Pairwise genetic distances (K2P and matrix analysis) revealed varying levels of differentiation among populations within each species, while the negative value in neutrality tests suggested potential/sudden population expansion for both species. The current study offers important insights into the genetic landscape and population dynamics of bat species in Pakistan. Future studies should incorporate additional genetic markers, morphological examinations, and ecological data to definitively characterize these potential new species and contribute to a more comprehensive understanding of Pakistan's bat fauna.},
}

@article {pmid40326708,
year = {2025},
author = {Lu, X and Pritko, DJ and Abravanel, ME and Huggins, JR and Ogunleye, O and Biswas, T and Ashy, KC and Woods, SK and Livingston, MWT and Blenner, MA and Birtwistle, MR},
title = {Genetically Encoded Fluorescence Barcodes Allow for Single-Cell Analysis via Spectral Flow Cytometry.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00807},
pmid = {40326708},
issn = {2161-5063},
abstract = {Genetically encoded, single-cell barcodes are broadly useful for experimental tasks such as lineage tracing or genetic screens. For such applications, a barcode library would ideally have high diversity (many unique barcodes), nondestructive identification (repeated measurements in the same cells or population), and fast, inexpensive readout (many cells and conditions). Current nucleic acid barcoding methods generate high diversity but require destructive and slow/expensive readout, and current fluorescence barcoding methods are nondestructive, fast, and inexpensive to readout but lack high diversity. We recently proposed a theory for how fluorescent protein combinations may generate a high-diversity barcode library with nondestructive, fast, and inexpensive identification. Here, we present an initial experimental proof-of-concept by generating a library of ∼150 barcodes from two-way combinations of 18 fluorescent proteins, 61 of which are tested experimentally. We use a pooled cloning strategy to generate a barcode library that is validated to contain every possible combination of the 18 fluorescent proteins. Experimental results using single mammalian cells and spectral flow cytometry demonstrate excellent classification performance of individual fluorescent proteins, with the exception of mTFP1, and of most evaluated barcodes, with many true positive rates >99%. The library is compatible with genetic screening for hundreds of genes (or gene pairs) and lineage tracing hundreds of clones. This work lays a foundation for greater diversity libraries (potentially ∼10[5] and more) generated from hundreds of spectrally resolvable tandem fluorescent protein probes.},
}

@article {pmid40322669,
year = {2025},
author = {Prasetiya, FS and Jauffrais, T and Mohamed-Benkada, M and Callac, N and Ansquer, D and Yılmaz, E and Lemieux, C and Turmel, M and Mouget, JL and Prabowo, DA and Purbani, DC and Noerdjito, DR and Fahmi, V and Arsad, S and Gastineau, R},
title = {Diving into Diversity: Hasleaberepwari (Bacillariophyceae, Naviculaceae), a new species of marine diatom from New Caledonia.},
journal = {PhytoKeys},
volume = {255},
number = {},
pages = {215-234},
pmid = {40322669},
issn = {1314-2011},
abstract = {The current article introduces and describes Hasleaberepwari sp. nov., a new species of diatom discovered in the vicinity of Boulouparis, New Caledonia. Under light microscopy, H.berepwari sp. nov. strongly resembles Hasleapseudostrearia, but preliminary molecular barcoding conducted using partial 18S and rbcL genes suggested that it was a distinct species. This was confirmed first by scanning electron microscopy which showed the differences in stria densities between both species. A short-reads genome-skimming protocol applied on H.berepwari sp. nov. led us to obtain its complete mitochondrial and plastid genomes. The mitogenome is 36,572 bp in length and as already observed among other species of Haslea spp., the nad6 and nad2 genes are fused within a single open-reading frame. The plastome is 131,897 bp length, and unlike the mitogenome, it is not colinear with those of H.pseudostrearia. The results derived from the sequencing of the plastome allowed to perform a 123-gene multigene maximum likelihood phylogeny that associates H.berepwari sp. nov. to H.pseudostrearia with maximum support at the nodes but also strictly distinguishes them, suggesting a greater genetic distance between these species than what has been previously observed between other marennine-producing species.},
}

@article {pmid40322611,
year = {2025},
author = {Javaheri Tehrani, S and Rezazadeh, E and Alaei Kakhki, N and Nourani, L and Ebadi, V and Karimi, S and Karami, M and Ashouri, F and Sarshar, A and Gossmann, TI and Aliabadian, M},
title = {DNA barcoding of passerine birds in Iran.},
journal = {ZooKeys},
volume = {1236},
number = {},
pages = {19-39},
pmid = {40322611},
issn = {1313-2989},
abstract = {Exploring genetic diversity is essential for precise species delimitation, especially within taxonomically complex groups like passerine birds. Traditional morphological methods often fail to resolve species boundaries; however, DNA barcoding, particularly through the mitochondrial cytochrome c oxidase subunit I (COI) gene, provides a powerful complementary method for accurate species identification. This study establishes a comprehensive DNA barcode library for Iranian passerine birds, analyzing 546 COI sequences from 94 species across 23 families and 53 genera. There is a pronounced barcode gap, with average intraspecific divergence at 0.41% and interspecific divergence at 18.6%. Notable intraspecific variation emerged in the Persian nuthatch (Sittatephronota) and the Lesser whitethroat (Currucacurruca), while the European goldfinch (Cardueliscarduelis) and the grey-crowned goldfinch (Cardueliscaniceps) showed limited genetic differentiation despite marked morphological distinctions. Phylogenetic analysis revealed significant east-west genetic splits in C.curruca and S.tephronota, reflecting Iran's geographic and zoogeographic boundaries. These findings demonstrate the effectiveness of DNA barcoding in elucidating biogeographic patterns, emphasizing Iran's key role as an ornithological crossroads for avian biodiversity. Moreover, our results suggest that much of the genetic variation in the COI gene arises from synonymous mutations, highlighting the role of purifying selection in shaping mtDNA diversity across species.},
}

@article {pmid40321907,
year = {2025},
author = {Liang, RN and Lin, XH and An, MM and Zhao, GZ},
title = {Two new species of Penicillium (Eurotiales, Aspergillaceae) from China based on morphological and molecular analyses.},
journal = {MycoKeys},
volume = {116},
number = {},
pages = {255-274},
pmid = {40321907},
issn = {1314-4049},
abstract = {Penicillium is a large and significant genus of fungi, exhibiting widespread distribution across diverse substrates. Ongoing taxonomic and nomenclatural revisions have led to an annual increase in the number of newly described species. This study described two new Penicillium species, i.e., P.lentum and P.tibetense, discovered in China. They have been identified and characterized through morphological examination and both single gene and multigene phylogenetic analyses. Based on these analyses, P.lentum was classified within the section Brevicompacta, while P.tibetense was placed in the section Lanata-Divaricata. Both species exhibited the morphological features typical of their respective sections. Penicilliumlentum is characterized by restricted growth with dense colonies on agar media and predominantly generates terverticillate conidiophores. Penicilliumtibetense demonstrates rapid growth on media and has vigorous growth on CYA at 30 °C, producing biverticillate conidiophores. Comprehensive descriptions and detailed illustrations of these new species were presented. A morphological comparison between the new species and their closely related taxa was provided.},
}

@article {pmid40319451,
year = {2025},
author = {Baeza, JA and Umaña-Castro, R and Behringer, DC and Castillo, A},
title = {A cryptic species of the nemertean egg predator Carcinonemertes conanobrieni (Simpson et al., 2017) detected using a barcoding approach infects the Caribbean spiny lobster Panulirus argus (Latreille, 1804) in the southwestern Caribbean Sea.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/24701394.2025.2499461},
pmid = {40319451},
issn = {2470-1408},
abstract = {A recently discovered nemertean egg predator, Carcinonemertes conanobrieni, inhabiting Panulirus argus egg masses poses a potential threat to this ecologically and commercially relevant lobster. This study assessed the prevalence of C. conanobrieni in the southwestern Caribbean Sea; Costa Rica and Panama. Brooding females of P. argus were collected by fishermen near Punta Uva beach, Costa Rica (n = 17), and Guna Yala, Panama (n = 19) and examined for the presence of C. conanobrieni. Prevalence of C. conanobrieni in brooding lobsters, determined as the presence/absence of adults, juveniles, encysted juvenile worms, or carcinonemertid egg masses was 47.06% and 31.58% in Costa Rica and Panama, respectively. Moreover, when indirect evidence (empty capsules and/or dead embryos presumably attacked/consumed by worms) of the presence of C. conanobrieni in brooding lobsters is considered in addition to direct evidence, prevalence of C. conanobrieni in brooding lobsters was 64.71% and 47.37% in Costa Rica and Panama, respectively. The observations suggest that this parasitic worm completes its life cycle locally in the southwestern Caribbean. Notably, a Maximum Likelihood phylogenetic analysis based on a fragment of the mitochondrial cox1 gene clustered two specimens collected in Costa Rica together with four other specimens previously collected in Saint Kitts into a single fully supported monophyletic clade that segregated from a second clade containing six specimens of C. conanobrieni collected in Colombia, Florida, and Saint Kitts. The barcoding analysis suggests that there is an undescribed species of Carcinonemertes, anatomically like C. conanobrieni, infecting P. argus in Costa Rica.},
}

@article {pmid40318160,
year = {2025},
author = {Williams, DM},
title = {What is Fragilaria koensabbei and does it matter what it is called? (Meta)barcoding and the science of taxonomy.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70020},
pmid = {40318160},
issn = {1529-8817},
abstract = {Commentary is provided on the use of barcoding and metabarcoding in diatom studies and its broader relevance to the principles of taxonomy. The claims that taxonomy, however it is performed, is time-consuming and that it requires extensive expertise, due to a constantly evolving taxonomy, are questioned as good, even useful, criteria by which to judge a science.},
}

@article {pmid40317890,
year = {2025},
author = {Ang, YS and Low, DKX and Yung, LL},
title = {DNA-Programmed Reaction to Evaluate Specific IgE for Allergy Point-of-Care Testing.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e2500575},
doi = {10.1002/smll.202500575},
pmid = {40317890},
issn = {1613-6829},
support = {A-0009534-01-00//Singapore Ministry of Education Academic Research Fund/ ; A-0000065-97-00//NUS Resilience and Growth Postdoctoral Fellowship/ ; },
abstract = {A DNA-programmed reaction to evaluate non-nucleic acids inputs with computation speed (≈30 min) and sensitivity (sub-picomolar) suitable for analyzing physiologically relevant biomarkers in a one-pot format and point-of-care testing setting is reported. Specifically, a DNA programme based on the proximity-activation exponential amplification reaction (PEAR) is designed to evaluate specific IgE (sIgE) against Der p 2 implicated in dust mite allergy which affects millions worldwide. In this work, we tailored the molecular components of the input-to-oligo barcode conversion module as an AND gate to detect inputs with binding specificity to Der p 2 antigen and is of an IgE isotype. In addition, an in situ biotinylation method is developed to generate amplified oligo barcodes amendable for direct visualization on a lateral flow format. As a proof-of-concept demonstration of its potential clinical utility, 21 clinical samples are evaluated by the as-developed sIgE PEAR programme using the dual readout modality of real-time fluorescence measurement for precise input quantification and simple lateral flow yes/no answer.},
}

@article {pmid40316679,
year = {2025},
author = {McFadden, CS and Erickson, KL and Lane, A and Nassongole, B and Aguilar, S and Dunakey, SK and Durkin, KM and Lalas, JAA and Kushida, Y and Macrina, L and Minor, NP and Morales-Paredes, M and Nelson, J and Peddada, A and Poole, S and Porto, R and Purow-Ruderman, R and Snyder, KE and Wismar, T and Samimi-Namin, K and Baria-Rodriguez, MV and Benzoni, F and Huang, D and Reimer, JD and Paulay, G and Quattrini, AM and Ekins, M and Benayahu, Y},
title = {Biodiversity and biogeography of zooxanthellate soft corals across the Indo-Pacific.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15461},
pmid = {40316679},
issn = {2045-2322},
support = {DEB-1929319//National Science Foundation/ ; DEB-1856245//National Science Foundation/ ; Rasmussen Summer Research Fund//Harvey Mudd College/ ; Munzer Summer Research Fund//Harvey Mudd College/ ; Emily Mudd Summer Research Fund//Harvey Mudd College/ ; baseline funds//King Abdullah University of Science and Technology/ ; BSF-2019624//United States - Israel Binational Science Foundation/ ; },
abstract = {Documentation of biodiversity and its geographical distribution is necessary to understand the processes and drivers of evolutionary diversification as well as to guide conservation and management initiatives. Among the most emblematic patterns of biodiversity in the world's oceans is the Coral Triangle (Indo-Australian Archipelago), widely recognized to be the center of species richness for a variety of marine life forms. The distribution of biodiversity remains incompletely documented, however, for a majority of reef-associated invertebrate taxa, including the zooxanthellate soft corals (Octocorallia) that dominate hard substrate on many Indo-Pacific reefs. We used a genetic approach to document the diversity of Indo-Pacific soft corals, sequencing two single-locus barcoding markers for > 4400 soft coral specimens and assigning individuals to molecular operational taxonomic units as proxies of species. We document two centers of species richness for zooxanthellate soft corals, one in the Indo-Australian Archipelago and a second, equally diverse center in the Western Indian Ocean. Centers of endemicity for soft corals are coincident with these centers of species richness, although the peripheral Red Sea and Hawaii also support high proportions of endemic taxa. The patterns documented here suggest that biogeographic distributions of soft coral families may be driven in part by larval dispersal potential: taxa with benthic larvae are absent from most oceanic islands of the central Pacific and are represented by higher proportions of endemic taxa in other geographic regions. Our findings demonstrate the distinct biogeographic patterns among reef taxa and underscore the need to document and analyze species distributions of more reef-associated invertebrate groups to derive a complete picture of reef biogeography.},
}

@article {pmid40314098,
year = {2025},
author = {Wei, YH and Lin, F},
title = {Barcodes based on nucleic acid sequences: Applications and challenges (Review).},
journal = {Molecular medicine reports},
volume = {32},
number = {1},
pages = {},
doi = {10.3892/mmr.2025.13552},
pmid = {40314098},
issn = {1791-3004},
mesh = {Humans ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Nucleic Acids/genetics ; Neoplasms/genetics/pathology ; Cell Differentiation ; Stem Cells/metabolism/cytology ; },
abstract = {Cells are the fundamental structural and functional units of living organisms and the study of these entities has remained a central focus throughout the history of biological sciences. Traditional cell research techniques, including fluorescent protein tagging and microscopy, have provided preliminary insights into the lineage history and clonal relationships between progenitor and descendant cells. However, these techniques exhibit inherent limitations in tracking the full developmental trajectory of cells and elucidating their heterogeneity, including sensitivity, stability and barcode drift. In developmental biology, nucleic acid barcode technology has introduced an innovative approach to cell lineage tracing. By assigning unique barcodes to individual cells, researchers can accurately identify and trace the origin and differentiation pathways of cells at various developmental stages, thereby illuminating the dynamic processes underlying tissue development and organogenesis. In cancer research, nucleic acid barcoding has played a pivotal role in analyzing the clonal architecture of tumor cells, exploring their heterogeneity and resistance mechanisms and enhancing our understanding of cancer evolution and inter‑clonal interactions. Furthermore, nucleic acid barcodes play a crucial role in stem cell research, enabling the tracking of stem cells from diverse origins and their derived progeny. This has offered novel perspectives on the mechanisms of stem cell self‑renewal and differentiation. The present review presented a comprehensive examination of the principles, applications and challenges associated with nucleic acid barcode technology.},
}

Humans
*DNA Barcoding, Taxonomic/methods
Animals
*Nucleic Acids/genetics
Neoplasms/genetics/pathology
Cell Differentiation
Stem Cells/metabolism/cytology

@article {pmid40313148,
year = {2025},
author = {Seo, CW and Yoo, S and Cho, Y and Kim, JS and Steinegger, M and Lim, YW},
title = {FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {4},
pages = {e2411017},
doi = {10.71150/jm.2411017},
pmid = {40313148},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; 2023R1A2C1005130//Ministry of Science and ICT/ ; NIBR202304107//National Institute of Biological Resources/ ; NIBR202402106//National Institute of Biological Resources/ ; },
mesh = {*Phylogeny ; *Fungi/classification/genetics/isolation & purification ; *Software ; Sequence Analysis, DNA ; DNA, Fungal/genetics ; Databases, Nucleic Acid ; },
abstract = {The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.},
}

*Phylogeny
*Fungi/classification/genetics/isolation & purification
*Software
Sequence Analysis, DNA
DNA, Fungal/genetics
Databases, Nucleic Acid

@article {pmid40307692,
year = {2025},
author = {Shen, Z and Feng, Y and Möller, M and Burgess, KS and Qin, H and Yang, J and Mo, Z and Li, H and Li, D and Gao, L},
title = {Genomic DNA barcodes provide novel insights into species delimitation in the complex Camellia sect. Thea (Theaceae).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {570},
pmid = {40307692},
issn = {1471-2229},
support = {2024PVA0087//Chinese Academy of Sciences (CAS) President's International Fellowship Initiative/ ; 202101BC070003//Key Basic Research Program of Yunnan Province, China/ ; 31970363//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Species delimitation within Camellia sect. Thea is taxonomically challenging due to its complex evolutionary history. This study aims to utilize nuclear and chloroplast data as genomic DNA barcodes to delimit species within this economically important group of plants.

RESULTS: Whole genome sequencing (WGS) data were obtained for 98 accessions representing all but one species in C. sect. Thea. Based on 759 high-quality SCNs, 98 whole chloroplast genomes, and by using 2× coverage clean reads from WGS for Skmer analyses, we found that combining the findings from these three data sets resulted in nearly complete species delimitation and resolution of all interspecific relationships within C. sect. Thea. We also found support for the taxonomic elevation of two varieties (C. sinensis var. assamica and C. tachangensis var. remotiserrata) to species status (C. assamica and C. remotiserrata, respectively). Furthermore, we confirmed that C. formosensis represents a distinct species. Gene tree discordances, chloroplast-nuclear conflicts and complex network-like phylogenetic relationships were observed in C. sect. Thea.

CONCLUSION: Compared with the use of single parentally inherited chloroplast data sources, utilizing both uniparentally inherited chloroplast data and biparentally inherited nuclear data improved the species delimitation of taxa within C. sect. Thea. The intricate phylogenetic relationships observed are likely a result of widespread past hybridization and chloroplast capture events among species within this group, which may have blurred the species boundaries. Our novel approach to species delimitation within C. sect. Thea may serve as a blueprint for employing genomic DNA barcodes in other taxa with complex histories, and will significantly contribute to the conservation of cultivated tea plant species and their wild relatives.},
}

@article {pmid40306561,
year = {2025},
author = {Cai, FM and Jiang, S and Daly, P and Bakhshi, M and Cartwright, K and Druzhinina, IS},
title = {Guidelines toward ecologically-informed bioprospecting for microbial plastic degradation.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108590},
doi = {10.1016/j.biotechadv.2025.108590},
pmid = {40306561},
issn = {1873-1899},
abstract = {Biological degradation of plastics by microbial enzymes offers a sustainable alternative to traditional waste management methods that often pollute the environment. This review explores ecologically-informed bioprospecting for microorganisms possessing enzymes suitable for biological plastic waste treatment. Natural habitats enriched in plastic-like polymers, such as insect-derived polyesters, epicuticular microbial biofilms in the phyllosphere of plants in extreme environments, or aquatic ecosystems, are highlighted as promising reservoirs for bioprospecting. Anthropogenic habitats, including plastic-polluted soils and the plastisphere, have yielded potent enzymes such as PETases and cutinases, which are being exploited in biotechnology. However, bioprospecting in plastispheres and artificial environments frequently leads to the isolation of environmental opportunistic microorganisms, such as Pseudomonas aeruginosa, Aspergillus fumigatus, Parengyodontium album, or species of Fusarium, which are capable of becoming human and/or plant pathogens. These cases necessitate stringent biosecurity measures, including accurate molecular identification, ecological assessment, and containment protocols. Beyond advancing bioprospecting approaches toward a broader scope of relevant habitats, this review underscores the educational value of such screenings, specifically, in understudied natural habitats, emphasizing its potential to uncover novel enzymes and microorganisms and engage the next generation of researchers in interdisciplinary study integrating environmental microbiology, molecular biology, enzymology, polymer chemistry, and bioinformatics. Finally, we offer guidelines for microbial bioprospecting in various laboratory settings, ranging from standard environmental microbiology facilities to high-biosecurity facilities, thereby maximizing the diversity of scientists who may contribute to addressing urgent environmental challenges associated with plastic waste.},
}

@article {pmid40303148,
year = {2024},
author = {Yap, PSX and Yeo, LF and Teh, CSJ and Dhanoa, A and Phipps, ME},
title = {Plasmid-Mediated Co-Occurrence of mcr-1.1 in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli Isolated From the Indigenous Seminomadic Community in Malaysia.},
journal = {Transboundary and emerging diseases},
volume = {2024},
number = {},
pages = {9223696},
pmid = {40303148},
issn = {1865-1682},
mesh = {Malaysia/epidemiology ; *beta-Lactamases/genetics/metabolism ; *Escherichia coli/genetics/drug effects/enzymology/isolation & purification ; *Plasmids/genetics ; Humans ; *Escherichia coli Infections/microbiology/epidemiology ; *Escherichia coli Proteins/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; },
abstract = {The growing prevalence of commensal antibiotic resistant Escherichia coli poses a significant concern for the global spread of antibiotic resistance. Stool samples (n = 35) from a seminomadic indigenous community in Malaysia, the Jehai, were screened for multidrug-resistant bacteria, specifically the extended-spectrum β-lactamase (ESBL) producers. Subsequently, whole-genome sequencing was used to provide genomic insights into eight ESBL-producing E. coli that colonised eight individuals. The ESBL E. coli isolates carry resistance genes from various antibiotic classes such as the β-lactams (bla TEM, bla CTX-M-15 and bla CTX-M-55), quinolones (gyrA, qnrS and qnrS1) and aminoglycosides (aph(3')-Ia, aph(6)-Id and aac(3)-IId). Three concerning convergence of ESBL, colistin and metal resistance determinants, with three plasmids from H-type lineage harbouring bla CTX-M and mcr-1.1 genes were identified. Using the Oxford Nanopore Technology (ONT) Native Barcoding Kit (SQK-NBD114.24) in conjunction with the R10.4.1 flow cell, which achieved an average read accuracy (Q > 10) of 99.84%, we further characterised the mcr-1.1-bearing plasmids, ranging in size from 25 to 28 kb, from three strains of E. coli. This report represents the first whole genome analysis of multidrug-resistant bacteria, specifically those resistant to colistin, found within the indigenous population in Malaysia. It strongly indicates that the pertinent issue of colistin resistance in the country is far more significant than previously estimated.},
}

Malaysia/epidemiology
*beta-Lactamases/genetics/metabolism
*Escherichia coli/genetics/drug effects/enzymology/isolation & purification
*Plasmids/genetics
Humans
*Escherichia coli Infections/microbiology/epidemiology
*Escherichia coli Proteins/genetics/metabolism
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Feces/microbiology

@article {pmid40302921,
year = {2025},
author = {Goraichuk, IV and Suarez, DL},
title = {Custom barcoded primers for influenza A nanopore sequencing: enhanced performance with reduced preparation time.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1545032},
pmid = {40302921},
issn = {2235-2988},
mesh = {*Nanopore Sequencing/methods ; *Influenza A virus/genetics/isolation & purification ; Animals ; *DNA Primers/genetics ; Humans ; Influenza in Birds/virology ; Whole Genome Sequencing/methods ; Influenza, Human/virology ; *DNA Barcoding, Taxonomic/methods ; Genome, Viral ; Time Factors ; Polymorphism, Single Nucleotide ; },
abstract = {Highly pathogenic avian influenza is endemic and widespread in wild birds and is causing major outbreaks in poultry worldwide and in U.S. dairy cows, with several recent human cases, highlighting the need for reliable and rapid sequencing to track mutations that may facilitate viral replication in different hosts. SNP analysis is a useful molecular epidemiology tool to track outbreaks, but it requires accurate whole-genome sequencing (WGS) with sufficient read depth across all eight segments. In outbreak situations, where timely data is critical for controlling the spread of the virus, reducing sequencing preparation time while maintaining high-quality standards is particularly important. In this study, we optimized a custom barcoded primer strategy for influenza A whole-genome sequencing on the nanopore sequencing platform, combining the high performance of the Native Barcoding Kit with the prompt preparation time of the Rapid Barcoding Kit. Custom barcoded primers were designed to perform barcode attachment during RT-PCR amplification, eliminating the need for separate barcoding and clean-up steps, thus reducing library preparation time. We compared the performance of the custom barcoded primer method with the Native and Rapid barcoding kits in terms of read quality, read depth, and sequencing output. The results show that the custom barcoded primers provided performance comparable to the Native Barcoding Kit while reducing library preparation time by 2.3X compared to the Native kit and being only 15 minutes longer than the Rapid kit with better depth of sequencing. Additionally, the custom barcoded primer method was evaluated on a variety of clinical sample types. This approach offers a promising solution for influenza A sequencing, providing both high throughput and time efficiency, which significantly improves the time-to-result turnaround, making sequencing more accessible for real-time surveillance.},
}

*Nanopore Sequencing/methods
*Influenza A virus/genetics/isolation & purification
Animals
*DNA Primers/genetics
Humans
Influenza in Birds/virology
Whole Genome Sequencing/methods
Influenza, Human/virology
*DNA Barcoding, Taxonomic/methods
Genome, Viral
Time Factors
Polymorphism, Single Nucleotide

@article {pmid40297676,
year = {2025},
author = {Usmani, S and Gebhardt, ME and Simubali, L and Saili, K and Hamwata, W and Chilusu, H and Muleba, M and McMeniman, CJ and Martin, AC and Moss, WJ and Norris, DE and Ali, RLMN},
title = {Phylogenetic taxonomy of the Zambian Anopheles coustani group using a mitogenomics approach.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-5976492/v1},
pmid = {40297676},
issn = {2693-5015},
abstract = {Background Mosquito species belonging to the Anopheles coustani group have been implicated in driving residual malaria transmission in sub-Saharan Africa and are regarded as an established primary vector in Madagascar. The morphological identification of mosquitoes in this group is challenging due to cryptic features and their molecular confirmation is difficult due to a paucity of reference sequence data representing all members of the group. Conventional molecular barcoding with the cytochrome oxidase I (COI) gene and the internal transcribed spacer 2 (ITS2) region targets is limited in their discrimination and conclusive identification of members of species complexes. In contrast, complete mitochondrial genomes (mitogenomes) have demonstrated much improved power over barcodes to be useful in rectifying taxonomic discrepancies in Culicidae. Methods We utilized a genome skimming approach via shallow shotgun sequencing on individual mosquito specimens to generate sequence reads for mitogenome assembly. Bayesian inferred phylogenies and molecular dating estimations were perfomed on the concatenated protein coding genes using the Bayesian Evolutionary Analysis by Sampling Trees 2 (BEAST 2) platform. Divergence estimates were calibrated on published calucations for Anopheles - Aedes . Results This study generated 17 new complete mitogenomes which were comprable to reference An. coustani mitogenomes in the GenBank repository by having 13 protein coding, 22 transfer RNA and 2 ribosomal RNA genes, with an average length of 15,400 bp and AT content of 78.3%. Bayesian inference using the concatenated protein coding genes from the generated and publicly available mitogenomes yielded six clades: one for each of the four taxa targeted in this study, the GenBank references, and a currently unknown species. Divergence times estimated that the An. coustani group separated from the An. gambiae complex approximately 110 million years ago (MYA), and members within the complex diverged at times points ranging from~34 MYA to as recent as ~7 MYA. Conclusions These findings demonstrate the value of mitochondrial genomes in differentiating cryptic taxa and help to confirm morphological identities of An. coustani s.s. , An. paludis , An. zeimanni and An. tenebrosus . Divergence estimates with the An. coustani group are similar to those for well-studied anopheline vector groups. These analyses also highlight the likely prescence of other cryptic An. coustani group members circulating in Zambia.},
}

@article {pmid40296507,
year = {2025},
author = {Dong, X and Edwards, S and Deng, YM and Dapat, C and Hirankitti, A and Wordsworth, R and Whitney, P and Baird, R and Freeman, K and Daley, AJ and Barr, IG},
title = {An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing.},
journal = {Influenza and other respiratory viruses},
volume = {19},
number = {5},
pages = {e70106},
doi = {10.1111/irv.70106},
pmid = {40296507},
issn = {1750-2659},
support = {//Department of Health and Aged Care, Australian Government/ ; },
mesh = {Humans ; *Respiratory Syncytial Virus Infections/virology/diagnosis ; *Whole Genome Sequencing/methods ; *Respiratory Syncytial Virus, Human/genetics/isolation & purification ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; Nanopores ; Australia ; *Nanopore Sequencing/methods ; Multiplex Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; },
abstract = {BACKGROUND: Whole-genome sequencing (WGS) provides critical insights into the respiratory syncytial virus (RSV) transmission and any emerging mutations that could impair the efficacy of monoclonal antibodies or vaccines that have been recently licenced for clinical use worldwide. However, the ability to sequence RSV genomes at large scale is limited by expensive and time-consuming sequencing methods. Oxford Nanopore Technology (ONT) offers significant improvements in next generation sequencing (NGS) both in turnaround time and cost, compared with other platforms for viral WGS.

METHODS: We have developed and modified an RSV long amplicon-based WGS protocol for the ONT platform using a one-step multiplex RT-PCR assay and the rapid barcoding kit. One hundred thirty-five RSV positive Australian clinical specimens (91 RSV-A and 44 RSV-B) sampled in 2023 with cycle threshold (Ct) values between 14 to 35 were tested in this study. This ONT workflow was compared with other recent RSV WGS amplification assays based on short amplicons.

RESULTS: A PCR amplicon clean-up step prior to library preparation significantly improved WGS result for samples with poor amplicon generation, but it is not necessary or beneficial for ones that generated high concentrations of amplicons. Overall, a success rate of 85.9% was achieved for WGS. This method performed as well as the more complex short amplicon methods in terms of genome coverage and sequencing depth.

CONCLUSIONS: The workflow described here was highly successful in generating RSV WGS on ONT platform and had improved turnaround times and excellent results with RSV clinical samples with Ct values up to 30.},
}

Humans
*Respiratory Syncytial Virus Infections/virology/diagnosis
*Whole Genome Sequencing/methods
*Respiratory Syncytial Virus, Human/genetics/isolation & purification
*Genome, Viral
*High-Throughput Nucleotide Sequencing/methods
Nanopores
Australia
*Nanopore Sequencing/methods
Multiplex Polymerase Chain Reaction/methods
Sensitivity and Specificity

@article {pmid40295995,
year = {2025},
author = {Jiang, S and Ding, Y and Zhao, G and Ye, S and Liu, S and Yin, Y and Li, Z and Zou, X and Xie, D and You, C and Guo, X},
title = {Species-specific RNA barcoding technology for rapid and accurate identification of four types of influenza virus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {409},
pmid = {40295995},
issn = {1471-2164},
support = {H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; H202191490139//Key Research & Development Project of Nanhua Biomedical/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 32372124//National Natural Science Foundation of China/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; 2021M701160//China Postdoctoral Science Foundation/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; XCX2024138//The Undergraduate Innovation and Entrepreneurship Training Program/ ; },
abstract = {BACKGROUND: The influenza virus (IV) is responsible for seasonal flu epidemics. Constant mutation of the virus results in new strains and widespread reinfections across the globe, bringing great challenges to disease prevention and control. Research has demonstrated that barcoding technology efficiently and cost-effectively differentiates closely related species on a large scale. We screened and validated species-specific RNA barcode segments based on the genetic relationships of four types of IVs, facilitating their precise identification in high-throughput sequencing viral samples.

RESULTS: Through the analysis of single nucleotide polymorphism, population genetic characteristics, and phylogenetic relationships in the training set, 7 IVA type, 29 IVB type, 40 IVC type, and 5 IVD type barcode segments were selected. In the testing set, the nucleotide-level recall rate for all barcode segments reached 96.86%, the average nucleotide-level specificity was approximately 55.27%, the precision rate was 100%, and the false omission rate was 0%, demonstrating high accuracy, specificity, and generalization capabilities for species identification. Ultimately, all four types of IVs were visualized in a combination of one-dimensional and two-dimensional codes and stored in an online database named Influenza Virus Barcode Database (FluBarDB, http://virusbarcodedatabase.top/database/index.html).

CONCLUSION: This study validates the effective application of RNA barcoding technology in the detection of IVs and establishes criteria and procedures for selecting species-specific molecular markers. These advancements enhance the understanding of the genetic and epidemiological characteristics of IVs and enable rapid responses to viral genetic mutations.},
}

@article {pmid40293989,
year = {2025},
author = {Hasan, M and Kambayashi, C and Anik, ZH and Islam, MS},
title = {Cryptic biodiversity of freshwater fish species in Bangladesh.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0318982},
doi = {10.1371/journal.pone.0318982},
pmid = {40293989},
issn = {1932-6203},
mesh = {Bangladesh ; *Biodiversity ; Animals ; Fresh Water ; Phylogeny ; *Fishes/genetics/classification ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; },
abstract = {Unrecognized cryptic species impede conservation planning and biodiversity assessments. DNA barcoding has tremendously expanded the number of novel and cryptic species in biological science. Despite few sporadic studies, the exact number of freshwater species found in Bangladesh is not known. To assess this biodiversity, we sequenced the COI gene of 124 freshwater specimens, which were gathered from various localities around Bangladesh. Seven cryptic species hidden among the currently studied specimens were identified based on the findings of phylogenetic and species delimitation analyses. The preliminary assessment also encompassed a restricted morphological examination of these cryptic taxa. The appearance of cryptic species, some of them possibly endemic, has been hypothesized. This raises concerns regarding the true diversity and evolutionary history of freshwater species in Bangladesh, which are significantly underrepresented in the current systematic frameworks that do not account for DNA data. Our current study provides baseline data that might aid local ichthyologists in their quest to identify additional new species by combining several variables (morphology and ecology). Further research is warranted to protect the priceless freshwater species in Bangladesh.},
}

Bangladesh
*Biodiversity
Animals
Fresh Water
Phylogeny
*Fishes/genetics/classification
DNA Barcoding, Taxonomic
Electron Transport Complex IV/genetics

@article {pmid40285927,
year = {2025},
author = {Lee, YI and Zahn, FE and Xie, QY and Wu, SH and Gebauer, G},
title = {Diverse mycorrhizal associations and nutrition in Didymoplexis orchids.},
journal = {Mycorrhiza},
volume = {35},
number = {3},
pages = {34},
pmid = {40285927},
issn = {1432-1890},
support = {107-2923-B-178-001-MY3//Ministry of Science and Technology, Taiwan/ ; Deutsche Forschungsgemeinschaft GE 565/9-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Mycorrhizae/physiology/classification ; *Orchidaceae/microbiology ; Symbiosis ; Taiwan ; },
abstract = {Fully mycoheterotrophic (FMH) orchids rely entirely on mycorrhizal fungi for carbon and nutrients, with tropical Asian FMH orchids typically associating with saprotrophic fungi, though some known relationships also with ectomycorrhizal fungi, leaving much to learn about their fungal partners. Didymoplexis belongs to tribe Gastrodieae, which represents one of the largest fully mycoheterotrophic orchid lineages. Although mycorrhizal associations of its sister genus Gastrodia have been relatively well-studied, those of Didymoplexis remain largely unexplored. Here, we used molecular barcoding to analyze fungal associations and stable isotope analysis to elucidate the nutritional strategies of Didymoplexis micradenia, Didymoplexis pallens, and Didymoplexis siamensis in subtropical and tropical forests across Taiwan. In Didymoplexis pallens and Didymoplexis micradenia, most fungal partners were litter-decaying fungi (Mycena, Clitocybula, Marasmius, Gymnopus) with smaller contributions from ectomycorrhizal and rhizoctonia fungi. In Didymoplexis siamensis, ectomycorrhizal fungi dominated, particularly Sebacinales, however, with additional associations with wood-decaying Delicatula. The pattern of carbon and nitrogen isotope enrichments found for the three Didymoplexis species was in the typical range known for fully mycoheterotrophic orchids associated with litter- or wood-decaying fungi. [15]N enrichments of all investigated Didymoplexis species distinguished from fully mycoheterotrophic orchids associated with ectomycorrhizal fungi. Despite its ectomycorrhizal association, Didymoplexis siamensis was weakly enriched in [15]N and more enriched in [13]C than found for exclusively ectomycorrhizal fully mycoheterotrophic orchids. Thus, Didymoplexis siamensis covered its carbon and nitrogen demand obviously through the additional association with wood-decaying Delicatula. These findings enhance our understanding of the diverse fungal associations and physiological ecology of Didymoplexis species in subtropical and tropical ecosystems.},
}

*Mycorrhizae/physiology/classification
*Orchidaceae/microbiology
Symbiosis
Taiwan

@article {pmid40284697,
year = {2025},
author = {Montalvo-Sabino, E and Villegas-Pingo, M and Zumaeta, J and Gonzales, L and Tapia-Limonchi, R and Moreno, M and González, CR and Chenet, SM},
title = {Molecular Identification of Anopheles (Diptera: Culicidae) Species in Native Communities of a Northeastern Region of Peru.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040861},
pmid = {40284697},
issn = {2076-2607},
support = {N°: 050-2021-FONDECYT//PROCIENCIA/ ; },
abstract = {BACKGROUND: Malaria is a severe health problem in native communities of Condorcanqui in the Amazonas region of Peru. Recently, the number of malaria cases has increased considerably following a Plasmodium falciparum outbreak in 2019. However, there is no information on the anophelines acting as Plasmodium vectors in this area. This study aimed to identify Anopheles species circulating in previously unexplored native communities of Condorcanqui. Additionally, we sought to detect the presence of DNA from P. vivax and P. falciparum parasites in mosquitoes.

METHODS: During three exploratory visits between March and September 2022, 453 mosquitoes were collected using Shannon traps and CDC light traps. Only specimens morphologically identified as Anopheles sp. were subjected to molecular confirmation through PCR amplification and sequencing of the Cox1 barcode region. Plasmodium parasites were detected using nested PCR targeting of the 18S rRNA subunit, while human blood meal feeding was evaluated using a human β-globin marker.

RESULTS: A total of 66 specimens were molecularly confirmed as anopheline species: An. benarrochi B, An. triannulatus, An. Costai, and An. nimbus. Six specimens of An. benarrochi B were exclusively positive for Plasmodium parasites by PCR. Moreover, four specimens tested positive for Plasmodium and the presence of human blood, suggesting the anthropophilic behavior of An. benarrochi B and its possible role as a potential malaria vector in this area.

CONCLUSIONS: In conclusion, while this study provides valuable insights into the potential role of Anopheles benarrochi as a malaria vector in Amazonas, further research is essential to fully understand its behavior and transmission dynamics in the region.},
}

@article {pmid40283945,
year = {2025},
author = {Yang, M and Yuan, Y and Wei, J and Pei, Y and Niu, Y and Zhao, Y and Kong, X and Zhang, Z},
title = {Comparison of the Blood-Brain Barrier Penetration Ability and Anti-Neuroinflammatory Activity of Chromones in Two Types of Agarwood.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/ph18040510},
pmid = {40283945},
issn = {1424-8247},
support = {CI2021A04009//the Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; },
abstract = {Background/Objectives: Agarwood has a good neuroprotective effect and is often used to relieve anxiety and treat insomnia. This study compared the similarities and differences in the chromone components of two types of agarwood. It further investigated the absorption and brain distribution characteristics of these components in rats and their neuroprotective effects mediated through anti-neuroinflammatory pathways. Methods: This study confirmed, through ITS2 barcoding and chloroplast genome analysis, that both the ordinary and Qi-Nan agarwood are derived from Aquilaria sinensis. A comparative analysis of chromones in ethanol extracts derived from ordinary and Qi-Nan agarwood, as well as those capable of penetrating the blood-brain barrier in vivo, was conducted using UPLC-Q-TOF-MS. Subsequently, an in vitro neuroinflammatory model was established via lipopolysaccharide (LPS)-stimulated BV-2 cells to evaluate the anti-neuroinflammatory activity of differential chromones. Results: UPLC-Q-TOF-MS characterization revealed the chromone components in the two types of agarwood: A total of 81 chromone compounds were identified in the ethanol extracts of ordinary agarwood (OAE) (20 THPECs, 42 FTPECs, and 19 BI), while 41 were identified in the ethanol extracts of Qi-Nan agarwood (QNE) (11 THPECs and 30 FTPECs). Pharmacokinetic analysis in rats showed that 14 components from OAE (eight THPECs and six FTPECs) penetrated the rat serum, and 10 of these 14 components penetrated the blood-brain barrier (BBB). Twelve FTPECs from QNE penetrated the rat serum, all of which penetrated the BBB. The total peak area of the total ion current (TIC) was calculated for the samples, and the TIC of the serum was compared to that of the brain tissue from the same rat to roughly estimate the ratio. The results demonstrated that the capability of FTPECs to traverse the blood-brain barrier is substantially superior to that of THPECs. Correspondingly, only FTPECs were detected using DESI-MS imaging; no THPECs were detected in rat brain tissue, and DESI-MS imaging localized FTPECs to neuroanatomic regions (cerebral cortex, thalamus, and hippocampus). In vitro neuroinflammatory assays revealed the superior anti-inflammatory efficacy of QNE over OAE (IL-6/TNF-α suppression, p < 0.05), correlating with its FTPEC-rich composition. Conclusions: Structure-activity relationships identified FTPECs as potent inhibitors of pro-inflammatory cytokines, exhibiting enhanced BBB penetration (blood-brain relative abundance > 1). These findings establish FTPECs as prioritized candidates for CNS-targeted therapeutics, with QNE's pharmacological superiority attributed to its FTPEC dominance and optimized BBB transit capacity.},
}

@article {pmid40282357,
year = {2025},
author = {Jung, J and Kim, HJ and Kim, JH},
title = {Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex.},
journal = {Genes},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/genes16040398},
pmid = {40282357},
issn = {2073-4425},
support = {KNA1-1-13, 14-1//Korea National Arboretum/ ; },
mesh = {Phylogeny ; *Polygonatum/genetics/classification ; *Genome, Plastid/genetics ; Republic of Korea ; *Plastids/genetics ; },
abstract = {Background/Objectives:Polygonatum grandicaule Y.S.Kim, B.U.Oh & C.G.Jang (Asparagaceae Juss.), a Korean endemic species, has been described based on its erect stem, tubular perianth shape, and pedicel length. However, its taxonomic status remains unclear due to limited molecular data. Methods: This study presents the complete plastid genomes (plastomes) of two P. grandicaule individuals and its close relative, P. odoratum (Mill.) Druce var. thunbergii (C.Morren & Decne.) H.Hara. Results: The plastomes, ranging from 154,578 to 154,579 base pairs (bp), are identical to those of P. falcatum A.Gray, P. odoratum var. odoratum, and another Korean endemic species, P. infundiflorum Y.S.Kim, B.U.Oh & C.G.Jang. All contain 78 plastid protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes, except for the pseudogene infA. Phylogenetic analyses using 78 plastid PCGs and whole intergenic spacer (IGS) regions strongly support the three sections within Polygonatum Mill. and show that P. odoratum and its variety are nested within P. falcatum, P. grandicaule, and P. infundiflorum. Conclusions: Given the limited genomic variation and phylogenetic relationships, we propose treating P. falcatum, P. grandicaule, and P. infundiflorum as part of the P. odoratum complex, despite their morphological differences. This study offers valuable putative molecular markers for species identification and supports the application of plastome-based super-barcoding in the morphologically diverse genus Polygonatum.},
}

Phylogeny
*Polygonatum/genetics/classification
*Genome, Plastid/genetics
Republic of Korea
*Plastids/genetics

@article {pmid40281442,
year = {2025},
author = {Tseng, YH and Chien, HC and Zhu, GX},
title = {Comparative plastome analyses and phylogenetic insights of Elatostema.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {537},
pmid = {40281442},
issn = {1471-2229},
support = {MOST 111-2621-B-005-001-MY3//National Science and Technology Council, Taiwan/ ; },
mesh = {*Phylogeny ; *Genome, Plastid/genetics ; Evolution, Molecular ; *Plastids/genetics ; },
abstract = {BACKGROUND: Elatostema, one of the largest genera in Urticaceae, comprises approximately 570 species. The taxonomic delimitation of Elatostema and its closely related genera, Elatostematoides and Procris and the infrageneric classification of Elatostema, have historically been challenging. Previous studies have been limited by insufficient molecular data, hindering our understanding of species-level relationships and the evolution of plastid genomes in this group. To address these limitations, we assembled and analyzed a comprehensive plastome analysis of 42 species across Elatostema and its allied genera. Our study focused on plastome structure, sequence diversity, and phylogenetic relationships to elucidate the evolutionary history of these taxa.

RESULTS: Our findings reveal that Elatostema plastomes exhibit a typical quadripartite structure, with genome sizes ranging from 149,152 bp to 164,019 bp. Comparative analysis of plastome structures across Elatostema and its related genera indicates high conservation in genome size, structure, gene content, and inverted repeat boundary configuration. Our findings indicate a strong association between the length of small single-copy (SSC) regions and phylogenetic grouping within Elatostema and between Elatostema, Elatostematoides and Procris. The length variations in the ndhF-rpl32, rpl32-trnL, and rps15-SSC/IRa regions may account for this observed correlation, highlighting the utility of SSC sequences in resolving phylogenetic relationships within this genus. Furthermore, we identified seven highly variable regions with potential as DNA barcodes for species identification and phylogenetic analysis. Our phylogenomic analysis provides robust support for the taxonomic delimitation of Elatostema s.l. into three distinct genera: Elatostema, Procris, and Elatostematoides. We also reconfirm the infrageneric classification of Elatostema into four major clades.

CONCLUSIONS: The utilization of plastome sequences has enabled a highly resolved phylogenetic framework, shedding light on the evolutionary history and speciation mechanism within Elatostema, particularly its species-rich core Elatostema clade. These findings provide a valuable foundation for future taxonomic revisions and evolutionary studies within this challenging plant group.},
}

*Phylogeny
*Genome, Plastid/genetics
Evolution, Molecular
*Plastids/genetics

@article {pmid40281336,
year = {2025},
author = {Xu, Z and Lyu, Y and Chen, H and Chen, Y and Wang, Y},
title = {Single-nucleus total RNA sequencing of formalin-fixed paraffin-embedded samples using snRandom-seq.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40281336},
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 = {Formalin-fixed paraffin-embedded (FFPE) samples represent a vast and valuable resource of patient material, often linked to extensive clinical history and follow-up data. However, achieving single-cell or single-nucleus RNA (sc/snRNA) profiling in these archived tissues remains challenging. To address this, we have developed snRandom-seq, a droplet- and random primer-based single-nucleus total RNA sequencing technology specifically designed for FFPE tissues. This method captures total RNAs by using random primers and demonstrates a low doublet rate (0.3%), increased RNA coverage and enhanced detection of non-coding and nascent RNAs compared to state-of-the-art high-throughput sc/snRNA-seq technologies. This protocol provides a comprehensive guide to isolating single nuclei from FFPE samples; performing in situ DNA blocking, reverse transcription and dA tailing reactions; barcoding single-nucleus droplets; and preparing sequencing libraries. The entire snRandom-seq process can be completed in 4 d. This platform serves as a powerful tool for snRNA-seq of clinical specimens, with broad applications in studying complex biological systems.},
}

@article {pmid40280882,
year = {2025},
author = {Sudermann, MA and Foster, ZSL and Dawson, SCL and Phan, H and Fieland, VJ and Martin, FN and Chang, JH and Grünwald, NJ},
title = {Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0043-FI},
pmid = {40280882},
issn = {0031-949X},
abstract = {Metabarcoding is a widely used approach relying on short DNA sequences to identify organisms present in a community. While established workflows exist for analysis of single metabarcodes, these are cumbersome when multiple metabarcodes are required to study diverse taxa, such as those in plant- and soil-associated microbial communities, or when analyzing newly developed metabarcodes. To address this, we developed demulticoder, an R package automating the use of DADA2 to analyze data derived from multiple metabarcodes. It has novel capabilities that streamline data analysis by reducing the number of manual input steps and enabling automated processing of multiplexed metabarcodes. Additionally, demulticoder modularizes data processing to allow iterative quality control and reformats data for downstream analyses. We also updated the oomycete specific rps10 barcode database by revising the taxonomic information of select entries based on updates to the classifications within the NCBI Taxonomy database. A multiplex sequenced dataset consisting of ITS1 and rps10 metabarcodes from 162 samples and 12 controls was analyzed to compare demulticoder against a standard analysis workflow. Demulticoder required manual input at only four steps in comparison to 28 steps required for the standard workflow. Data quality and results from downstream exploratory, diversity, and differential abundance analyses were comparable to those from the standard workflow. Demulticoder is versatile and can be used to analyze datasets consisting of single metabarcodes, multiplexed and pooled metabarcode types, and different metabarcode types generated in separate experiments. The demulticoder R package, example datasets, and instructions are publicly accessible and open source.},
}

@article {pmid40280670,
year = {2025},
author = {Zamri, NAS and Baharudin, S and Harun, AAC and Ariffin, NA and Khong, HY and Wahab, W and Kamaludeen, J and Zakariah, MI and Tosin, OV and Manaf, SR},
title = {Parasite infestation in red hybrid Tilapia across Sarawak: Morphological, DNA barcoding and water quality assessment under different culture systems.},
journal = {Veterinary parasitology, regional studies and reports},
volume = {60},
number = {},
pages = {101238},
doi = {10.1016/j.vprsr.2025.101238},
pmid = {40280670},
issn = {2405-9390},
mesh = {Animals ; *Fish Diseases/parasitology/epidemiology ; Aquaculture/methods ; DNA Barcoding, Taxonomic/veterinary ; *Tilapia/parasitology ; *Water Quality ; Prevalence ; *Ectoparasitic Infestations/veterinary/epidemiology/parasitology ; Phylogeny ; Trematoda/genetics ; *Parasitic Diseases, Animal/epidemiology/parasitology ; Cichlids ; },
abstract = {Red Hybrid Tilapia (RHT) is a vital species in aquaculture but remains highly vulnerable to parasitic infestations, which can compromise productivity and overall fish health. This study assessed the prevalence, intensity, and species identification of ecto- and endoparasites in RHT across different aquaculture systems in Sarawak from May to December 2022. A total of 120 RHT samples were analyzed using both morphological and molecular approaches. Results indicated a high prevalence of ectoparasites in ST1, ST2, and ST3 (100 %) compared to ST4 (96.67 %). Trichodina spp. was the most common ectoparasite (70.83 %), while molecular analysis identified Cichlidogyrus thurstonae. Endoparasites were detected only in ST1, with greater occurrence in the intestine (53 %) than in the stomach (40 %). Despite being morphologically identified as a Digenean Trematode, BLAST and phylogenetic analysis failed to provide a definitive match, suggesting a potentially novel species. Interestingly, water quality parameters did not vary significantly across sites, implying that parasite prevalence is more influenced by aquaculture system design, stocking density, and management practices rather than environmental factors alone. Poor biosecurity, high fish densities, and insufficient parasite control measures may contribute to high infestation rates. This study highlights the need for enhanced biosecurity protocols, regular parasite monitoring, and improved management strategies to mitigate parasitic infections. The findings provide valuable baseline data for sustainable RHT farming, emphasizing the importance of proactive health management to ensure long-term productivity and food security.},
}

Animals
*Fish Diseases/parasitology/epidemiology
Aquaculture/methods
DNA Barcoding, Taxonomic/veterinary
*Tilapia/parasitology
*Water Quality
Prevalence
*Ectoparasitic Infestations/veterinary/epidemiology/parasitology
Phylogeny
Trematoda/genetics
*Parasitic Diseases, Animal/epidemiology/parasitology
Cichlids

@article {pmid40278563,
year = {2025},
author = {Ingegneri, M and Smeriglio, E and Zebbiche, Y and Cornara, L and Visalli, L and Smeriglio, A and Trombetta, D},
title = {The Dark Side of "Smart Drugs": Cognitive Enhancement vs. Clinical Concerns.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/toxics13040247},
pmid = {40278563},
issn = {2305-6304},
abstract = {The European Union Drugs Agency has emphasized the increasing difficulty in monitoring the drug market due to the emergence of new psychoactive substances, often marketed as legal highs. The proliferation of fake pharmacies, drugstores, and e-commerce platforms has made access to illicit substances alarmingly rapid and inexpensive. These substances are readily available without medical prescriptions, lacking proper risk assessments or monitoring of potential adverse effects, raising significant public health concerns. Today, the relentless pursuit of validation and success-often, at any cost-has led to an exponential rise in the use of cognitive and mood enhancers. Such substances are frequently consumed to manage demands related to work, diet, sexuality, sleep, achievement, and interpersonal relationships. Consequently, investigating these phenomena is critically important for institutions, as they represent a serious threat to individual development and health. Developing effective preventive and protective systems is essential. This review provides an overview of currently available smart drugs, discussing their desired and adverse neuropharmacological effects, psychological implications, and cognitive decline resulting from their excessive and unregulated use. This review concludes that a multidisciplinary approach combining molecular identification, micro-morphological analysis, and chemical characterization is crucial for the accurate detection, monitoring, and risk mitigation of new psychoactive substances.},
}

@article {pmid40278070,
year = {2025},
author = {Baramidze, V and Sella, L and Japaridze, T and Dzotsenidze, N and Lamazoshvili, D and Abashidze, N and Basilidze, M and Tomashvili, G},
title = {A Barcoded ITS Primer-Based Nanopore Sequencing Protocol for Detection of Alternaria Species and Other Fungal Pathogens in Diverse Plant Hosts.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040249},
pmid = {40278070},
issn = {2309-608X},
support = {YS 18-1446//Shota Rustaveli National Science Foundation/ ; },
abstract = {Alternaria is a genus that contains several important plant pathogens affecting nearly 400 plant species worldwide, including economically important crops such as grapes, citrus, and ornamental plants. Rapid, scalable, and efficient methods of pathogen detection are crucial for managing plant diseases and ensuring agricultural productivity. Current amplicon sequencing protocols for Alternaria detection often require the enzymatic barcoding of amplicons, increasing hands-on time, cost, and contamination risk. We present a proof-of-concept study using custom barcoded primers, combining universal primers targeting ITS1 and ITS2 regions (600 bp) coupled with Oxford Nanopore Technologies (ONT) barcode sequences. Sequencing was performed on infected grapevine, mandarin orange, thuja, and maple tree samples. In total, we analyzed 38 samples using qPCR; 8 tested positive for Alternaria, which were sequenced using a newly developed protocol. As a result, we could identify Alternaria in every positive sample, and besides the pathogen of interest, we could identify the associated mycobiome. This protocol reduces hands-on time and cost, making a significant advancement over current sequencing methods. Future work will focus on optimizing our approach for high-throughput sequencing of up to 96 samples and determining the method's applicability for large-scale mycobiome analysis.},
}

@article {pmid40276957,
year = {2025},
author = {Mavridis, K and Evangelou, V and Grigoriadou, AM and Papachristos, DP and Vontas, J},
title = {Molecular surveillance of resistance mutations in invasive populations of Spodoptera frugiperda in Europe, for evidence-based pest control.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8849},
pmid = {40276957},
issn = {1526-4998},
support = {InnoPP-TAEDR-0535675//European Union - National Recovery and Resilience Plan Greece 2.0- NextGenerationEU/ ; 101212676//European Union's Horizon Europe research and innovation program EUFAWREADY/ ; //Hellenic Ministry of Rural Development and Food/ ; },
abstract = {BACKGROUND: The invasive fall armyworm (Spodoptera frugiperda, FAW), a highly destructive pest affecting more than 350 plant species, has recently invaded Europe raising urgent management concerns. Insecticide resistance profiling is essential to support evidence-based pest control strategies. In this study, we analyzed target-site insecticide resistance mutations in FAW populations from Greece to inform pest control strategies. In addition, DNA barcoding through cytochrome oxidase subunit 1 (COI) gene sequencing was used to trace the pest's geographic origin and potential invasion pathways.

RESULTS: All Spodoptera frugiperda specimens in Greece were identified as the rice strain, exhibiting two almost balanced haplotypes (Haplotype 1: 58.6%; Haplotype 2: 41.4%), suggesting a likely origin from a single, genetically diverse source population. Resistance-associated mutations were identified in the ABCC2 gene (A > G single-nucleotide polymorphism (SNP); up to 80.9%) and the Ace-1 gene (F290V: up to 37.5%; A201S: up to 3.85%), conferring resistance to Bacillus thuringiensis (Bt) and organophosphates/carbamates, respectively. By contrast, no resistance-associated mutations were detected for other key insecticides (diamides, pyrethroids, oxadiazines, spinosyns, and avermectins), suggesting their current efficacy in Greece.

CONCLUSION: This study provides a critical baseline for monitoring insecticide resistance in invasive FAW populations in Europe, supporting the development of sustainable integrated pest management strategies in line with the European Union Green Deal. Continuous monitoring with molecular diagnostics, alongside complementary bioassays, is recommended to mitigate the impact of FAW on European agriculture. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid40276244,
year = {2025},
author = {He, ZS and Yang, JX and Huang, JL and Li, DZ and Yang, JB},
title = {Specimen Identification Through Multilocus Species Tree Constructed From Single-Copy Orthologs (SCOs): A Case Study in Cymbidium Subgenus Jensoa.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71323},
pmid = {40276244},
issn = {2045-7758},
abstract = {Standard barcodes and ultra-barcode encounter significant challenges when delimiting and discriminating closely related species characterized by deep coalescence, hybrid speciation, gene flow, or low sequence variation. Single-copy orthologs (SCOs) have been widely recognized as standardized nuclear markers in metazoan DNA taxonomy, yet their application in plant taxonomy remains unexplored. This study evaluates the efficacy of SCOs for identifying recently diverged species within the Cymbidium subgenus Jensoa, where ultra-barcodes have previously shown limited resolution. Remarkably, over 90% of the 9094 targeted reference SCOs, inferred from three Cymbidium genomes, were successfully retrieved for all 11 representative species in subg. Jensoa using ALiBaSeq at a minimal 5× depth from whole genome shotgun sequences. The species tree, reconstructed from multiple refined SCO matrices under the coalescent model, effectively distinguished all species and identified mislabeled or misidentified specimens. The comprehensive and refined SCO matrices produced by our pipeline not only enhance phylogenetic analysis but also improve the precision of species diagnosis. Additionally, biparentally inherited SCOs, serving as multi-locus markers, not only augment the effectiveness of DNA barcoding but also support a transition to multi-locus, species-tree-based specimen assignment strategies.},
}

@article {pmid40271218,
year = {2025},
author = {Tomsia, M and Grzywacz, A and Szpila, K and Walczak, K and Mahlerová, K and Vaněk, D and Matuszewski, S},
title = {Human costal cartilage, tooth cavities, and femur nutrient canals-new niches for insects used in forensic entomology.},
journal = {Forensic sciences research},
volume = {10},
number = {2},
pages = {owae028},
doi = {10.1093/fsr/owae028},
pmid = {40271218},
issn = {2471-1411},
abstract = {UNLABELLED: The study aimed to analyze the entomological material collected during 13 autopsies performed on the unidentified cadavers revealed at different stages of decay in the Upper Silesia Region (Poland) over 2016-2022. During the preparation of human tissues for genetic identification, we revealed larvae, puparia, and adult insects in previously undescribed locations: costal cartilage, femur nutrient canals (foramen nutrients), and tooth cavities. The taxonomical assessment was done using morphological examination or DNA barcoding, where necessary. Based on our observations, we conclude that the apical constriction, foramen, and cavities may serve as migration paths inside teeth, and the femur nutrient canals to the bone marrow. The study also revealed that the beetle Necrobia ruficollis (Fabricius, 1775) and the moth family Pyralidae Latreille, 1802 (Phycitinae) moths can form pupal chambers inside the costal cartilage, indicating that these insects can complete their life cycle inside this cache. We believe that the newly reported locations of carrion insects in human remains may be relevant to forensic entomology, as they provide new opportunities to collect insect evidence.

KEY POINTS: Costal cartilage may serve as an occasional cache for adults and immatures of carrion insects.Tooth cavities and apical foramen may serve as entryways for necrophilous insect larvae.Insect larvae use nutrient canals as migratory pathways to the bone marrow.},
}

@article {pmid40270798,
year = {2025},
author = {Kireta, D and van Dijk, KJ and Crotty, S and Malik, A and Bell, K and Hogendoorn, K and Lowe, AJ},
title = {A Novel Approach for Pollen Identification and Quantification Using Hybrid Capture-Based DNA Metabarcoding.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71311},
doi = {10.1002/ece3.71311},
pmid = {40270798},
issn = {2045-7758},
abstract = {Pollen identification (ID) and quantification is important in many fields, including pollination ecology and agricultural sciences, and efforts to explore optimal molecular methods for identifying low concentrations of DNA from plant mixtures are increasing, but quantifying mixture proportions remains challenging. Traditional pollen ID using microscopy is time-consuming, requires expertise and has limited accuracy and throughput. Molecular barcoding approaches being explored offer improved accuracy and throughput. The common approach, amplicon sequencing, employs PCR amplification to isolate DNA barcodes, but introduces significant bias, impairing downstream quantification. We apply a novel molecular hybrid capture approach to artificial pollen mixtures to improve upon current taxon ID and quantification methods. The method randomly fragments DNA and uses RNA baits to capture DNA barcodes, which allows for PCR duplicate removal, reducing downstream quantification bias. Four reference databases were used to explore identification and quantification. A restricted matK database containing only mixture species yielded sequence proportions highly correlated with input pollen proportions, demonstrating the potential usefulness of hybrid capture for metabarcoding and quantifying pollen mixtures. Identification power was further tested using two reference libraries constructed from publicly available sequences: the matK plastid barcode and RefSeq complete chloroplast references. Single barcode-based taxon ID did not consistently resolve to species or genus level. The RefSeq chloroplast database performed better qualitatively but had limited taxon coverage (relative to species used here) and introduced ID issues. At the family level, both databases yielded comparable qualitative results, but the RefSeq database performed better quantitatively. Whilst the method developed here has tremendous potential, the choice and expansion of reference databases remains one of the most important factors allowing qualitative and quantitative accuracy using the full set of genomic regions screened by this hybrid capture method.},
}

@article {pmid40270465,
year = {2025},
author = {Borer, G and Monteiro, C and Lima, FP and Martins, FMS},
title = {Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14115},
doi = {10.1111/1755-0998.14115},
pmid = {40270465},
issn = {1755-0998},
support = {BIOINTERACT/https://doi.org/10.54499/2022.02887//Fundação para a Ciência e a Tecnologia/ ; CEECInd/10.54499/CEECIND/03185/2018/CP1546/CP164//Fundação para a Ciência e a Tecnologia/ ; OceanLog/10.54499/PTDC/BIA-BMA/4848/2021//Fundação para a Ciência e a Tecnologia/ ; ANERIS/101094924//Horizon 2020 Framework Programme/ ; FutureMares/869300//Horizon 2020 Framework Programme/ ; NORTE-01-0246-FEDER-000063//European Commission/ ; },
abstract = {Large biogeographical shifts in marine communities are taking place in response to climate change and biological invasions yet we still lack a full understanding of their diversity and distribution. An important example of this is turf and foliose algae that are key coastal primary producers in several regions and are expanding into new environments. Traditionally, monitoring turf and foliose algae communities involves species identification based on morphological traits, which is challenging due to their reduced dimensions and highly variable morphology. Molecular methods promise to revolutionise this field, but their effectiveness in detecting turf and foliose algae has yet to be tested. Here, we evaluate the performance of DNA metabarcoding (COI and rbcL markers) and morphological identification (in situ and photoquadrat) to describe intertidal turf and foliose algae communities along the Portuguese coast. Both molecular markers detected more taxa than the morphological methods and showed greater discrimination of turf and foliose algae communities between regions, matching our knowledge of the geographical and climatic patterns for the region. In sum, our multi-marker metabarcoding approach was more efficient than morphology-based methods in characterising turf and foliose algae communities along the Portuguese coast, differentiating morphologically similar species, and detecting unicellular organisms. However, certain taxa that were identified by in situ and photoquadrat approaches were not detected through metabarcoding, partly due to lack of reference barcodes or taxonomic resolution. Metabarcoding emerges as a valuable tool for monitoring these communities, particularly in long-term programmes requiring accuracy, speed, and reproducibility.},
}

@article {pmid40270210,
year = {2025},
author = {Pedersen, FB and Hauge, AW and Hansen, JF and Andersen, LS and Blomsterberg, S and Bruunsgaard, H},
title = {Cost-Effective and Highly Scalable Typing of HLA Classes I and II Genes of up to 96 Individuals Using Nanopore Sequencing.},
journal = {HLA},
volume = {105},
number = {4},
pages = {e70164},
doi = {10.1111/tan.70164},
pmid = {40270210},
issn = {2059-2310},
support = {FF 2022/01//Bloddonorernes Forskningsfond/ ; },
mesh = {Humans ; *Histocompatibility Testing/methods/economics ; *Nanopore Sequencing/economics/methods ; Cost-Benefit Analysis ; Alleles ; *Histocompatibility Antigens Class II/genetics ; Multiplex Polymerase Chain Reaction/economics ; },
abstract = {HLA typing of large donor registries and biobanks as well as acute single patient/donor samples remains expensive, slow and logistically challenging, despite recent developments in the field. We have tested and validated a cost-effective, accurate and highly scalable method for typing specific genes in the HLA region. This enables HLA typing from 1 to 96 individuals simultaneously, using a targeted PCR and Native Barcoding kit from Oxford Nanopore Technologies. A primer set for seven HLA genes (HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1) was developed to work in a multiplex PCR reaction. The resulting amplicons provide a possible four-field resolution of the HLA Class I genes and G-group resolution of the HLA Class II genes. The entire process, from DNA to HLA typing result, takes a total of 5.5-10.5 h depending on the number of samples processed simultaneously. Data analysis was conducted using NGSEngine-Turbo from GenDx (Utrecht, The Netherlands), with analysis time ranging from 1 to 5 min per sample. Samples from 96 Danish registered stem cell donors were typed using this method. One allele out of 1128 analysed alleles was inaccurately called homozygous, leading to an accuracy of 99.91%. The rapid turnaround, low cost and high accuracy make this new method highly relevant for HLA typing of large biobanks and donor registries, as well as for acute single samples. HLA typing can be obtained within 1 day, with a cost per sample of approximately €7 when 96 samples are sequenced simultaneously.},
}

Humans
*Histocompatibility Testing/methods/economics
*Nanopore Sequencing/economics/methods
Cost-Benefit Analysis
Alleles
*Histocompatibility Antigens Class II/genetics
Multiplex Polymerase Chain Reaction/economics

@article {pmid40269967,
year = {2025},
author = {Isiye, E and Valcarcel Olmeda, A and Curran, T and O'Neill, D and de Waal, T and Barry, G and O'Hanlon, A and O'Shaughnessy, J and Keohane McCarthy, N and Vellinga, A and Jenkinson, A and Johnson, A and Barrett, D and Costello, S and Zintl, A and O'Meara, D},
title = {Molecular characterisation of common Culicoides biting midges (Diptera: Ceratopogonidae) in Ireland.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {149},
pmid = {40269967},
issn = {1756-3305},
mesh = {Animals ; *Ceratopogonidae/genetics/classification/virology ; Ireland ; *Insect Vectors/genetics/classification/virology ; DNA Barcoding, Taxonomic ; Phylogeny ; Electron Transport Complex IV/genetics ; Genetic Variation ; Bluetongue virus ; Bluetongue/transmission ; Female ; },
abstract = {BACKGROUND: Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques.

METHODS: Adult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. In addition, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland.

RESULTS: DNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides spp. that could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector.

CONCLUSIONS: DNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.},
}

Animals
*Ceratopogonidae/genetics/classification/virology
Ireland
*Insect Vectors/genetics/classification/virology
DNA Barcoding, Taxonomic
Phylogeny
Electron Transport Complex IV/genetics
Genetic Variation
Bluetongue virus
Bluetongue/transmission
Female

@article {pmid40266812,
year = {2025},
author = {Wu, Y and Liu, Y and Huang, Z and Yin, H and Xu, X},
title = {New Species of the Purse-Web Spider Genus Atypus Latreille, 1804 from Southern China (Araneae, Atypidae), with the General Natural History of Atypus Spiders.},
journal = {Insects},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/insects16030301},
pmid = {40266812},
issn = {2075-4450},
support = {32070429/31772423/31471963/31372160//National Natural Sciences Foundation of China/ ; 2023JJ30399//Hunan Provincial Natural Science Foundation of China/ ; CX20230525//Hunan Provincial Innovation Foundation for Postgraduate/ ; },
abstract = {Three species of the purse-web spider genus Atypus Latreille, 1804, collected from Hunan and Sichuan Provinces of China, are diagnosed and described as new to science: A. yaozu sp. nov. (♂♀), A. siyiensis sp. nov. (♂♀) and A. yanjingensis sp. nov. (♂♀). Detailed descriptions, photographs and DNA barcodes of the three new species and a distribution map of Atypus species in China are provided. Additionally, we enrich the general natural history of the genus Atypus through a decade of observation.},
}

@article {pmid40265169,
year = {2025},
author = {Renou, L and Sun, W and Friedrich, C and Galant, K and Conrad, C and Consalus, A and Plantier, E and Schallmoser, K and Krisch, L and Barroca, V and Devanand, S and Dechamps, N and Reinisch, A and Martinovic, J and Magnani, A and Faivre, L and Lewandowski, D and Calvo, J and Perie, L and Kosmider, O and Pflumio, F},
title = {Orchestration of human multi-lineage hematopoietic cell development by humanized in vivo bone marrow models.},
journal = {HemaSphere},
volume = {9},
number = {4},
pages = {e70120},
pmid = {40265169},
issn = {2572-9241},
abstract = {Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate the differentiation and preservation of hematopoietic stem and progenitor cells (HSPCs). Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, but the physiology of these models is questioned as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h) in vivo BM model, developed from fetal (F/) and post-natal (P-N/) mesenchymal stromal cell (MSC) differentiation (called hOssicles [hOss]), in which human hematopoietic cells are generated following the transplantation of CD34[+] cells. Serial isolation and transplant experiments of hMSCs and HSPCs from hOss revealed the dynamic nature of these hBM niches. hOss modified human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels, with no major transcriptional changes in HSPCs at the single-cell level. Clonal tracking using genetic barcodes highlighted hematopoietic cell cross-talks between the endogenous murine BM and hOss and differences in clonal myeloid/multipotent cell production between F/hOss and P-N/hOss, uncovering ontogeny-related impact of the BM on human hematopoietic cell production.},
}

@article {pmid40263935,
year = {2025},
author = {Becker, J and Domenger, C and Choksi, P and Krämer, C and Baumgartl, C and Maiakovska, O and Kim, JJ and Weinmann, J and Huber, G and Schmidt, F and Thirion, C and Müller, OJ and Willenbring, H and Grimm, D},
title = {Identification of a robust promoter in mouse and human hepatocytes by in vivo biopanning of a barcoded AAV library.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2025.04.027},
pmid = {40263935},
issn = {1525-0024},
abstract = {Recombinant adeno-associated viruses (AAV) are leading vectors for in vivo human gene therapy. An integral vector element are promoters, which control transgene expression in either a ubiquitous or cell-type-selective manner. Identifying optimal capsid-promoter combinations is challenging, especially when considering on- versus off-target expression. Here, we report a pipeline for in vivo promoter biopanning in AAV building on our AAV capsid barcoding technology and illustrate its potential by screening 53 promoters in 16 murine tissues using an AAV9 vector. Surprisingly, the 2.2 kb human glial fibrillary acidic protein (GFAP) promoter was the top hit in the liver, where it outperformed robust benchmarks such as the human alpha-1-antitrypsin promoter or the clinically used liver-specific promoter 1 (LP1). Analysis of hepatic cell populations revealed preferred GFAP promoter activity in hepatocytes. Notably, the GFAP promoter also surpassed the LP1 and cytomegalovirus (CMV) promoters in human hepatocytes engrafted in an immune-deficient mouse. These findings establish the GFAP promoter as an exciting alternative for research and clinical applications requiring efficient and specific transgene expression in hepatocytes. Our pipeline expands the arsenal of technologies for high-throughput in vivo screening of viral vector components and is compatible with capsid barcoding, facilitating the combinatorial interrogation of complex AAV libraries.},
}

@article {pmid40263541,
year = {2025},
author = {Boutelle, AM and Mabene, AR and Yao, D and Xu, H and Wang, M and Tang, YJ and Lopez, SS and Sinha, S and Demeter, J and Cheng, R and Benard, BA and McCrea, EM and Valente, LJ and Drainas, AP and Fischer, M and Majeti, R and Petrov, DA and Jackson, PK and Yang, F and Winslow, MM and Bassik, MC and Attardi, LD},
title = {Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network.},
journal = {Cell death and differentiation},
volume = {},
number = {},
pages = {},
pmid = {40263541},
issn = {1476-5403},
support = {R35CA197591//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; T32CA009302//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01CA234349//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 28IP-0037//Tobacco-Related Disease Research Program (TRDRP)/ ; T31DT1713//Tobacco-Related Disease Research Program (TRDRP)/ ; },
abstract = {TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seq[Ultra] somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.},
}

@article {pmid40263346,
year = {2025},
author = {Yamamoto, PK and Takasuka, K and Mori, M and Masuda, T and Kono, N},
title = {Non-invasive molecular species identification using spider silk proteomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13844},
pmid = {40263346},
issn = {2045-2322},
support = {23K21203//Japan Society for the Promotion of Science/ ; },
abstract = {Accurate species identification is essential in biology, ecology, medicine, and agriculture, yet traditional methods relying on morphological characteristics often fail due to phenotypic plasticity and cryptic species. These limitations are particularly pronounced in small organisms with minimal distinguishing features. DNA barcoding has become a popular alternative; however, it requires invasive tissue sampling, making it unsuitable for delicate or rare organisms like insects and spiders. To address this challenge, we propose a non-invasive molecular method using proteomic analysis focused on species-specific protein sequences in spider silk, offering a viable solution for species identification without harming specimens. We developed a universal silk-dissolving method, followed by sequence similarity analysis to classify species into those identifiable at the species level and those distinguishable only to a group of closely related species. A bioinformatics pipeline was established to analyze peptide sequences, achieving 96% accuracy across 15 spider species, even in the presence of contaminants. This technique complements DNA barcoding and can be extended to other organisms producing biological materials. It holds promise in pest management, medical diagnostics, and improving public health by enabling accurate species identification without invasive procedures.},
}

@article {pmid40262372,
year = {2025},
author = {Finney, J and Kuraoka, M and Song, S and Watanabe, A and Liang, X and Liao, D and Moody, MA and Walter, EB and Harrison, SC and Kelsoe, G},
title = {Fluorescence-barcoded cell lines stably expressing membrane-anchored influenza neuraminidases.},
journal = {Vaccine},
volume = {56},
number = {},
pages = {127157},
doi = {10.1016/j.vaccine.2025.127157},
pmid = {40262372},
issn = {1873-2518},
abstract = {The discovery of broadly protective antibodies to the influenza virus neuraminidase (NA) has raised interest in NA as a vaccine target. However, recombinant, solubilized tetrameric NA ectodomains are often challenging to express and isolate, hindering the study of anti-NA humoral responses. To address this obstacle, we established a panel of 22 non-adherent cell lines stably expressing native, historical N1, N2, N3, N9, and NB NAs anchored on the cell surface. The cell lines are barcoded with fluorescent proteins, enabling high-throughput, 16-plex analyses of antibody binding with commonly available flow cytometers. The cell lines were at least as efficient as a Luminex multiplex binding assay at identifying NA antibodies from a library of unselected clonal IgGs derived from human memory B cells. The cell lines were also useful for measuring the magnitude and breadth of the serum antibody response elicited by experimental infection of rhesus macaques with influenza virus. The membrane-anchored NAs are catalytically active and are compatible with established sialidase activity assays. NA-expressing K530 cell lines therefore represent a useful tool for studying NA immunity and evaluating influenza vaccine efficacy.},
}

@article {pmid40262024,
year = {2025},
author = {Tong, Y and Wang, H and Li, H and Jia, Y and Zhou, Z},
title = {Molecular Diet Analysis of Leaf-Grazing Katydids Based on DNA Barcoding.},
journal = {Archives of insect biochemistry and physiology},
volume = {118},
number = {4},
pages = {e70062},
doi = {10.1002/arch.70062},
pmid = {40262024},
issn = {1520-6327},
support = {//This study was supported by Engineering Research Center of Ecological Safety and Conservation in Beijing-Tianjin-Hebei (Xiong'an New Area) of MOE, China (2024-11)./ ; },
abstract = {The diversity of herbivorous insects is associated with host plant diversity. The determination of dietary profile is a central topic in insect ecology. DNA barcoding, that is, taxon identification using a standardized DNA region, have been important to the recent advances in food web understandings. In this study, three commonly plant barcoding loci (i.e., rbcL, matK, and trnH-psbA) were chosen for screening of ingested plant DNA in 207 specimens of 18 leaf-grazing katydid species representing 4 subfamilies in China. The obtained sequences were queried against the Barcode of Life Database (BOLD) and GenBank for taxa identification. The results of identification were as follow: 3 Conocephalinae species consumed 10 plant families, with preference for Poaceae; 1 Mecopodinae species consumed 18 plant families, with preference for Fabaceae and Vitaceae; 11 Phaneropterinae species consumed 43 plant families, with preference for Juglandaceae; 3 species Pseudophyllinae species consumed 9 plant families, with preference for Balsaminaceae. Among these, only 81 out of 207 samples were identified at the species level when compares with NCBI and BOLD database. Our study added a significant amount of dietary information for leaf-grazing katydids in China. It is crucial to fully understand coevolution of katydids and plant, katydids diet resource requirements, and best practices for habitat conservation.},
}

@article {pmid40261157,
year = {2025},
author = {Kumar, A and Mishra, DK and Kanojiya, S},
title = {Identification of Botanicals Based on Their Mass Spectrum Fingerprints Using Ultra-Performance Liquid Chromatography-Mass Spectrometry.},
journal = {Journal of mass spectrometry : JMS},
volume = {60},
number = {5},
pages = {e5131},
doi = {10.1002/jms.5131},
pmid = {40261157},
issn = {1096-9888},
support = {YSS/2015/001048//Science & Engineering Research Board (SERB) DST Government of India/ ; },
mesh = {Chromatography, High Pressure Liquid/methods ; *Mass Spectrometry/methods ; *Plants, Medicinal/chemistry/classification ; *Plant Extracts/chemistry/analysis ; Liquid Chromatography-Mass Spectrometry ; },
abstract = {In the current scenario, herbal raw materials are identified via morphotaxonomy, microscopic pharmacognosy, or DNA barcoding. However, these methods do not reveal their chemical integrity, while plant raw materials play a crucial role in the quality of plant-based medicine. To overcome this limitation, we used a mass spectrometry-based method to identify 30 botanicals. This assay followed a standard operating procedure (SOP) from sample preparation to the reference library's mass spectrum fingerprint (MSFP) search. The MS1 score showed a similarity index between the input data and the reference mass spectrum. A more than 50% MS1 score was the critical threshold for accurately identifying botanicals based on their chemical integrity. Interestingly, the analysis of 30 different plant species yielded no false results. The results were 100% accurate and selective for tested botanical samples. However, we found that the standard deviation of analytical assays and biological replicates was ± 3.5 and ± 6.3 (MS1 score) for all analyzed samples, respectively. Intraspecies variability showed MS1 scores > 50% ± 10, whereas interspecies variability was observed with MS1 scores < 50% ± 10. The MS1 score was observed, dependent on the plant species, ranging from 53.00% (± 2.65) to 89.76% (± 4.08). In addition, the method was tested to see how seasonal and geographical changes affected search results. The MS1 score changed by less than 15%. We simultaneously created a chemical barcode (unique molecular weight sequence) for each plant species to validate search results and ensure the reliable identification of botanicals.},
}

Chromatography, High Pressure Liquid/methods
*Mass Spectrometry/methods
*Plants, Medicinal/chemistry/classification
*Plant Extracts/chemistry/analysis
Liquid Chromatography-Mass Spectrometry

@article {pmid40260151,
year = {2025},
author = {Shapkin, V and Caboň, M and Kolařík, M and Adamčíková, K and Baldrian, P and Michalková, T and Větrovský, T and Adamčík, S},
title = {Protein Coding Low-Copy rpb2 and ef1-α Regions Are Viable Fungal Metabarcoding DNA Markers Which Can Supplement ITS for Better Accuracy.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71352},
pmid = {40260151},
issn = {2045-7758},
abstract = {The nuclear ribosomal DNA Internal Transcribed Spacer (ITS) region is used as a universal fungal barcode marker, but often lacks a significant DNA barcoding gap between sister taxa. Here we tested the reliability of protein coding low-copy genes as alternative barcode markers. Mock communities of three unrelated agaric genera (Dermoloma, Hodophilus, and Russula) representing lineages of closely related species were sequenced by the Illumina platform targeting the ITS1, ITS2, the second largest subunit of RNA polymerase II gene (rpb2) and the transcription elongation factor 1-alpha gene (ef1-α) regions. Species representation and their relative abundances were similar across all tested barcode regions, despite a lower copy number in protein coding markers. ITS1 and ITS2 required more sophisticated sequence filtering because they produced a high number of chimeric sequences requiring reference-based chimera removal and had a higher number of sequence variants per species. Although clustering of filtered ITS sequences resulted in an average higher number of correctly clustered units at optimal similarity thresholds, these thresholds varied substantially among genera. Best-fitted thresholds of low-copy markers were more consistent across genera but frequently lacked species resolution due to low intraspecific variability. At some thresholds, we observed multiple species lumped together, and at the same time, species split into multiple partial clusters, which should be taken into consideration when assessing the best clustering thresholds and taxonomic identity of clusters. To achieve the best taxonomic resolution and improve species detection, we recommend combining different markers and applying additional reference-based sorting of clusters. The current availability of rpb2 and ef1-α reference sequences in public databases is far from being complete for all fungal groups, but a combined marker approach can be used for group-specific studies that can build reference data for their own purposes.},
}

@article {pmid40260148,
year = {2025},
author = {Wong, A and Eizirik, E and Koepfli, KP and de Ferran, V and Shihepo, T and Lay, AR and Zumbroich, J and Rooney, N and Marker, L and Schmidt-Küntzel, A},
title = {Identifying Cryptic Mammals With Non-Invasive Methods: An Effective Molecular Species Identification Tool to Survey Southern African Terrestrial Carnivores.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71223},
pmid = {40260148},
issn = {2045-7758},
abstract = {Carnivores play a vital role in ecosystem health and are thus an important focus for conservation management. Non-invasive methods have gained traction for carnivore monitoring as carnivores are often elusive and wide-ranging, making visual counts particularly difficult. Faecal mini-barcoding combines field collection of scats with genetic analysis for species identification. Here, we assessed the applicability of a mini-barcode based on the mitochondrial ATP6 gene in southern Africa. We predicted amplification success based on in silico evaluation of reference sequences from 34 of the 42 terrestrial carnivore species existing in southern Africa, including the Congo clawless otter (Aonyx congicus) for which we contributed a mitochondrial assembly. We further tested amplification success on available reference samples of 23 species. We expanded the existing ATP6 mini-barcode reference database by contributing additional sequences for 22 species, including the Cape genet (Genetta tigrina) and the side-striped jackal (Lupulella adusta) for which no complete mini-barcode sequences were available on GenBank, and compiled a representative reference dataset of 61 unique sequences as a tool for species identification. As a proof of principle, we applied the ATP6 mini-barcode to a small scat-based carnivore survey conducted in Namibia 13 years prior, which showed a 95% identification success and detected six species among 157 samples collected. With southern Africa's mammalian carnivores facing escalating threats, this robust mini-barcode offers a vital tool for accurate species identification from non-invasive samples, enabling crucial monitoring and conservation efforts.},
}

@article {pmid40259706,
year = {2025},
author = {Woodford, DJ and Magoro, M and Kadye, WT and Scheepers, M and Sithole, Y and Mutizwa, TI and Ntokoane, T and Chakona, A},
title = {Freshwater fishes of the Waterberg aquatic ecoregion, South Africa: Diversity, taxonomic conflicts and conservation concerns.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70007},
pmid = {40259706},
issn = {1095-8649},
support = {FBIP-211006643719//National Research Foundation/ ; IBIP-BS13100251309//National Research Foundation/ ; FBIC200227507229//National Research Foundation/ ; },
abstract = {Southern Africa is a region denoted by both high levels of fish diversity, some of it cryptic and unrecognised by current taxonomy, and severely threatened freshwater ecosystems. The Waterberg, a key aquatic ecoregion of the greater Limpopo River basin in South Africa, represents an area with high terrestrial conservation value but is lacking in aquatic biodiversity information. This study characterised this unique aquatic ecoregion's fish diversity, their biogeographic patterns and threats to this biodiversity. A total of 29 fish species (11 families, 19 genera) were identified, with many distinct upland fish communities occurring within the high-altitude headwaters of the ecoregion, whereas lowland fish communities tended to be more homogeneous. Mitochondrial CO1 barcoding revealed genetically distinct lineages in four presumed-widespread southern African species: the shortfin barb, Enteromius brevipinnis (Jubb, 1966); hyphen barb, Enteromius bifrenatus (Fowler, 1935); straightfin barb, Enteromius paludinosus (Peters, 1852) and snake catfish, Clarias theodorae Weber, 1897, that were restricted to the Waterberg aquatic ecoregion. The level of genetic divergence suggests that these four Waterberg-restricted lineages are likely new candidate species. These findings indicate the Waterberg to be a biogeographic island within the greater Zambezian ichthyofaunal region of southern Africa, which should be prioritised for aquatic ecosystem conservation. Current terrestrial conservation structures in the region, encapsulated within the Waterberg Biosphere Reserve, appear to protect this distinct ichthyofauna from human land-use-derived impacts. Nonetheless, the presence of the invasive predatory largemouth bass (Micropterus nigricans) inside the biosphere represents a credible conservation threat. Engagement with biosphere stakeholders will be critical for managing this threat to the Waterberg's unique ichthyofauna going forward.},
}

@article {pmid40258808,
year = {2025},
author = {van der Toorn, W and Bohn, P and Liu-Wei, W and Olguin-Nava, M and Gribling-Burrer, AS and Smyth, RP and von Kleist, M},
title = {Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3742},
pmid = {40258808},
issn = {2041-1723},
support = {390685689//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KI2016//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 955974//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; VH-NG-1347//Helmholtz Association/ ; ANR 20-SFRI-0012//Université de Strasbourg (University of Strasbourg)/ ; },
mesh = {*SARS-CoV-2/genetics ; RNA, Viral/genetics ; Humans ; *Sequence Analysis, RNA/methods ; *Nanopore Sequencing/methods ; COVID-19/virology ; *Nanopores ; Software ; Algorithms ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate adapter-barcoding and demultiplexing approach for dRNA-seq with SQK-RNA002 and SQK-RNA004 chemistries. WarpDemuX enhances speed and accuracy by fast processing of the raw nanopore signal, use of a light-weight machine-learning algorithm and design of optimized barcode sets. We demonstrate its utility by performing rapid phenotypic profiling of different SARS-CoV-2 viruses through multiplexed sequencing of longitudinal samples on a single flowcell, identifying systematic differences in transcript abundance and poly(A) tail lengths during infection. Additionally, integrating WarpDemuX into sequencing control software enables real-time enrichment of target molecules through barcode-specific adaptive sampling, which we demonstrate by enriching low abundance viral RNA. In summary, WarpDemuX represents a broadly applicable, high-performance, economical multiplexing solution for dRNA-seq, facilitating advanced (epi-) transcriptomic research.},
}

*SARS-CoV-2/genetics
RNA, Viral/genetics
Humans
*Sequence Analysis, RNA/methods
*Nanopore Sequencing/methods
COVID-19/virology
*Nanopores
Software
Algorithms
Machine Learning
High-Throughput Nucleotide Sequencing/methods

@article {pmid40258437,
year = {2025},
author = {Kioulos, I and Grigoriadou, AM and Papadakis, A and Vontas, J and Mavridis, K},
title = {Molecular genotyping of pyrethroid resistant mutations and their haplotypes in bed bug populations from Greece.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107624},
doi = {10.1016/j.actatropica.2025.107624},
pmid = {40258437},
issn = {1873-6254},
abstract = {The resurgence of bed bugs poses significant risks to public health and tourism-driven economies in Southern Europe, including Greece. Control efforts largely rely on pyrethroids; however, the widespread selection of knockdown resistance (kdr) mutations has compromised their effectiveness. Molecular monitoring is therefore essential for accurate species identification and resistance surveillance to support evidence-based pest management strategies. In this study, we analyzed bed bug populations collected from Athens, Thessaloniki, and Heraklion between 2021 and 2024. Species identification was performed via DNA barcoding of the cytochrome oxidase I (COI) gene, while kdr mutations in the voltage-gated sodium channel (VGSC) gene-specifically V419L, L925I, and I936F-were assessed to determine their frequencies and haplotype distributions. All specimens were identified as Cimex lectularius. The L925I mutation reached fixation (100%) in Thessaloniki and Heraklion, while V419L was detected at frequencies of 30.00% and 50.00%, respectively; I936F was not detected in these populations. In Athens, L925I was highly prevalent (98.40%), while V419L (5.27%) and I936F (0.60%) were detected at lower frequencies. Haplotype analysis revealed Haplotype B (L925I only) as the most common in Athens (91.20%) and Thessaloniki (60.0%), while Haplotype C (L925I + V419L) predominated in Heraklion (76.92%). Additional haplotypes were identified in Athens, including Haplotype B[b] (L925I + I936F), marking its first detection in Europe. These findings highlight the widespread presence of kdr mutations and underscore the urgent need for integrated pest management (IPM) strategies, incorporating resistance monitoring, alternative insecticides, and non-chemical control methods to mitigate the growing challenge of pyrethroid resistance in bed bugs.},
}

@article {pmid40257565,
year = {2025},
author = {Marsolier, J and Moutaux, E and Grosselin, K and Griffiths, A and Vallot, C},
title = {Single-cell Epigenomic Profiling with High-throughput Droplet scChIP-seq.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2919},
number = {},
pages = {213-239},
pmid = {40257565},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Epigenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Histones/genetics ; Microfluidics/methods ; *Epigenesis, Genetic ; },
abstract = {Our high-throughput scChIP-seq approach combines droplet microfluidics with single-cell DNA barcoding to study the heterogeneity of epigenomes (H3K27me3, H3K4me3, H3K27Ac, H3K4me1) in a cellular population of several thousand cells with a coverage of up to 10,000 unique loci per cell.},
}

*Single-Cell Analysis/methods
*Epigenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Humans
Histones/genetics
Microfluidics/methods
*Epigenesis, Genetic

@article {pmid40253081,
year = {2025},
author = {Llera-Oyola, J and Pérez-Moraga, R and Parras, M and Rosón, B},
title = {How to view the female reproductive tract through single-cell looking glasses.},
journal = {American journal of obstetrics and gynecology},
volume = {232},
number = {4S},
pages = {S21-S43},
doi = {10.1016/j.ajog.2024.08.040},
pmid = {40253081},
issn = {1097-6868},
mesh = {Female ; Humans ; *Single-Cell Analysis/methods ; *Genitalia, Female/cytology ; Sequence Analysis, RNA ; Pregnancy ; },
abstract = {Single-cell technologies have emerged as an unprecedented tool for biologists and clinicians, allowing them to assess organs and tissues at the level of individual cells. In the field of women's reproductive biology, single-cell studies have provided insights into the cellular and molecular processes that regulate reproductive and obstetrical functions in health and disease. The knowledge that these studies generate is helping clinicians to improve the understanding and diagnosis of infertility related issues or pregnancy complications and to find new avenues for their treatment. However, navigating the expansive landscape of this type of transcriptomic data analysis represents a pivotal challenge in current research. Single cell RNA sequencing involves isolating cells into droplets, reverse transcribing RNA to generate complementary DNA, with each droplet content uniquely labeled by a barcode. Upon sequencing the complementary DNAs, the barcodes enable the reassignment of sequencing reads to individual droplets, facilitating the reconstruction of the cellular landscape of the sample obtained from a tissue or organ and beyond. Researchers, equipped with the metaphorical 'single-cell glasses,' must adequately choose from a plethora of strategies to dissect and interpret cellular information. Sophisticated algorithms and the decision-making process are often underestimated, resulting in artefactual or cumbersome interpreted results. Computational biologists apply and innovate computational tools designed to process, model, and interpret expansive datasets. The ramifications of their work extend far beyond the realm of data processing; they give shape to the outcome of analyses, playing a pivotal role in drawing meaningful conclusions from the wealth of information garnered. In this review, we describe the wide variety of approaches and analytical steps available with enough detail to gain a concise picture of what a complete examination of a single-cell dataset would be. We commence with a discussion on key points in experimental design, highlighting crucial questions one should consider. Following this, we delve into the various preprocessing and quality control steps essential for any single-cell dataset. The subsequent section offers a detailed guide on constructing a single-cell atlas, exploring nuances such as differential characteristics in visualization and clustering techniques, as well as strategies for assigning identity to cell populations through gene marker annotations. Moving beyond the creation of an atlas, we explore methods for investigating pathological conditions. This involves conducting cell population comparison tests between conditions and analyzing specific cell-to-cell communications and cellular differentiation trajectories in both health and disease scenarios. This work aims to furnish a newcomer researcher and/or clinician with essential guidelines to embark on a single-cell adventure without succumbing to common pitfalls. By bridging the gap between theory and practice, it facilitates the translation of single-cell technologies into clinically relevant applications. Throughout the manuscript, practical examples of its usage in women's reproductive health studies are provided. Various sections delve into specific clinical scenarios, demonstrating how these guidelines can be instrumental in unraveling the molecular landscapes of diseases and physiological processes related to women's reproduction.},
}

Female
Humans
*Single-Cell Analysis/methods
*Genitalia, Female/cytology
Sequence Analysis, RNA
Pregnancy

@article {pmid40248651,
year = {2025},
author = {Liu, WW and Yin, CZ and Zhang, ZX and Wang, XS and Meng, Z and Zhang, XG and Wang, S},
title = {Four new species of Beltraniella (Amphisphaeriales, Beltraniaceae) revealed by morphology and phylogenetic analyses from China.},
journal = {MycoKeys},
volume = {116},
number = {},
pages = {125-144},
pmid = {40248651},
issn = {1314-4049},
abstract = {Beltraniella is a widely-distributed genus on Earth, although its abundance is relatively limited in relation to other dematiaceous hyphomycetes. In the present study, diseased leaves of Myristicafragrans and decaying leaves were collected from Hainan and Sichuan Province. Fungal DNA was amplified and sequenced using two barcodes, the internal transcribed spacer (ITS) and large subunit of ribosomal RNA (LSU), and phylogenetic analyses were conducted through maximum likelihood (ML) and Bayesian inference (BI) algorithms. Four new species of Beltraniella, B.dujiangyanensis, B.jianfengensis, B.myristicae, and B.xinglongensis are identified through phylogenetic analyses and morphological comparison during a survey of fungal diversity in Hainan and Sichuan Provinces, China. Detailed descriptions of the morphological characteristics of these four new species are provided and illustrated with figures.},
}

@article {pmid40248647,
year = {2024},
author = {Wibisana, JN and Plessy, C and Dierckxsens, N and Masunaga, A and Miao, J and Luscombe, NM},
title = {The complete mitogenome of an unidentified Oikopleura species.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {1357},
pmid = {40248647},
issn = {2046-1402},
mesh = {*Genome, Mitochondrial ; Animals ; *Urochordata/genetics/classification ; Japan ; Sequence Analysis, DNA ; },
abstract = {Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of Oikopleura dioica. This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.},
}

*Genome, Mitochondrial
Animals
*Urochordata/genetics/classification
Japan
Sequence Analysis, DNA

@article {pmid40248491,
year = {2025},
author = {Fulci, V},
title = {Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf044},
pmid = {40248491},
issn = {2631-9268},
mesh = {*Software ; *Gene Expression Profiling/methods ; *Transcriptome ; Humans ; Sequence Analysis, RNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Recently, several protocols repurposing the Illumina flow cells or DNA nanoballs as an RNA capture device for spatial transcriptomics have been reported. These protocols yield high volumes of sequencing data which are usually analyzed through the use of high-performance computing clusters. I report Fast analysis of Spatial Transcriptomic (FaST), a novel pipeline for the analysis of subcellular resolution spatial transcriptomics datasets based on barcoding. FaST is compatible with OpenST, seq-scope, Stereo-seq, and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of >500 M million reads in as little as 1 h on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented Spatial Transcriptomics datasets suitable for subsequent analysis through commonly used packages (e.g scanpy or seurat). Notably, the pipeline I present relies on the spateo-release package for RNA segmentation and does not require hematoxylin/eosin or any other imaging procedure to guide cell segmentation. Nevertheless, integration with other software for imaging-guided cell segmentation is still possible. FaST is publicly available on github (https://github.com/flcvlr/FaST).},
}

*Software
*Gene Expression Profiling/methods
*Transcriptome
Humans
Sequence Analysis, RNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid40248452,
year = {2025},
author = {Hrivniak, Ľ and Sroka, P and Godunko, RJ and Martynov, AV and Palatov, DM and Bojková, J},
title = {Discovering diversity of Central Asian and Himalayan Epeorus (Caucasiron) mayflies (Ephemeroptera, Heptageniidae) using DNA barcoding and morphology.},
journal = {ZooKeys},
volume = {1234},
number = {},
pages = {89-125},
pmid = {40248452},
issn = {1313-2989},
abstract = {The mayflies of the genus Epeorus Eaton, 1881 subgenus Caucasiron Kluge, 1997 are distributed from the eastern Mediterranean to the mountains of south-west China. In contrast to the Caucasus, the Mediterranean and Irano-Anatolian regions, where E. (Caucasiron) represents one of the most extensively studied mayfly taxa, the species diversity in the more eastern mountains of Asia has been studied only sporadically. In this study, the species diversity of E. (Caucasiron) from the mountains of Central Asia (Pamir, Tian Shan) and the western part of the Himalayas was analysed using DNA barcoding and the morphology of larvae and adults. The distance- and phylogenetic tree-based molecular species delimitation analyses revealed five E. (Caucasiron) species occurring in the study area. Three of them did not correspond morphologically to any known species of the genus Epeorus. These species were described herein as E. (C.) himalayensis Hrivniak & Sroka, sp. nov., E. (C.) lanceolatus Hrivniak & Sroka, sp. nov. and E. (C.) lineatus Hrivniak & Sroka, sp. nov. All new species were compared with other representatives of the subgenus and other related species of the genus Epeorus, and appropriate morphological diagnostic characters were provided. Morphological revision, main diagnostic characters, and information on the distribution of E. (C.) guttatus Braasch & Soldán, 1979 and two other potentially related Epeorus species from the area, E.psi Eaton, 1885 and E.suspicatus (Braasch, 2006), are also given.},
}

@article {pmid40247933,
year = {2025},
author = {Moulin, N},
title = {MANGF: a reference library of DNA barcodes for Mantodea from French Guiana (Insecta, Dictyoptera).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e149486},
pmid = {40247933},
issn = {1314-2828},
abstract = {BACKGROUND: Mantodea plays a special role in the food chain as a group charismatic generalist predators. They regulate invertebrate populations while themselves being prey for many larger animals such as reptiles and birds. The present study focuses on Fench Guiana where about 78 species are known within eight families. This diversity represents a challenge for specimen identification.

NEW INFORMATION: The MANGF project aims at developing a DNA metabarcoding approach to facilitate and enhance the monitoring of mantises as indicators in ecological studies. As a first step towards that goal, we assembled a library of DNA barcodes using the standard genetic marker for animals, i.e. a portion of the COI mitochondrial gene. In the present contribution, we release a library including 425 records representing 68 species in eight different families. Species were identified by expert taxonomists and each record is linked to a voucher specimen to enable future morphological examination. We also highlight and briefly discuss cases of low interspecific divergences, as well as cases of high intraspecific divergences that might represent cases of overlooked or cryptic diversity.},
}

@article {pmid40246065,
year = {2025},
author = {Oskolas, H and Nogueira, FCN and Domont, GB and Yu, KH and Semenov, YR and Sorger, P and Steinfelder, E and Corps, L and Schulz, L and Wieslander, E and Fenyö, D and Kárpáti, S and Holló, P and Kemény, LV and Döme, B and Megyesfalvi, Z and Pawłowski, K and Nishimura, T and Kwon, H and Encarnación-Guevara, S and Szasz, AM and Veréb, Z and Gyulai, R and Németh, IB and Appelqvist, R and Rezeli, M and Baldetorp, B and Horvatovich, P and Malmström, J and Pla, I and Sanchez, A and Knudsen, B and Kiss, A and Malm, J and Marko-Varga, G and Gil, J},
title = {Comprehensive biobanking strategy with clinical impact at the European Cancer Moonshot Lund Center.},
journal = {Journal of proteomics},
volume = {},
number = {},
pages = {105442},
doi = {10.1016/j.jprot.2025.105442},
pmid = {40246065},
issn = {1876-7737},
abstract = {This white paper presents a comprehensive biobanking framework developed at the European Cancer Moonshot Lund Center that merges rigorous sample handling, advanced automation, and multi-omic analyses to accelerate precision oncology. Tumor and blood-based workflows, supported by automated fractionation systems and standardized protocols, ensure the collection of high-quality biospecimens suitable for proteomic, genomic, and metabolic studies. A robust informatics infrastructure, integrating LIMS, barcoding, and REDCap, supports end-to-end traceability and realtime data synchronization, thereby enriching each sample with critical clinical metadata. Proteogenomic integration lies at the core of this initiative, uncovering tumor- and blood-based molecular profiles that inform cancer heterogeneity, metastasis, and therapeutic resistance. Machine learning and AI-driven models further enhance these datasets by stratifying patient populations, predicting therapeutic responses, and expediting the discovery of actionable targets and companion biomarkers. This synergy between technology, automation, and high-dimensional data analytics enables individualized treatment strategies in melanoma, lung, and other cancer types. Aligned with international programs such as the Cancer Moonshot and the ICPC, the Lund Center's approach fosters open collaboration and data sharing on a global scale. This scalable, patient-centric biobanking paradigm provides an adaptable model for institutions aiming to unify clinical, molecular, and computational resources for transformative cancer research.},
}

@article {pmid40245615,
year = {2025},
author = {Wu, Q and Nakano, T and Ishida, S and Komai, T and Fujiwara, Y and Yoshida, T and Kawato, M and Oka, SI and Fujikura, K and Miya, M and Minamoto, T},
title = {Development of universal PCR primers for the environmental DNA metabarcoding of cephalopod (Mollusca) diversity.},
journal = {Marine environmental research},
volume = {208},
number = {},
pages = {107094},
doi = {10.1016/j.marenvres.2025.107094},
pmid = {40245615},
issn = {1879-0291},
abstract = {Cephalopods play crucial roles in marine ecosystems, acting as both predators and prey for apex predators, thereby contributing to the distribution of energy and nutrients across the food web. Traditional net capture methods are often ineffective for studying cephalopods owing to their wide distribution in marine environments, necessitating the development of simple and efficient surveying techniques to assess cephalopod diversity. Therefore, in this study, we aimed to establish universal polymerase chain reaction primers specifically targeting mitochondrial 16S rRNA genes for environmental DNA metabarcoding in cephalopods. Two primer sets, Cep16S_D and Cep16S_O, were designed for squids and octopuses, respectively. Taxonomic specificity, resolution, and coverage of these primers were evaluated via in silico and in vitro analyses. Additionally, efficiency of these primer sets was assessed using tissue samples and mock communities. Finally, their applicability and performance were tested at various depths. The developed primers exhibited a relatively large amplification size with mixed bases that enhanced their amplification efficiency and sensitivity for cephalopod detection. We successfully identified cephalopod species with different body sizes, from small species, such as Heteroteuthis dagamensis, to large species, such as Architeuthis dux, at varying water depths. Overall, the primer sets established in this study serve as powerful tools to study cephalopod diversity and exhibit great potential for barcoding and genetic diversity investigations.},
}

@article {pmid40242636,
year = {2025},
author = {Munkhtulga, D and Baasanmunkh, S and Nyamgerel, N and Park, JH and Tsegmed, Z and Tojibaev, KS and Choi, HJ},
title = {Morphological and phylogenetic analysis approach to three new species and a new section of Astragalus (Fabaceae) from Mongolia.},
journal = {PhytoKeys},
volume = {255},
number = {},
pages = {51-73},
pmid = {40242636},
issn = {1314-2011},
abstract = {Astragalus L. is the largest genus worldwide, comprising more than 3,100 species belonging to 250 sections. In Mongolia, approximately 130 species, including 15 endemic and 25 subendemic species have been previously recognized from 42 sections and 6 subgenera. In this study, we investigated several species within section Laguropsis in Mongolia based on extensive morphological analyses and molecular evidence. Based on these results, we describe three new species and a new section. Two of the newly described species, A.oyunicus and A.teshigicus, belong to the section Laguropsis, whereas the remaining species, A.uvsicus, is the type species of the new section Uvsicus. Furthermore, our findings revealed that (i) A.tamiricus, previously considered endemic to Mongolia, is an additional synonym of A.laguroides, and (ii) A.gobi-altaicus, previously a synonym of A.laguroides, is an independent species. Finally, we provide taxonomic nomenclature, morphological observations, distribution maps and wild photo illustrations of each species.},
}

@article {pmid40238250,
year = {2025},
author = {Zhao, J and Yang, W and Cai, H and Cao, G and Li, Z},
title = {Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/foods14071116},
pmid = {40238250},
issn = {2304-8158},
support = {Grant No. ZDYF2024GXJS316//Key Research and Development Projects in Hainan Province/ ; },
abstract = {Addressing the pervasive issue of food adulteration and fraud driven by economic interests has long presented a complex challenge. Such adulteration not only compromises the safety of the food supply chain and destabilizes the market economy but also poses significant risks to public health. Food adulteration encompasses practices such as substitution, process manipulation, mislabeling, the introduction of undeclared ingredients, and the adulteration of genetically modified foods. Given the diverse range of deceptive methods employed, genomics-based identification techniques have increasingly been utilized for detecting food adulteration. Compared to traditional detection methods, technologies such as polymerase chain reaction (PCR), next-generation sequencing (NGS), high-resolution melt (HRM) analysis, DNA barcoding, and the CRISPR-Cas system have demonstrated efficacy in accurately and sensitively detecting even trace amounts of adulterants. This paper provides an overview of genomics-based approaches for identifying food adulteration, summarizes the latest applications in certification procedures, discusses current limitations, and explores potential future trends, thereby offering new insights to enhance the control of food quality and contributing to the development of more robust regulatory frameworks and food safety policies.},
}

@article {pmid40237570,
year = {2025},
author = {Bignotto, TS and de Souza, HB and da Silva Bronzim, RC and Maniglia, TC and Baumgartner, D},
title = {Integrative morphometric and molecular analyses reveal possible genetic contamination of silver catfish populations of the genus Rhamdia in Neotropical River basins.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70057},
pmid = {40237570},
issn = {1095-8649},
abstract = {Rhamdia quelen, Rhamdia branneri and Rhamdia voulezi are morphologically similar species that, until recently, were considered synonymous. Although R. quelen has wide distribution in the Neotropical region, R. branneri and R. voulezi are sympatric and endemic species of the Iguaçu River basin. We used an integrative approach, including morphometric and molecular data (barcodes DNA, COI gene), to assist in the identification and delimitation of these species. We also intended to investigate genetic contamination of the Paraná III and lower Iguaçu River basins, as silver catfish production has increased in southern Brazil, and accidental or occasional escapes to nature may pose risks to the genetic integrity of native populations. COI sequences and morphometric data were efficient in the characterization and differentiation of Rhamdia species and may be helpful tools in correctly identifying R. quelen, R. branneri and R. voulezi. Both morphometric and molecular analyses indicated the segregation of specimens into three groups. Although this separation coincided with the taxonomy and the collection site in the morphometric analyses, the taxonomic identification of most samples did not coincide with the molecular identification. This fact may be due to (i) incorrect morphological identification and/or (ii) escapes of pure species and/or interspecific hybrids from fish farms. The detection of COI haplotypes of R. quelen in the lower Iguaçu River, as well as COI haplotypes of R. branneri and R. voulezi in the Paraná III basin, combined with the morphometric and morphological characteristics of the specimens, reinforces the occurrence of hybrid specimens in these river basins. These results reveal the importance of characterizing species and interspecific hybrids of Rhamdia and the urgency to regulate aquaculture activities.},
}

@article {pmid40236044,
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.31.646279},
pmid = {40236044},
issn = {2692-8205},
abstract = {UNLABELLED: 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.

AUTHOR SUMMARY / IMPORTANCE: Polyomavirus infections, mostly benign but potentially fatal for immunocompromised individuals, undergo acute and long-term persistent infections. Typically, polyomavirus-associated diseases arise due to virus infection occurring in the context of a persistently infected individual. However, little is understood regarding the mechanisms of how polyomaviruses establish, maintain, and reactivate from persistent infection. We developed a non-invasive virus shedding assay combining barcoded murine polyomavirus, massively parallel sequencing technology, and novel computational approaches to track long-term infections in mice. We expect these methods to be of use not only to the study of DNA viruses but also for understanding persitent infection of diverse microbes. The study revealed organ-specific virus reservoirs and two distinct shedding patterns: constant low-level shedding of numerous barcodes and episodic high-level shedding of few barcodes. Over time, the diversity of shed barcodes decreased substantially. These findings suggest a persistent low-level infection in multiple reservoirs, with occasional bursts of replication in a small subset of infected cells. This combination of broad reservoirs and varied shedding mechanisms may contribute to polyomavirus success in transmission and maintaining long-term infections.},
}

@article {pmid40236020,
year = {2025},
author = {Tasca, JA and Doherty, JF and Shields, EJ and Mudiyanselage, SD and Reich, LN and Sarma, K and Garcia, BA and Bonasio, R},
title = {Pooled scanning of protein variants identifies novel RNA-binding mutants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.02.646914},
pmid = {40236020},
issn = {2692-8205},
abstract = {Binding to RNA has been observed for an ever-increasing number of proteins, which often have other functions. The contributions of RNA binding to protein function are best discerned by studying separation-of-function mutants that hamper interaction with RNA without affecting other aspects of protein function. To design these mutants, we need precise knowledge of the residues that contribute to the affinity of the protein for its RNA ligands. Here, we present RBR-scan: a technology to simultaneously measure RNA-binding affinity of a large number of protein variants. We fused individual variants with unique peptide barcodes optimized for detection by mass spectrometry (MS), purified protein pools from single bacterial culture, and assayed proteins in parallel for RNA binding. Mutations in the MS2 coat protein known to impair RNA-binding were correctly identified, as well as a previously unreported mutant, which we validated with orthogonal biochemical methods. We used RBR-scan to discover novel RNA-binding mutants in the cancer-associated splicing regulator SRSF2. Together, our results demonstrate that RBR-scan is a powerful and scalable platform for linking RNA-binding affinity to protein sequence, offering a novel strategy to decode the functional consequences of protein-RNA interactions.},
}

@article {pmid40235722,
year = {2025},
author = {Chai, Y and Tian, T and Wang, L and Wei, J and Xu, Y and Liu, P and Xiang, C and Yue, M},
title = {Using Plant DNA Barcodes and Functional Traits to Assess Community Assembly of Quercus Forests at Different Scales in the Semiarid Loess Plateau of China.},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71103},
pmid = {40235722},
issn = {2045-7758},
abstract = {Trait and evolutionary differences among coexisting species are increasingly used to comprehend the processes shaping communities. However, they do not consistently yield congruent insights due to methodological limitations and scale dependence. Utilizing two plastid DNA genes (rbcL and matK) and one nuclear DNA gene (internal transcribed spacer, ITS), we first constructed the phylogenies of 147 woody species from 98 line transects in the forest areas of the Loess Plateau and subsequently measured three functional traits. Five plots (2500 m[2]) were constructed within Quercus forests to analyze the functional and phylogenetic structures at three spatial scales (100, 400, 2500 m[2]) and two vertical structural layers (tree colonization and shrub layer). In contrast to the phylogenetic convergence observed at the genus level, using plant DNA barcodes, we found that the entire forest communities and the tree layer exhibited phylogenetic randomness across all three spatial scales; even the shrub layer showed phylogenetic overdispersion with increasing scale. Specific leaf area (SLA) exhibited functional convergence in both the shrub and tree layers. In contrast, seed mass (SM) and plant height (PH) displayed distinct functional structures. In the tree layer, these traits showed phylogenetic overdispersion, while in the shrub layer, they demonstrated functional convergence. This contrast highlights the different ecological roles and processes at play in the two layers. Specifically, the scale dependency of assembly patterns in the shrub layer was more pronounced than in the tree layer for both functional and phylogenetic structures. Our findings underscore the significance of employing DNA barcodes to assess the phylogenetic structure of communities with closely related coexisting species and emphasize niche-based functional assembly and multi-process phylogenetic assembly among vertical structural layers in the Quercus community. Decoupling functional and phylogenetic disparities between species could facilitate the understanding of complex species differences influencing community assembly.},
}

@article {pmid40234750,
year = {2025},
author = {Shen, X and Li, Y and Liu, Y and Jiang, D},
title = {Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus).},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {475},
pmid = {40234750},
issn = {1471-2229},
support = {2021C02071-4-2//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; },
abstract = {BACKGROUND: Cherries, a subgenus of Cerasus within Rosaceae, as fruit trees with high economic value and elegant garden plants, have broad prospects for development and utilization. However, traditional morphology and molecular data have struggled to accurately identify cherry species due to their extensive overlap in the distribution, frequent hybridization, both open and closed flowers, hysteranthy and limited species coverage, hindering the advancement of the cherry industry. In this study, 61 well-documented cherry species were collected and whole chloroplast genome data was used to develop an effective DNA identification system for precise species identification.

RESULTS: 36 new cherry chloroplast genomes were added to the public database, resulting in the most comprehensive phylogenetic relationship of cherry species to date. While whole chloroplast genome data achieved an 85.26% species identification success rate, it did not fully resolve all species identification. Relying solely on whole chloroplast genome data is resource-intensive. Therefore, we explored using highly variable regions, species-specific SNPs, and structural variations for accurate species identification. This study revealed that 14 newly developed DNA barcodes could identify 71.88% of cherry samples, while 106 SNPs and Indels allowed for precise identification of 59 out of 61 cherry species.

CONCLUSIONS: This study not only clarified the phylogenetic relationships of major cherry species but also developed a precise identification system, providing a robust tool for accurate species identification and laying a solid foundation for breeding and the broader promotion of cherry species.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid40231940,
year = {2025},
author = {Grbin, D and Zrnčić, S and Oraić, D and Alfier, M and Cindrić, M and Jović, L and Sučec, I and Zupičić, IG},
title = {Seafood Labeling in Croatia: Molecular Evidence and Regulatory Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/foods14060917},
pmid = {40231940},
issn = {2304-8158},
support = {Project MetaPatvor NPOO.C3.2.R3-I1.04.0122//European Union NextGenerationEU/ ; },
abstract = {Fisheries and aquaculture play a crucial role in global food security, yet species mislabeling remains a persistent challenge, undermining consumer trust and market transparency. Proper food labeling is essential for protecting public health due to the presence of unknown toxic or allergenic substances and preventing illegally sourced products from entering the market. Despite extensive research across Europe, seafood mislabeling in Croatia has remained unexplored. This study aims to provide the first comprehensive assessment of seafood labeling accuracy in Croatia, where fisheries are integral to the coastal economies and tourism. Using DNA barcoding of the COI gene, 109 seafood samples were collected over two years from various sources, including restaurants, markets, and fishing vessels, and analyzed for potential mislabeling. Results revealed a mislabeling rate of 3% among fish samples and 20% among cephalopods, with notable substitutions, such as the yellowfin tuna mislabeled as bigeye tuna and Bluefin tuna and the European squid mislabeled as Patagonian squid. Additionally, 38.5% of samples were partially labeled, while 32% lacked clear country-of-origin information, complicating traceability. While the findings align with the mislabeling rates in other European countries, this study underscores the ongoing challenges in seafood labeling compliance. Establishing standardized monitoring protocols will be essential for improving comparability and effectively addressing seafood fraud.},
}

@article {pmid40228207,
year = {2025},
author = {Leibovich, N and Goyal, S},
title = {Limitations and optimizations of cellular lineages tracking.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012880},
doi = {10.1371/journal.pcbi.1012880},
pmid = {40228207},
issn = {1553-7358},
mesh = {*Cell Lineage/genetics ; Computational Biology/methods ; *DNA Barcoding, Taxonomic/methods ; *Cell Tracking/methods ; Humans ; Animals ; },
abstract = {Tracking cellular lineages using genetic barcodes provides insights across biology and has become an important tool. However, barcoding strategies remain ad hoc. We show that elevating barcode insertion probability and thus increasing the average number of barcodes within the cells, adds to the number of traceable lineages but may decrease the accuracy of lineages inference due to reading errors. We establish the trade-off between accuracy in tracing lineages and the total number of traceable lineages, and find optimal experimental parameters under limited resources concerning the populations size of tracked cells and barcode pool complexity.},
}

*Cell Lineage/genetics
Computational Biology/methods
*DNA Barcoding, Taxonomic/methods
*Cell Tracking/methods
Humans
Animals

@article {pmid40226864,
year = {2025},
author = {Huang, Y and Zhang, Z and Yang, T and Zhang, Y and Cheng, X and Kang, Y and Guang, Y and Zou, Y and Zhang, X and Luo, Z and Chen, J and Cheng, W},
title = {Gemini Molecular Assembly Colocalization (GOAL): Accurate and Efficient Fusion Genotyping for Chronic Myeloid Leukemia Intelligent Diagnosis.},
journal = {Small methods},
volume = {},
number = {},
pages = {e2500194},
doi = {10.1002/smtd.202500194},
pmid = {40226864},
issn = {2366-9608},
support = {82372334//National Natural Science Foundation of China/ ; 82302621//National Natural Science Foundation of China/ ; U24A20751//National Natural Science Foundation of China/ ; KJZD-K202200404//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; KJQN202300435//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; CSTB2023NSCQ-LZX0022//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; W0183//Future Medical Youth Innovation Team Development Support Program Project of Chongqing Medical University/ ; CYYY-DSTDXM-202305//The First Affiliated Hospital of Chongqing Medical University Graduate Tutor Team Building Project Grants/ ; CYYY-YJSJXCX-202303//The First Affiliated Hospital of Chongqing Medical University Graduate Teaching Innovation Team Project Grants/ ; },
abstract = {RNA small fragment aberrances are associated with diseases by mediating a range of pathogenesis and pathological processes. DNA assembly-based barcoding and amplification technologies are currently being actively explored for RNA in situ analysis. However, these modular integrated DNA assembly processes are inevitably accompanied with false positive signals caused by unexpected misassembly. Completely avoiding this phenomenon through simple and universal methods is challenging. Here, a novel dual-input to dual-output in situ analysis paradigm is proposed, aiming to improve target specificity through co-recognition (dual-input) and to eliminate false positive misassembly through fluorescent signal co-localization (dual-output). Based on this paradigm, Gemini molecular assembly co-localization (GOAL) in situ imaging system is launched to accurately distinguish the fusion gene subtypes associated with chronic myeloid leukemia (CML), and to precisely report the proportion of minimum residual cancer cells in clinical samples by intelligent co-localization counting and sorting. GOAL achieves highly sensitive and accurate genotyping recognition of 0.01% CML tumor cells and realizes fully automatic rapid diagnosis with a customized Intelligent Cell Image Sorter (iCis). iCis-assisted GOAL represents an innovative and versatile molecular toolkit for accurate, rapid, user-friendly, and professional-independent profiling of cancer cells with RNA small fragment aberrances, providing efficient clinical decision support for disease diagnosis.},
}