@article {pmid40642430,
year = {2025},
author = {Muñoz, I and Clark, PF and Cuesta, JA},
title = {The systematic status of Afropisasanctaehelenae (Chace, 1966) (Decapoda, Brachyura, Majoidea, Epialtidae): morphological and molecular evidence.},
journal = {ZooKeys},
volume = {1243},
number = {},
pages = {225-240},
pmid = {40642430},
issn = {1313-2989},
abstract = {Afropisasanctaehelenae (Chace, 1966) was originally described from three specimens collected from Saint Helena Island, South Atlantic, and assigned to Pisa Leach, 1814. It is a poorly known species, and until now, no new records have been reported. Recently, this species was transferred to a new genus, Afropisa Muñoz, García-Raso, González, Lopes, dos Santos & Cuesta, 2023, based exclusively on morphology. Nearly 60 years on from the original description, another eight specimens of A.sanctaehelenae have been made available for further study and sequencing. Mitochondrial 16S rRNA and cytochrome c oxidase subunit I sequences confirm the assignment of this Chace species to Afropisa. Photographs of the male holotype and female paratype confirmed the presence of additional characters; consequently, the present work provides a redescription of this species.},
}

@article {pmid40642429,
year = {2025},
author = {Reemer, M and Mengual, X},
title = {Revision of the Neotropical species of the hoverfly genus Serichlamys Curran, 1925 (Diptera, Syrphidae, Microdontinae).},
journal = {ZooKeys},
volume = {1243},
number = {},
pages = {51-106},
pmid = {40642429},
issn = {1313-2989},
abstract = {The Neotropical species of the hoverfly genus Serichlamys Curran, 1925 are revised. A total number of 14 Neotropical species are recognized, two of which were previously described, namely S.mitis (Curran, 1940) and S.mus (Curran, 1936). The other 12 species are here described for the first time: S.boti Reemer, sp. nov., S.chloraspis Reemer, sp. nov., S.melamitis Reemer, sp. nov., S.mellimitis Reemer, sp. nov., S.pallitarsis Reemer & Mengual, sp. nov., S.serpentiphallus Reemer, sp. nov., S.simpliciphallus Reemer, sp. nov., S.spathulata Reemer, sp. nov., S.trigonoides Reemer, sp. nov., S.varicaudata Reemer & Mengual, sp. nov., S.vexilliphallus Reemer & Mengual, sp. nov., and S.xanthocnemia Reemer, sp. nov. An identification key is provided including all the recognised species. The distribution of the genus in the Neotropical region is shown to be disjunct, with one group of species in the northwest of the South American landmass and another group in southeastern Brazil.},
}

@article {pmid40642427,
year = {2025},
author = {Qiao, CH and Xu, YQ and Wang, HS},
title = {A new genus of Orgyiini (Lepidoptera, Erebidae, Lymantriinae) from China, with description of a new species.},
journal = {ZooKeys},
volume = {1243},
number = {},
pages = {131-142},
pmid = {40642427},
issn = {1313-2989},
abstract = {A new genus, Cyclomacula Qiao & Wang, gen. nov., is established to accommodate a new species and three new combinations from China: C.medogensis Qiao & Wang, sp. nov., C.glaucinoptera (Collenette, 1934), comb. nov., C.dudgeoni (Swinhoe, 1907), comb. nov. and C.flavimacula (Moore, 1865), comb. nov. Images of adults and genitalia of all currently recognized Cyclomacula species are provided, with illustrations of wing venation of the type species in the new genus. A key to species of the genus is presented, along with DNA barcode data.},
}

@article {pmid40638508,
year = {2025},
author = {Cardoso, SF and Pinheiro, IC and Kikuti, LAO and Yoshikawa, AAG and Pitaluga, AN and Rona, LDP},
title = {Expanded range of Haemagogus leucocelaenus in yellow fever hotspots: new findings from Santa Catarina State, southern Brazil.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {120},
number = {},
pages = {e240240},
pmid = {40638508},
issn = {1678-8060},
mesh = {Brazil ; Animals ; Yellow Fever/transmission ; *Mosquito Vectors/classification/genetics/anatomy & histology ; Polymerase Chain Reaction ; *Culicidae/classification/genetics/anatomy & histology ; Female ; Electron Transport Complex IV/genetics ; Male ; Phylogeny ; *Animal Distribution ; },
abstract = {BACKGROUND: The Haemagogus genus includes nine mosquito species reported in Brazil, each with distinct distribution patterns. Haemagogus leucocelaenus, a major yellow fever vector, is widely distributed throughout the country, while Haemagogus leucophoebus, a morphologically similar species, has only been identified in Acre State.

OBJECTIVES: This study evaluated the presence of Haemagogus species in southern Brazil by comparing their morphological and molecular characteristics.

METHODS: Mosquitoes were collected from five municipalities in southern Santa Catarina State, Brazil. Each specimen was identified morphologically and photographed. Genomic DNA was extracted, and a Cytochrome C Oxidase Subunit I (COI) gene fragment was amplified using polymerase chain reaction (PCR). The positive amplicons were sequenced for molecular identification.

FINDINGS: New records of Hg. leucocelaenus were found in Santa Rosa de Lima, Rio Fortuna, Braço do Norte, São Martinho, and Pedras Grandes, located at the southern edge of the Atlantic Forest. This study expands the known distribution of Hg. leucocelaenus, the only Haemagogus species identified in the area, with 91 specimens collected. Although some specimens exhibited morphological variations that might lead to misidentification as Hg. leucophoebus, molecular identification confirmed that all were Hg. leucocelaenus.

MAIN CONCLUSIONS: This study is the first to report Hg. leucocelaenus in Santa Catarina, Brazil, and provides DNA barcoding sequences from southern Brazil. This method offers a reliable alternative for species identification, especially when combined with morphological analysis. Further molecular studies are needed to determine whether the morphological variations observed indicate intraspecific differences.},
}

Brazil
Animals
Yellow Fever/transmission
*Mosquito Vectors/classification/genetics/anatomy & histology
Polymerase Chain Reaction
*Culicidae/classification/genetics/anatomy & histology
Female
Electron Transport Complex IV/genetics
Male
Phylogeny
*Animal Distribution

@article {pmid40638159,
year = {2025},
author = {Sekiguchi, S and Kohtsuka, H and Kakui, K},
title = {First Record of the Deep-Sea Sea Spider Bathypallenopsis californica (Arthropoda: Pycnogonida) from the Northwestern Pacific, with a Note on an Attached Crinoid.},
journal = {Zoological science},
volume = {42},
number = {3},
pages = {335-341},
doi = {10.2108/zs250004},
pmid = {40638159},
issn = {0289-0003},
mesh = {Animals ; Male ; Pacific Ocean ; Animal Distribution ; *Arthropods/anatomy & histology/genetics/classification ; Phylogeny ; *Spiders/anatomy & histology ; Electron Transport Complex IV/genetics ; },
abstract = {We report the first record of the pallenopsid pycnogonid species Bathypallenopsis californica (Schimkewitsch, 1893) from the northwestern Pacific. Based on one male specimen collected from 1987-2007 m depth off the southeastern coast of Hokkaido, Japan, we redescribe the species and present its cytochrome c oxidase subunit I (COI) sequence for use in future DNA barcoding. We found a cystidean-stage crinoid on the leg-1 femur of the sea spider, representing the first record of a cystidean found on a sea spider. BLAST searches for COI and 28S sequences revealed that the crinoid was Florometra asperrima (Clark, 1907).},
}

Animals
Male
Pacific Ocean
Animal Distribution
*Arthropods/anatomy & histology/genetics/classification
Phylogeny
*Spiders/anatomy & histology
Electron Transport Complex IV/genetics

@article {pmid40636447,
year = {2025},
author = {Heng, X and Li, F and Xie, D and Wang, A and Liu, C and Yang, Y},
title = {Species diversity of oysters (Mollusca, Bivalvia) in the intertidal zone of Hainan Island revealed by DNA barcoding analysis.},
journal = {ZooKeys},
volume = {1241},
number = {},
pages = {247-260},
pmid = {40636447},
issn = {1313-2989},
abstract = {The family Ostreidae (Mollusca, Bivalvia) is an important component of marine ecosystems. The unique location and marine environment of Hainan Island provide diverse habitats for oysters. However, in recent years, oyster resources of Hainan Island have been under severe threats due to environmental pollution and habitat destruction. To better protect and utilize these biological resources, this study conducted systematic identification of naturally distributed oysters on Hainan Island using DNA barcoding technology. The results revealed the presence of 17 lineages, belonging to 14 species of oysters. The interspecies genetic distances for the COI gene sequences ranged from 10.09% to 31.72%, with notable DNA barcode gaps observed between intra- and interspecies. Additionally, the interspecies genetic distances for the 28S rRNA gene sequences varied between 0.24% and 14.03%. The DNA barcoding analysis indicated the existence of cryptic lineages within Saccostreacuccullata (Born, 1778). Furthermore, the study highlighted that Saccostreamalabonensis (Faustino, 1932) is the most prevalent and dominant species along the Hainan Island coastline, attributed to its ability to adapt to a wide range of salinity levels. When comparing the species diversity of oysters between the western and eastern coasts of Hainan Island, it was found to be higher on the western coast. This disparity is likely influenced by geographical factors and human activities. Specifically, the western coast, situated in the Beibu Gulf, benefits from relatively stable water quality and numerous river inflows, providing abundant phytoplankton and optimal growth conditions for oyster larvae. Conversely, the eastern coast experiences frequent human activities, such as aquaculture and tourism, which may contribute to the decline in species diversity in this region. Overall, this study enhances our understanding of the species diversity of oysters on Hainan Island and provides scientific evidence that is crucial for the development, protection, and sustainable utilization of these valuable oyster resources.},
}

@article {pmid40634378,
year = {2025},
author = {Pizzigalli, C and Regalla, A and Palmeirim, AF and Palma, L and Lopes-Lima, M and Razgour, O and Godinho, R and Intipe, WA and Brito, JC},
title = {Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24703},
pmid = {40634378},
issn = {2045-2322},
support = {2020.05054.BD//Fundação para a Ciência e a Tecnologia/ ; FCT - InBIO Programático FUI 2020-2023 (UIDP/50027/2020)//Fundação para a Ciência e a Tecnologia/ ; CEECINSTLA/00020/2022//Fundação para a Ciência e a Tecnologia/ ; 2022.07926. CEECIND//Fundação para a Ciência e a Tecnologia/ ; CEECINST/00014/2018/CP1512/CT0001//Fundação para a Ciência e a Tecnologia/ ; Projects GW_ICE-01, GW_CIB_02 and 03//Elephant Crisis Fund (Save the Elephants/Wildlife Conservation Network)/ ; },
mesh = {*Alligators and Crocodiles/genetics/physiology/classification ; Animals ; Guinea-Bissau ; *Conservation of Natural Resources ; *Biodiversity ; Ecosystem ; },
abstract = {Challenges in freshwater organism conservation in West Africa are worsened by significant knowledge gaps, even for charismatic species like crocodiles. This study addresses these gaps by assessing crocodile diversity, distribution, and conservation threats in Guinea-Bissau, where existing data is outdated. We used visual surveys, inquiries, molecular barcoding, camera trapping, and bibliographic reviews to investigate crocodile populations. Notably, we found evidence suggesting the Nile crocodile (Crocodylus niloticus), previously thought extinct in West Africa since about 200 years, may persist in Guinea-Bissau's Cacheu region. We also confirmed the presence of the West African crocodile (Crocodylus suchus) in major river basins and coastal lagoons, including the Bijagós Archipelago, and the West African dwarf crocodile (Osteolaemus cf. tetraspis) in the southern mainland and the Bijagós Archipelago. Habitat loss and deliberate killings were identified as major threats. Standardized surveys and genetic sampling are essential to assess population size, connectivity, and genetic diversity, informing evolutionary studies and conservation planning. Conservation efforts should prioritize habitat protection through community-managed reserves and restoration initiatives. Additionally, engaging local communities to raise awareness and develop conflict mitigation strategies is crucial, particularly in areas with human-crocodile interactions.},
}

*Alligators and Crocodiles/genetics/physiology/classification
Animals
Guinea-Bissau
*Conservation of Natural Resources
*Biodiversity
Ecosystem

@article {pmid40633110,
year = {2025},
author = {Cheng, W and Zeng, W and Fan, J and Li, J and Wu, Y and Chen, Y and Yang, X and Wang, K and Huang, J},
title = {Molecular Encoded Beads with DNA Duplex Programming Fluorophore-Quencher Distance for Multiplexed Detection.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c01774},
pmid = {40633110},
issn = {1520-6882},
abstract = {Currently, the leading-edge bead encoding technique adopts the dye-doped strategy, which requires the construction of an encoded bead library in advance and is limited by strict material and technical barriers. Here, we report a simple, versatile, and plug-and-play bead encoding strategy, which uses bead surface DNA encoding instead of a dye-doped strategy. This is a fluorophore-quencher (F-Q) distance encoded strategy through the different Q-labeled positions at the DNA duplex, thereby changing the FRET efficiency. The strategy can simultaneously realize target capture and encoding on a bead surface, which greatly simplifies the process and reduces detection costs. In this work, we encoded 9-plex barcodes through the strategy and decoded them by 2-channel fluorescence flow cytometry. It is a modular technique that enables seamless integration with additional signal amplifier units. Herein, we constructed three kinds of multiplexed nucleic acid detection models, including "direct capture", "capture and then amplify", and "amplify and then capture", that enrich the encoding toolbox for bead-based multiplexed detection.},
}

@article {pmid40632720,
year = {2025},
author = {Shumba, K and Bor, J and Nattey, C and Gareta, D and Lauren, E and Macleod, W and Fox, MP and Puren, A and Mlisana, K and Onoya, D},
title = {Record linkage without patient identifiers: Proof of concept using data from South Africa's national HIV program.},
journal = {PLOS global public health},
volume = {5},
number = {7},
pages = {e0004835},
pmid = {40632720},
issn = {2767-3375},
abstract = {Linkage between health databases typically requires patient identifiers such as names and personal identification numbers. We developed and validated a record linkage strategy to combine administrative health databases without identifiers for South Africa's public sector HIV program. We linked CD4 counts and HIV viral loads from South Africa's TIER.Net with the National Health Laboratory Service (NHLS) database for patients receiving care between 2015-2019 in Ekurhuleni District (Gauteng Province). Linkage variables were result value, specimen collection date, facility of collection, year and month of birth, and sex. We used three matching strategies: exact matching on exact values of all variables, caliper matching allowing a ± 5 day window on result date, and specimen barcode matching using unique specimen identifiers. A sequential linkage approach applied specimen barcode, followed by exact, and then caliper matching. Exact and caliper matching were validated using barcodes (available for 34% of records in TIER.Net) as a "gold standard". Performance measures were sensitivity, positive predictive value (PPV), share of patients linked, and percent increase in data points. We attempted to link 2,017,290 laboratory test results from TIER.Net (523,558 unique patients) with 2,414,059 NHLS test results. Exact matching achieved 69.0% sensitivity and 95.1% PPV. Caliper matching achieved 75% sensitivity and 94.5% PPV. Sequential linkage matched 41.9% using specimen barcodes, 51.3% through exact matching, and 6.8% through caliper matching, for 71.9% (95% CI: 71.9, 72.0) of test results matched overall, with 96.8% (95% CI: 96.7, 97.1) PPV and 85.9% (95% CI: 85.7, 85.9) sensitivity. This linked 86.0% (95% CI: 85.9, 86.1) of TIER.Net patients to the NHLS (N = 1,450,087), increasing laboratory results in TIER.Net by 62.6%. Linkage of TIER.Net and NHLS without patient identifiers attained high accuracy and yield without compromising privacy. The integrated cohort provides a more complete laboratory test history and supports more accurate HIV program indicator estimates.},
}

@article {pmid40631198,
year = {2025},
author = {Villegas, NK and Tran, MH and Keller, A and Plesa, C},
title = {BAR-CAT: Targeted Recovery of Synthetic Genes via Barcode-Directed CRISPR-dCas9 Enrichment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.27.658158},
pmid = {40631198},
issn = {2692-8205},
abstract = {Modern gene-synthesis platforms let us probe protein function and genome biology at unprecedented scale. Yet in large, diverse gene libraries the proportion of error-free constructs decreases with length due to the propagation of oligo synthesis errors. To rescue these rare, error-free molecules we developed BAR-CAT (Barcode-Assisted Retrieval CRISPR-Activated Targeting), an in-vitro enrichment method that couples unique PAM-adjacent 20-nt barcodes to each library member and uses multiplexed dCas9-sgRNA complexes to fish out the barcodes corresponding to perfect assemblies. After a single 15-min reaction and optimized wash regime (BAR-CAT v1.0), three low-abundance targets in a 300, 000-member test library were enriched 600-fold, greatly reducing downstream requirements. When applied to 384x and 1, 536x member DropSynth gene libraries, BAR-CAT retrieved up to 122-fold enrichment for 12 targets and revealed practical limits imposed by sgRNA competition and library complexity, which now guide ongoing protocol scaling. By eliminating laborious clone-by-clone validation and working directly on plasmid libraries, BAR-CAT provides a versatile platform for recovering perfect synthetic genes, subsetting large libraries, and ultimately lowering the cost of functional genomics at scale.},
}

@article {pmid40630932,
year = {2025},
author = {Zajac, N and Zhang, Q and Bratus-Neuenschwander, A and Qi, W and Bolck, HA and Karakulak, T and Oltra, TC and Moch, H and Kahraman, A and Rehrauer, H},
title = {Comparison of single-cell long-read and short-read transcriptome sequencing via cDNA molecule matching: quality evaluation of the MAS-ISO-seq approach.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf089},
pmid = {40630932},
issn = {2631-9268},
mesh = {*DNA, Complementary/genetics ; *Single-Cell Analysis/methods ; Humans ; *Transcriptome ; *Gene Expression Profiling/methods ; *Sequence Analysis, RNA/methods ; Gene Library ; *High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Single-cell RNA sequencing is used for profiling gene expression differences between cells. It can be performed with short reads, which provide high-throughput and high-quality information at the gene level, or with long reads, which provide isoform resolution via preserving full-length transcripts. It is, however, unclear how comparable the data is between the two methods. We investigate the types of bias introduced at the library preparation and the bioinformatic processing steps on the transcripts recovered from long- and short-read sequencing, and the effects of filtering, enabled by sequencing of full-length transcripts, on gene expression. For each sample, we sequenced the same 10x Genomics 3' complementary DNA (cDNA) using Illumina short reads and Pacific Biosciences long reads and cross-compared each molecule matched through cell barcode and unique molecular identifier. We find that both methods render highly comparable results and recover a large proportion of cells and transcripts. However, platform-dependent cDNA library processing and data analysis steps introduce biases. Short-read sequencing provided higher sequencing depth, but long-read sequencing allowed for retaining transcripts shorter than 500 bp and for removal of degraded cDNA contaminated by template switching oligos. Filtering of artefacts, identifiable only from full-length transcripts, reduces gene count correlation between the two methods.},
}

*DNA, Complementary/genetics
*Single-Cell Analysis/methods
Humans
*Transcriptome
*Gene Expression Profiling/methods
*Sequence Analysis, RNA/methods
Gene Library
*High-Throughput Nucleotide Sequencing/methods

@article {pmid40630502,
year = {2025},
author = {Meleshko, D and Yang, R and Maharjan, S and Danko, DC and Korobeynikov, A and Hajirasouliha, I},
title = {Blackbird: structural variant detection using synthetic and low-coverage long-reads.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf151},
pmid = {40630502},
issn = {2635-0041},
abstract = {MOTIVATION: Recent benchmarks show that most structural variations, especially within 50-10,000 bp range cannot be resolved with short-read sequencing, but long-read structural variant callers perform better on the same datasets. However, high-coverage long-read sequencing is costly and requires substantial input DNA. Reducing coverage lowers cost but significantly impacts the performance of existing structural variation (SV) callers. Synthetic long-read technologies offer long-range information at lower cost, but leveraging them for SVs under 50 kbp remains challenging.

RESULTS: We propose a novel hybrid alignment- and local-assembly-based algorithm, Blackbird, that uses synthetic long reads and low-coverage long reads to improve structural variant detection. Instead of relying on whole-genome assembly, Blackbird uses a sliding window approach and synthetic long-read barcode information to assemble local segments, integrating long reads to improve structural variant detection accuracy. We evaluated Blackbird on real human genome datasets. On the HG002 Genome in a Bottle (GIAB) benchmark, Blackbird in hybrid mode demonstrated results comparable to state-of-the-art long-read tools, while using less long-read coverage. Blackbird requires only 5 × coverage to achieve F1-scores (0.835 and 0.808 for deletions and insertions) similar to PBSV and Sniffles2 using 10 × PacBio Hi-Fi long-read coverage.

Blackbird is available at https://github.com/1dayac/Blackbird.},
}

@article {pmid40628719,
year = {2025},
author = {Gencel, M and Cofino, GM and Hui, C and Sahaf, Z and Gauthier, L and Matta, C and Gagné-Leroux, D and Tsang, DKL and Philpott, DP and Ramathan, S and Menendez, A and Bershtein, S and Serohijos, AWR},
title = {Quantifying the intra- and inter-species community interactions in microbiomes by dynamic covariance mapping.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6314},
pmid = {40628719},
issn = {2041-1723},
support = {PG-408523//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; RGPIN-2016-06566//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; CRC-2022-00138//Canada Research Chairs (Chaires de recherche du Canada)/ ; 89967//National Research Foundation (NRF)/ ; },
mesh = {Animals ; *Escherichia coli/genetics/physiology/drug effects ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; *Microbial Interactions ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Mice, Inbred C57BL ; },
abstract = {A microbiome's composition, stability, and response to perturbations are governed by its community interaction matrix, typically quantified through pairwise competition. However, in natural environments, microbes encounter multispecies interactions, complex conditions, and unculturable members. Moreover, evolutionary and ecological processes occur on overlapping timescales, making intra-species clonal diversity a critical but poorly understood factor influencing community interactions. Here, we present Dynamic Covariance Mapping (DCM), a general approach to infer microbiome interaction matrices from abundance time-series data. By combining DCM with high-resolution chromosomal barcoding, we quantify inter- and intra-species interactions during E. coli colonization in the mouse gut under three contexts: germ-free, antibiotic-perturbed, and innate microbiota. We identify distinct temporal phases in susceptible communities: (1) destabilization upon E. coli invasion, (2) partial recolonization of native bacteria, and (3) a quasi-steady state where E. coli sub-lineages coexist with resident microbes. These phases are shaped by specific interactions between E. coli clones and community members, emphasizing the dynamic and lineage-specific nature of microbial networks. Our results reveal how ecological and evolutionary dynamics jointly shape microbiome structure over time. The DCM framework provides a scalable method to dissect complex community interactions and is broadly applicable to bacterial ecosystems both in vitro and in situ.},
}

Animals
*Escherichia coli/genetics/physiology/drug effects
Mice
*Gastrointestinal Microbiome/drug effects/genetics
*Microbial Interactions
*Microbiota
Anti-Bacterial Agents/pharmacology
Mice, Inbred C57BL

@article {pmid40628201,
year = {2025},
author = {Saberi-Pirooz, R and Aghamir, F and Ahmadzadeh, F},
title = {Assessing the response of two soil engineering groups to reforestation in the Hyrcanian forests.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126410},
doi = {10.1016/j.jenvman.2025.126410},
pmid = {40628201},
issn = {1095-8630},
abstract = {Many forest ecosystems are becoming more vulnerable due to human activities and the considerable effects of forest exploitation. Furthermore, forest management practices often overlook the importance of biodiversity, focusing primarily on timber production and economic gain. The Hyrcanian forests, in particular, face significant challenges due to a combination of factors such as deforestation, climate change, and invasive species. This study aims to explore the impact of reforestation on the diversity, abundance, and community structure of two key groups of soil engineers: earthworms and ants. These groups were chosen due to findings from a previous study indicating their higher abundance in this region. Additionally, it aims to determine which of these groups is more significantly impacted. The study was conducted in both natural and planted forests across three locations in the central region of these forests. Samples were collected from 72 quadrats and 48 transects. A total of 251 samples were collected for earthworms and 410 samples for ants. Then, the samples were sorted into morphological operational taxonomic units (MorphOTUs) based on morphological characteristics. DNA barcoding studies were performed using the cytochrome c oxidase subunit 1 (COI) gene to determine the molecular OTUs. After that, the difference in OUT richness, abundance and composition between natural and planted forests was investigated using statistical analysis. In the current research, 16 and 19 OTUs were recognized for earthworms and ants, respectively. The results indicated that ant abundance was significantly higher in natural forests (n = 263) compared to planted forests (n = 147). However, the difference in earthworm numbers was negligible (n = 125 in natural and n = 126 in planted forests). The community compositions of both groups did not show significant differences between these forests. The difference between ants and earthworm abundance indicates that ants play a key role as pioneer species in the colonization process, followed by other groups (earthworms) that have settled in the planted forests. The study emphasizes the significance of a genetic approach to understanding the biodiversity of both groups. We believe that integrating both groups will improve the effectiveness of bioindicators in these areas. It is crucial to recognize the biodiversity of soil invertebrates for monitoring natural forests and developing effective reforestation policies, which are essential for fostering resilient ecosystems.},
}

@article {pmid40627868,
year = {2025},
author = {Moreno-Torres, K and Prieto, C and Pyrcz, TW},
title = {Single-Locus species delimitation of Pronophilina butterflies (Nymphalidae: Satyrini) in the Colombian Andes: Congruence between morphology and MOTUs.},
journal = {Genome},
volume = {},
number = {},
pages = {},
doi = {10.1139/gen-2025-0041},
pmid = {40627868},
issn = {1480-3321},
abstract = {The subtribe Pronophilina (Nymphalidae: Satyrinae: Satyrini) is one of the most diverse subtribes within the Lepidoptera. In Colombia, these butterflies are distributed throughout the Andes, where they play a key role in montane ecosystems and exhibit high levels of endemism. Despite their complex genital morphology, species within the same genus often exhibit highly similar wing patterns, complicating taxonomic identification. In this study, we analyzed the concordance between DNA barcode-based species delimitation and morphological identifications using 334 cytochrome c oxidase subunit I (COI) barcodes from 94 a priori identified morphospecies in Colombia. We applied four molecular species delimitation methods (ABGD, RESL, PTP, and ASAP), delimitating between 98-108 molecular operational taxonomic units (MOTUs). Overall, the methods showed high consistency, with high congruence between morphological and molecular delimitations (81%). Additionally, 96.8% of the morphospecies exhibited a barcode gap, indicating clear genetic differentiation. However, we found some inconsistencies, including six cases of species merging and 12 cases of species splitting. Our findings underscore the utility of DNA barcoding for species delimitation in Pronophilina, while highlighting the need for integrative approaches to resolve taxonomic uncertainties in this diverse group.},
}

@article {pmid40624534,
year = {2025},
author = {Ma, J and Jin, W and Rong, L and Gao, Z and Hazrat, Z and Shakhawat, HM and Long, F and Zhang, Z and Huang, J and Lu, X and Jin, G and Zhou, Z},
title = {IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {196},
pmid = {40624534},
issn = {1474-760X},
support = {T13-602/21N//University Grants Committee/ ; KJ012019517//High-level Hospital Construction Project of Guangdong Provincial People's Hospital/ ; 2021B1515130004//Guangdong-Dongguan Joint Research Scheme Guangdong-Hong Kong-Macau Program/ ; JCYJ20210324 114408024//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; },
mesh = {*Single-Cell Analysis/methods ; Animals ; Mice ; Chromatin/metabolism ; *DNA/metabolism ; Female ; Transcription Factors/metabolism ; High-Throughput Nucleotide Sequencing/methods ; Mammary Glands, Animal/metabolism ; Histone Code ; },
abstract = {Single-cell profiling protein-chromatin interactions is often constrained by complex workflows, high cost, or dependence on specialized equipment. We present indexed tagmentation-based single-cell CUT&Tag-sequencing (IT-scC&T-seq), a modular, plate-based strategy using three-round combinatorial barcoding. IT-scC&T-seq robustly profiles histone modifications and transcription factors with high specificity and throughput, supporting simultaneous analysis of multiple samples and epitopes. Notably, it enables sensitive single-cell mapping of lamina-associated domains, low-abundance chromatin features previously difficult to resolve. Applied to adult mouse mammary gland, the method reveals cell-type-specific chromatin landscapes and lineage-regulatory dynamics. Together, IT-scC&T-seq provides a scalable, cost-effective, and broadly accessible approach for high-resolution chromatin profiling.},
}

*Single-Cell Analysis/methods
Animals
Mice
Chromatin/metabolism
*DNA/metabolism
Female
Transcription Factors/metabolism
High-Throughput Nucleotide Sequencing/methods
Mammary Glands, Animal/metabolism
Histone Code

@article {pmid40624060,
year = {2025},
author = {Maurya, S and Sukhramani, G and Lee, C and Jo, S and Kim, J and Jeong, EJ and Zamora, NA and Garcia, R and Zhang, Z and Choi, S and Choudhary, RK and Kim, SY},
title = {Comparative plastome evaluation, phylogenomic analysis, and DNA signatures of medicinally important malvaceous genera and their adulterants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24285},
pmid = {40624060},
issn = {2045-2322},
support = {313-5661-6703/2K23/1//CSIR/ ; IF210309//DST-INSPIRE/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; KGM1172511//Korea Research Institute of Bioscience and Biotechnology/ ; },
mesh = {Phylogeny ; *DNA, Plant/genetics ; *Plants, Medicinal/genetics/classification ; DNA Barcoding, Taxonomic ; Drug Contamination ; Microsatellite Repeats ; India ; },
abstract = {The Bala group of plants, classified under the Malvaceae family, is acknowledged in the Ayurvedic Pharmacopoeia of India and is well-known for its medicinal uses, especially in boosting vitality and addressing neurological and cardiovascular conditions. The key genera of this group, such as Sida and Abutilon, are highly valued in traditional medicine; however, the efficacy of herbal formulations is frequently compromised by adulterants from morphologically similar genera like Malvastrum and Malva. To address this critical challenge, our study focuses on plastome sequencing of various Bala group taxa and their adulterants, aiming to delineate DNA signatures for key species and provide a robust strategy against adulteration. Comprehensive analyses of plastomes from Sida, Abutilon, Malvastrum, and Malva reveal distinct indels, simple sequence repeats (SSRs), and tandem repeats across coding and non-coding regions, as well as potential DNA barcodes within specific intergenic regions. Investigations into gene composition, genetic variations, and nucleotide diversity further elucidate phylogenetic relationships within the Malveae tribe. Phylogenomic analyses clarify the placement of the Bala group and its adulterants, offering robust insights into their evolutionary context. This study underscores the utility of plastome-based approaches in safeguarding the authenticity of Bala group herbal drugs and highlights the broader implications for quality assurance in traditional medicine.},
}

Phylogeny
*DNA, Plant/genetics
*Plants, Medicinal/genetics/classification
DNA Barcoding, Taxonomic
Drug Contamination
Microsatellite Repeats
India

@article {pmid40623487,
year = {2025},
author = {Chotelersak, K and Machida, R and Thipaksorn, A and Samung, Y and Ruangsittichai, J},
title = {Mitochondrial COI barcoding of pulicidae fleas and ultrastructural differentiation of the cat flea by scanning electron microscopy.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105793},
doi = {10.1016/j.meegid.2025.105793},
pmid = {40623487},
issn = {1567-7257},
abstract = {Fleas are widespread ectoparasites found across the globe-even in polar regions-and exhibit low host specificity, allowing them to infest both humans and animals, including birds. They feed on the blood of their hosts and serve as vectors for various infectious diseases, particularly in tropical and subtropical regions. In this study, the COI barcodes and ultrastructural characteristics using scanning electron microscopy (SEM) were performed to confirm classical morphological identification of cat flea taxonomic levels. Four species of medically important Pulicidae fleas were collected from hosts in various provinces of Thailand and identified based on their distinctive morphological characteristics: Xenopsylla cheopis, Echidnophaga gallinacea, Ctenocephalides felis and Ctenocephalides orientis. Phylogenetic analyses and calculated sequence distance based on mitochondrial COI barcodes were performed. The four species clearly formed monophyletic groups with low intraspecific distance (0 % -0.24 %) and high interspecific distance (4.60 % -21.26 %). Ctenocephalides felis and C. orientis were separated at the closely related level and separated into distinct clusters, with a sequence distance of 8.42 %. and C. orientis has shown closely genetic relationship with C. canis (4.60 %). Scanning electron microscopy (SEM) revealed ultrastructural characteristics that clearly differentiate C. felis and C. orientis, including differences in head shape and minute bristles on the dorsal end of the antennal fossa. Specifically, C. felis frons are elongated and pointed anteriorly, whereas C. orientis frons are short and rounded anteriorly. Additionally, the C. orientis female has 3-4-min bristles at the dorsal end of the antennal fossa, while this structure is absent in the C. felis female but present and numerous (with 13-18 bristles) in all males of the genus Ctenocephalides. Fleas were identified, and their sex or ambiguous structures were determined using a stereoscope or low-power binocular microscope. DNA barcoding and ultrastructural analysis using SEM for differentiation of structures of taxonomic significance are useful for subspecies/species identification.},
}

@article {pmid40622985,
year = {2025},
author = {Oladipo, SO and Everett, A and Durand, JD and Adelakun, KM and Dieudonne, WP and Maame, A and Nneji, IC and Ayoola, AO and Atofarati, OT and Kachi, JB and Nneji, LM},
title = {Morphology, DNA Barcoding and Range Extension of a Poorly Known Freshwater Stingray Fontitrygon garouaensis Stauch & Blanc, 1962 from Nigerian Inland Water.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf125},
pmid = {40622985},
issn = {1557-7023},
abstract = {Increasingly sophisticated taxonomic tools have enhanced our understanding of species diversity and phylogenetic relationships in elasmobranchs. Nevertheless, ichthyologists continue to face challenges in resolving the taxonomic placement and authentication of some taxa, particularly those originally described based on morphology. The recently described genus Fontitrygon comprises several Atlantic dasyatid stingrays whose phylogenetic positions have remained unresolved due to the lack of molecular data. In this study, we employed an integrative taxonomic approach to identify and determine the phylogenetic position of the understudied Fontitrygon garouaensis from Nigeria. Specimens were collected from freshwater ecosystems along the Jebba and Lokoja stretches of the River Niger in Nigeria. Comparative morphological analysis distinguished F. garouaensis from other Fontitrygon species by the presence of a depressed central spine shaft with flanges extending along either side, a flattened oval disc, an obtuse snout, a whip-like tail bearing a sting, a broad and elongated snout, small pelvic fins, and radially arranged pectoral fins. Additionally, morphological measurements of the newly collected F. garouaensis were consistent with those of the syntype and holotype, confirming species identification. Phylogenetic analyses based on mitochondrial Cytochrome c Oxidase Subunit I (COI) gene sequences recovered Fontitrygon as a monophyletic lineage and identified F. garouaensis as the sister taxon to F. margarita and F. margaritella. This study provides an integrative taxonomic assessment of F. garouaensis, clarifying its species identity and confirming the presence of F. garouaensis from the upstream of the Jebba stretch of the River Niger. We, therefore, propose an update to its IUCN geographic range.},
}

@article {pmid40622584,
year = {2025},
author = {Chen, X and Han, S and Zhao, D and Li, Z},
title = {Intraductal Injection of Adenoviruses to Perform Lineage Tracing in the Mammary Gland.},
journal = {Journal of mammary gland biology and neoplasia},
volume = {30},
number = {1},
pages = {10},
pmid = {40622584},
issn = {1573-7039},
support = {R01 CA222560/NH/NIH HHS/United States ; W81XWH-15-1-0100//U.S. Department of Defense/ ; SG-0062-10//Harvard Stem Cell Institute/ ; },
mesh = {Animals ; Female ; *Cell Lineage ; *Adenoviridae/genetics ; Humans ; *Mammary Glands, Animal/pathology/metabolism/virology/cytology ; Mice ; *Mammary Glands, Human/pathology ; *Breast Neoplasms/pathology/genetics ; Integrases/genetics ; Epithelial Cells/metabolism ; Cell Differentiation ; },
abstract = {Lineage tracing is a fundamental tool in developmental biology and cancer research, providing critical insights into cell fate decisions, tissue homeostasis and tumor initiation. The mammary gland is a highly dynamic organ with a complex cellular hierarchy, making it an ideal system for lineage-tracing studies. Classic approaches, such as tamoxifen-inducible CreER/loxP recombination, have significantly advanced our understanding of mammary epithelial cell (MEC) differentiation, homeostasis, and transformation. However, these methods have limitations, including potential effects of tamoxifen on estrogen signaling, low mammary gland specificity, and the requirement for transgenic model creation and mouse breeding. Adenovirus-Cre (Ad-Cre)-based lineage tracing has emerged as a powerful alternative, enabling rapid and organ-specific recombination. This review provides a comprehensive evaluation of the Ad-Cre approach in mammary gland biology, comparing its efficiency, specificity, and technical advantages over the CreER-based method. We discuss applications of Ad-Cre intraductal injection-based lineage tracing in mapping MEC fates, identifying the cellular origins of breast cancer, and modeling tumor progression. Additionally, we highlight its ability to induce genetic marking at a clonal level, facilitating precise investigations into MEC plasticity and tumor cell heterogeneity. Despite its advantages, Ad-Cre lineage tracing also presents challenges, such as low cell-targeting efficiency and potential effect on the mammary gland immune microenvironment. Future advancements, including the integration of CRISPR-based barcoding, may further enhance its utility for high-resolution fate mapping. By summarizing recent advancements and comparative analyses, this review underscores the significance of Ad-Cre lineage tracing as a versatile and powerful tool in mammary gland biology and breast cancer research.},
}

Animals
Female
*Cell Lineage
*Adenoviridae/genetics
Humans
*Mammary Glands, Animal/pathology/metabolism/virology/cytology
Mice
*Mammary Glands, Human/pathology
*Breast Neoplasms/pathology/genetics
Integrases/genetics
Epithelial Cells/metabolism
Cell Differentiation

@article {pmid40621477,
year = {2025},
author = {Hayal, TB and Mulla, AA and Allan, DSJ and Duncan, BB and Joshi, S and Hong, SG and Basar, R and Rezvani, K and Childs, RW and Wu, C and Dunbar, CE},
title = {Optimization of lentiviral delivery of barcoded anti-CD20 chimeric antigen receptors into rhesus macaque and human natural killer cells.},
journal = {Molecular therapy. Methods & clinical development},
volume = {33},
number = {2},
pages = {101473},
pmid = {40621477},
issn = {2329-0501},
abstract = {Natural killer (NK) cells are pivotal in immunosurveillance and hold great potential for immunotherapy due to their ability to target malignant cells. Their low risk of causing graft-versus-host disease (GvHD) post-allogenic transplantation underscores their potential as an off-the shelf cellular therapy tool. Advances in genetic engineering focus on improving NK targeting, persistence, and fitness. However, NK cells pose challenges for lentiviral transduction, which are clinically relevant and safe. In this study, we identified Poloxamer 407 (P407) as a novel transduction enhancer for rhesus macaque (RM) and human NK cells. We found that P407 significantly improved transduction efficiency, achieving up to 60% in expanded RM NK cells, without compromising cell viability or functionality. Additionally, P407 facilitated the expression of anti-CD20 chimeric antigen receptors (CARs) with or without interleukin (IL)-15. In a xenograft mouse model, CAR-IL15 NK cells demonstrated superior anti-tumor activity, and maintained higher clonal diversity tracked by genetic barcoding compared to CAR-NK cells lacking IL-15 in vivo. Additionally, in human NK cells, P407 combined with the TBK1/IKKε inhibitor, BX795, further improved lentivirus-mediated transduction. This study is the first to engineer NK cells from a clinically relevant rhesus macaque model in an adaptive cell therapy context and highlights P407's potential as a transduction enhancer.},
}

@article {pmid40621193,
year = {2025},
author = {Imran Hossain, NM and Jony, ME and Emon, SR and Sifat, NI and Rahman, MA and Shomrat, MGM and Jony, MMA},
title = {University Student's Knowledge, Practices, and Perceptions of Food Packaging Labels in Bangladesh: A Cross-Sectional Study.},
journal = {Food science & nutrition},
volume = {13},
number = {7},
pages = {e70567},
pmid = {40621193},
issn = {2048-7177},
abstract = {Food packaging labels play a crucial role in ensuring consumer safety and aiding informed decision-making. However, in Bangladesh, limited research exists on students' understanding and use of food packaging labels. This cross-sectional study assessed the knowledge, practices, and consumer preferences of food labeling among 397 students from various public and private universities across Bangladesh. A self-administered questionnaire, developed based on food safety regulations, was used for data collection. The study employed convenience sampling, and data analysis was conducted using SPSS 27.0, including descriptive statistics, Chi-square tests, and Spearman's rho correlation to evaluate relationships between knowledge and practices. The study found that 74.8% of students had adequate knowledge of food labeling, with high awareness of "Expiry Date" and "Nutritional Information," but limited understanding of "Batch Number" and "Packaging Symbols". Only 44.3% demonstrated good labeling practices, with gaps in checking "Best Before" dates, allergen content, and barcodes. Gender and residential background significantly influenced knowledge and practices (p < 0.001), with females and urban students performing better. A significant positive correlation (r s = 0.524, p < 0.01) indicated that higher knowledge led to better practices. Consumer preferences emphasized food protection, quality, and sustainability, with Kraft/Carton as the preferred packaging material. Although students possess sufficient knowledge, their labeling practices remain lacking, highlighting the need for targeted educational initiatives and policy measures to address this gap and encourage more informed food choices.},
}

@article {pmid40619368,
year = {2025},
author = {Luo, J and Zheng, X and Xin, Q and Liu, M and Zhang, J and Chen, W and Chen, C and Zhang, C and Wan, G and Xia, C and Lu, J},
title = {Glycyrrhiza plastid paternal inheritance and a new DNA barcode provide new strategies for molecular identification of three medicinal licorice hybrid complexes.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {885},
pmid = {40619368},
issn = {1471-2229},
support = {31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; 31760046, 32360053//National Natural Science Foundation of China/ ; },
}

@article {pmid40616113,
year = {2025},
author = {Ramdini, C and Calvez, E and Houy, O and Gréaux, C and Dollin, C and Pocquet, N and Almeras, L and Sonor, F and Déliscar-Jourdan, G and Vega-Rúa, A},
title = {First report of Aedes albopictus in Saint Barthélemy (French West Indies) confirmed by morphological, molecular and MALDI-TOF mass spectrometry approaches.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {258},
pmid = {40616113},
issn = {1756-3305},
support = {"Une santé" 2021-2027//Programme Opérationnel FEDER-Guadeloupe-Conseil Regional/ ; "Une santé" 2021-2027//Programme Opérationnel FEDER-Guadeloupe-Conseil Regional/ ; "Une santé" 2021-2027//Programme Opérationnel FEDER-Guadeloupe-Conseil Regional/ ; ARS/DSS/N°2023-08//Collaboration convention Regional Health Agency and Institut Pasteur Guadeloupe/ ; },
mesh = {Animals ; *Aedes/genetics/anatomy & histology/classification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Mosquito Vectors/anatomy & histology/genetics/classification ; Guadeloupe ; Electron Transport Complex IV/genetics ; Introduced Species ; Female ; },
abstract = {Aedes albopictus is a mosquito vector of arboviruses that is native to southeast Asia. However, this invasive species has spread worldwide. It arrived in the Caribbean in 1993, but had never been recorded in the French Territories of the Americas. We report here the first detection of Aedes albopictus in Saint Barthélemy, Guadeloupe confirmed by morphological criteria, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), and cytochrome c oxidase 1 (cox1) gene barcoding. The presence of this invasive mosquito species in Saint Barthélemy, an island with daily aerial or maritime connections to the French Departments of the Americas, raises concerns about the risk of its introduction into these territories, as well as into other Caribbean countries. It also emphasizes the urgent need to locally reinforce vector surveillance and control measures to prevent the further spread of this mosquito vector.},
}

Animals
*Aedes/genetics/anatomy & histology/classification
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Mosquito Vectors/anatomy & histology/genetics/classification
Guadeloupe
Electron Transport Complex IV/genetics
Introduced Species
Female

@article {pmid40615598,
year = {2025},
author = {Shah, M and Sieber, G and Deep, A and Beisser, D and Boenigk, J},
title = {Unravelling the temporal dynamics of community functions in protists induced by treated wastewater exposure using metatranscriptomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23957},
pmid = {40615598},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; *Transcriptome ; Ecosystem ; Fresh Water/microbiology ; *Eukaryota/genetics ; },
abstract = {The discharge of treated wastewater (TWW) into freshwater ecosystems poses a significant impact on microbial communities, particularly protists, which play a crucial role in nutrient cycling and ecosystem stability. While the ecological effects of TWW on microbial diversity have been studied, understanding the functional responses of protist communities remains limited. This study employs metatranscriptomics to unravel the temporal dynamics of protist community functions in response to TWW exposure. Using mesocosm experiment, water samples were analyzed over a ten-day period to monitor shifts in metabolic pathways and community interactions. Our results indicate that processed metatranscriptomic data, focusing on treatment-significant pathways, is more sensitive than traditional methods, such as meta-barcoding, and non-target screening, in detecting wastewater-induced perturbations. Early exposure to TWW significantly altered expression of pathways associated with signal transduction and environmental interaction, while general metabolic pathways showed resilience. Over time, the protist community showed signs of adaptation with expression levels stabilizing towards the end of the experiment. This study underscores the importance of focussing on functional shifts rather than just taxonomic changes for assessing wastewater impacts on freshwater ecosystems. Our findings advocate for the use of metatranscriptomics as a robust indicator for TWW detection, aiding in development of targeted environmental management strategies.},
}

*Wastewater/microbiology
*Transcriptome
Ecosystem
Fresh Water/microbiology
*Eukaryota/genetics

@article {pmid40614237,
year = {2025},
author = {Zhao, Y and Chen, X and Zhou, T and Zhang, R and Zhao, F and Zhang, X},
title = {Complete chloroplast genome sequence and phylogenetic analysis of Symphytum officinale.},
journal = {Genetics and molecular biology},
volume = {48},
number = {2},
pages = {e20240258},
pmid = {40614237},
issn = {1415-4757},
abstract = {Symphytum officinale is a perennial herb belonging to the Boraginaceae. Here, we sequenced the complete chloroplast (cp) genomes of S. officinale using Illumina sequencing technology. The results revealed that the cp genome is 148,149 bp in length and exhibits a typical quadripartite structure, with a pair of inverted repeat regions (IR) comprising 27,001 bp, a large single-copy (LSC) region comprising 77,366 bp, and a small single-copy (SSC) region comprising 16,781 bp. The sequence contained 133 unique genes, including 86 protein-coding genes, 37 transfer RNAs, eight ribosomal RNAs, and two pseudogenes. Six tandem, 42 dispersed, and 38 simple sequence repeats were identified. Sequence divergence analysis across 21 Boraginaceae species revealed that the most divergent regions, potentially serving as specific DNA barcodes, were found in non-coding spacers. A comparative analysis of the IR/SC boundary regions of the 21 Boraginaceae species revealed IR expansion events in S. officinale. Phylogenetic analysis based on 63 protein-coding genes demonstrated that S. officinale was closely related to Nonea vesicaria. This represents the first cp genome sequenced in Symphytum, and our results provide valuable genetic information for future population and phylogenetic studies of Boraginaceae.},
}

@article {pmid40612707,
year = {2025},
author = {Barratt, JLN and Jacobson, D and Pierre-Louis, E and Bajic, M and Kelley, J and Patel, DS and Goldman, I and Zhou, Z and Shi, YP and Ridpath, A and Mace, K and Carlson, C and Sutcliffe, A and Butler, Q and Morrison, A and Stanek, D and Tomson, K and Blackmore, C and Cannons, A and Rollo, S and Wang, C and Tuladhar, R and Clemons, B and Madison-Antenucci, S and Mergen, K and White, J and Antwi, M and Rothfeldt, L and Lazenby, K and Hedges, S and Shray, JN and Courtney, A and Boyanton, B and Qvarnstrom, Y and Freeman, M and Raphael, BH},
title = {Genetic characterization of Plasmodium vivax linked to autochthonous malaria transmission in the US (2023) using Illumina AmpliSeq technology: a genetic epidemiology study.},
journal = {Lancet regional health. Americas},
volume = {48},
number = {},
pages = {101159},
pmid = {40612707},
issn = {2667-193X},
abstract = {BACKGROUND: Malaria is a mosquito borne disease caused by parasites of the genus Plasmodium. In 2023, the United States (US) experienced nine cases of autochthonous Plasmodium vivax malaria transmission; seven in Florida, one in Texas, and another in Arkansas. These were the first autochthonous cases since 2003 when a cluster was identified in Florida. The aim of this study was to genetically characterize the implicated P. vivax isolates in order to complement epidemiologic investigations of these cases.

METHODS: A custom Illumina AmpliSeq sequencing panel capturing 495 amplicons was designed. This panel was used to ascertain whether these 2023 cases were related, and assess if they were associated with a single or separate introduction events. Sequence data were hierarchically clustered and a Naïve Bayes classification approach was used to assign genotypes to a probable geographic origin based on 113 'geo-informative' SNPs captured by the panel. Genotypes associated with the 2023 Arkansas, Texas, and Florida cases were clustered alongside those sequenced from archived blood samples from the 2003 Florida case-patients, a set of reference strains, and other travel-associated specimens. Microsatellite analysis was performed on a subset of samples from these autochthonous cases to complement the AmpliSeq analysis.

FINDINGS: The 2023 autochthonous Florida cases were genetically linked as were the 2003 Florida cases. The 2023 and 2003 Florida clusters were genetically distinct, and the two Florida clusters were distinct from the 2023 Texas and Arkansas cases, which were also distinct from each other. These genotypes classified to the Central or South American region using the Naïve Bayes classifier, including those from the 2003 cluster.

INTERPRETATION: These data support that at least three distinct P. vivax introduction events in the US in 2023, involving parasites possessing genetic signatures consistent with Central or South America.

FUNDING: This work was supported by the National Center for Emerging and Zoonotic Infectious Diseases at the US Centers for Disease Control and Prevention.},
}

@article {pmid40608992,
year = {2025},
author = {Fedosov, A and Bouchet, P and Dekkers, A and Gori, S and Huang, SI and Kantor, Y and Lemarcis, T and Marrow, M and Ratti, C and Rosenberg, G and Salisbury, R and Zvonareva, S and Puillandre, N},
title = {The phylogeny and systematics of the Costellariidae (Caenogastropoda: Turbinelloidea) revisited.},
journal = {Invertebrate systematics},
volume = {39},
number = {},
pages = {},
doi = {10.1071/IS24101},
pmid = {40608992},
issn = {1447-2600},
mesh = {Animals ; *Phylogeny ; *Gastropoda/classification/genetics/anatomy & histology ; DNA Barcoding, Taxonomic ; },
abstract = {The marine neogastropod family Costellariidae constitutes a large radiation encompassing 647 living species, widely distributed in tropical seas, with their highest diversity in the Central Indo-Pacific. The systematics of the family has undergone profound changes in the mid-2010s, when relationships within Costellariidae were critically revised based on molecular (multilocus) data from 80 species. Whereas four new genera were described, and two more transferred to Costellariidae from Ptychatractidae, relationships of some key lineages could not be resolved due to the incomplete taxonomic and geographic coverage. In the present study we combine an analysis of an extensive DNA-barcoding dataset with phylogenomics to propose a robust new phylogenetic hypothesis and revise the genus-level systematics of the family. Species delimitation was performed for a Cox1 dataset of 1475 specimens, which revealed 221 secondary species hypotheses (SSHs). The phylogeny was reconstructed from a 1003 loci dataset for 70 species representing all but two of the revealed major costellariid lineages. Maximum likelihood (ML) and Bayesian inference (BI) arrived at nearly identical topologies with full support for all backbone nodes but one, providing a robust framework for a new classification. We treat Turricostellaria as a synonym of Tosapusia. Further, based on a re-evaluation of the identity of the type species of Pusia , we conclude that the name should be applied to a Caribbean lineage, previously treated as a part of Vexillum . Consequently, the Indo-Pacific species of Pusia (Pusia) are here reassigned to a new genus Eupusia , and two other subgenera, Ebenomitra and Vexillena , are raised to full genera. Eight further new genera are described based on phylogenomics: Bathythala , Canaripusia and Caribbonus from the Caribbean in deep water, Pilgrivexillum , Pacifilux , Ponderiola and Cernohorskyola from the Central and southern Indo-Pacific, and Kilburniola from the south-western Indian Ocean. From a total of 25 SSHs corresponding to undescribed species, 23 are described herein in the genera Austromitra (1), Bathythala (1), Canaripusia (1), Caribbonus (3), Costapex (4), Eupusia (1), Kilburniola (1), Pilgrivexillum (1), Pusia (2), Thala (1), Tosapusia (1) and Vexillum (6). ZooBank: urn:lsid:zoobank.org:pub:0791EF1F-7F77-4F02-A447-40798388C7FE.},
}

Animals
*Phylogeny
*Gastropoda/classification/genetics/anatomy & histology
DNA Barcoding, Taxonomic

@article {pmid40605502,
year = {2025},
author = {Kuitunen, S and Laakkonen, L and Janhunen, K and Kvarnström, K and Linden-Lahti, C},
title = {Facilitators and Barriers Associated With the Use of Barcode Technologies in Drug Preparation and Administration in Hospital Settings-A Narrative Review of Qualitative Studies.},
journal = {Journal of patient safety},
volume = {},
number = {},
pages = {},
doi = {10.1097/PTS.0000000000001381},
pmid = {40605502},
issn = {1549-8425},
abstract = {OBJECTIVES: Barcode technologies are commonly used in hospital settings to improve medication safety. However, the implementation of these systems poses several challenges. This narrative review aims to synthesize qualitative studies exploring the facilitators and barriers associated with using barcode technologies in clinical environments.

METHODS: This review is grounded in the theory of systems-based risk management. A comprehensive literature search was conducted in November 2022 across 3 databases: CINAHL; MEDLINE (Ovid); and Scopus. Two independent reviewers utilized a predetermined SPIDER (Sample; Phenomenon of Interest; Design; Evaluation; Research type) tool for article selection by using Covidence software. The qualitative data from the selected studies were systematically summarized.

RESULTS: The search found 197 articles, of which 11 studies from 6 countries met the inclusion criteria. All included studies identified barriers, while 7 studies also highlighted facilitators. Seven common themes emerged as facilitators and barriers: efficacy; implementation; leadership; medication safety; process; technology; and user experience. Three themes-materials; system design; and work environment-were exclusively associated with barriers. Workarounds, such as bypassing barcoding, omitting process steps, and unauthorized process steps, were reported in 8 studies as responses to the barriers.

CONCLUSIONS: This review underscores the complexity of implementing and maintaining high-leverage, technology-based systemic defenses in clinical practice. The findings provide a foundation for the improvement of the safety and usability of barcode technologies in hospital settings. Future research should focus on developing and testing interventions that address the identified barriers and enhance the facilitators to optimize the use of barcode systems.},
}

@article {pmid40605267,
year = {2025},
author = {Calegari, BB and Freyhof, J and Waldock, C and Wegscheider, B and Josi, D and Rüber, L and Seehausen, O},
title = {Two new species of stone loaches of the genus Barbatula (Cypriniformes: Nemacheilidae) from Europe with a neotype designation of B. barbatula (Teleostei: Nemacheilidae).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70108},
pmid = {40605267},
issn = {1095-8649},
support = {//Kanton Bern/ ; //Wyss Academy for Nature/ ; //Swiss Federal Office of the Environmental/ ; },
abstract = {Ten species of Barbatula are recognised in Europe, west of the Urals: B. barbatula, B. caucasica, B. hispanica, B. leoparda, B. pironae, B. quignardi, B. sturanyi, B. taurica, B. vardarensis and B. zetensis, with B. caucasica and B. taurica formerly considered subspecies of B. barbatula. A comprehensive dataset of the DNA barcoding gene coI recovered four major clades within Europe: three in Eastern Europe including B. caucasica, B. pironae, B. sturanyi, B. taurica, B. vardarensis and B. zetensis, and one in Western Europe including B. barbatula, B. hispanica and B. leoparda. The results further indicated several genetic lineages, representing potentially new species. Recent surveys in Switzerland revealed two new species of Barbatula, within the Western clade, which are herein described. Barbatula fluvicola, a new species, inhabits streams and rivers in the upper and middle Rhine drainage in Switzerland and Germany, as well as the upper Danube drainage in Germany and Austria. Barbatula ommata, a new species, is mostly confined to lakes of the Aare-Rhine system. The two new species overlap geographically in Switzerland, where they occupy different habitats. Morphological differences, species delimitation analyses, phylogenetic reconstruction and genetic distances based on the coI gene corroborates the recognition of the two new species. To stabilise the nomenclatural status and the consequent use of the nomen B. barbatula, we are herein designating an unambiguously identifiable neotype from the Lez River population, previously recognised as B. quignardi, to clarify the identity of the nominal species Cobitis barbatula Linnaeus, 1758.},
}

@article {pmid40601148,
year = {2025},
author = {Martínez-Moreno, JM and Llamas-Urbano, A and Barbarroja, N and Pérez-Sánchez, C},
title = {Proteomics by qPCR Using the Proximity Extension Assay (PEA).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2929},
number = {},
pages = {129-142},
pmid = {40601148},
issn = {1940-6029},
mesh = {*Proteomics/methods ; Humans ; *Real-Time Polymerase Chain Reaction/methods ; Software ; Immunoassay/methods ; },
abstract = {The Proximity Extension Assay (PEA) is an innovative technology developed by Olink Proteomics that has revolutionized proteomics research. This method enables the simultaneous detection of hundreds of proteins using a minimal sample volume (1 microliter), combining the specificity of antibody-based immunoassays with the sensitivity of quantitative PCR (qPCR). The PEA process relies on the binding of two antibodies, each conjugated with unique DNA sequences, to a target protein. Upon proximity, these DNA sequences hybridize, forming a molecular barcode that is subsequently amplified by PCR, ensuring high specificity and minimizing cross-reactivity-an issue commonly encountered in multiplexed immunoassays. This chapter provides a detailed overview of the technical and methodological aspects of PEA, including the incubation, extension, amplification, and detection steps, as well as the quality control measures implemented in the Olink[®] NPX Signature software for data analysis. This technology has been applied in more than 2000 peer-reviewed studies, demonstrating its potential for biomarker discovery in diagnostics, prognostics, and personalized medicine across various diseases. The integration of PEA into biomedical research continues to enhance the precision and reproducibility of proteomics studies.},
}

*Proteomics/methods
Humans
*Real-Time Polymerase Chain Reaction/methods
Software
Immunoassay/methods

@article {pmid40597261,
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 = {Malaria journal},
volume = {24},
number = {1},
pages = {203},
pmid = {40597261},
issn = {1475-2875},
support = {T32AI138953/NH/NIH HHS/United States ; T32AI138953/NH/NIH HHS/United States ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; U19AI089680//The National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; },
mesh = {Animals ; *Anopheles/classification/genetics ; *Phylogeny ; *Genome, Mitochondrial ; Zambia ; *Mosquito Vectors/classification/genetics ; },
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 similarity of 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. The goal of this study was to characterize the phylogenetic taxonomy of Zambian members of the An. coustani group by generating and then using complete mitochondrial genomes for phylogenetic rectification.

METHODS: A genome skimming approach was utilized 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 for members of the An. coustani group based 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 Anopheles 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 sensu stricto, Anopheles paludis, Anopheles zeimanni and Anopheles tenebrosus. Divergence estimates within the An. coustani group are similar when compared to species with morphologically distinct features. These analyses also highlight the likely presence of other cryptic An. coustani group members circulating in Zambia.},
}

Animals
*Anopheles/classification/genetics
*Phylogeny
*Genome, Mitochondrial
Zambia
*Mosquito Vectors/classification/genetics

@article {pmid40596413,
year = {2025},
author = {Wilcken, CF and da Mota, TA and de Oliveira, CH and de Carvalho, VR and Benso, LA and Gabia, JA and Wilcken, SRS and Furtado, EL and Schiff, NM and de Camargo, MB and Ribeiro, MF},
title = {Sirex obesus (Hymenoptera: Siricidae) as invasive pest in pine plantations in Brazil.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22522},
pmid = {40596413},
issn = {2045-2322},
mesh = {Animals ; Brazil ; *Pinus/parasitology ; *Hymenoptera/genetics/classification/physiology ; *Introduced Species ; Female ; DNA Barcoding, Taxonomic ; Male ; },
abstract = {The genus Sirex (Hymenoptera: Siricidae) consists of 29 species including the Sirex Woodwasp, Sirex noctilio, which is the main insect pest of pine plantations in the Southern Hemisphere including Brazil. In 2023, a species of Sirex similar to S. noctilio was discovered in Southeastern Brazil infesting pine plantations and causing tree mortality of up to 40%. We definitively identified this species as Sirex obesus based on both morphological characters and DNA barcodes. It is a species indigenous to the Southwestern United States and Northern and Central Mexico with little information available regarding its biology and control. This is the first record of S. obesus in Brazil and the first record of the species outside of North America. We document details about S. obesus occurrence in Brazil, describe preliminary damage caused in pine plantations and provide a partial list of natural enemies.},
}

Animals
Brazil
*Pinus/parasitology
*Hymenoptera/genetics/classification/physiology
*Introduced Species
Female
DNA Barcoding, Taxonomic
Male

@article {pmid40595485,
year = {2025},
author = {Li, J and Crown, A and Ney, P and Yekhanin, S and Partap, A and Shirole, A and Jiang, H and Russ, S and Gordon, M and Aroh, A and Nivala, J and Badam, A and Ranganathan, V and Strauss, K and Chandra, R and Chen, YJ},
title = {Hybridization-encoded DNA tags with paper-based readout for anti-forgery raw material tracking.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5832},
pmid = {40595485},
issn = {2041-1723},
mesh = {*DNA/genetics/chemistry ; *Paper ; *Nucleic Acid Hybridization/methods ; Cell Phone ; *Product Labeling/methods ; Radio Frequency Identification Device/methods ; },
abstract = {Tracking and tracing raw materials is crucial for securing global supply chains. Conventional methods like barcodes and Radio Frequency Identification (RFID) tags are effective but fall short in ensuring raw material traceability and anti-counterfeiting. This work introduces DNA as a powerful tool for source tracking, leveraging its invisibility, safety, and seamless product integration. We present DNATags-engineered DNA mixtures enabling product labeling with error tolerance-readable in the field via paper tickets that fluoresce under a mobile phone and filter device. Additionally, DNATrack employs DNA Hybridization Encoding (HyEn) for enhanced anti-forgery security. Although current costs are higher ($2-$4 per read and write), declining DNA synthesis costs, along with DNA's unique advantages, make this approach a promising solution for future supply chain management.},
}

*DNA/genetics/chemistry
*Paper
*Nucleic Acid Hybridization/methods
Cell Phone
*Product Labeling/methods
Radio Frequency Identification Device/methods

@article {pmid40595213,
year = {2025},
author = {Cannet, A and Chane, CS and Histace, A and Akhoundi, M and Romain, O and Jacob, P and Sereno, D and Souchaud, M and Bousses, P and Sereno, D},
title = {Application of wings interferential patterns (WIPs) and deep learning (DL) to classify some Culex. spp (Culicidae) of medical or veterinary importance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21548},
pmid = {40595213},
issn = {2045-2322},
mesh = {Animals ; *Deep Learning ; *Wings, Animal/anatomy & histology ; *Culex/classification/anatomy & histology ; Neural Networks, Computer ; },
abstract = {In this paper, we test the possibility of using Wing Interference Patterns (WIPs) and deep learning (DL) for the identification of Culex mosquitoes species to evaluate the extent to which a generic method could be developed for surveying Dipteran insects of major importance to human health. Previous applications of WIPs and DL have successfully demonstrated their utility in identifying Anopheles, Aedes, sandflies, and tsetse flies, providing the rationale for extending this approach to Culex. Accurate identification of these mosquitoes is crucial for vector-borne disease control, yet traditional methods remain labor-intensive and are often hindered by cryptic species or damaged samples. To address these challenges, we applied WIPs, generated by thin-film interference on wing membranes, in combination with convolutional neural networks (CNNs) for species classification. Our results achieved over [Formula: see text] genus-level accuracy and up to [Formula: see text] species-level accuracy. Nonetheless, challenges with underrepresented species emphasize the need for larger datasets and complementary techniques such as molecular barcoding. This study highlights the potential of WIPs and DL to enhance mosquito identification and contribute to scalable tools for broader surveys of health-relevant Dipteran insects.},
}

Animals
*Deep Learning
*Wings, Animal/anatomy & histology
*Culex/classification/anatomy & histology
Neural Networks, Computer

@article {pmid40595196,
year = {2025},
author = {Sraphet, S and Javadi, B},
title = {Exploring genetic diversity and genomic insights of Bacillus subtilis isolates from cassava rhizosphere using molecular barcoding and whole genome sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22708},
pmid = {40595196},
issn = {2045-2322},
support = {งป11773/2566//Suan Sunandha Rajabhat University/ ; },
mesh = {*Bacillus subtilis/genetics/isolation & purification/classification ; *Manihot/microbiology ; *Rhizosphere ; *DNA Barcoding, Taxonomic/methods ; *Genetic Variation ; Phylogeny ; *Genome, Bacterial ; Whole Genome Sequencing/methods ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Genomics/methods ; },
abstract = {Bacillus subtilis plays a significant role in both agriculture and industry. It is commonly isolated from agricultural environments, particularly various soil types. This study aimed to investigate DNA barcoding and whole-genome sequencing of B. subtilis strains, focusing on those specific to the cassava rhizosphere. Genetic identification and diversity of B. subtilis strains isolated from the rhizosphere of the Piroon 2 cassava cultivar were initially characterized using 16 S rDNA, a molecular marker for species-level identification. To explore strain-specific biodiversity within B. subtilis, repetitive DNA elements-specifically extragenic palindromic and BOX sequences-were analyzed across the genomes of the isolated strains. These repetitive sequences revealed two main structural patterns, providing clear and distinct genomic fingerprints for biodiversity analysis. The results showed that both REP and BOX sequences were highly conserved within specific regions of the B. subtilis genome, resulting in reliable and reproducible DNA patterns suitable for whole-genome phylogenetic analysis. While the 16 S rDNA approach showed a high sequence similarity among the B. subtilis strains (99.98%), whole-genome analysis using repetitive sequences allowed for clearer differentiation, with phylogenetic distances exceeding 97%. Whole-genome sequencing of the elite strain BsPr8 was performed using the Illumina MiSeq platform. The sequencing results yielded 56 contigs, with an average GC content of 43.67% and a total genome size of approximately 4,050 Kbp. Genome annotation identified 3,575 proteins with functional assignments, including 1,055 enzymes classified by Enzyme Commission numbers. The PATRIC database further annotated 3,937 genus-specific protein families. Additionally, 45 genes homologous to known antibiotic resistance genes were identified within the BsPr8 genome. These findings have important implications for sustainable agricultural practices and cassava cultivation. By elucidating the genetic diversity and genomic characteristics of B. subtilis strains, this study facilitates the identification of beneficial traits-such as plant growth promotion, pathogen suppression, and improved nutrient uptake. These strains hold potential for development as biofertilizers or biopesticides, offering an environmentally friendly alternative to conventional chemical inputs.},
}

*Bacillus subtilis/genetics/isolation & purification/classification
*Manihot/microbiology
*Rhizosphere
*DNA Barcoding, Taxonomic/methods
*Genetic Variation
Phylogeny
*Genome, Bacterial
Whole Genome Sequencing/methods
Soil Microbiology
RNA, Ribosomal, 16S/genetics
Genomics/methods

@article {pmid40594022,
year = {2025},
author = {Liu, Y and Xie, Y and Wang, Y and Zong, Y and Liu, Y and Li, C and Dong, J},
title = {The development and application of mini-barcodes from mitochondrial DNA for identifying medicinal leeches from traditional medicines.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20444},
pmid = {40594022},
issn = {2045-2322},
support = {31801957//National Natural Science Foundation of China/ ; 32100334//National Natural Science Foundation of China/ ; BK20181471//Natural Science Foundation of Jiangsu Province, China/ ; BK20210897//Natural Science Foundation of Jiangsu Province, China/ ; D2020009//Scientific Research Foundation for the Talents by Xuzhou Medical University/ ; },
mesh = {Animals ; *Leeches/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Mitochondrial/genetics ; Phylogeny ; Medicine, Chinese Traditional ; },
abstract = {Species-specific efficacy necessitates accurate identification of medicinal leeches, but standard DNA barcoding often fails with degraded DNA from traditional medicines. This deficiency highlights the need for mini-barcoding. This study aimed to develop and validate mini-barcode markers for three Chinese Pharmacopoeia-listed leech species: Whitmania pigra, Whitmania acranulata and Hirudo nipponia. Four novel mini-barcode primer sets (ND1F1/R1, 12SF1/R1, 16SF1/R1 and COX1F1/R1) were developed and validated using seven morphologically identified specimens and subsequently tested on 16 commercial leech products. DNA extractions were performed using both single-tube and column purification kits, with the latter yielding superior DNA quality and meeting the requirements for following PCR amplification. The PCR results confirmed the validation of four candidate mini-barcodes targeting specific genetic regions, which produced results in 13 out of 16 commercial leech products. Mini-barcode sequences from morphologically identified W. pigra specimens exhibit > 95% identity to the complete ND1, 12S rDNA, 16S rDNA, and COX1 sequences (EU304459), whereas sequences from H. nipponia and W. acranulata show < 85% identity, and among leech-derived products only the proprietary Chinese medicine Maxuekang exhibits lower identity. Both the optimal partition of ASAP and phylogenetic tree identified three distinct groups correlating with the morphological species: W. pigra, W. acranulata, and H. nipponia. Mislabeled species have been uncovered in proprietary Chinese medicine, notably the claimed Hirudo nipponia, which was replaced by W. pigra. The results highlight the value of mini-barcodes in enhancing product quality control and offer a reliable method for accurate species identification in traditional and commercial leech-based medicines. This advance supports safer and more effective utilization of medicinal leeches and advocates for their integration into regulatory standards.},
}

Animals
*Leeches/genetics/classification
*DNA Barcoding, Taxonomic/methods
*DNA, Mitochondrial/genetics
Phylogeny
Medicine, Chinese Traditional

@article {pmid40593543,
year = {2025},
author = {Yang, L and Liu, F and Hahm, H and Okuda, T and Li, X and Zhang, Y and Kalyanaraman, V and Heitmeier, MR and Samineni, VK},
title = {Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5557},
pmid = {40593543},
issn = {2041-1723},
support = {R01DK128475//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01DK140445//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01DK139386//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01DA056829//U.S. Department of Health & Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; },
mesh = {Animals ; *Neurons/metabolism/cytology ; Female ; Mice ; Single-Cell Analysis/methods ; Dependovirus/genetics ; Mice, Inbred C57BL ; Brain/metabolism/cytology ; Epigenesis, Genetic ; },
abstract = {Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons in female mice. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.},
}

Animals
*Neurons/metabolism/cytology
Female
Mice
Single-Cell Analysis/methods
Dependovirus/genetics
Mice, Inbred C57BL
Brain/metabolism/cytology
Epigenesis, Genetic

@article {pmid40593007,
year = {2025},
author = {Liang, Z and Chen, X and Xie, Y and He, F and Zhang, L and Zhu, X and Lu, T},
title = {An integrated widely targeted metabolomics and network pharmacology study of Persicaria runcinata var. Sinensis against arthritis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20499},
pmid = {40593007},
issn = {2045-2322},
support = {QKHJC-ZK[2021]-YB156//Guizhou Province Science and Technology Department Support Plan/ ; 24141900201//Project of Shanghai Science and Technology Commission/ ; gzwkj 2021-245//Science and Technology Foundation of Health Commission of Guizhou Province/ ; },
mesh = {*Metabolomics/methods ; *Network Pharmacology/methods ; Animals ; Phylogeny ; *Arthritis/drug therapy/metabolism ; *Plant Extracts/pharmacology/chemistry ; Tandem Mass Spectrometry ; DNA Barcoding, Taxonomic ; Chromatography, High Pressure Liquid ; },
abstract = {The present study aimed to investigate the material basis of Persicaria runcinata var. sinensis (Hemsl.) Bo Li using widely targeted metabolomics and network pharmacology techniques. Efforts were also made to establish a DNA barcode for P. runcinata var. sinensis. Widely targeted metabolomics technique of Ultra performance liquid chromatography-mass spectrometry(UPLC-MS/MS) was employed to detect and analyze the metabolites in P. runcinata var. sinensis. Network pharmacology was used to screen and analyze metabolites with high content and pharmacological effects. DNA extraction, Polymerase chain reaction(PCR) amplification, sequence alignment, and phylogenetic tree construction were performed to establish the DNA barcode. A total of 716 metabolites were detected in Miao ethnomedicine P. runcinata var. sinensis, with key targets, enriched functions, and pathways identified using network pharmacology. The DNA sequence for the ITS2 primer of P. runcinata var. sinensis was determined and a phylogenetic tree was generated. Metabolite enrichment in P. runcinata var. sinensis revealed potential therapeutic compounds for arthritis. The study's approach provided theoretical support for understanding the substance basis and therapeutic effects of P. runcinata var. sinensis. Additionally, the high homology level with various Polygonum species provided the foundation for molecular identification in ethnomedicine.},
}

*Metabolomics/methods
*Network Pharmacology/methods
Animals
Phylogeny
*Arthritis/drug therapy/metabolism
*Plant Extracts/pharmacology/chemistry
Tandem Mass Spectrometry
DNA Barcoding, Taxonomic
Chromatography, High Pressure Liquid

@article {pmid40590343,
year = {2025},
author = {Gao, Y and Liu, J and Huang, S and Du, N and Zhang, G and Li, Y},
title = {Recent advances in DNA-encoded libraries.},
journal = {Chemical communications (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5cc02904j},
pmid = {40590343},
issn = {1364-548X},
abstract = {The DNA-encoded library (DEL), a novel high-throughput screening platform that synergistically combines the strengths of combinatorial chemistry and genetic barcoding, has transitioned from a theoretical framework to a valuable technology within the pharmaceutical research landscape. As an emerging platform for drug discovery, DEL technology has undergone rapid evolution over the past thirty years. This review aims to highlight remarkable advancements in DELs over the past five years across multiple dimensions, including encoding methods, DEL-compatible chemistry, selection methods, library design, and hit picking. It also delves into the issues that have been successfully addressed and the breakthroughs achieved. Finally, this review proposes practical strategies and outlines future research directions that have the potential to further propel the development of DELs in the upcoming five years, aiming to provide valuable insights for drug discovery endeavors.},
}

@article {pmid40590201,
year = {2025},
author = {Liu, Y and Shen, F and Wang, L and Dou, J and Dong, T and Li, M and Wang, Q and Dong, S and Zhang, G and Zhao, J and Li, L and Shi, S},
title = {Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70004},
doi = {10.1111/1755-0998.70004},
pmid = {40590201},
issn = {1755-0998},
support = {C2019205175//Natural Science Foundation of Hebei Province/ ; C2022402017//Natural Science Foundation of Hebei Province/ ; S23B053//Humanities and Social Science Research Fund of Hebei Normal University/ ; 221490222A//Shijiazhuang Science and Technology Bureau/ ; },
abstract = {Mosses represent the most species-diverse clade of bryophytes and are among the earliest land plants. These diminutive organisms hold substantial ecological importance and have significant applications in horticulture and medicine. However, their study, development and utilisation are impeded by the complex identification process and scarcity of researchers specialising in moss taxonomy. The advancement of DNA barcoding technology presents an opportunity for precise moss identification. Present molecular markers primarily originate from angiosperm research and may not be optimal for moss species. This study aims to identify suitable DNA barcodes for mosses at the chloroplast genome level. Utilising 61 complete chloroplast genome datasets of mosses, including 14 orders, 23 families and 60 species, this research presented the first construction of a reliable phylogenetic tree at the family level of mosses using whole chloroplast genomes, enabling accurate identification of most samples. Based on nucleotide polymorphism in the complete chloroplast genome, 12 highly variable regions were selected as candidate DNA barcodes for mosses. Experimental validation of the newly designed primers demonstrated high universality (> 90%). The resolution verification experiment, employing DNA barcodes from 103 samples representing 21 families and 48 genera, confirmed the efficacy of atpB-rbcL, psaI-accD, ycf2, ycf1, matK, rpoB-trnC and clpP as reliable DNA barcodes for mosses. The study also revealed inconsistencies in the chloroplast genome structures of mosses submitted to public databases, which hinder subsequent research. Consequently, we recommend that researchers upload data with a designated reference genome in future submissions.},
}

@article {pmid40587582,
year = {2025},
author = {Langsiri, N and Banlunara, W and Klaychontee, O and Worasilchai, N and Cognialli, R and de Queiroz-Telles, F and Spruijtenburg, B and de Groot, T and Meijer, EFJ and Chindamporn, A},
title = {Targeted long-read sequencing analysis and antifungal susceptibility profiles of Sporothrix schenckii isolates from Thailand.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {6},
pages = {e0013253},
doi = {10.1371/journal.pntd.0013253},
pmid = {40587582},
issn = {1935-2735},
abstract = {Sporothrix spp. are dimorphic fungi capable of undergoing morphological changes in response to temperature variations. The genus Sporothrix includes the species S. schenckii sensu stricto, S. brasiliensis, S. globosa, and S. luriei that cause sporotrichosis, which can range from local skin infections to systemic infections in immunocompromised individuals. As these species are morphologically similar, molecular techniques that utilize barcoding genes are required for accurate identification. While the Internal Transcribed Spacer (ITS) region is the universal fungal barcode, the calmodulin gene offers higher resolution for phylogenetic classification of Sporothrix using Sanger sequencing. This study evaluated the ability of long-read nanopore sequencing of calmodulin and ITS to identify species level and allow phylogenetic analysis of Sporothrix strains isolated from humans and felines in Thailand. We found that the calmodulin sequencing with Oxford Nanopore Technology (ONT) consistently classified all isolates as S. schenckii sensu stricto, whereas the ITS region showed a lower discriminatory power, complicating species identification in some isolates. The phylogenetic analysis of the calmodulin region indicated that all isolates localized in a specific S. schenckii sensu stricto subclade together with other isolates from Southeast Asia, while the three residual S. schenckii subclades were associated with other geographical locations. Antifungal susceptibility testing on all Sporothrix strains demonstrated elevated in vitro minimum inhibitory concentrations (MICs) to itraconazole for 8 out of 26 isolates. Altogether, this study demonstrated that ONT sequencing of calmodulin allows accurate species identification and phylogenetic analysis of S. schenckii sensu stricto isolates from Thailand, of which some also demonstrated elevated MIC values for itraconazole.},
}

@article {pmid40587561,
year = {2025},
author = {Hwang, K and Veith, A and Duro, L and Wood, D and Chatterjee, G and Cajigas, Y and Lee, JH and Vasaturo, A},
title = {High-Throughput Automated Multiplex Immunofluorescence Assays for Translational Research.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/67584},
pmid = {40587561},
issn = {1940-087X},
mesh = {Humans ; *Fluorescent Antibody Technique/methods ; *Translational Research, Biomedical/methods ; *High-Throughput Screening Assays/methods ; },
abstract = {Multiplex immunofluorescence (mIF) is an advanced technique that allows for detailed, spatially resolved analysis of tissue samples by visualizing multiple protein biomarkers within a single section. However, most mIF technologies face significant tradeoffs between sensitivity and throughput when multiplexing, posing a critical limitation for robustly detecting low-abundance biomarkers across multiple tissue sections. A new approach for mIF uses unique DNA barcodes linked to antibodies, which are amplified through a parallel single-molecule amplification mechanism. This method achieves staining quality highly comparable to clinical-grade immunohistochemistry (IHC) while providing high multiplexing capabilities and high-throughput whole-slide imaging. This assay involves amplifying a cocktail of DNA-barcoded antibodies on the tissue, followed by sequential rounds of detection steps to visualize four fluorescent-labeled oligonucleotides per cycle. This process thus enables the detection of eight or more biomarkers per tissue sample. Key steps in this method include automated tissue preparation, application of primary antibodies conjugated with DNA barcodes, signal amplification, and iterative cycles of detection, imaging, and signal removal. Image acquisition is followed by image registration and single-cell analysis using an AI-enhanced spatial image data science platform. For this study, the protocol was applied to formalin-fixed, paraffin-embedded (FFPE) multi-tissue micro-arrays (TMAs), including tonsil, melanoma, colon, and lymph node cores in triplicate. Advanced mIF technologies provide more insights into the tumor response, the tumor microenvironment, and the immune landscape. By overcoming the inherent tradeoffs between sensitivity, multiplexing capabilities, and imaging throughput, researchers can now aim to understand the heterogeneity of challenging molecular signatures and biomarkers of therapeutic responses.},
}

Humans
*Fluorescent Antibody Technique/methods
*Translational Research, Biomedical/methods
*High-Throughput Screening Assays/methods

@article {pmid40587398,
year = {2025},
author = {Loudig, O and Ben-Dov, IZ and Shapiro, B and Mitchell, MI and Lachica, M and Topilow, A and Liu, C and Ronan, M},
title = {Ultrasensitive cDNA Library Preparation for Next-generation Sequencing of MicroRNAs from Small Extracellular Vesicles.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/67154},
pmid = {40587398},
issn = {1940-087X},
mesh = {*MicroRNAs/genetics/analysis ; *Gene Library ; *Extracellular Vesicles/genetics/chemistry ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; },
abstract = {Recent studies demonstrate that small extracellular vesicles (sEVs), which are found in all biofluids, play critical roles in intercellular communication by channeling proteins, DNA, and RNAs. MicroRNAs (miRNAs) that are packaged in sEVs have emerged as critical deliverable regulators in recipient cells. Since sEVs secreted by normal and diseased cells carry different miRNA cargos, recent sEV-miRNA profiling studies suggest that they may help identify novel circulating biomarkers. However, cell/disease-specific sEVs circulating in diverse biofluids, once isolated, provide low miRNA quantities, which are generally difficult to quantify using conventional spectrometric methodologies. Small non-coding RNA Next Generation Sequencing (NGS), which allows for the amplification of cloned miRNA sequences, offers a valuable opportunity to evaluate the miRNA cargos of sEVs. Unfortunately, commercial cDNA library preparation procedures often require RNA inputs well above the unquantifiable amounts available from isolated sEVs. Thus, considering the robustness and multiplexing capabilities of our existing cDNA library preparation procedure (i.e., initially optimized for the analysis of low-input, highly degraded, formalin-fixed paraffin-embedded (FFPE) RNA), we sought to evaluate its applicability for the analysis of sEV miRNAs. Importantly, taking into account the recent technical clustering improvements of sequencing chips, we sought to adapt our transcript barcoding approach within a paired-end, dual index-compatible cDNA library preparation workflow to enhance our sequencing and multiplexing capabilities. Using RNA extracted from 8.4 × 10[9] sEVs in 16 replicates, and from decreasing amounts of sEVs from 10[10] sEVs to as low as 2.5 × 10[7] sEVs, we evaluated the reproducibility and sensitivity of this methodology. The data demonstrate that the 16 3' adenylated DNA barcodes allow for highly reproducible and sensitive detection of sEV-miRNA profiles across repeats using as low as 3.15 pg of total small non-coding RNAs or 1.35 pg of miRNAs.},
}

*MicroRNAs/genetics/analysis
*Gene Library
*Extracellular Vesicles/genetics/chemistry
*High-Throughput Nucleotide Sequencing/methods
Humans

@article {pmid40584258,
year = {2025},
author = {Mortlock, M and Geldenhuys, M and Keith, M and Rademan, R and Swanepoel, LH and Von Maltitz, EF and Kearney, T and Markotter, W},
title = {Paramyxo- and coronavirus diversity and host associations in non-volant small mammals: evidence of viral sharing.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf041},
pmid = {40584258},
issn = {2057-1577},
abstract = {Rodents and other non-volant small mammals (like shrews) maintain major ecological and epidemiological roles as reservoirs of zoonotic pathogens. Their presence within human-modified landscapes and interfaces with people, wildlife, and livestock create frequent opportunities for viral spillover. Despite this, the pathogen diversity and true risk of viral transmission are poorly understood by these hosts in Africa. Here, we explored the diversity and host association of paramyxoviruses and coronaviruses in non-volant small mammals from South Africa through longitudinal and opportunistic sample collection and molecular detection of viral RNA and host genetic barcoding. A high diversity of viruses was identified, with prevalences of 11.9% and 1.79% for paramyxoviruses and coronaviruses, respectively. Five instances of coinfections involving multiple paramyxoviruses and a coronavirus were detected, as well as nine Bayesian-supported paramyxovirus host genus, subfamily, and family switching, signifying frequent unrestrained viral sharing. Though the zoonotic potential of these identified viruses is unknown, the frequency of host switching suggests that these viruses may be more prone to adaptation to new host species or utilize highly conserved entry mechanisms. This highlights the risks for potential cross-species transmission events to livestock, domestic animals, and people, warranting continued surveillance.},
}

@article {pmid30889932,
year = {2019},
author = {Morello, L and Braglia, L and Gavazzi, F and Gianì, S and Breviario, D},
title = {Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices.},
journal = {Genes},
volume = {10},
number = {3},
pages = {},
pmid = {30889932},
issn = {2073-4425},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Food/*classification/standards ; Food Industry ; Plant Proteins/genetics ; Plants/classification/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tubulin/*genetics ; },
abstract = {The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.},
}

Animals
DNA Barcoding, Taxonomic/*methods
Food/*classification/standards
Food Industry
Plant Proteins/genetics
Plants/classification/genetics
Polymorphism, Genetic
Sequence Analysis, DNA
Tubulin/*genetics

@article {pmid40584119,
year = {2025},
author = {Marín-Villa, J and López-Herrera, A and Gómez-Ruiz, DA and Restrepo-Rodas, DC and Sánchez-Rodríguez, G and Úsuga-Monroy, C},
title = {Mitochondrial markers (cytochrome c oxidase subunit I and 16S ribosomal RNA) as supporting biomarkers for wild bird identification.},
journal = {Veterinary world},
volume = {18},
number = {5},
pages = {1389-1399},
pmid = {40584119},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Illegal wildlife trafficking is a critical threat to biodiversity, particularly in megadiverse countries such as Colombia. Birds, notably psittacines, are among the most targeted taxa. Morphological identification is often insufficient, especially when dealing with cryptic species or degraded samples. This study aimed to assess the utility of mitochondrial markers cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) as molecular tools for species-level identification of psittacines housed at the Conservation Park of Medellín.

MATERIALS AND METHODS: Six adult psittacines from the genera Ara and Pionus were selected based on availability. Blood samples were collected and genomic DNA was extracted using a commercial kit. Polymerase chain reaction amplification of partial COI and 16S rRNA gene fragments was performed, followed by Sanger sequencing. Sequence identity was confirmed using BLASTn and the Barcode of Life Data System (BOLD). Phylogenetic relationships were analyzed using Neighbor-Joining, Maximum Likelihood, and Bayesian Inference approaches.

RESULTS: Molecular results showed 100% concordance with prior morphological identification for all six individuals. COI and 16S rRNA sequences allowed clear species-level identification with similarity values >98%. Phylogenetic analyses for both markers yielded congruent tree topologies, with high branch support (>90%), further validating species identification. Maximum interspecific divergence for COI was observed between Ara macao and Pionus fuscus (0.15980), while 16S rRNA showed lower divergence values. All generated sequences were submitted to GenBank and BOLD in accordance with findable, accessible, interoperable, reusable principles.

CONCLUSION: This study confirms the robustness of COI and 16S rRNA mitochondrial markers in accurately identifying psittacine species. The integration of molecular and morphological approaches enhances forensic investigations, facilitates biodiversity conservation, and contributes to efforts against wildlife trafficking. Expanding genetic databases for Neotropical avifauna, especially for commonly trafficked species, is imperative. Future research should adopt integrative genomic approaches involving nuclear markers to overcome the maternal inheritance limitation of mitochondrial DNA.},
}

@article {pmid40583309,
year = {2025},
author = {Li, J and Zhai, R and Xiao, H and Chen, Y and Cheng, W and Yang, X and Wang, K and Yang, Y and Huang, J},
title = {Ultrahigh-Capacity Vertical Encoded Micro-Spherical Nucleic Acids for Multiplexed Detection.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c02444},
pmid = {40583309},
issn = {1520-6882},
abstract = {Here, we report a DNA-programmable microsphere encoding platform using spatially organized fluorophores on magnetic cores with elongated DNA scaffolds. By engineering vertically stratified DNA scaffolds on paramagnetic microspheres, we achieved orthogonal spectral separation of 2-3 fluorophores through spatial confinement, generating 96 distinct two-color and 536 three-color barcodes via tunable stoichiometric control. We validated the platform's utility for nucleic acid multiplexing by demonstrating simultaneous detection of multiple targets, establishing a foundation for scalable high-order multiplexing. The system circumvents material compatibility restrictions inherent to conventional approaches, resolves spatial encoding conflicts through programmable DNA nanostructures, and achieves exponential encoding scalability. By synergizing the operational advantages of liquid-phase microsphere assays with the precision of DNA nanotechnology, this work establishes a new paradigm for high-throughput multiplexed diagnostics, offering unprecedented potential for precision medicine and large-scale biomedical analysis.},
}

@article {pmid40582202,
year = {2025},
author = {Huo, X and Xie, Y and Hu, Y and Wang, Z and Sheng, Y and Qi, H and Shao, H and Ma, Q and Yu, W and Dong, X},
title = {Electrospun perovskite quantum dots-based Janus microribbons film with white light and multicolor luminescence for optical data storage and anti-counterfeiting.},
journal = {Journal of colloid and interface science},
volume = {699},
number = {Pt 2},
pages = {138276},
doi = {10.1016/j.jcis.2025.138276},
pmid = {40582202},
issn = {1095-7103},
abstract = {In order to attain white light or multicolor luminescence of perovskite quantum dots (PQDs) materials, the prevalent method involves directly blending PQDs with different type and composition of halogen anions. However, this method allows uncontrolled halogen anion exchange between the different PQDs, thereby leading to alterations in the final fluorescence color of the material. To address this problem, we creatively design and fabricate a PQDs-based Janus microribbons film (Janus-MRF) with white light emission and multicolor fluorescence under multi-wavelength stimulation by a parallel electrospinning. [CsPbCl1.5Br1.5/Eu(BA)3phen/PS]//[CsPbBr3/Eu(BA)3phen/PS] (BA = benzoate radical, phen = 1,10-phenanthroline, PS = polystyrene) Janus microribbon (Janus-MR) serves as fundamental structural unit of Janus-MRF, CsPbCl1.5Br1.5 and CsPbBr3 PQDs respectively provide blue and green fluorescence, and Eu(BA)3phen offers red fluorescence. The introduction of Janus structure in Janus-MR allows the interior of the Janus-MR to form two independent microscopic domains, confining CsPbCl1.5Br1.5 PQDs and CsPbBr3 PQDs to their respective domains and avoiding halogen anion exchange caused by direct contact between the two PQDs and obtaining superior and designed macroscopic fluorescence. Owing to the disparity in optimal excitation wavelengths between PQDs and Eu(BA)3phen, white light and multicolor emissions of Janus-MRF can be achieved under multi-wavelength stimulation. Furthermore, the fluorescent color of Janus-MRF is sensitive to temperature changes. As an applicative demonstration of Janus-MRF, different sub-barcodes are obtained by using the identifiable fluorescence spectra emitted by Janus-MRF under multi-wavelength stimulation and the sensitivity of fluorescent color of Janus-MRF to temperature changes, and further these sub-barcodes are integrated into the large photonic barcodes encoding library for high-volume data storage and advanced anti-counterfeiting applications. This work provides a novel idea and strategy for advancing fabrication and application of materials based on PQDs.},
}

@article {pmid40580296,
year = {2025},
author = {Magbanua, ZV and Hsu, CY and Pechanova, O and Arick, M and Peterson, DG},
title = {Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2943},
number = {},
pages = {189-204},
pmid = {40580296},
issn = {1940-6029},
mesh = {*Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Polymorphism, Single Nucleotide ; DNA Restriction Enzymes/metabolism ; Animals ; Gene Library ; Polymerase Chain Reaction/methods ; Gossypium/genetics ; },
abstract = {ddRAD-Seq is a reduced representation sequencing technique that results in sequence datasets that can be compared and used to identify SNPs. We present an improved ddRAD-Seq protocol that increases efficiency and decreases the time to complete a ddRAD-Seq experiment. It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Enzyme deactivation steps are eliminated, library amplification and barcoding are completed in one PCR step, highly-efficient and precise size selection with BluePippin system and cleanup steps using magnetic beads are consolidated at the end of the library generation step. The SNPs that we identified using this streamlined protocol were validated in population and evolutionary studies of cotton (plant) (Magbanua et al., Anal Biochem 662:115001, https://doi.org/10.1016/j.ab.2022.115001 , 2023) and rohu carp (animal) (Arick et al., G3 (Bethesda) 13, https://doi.org/10.1093/g3journal/jkad009 , 2023).},
}

*Sequence Analysis, DNA/methods
*High-Throughput Nucleotide Sequencing/methods
Polymorphism, Single Nucleotide
DNA Restriction Enzymes/metabolism
Animals
Gene Library
Polymerase Chain Reaction/methods
Gossypium/genetics

@article {pmid40580295,
year = {2025},
author = {Torres, A and Gaudino, R},
title = {Long-Range Targeted Nanopore Ligation Sequencing Workflow for Targeted Amplicon Sequencing of Secondary Metabolite Gene.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2943},
number = {},
pages = {177-188},
pmid = {40580295},
issn = {1940-6029},
mesh = {*Nanopore Sequencing/methods ; Workflow ; *Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; Polymerase Chain Reaction/methods ; DNA, Plant/genetics ; *Plants/genetics/metabolism ; Nanopores ; },
abstract = {This chapter presents protocols for advanced genotyping and genetic analysis in plant science, utilizing DNA extracted from FTA samples and leaf tissue. Targeted long range PCR is employed to uncover allelic and structural variations within genes of interest, while targeted long-read nanopore sequencing offers a comprehensive view of gene targets in their native and enriched forms. The protocol for nanopore sequencing encompasses DNA preparation, barcoding of up to 96 samples, adapter ligation, purification, and sequencing, culminating in the generation of raw data files (pod5 or fastq) suitable for further analysis. Together, these methods provide a powerful toolkit for plant diagnostics and breeding.},
}

*Nanopore Sequencing/methods
Workflow
*Sequence Analysis, DNA/methods
*High-Throughput Nucleotide Sequencing/methods
Polymerase Chain Reaction/methods
DNA, Plant/genetics
*Plants/genetics/metabolism
Nanopores

@article {pmid40577524,
year = {2025},
author = {Rajasegaran, P and Tan, KK and Khoo, JJ and Mansor, MS and Ahmad Khusaini, MKS and AbuBakar, S and Ya'cob, Z and Makepeace, BL},
title = {Molecular species delimitation analysis of Leptotrombidium spp. and other chigger species parasitizing birds in Malaysia.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf078},
pmid = {40577524},
issn = {1938-2928},
support = {ICA\R1\191058//Royal Society International Collaboration Award/ ; },
abstract = {Trombiculid mites (Acariformes) are unique among arthropods of medical importance in that only the larval instar (chigger) is parasitic, which can result in the transmission of zoonotic scrub typhus. The use of molecular approaches for chigger species discrimination has been very limited until recently, especially for those parasitizing bird hosts, where data remain scarce. Here, we aimed to generate DNA barcodes of chiggers parasitizing birds in Malaysia based on the mitochondrial cytochrome c oxidase subunit I (COI) gene following DNA extraction, PCR and sequencing. Fifty-four COI sequences from 8 bird-associated chigger species in Malaysia were combined with 50 GenBank sequences comprising 7 genera from various countries for DNA barcode and phylogenetic analysis. The correct identification rates for the 95 COI barcodes were 96.84% (Best Match) and 86.31% (Best-Close Match). DNA barcode analyses effectively clustered the 8 nominal species from this study into their respective genera. Genetic divergence of less than 3% was observed within Ascoschoengastia lorius, Neoschoengastia gallinarum, Parascoschoengastia heynemani, Leptotrombidium imphalum, and Blankaartia acuscutellaris, all of which formed a monophyletic clade, confirming their conspecific nature. Conversely, intraspecific divergences of 17.64%, 15.49%, and 11.63% were obtained for Toritrombicula densipiliata, Odontacarus audyi, and Leptotrombidium deliense. These divergences, supported by evidence of distinct entities through delimitation analyses, indicate potential cryptic diversity within these populations. In conclusion, this study represents the first molecular genetic analysis of bird chiggers in Malaysia, revealing varying levels of genetic divergence. Our findings highlight the utility of DNA barcoding for understanding chigger diversity and aiding in accurate identification.},
}

@article {pmid40577080,
year = {2025},
author = {Butti, P and Bellusci, F and Brambilla, E and Branduardi, P},
title = {Genomically integrated cassettes swapping: bringing modularity to the strain level in Saccharomyces cerevisiae.},
journal = {FEMS yeast research},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsyr/foaf032},
pmid = {40577080},
issn = {1567-1364},
abstract = {A large variety of synthetic biology toolkits for the introduction of multiple expression cassettes is available for Saccharomyces cerevisiae. Unfortunately, none of these tools is designed to allow the modification-exchange or removal-of the cassettes already integrated into the genome in a standardised way. The application of the modularity principle therefore ends to the steps preceding the final host engineering, making microbial cell factories construction stiff and strictly sequential. In this work we describe a system that easily allows CRISPR-mediated swapping or removal of previously integrated cassettes, thus bringing the modularity to the strain level, enhancing the possibility of modifying existing strains with a reduced number of steps. In the system, each cassette is tagged with specific barcodes, which can be used as targets for CRISPR nucleases (Cas9 and Cas12a), allowing the excision of the construct from the genome and its substitution with another expression cassette or the restoration of the wild type locus in one single standardised step. The system has been applied to the previously developed Easy-MISE toolkit and tested by swapping fluorescent protein expression cassettes with an efficiency of ∼90% quantified by PCR and flow cytometry.},
}

@article {pmid40575388,
year = {2025},
author = {Li, X and Li, X and Tong, L and Hu, L and Hong, Y and Zhou, R and Li, Z and Dong, M and Hou, J and Xu, T and Zhong, W},
title = {Systematic Evaluation of Isolation Techniques and Freeze-Thaw Effects on Plasma Extracellular Vesicle Heterogeneity and Subpopulation Profiling.},
journal = {Journal of extracellular biology},
volume = {4},
number = {6},
pages = {e70058},
pmid = {40575388},
issn = {2768-2811},
abstract = {Extracellular vesicles (EVs) are increasingly recognized as promising disease biomarkers and therapeutic carriers. However, standardizing blood-derived EV isolation remains challenging due to the heterogeneity of EV populations and variability among isolation techniques. In this study, we systematically evaluated three distinct EV isolation methods, including asymmetrical flow field-flow fractionation (AF4), size-exclusion chromatography (SEC) and automated centrifugal microfluidic disc system combined with functionalized membranes (Exo-CMDS), to compare their efficiency in isolating EVs from both freshly frozen and freeze-thawed plasma samples. We utilized an integrative approach combining Proximity-dependent Barcoding Assay (PBA) for single-EV surface protein profiling, Liquid Chromatography-Mass Spectrometry (LC-MS/MS) for bulk proteomic analysis, along with transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA) to assess EV yield, morphology, surface protein expression and subpopulation diversity. Our results revealed significant differences in three EV isolation methods. AF4 is particularly enriched for EV subpopulations expressing high levels of classical tetraspanins (e.g., CD81, CD9 and CD151), and single-pass membrane proteins (e.g., ITGA4 and ITAGB1). Exo-CMDS demonstrated the highest reproducibility across samples, isolating specific EV subpopulations enriched in markers like CD5. SEC provided the highest yield but co-isolated significant amounts of non-vesicular particles, including lipoproteins. The findings contribute valuable insights toward standardized and reliable EV isolation practices for research and clinical applications.},
}

@article {pmid40574733,
year = {2025},
author = {Fumo, JT and Nichols, PK and Ely, T and Marko, PB and Moran, AL and Powell, BS and Williams, TM and Kosaki, RK and Smith, CM and Lopes, KH and Smith, JE and Spalding, HL and Krueger-Hadfield, SA and McDermid, KJ and Hauk, BB and Morioka, J and O'Brien, K and Kennedy, B and Leliaert, F and Fujii, MT and Nelson, WA and Draisma, SGA and Sherwood, AR},
title = {A predictive framework for identifying source populations of non-native marine macroalgae: Chondria tumulosa in the Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19610},
pmid = {40574733},
issn = {2167-8359},
mesh = {Pacific Ocean ; *Seaweed/classification/genetics ; *Rhodophyta/classification/genetics ; Hawaii ; Ecosystem ; *Introduced Species ; },
abstract = {The cryptogenic marine red alga Chondria tumulosa was first observed in 2016 in subtidal habitats at Manawai (Pearl and Hermes Atoll) in the Papahānaumokuākea Marine National Monument (PMNM), Hawai'i. Without molecular or morphological matches to any known species, it was described in 2020 and declared cryptogenic. This alga has substantially increased in benthic cover and has been discovered on two additional atolls in PMNM: Kuaihelani (Midway) and Hōlanikū (Kure). It exhibits several characteristics indicative of non-native origins including putative prior absence in the region, persistence in high densities over nearly a decade, apparent lack of native herbivore pressure, and strong tetrasporophytic bias. Importantly, it is negatively impacting the culturally and ecologically valuable reefs of PMNM. The geographical origin of this putative invasion is unknown, and there are no published reports of the species occurring anywhere other than PMNM. The central Pacific location of Hawai'i allows a broad range of potential sources for the origin of C. tumulosa. Taxonomic ambiguities within the genus Chondria and challenges associated with sampling necessitate the development of a narrowed set of search locations and efficient search strategies to detect the species outside of PMNM. Attachment to floating debris is a potential introduction vector for C. tumulosa into PMNM, and an oceanographic model was used to identify the most likely source locations for this pathway between 2000 and 2015, including Japan in the western Pacific, Johnston Atoll, the Line Islands including Palmyra Atoll in the central Pacific, and Clipperton Atoll and the Galápagos Islands in the eastern Pacific. We used a recently developed and validated eDNA assay for detecting C. tumulosa from three of the regions of interest to screen for C. tumulosa with no samples yielding positive detections. We provide a framework for investigating positive eDNA field detections using in-water surveys, microscopy, and DNA barcoding. A parallel sampling effort targeting preserved specimens stored in global herbaria is also presented, which did not yield any detections. Several Chondria species remain targets for sequencing from global herbaria. Identification of the native range of C. tumulosa is a critical step that will allow for an evaluation of its evolutionary ecology and any shifts that may have occurred that facilitated its putative invasion and subsequent spread, offering insights crucial for the development of mitigation strategies to safeguard PMNM against further risk.},
}

Pacific Ocean
*Seaweed/classification/genetics
*Rhodophyta/classification/genetics
Hawaii
Ecosystem
*Introduced Species

@article {pmid40573282,
year = {2025},
author = {Wang, W and Liu, Y and Lou, W and Chen, L and Xie, T and Wang, Z and Ma, Y and Gao, H},
title = {A Comprehensive Quality Evaluation System for Medicinal Leeches by Integrating Macromolecular Protein Analysis and Small-Molecule Marker Detection as Well as Quantitative Bioassays.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {6},
pages = {},
pmid = {40573282},
issn = {1424-8247},
support = {No. CI2021A05053//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; No. CI2021A04401//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; No. 2023YFC3504000//National Key R&D Program of China/ ; No. ZYJGKX202414//Fundamental Research Funds for the Central public welfare research institutes/ ; },
abstract = {Background/Objectives: Medical leech (Hirudo in the Chinese Pharmacopoeia) is renowned in traditional medicine for its significant antithrombin activity. As an animal-derived medicine with complex and incompletely understood composition, its insufficient quality control measures are met with widespread counterfeiting caused by limited animal resources and rising demand. Methods: In this study, an integrated quality evaluation strategy guided by "Totality of the Evidence" (TOE) method is proposed. This strategy combines chemical characterization of small and macromolecular components with bioassays relevant to its clinical functions. A total of 28 batches of samples were analyzed, comprising 23 genuine and 5 counterfeit batches. Species origins were identified by morphology and DNA barcoding. Chemical characterization included TLC, HPLC and UPLC-QTOF-MS/MS for small molecules, and SDS-PAGE with HPLC-Orbitrap Fusion Lumos Tribrid-MS for macromolecules. Antithrombotic activity was assessed by thrombin titration and platelet aggregation assays. Results: Several characteristic components were discovered and identified as key quality control markers, including eight small molecules such as an unreported compound SZ-1, plus seven major differential proteins across species. Based on these markers, accurate and rapid authentication methods were established using SDS-PAGE for macromolecules, and both HPLC and TLC for small molecules. Furthermore, using bioassay methods we established for quality evaluation, Hirudo nipponica exhibits potent anti-thrombin activity and inhibits platelet aggregation, while Whitmania pigra shows weak anti-thrombin activity and promotes platelet aggregation. Conclusions: This quality evaluation strategy is not only applicable for the quality assessment of genuine Hirudo products of different origins, but also for distinguishing medical leeches from their counterfeits.},
}

@article {pmid40569485,
year = {2025},
author = {Hazarika, TK and Momin, MD and Ibrahim, KS and Lalrinzuala, P and Dutta, H and Singh, TS and Debbarma, P and Das, J and Bora, A},
title = {Morphological and molecular insights into the wild Ficus species of Mizoram, Northeast India.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {643},
pmid = {40569485},
issn = {1573-4978},
mesh = {*Ficus/genetics/anatomy & histology/classification ; India ; Phylogeny ; Genetic Variation/genetics ; DNA Barcoding, Taxonomic/methods ; Fruit/genetics ; },
abstract = {BACKGROUND: The genus Ficus L., commonly known as fig and belonging to the family Moraceae, is widely distributed across tropical and subtropical regions of Asia, Africa, America, and Australia. Ficus species hold significant importance in horticulture and traditional medicine due to their aesthetic, edible, and therapeutic properties. Nevertheless, the pronounced morphological diversity and intricate genetic makeup of these species require the application of molecular techniques for precise identification and comprehensive assessment of genetic diversity.

METHODS AND RESULTS: This study focuses on the morphological, molecular characterization, and phylogeny of wild Ficus species in Mizoram, Northeast India. Morphological traits of the plants and fruits were observed, and molecular analysis was conducted using DNA barcoding of the rbcL gene, with the resulting sequences submitted to NCBI GenBank. Significant variation in morphological traits was observed among the studied Ficus species. Phylogenetic analysis based on rbcL gene sequences confirmed genetic diversity, with notable genetic similarity identified in Ficus velutina (MTMZU12 and MTMZU13) despite their morphological similarity.

CONCLUSIONS: The study underscores how genetic and environmental factors shape morphology and shows that integrating molecular and morphological data improves phylogenetic resolution in Northeast India, a critical biodiversity hotspot.},
}

*Ficus/genetics/anatomy & histology/classification
India
Phylogeny
Genetic Variation/genetics
DNA Barcoding, Taxonomic/methods
Fruit/genetics

@article {pmid40567577,
year = {2025},
author = {Sire, L and Martin, C and Parmain, G and Bézier, A and Herniou, EA and Bouget, C and Lopez-Vaamonde, C},
title = {Incorporating Neglected Insect Larvae in Species Inventories: DNA Barcoding as an Effective Tool for All-Stage Invertebrate Identification in Tree Holes.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71586},
pmid = {40567577},
issn = {2045-7758},
abstract = {Invertebrates, especially insects, are an integral part of biodiversity. Many species live in forest ecosystems where they play a key role in decomposing wood and maintaining ecosystem functions. Nevertheless, global changes, like fires, storms, and pest outbreaks, are impacting insect diversity, reinforcing the need for long-term biomonitoring to understand and tackle these issues. Forests are heterogeneous ecosystems with tree-related microhabitats (TReMs) such as tree holes, which are important for ecosystem diversity. Conventional identification approaches for species inventories are frequently hampered by the extensive and hidden diversity of insect larval stages. Thus, there is a crucial need to develop tools that facilitate inventories of these ecological niches and allow the incorporation of such hidden diversity into long-term monitoring studies. To that end, we explored the biodiversity found in tree holes within French state forests using DNA barcoding and addressed challenges associated with traditional morphological identification methods. Results demonstrate the successful application of DNA barcoding in identifying nearly 62% of all invertebrates sampled from tree holes to the species level. Sampled invertebrates comprised 44% of larvae (566 individuals), of which nearly 50% could be assigned a species name. In total, 108 species and 173 barcode index numbers (BINs, used as species proxy) were molecularly inventoried, and 39% of these identified species were solely represented by larvae in our sampling. Our study highlights the usefulness of DNA-based identification methods and the significance of including larvae in biodiversity assessments to gain insights into species abundance and functional diversity. It also underscores the necessity of ongoing and parallel developments of DNA reference libraries to improve species molecular identification rates and accuracy, and the need to investigate potential non-destructive alternatives for biomonitoring. These efforts aim to ensure thorough and precise monitoring of invertebrate communities in tree holes and similar microhabitats.},
}

@article {pmid40567417,
year = {2025},
author = {Pasquariello, M and Martinelli, T and Paris, R and Moschella, A and Colombo, R and Di Bello, A and Frigerio, J and Kheloufi, A and Mirzaabolghasemi, MA and Puglisi, D and Esposito, S and Scalercio, S and Virzì, N and De Vita, P and Pecchioni, N and Bassolino, L},
title = {Exploring the chemotypic variability of Silybum marianum and Silybum eburneum by biochemical and genetic characterization.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1584104},
pmid = {40567417},
issn = {1664-462X},
abstract = {The Silybum genus belonging to the Asteraceae family, is composed of two species, marianum and eburneum, although, in the past, their classification was not always appropriate. While Silybum marianum is very well known since ancient times for the medicinal properties of a blend of different flavonolignans contained in the achenes and named silymarin, very little information is available about Silybum eburneum chemodiversity. Here, we describe the biochemical characterization of a wide ex situ germplasm collection including 83 wild Silybum accessions collected during ad hoc sampling campaigns in Italy, Spain, Iran and Algeria as well as accessions acquired by seed GenBanks and studied at both population and single plant level. Interestingly, our results confirm the presence of only three chemotypes in S. marianum, namely A, B and C. Conversely, S. eburneum accessions, exhibit a distinct and stable chemotype (D) where isosilychristin is the predominant silymarin component. Additionally, DNA barcoding based on the ribosomal DNA region ITS2 combined with morphological phenotyping and chemotyping, successfully resolves frequently found mistakes in the identification of the two species. These findings significantly expand our knowledge of the global biodiversity of the Silybum genus and provide valuable insights for future breeding programs and potential applications in nutrition and human health sciences.},
}

@article {pmid40567021,
year = {2025},
author = {Xu, L and Chen, R and Wang, X and Liu, D and Liu, Y and Zhao, CX},
title = {DNA Barcoding-Enabled Tracking of Lipid Nanoparticles: Drug-Loading-Dependent Biodistribution and Tumor Microenvironment Targeting.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2501914},
doi = {10.1002/adhm.202501914},
pmid = {40567021},
issn = {2192-2659},
support = {APP2008698//National Health and Medical Research Council/ ; },
abstract = {Lipid nanoparticles (LNPs) are versatile drug delivery systems, yet the impact of drug loading (DL) on their biodistribution and cellular uptake remains poorly understood. Optimizing drug loading is crucial for enhancing therapeutic efficacy and safety, as higher loading allows for lower LNP doses, reducing overall nanomaterial burden. Addressing this knowledge gap is essential for advancing LNP-based cancer therapies. This study integrates DNA barcoding technology with LNPs to evaluate their in vivo delivery behaviors under varying drug loadings. Using a sequential nanoprecipitation method, DNA-barcoded LNPs with low (1%), medium (16%), and high (26%) drug loadings are fabricated, each tagged with a unique DNA barcode for precise tracking. Pooled LNPs are intravenously administered to tumor-bearing mice, and their biodistribution across organs is quantified via qPCR. High drug-loading LNPs demonstrate preferential accumulation in the spleen, while low drug-loading LNPs exhibit higher liver accumulation, suggesting faster clearance. Cellular uptake analysis reveals enhanced uptake of high drug-loading LNPs by tumor-associated macrophages within the tumor microenvironment (TME). This study establishes a robust platform for simultaneous and high-sensitivity monitoring of LNP behaviors, significantly reducing animal use and interanimal variability. The findings guide the rational design for developing optimal LNPs for cancer therapies targeting specific TME components.},
}

@article {pmid40565578,
year = {2025},
author = {Peña, F and Univaso, L and Román-Figueroa, C and Paneque, M},
title = {In Silico Genomic Analysis of Chloroplast DNA in Vitis Vinifera L.: Identification of Key Regions for DNA Coding.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
pmid = {40565578},
issn = {2073-4425},
support = {40035912-0/2022//FIC-Ñuble/ ; },
mesh = {*Vitis/genetics/classification ; *Genome, Chloroplast/genetics ; *DNA, Chloroplast/genetics ; Phylogeny ; Microsatellite Repeats/genetics ; DNA Barcoding, Taxonomic/methods ; Genomics/methods ; Chloroplasts/genetics ; Computer Simulation ; },
abstract = {BACKGROUND/OBJECTIVES: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding.

METHODS: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties.

RESULTS: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine-cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers.

CONCLUSIONS: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera.},
}

*Vitis/genetics/classification
*Genome, Chloroplast/genetics
*DNA, Chloroplast/genetics
Phylogeny
Microsatellite Repeats/genetics
DNA Barcoding, Taxonomic/methods
Genomics/methods
Chloroplasts/genetics
Computer Simulation

@article {pmid40565551,
year = {2025},
author = {Guo, X and Huang, W and Zhao, Z and Xue, D and Wu, Y},
title = {Comparative Analysis of Plastomes of Artemisia and Insights into the Infra-Generic Phylogenetic Relationships Within the Genus.},
journal = {Genes},
volume = {16},
number = {6},
pages = {},
pmid = {40565551},
issn = {2073-4425},
support = {LQ24C020002//Zhejiang Provincial Natural Science Foundation/ ; 32270215//National Natural Science Foundation of China/ ; },
mesh = {*Artemisia/genetics/classification ; *Phylogeny ; *Genome, Chloroplast/genetics ; Evolution, Molecular ; Base Composition ; },
abstract = {Background: Artemisia is a large and complex genus comprising about 500 species. Currently, only a limited number of plastomes (the chloroplast genome) of Artemisia are available. Their structures have not been comparatively analyzed, and a phylogenetic backbone based on plastome-scale data is still lacking. This situation has greatly hindered our understanding of the plastome variation patterns and infra-generic relationships of the genus. Methods: We newly sequenced 34 Artemisia plastomes representing 30 species and three varieties. Combining this with previously published plastomes, we comparatively analyzed their structure and constructed phylogenetic relationships using the protein-coding sequences (CDS) of plastomes. Results: Our analyses indicated that the Artemisia plastomes are conserved in terms of their structure, GC content, gene number, and order. The sequence divergence is higher in the LSC and SSC regions than in the IR regions. Three protein-coding genes and four non-coding regions, i.e., accD, petG, ycf1, rpoC1-rpoC2, rpoC2-rps2, trnG(UCC)-trnfM(CAU), and ndhG-ndhI, were highly diverse and could be chosen as candidates of DNA barcodes. Phylogenetic trees were divided into several clades, and all four main subgenera were not monophyletic. Additionally, the phylogenetic position of A. stracheyi is still controversial. Conclusions: Plastomes can provide important information for phylogenetic constructions. This study provides insights into the infra-generic relationships within Artemisia and also lays a foundation for future evolutionary studies of this genus.},
}

*Artemisia/genetics/classification
*Phylogeny
*Genome, Chloroplast/genetics
Evolution, Molecular
Base Composition

@article {pmid40565087,
year = {2025},
author = {Li, J and Zhang, Y and Liu, Y and Wei, S and Huang, Z and Chen, L and Huang, H},
title = {Comprehensive Analysis of Genetic and Morphological Diversity in Echinochloa spp. Populations Infesting Paddy Fields in Ningxia, China.},
journal = {International journal of molecular sciences},
volume = {26},
number = {12},
pages = {},
pmid = {40565087},
issn = {1422-0067},
mesh = {*Echinochloa/genetics/classification/anatomy & histology ; DNA Barcoding, Taxonomic ; *Genetic Variation ; China ; Phylogeny ; *Plant Weeds/genetics ; Herbicide Resistance/genetics ; },
abstract = {Barnyard grass is the most problematic weed in paddy fields in Ningxia. Its substantial morphological variation complicates both identification and control, yet the genetic diversity of barnyard grass infesting paddy fields in Ningxia has not been thoroughly studied. In this research, we analyzed the genetic diversity of 46 barnyard grass populations from Ningxia's paddy fields based on the assessment of morphological traits, DNA barcoding, and SCoT-targeted gene markers. Nine morphological traits were quantitatively analyzed, among which three phenological traits, i.e., leaf length, stem diameter, and plant height, exhibited notable variations. Correlational analysis revealed a positive relationship between morphological traits and multi-herbicide resistance profiles. To assess genetic diversity, four DNA barcodes (ITS, psbA, matK, and trnL-F) were used, among which ITS demonstrated the strongest potential in single-gene barcoding for barnyard grass species identification. Cluster analysis based on ITS barcode sequences was performed to group the populations into five main categories. Additionally, SCoT marker analysis using six primers was performed to classify the 46 barnyard grass samples into five groups. The results showed that the predominant barnyard grass species in Ningxia were E. colona, E. crus-galli var. Formosensis, E. crusgalli, E. oryzoides, and E. crusgalli var. Zelayensis, with E. colona being the most prevalent. The differences observed between the morphological and molecular marker-based classifications were method-dependent. However, both SCoT molecular marker technology and DNA barcoding contributed to identifying the genetic diversity of barnyard grass. Taken together, our study revealed significant morphological and genetic variations among barnyard grass populations, which correlated with herbicide sensitivity in Ningxia's paddy fields, underscoring the necessity for an integrated weed management approach to combat this troublesome weed species.},
}

*Echinochloa/genetics/classification/anatomy & histology
DNA Barcoding, Taxonomic
*Genetic Variation
China
Phylogeny
*Plant Weeds/genetics
Herbicide Resistance/genetics

@article {pmid40564765,
year = {2025},
author = {Yalçın, E and Aslan, S and Toğaçar, M and Demir, SC},
title = {A Hybrid Artificial Intelligence Approach for Down Syndrome Risk Prediction in First Trimester Screening.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
doi = {10.3390/diagnostics15121444},
pmid = {40564765},
issn = {2075-4418},
abstract = {Background/Objectives: The aim of this study is to develop a hybrid artificial intelligence (AI) approach to improve the accuracy, efficiency, and reliability of Down Syndrome (DS) risk prediction during first trimester prenatal screening. The proposed method transforms one-dimensional (1D) patient data-including features such as nuchal translucency (NT), human chorionic gonadotropin (hCG), and pregnancy-associated plasma protein A (PAPP-A)-into two-dimensional (2D) Aztec barcode images, enabling advanced feature extraction using transformer-based deep learning models. Methods: The dataset consists of 958 anonymous patient records. Each record includes four first trimester screening markers, hCG, PAPP-A, and NT, expressed as multiples of the median. The DS risk outcome was categorized into three classes: high, medium, and low. Three transformer architectures-DeiT3, MaxViT, and Swin-are employed to extract high-level features from the generated barcodes. The extracted features are combined into a unified set, and dimensionality reduction is performed using two feature selection techniques: minimum Redundancy Maximum Relevance (mRMR) and RelieF. Intersecting features from both selectors are retained to form a compact and informative feature subset. The final features are classified using machine learning algorithms, including Bagged Trees and Naive Bayes. Results: The proposed approach achieved up to 100% classification accuracy using the Naive Bayes classifier with 1250 features selected by RelieF and 527 intersecting features from mRMR. By selecting a smaller but more informative subset of features, the system significantly reduced hardware and processing demands while maintaining strong predictive performance. Conclusions: The results suggest that the proposed hybrid AI method offers a promising and resource-efficient solution for DS risk assessment in first trimester screening. However, further comparative studies are recommended to validate its performance in broader clinical contexts.},
}

@article {pmid40562837,
year = {2025},
author = {de Medeiros, BAS and Cai, L and Flynn, PJ and Yan, Y and Duan, X and Marinho, LC and Anderson, C and Davis, CC},
title = {A composite universal DNA signature for the tree of life.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {40562837},
issn = {2397-334X},
support = {DEB-0544039//National Science Foundation (NSF)/ ; },
abstract = {Species identification using DNA barcodes has revolutionized biodiversity sciences. However, conventional barcoding methods may lack power and universal applicability across the tree of life. Alternative methods based on whole genome sequencing are hard to scale due to large data requirements. Here we develop a novel DNA-based identification method, varKoding, using exceptionally low-coverage genome skim data to create two-dimensional images representing the genomic signature of a species. Using these representations, we train neural networks for taxonomic identification. Applying a taxonomically verified novel genomic dataset of Malpighiales plant accessions, we optimize training hyperparameters and find the highest performance by combining a transformer architecture with a new modified chaos game representation. Greater than 91% precision is achieved despite minimal input data, exceeding alternative methods tested. We illustrate the broad utility of varKoding across several focal clades of eukaryotes and prokaryotes. We also train a model capable of identifying all species in the Sequence Read Archive of the National Center for Biotechnology Information using less than 10 Mbp sequencing data with 96% precision and 95% recall and robust to sequencing platforms. The varKoding approach offers enhanced computational efficiency and scalability, minimal data inputs robust to sequencing details and modularity for further development in biodiversity science.},
}

@article {pmid40559832,
year = {2025},
author = {González-Velo, M and Espinosa-Sánchez, A and Ripa, A and Hurtado-Preciado, MA and Martínez-Estéllez, MAH and Fernández-García, JL and Bazo-Pérez, C},
title = {Contributions to Knowledge of the Dictyocaulus Infection of the Red Deer.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
pmid = {40559832},
issn = {2306-7381},
abstract = {Dictyocaulosis is a parasitic disease that affects ungulate species, including red deer (Cervus elaphus). The genus Dictyocaulus comprises eighteen species, but only four have been reported to infect red deer. The disease is characterized by respiratory tract infection, particularly in the lungs, bronchi, and bronchioles, leading to inflammatory and hemorrhagic microscopic lesions, as well as emphysema and edema. The biological cycle involves a female ovipositing larvated eggs in the bronchi and trachea, which are expelled to the exterior through coughing or feces, releasing L1 into the environment. In this study, 106 adult red deer were collected from seven locations in Extremadura (Spain). Eight positive lungs were initially assessed by morphological identification, revealing a mean intensity of 13.3 adult worms per infected lung, with a global decrease to an average of 1.8 adult worms per sampled lung. The presence of adult worms in the upper and middle respiratory tract was confirmed through anatomopathological analysis. Molecular identification was performed by sequencing the COI gene. The results indicated the presence of three genetic groups, supported by significant subdivision using the ɸST measure. D. cervi and D. viviparus exhibited their respective matrilineal ancestry, while D. eckerti and D. cervi demonstrated matrilineal sharing. Consequently, the possibility of introgression between these two species was suggested. Although D. viviparus had previously been identified in the same Spanish region based on morphological characteristics, D. cervi and D. eckerti were reported for the first time in the explored geographic area.},
}

@article {pmid40559028,
year = {2025},
author = {Shah, HK and Fathima, PA and Rahi, M and Saini, P},
title = {Report of a New Sand Fly (Diptera: Psychodidae) Species, Sergentomyia (Neophlebotomus) pradeepii n. sp. from Madhya Pradesh, India.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
pmid = {40559028},
issn = {2075-4450},
support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; },
abstract = {Madhya Pradesh, a biodiversity-rich state in central India, reports sporadic non-indigenous leishmaniasis cases. Systematic entomological surveillance as part of molecular xenomonitoring in sand flies led to the discovery of a new species, Sergentomyia (Neophlebotomus) pradeepii n. sp. (Diptera: Psychodidae), from Johariya village in Sagar district, Madhya Pradesh, India. A systematic cross-sectional survey of sand flies was conducted in Bhopal, Sagar, and Hoshangabad districts of Madhya Pradesh. Standard collection methods were employed for two months, i.e., from July to August 2023. DNA barcoding targeting the mitochondrial Cytochrome c oxidase subunit I (COI) gene was performed, and the generated sequences were phylogenetically analyzed. Se. (Neo.) pradeepii, a newly recorded sand fly species, is reported in this study. Its taxonomic relationship to other congeners of subgenus Neophlebotomus is discussed. COI barcoding and phylogenetic analysis established that the specimens fit into the same taxonomic group, exhibiting negligible gene flow within the population, while a 13.4% genetic distance from congeners establishes it as a separate species. Madhya Pradesh, with its rich biodiversity and favorable conditions for sand fly proliferation, lacks systematic entomological surveillance. This study enhances the knowledge of the state's sand fly fauna by reporting and providing a detailed morphological and molecular description of the new species.},
}

@article {pmid40559020,
year = {2025},
author = {Wang, B and Ha, S and Cai, J and Ma, Y and Li, D and Chen, J and Deng, J},
title = {Exploratory Study on DNA Barcode Combined with PCR-HRM Technology for Rapid and Accurate Identification of Necrophilous Fly Species.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
pmid = {40559020},
issn = {2075-4450},
support = {Grant No. 82060341, Grant No. 82471916, Grant No. 81560304//National Natural Science Foundation of China/ ; Grant No.2024D14016//Research Innovation Team Project of Xinjiang/ ; Grant No.XYD2024C05//Research Innovation Team Project of Xinjiang Medical University,/ ; Grant No. YSPTZX202134//Hainan academician innovation platform scientific research project/ ; Grant No. HYYS2021A06//Innovative Scientific Research Project for Postgraduates of Hainan Medical College/ ; },
abstract = {Molecular species identification plays an increasingly important role in forensic entomology and is centered on selecting appropriate DNA barcodes, which there are not yet enough of. Such identification is decisive in discovering a better DNA barcode for the identification of necrophilous fly species. Here, we analyzed 10 common necrophilous fly species found on Hainan Island; designed 12 pairs of fly-specific primers from different mitochondrial regions; screened two fly DNA barcodes with better results than those of published studies, which were used as controls; and employed a high-resolution melting (HRM) curve to construct PCR-HRM technology systems for rapid and efficient necrophilous fly species identification. The results showed that, among the 14 DNA barcoding PCR-HRM systems, the newly designed COXII-519/COXII-615 primer was the best, which identified 10 necrophilous fly species in one test. The second-best system was the C1-J-2495/C1-N-2800 primer published in the literature, which identified six fly species in one test. Moreover, since the COXII-519/COXII-615 primer system performed successfully in both stale (stored over two years) and larval samples due to its short amplificated fragment (shorter than 97 bp), it may serve as a new efficient DNA barcode for necrophilic fly species identification. The new DNA barcoding PCR-HRM system established in this study enables the rapid and accurate identification of necrophilic fly species.},
}

@article {pmid40558994,
year = {2025},
author = {Wu, J and Li, D and Balan, RK and George, S and Peacock, L and Pal, C},
title = {Comparative Assessment of Environmental DNA and Bulk-Sample Metabarcoding in Biosecurity Surveillance for Detecting Biting Midges (Ceratopogonidae).},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
pmid = {40558994},
issn = {2075-4450},
support = {405732//Ministry for Primary Industries/ ; },
abstract = {Biting midges, Culicoides spp. (Diptera: Ceratopogonidae), are significant vectors capable of transmitting arboviruses, such as bluetongue virus, to livestock. New Zealand is free of Culicoides, and a national surveillance programme is in place for the early detection of an incursion. Traditionally, insect trap samples from the surveillance programme are analyzed using morphology-based diagnostics under microscopes, which is time-consuming and relies on specialized taxonomic expertise. Here, we assessed the effectiveness of DNA metabarcoding using insect bulk samples and environmental DNA (eDNA) from liquid samples collected in surveillance traps. Two Cytochrome oxidase I (COI) barcoding primer sets were employed to study biodiversity and detect exotic species. The results indicated that DNA metabarcoding with homogenized insect bulk samples had a higher overall detection accuracy rate (over 81% for both primer pairs) compared to ethanol fluid-derived eDNA samples from traps (68.42% and 55.26% for the primer sets LCO1490/HCO2198 and mlCOIintF/jgHCO2198, respectively) based on congruence with morphological identification. Detection failures were likely due to eDNA extraction issues or low target species abundance. Both approaches showed similar insect community composition and diversity in the surveillance trap samples, suggesting the potential of DNA metabarcoding for biosecurity surveillance and biodiversity assessments. Overall, DNA metabarcoding using bulk insect samples could enhance the efficiency of Culicoides surveillance, reducing workload and screening time.},
}

@article {pmid40558971,
year = {2025},
author = {Motato-Vásquez, V and Vinasco-Diaz, LK and Londoño-Caicedo, JM and Bolaños-Rojas, AC},
title = {Hidden Treasures of Colombia's Pacific Mangrove: New Fungal Species and Records of Macrofungi (Basidiomycota).},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
pmid = {40558971},
issn = {2309-608X},
abstract = {Mangrove-associated fungi represent a diverse but understudied group of eukaryotic organisms, especially in the Neotropics. The Colombian Pacific region, with approximately 1300 km of coastline covered with 194,880 ha of mangrove forests that remain largely unexplored for macrofungal diversity, is recognized as a global biodiversity hotspot. This study aimed to catalog the macrofungi associated with mangrove ecosystems in Colombia, integrating morphological characterization and molecular phylogenetics, focusing on three Valle del Cauca Pacific coast localities. A total of 81 specimens were collected from both living trees and decaying wood. Detailed macroscopic and microscopic analyses were conducted, and DNA sequences from two ribosomal DNA barcode regions (ITS and LSU) were generated for 43 specimens. Three new species-Neohypochnicium manglarense, Phlebiopsis colombiana, and Porogramme bononiae-were documented. In addition, eight species were reported as new records for both Colombia and mangrove ecosystems, including Microporus affinis, Paramarasmius palmivorus, Phlebiopsis flavidoalba, Porogramme brasiliensis, Resinicium grandisporum, Trametes ellipsospora, T. menziesii, and T. polyzona. Although previously recorded in Colombian terrestrial ecosystems, Lentinus scleropus and Oudemansiella platensis are globally reported here for the first time from mangrove habitats. Furthermore, Fomitopsis nivosella and Punctularia strigosozonata were documented for the first time in Colombia. This study addresses the first exploration of mangrove-associated macrofungi in the country and provides new insights into the hidden fungal diversity and potential of mangrove ecosystems as a latent niche for basidiomycete dispersal along Colombia's Pacific coast.},
}

@article {pmid40557963,
year = {2025},
author = {Shynggyskyzy, N and Madsen, CK and Gregersen, PL and Rasmussen, J and Jørgensen, U and Brinch-Pedersen, H},
title = {Digital PCR enables direct root biomass quantification and species profiling in soil samples.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf276},
pmid = {40557963},
issn = {1532-2548},
abstract = {Roots support plant growth and resilience and are a major route for carbon sequestration. Thus, the study of roots in agricultural and natural systems is essential to develop strategies to mitigate and adjust to climate change. Methods to quantify root biomass in mono- and mixed crop systems are therefore in high demand. A promising approach is to exploit the correlation between root biomass and nuclear DNA. The use of qPCR for the quantitative analysis of root samples has been reported. Here, we show how digital PCR can be used to quantify root DNA from soil samples harboring single species or species mixtures. This molecular method has several advantages over more time-consuming methods, including enhanced sensitivity and absolute quantification of target DNA, increased accuracy and reliability, and the ability to quantify roots directly from soil in different species mixtures. We developed a DNA-based digital droplet PCR (ddPCR) method for root species profiling and biomass quantification directly from soil samples under semi-field conditions. Our findings suggest that implementing this ddPCR method can substantially simplify and improve root quantification of specific species, even in crop mixtures. This method offers a more time- and labor-efficient alternative to traditional techniques (e.g., root separation or C13 labeling). The complement of primer-probe sets presented here can be continuously expanded to include additional plant species, thus broadening the scope of this DNA-based ddPCR method.},
}

@article {pmid40556097,
year = {2025},
author = {Aristya, GR and Budiman, MS and Kasiamdari, RS and Widiastuti, A and Arif, MF},
title = {Genetic Variation and Phylogenetic Analysis of Strawberry (Fragaria spp.) on Yogyakarta and Central Java, Indonesia, Based on rbcL DNA Barcoding.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {28},
number = {3},
pages = {121-130},
doi = {10.3923/pjbs.2025.121.130},
pmid = {40556097},
issn = {1812-5735},
mesh = {Indonesia ; *Phylogeny ; *Genetic Variation/genetics ; *Fragaria/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; Haplotypes ; *DNA, Plant/genetics ; Fruit/genetics ; },
abstract = {Background and Objective: Strawberry (Fragaria spp.) is known for producing fruit with high economic value and significant nutritional content. Recently, the growing diversity of cultivated strawberries in Indonesia has made it challenging to distinguish the original characteristics of early ancestors and identify superior traits. The DNA barcoding, mainly through the chloroplast gene rbcL, offers a precise and detailed method for this identification. This research aims to reconstruct a phylogenetic tree, analyze genetic variation and determine the haplotype distribution of six strawberry cultivars from Java, particularly Yogyakarta and Central Java, based on the rbcL gene. Materials and Methods: The rbcL gene was amplified using DNA amplification techniques with rbcL-F and rbcL-R primers. The resulting data were analyzed to construct a phylogenetic tree using ML via IQtree software and BI using MrBayes software. The alignment results were used to determine genetic distances and identify polymorphic sites. This study assessed intraspecific genetic variation by examining h, identifying polymorphic sites, generating a haplotype network using PopART v1.7 and conducting PCoA with GenAIEx 6.503. Results: The results showed that the rbcL gene was successfully amplified with a length of 1,221 bp after alignment with the GenBank database. Phylogenetic analysis using ML revealed that the six cultivars formed a single clade with a bootstrap value of 97. BI similarly indicated the formation of one clade with a posterior probability value of 1. Haplotype analysis showed that the cultivars 'Californica', 'Knia', 'Mencir', 'Moha' and 'Geolhyang' belonged to the same haplotype group, while the 'Bali×Jumbo' cultivar was placed in a different group. Conclusion: Haplotype network analysis and PCoA further indicated that the genetic variation of Indonesian strawberries, as assessed through the rbcL gene, is similar to strawberries from the United States and China.},
}

Indonesia
*Phylogeny
*Genetic Variation/genetics
*Fragaria/genetics/classification
*DNA Barcoding, Taxonomic/methods
Haplotypes
*DNA, Plant/genetics
Fruit/genetics

@article {pmid40555940,
year = {2025},
author = {Zhai, J and Li, X and Dong, F and Ema, H},
title = {How Faithful Flt3-Cre Mouse is to Hematopoietic Lineage Tracing?.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {40555940},
issn = {2629-3277},
abstract = {Flt3 gene expression is known to occur at a specific development stage of hematopoiesis in mice. Flt3-Cre reporter mice have been utilized in lineage tracing studies. This review systematically evaluates different Flt3-Cre reporter constructs, focusing on labeling efficiency and consistency with endogenous Flt3 expression patterns. We discuss the strengths and limitations associated with employing marker gene expression in lineage tracing. Furthermore, this lineage tracing strategy is compared with clonal tracing strategies such as barcoding and single-cell transplantation. Finally, we propose comparing hematopoietic stem cells identified by barcoding with those identified by transplantation to know the relationship between HSCs in non-stress and stress conditions. HIGHLIGHTS: • Flt3-Cre reporter mice are excellent models to understand hematopoiesis but may not necessarily reflect endogenous expression of Flt3. • The labeling efficiency significantly differs among the Flt3-Cre reporter mice.},
}

@article {pmid40555399,
year = {2025},
author = {Lindenmaier, MP and Bernart, MW and Brinckmann, JA},
title = {Advanced Methodologies for the Quality Control of Herbal Supplements and Regulatory Considerations.},
journal = {Phytochemical analysis : PCA},
volume = {},
number = {},
pages = {},
doi = {10.1002/pca.70000},
pmid = {40555399},
issn = {1099-1565},
abstract = {INTRODUCTION: Herbal supplements and OTC herbal drugs enjoy wide popularity with consumers but their quality has been questioned by genomic methods of testing. Due to complex regulatory environments in Europe and North America, the quality assurance of herbal preparations depends on protocols, which can significantly differ between the respective national and supranational drug control agencies. Modern methods of analysis combine genetic testing (DNA barcoding) with advanced chromatographic techniques as well as traditional microscopic and macroscopic tests to detect adulterants and undesirable constituents of herbs, including alkylphenols, aristolochic acids, and pyrrolizidine alkaloids.

OBJECTIVE: This review will give an account of current trends in herbal drug analysis and explain the shortcomings of existing methodologies. The article will also discuss regulatory protocols, compendial methods and differentiate between dietary supplement testing regimens and the requirements for approved herbal drugs. The purpose of this review is to document current trends in genetic testing and reveal future developments in drug analysis to reduce the possibility of adulterations and assure the authenticity of herbal products.

RESULTS: Chemometric methods and orthogonal approaches aid in the deconvolution of chromatographic and spectral data while expanding databases for nucleotide sequences and mineable spectra support method development in herbal analysis.

CONCLUSION: Genetic testing of herbal products has further increased the capabilities to detect minute adulterations, but such assays are only meaningful in combination with chromatographic and spectroscopic analysis. Despite the advancement of genomic testing, chemometrics, UHPLC and mass spectrometry, cost-effective quality control techniques such as HPTLC in conjunction with microscopic and macroscopic examination remain important particularly in regulated environments.},
}

@article {pmid40552098,
year = {2025},
author = {Ramanan, A and Quek, KH and Chung Mae Sze, N and Oo Xinyen, NI and Kim Hyun Soo, D and Sung, C and Dimitrov, V and Nix, RP and Sng, MHM and Lim, PXJ and Lim, EXY and Wainwright, BJ},
title = {In Troubled Waters: Applying DNA Barcoding to Monitor Singapore's Shark Fin Trade.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71607},
pmid = {40552098},
issn = {2045-7758},
abstract = {The global fin trade poses a significant threat to shark populations; many species of shark are at risk of extinction due to overfishing and unsustainable practices. This study examines the fin trade in Singapore, a globally significant fin trading hub, market and transit point. Using DNA barcoding techniques, we attempted to determine the species of origin for 300 processed fins that could not be identified by visual techniques. Fins were collected from a variety of outlets across Singapore. We identified 12 species, eight of which were identified as threatened on the IUCN Red List of threatened species (critically threatened n = 2, endangered n = 4 & vulnerable n = 2). Of all the samples we identified to the species or genus level, 13 (12 species and 1 entire genus) are listed on CITES Appendix II. This listing means that international trade has to be controlled to prevent further population declines and utilisation incompatible with their survival. Ninety-eight percent of all the identifications made in this work belonged to species that are listed on CITES Appendix II. Demonstrating the importance of regular and repeated monitoring, we identified the blackchin guitarfish (Glaucostegus cemiculus); this is the first occurrence of fins from this species within Singapore and the wider Southeast Asian region. This is a CITES Appendix II listed species and one that has been designated as critically endangered by the IUCN. Without repeated monitoring, the presence of this species in Singpaore would likely have gone undetected.},
}

@article {pmid40549669,
year = {2025},
author = {Surwase, SS and Zhou, XMM and Luly, KM and Zhu, Q and Talebian, N and Anders, RA and Green, JJ and Tzeng, SY and Sunshine, JC},
title = {DNA-barcode-based Multiplex Immunofluorescence Imaging to Analyze FFPE Specimens from Genetically Reprogrammed Murine Melanoma.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/68124},
pmid = {40549669},
issn = {1940-087X},
mesh = {Animals ; Mice ; Paraffin Embedding/methods ; *Fluorescent Antibody Technique/methods ; *Melanoma/genetics/pathology/chemistry ; *Melanoma, Experimental/genetics/pathology/chemistry ; Formaldehyde/chemistry ; *DNA/genetics/chemistry ; Tumor Microenvironment ; Tissue Fixation/methods ; },
abstract = {Presented here is an emerging DNA-barcode-based multiplex imaging technique based on Co-Detection-by-indEXing that analyzes the spatial proteomics of tissue microenvironments. Successful imaging requires a repertoire of well-designed and properly validated antibody panels, but very few currently exist for formalin-fixed paraffin-embedded (FFPE) samples. FFPE offers several advantages over fresh-frozen specimens, such as widespread availability, ease of handling and storage, and the ability to make tissue microarrays (TMAs). Here, we present a protocol to develop an antibody panel for visualizing and analyzing FFPE tissues from a murine melanoma model treated with nanoparticles, which deliver plasmid DNA encoding immunologic signals for tumor microenvironment reprogramming. We also describe an image analysis pipeline using open-source computational tools for annotating tissues, segmenting cells, processing proteomics data, phenotyping cell populations, and quantifying spatial metrics. The protocol offers applications for designing antibody panels in murine FFPE and generating novel insights into the spatial proteomics of complex tissue microenvironments.},
}

Animals
Mice
Paraffin Embedding/methods
*Fluorescent Antibody Technique/methods
*Melanoma/genetics/pathology/chemistry
*Melanoma, Experimental/genetics/pathology/chemistry
Formaldehyde/chemistry
*DNA/genetics/chemistry
Tumor Microenvironment
Tissue Fixation/methods

@article {pmid40547570,
year = {2025},
author = {Mwamula, AO and Bae, CH and Lee, DG and Kim, YS and Lee, YD and Lee, DW},
title = {Description and molecular characterization of Geraldius jejuensis n. sp. (Nematoda: Chambersiellidae) from Korea.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250023},
pmid = {40547570},
issn = {0022-300X},
abstract = {A new species of the genus Geraldius isolated from the wood of a dead black pine tree is characterized using morphological data and molecular DNA barcodes. Geraldius jejuensis n. sp. is characterized by its lateral fields with two incisures; lip region conoid to rounded and continuous with body; hemizonid and excretory pore located posterior to nerve ring; excretory pore opening just at the beginning of hemizonid or within the contour of hemizonid; vulva a transverse slit in ventral view; opening in a depression, creating a circular profile in lateral view; rectum 1.4 to 1.7 times longer than anal body diameter; phasmids located 55.0 to 78.5 μm from anal opening; tail elongated, 146.0 to 177.0 μm long; gubernaculum 27.0 to 33.5 μm long, caudal papillae arrangement of seven pairs pre-cloacal, two adcloacal, and six post-cloacal; and three additional midventral papillae on anterior cloacal lip. The new species was compared with the three known species of the genus, including G. bakeri, G. galapagoensis and G. inserrai. The phylogenetic relationships among species were reconstructed using 18S-rRNA and 28S-rRNA gene sequences. Inferences from both genes corroborate the close morphological relationships between Geraldius and Diastolaimus.},
}

@article {pmid40546919,
year = {2025},
author = {Levenson, HK and Tembrock, LR and Zink, FA and Mollet, KA and Tarpy, DR},
title = {Redefining the Geographic Distribution of Two Cryptic Halictus (Hymenoptera: Halictidae) Species in the Eastern United States.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71570},
pmid = {40546919},
issn = {2045-7758},
abstract = {Incomplete characterization of cryptic species complexes in pollinator communities can limit our understanding of ecosystem function, population dynamics, effects of environmental perturbations, and conservation planning. Molecular tools to distinguish morphologically indistinguishable bee species are therefore necessary but require refinement and validation to make robust inferences. Here we present newly developed primers and demonstrate their successful use for identification of two cryptic bee species, Halictus ligatus and Halictus poeyi, with overlapping ranges in the mid-Atlantic USA. We found that H. ligatus is present at higher elevations while H. poeyi is present at lower elevations, with both species present at three sample sites in central North Carolina, USA. The data generated in this study was combined with publicly available sequence data and analyzed to make inferences about the species ranges of these two bees in the Western Hemisphere. These clarified species distributions help us better understand local pollinator communities, associated habitat features, and abiotic conditions amenable to each, as well as provide insights into patterns related to their speciation.},
}

@article {pmid40546907,
year = {2025},
author = {Teixeira, MAL and Aylagas, E and Pearman, JK and Carvalho, S},
title = {Gaps and Data Ambiguities in DNA Reference Libraries: A Limiting Factor for Molecular-Based Biodiversity Assessments Using Annelids as a Case Study.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71544},
pmid = {40546907},
issn = {2045-7758},
abstract = {Regional DNA reference libraries are essential to improve the accuracy of molecular-based biodiversity assessments, species identification and conservation. However, these libraries are often incomplete, limiting the full potential of molecular tools. In this study, we evaluated the completeness of DNA barcode reference data for annelids from the Red Sea, Arabian Gulf and Gulf of Oman and examined its implications for biodiversity assessments. A database of 2291 worldwide annelid species and 3131-4047 Molecular Operational Taxonomic Units (MOTUs) was compiled from the Barcode of Life Data System (BOLD). Two regional checklists -OBIS (498 species) and Wehe & Fiege (892 species)-were cross-referenced against this database to identify coverage gaps and taxonomic inconsistencies. Only 24% and 23% of species in each checklist, respectively, had corresponding barcodes, and just three species were sampled from the region. Additionally, 43% of BOLD's Barcode Index Numbers (BINs) revealed taxonomic ambiguities. To further assess local annelid biodiversity, we analysed a metabarcoding dataset from 135 Autonomous Reef Monitoring Structures (ARMS) deployed on shallow reefs in the region. This yielded 5375 Amplicon Sequence Variants (ASVs), with 55% classified only to class or phylum level. Of the 1350 MOTUs identified, either none to just 14 species-level identifications were found depending on the taxonomic classification method and database, 10 of which appear to be cryptic species complexes. Based on proposed MOTU/species ratios, we estimate approximately 992 annelid species in the ARMS dataset, highlighting underexplored regional diversity. Manual inspection of clustered ASVs also revealed potential pseudogene artifacts, taxonomic misidentifications up to the class level and underestimation of species matches due to discordant MOTUs. These findings underscore the urgent need to expand regional reference libraries, apply integrative taxonomy and implement refined, user-defined MOTU clustering algorithms to improve molecular biodiversity assessments in the region.},
}

@article {pmid40546449,
year = {2025},
author = {Biketova, AY and Svetasheva, TY and Taylor, AFS and Simonini, G and Gelardi, M and Morozova, OV and Polemis, E and Muñoz, JA and Albert, L and Saitta, S and Wasser, SP and Nevo, E and Zervakis, GI and Vizzini, A and Dima, B},
title = {Morphological and molecular re-assessment of European and Levantine species of the genus Hortiboletus (Boletaceae).},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e144731},
pmid = {40546449},
issn = {2210-6340},
abstract = {Hortiboletus (the former Xerocomusrubellus species complex) is one of the most taxonomically critical and difficult genera for species identification in the family Boletaceae. Here, we provide a detailed morphological and molecular re-assessment of European and Levantine species of Hortiboletus. A new species, H.hershenzoniae, is described from Israel. It is sister to H.engelii and associated with the evergreen oak Quercuscalliprinos and potentially also with Q.ithaburensis. Based on the sequence retrieved from INSDC, this species is also found in Lebanon. Accurate morphological descriptions, comprehensive sampling, type studies, biogeography, macro- and microphotographs and a historical overview on the nomenclatural issues surrounding H.rubellus, H.bubalinus, H.engelii, and H.hershenzoniae are given. An epitype collection is designated for H.rubellus. A key is provided for identification of the European and Levantine taxa. In addition, we propose a novel taxonomic combination Hortiboletusflavorubellus, which is conspecific with Boletusrubellusvar.flammeus, based on the DNA barcoding and phylogenetic analysis of type material. Boletusharrisonii is also shown to be conspecific with H.campestris. A multilocus phylogenetic analysis of four markers (ITS, LSU, tef1-α, and rpb2) reveals that Hortiboletus is a sister genus to Xerocomellus. Using the Genealogical Concordance Phylogenetic Species Recognition method, at least 19 phylogenetic species and eight putative phylogenetic species of the genus Hortiboletus can be delimited. Based on multilocus analysis, it contains from 24 to 25 species-level clades worldwide, 17 out of which represent known species, one newly described and potentially six to seven undescribed species. Tandem repeat insertions within the ITS region (both in ITS1 and ITS2) are reported for the first time, not only in the genus Hortiboletus, but in the entire subfamily Boletoideae. Their identification and characterisation were based on Tandem Repeat Finder analysis and visual assessment of the ITS alignment.},
}

@article {pmid40541962,
year = {2025},
author = {Whiting, FJH and Mossner, M and Gabbutt, C and Kimberley, C and Barnes, CP and Baker, AM and Yara-Romero, E and Sottoriva, A and Nichols, RA and Graham, TA},
title = {Quantitative measurement of phenotype dynamics during cancer drug resistance evolution using genetic barcoding.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5282},
pmid = {40541962},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; 202778/Z/16/Z//Wellcome Trust (Wellcome)/ ; A19771//Cancer Research UK (CRUK)/ ; DRCNPG-May21_100001//Cancer Research UK (CRUK)/ ; },
mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; Phenotype ; Cell Line, Tumor ; Fluorouracil/pharmacology ; *Colorectal Neoplasms/genetics/drug therapy ; HCT116 Cells ; *DNA Barcoding, Taxonomic/methods ; Evolution, Molecular ; },
abstract = {Cancer treatment frequently fails due to the evolution of drug-resistant cell phenotypes driven by genetic or non-genetic changes. The origin, timing, and rate of spread of these adaptations are critical for understanding drug resistance mechanisms but remain challenging to observe directly. We present a mathematical framework to infer drug resistance dynamics from genetic lineage tracing and population size data without direct measurement of resistance phenotypes. Simulation experiments demonstrate that the framework accurately recovers ground-truth evolutionary dynamics. Experimental evolution to 5-Fu chemotherapy in colorectal cancer cell lines SW620 and HCT116 validates the framework. In SW620 cells, a stable pre-existing resistant subpopulation was inferred, whereas in HCT116 cells, resistance emerged through phenotypic switching into a slow-growing resistant state with stochastic progression to full resistance. Functional assays, including scRNA-seq and scDNA-seq, validate these distinct evolutionary routes. This framework facilitates rapid characterisation of resistance mechanisms across diverse experimental settings.},
}

Humans
*Drug Resistance, Neoplasm/genetics
Phenotype
Cell Line, Tumor
Fluorouracil/pharmacology
*Colorectal Neoplasms/genetics/drug therapy
HCT116 Cells
*DNA Barcoding, Taxonomic/methods
Evolution, Molecular

@article {pmid40539248,
year = {2025},
author = {Stegemann, J and Augustin, MN and Ackermann, J and Fizzi, NEH and Neutsch, K and Gregor, M and Herbertz, S and Kruss, S},
title = {Levodopa Sensing with a Nanosensor Array via a Low-Cost Near Infrared Readout.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c02320},
pmid = {40539248},
issn = {1520-6882},
abstract = {Near infrared (NIR) signals are beneficial for biomedical applications due to reduced light absorption, scattering, and autofluorescence in this range, which promises higher signal-to-noise ratios (SNR). Single-walled carbon nanotubes (SWCNTs) fluoresce in the NIR (800-1700 nm) and serve as building blocks for biosensors. To quantify the benefits of NIR fluorescence biosensing, we simulate the SNR considering wavelength-dependent scattering/absorption, autofluorescence, dark currents, and excitation background. We also compare Si and InGaAs PIN phototdiodes (pn diode with an additional intrinsic layer) as detectors for the NIR region. The simulation shows that the SNR of fluorophores in the NIR is higher, but InGaAs detectors are outperformed by Si detectors in the short NIR (<1050 nm). This was also validated in experiments with (6,5)-SWCNTs (emission 990 nm), showing a 1.2-fold higher SNR for Si PIN photodiodes. Next, SWCNTs were chemically modified to create sensor arrays/barcodes that detect levodopa. Monitoring levodopa blood levels is a crucial step for personalized Parkinson's disease treatment. We then combine nanosensors and detectors to engineer a portable low-cost fluorescence reader that scans (6,5)-SWCNT sensor barcodes. It detects levodopa at relevant concentrations (10 μM) in human blood serum. Thus, we combine NIR fluorescent sensors with high SNR and low-cost Si detectors to make use of beneficial NIR signals, which opens opportunities for point-of-care applications.},
}

@article {pmid40539017,
year = {2025},
author = {Vélez, M and Rödel, MO and Carvajal, V and Donoso, DA and Guerra, MA},
title = {First report of flesh-fly (Diptera: Sarcophagidae) myiasis in little-devil poison frog (Anura: Dendrobatidae) from Ecuador.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {27},
number = {},
pages = {101093},
pmid = {40539017},
issn = {2213-2244},
abstract = {We report a case of myiasis in the poison frog Oophaga sylvatica from the Canandé Reserve located in the Chocó region of northwestern Ecuador. We identified the causal agents as larvae of flesh flies, Sarcophagidae, by means of DNA barcoding and morphological features. This represents the first record of myiasis in an anuran in Ecuador and the second record for Dendrobatidae in the Neotropics. This observation may constitute a case of facultative parasitism where larvae are deposited in the frog's wounds, but further research is needed to understand the biological mechanisms underlying this interaction.},
}

@article {pmid40533248,
year = {2025},
author = {Chen, Y and Li, H and Zhao, T and Cui, J and Song, W and Li, H and Fan, G and Chen, R},
title = {Fluorescence Visual Identification of Four Main Varieties of Tibetan Medicinal Berberis cortex Based on Site-Specific PCR Technology.},
journal = {Phytochemical analysis : PCA},
volume = {},
number = {},
pages = {},
doi = {10.1002/pca.70002},
pmid = {40533248},
issn = {1099-1565},
support = {82374001//National Natural Science Foundation of China/ ; 2023MS081//Special Project for Traditional Chinese Medicine Research of Sichuan Provincial Administration of Traditional Chinese Medicine/ ; KJYYB2306//Innovation and Entrepreneurship Projects for College Students in Chengdu University of Traditional Chinese Medicine Science and Technology Park/ ; 202410633067//National Undergraduate Training Program for Innovation and Entrepreneurship/ ; },
abstract = {BACKGROUND: Berberis cortex is a typical multi-origin species in Tibetan medicine, with varying medicinal effects among different species. Establishing a rapid and accurate identification method for the major species of Tibetan medicinal B. cortex, including Berberis vernae Schneid. (SY), Berberis diaphana Maxim. (XH), Berberis kansuensis Schneid. (GS), and Berberis dictyophylla Franch. (CHZ), is conducive to the quality control of B. cortex.

METHODS: Site-specific PCR visualization using SYBR Green I was developed based on rbcL SNP sites for SY, GS, and CHZ. For XH, which cannot be differentiated through rbcL and other barcoding SNP sites, RAPD-PCR methodology was employed to screen for species-specific sequences. A site-specific amplification visualization system was subsequently developed based on the identified sequence.

RESULTS: The developed site-specific PCR visualization systems demonstrated excellent sensitivity, with all systems capable of detecting genomic DNA at concentrations as low as 100 fg. These systems were employed to analyze 16 batches of actual B. cortex samples. The analysis revealed that four samples were identified as SY, six samples as GS, two samples as CHZ, and three samples as XH. All results were concordant with sequencing data. One remaining negative sample was confirmed through sequencing as adulterated with Phellodendri Chinensis Cortex. Further authentication of 10 batches of Tibetan patent medicines containing B. cortex revealed that 2 batches contained both SY and GS, one batch contained both SY and CHZ, three batches contained exclusively GS, and three batches contained XH.

CONCLUSION: A site-specific PCR fluorescence visual identification system has been developed for the authentication of four major B. cortex species, enabling accurate identification of botanical origins in both B. cortex crude materials and Berberis-containing Tibetan patent medicines.},
}

@article {pmid40531408,
year = {2025},
author = {Modeel, S and Chaurasia, M and Siwach, S and Dolkar, P and Negi, RK and Negi, RK},
title = {Mitochondrial Perspective on Species Complexes and Evolutionary Dynamics Within Genus Channa.},
journal = {Biochemical genetics},
volume = {},
number = {},
pages = {},
pmid = {40531408},
issn = {1573-4927},
support = {F. No. EEQ/2019/000214//Science and Engineering Research Board/ ; },
abstract = {The genus Channa, commonly known as Snakeheads comprises a diverse variety of species that hold great significance in the commercial sectors. Their complexity and genetic variety show how adaptable they are to different environmental settings and shed light on their evolutionary history. To delve into the genetic intricacies of the genus Channa, we analyzed mitochondrial genetic diversity using 1372 COI sequences obtained from the Barcode of Life Data System (BOLD) database. The metadata and phylogenetic analysis revealed the presence of species complex within C. gachua and C. marulius, suggesting the potential existence of intra and inter-clades within one species group. Further, we selected four ecologically and economically important taxonomic groups to study their haplotype diversity and genetic differentiation. These species/taxonomic groups include C. striata, C. punctata, gachua species complex, and marulius species complex. The analysis indicated a substantial level of genetic differentiation and haplotype diversity in species groups indicating high gene flow within populations. Mitochondrial introgression and species complexes account for a significant section of errors in DNA barcodes, which are two of the primary challenges associated with employing DNA barcoding to identify species. Highlighting these challenges and ongoing uncertainties in specific taxonomic groups of genus Channa, the study argues that the efficacy of DNA barcoding and the genetic integrity of wild variation may be weakened when speciation results in the establishment of numerous cryptic taxa in a species complex.},
}

@article {pmid40529295,
year = {2025},
author = {Zhang, J and Zhang, C and Zhong, Y},
title = {On small huntsman spiders (Araneae, Philodromidae) occurring in Guizhou and Hubei provinces, China.},
journal = {ZooKeys},
volume = {1240},
number = {},
pages = {327-368},
pmid = {40529295},
issn = {1313-2989},
abstract = {Spiders of the family Philodromidae Thorell, 1869 from Guizhou and Hubei provinces, China are studied. A total of three genera and seven species are reported and illustrated, comprising Sinodromuslanyue sp. nov. (newly recorded genus for Hubei), and all known species from both provinces: Philodromusauricomus L. Koch, 1878, P.guiyang Long & Yu, 2022, P.subaureolus Bösenberg & Strand, 1906, P.paiki Jang, Lee, Yoo & Kim, 2024 (the previously records of P.spinitarsis Simon, 1895 from Guizhou and Hubei are presumed to be misidentifications, and should belong to P.paiki), P.rufus Walckenaer, 1826 (new record for Hubei) and Tibellusjaponicus Efimik, 1999 (new record for Hubei). Detailed descriptions, diagnoses, and illustrations of S.lanyue sp. nov. and P.guiyang are given, and the male of P.guiyang is diagnosed and described in English for the first time. The other five species are also re-illustrated. Their DNA barcodes were obtained for species delimitation, matching of sexes and future use.},
}

@article {pmid40527675,
year = {2025},
author = {Carrasco-Lozano, EC and Carrillo-Ordóñez, GA and Torres-Suarez, G and Noa-Carrazana, JC},
title = {Identification of Dysmicoccus brevipes and its association with PMWaV-1, -2, and -3 in Hawaiiana cultivar and MD-2 hybrid pineapple in Peru.},
journal = {Bulletin of entomological research},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/S000748532510014X},
pmid = {40527675},
issn = {1475-2670},
abstract = {Pineapple cultivation is of economic importance for farmers; however, pineapple production can be affected by pests and diseases. Recently, the presence of mealybugs and pineapple mealybug wilt-associated viruses (PMWaV)-1, -2, and -3 has been reported in the provinces of Satipo and Chanchamayo, in Peru's central jungle. This study aimed to molecularly identify mealybugs collected from the Hawaiiana cultivar and the MD-2 hybrid in those provinces to determine if they are indeed hosts of the PMWaV-1, -2, and -3. Through amplification and sequencing of the internal transcribed spacer ribosomal genes, the mealybugs were identified as Dysmicoccus brevipes. In the phylogenetic analysis of these D. brevipes, Peruvian isolates were associated with isolates from India, China, Taiwan, and Japan. In addition, our results confirmed the presence of PMWaV-1, -2, and -3 in all mealybug specimens collected from both the Hawaiiana cultivar and the MD-2 hybrid tested, with these PMWaVs showing a 99% sequence identity with others recently reported in Peru. Therefore, D. brevipes is a host and probable vector of PMWaV-1, -2, and -3 for the cultivar Hawaiiana and the hybrid pineapple MD-2 in Satipo and Chanchamayo, Peru. Based on these findings and observations of crop management strategies in these provinces, we recommend integrated management practices to control this pest.},
}

@article {pmid40526730,
year = {2025},
author = {Hussain, J and Afzal, G and Haider, MZ and Qadeer, I and Perveen, S and Ahmad, HI and El-Mansi, AA and Gadallah, AA and Sakran Abass, K},
title = {Genetic diversity and phylogenetic relationships of Calotes and Uromastyx in the Cholistan Desert, Pakistan, based on COI gene analysis.},
journal = {PloS one},
volume = {20},
number = {6},
pages = {e0324053},
pmid = {40526730},
issn = {1932-6203},
mesh = {Animals ; Pakistan ; *Phylogeny ; *Lizards/genetics/classification ; *Genetic Variation ; *Electron Transport Complex IV/genetics ; Desert Climate ; DNA, Mitochondrial/genetics ; Haplotypes ; Bayes Theorem ; DNA Barcoding, Taxonomic ; },
abstract = {The Cholistan Desert of Pakistan harbors unique reptile diversity, including ecologically significant agamid lizards of the genera Calotes and Uromastyx, yet their genetic structure remains poorly understood. This study presents the first mitochondrial DNA barcode assessment of these taxa in the region, analyzing 658 bp of the cytochrome c oxidase I (COI) gene from 19 specimens collected across seven desert sites. We employed a combination of distance-based (p-distance, K2P) and phylogenetic methods (Maximum Likelihood, Bayesian Inference) to evaluate genetic diversity and evolutionary relationships. Results revealed pronounced divergence between genera (24-30% K2P distance), with Uromastyx populations showing remarkably low intraspecific variation (0-1%), contrasting with higher diversity in Calotes (0-14%). Demographic analyses suggested stable populations (Tajima's D = 0.93, p > 0.10), though haplotype networks indicated limited gene flow (Nm = 0.12). Our findings: (1) provide the first genetic baseline for these ecologically important desert lizards, (2) identify Uromastyx as potentially more vulnerable to genetic erosion, and (3) demonstrate the utility of COI barcoding for rapid biodiversity assessment in understudied arid ecosystems. The study highlights the Cholistan Desert as an evolutionary significant zone for agamid lizards while underscoring the need for integrated taxonomic approaches to address potential cryptic diversity. All sequence data are publicly available (GenBank PQ896696-PQ896705) to support future conservation genomic studies.},
}

Animals
Pakistan
*Phylogeny
*Lizards/genetics/classification
*Genetic Variation
*Electron Transport Complex IV/genetics
Desert Climate
DNA, Mitochondrial/genetics
Haplotypes
Bayes Theorem
DNA Barcoding, Taxonomic

@article {pmid40526297,
year = {2025},
author = {Vargas-Ortiz, M and Parra, LE},
title = {A New Species of Physocleora Warren 1897 (Lepidoptera: Geometridae) from Atacama and Puna Provinces, Northernmost Chile.},
journal = {Neotropical entomology},
volume = {54},
number = {1},
pages = {72},
pmid = {40526297},
issn = {1678-8052},
mesh = {Animals ; Chile ; Phylogeny ; Male ; Female ; *Moths/classification/anatomy & histology/genetics ; DNA Barcoding, Taxonomic ; },
abstract = {Riparian zones of the Atacama Desert and slopes of the Andes mountain range host a diversity of insect species still unknown, and some lineages of different species of Geometridae have been discovered in recent years in such areas. Here, we describe Physocleora polyphaga Vargas-Ortiz & Parra sp.nov., a polyphagous species closely related to several native plants, distributed in coastal valleys and slopes of the Andes mountain range in the northernmost Chile. We present their diagnostic morphological characteristics, some ecological traits, and a representation of its evolutionary history within Physocleora Warren 1897 from DNA barcode sequence data. To validate the hypothesis of conspecificity of the specimens found, we use species delimitation methods based on genetic distances and phylogenetics.},
}

Animals
Chile
Phylogeny
Male
Female
*Moths/classification/anatomy & histology/genetics
DNA Barcoding, Taxonomic

@article {pmid40525968,
year = {2025},
author = {Lopez-Echartea, E and Dusek, N and Misialek, M and Mahmud-Un-Nabi, MA and Williamson, R and Marathe, K and Geddes, BA},
title = {Culturomics from field-grown crop plants using dilution to extinction, two-step library preparation and amplicon sequencing.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {6},
pages = {},
pmid = {40525968},
issn = {1465-2080},
mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/growth & development ; *Zea mays/microbiology ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Plant Roots/microbiology ; *Pisum sativum/microbiology ; *Crops, Agricultural/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; Gene Library ; Soil Microbiology ; },
abstract = {Culturomics approaches have advanced microbial research by enabling the high-throughput isolation and characterization of a broader range of bacterial taxa, including some previously considered unculturable. Here, we present the testing and optimization of a protocol for isolating and identifying hundreds of cultivable microbes from field-grown plants. This protocol was tested and optimized using the root microbiomes of field-grown corn and pea plants under varying environmental conditions in ND, USA. By employing dilution-to-extinction culturing and a two-step barcoding PCR strategy targeting the V4 region of the 16S rRNA gene, we identified over 200 unique bacterial isolates. The optimized bioinformatic pipeline, built around the DADA2 package, ensured accurate amplicon sequence variant detection and taxonomy assignment. The resulting bacterial isolates span diverse phylogenetic groups, including plant-associated taxa known for promoting plant growth and mitigating stress. Our findings highlight the value of culturomics in generating microbial collections for synthetic community design and advancing plant-microbe interaction research. The protocol's scalability, cost-effectiveness and robust performance demonstrate its potential for widespread application in agricultural microbiome studies.},
}

RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/growth & development
*Zea mays/microbiology
*Microbiota/genetics
Phylogeny
DNA, Bacterial/genetics
Plant Roots/microbiology
*Pisum sativum/microbiology
*Crops, Agricultural/microbiology
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Gene Library
Soil Microbiology

@article {pmid40525124,
year = {2025},
author = {Eygeris, Y and Jozic, A and Henderson, MI and Nelson, D and Sahay, G},
title = {Exploring the potential of saponins as adjuvants in lipid-nanoparticle-based mRNA vaccines.},
journal = {Molecular therapy. Methods & clinical development},
volume = {33},
number = {2},
pages = {101495},
pmid = {40525124},
issn = {2329-0501},
abstract = {Saponins are a class of phytocompounds known for their amphiphilic properties. Here, we have evaluated incorporation of 40 saponins into a model lipid nanoparticle (LNP) formulation and evaluated their performance in vitro and in vivo. We reasoned that the surfactant activity of saponins could be beneficial in the context of cell and gene therapy due to the disruption of the intracellular membranes. We established formulation methodology to incorporate saponins into LNPs and measured their endosomal disruption and transfection efficiency with DNA barcode and mRNA cargoes. We identified two saponins-quillaic acid and macranthoidin B-that increase the LNP transfection efficiency and endosomal disruption. Saponin formulations demonstrated cargo-dependent activation of the innate immune system, as measured by the cell-based assays of interferon regulatory factor (IRF) and NF-κB pathway activation. Quillaic acid LNPs resulted in higher titers of anti-OVA IgG2a in the vaccination studies compared to a "naive" LNP control, which suggests a more Th1-biased immunopathology of these vaccines. As Th2-biased vaccines can trigger an allergic response, an mRNA vaccine with a balanced Th1/Th2 response is more favorable for translation into the clinic. Overall, quillaic acid may serve as an adjuvant for mRNA vaccines and potentially decrease the risk of vaccine-associated adverse events.},
}

@article {pmid40524962,
year = {2025},
author = {Parreño, MA and Werle, S and Buydens, L and Spitz, J and Härtl, F and Montoya, J and Ruedenauer, F and Arisoy, B and Seiler, R and Leroy, C and Feng-Spitz, Q and Nebauer, CA and Ferrari, A and Proessl, N and Borchardt, R and Peters, B and Siebler, S and Reese, M and Schumacher, N and Phung, T and Schildt, K and Ebensberger, J and Seiler, M and Reiter, P and Beelaert, S and Buydens, M and Koirala, S and Moreniere, J and Tänzler, R and Alaux, C and Filipiak, M and Meeus, I and Piot, N and Kuhlmann, M and Requier, F and Klein, A and Brunet, JL and Henry, M and Keller, A and Leonhardt, SD},
title = {Data on visitation records from wild bees and plants along a land use gradient in Germany and Belgium: laboratory work and protocol description for barcoding.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111672},
pmid = {40524962},
issn = {2352-3409},
abstract = {The dataset contains information on plant-bee interactions in an agricultural landscape with diverse intensities of land use management, in Germany and Belgium. It was collected during spring and early summer in 2020 and 2021 using two complementary types of sampling: standardized transects (5 transects of 50 m long in 1 h of netting) and targeted sampling in which flowers were observed for diverse periods of times, anywhere in an area of 50 to 150 m[2]. The species identity was obtained with field keys and DNA barcoding. The dataset is of use for building pollinator networks and in combination with other datasets on environmental characteristics of the area to better understand species distributions and interactions. Indeed, we include in the dataset information on environmental parameters from the plots of sampling (spatial coordinates, land use intensity index, landscape heterogeneity index, plant diversity), which can support further correlational analyses.},
}

@article {pmid40519893,
year = {2025},
author = {Balaji, R and Easwaran, S and Devanathan, K and Sharma, S and Alqahtani, T and Uti, DE and Malik, T},
title = {Unfolding the Complete Chloroplast Genome of Myrica esculenta Buch.-Ham. ex D.Don (1825): Advancing Phylogenetic Insights Within Fagales and Pioneering DNA Barcodes for Precise Species Identification.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71566},
pmid = {40519893},
issn = {2045-7758},
abstract = {This study aims to delineate the chloroplast (cp) genome of Myrica esculenta Buch.-Ham. ex D.Don (1825), a traditional medicinal plant from the Myricaceae family, to elucidate its phylogenetic relationships within the Fagales order. The objective was to assemble the complete cp genome and assess its utility as a molecular marker for species identification and evolutionary analysis. The methodology involved assemby of the cp genome of M. esculenta, which was found to be 159,538 base pairs (bp) in length and exhibited a typical quadripartite structure. This included an 88,830 bp large single-copy (LSC) region, an 18,810 bp small single-copy (SSC) region, and two inverted repeats each of 25,949 bp. Phylogenetic analysis utilized the ycf1 gene sequences from 13 Fagales species. Results indicated that M. esculenta and other Myrica species form a monophyletic clade, with the ycf1 gene showing substantial divergence, suggesting its potential as a novel DNA barcode marker. This marker could significantly improve the resolution of species identification beyond traditional morphological methods. Future perspectives include expanding the genomic datasets across the Myrica genus to enhance the phylogenetic framework and further refine the utility of the ycf1 gene as a DNA barcode for broader applications in plant breeding, herbal drug authentication, and evolutionary studies.},
}

@article {pmid40509709,
year = {2025},
author = {Schumacher, JD and Dusek, N and Mendoza-Suárez, M and Geddes, BA},
title = {Adaptation of Plasmid-ID Technology for Evaluation of N2-Fixing Effectiveness and Competitiveness for Root Nodulation in the Sinorhizobium-Medicago System.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70118},
doi = {10.1111/1462-2920.70118},
pmid = {40509709},
issn = {1462-2920},
support = {FF-NIA21-0000000061m//Foundation for Food and Agriculture Research/ ; //U.S. Alfalfa Farmer Research Initiative of the National Alfalfa & Forage Alliance/ ; },
mesh = {*Plasmids/genetics ; *Nitrogen Fixation ; *Plant Root Nodulation ; Symbiosis ; *Sinorhizobium/genetics/physiology/metabolism ; Plant Roots/microbiology ; *Medicago sativa/microbiology ; },
abstract = {Maximising the nitrogen fixation occurring in rhizobia-legume associations represents an opportunity to sustainably reduce nitrogen fertiliser inputs in agriculture. High-throughput measurement of symbiotic traits has the potential to accelerate the identification of elite rhizobium/legume associations and enable novel research approaches. Plasmid-ID technology, recently deployed in Rhizobium leguminosarum, facilitates the concurrent assessment of rhizobium nitrogen-fixing effectiveness and competitiveness for root nodulation. This study adapts Plasmid-ID technology to function in Sinorhizobium species that are central models for studying rhizobium-legume associations and form economically important symbioses with alfalfa. New Sino-Plasmid-IDs were developed and tested for stability and their ability to measure competitiveness for root nodulation and nitrogen-fixing effectiveness. Rhizobial competitiveness is measured by identifying strain-specific nucleotide barcodes using next-generation sequencing, whereas effectiveness is measured by GFP fluorescence driven by the synthetic nifH promoter. Sino-Plasmid-IDs allow researchers to efficiently study competitiveness and effectiveness in a multitude of Sinorhizobium strains simultaneously.},
}

*Plasmids/genetics
*Nitrogen Fixation
*Plant Root Nodulation
Symbiosis
*Sinorhizobium/genetics/physiology/metabolism
Plant Roots/microbiology
*Medicago sativa/microbiology

@article {pmid40509529,
year = {2025},
author = {Zdeňková, K and Čermáková, E and Vejl, P and Čermáková, A and Vašek, J},
title = {Analytical Methods for the Identification of Edible and Feed Insects: Focus on DNA-Based Techniques.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {40509529},
issn = {2304-8158},
support = {QK23020101//Ministry of Agriculture/ ; LM2023064//Ministry of Education Youth and Sports/ ; },
abstract = {The utilization of insects as a source of essential nutrients holds considerable promise, with the potential to serve as both feed and food. Consequently, there is a necessity to develop control systems, as the undeclared addition of insects to food products and/or non-compliance with labelling regulations may pose health risks and result in financial losses for consumers. This review describes methods for identifying and detecting insect species by targeting biomolecules such as DNA, proteins, saccharides, and metabolites, with a particular focus on DNA-based approaches. This review provides a detailed overview of the application of polymerase chain reaction (PCR) and DNA sequencing methods that are suitable for the analysis of edible and forage insects. The main focus is on identifying species that are approved for use as novel foods or insect feeds within the European Union (e.g., house cricket (Acheta domesticus), common mealworm (Tenebrio molitor), migratory locust (Locusta migratoria), lesser mealworm (Alphitobius diaperinus), black soldier fly (Hermetia illucens), banded cricket (Gryllodes sigillatus), field cricket (Gryllus assimilis), silkworm (Bombyx mori)). However, insect species of global relevance are also discussed. The suitability of DNA analysis methods for accurate species identification, detection of (un)labeled contaminants, and monitoring of genetic diversity has been demonstrated.},
}

@article {pmid40506553,
year = {2025},
author = {Raab, M and Schütz, L and Sommermann, L and Babin, D and Kampouris, I and Francioli, D and Grosch, R and Neumann, G and Deubel, A and Geistlinger, J and Bade, K and Rozhon, W},
title = {Two decades long-term field trial data on fertilization, tillage, and crop rotation focusing on soil microbes.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {986},
pmid = {40506553},
issn = {2052-4463},
support = {16DKWN019 - BioTrain//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0514A - E Program 524 BonaRes, Project DiControl//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 16DKWN019 - BioTrain//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {*Soil Microbiology ; *Crops, Agricultural/growth & development ; *Agriculture/methods ; *Microbiota ; Rhizosphere ; Germany ; Fertilizers ; Plant Roots/microbiology ; },
abstract = {Agricultural long-term field trials provide fundamental data on crop performance and soil characteristics under diverse management practices. This information represents essential knowledge for upcoming challenges in food and nutrition security. Data provided here have been compiled since 2004 from a nitrogen(N)-fertilization intensity, tillage, and crop rotation field trial in Central Germany including standardized metrics regarding soil management, physical soil properties, crop management, crop characteristics, yield, and harvest quality parameters. In 2015, the field trial became a member of the German Agricultural Soil Research Program BonaRes. Numerous measurement results were added including plant physiology and soil and rhizosphere microbiology. DNA of bacterial/archaeal and fungal microbiomes was sequenced in the rhizosphere and root-associated soil following a meta-barcoding approach. Taxonomic and relative abundance data were included in the dataset. The dataset is the first to include information on root characteristics, soil and rhizosphere microbiomes, and crop gene expression. We encourage reuse of these biological field trial data in terms of meta-analysis, modeling and AI approaches.},
}

*Soil Microbiology
*Crops, Agricultural/growth & development
*Agriculture/methods
*Microbiota
Rhizosphere
Germany
Fertilizers
Plant Roots/microbiology

@article {pmid40505585,
year = {2025},
author = {Holzmann, M and Siemensma, F},
title = {A new freshwater monothalamid (Rhizaria, Foraminifera) from the Pyrenees branching within a marine clade.},
journal = {European journal of protistology},
volume = {99},
number = {},
pages = {126156},
doi = {10.1016/j.ejop.2025.126156},
pmid = {40505585},
issn = {1618-0429},
mesh = {*Fresh Water/parasitology ; *Foraminifera/classification/genetics/cytology ; Phylogeny ; Species Specificity ; France ; },
abstract = {Monothalamous (single-chambered) foraminifera are widespread in marine benthic environments and are also a common part of freshwater and soil microbial communities. Based on molecular and morphological characteristics, seven non-marine families are currently recognized, branching either as sisters to marine clades or independently within the paraphyletic class Monothalamida. In this study, we describe a new monothalamous freshwater foraminifera sampled from a Pyrenean pond near the French town of Cauterets. We erect the novel genus Poseidonella, with its type species Poseidonella transaquatica sp. nov. The new species branches within the marine clade E, which includes the genera Psammophaga, Vellaria, Niveus, and Nellya. This represents the first evidence of a mixed clade comprising both marine and freshwater monothalamids, highlighting an ongoing transition from coastal marine environments to freshwater habitats.},
}

*Fresh Water/parasitology
*Foraminifera/classification/genetics/cytology
Phylogeny
Species Specificity
France

@article {pmid40504436,
year = {2025},
author = {Sahin, EC and Aydin, Y and Uncuoglu, AA},
title = {Assessing the accuracy of cp-DNA barcodes in Colchicum species identification.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {584},
pmid = {40504436},
issn = {1573-4978},
support = {111T854//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; FEN-C-DRP-141112-0335//Marmara Üniversitesi/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Chloroplast/genetics ; Species Specificity ; Phylogeny ; Sequence Analysis, DNA/methods ; DNA, Plant/genetics ; Genetic Variation ; Genotype ; },
abstract = {BACKGROUND: The genus Colchicum, belonging to the family Colchicaceae, holds significant economic and medicinal value globally. However, precise identification of many species within this genus is challenging. In order to address this obstacle, we carried out a study involving 155 genotypes from various locations in Türkiye to assess the effectiveness of DNA barcoding, specifically utilizing the matK, rbcL, trnH-psbA chloroplast DNA (cp-DNA) barcode regions, by comparing their effectiveness in distinguishing Colchicum species.

METHODS AND RESULTS: Following PCR amplification and sequence analysis, multiple sequence alignment was conducted. Stop codons were detected and sequences were cleaned. Conserved region identification, and GC content analysis were carried out. Species discrimination was analysed (best match, best close-match, all species barcodes functions). The Wilcoxon Ranked Sum test was used to assess differences in genetic variation within and between species. As a result, trnH-psbA emerged as the most effective locus for species differentiation, with significantly higher intra-specific (mean: 3.915) and inter-specific distances (maximum: 1.844) compared to matK and rbcL. matK displayed moderate identification success rates, while rbcL had the lowest performance. trnH-psbA excelled in the 'best match' and 'best close match' categories; rbcL recorded the highest incorrect identification rates.

CONCLUSION: This study highlights the importance of DNA barcoding, specifically the trnH-psbA locus, in distinguishing Colchicum species. The locus shows significantly higher genetic distances than the matK and rbcL loci, underscoring its effectiveness for species identification. These insights are crucial for comprehending the genetic diversity of Colchicum species and enhancing resources for future taxonomy and conservation efforts.},
}

*DNA Barcoding, Taxonomic/methods
*DNA, Chloroplast/genetics
Species Specificity
Phylogeny
Sequence Analysis, DNA/methods
DNA, Plant/genetics
Genetic Variation
Genotype

@article {pmid40502998,
year = {2025},
author = {Li, J and Li, S and Zhang, X and Yao, Z},
title = {Diversity survey of Pholcus spiders (Araneae, Pholcidae) from eastern Sichuan and neighboring areas, with descriptions of six new species.},
journal = {ZooKeys},
volume = {1240},
number = {},
pages = {39-64},
pmid = {40502998},
issn = {1313-2989},
abstract = {Thirteen spider species of the genus Pholcus Walckenaer, 1805 are reported from a diversity survey in eastern Sichuan and neighboring areas (northeastern Yunnan and western Guizhou). They belong to three species groups and include six newly described species: Pholcusqiaojia Li, Li & Yao, sp. nov. (♂♀, Yunnan) in the bidentatus group; P.aba Li, Li & Yao, sp. nov. (♂♀, Sichuan) and P.wenchuan Li, Li & Yao, sp. nov. (♂♀, Sichuan) in the crypticolens group; P.mengding Li, Li & Yao, sp. nov. (♂♀, Sichuan), P.miyi Li, Li & Yao, sp. nov. (♂♀, Sichuan) and P.yaan Li, Li & Yao, sp. nov. (♂♀, Sichuan) in the yichengicus group. P.bidentatus Zhu, Zhang, Zhang & Chen, 2005 is recorded from Yunnan for the first time and P.kunming Zhang & Zhu, 2009 is recorded from Guizhou and Sichuan for the first time. Detailed diagnoses, descriptions, photomicroscope images, and DNA barcodes of all newly described species are provided.},
}

@article {pmid40502055,
year = {2025},
author = {Morrison, J and Johnson, BK and Shen, H},
title = {Synthbar: A Lightweight Tool for Adding Synthetic Barcodes to Sequencing Reads.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40502055},
issn = {2692-8205},
abstract = {Preparation of single-cell sequencing libraries includes adding nucleotide barcodes to assist with pooling samples or cells together for sequencing. The popularity of droplet-based single-cell protocols has spurred the development of computational tools that expect the read structure of the assay to include a cell barcode (CB). Microwell plate-based protocols, such as the Switching Mechanism At the 5' end of the RNA Transcript (SMART) single-cell RNA sequencing (scRNA-seq) family of methods, typically do not add a CB as part of the library preparation method as there is typically one cell per well and standard unique dual indices are sufficient for multiplexing. While several tools exist to manipulate and parse varying single-cell read structures, no tool is currently available to easily add synthetic CBs to enable use of computational tooling that expects the presence of a CB, such as STARsolo, zUMIs, and Alevin. Synthbar fills this gap as a lightweight tool that is assay agnostic, can add user-defined CBs, and modify read structures.},
}