@article {pmid40907964,
year = {2025},
author = {Egizi, A and Bezhani, F and Jordan, RA and Price, DC},
title = {Parasitism of a US traveler by a nymphal Amblyomma tapirellum Dunn, 1933 (Ixodida: Ixodidae) and review of exotic tick interceptions on humans in the United States.},
journal = {Journal of medical entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jme/tjaf109},
pmid = {40907964},
issn = {1938-2928},
support = {NE2443//USDA-NIFA Multistate/ ; },
abstract = {A resident of Monmouth County, New Jersey, United States removed an engorged nymphal tick after returning from travel to Costa Rica. The tick was identified by cox1 barcoding as Amblyomma tapirellum Dunn, 1933, a Central American species whose immature stages are undescribed. This species is associated with wet, tropical forests, and most host records come from Baird's tapirs (Tapirus bairdii), though feeding on other mammalian orders and on humans has been observed. To date, no human pathogens have been detected in A. tapirellum, although very few specimens have been tested. The A. tapirellum reported here was screened for Rickettsia spp. via qPCR and additionally for bacterial pathogens via 16S amplicon sequencing, and no pathogens were detected. However, we report the presence of a Coxiella-like endosymbiont, common among -Amblyomma spp. We also briefly review 29 published records comprising 14 exotic hard tick species removed from US travelers returning from abroad, most commonly Amblyomma spp. from Africa. Due to the near-worldwide distribution of ticks and tick-borne disease as well as the growing frequency of international tourism, travelers are urged to prevent tick bites and physicians are encouraged to be mindful not only of native tick-borne diseases but potential exposure to exotic tick-borne diseases. There is also a need to improve identification resources for ixodids and for existing resources to be made more accessible.},
}

@article {pmid40906971,
year = {2025},
author = {Papadimitriou, M and Ahn, S and Diamond, BT and Lee, H and McIntyre, JB and Truger, M and Durante, MA and Ziccheddu, B and Osz, K and Landgren, O and Rasche, L and Bahlis, NJ and Neri, P and Maura, F},
title = {Timing genomic antigen loss in multiple myeloma treated with T-cell redirecting immunotherapies.},
journal = {Blood cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2643-3230.BCD-25-0005},
pmid = {40906971},
issn = {2643-3249},
abstract = {Genomic antigen loss is a recurring mechanism of resistance to chimeric antigen receptor T-cell (CAR-T) and T-cell engagers (TCE) in relapsed/refractory multiple myeloma (RRMM). Yet, it remains unclear whether these events are acquired under treatment or merely selected from pre-existing, undetectable clones. By leveraging chemotherapy mutational signatures as temporal barcodes within whole genome sequencing data, we could time genomic antigen escape in 4 out of 11 RRMM patients. In all cases, the biallelic loss was driven by genomic events acquired after exposure to BCMA- and GPRC5D-targeted CAR-T/TCE, and not present at baseline. Longitudinal digital PCR analysis corroborated that resistance mutations were undetectable at therapy initiation but emerged preceding relapse. Among 752 newly diagnosed patients only 2.7% and 9% had monoallelic inactivation of TNFRSF17 and GPRC5D, respectively, with no biallelic loss. Our findings suggest limited utility of mutational screening prior to CAR-T/TCE, while underscoring the importance of dynamic surveillance during therapy.},
}

@article {pmid40905664,
year = {2025},
author = {Thielecke, L and Nattamai, K and Hassan, A and Glauche, I and Geiger, H and Cornils, K},
title = {The impact of donor and recipient age on post-transplantation clonality in murine haematopoiesis.},
journal = {Stem cells (Dayton, Ohio)},
volume = {},
number = {},
pages = {},
doi = {10.1093/stmcls/sxaf059},
pmid = {40905664},
issn = {1549-4918},
abstract = {The sustained production of blood and immune cells is driven by a pool of hematopoietic stem cells (HSCs) and their offspring. Due to the intrinsic heterogeneity of HSCs, the composition of emergent clones changes over time, leading to a reduced clonality in aging mice and humans. Theoretical analyses suggest that clonal conversion rates and clonal complexity depend not only on HSC heterogeneity, but also on additional stress conditions. These insights are particularly relevant in the context of stem cell transplantations, which still remain the only curative option for many hematologic diseases, increasingly considered viable for elderly individuals. However, age-related clonal changes post-transplantation are not well understood. To address this, we conducted a barcode-based assessment of clonality to investigate post-transplantation changes in both homo- and hetero-chronic settings, combined with low- and high-intensity pre-conditioned recipients. A robust and polyclonal engraftment was observed across all groups, but with distinct differences in barcode diversity. In particular, transplanted aged HSCs showed no changes in clonality, regardless of recipient age or pre-conditioning. Young HSCs transplanted into severely pre-conditioned old hosts as well as under reduced pre-conditioning, allowed for full lymphoid reconstitution, but showed substantial differences in clonality. Also, myeloid lineage bias, a hallmark of aged HSCs, was confirmed at a clonal level across all experimental groups. Overall, we found that aged HSCs generally maintain clonal diversity similar to young HSCs, but notable differences emerge under hetero-chronic conditions and varying pre-conditioning regimens. These findings challenge current paradigms and underscore the complex interactions between aging and transplantation conditions.},
}

@article {pmid40905625,
year = {2025},
author = {Trull, A and Worthey, EA and Ianov, L},
title = {Scnanoseq: an nf-core pipeline for oxford nanopore single-cell RNA-sequencing.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf487},
pmid = {40905625},
issn = {1367-4811},
abstract = {MOTIVATION: Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge.

RESULTS: Here we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and transcript-level quantification. The scnanoseq pipeline is implemented using Nextflow and is built upon the nf-core framework, enabling portability across computational environments, scalability and reproducibility of results across pipeline runs. The nf-core/scnanoseq workflow follows best practices for analyzing single-cell and single-nuclei data, performing barcode detection and correction, genome and transcriptome read alignment, unique molecular identifier deduplication, gene and transcript quantification, and extensive quality control reporting.

AVAILABILITY: The source code, and detailed documentation are freely available at https://github.com/nf-core/scnanoseq and https://nf-co.re/scnanoseq under the MIT License. Documentation for the version of nf-core/scnanoseq used for this paper, including default parameters and descriptions of output files are available at https://nf-co.re/scnanoseq/1.1.0.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40904667,
year = {2025},
author = {Goren, M and Feldstein-Farkash, T},
title = {A new Pseudophoxinus species (Teleostei, Cypriniformes, Leuciscidae) from the upper Jordan River basin (Israel) with comments on the status of a few other congeneric species.},
journal = {ZooKeys},
volume = {1249},
number = {},
pages = {303-315},
pmid = {40904667},
issn = {1313-2989},
abstract = {A taxonomic reassessment of Pseudophoxinus populations in the upper Jordan River basin has revealed that specimens previously identified as Pseudophoxinus kervillei actually represent an undescribed species. In addition, earlier taxonomic revisions have shown that P. kervillei is a junior synonym of P. libani and should no longer be regarded as a valid species. In this study, we formally describe the newly recognized species as Pseudophoxinus galilaeus sp. nov. Pseudophoxinus galilaeus sp. nov. is characterized by 39-44 scales along the mid-lateral row, 13-17 pored lateral line scales, and 20-23 predorsal scales. It has 4-5 gill rakers on the lower arch of the first gill, with two being notably short. The species possesses 33-34 vertebrae; its dorsal fin originates at vertebrae 12 or 13, and its anal fin commonly originates at vertebra 19, occasionally extending to vertebra 20 or 21. Pseudophoxinus galilaeus sp. nov. inhabits ponds, lakes, and rivers with slow to moderate currents. A unique DNA barcoding signature (mtDNA COI) revealed that it differs from any other previously bar-coded Pseudophoxinus species. In phylogenetic analyses, it clustered with the Pseudophoxinus species from neighboring countries in the Levant region, suggesting a common ancestor for these species. This analysis shows that sequences of P. kervillei from Turkey differ from P. libani from Lebanon and Syria. Further morphological examination is needed to determine the status of the species.},
}

@article {pmid40902006,
year = {2025},
author = {Zhou, X and Feng, R and Ding, N and Cao, W and Liu, Y and Zhou, S and Deng, Y},
title = {Deep learning guided programmable design of Escherichia coli core promoters from sequence architecture to strength control.},
journal = {Nucleic acids research},
volume = {53},
number = {16},
pages = {},
doi = {10.1093/nar/gkaf863},
pmid = {40902006},
issn = {1362-4962},
support = {2024YFA0918000//National Key R&D Program of China/ ; BK20220089//Distinguished Young Scholars of Jiangsu Province/ ; BE2022322//Key R&D Project of Jiangsu Province/ ; 22378170//National Natural Science Foundation of China/ ; 22478156//National Natural Science Foundation of China/ ; 2022SP-T16-B//"Pilot Plan" Internet of Things Special Project/ ; },
mesh = {*Promoter Regions, Genetic ; *Escherichia coli/genetics ; *Deep Learning ; Gene Expression Regulation, Bacterial ; Gene Library ; },
abstract = {Core promoters are essential regulatory elements that control transcription initiation, but accurately predicting and designing their strength remains challenging due to complex sequence-function relationships and the limited generalizability of existing AI-based approaches. To address this, we developed a modular platform integrating rational library design, predictive modelling, and generative optimization into a closed-loop workflow for end-to-end core promoter engineering. Conserved and spacer region of core promoters exert distinct effects on transcriptional strength, with the former driving large-scale variation and the latter enabling finer gradation. Based on this insight, Mutation-Barcoding-Reverse Sequencing approach was used and constructed a synthetic promoter library comprising 112 955 variants with minimal redundancy and a 16 226-fold expression range. A Transformer-based model trained on this dataset achieved a Pearson correlation of 0.87 with experimentally measured promoter strengths. When combined with a conditional diffusion model, the system enabled de novo generation of promoter sequences with defined strengths, achieving a design-to-measurement correlation of 0.95 and maintaining high accuracy (R = 0.93) across varied sequence contexts. The designed promoters consistently preserved their intended strength gradients, demonstrating robust plug-and-play functionality. This work establishes a scalable and extensible platform (www.yudenglab.com) for deep learning-guided programmable design of Escherichia coli core promoters, enabling precise transcriptional control.},
}

*Promoter Regions, Genetic
*Escherichia coli/genetics
*Deep Learning
Gene Expression Regulation, Bacterial
Gene Library

@article {pmid40901798,
year = {2025},
author = {Bertrand, G and Levallois, O and Santesteban, CG and Nogues, N and Renac, V},
title = {Non-invasive fetal HPA genotyping by UMI-NGS: a robust method for antenatal diagnosis including 48 fetal DNA markers.},
journal = {Blood transfusion = Trasfusione del sangue},
volume = {},
number = {},
pages = {},
doi = {10.2450/BloodTransfus.1070},
pmid = {40901798},
issn = {2385-2070},
abstract = {BACKGROUND: Non-invasive fetal HPA typing is a valuable tool to identify the pregnancies at risk of fetal and neonatal alloimmune thrombocytopenia (FNAIT). Different approaches have been developed, mainly based on real-time PCR and droplet digital-PCR. Those methods have a limited ability to multiplex and require replicates due to the contamination risk. Moreover, in order to exclude false-negative results caused by insufficient cell-free fetal DNA, the presence of fetal DNA is usually assessed with a single epigenetic marker whereas large single-nucleotide variant (SNV) panels are now available to more accurately measure the sample's fetal fraction.

MATERIALS AND METHODS: We developed an innovative method for the simultaneous genotyping of HPA-1, -2, -3, -4, -5, -6, -9 and 15, in combination with a panel of 48 SNV markers, based on cell-free DNA target-enrichment with specific probes. An improved accuracy using NGS sequencing was reached with the Unique Molecular Identifiers (UMIs); these molecular barcodes are short sequences used to uniquely tag each molecule in a sample library.

RESULTS: 81 plasma samples were collected from French and Spanish pregnant women, from 10 to 40 weeks of gestation ([wg]; 4 samples <12 wg; 38 samples 13-24 wg; 39 samples >24 wg). The panel of 48 SNVs allowed a precise quantification of fetal DNA (range: 1.1%-16.1%). All samples but one gave concordant results with the confirmed HPA genotypes. One sample was discordant for HPA-2 and HPA-3, due to false negative cffDNA results for these two loci. However, a low amount of fetal fraction in that sample was effectively alerted by the SNV markers results.

DISCUSSION: In our experience, 16 samples can be simultaneously sequenced and analyzed in a 72 hours assay. UMIs NGS sequencing of HPA and SNV markers constitutes a robust and sensitive method for non-invasive fetal HPA genotyping.},
}

@article {pmid40901553,
year = {2025},
author = {Wei, F and Lin, Y and Tang, D and Liang, Y and Qin, S},
title = {Comparative analysis of complete chloroplast genomes of Flemingia prostrata and Flemingia macrophylla, two commonly used medicinal plants in southern China.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1591427},
doi = {10.3389/fpls.2025.1591427},
pmid = {40901553},
issn = {1664-462X},
abstract = {Flemingia prostrata and Flemingia macrophylla, belonging to the genus Flemingia, are ethnomedicinal plants that contain valuable medicinal and nutritional compounds. However, their medicinal materials are frequently confused in the Chinese medicinal materials market. Moreover, molecular genomic resources for this genus remain limited, which hinders phylogenetic studies. In this study, the complete chloroplast (cp) genomes of F. macrophylla and F. prostrata were sequenced to enable genome comparison and phylogenetic analysis. Both cp genomes exhibited typical quadripartite structures, with genome sizes of 152,937 bp for F. macrophylla and 153,033 bp for F. prostrata. Each genome consisted of a large single copy (LSC) region (83,594 and 83,701 bp, respectively), a small single copy (SSC) region (17,773 and 17,776 bp, respectively), and two inverted repeats (IR) regions (50,570 and 51,556 bp, respectively). A total of 129 genes were annotated in each cp genome, including 8 ribosomal RNAs, 83 protein-coding genes, and 37 transfer RNAs. Comparative analysis revealed that although the overall genome structure, codon usage bias, simple sequence repeats (SSRs), and dispersed repetitive sequences were relatively conserved between the two cp genomes, certain genomic variations were present. Specifically, 286 SNPs and 104 indels were identified, and psaJ-rps18 showed the highest variability and could serve as potential DNA barcode regions. Furthermore, phylogenetic analysis supported a close evolutionary relationship between the genus Flemingia and Cajanus. Divergence time estimation suggested that F. macrophylla and F. prostrata diverged approximately 0.26 million years ago (Mya). Finally, we successfully distinguished the two species using SSR markers. This study lays the foundation for enriching the molecular data and phylogenetic insights of this genus, as well as for the safe application of its medicinal materials.},
}

@article {pmid40900687,
year = {2024},
author = {Chou, TK and Huang, WC and Jhuang, WC and Liao, TY},
title = {Checklist and DNA Barcoding of the Scorpaenidae (Teleostei: Scorpaeniformes) in Taiwan.},
journal = {Zoological studies},
volume = {63},
number = {},
pages = {e37},
pmid = {40900687},
issn = {1810-522X},
abstract = {Species of the family Scorpaenidae are easily misidentified due to their similar appearances, a result of camouflaging to their surroundings. In recent years, many species from this family have been described, and generic placements of some species have been revised. Previously, there were 80 species belonging to 29 genera of the Scorpaenidae recorded in Taiwanese waters. However, their taxonomy has not been revised for decades. It is necessary to update the checklist of the Scorpaenidae occurring in Taiwanese waters based on updated morphological and molecular data. In the present study, we revised the Taiwanese scorpaenids based on 296 specimens and updated the checklist, amounting to a total of 85 species of 29 genera, of which Sebastapistes mauritiana (Cuvier) is a new record, and three species from the genera Phenacoscorpius, Scorpaenopsis, and Sebastapistes are unable to be identified to any species. Using molecular analysis, we conducted the first comprehensive DNA barcoding study of the Scorpaenidae from Taiwanese waters based on a partial cytochrome c oxidase I (COI) gene of 655 bps. A total of 118 COI sequences were generated from voucher specimens of 66 species (28 genera) identified based on morphological characters. The COI sequences of Parascorpaena maculipinnis, Scorpaena pepo, and Scorpaenopsis orientalis are new to online databases. According to the Kimura-2 Parameter (K2P) genetic distance, the mean interspecific variation (15.61%) was distinctly greater than the mean intraspecific variation (0.22%), suggesting a barcoding gap. The maximum likelihood tree showed that all lineages were supported by high bootstrap values.},
}

@article {pmid40898047,
year = {2025},
author = {Hu, Y and Wang, S and Xu, Z and Yan, S and Ali, M and Li, Z and Shao, J},
title = {Chloroplast genome comparison and taxonomic reassessment of Polygonatum sensu Lato (Asparagaceae): implications for molecular marker development in traditional medicinal plants.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {796},
pmid = {40898047},
issn = {1471-2164},
support = {32070370//National Natural Science Foundation of China/ ; },
abstract = {The Polygonati Rhizoma have generated significant market attention for their medicinal and culinary applications. However, morphological similarities and ambiguous species boundaries complicate the identification of genera and species, thereby impeding product development and utilization within Polygonatum sensu lato. Despite the widespread application of the chloroplast genome for taxonomic boundary revisions for Polygonatum s.l., a critical gap persist regarding their genomic applicability and the lack of standardized pipelines for developing species-specific molecular markers capable of rapid discrimination among species. This study aims to assess the effectiveness of chloroplast genomes in clarifying the current taxonomic status of the genera and species of Polygonatum s.l., and develop a reliable process for rapid identification of designated species from other species. A total of 21 chloroplast genomes were sequenced and assembled, and subsequent analyses included phylogenetic inference, multiple molecular species delimitation methods, and an automated screening framework were employed for subsequent analysis. Comparative analyses revealed relatively conserved chloroplast genomes, with notable variation limited primarily to the length of IR and LSC regions. By integrating multiple delimitation methods, the chloroplast genome validated 82.46% of the current classifications of Polygonatum s.l., demonstrating strong support (90.63%) for species represented by multiple sequences, yet only moderate support (70%) for those with single-sequence representation. Additionally, this study established and validated a scalable molecular marker development framework, spanning from identification of species-specific SNPs/InDels to the design of high-resolution molecular markers, illustrated through case studies involving Heteropolygonatum and three medicinally significant Polygonatum species.},
}

@article {pmid40897784,
year = {2025},
author = {Fantozzi, D and Sferra, G and Trupiano, D and Scippa, GS},
title = {Design and application of species-specific primers to Quercus cerris roots' identification in urban forests.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32298},
pmid = {40897784},
issn = {2045-2322},
support = {Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022 adopted by the Italian Ministry of University and Research, CUP: H73C22000300001, Project title "National Biodiversity Future Center-NBFC."//National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4-Call for Tender No. 3138 of 16 December 2021, rectified by Decree No. 3175 of 18 December 2021 of the Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; },
abstract = {Accurate species identification, the first crucial step for effective root studies, is a time-demanding, experience-based and error-prone process. Molecular methods are therefore needed to ensure this process, especially in urban settings where root sampling is challenging. Here, we developed a novel molecular method for root identification in complex environments. Specifically, we focused on detecting Quercus cerris-a species common in European cities and non-urban areas and used in afforestation-from bulk root samples, including those collected non-invasively. To achieve this, we conducted the first comprehensive analysis of candidate DNA regions to discriminate among Quercus species. Among the candidate sequences tested, ITS and ITS2 showed the highest discriminatory power compared to commonly used barcodes such as matK, psbA-trnH, rbcL, rpoC1, trnL-trnF. Based on this results, we designed specific primers to target ITS and ITS2 and we developed a PCR-based protocol capable of reliability and specificity detecting Q. cerris within mixed Quercus root samples. This method was then successfully applied to root bulk samples collected via excavation and non-invasive soil coring in the urban area of Campobasso (central Italy), with results validated through traditional identification techniques. The outcome is a novel, rapid, low-cost, and non-invasive molecular approach for monitoring Q. cerris roots. More broadly, this tool enable in situ root identification and mapping which support the study of root functioning and dynamics in ecosystems and is particularly valuable in challenging urban environments.},
}

@article {pmid40895702,
year = {2025},
author = {Hayashi, E and Amemiya, T and Tomita, T},
title = {Pitfalls of a Drug-Dispensing Audit Support System.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89200},
doi = {10.7759/cureus.89200},
pmid = {40895702},
issn = {2168-8184},
abstract = {Dispensing audit support systems that authenticate pharmaceuticals via barcodes have been introduced into clinical practice to prevent dispensing errors, yet they occasionally generate false warnings, complicating clinical usage. This study sought to identify drugs prone to weight-error false warnings in the C-correct II[®] dispensing audit support system and to clarify its operational problems. We investigated the drugs that caused false weight-error warnings in the system, confirming that such errors did occur. Furthermore, the drugs causing weight errors tended to be significantly heavier than those that did not. Accurately identifying and addressing such operational issues within dispensing audit support systems will minimize the risk of dispensing errors and ultimately enhance medical safety.},
}

@article {pmid40895230,
year = {2025},
author = {Mwamula, AO and Bae, CH and Kim, YS and Lee, DW},
title = {Description of a New Cryptic Rhabditid, Parasitorhabditis paraterebrana n. sp. (Nematoda: Rhabditidae), with Remarks on Two Known Species from Korea.},
journal = {Journal of nematology},
volume = {57},
number = {1},
pages = {20250027},
doi = {10.2478/jofnem-2025-0027},
pmid = {40895230},
issn = {0022-300X},
abstract = {A new cryptic species of the genus Parasitorhabditis isolated from the bark of a dead pine tree was characterized using morphological features, morphometrics, and DNA barcodes. Parasitorhabditis paraterebrana n. sp. is characterized by its stoma 20-24 μm in depth; tips of prorhabdions not bent inwards; metarhabdions with two subventral, and two subdorsal teeth; corpus longer than postcorpus; hemizonid 15.0-26.5 μm posterior to excretory pore; vulva-anus distance 21.5-31.5 μm, ca equal to or slightly less than vulval body diameter; rectum distinctly longer than anal body diameter; female tail cupola-shaped, conoid posteriorly, with an extended spike; male with slender spicules, nearly straight to minimally curved towards a nearly acute to a bluntly rounded tip; and bursa with 10 pairs of bursal rays, with a 2 + 3 + 2 + 3 typical pattern. It differs from the morphologically similar P. terebrana by the non-bent tips of prorhabdions, the corpus being longer than postcorpus, the bursal rays' pattern, and a more cupola-shaped tail in female and DNA barcodes. The DNA phylogenies using the 18S rRNA, 28S rRNA and COI gene markers showed well-supported sister relations of Parasitorhabditis paraterebrana n. sp. with P. terebrana and P. obtusa.},
}

@article {pmid40894274,
year = {2025},
author = {Wu, C and Tao, Z and Wang, Y and Luo, Y},
title = {The revision and phylogenetic position of Hippasa bifasciata Buchar, 1997 (Araneae, Lycosidae).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e166495},
doi = {10.3897/BDJ.13.e166495},
pmid = {40894274},
issn = {1314-2828},
abstract = {BACKGROUND: Hogna Simon, 1885 is the second-largest genus in the family Lycosidae after Pardosa C. L. Koch, 1847 (517 species), including 232 species so far. This genus has a cosmopolitan distribution spanning multiple continents. However, only four species (Hogna rubetra (Schenkel, 1963), Hogna trunca Yin, Bao & Zhang, 1996, Hogna jiafui Peng, Yin, Zhang & Kim, 1997 and Hogna arborea Lo, Wei & Cheng, 2023) have been recorded in China.

NEW INFORMATION: A new combination, Hogna bifasciata (Buchar, 1997), comb. nov. (from Yunnan and Sichuan Provinces in south-western China), is proposed with both morphological and molecular evidence. Detailed morphological descriptions, photographs, scanning electron micrographs and a distribution map are provided. This species is distinguished from congeners by the unique structure of the female epigyne and its somatic pattern. Molecular phylogenetic analyses suggest H. bifasciata (Buchar, 1997) and all analysed Hogna species cluster together within the subfamily Lycosinae and the species is sister to the group, including Hogna frondicola Emerton, 1885, Hogna carolinensis Walckenaer, 1805 and Hogna crispipes L. Koch, 1877.},
}

@article {pmid40892906,
year = {2025},
author = {Holmes, KE and Ferreri, LM and Elie, B and Ganti, K and Lee, CY and VanInsberghe, D and Lowen, AC},
title = {Viral expansion after transfer is a primary driver of influenza A virus transmission bottlenecks.},
journal = {PLoS biology},
volume = {23},
number = {9},
pages = {e3003352},
doi = {10.1371/journal.pbio.3003352},
pmid = {40892906},
issn = {1545-7885},
abstract = {For many viruses, narrow bottlenecks acting during transmission sharply reduce genetic diversity in a recipient host relative to the donor. Since genetic diversity represents adaptive potential, such losses of diversity are thought to limit the opportunity for viral populations to undergo antigenic change and other adaptive processes. Thus, a detailed picture of evolutionary dynamics during transmission is critical to understanding the forces driving viral evolution at an epidemiologic scale. To advance this understanding, we used a barcoded virus library and a guinea pig model of transmission to decipher where in the transmission process influenza A virus populations lose diversity. In inoculated guinea pigs, we show that a high level of viral barcode diversity is maintained. Within-host continuity in the barcodes detected across time furthermore indicates that stochastic effects are not pronounced within the inoculated hosts. Importantly, in both aerosol-exposed and direct contact animals, we observed many barcodes at the earliest time point(s) positive for infectious virus, indicating robust transfer of diversity through the environment. This high viral diversity is short-lived, however, with a sharp decline seen 1-2 days after initiation of infection. Although major losses of diversity at transmission are well described for influenza A virus, our data indicate that events that occur following viral transfer and during the earliest stages of natural infection have a central role in this process. This finding suggests that host factors, such as immune effectors, may have greater opportunity to impose selection during influenza A virus transmission than previously recognized.},
}

@article {pmid40892738,
year = {2025},
author = {Peiris, MALM and Nanayakkara, D and Silva, C and Abeysundara, SP and Wijesinghe, P},
title = {Barcode high-resolution melting (Bar-HRM) analysis to authenticate true cinnamon (Cinnamomum verum) from its adulterants and contaminants.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0328808},
pmid = {40892738},
issn = {1932-6203},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Cinnamomum zeylanicum/genetics/classification ; DNA, Plant/genetics ; *Food Contamination/analysis ; *Cinnamomum/genetics ; },
abstract = {Sri Lankan cinnamon, widely known as true cinnamon (Cinnamomum verum), is a world-renowned commodity. With the high market demand, many incidents have reported adulteration of true cinnamon with other cinnamon species such as Cinnamomum aromaticum, Cinnamomum burmanni, and Cinnamomum loureiroi. Moreover, the contamination of cinnamon products with fungi (Aspergillus flavus) has also significantly negatively impacted the cinnamon export market. Morphological and chemical detection of adulterations has limitations, benchmarking the necessity for precise and effective new detection methods. The current study reports gene-specific novel molecular markers that can be used in Barcode High-Resolution Melting (Bar-HRM) analysis to distinguish C. verum from other substitutes. Six barcode regions (rbcL, trnH-psbA, matK, ITS2, trnL, trnL-trnF) were analyzed. The results demonstrate that trnH-psbA can effectively discriminate all selected cinnamon species from one another. Novel markers were designed to target the diagnostic nucleotide variations found within the designated barcode regions. Commercial cinnamon products and authentic samples of C. verum were used to validate the assay, and the DNA extraction protocol was optimized to ensure the acquisition of high-quality DNA. Bar-HRM was performed with the novel markers, and the four major cinnamon species in the international market were successfully distinguished. The spiked-in A. flavus DNA was also detected in a cinnamon admixture. Hence, these Bar-HRM conditions with the novel gene-specific markers can serve as an economical, efficient, and promising assay to detect the authenticity and purity of cinnamon samples.},
}

*DNA Barcoding, Taxonomic/methods
*Cinnamomum zeylanicum/genetics/classification
DNA, Plant/genetics
*Food Contamination/analysis
*Cinnamomum/genetics

@article {pmid40890382,
year = {2025},
author = {Goulpeau, A and Hedde, M and Ganault, P and Lapied, E and Maggia, ME and Marcon, E and Decaëns, T},
title = {Biotic interactions and environmental filtering both determine earthworm alpha and beta diversity in tropical rainforests.},
journal = {Oecologia},
volume = {207},
number = {9},
pages = {151},
pmid = {40890382},
issn = {1432-1939},
support = {ANR-10-LABX-25-01//ANR/ ; ANR-10-LABX-41//ANR/ ; Our Planet Reviewed//Muséum National d'Histoire Naturelle/ ; CFREF-2015-00004//Canadian Center for DNA Barcoding/ ; BC-Wormbank APEGE 2013//CNRS/ ; },
mesh = {Animals ; *Oligochaeta ; *Biodiversity ; *Rainforest ; Ecosystem ; French Guiana ; Soil ; Tropical Climate ; },
abstract = {Understanding the relative importance of biotic interactions, multiple environmental drivers, and neutral processes in shaping community diversity and composition is a central question for both theoretical and applied ecology. We analysed a dataset describing 125 earthworm communities sampled in 10 localities in French Guiana. DNA barcodes were used to delimit operational taxonomic units (OTUs) that we considered as species surrogates to avoid the taxonomic deficit and calculate community-scale species richness and pair-wise Sørensen beta-diversity. We used log-ratio and generalised linear models to highlight the effects of biotic interactions and environment as drivers of alpha diversity, and generalised dissimilarity models to figure out the relative contribution of space and environment to beta-diversity at different spatial extents. Community-scale alpha diversity was mainly explained by habitat filtering (soil texture) and interspecific competition that limit the number of locally co-existing species. Beta diversity between pairs of communities was mainly explained by distance when comparing communities in similar habitats, by topography and available soil phosphorus when comparing communities in different habitats, and by distance, elevation and climate when comparing all possible pairs of communities. While community composition is determined locally by neutral processes and environmental filtering, biogeographic processes linked to dispersal limitation and adaptation to local environment are the most influential on a regional scale. This highlights the complex interplay of dispersal limitation, biotic interactions and environmental filtering during the process of community assembly.},
}

Animals
*Oligochaeta
*Biodiversity
*Rainforest
Ecosystem
French Guiana
Soil
Tropical Climate

@article {pmid40890121,
year = {2025},
author = {Gao, M and Barile, M and Chabra, S and Haltalli, M and Calderbank, EF and Chao, Y and Zheng, W and Wilson, NK and Laurenti, E and Göttgens, B and Huang, Y},
title = {CLADES: a hybrid NeuralODE-Gillespie approach for unveiling clonal cell fate and differentiation dynamics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8174},
pmid = {40890121},
issn = {2041-1723},
support = {62222217//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Cell Differentiation/genetics ; *Cell Lineage/genetics ; *Single-Cell Analysis/methods ; Clone Cells/cytology ; Algorithms ; Animals ; Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Mice ; Stochastic Processes ; },
abstract = {Recent lineage tracing based single-cell techniques (LT-scSeq), e.g., the Lineage And RNA RecoverY (LARRY) barcoding system, have enabled clonally resolved interpretation of differentiation trajectories. However, the heterogeneity of clone-specific kinetics remains understudied, both quantitatively and in terms of interpretability, thus limiting the power of barcoding systems to unravel how heterogeneous stem cell clones drive the overall cell population dynamics. Here, we present CLADES, a NeuralODE-based framework to faithfully estimate the clone and population-specific kinetics from both newly generated and publicly available LARRY LT-scSeq data. By incorporating a stochastic simulation algorithm (SSA) and differential expression gene (DEGs) analysis, CLADES yields the summary of cell division dynamics across differentiation time-courses and reconstructs the lineage tree of the progenitor cells in a quantitative way. Moreover, clone-level behaviors can be grouped into characteristic types by pooling individual clones into meta-clones for analyses at various resolutions. Finally, we show that meta-clone specific cellular behaviors identified by CLADES originate from hematopoietic stem and progenitor cells in distinct transcriptional states. In conclusion, we report a scalable approach to robustly quantify clone-specific differentiation kinetics of cellular populations for time-series systems with static barcoding designs.},
}

*Cell Differentiation/genetics
*Cell Lineage/genetics
*Single-Cell Analysis/methods
Clone Cells/cytology
Algorithms
Animals
Hematopoietic Stem Cells/cytology/metabolism
Humans
Mice
Stochastic Processes

@article {pmid40887508,
year = {2025},
author = {Wongsuwan, P and Tansawat, R and Khaoiam, P and Rattanakrajang, P and Phokham, B and Uthairangsee, A and Picheansoonthon, C and Sukrong, S},
title = {Integrating untargeted volatile metabolomics and molecular evidence supporting chemotaxonomy in Kaempferia species for more effective identification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32020},
pmid = {40887508},
issn = {2045-2322},
support = {GCUGR1125671060D//The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund)/ ; GCUGR1125671060D//The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund)/ ; },
mesh = {*Metabolomics/methods ; *Zingiberaceae/metabolism/classification/genetics/chemistry ; Gas Chromatography-Mass Spectrometry ; Phylogeny ; *Oils, Volatile ; *Volatile Organic Compounds/metabolism/analysis ; DNA Barcoding, Taxonomic ; },
abstract = {Kaempferia L., a medicinal genus of Zingiberaceae family, is widely distributed from India to Southeast Asia and is rich in terpenoids, flavonoids, phenolics, and volatile oils. Recently, it has gained attention for its diverse biological activities, including antioxidant, anticancer, analgesic, anti-inflammatory, and anti-tuberculosis effects. However, several Kaempferia species complexes exhibit similar morphological characteristics, making identification and classification challenging. This study integrates morphology, molecular phylogeny, and phytochemistry to identify and distinguish Kaempferia species. Phylogenetic relationships were reconstructed using four DNA barcoding markers: one nuclear region (ITS) and three chloroplast markers (matK, rbcL, and psbA-trnH). Untargeted metabolomic analysis using SPME-GC-MS, combined with multivariate statistical analyses, was employed to resolve species relationships and display volatile profiles among 15 Kaempferia species from two subgenera. A total of 217 metabolites were identified by the SPME-GC-MS technique. Variable Importance in Projection (VIP ≥ 1.5) analysis indicated 30 key metabolites, primarily sesquiterpenes, as specific chemotaxonomic markers. This study provides a comprehensive chemical profile of Kaempferia species and highlights metabolomic differences among them. Our findings emphasize the importance of integrating morphological, molecular, and phytochemical approaches for precise identification of closely related species, particularly within Kaempferia. This chemotaxonomic research also provides further applications for species authentication in pharmaceuticals and medicine.},
}

*Metabolomics/methods
*Zingiberaceae/metabolism/classification/genetics/chemistry
Gas Chromatography-Mass Spectrometry
Phylogeny
*Oils, Volatile
*Volatile Organic Compounds/metabolism/analysis
DNA Barcoding, Taxonomic

@article {pmid40887478,
year = {2025},
author = {Luce, JJ and Reardon-Lochbaum, CA and Cadinu, P and Xu, RJ and Aceves-Salvador, J and Semizoglou, E and Wong, B and Lopez, I and Cantor, AB and Renthal, W and Moffitt, JR},
title = {Protocol optimization improves the performance of multiplexed RNA imaging.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32030},
pmid = {40887478},
issn = {2045-2322},
support = {5T32HL007574/HL/NHLBI NIH HHS/United States ; R01HL159106/HL/NHLBI NIH HHS/United States ; R01HL159106/HL/NHLBI NIH HHS/United States ; U19NS130617/NS/NINDS NIH HHS/United States ; U19NS130617/NS/NINDS NIH HHS/United States ; R01GM143277/GM/NIGMS NIH HHS/United States ; },
mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA/genetics/analysis ; Humans ; Animals ; *Single Molecule Imaging/methods ; },
abstract = {Spatial transcriptomics has emerged as a powerful tool to define the cellular structure of diverse tissues. One such method is multiplexed error robust fluorescence in situ hybridization (MERFISH). MERFISH identifies RNAs with error tolerant optical barcodes generated through sequential rounds of single-molecule fluorescence in situ hybridization (smFISH). MERFISH performance depends on a variety of protocol choices, yet their effect on performance has yet to be systematically examined. Here we explore a variety of properties to identify optimal choices for probe design, hybridization, buffer storage, and buffer composition. In each case, we introduce protocol modifications that can improve performance, and we show that, collectively, these modified protocols can improve MERFISH quality in both cell culture and tissue samples. As RNA FISH-based methods are used in many different contexts, we anticipate that the optimization experiments we present here may provide empirical design guidance for a broad range of methods.},
}

*In Situ Hybridization, Fluorescence/methods
*RNA/genetics/analysis
Humans
Animals
*Single Molecule Imaging/methods

@article {pmid40883593,
year = {2025},
author = {Nama, S and Shanmughan, A and Akter, S and K, AW and Bhushan, S and Ramteke, K and Deshmukhe, G and Jaiswar, AK and Kumar, AP and Nayak, BB},
title = {DNA barcoding reveals the temporal variation of ichthyoplankton assemblages and their relationship with environmental variables in a tropical mangrove estuary.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {9},
pages = {1060},
doi = {10.1007/s10661-025-14473-w},
pmid = {40883593},
issn = {1573-2959},
mesh = {*Estuaries ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Environmental Monitoring ; Animals ; Seasons ; *Wetlands ; Plankton ; *Zooplankton/classification/genetics ; Fishes/classification ; },
abstract = {Seasonal ichthyoplankton dynamics and their relationship with environmental parameters were studied in the Karanja mangrove estuary from January 2022 to March 2023 to determine ichthyoplankton biodiversity. Twenty-four ichthyoplankton species from 16 families and 3 orders were identified using morphological characteristics and DNA barcoding methods. The most dominant family was Mugilidae, contributing 20% of the total ichthyoplankton assemblage, followed by Engraulidae (12%). The maximum abundance of ichthyoplankton was recorded during the monsoon seasons, indicating that Karanja estuary can be a spawning ground for Mugil cephalus, Osteomugil perusii, Stolephorus insularis, Thryssa hamiltonii, Escualosa thoracata, Terapon jarbua, and Dendrophysa russelii. Redundancy analysis (RDA) and biotic-environmental (BIO-ENV) analysis revealed that water temperature, salinity, dissolved oxygen, nitrate, and transparency were the prevailing environmental factors affecting seasonal variation of ichthyoplankton in the estuary. The Shannon-Wiener index (index = 2.54), Margalef index (index = 2.60), and Pielou's index (index = 0.95) indicate diverse ichthyoplankton dynamics in the estuary. This is the first report of ichthyoplankton biodiversity from the Karanja estuary using integrated taxonomy, with the first-time documentation of Tridentiger barbatus and Scombrops sp. in the region. These findings provide valuable insights into the intricate interactions between environmental factors, food plankton, and ichthyoplankton assemblages, which will be crucial for biodiversity inventories, effective management, and sustainability of resources.},
}

*Estuaries
*DNA Barcoding, Taxonomic
*Biodiversity
*Environmental Monitoring
Animals
Seasons
*Wetlands
Plankton
*Zooplankton/classification/genetics
Fishes/classification

@article {pmid40883345,
year = {2025},
author = {Shah, HK and Fathima, PA and Gupta, B and Rahi, M and Saini, P},
title = {Molecular identification of wild caught phlebotomine sand flies (Diptera, Psychodidae) by mitochondrial DNA barcoding in India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31950},
pmid = {40883345},
issn = {2045-2322},
support = {6/9-7(331)/2020/ECD-II//Indian Council of Medical Research/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; India ; Phylogeny ; *Psychodidae/genetics/classification ; Electron Transport Complex IV/genetics ; *DNA, Mitochondrial/genetics ; },
abstract = {Sand flies are medically important insects with diverse distributions and roles in pathogen transmission. Globally, over a thousand species have been documented, with Indian sand fly fauna currently comprising 71 species. Traditional morphological identification faces challenges due to specimen damage and the presence of cryptic species. This study utilizes DNA barcoding of the mitochondrial marker, cytochrome c oxidase subunit I (COI) to enhance accurate identification of Indian sand flies. A total of 10,456 sand flies, representing 31 species, were collected from 26 districts across six Indian states between 2018 and 2024. Legs from voucher specimens were used to generate ~ 720 bp COI sequences, which were analyzed phylogenetically. In total, 169 COI sequences were generated. A common 570 bp region was selected for final analysis. The gene showed an AT-rich composition with a GC content of 34.8%. Maximum likelihood phylogenetic analysis, supported by ABGD and ASAP species delimitation methods, confirmed the majority of morphological identifications. Species delimitation analyses using ABGD, ASAP, and bPTP grouped the specimens into 32, 34, and 68 clusters, respectively, with bPTP showing evidence of over splitting. Despite this, COI-based classification proved effective in delineating species boundaries and serves as a reliable tool for the DNA barcoding of sand fly species.},
}

Animals
*DNA Barcoding, Taxonomic/methods
India
Phylogeny
*Psychodidae/genetics/classification
Electron Transport Complex IV/genetics
*DNA, Mitochondrial/genetics

@article {pmid40881467,
year = {2025},
author = {Dadykin, IA and Pereboev, DD},
title = {Revision of Lathonurarectirostris (O.F. Müller, 1785) (Anomopoda, Macrothricidae) leads to translocation of East Asian populations to a separate species, Lathonurabekkerae sp. nov.},
journal = {ZooKeys},
volume = {1249},
number = {},
pages = {147-192},
doi = {10.3897/zookeys.1249.154922},
pmid = {40881467},
issn = {1313-2989},
abstract = {The family Macrothricidae (Branchiopoda: Anomopoda) remains one of the least studied groups of water fleas (Cladocera). One of macrothricids with an unclear phylogenetic status is Lathonura Lilljeborg, 1853 comprising a single universally accepted valid species, L.rectirostris (O.F. Müller, 1785). Despite its wide distribution in the Northern Hemisphere, no studies were conducted to prove conspecificity of L.rectirostris from different regions and properly describe its gamogenetic stages. Here, the morphological and genetic diversity of Lathonura in the Holarctic is revised. Our results show that in East Eurasia and Alaska a separate species of the genus occurs, L.bekkerae sp. nov., which differs from L.rectirostris s. str. by the posteroventral valve armature, structure of antenna I, and ephippium ornamentation. Mitochondrial DNA barcoding supports separation of L.bekkerae sp. nov. and reveals a deeply divergent clade of L.rectirostris s. l. in Canada, for which parthenogenetic females are morphologically indistinct from those of L.rectirostris s. str. Lathonura distribution fits well to the known patterns of Anomopoda biogeography. Males of Lathonura possess two additional setae at antenna II basipodite, P1 with a subdistal lobe lacking setae, P1 IDL with a hook and an additional seta, and an unmodified postabdomen. As noted in some previous studies, Lathonura likely represents a phylogenetic lineage distinct from the subfamily Macrothricinae, differing from most macrothricines by the absence of Fryer's fork at P1 inner endite anterior setae and presence of P1 accessory seta. However, the phylogenetic position of the genus and its diversity in South Eurasia, Africa, and North America requires further studies.},
}

@article {pmid40880439,
year = {2025},
author = {Stein, F and Gailing, O},
title = {Identification of BOLD engine deficiencies and suggestions for improvement based on a curated Tachina (Diptera) record set.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0331216},
doi = {10.1371/journal.pone.0331216},
pmid = {40880439},
issn = {1932-6203},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Diptera/genetics/classification ; Algorithms ; },
abstract = {The increasing number of Barcode of Life Database (BOLD) records per species and genus leads to contradictory species assignments within Barcode Index Numbers (BINs), serving as identifiers for the BOLD ID engine. To examine these issues, we analyzed a dataset comprising original and curated BOLD records for the genus Tachina (Insecta: Tachinidae), based on a previous publication. This dataset included both published and private records. We were able to assess the performance of the BOLD engine's species determination algorithm, Refined Single Linkage (RESL), and compare it to Assemble Species by Automatic Partitioning (ASAP). Additionally, we investigated the usage of BINs by the BOLD v4 ID engine. Our analysis confirmed that BOLD queries primarily rely on BINs for species identification, although some cases deviated from this pattern, resulting in species matches inconsistent with the assigned BIN species. ASAP was found to be superior to RESL due to RESL's adherence to the concept of the DNA barcoding gap. Moreover, we found that taxonomic misassignments, inconsistencies in BIN formation, and missing metadata also contribute significantly to unreliable identifications. These problems appear to stem from both algorithmic limitations and deficiencies in submission and post-submission processes. Moreover, we noted that the default mode of the BOLD v4 ID engine integrates both private and published data, leading to public records based solely on COI-based identifications. However, this issue may now be mitigated, as the BOLD v5 ID engine default mode exclusively employs published data. To enhance BOLD's reliability, we propose improvements to submission and post-submission processes. Without such amendments, the accumulation of contradictory species assignments within BINs will continue to rise and the reliability of specimen identification by BOLD will decrease.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Diptera/genetics/classification
Algorithms

@article {pmid40877266,
year = {2025},
author = {Le, TTM and Jin, L and Wang, RJ and Deng, YF and Yan, HF and Ge, XJ},
title = {A DNA barcode reference library of native seed plants in the Guangdong-Hong Kong-Macao Greater Bay Area.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1505},
pmid = {40877266},
issn = {2052-4463},
mesh = {*DNA Barcoding, Taxonomic ; China ; *Seeds/genetics ; Biodiversity ; *Plants/genetics/classification ; Ecosystem ; },
abstract = {The Guangdong-Hong Kong-Macao Greater Bay Area (GBA) is a critical region in the Pearl River Delta along the South China coast and has a remarkably diverse seed plant species. However, factors such as rapid urbanization and climate change are increasingly impacting the resilience of the Greater Bay Area's ecosystems. While morphology identification has many drawbacks such as slow process, incorrect identifications, and unreliable for distinguishing species at the growth stage; DNA barcoding has become a valuable tool in plant taxonomy by effectively overcoming many limitations of traditional methods. In this study, we constructed a comprehensive DNA barcoding database for native seed plants in the GBA using three barcodes (matK, rbcL, and ITS2). A total of 2864 native species from 1117 genera and 192 families were represented, of which 695 individuals from 516 species that were newly generated. This study enhances sustainable management and accurate identification of species, facilitates research on plant evolution and ecology, and supporting biodiversity monitoring and conservation efforts within the Greater Bay Area.},
}

*DNA Barcoding, Taxonomic
China
*Seeds/genetics
Biodiversity
*Plants/genetics/classification
Ecosystem

@article {pmid40875882,
year = {2025},
author = {Chen, A and Lan, F and Ding, Y and Tian, R and Zheng, W and Wu, Q and Zhang, P and Fang, X and Yang, C},
title = {In Situ MicroRNA Profiling of Single Tumor Extracellular Vesicles for Precise Prostate Cancer Diagnosis.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c02902},
pmid = {40875882},
issn = {1520-6882},
abstract = {MicroRNAs (miRNAs) packaged within extracellular vesicles (EV) exhibit remarkable stability in circulation and reflect the genetic and epigenetic characteristics of their parent cells, making them promising biomarkers for cancer diagnosis. However, the intrinsic heterogeneity of EV populations and the low abundance of miRNAs in early stage cancer pose a challenge in the sensitive detection of miRNAs in tumor-cell-derived EV (TEV). Herein, we present a one-pot strategy named miR-nSTEV for specific recognition and in situ miRNA profiling of TEV at the single-particle level for precise prostate cancer (PCa) diagnosis. Utilizing dual-surface protein recognition (CD63 and EpCAM) and orthogonal DNA barcoding-based fusion between the identified TEV and DNA-tagged liposome encapsulating variant miRNA probes (Tag-Lipo probes), our approach enables selective isolation and precise miRNA analysis of individual TEVs by nanoflow cytometry (nFCM). By integrating dual-protein sorting, DNA-directed fusion, and nFCM detection into one platform, miR-nSTEV effectively eliminates interference from free nucleic acids and RNases, significantly enhancing the detection fidelity. As a proof of concept, we profiled six PCa-associated miRNAs (miR-153, miR-183, miR-18A, miR-181, miR-429, and miR-940) in both cell culture medium and clinical plasma samples. The miR-nSTEV assay demonstrated superior diagnostic performance, achieving 100% accuracy in distinguishing PCa patients from healthy donors (HD), outperforming conventional RT-qPCR while simplifying the workflow. Overall, miR-nSTEV offers a robust, sensitive, and noninvasive tool for real-time TEV miRNA analysis, paving the way for early detection and precision diagnostics in PCa patients.},
}

@article {pmid40874976,
year = {2025},
author = {Jiang, F and Yan, L and Jing, X and Chen, G and Wang, Y and Zhao, C and Huang, Y},
title = {Insights into traditional Chinese medicine: molecular identification of black-spotted tokay gecko, Gekko reevesii, and related species used as counterfeits based on mitochondrial 16S rRNA gene sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/24701394.2025.2550967},
pmid = {40874976},
issn = {2470-1408},
abstract = {Authentication of traditional Chinese medicine (TCM) is challenging due to DNA degradation in Chinese medicinal materials, which are usually processed and stored dry. The standard DNA barcoding length (648 bp) or longer are difficult to amplify, which makes it difficult to identify adulterants in Chinese medicinal materials. In this study, we used the mitochondrial 16S rRNA gene (< 200bp) as a barcode to differentiate black-spotted tokay geckoes (Gekko reevesii) from the related species used as counterfeits. We collected 63 specimens from 17 species of G. reevesii and their counterfeits, and each specimen generated a 189 bp 16S rRNA gene sequence. The average uncorrected p-distances within genuine G. reevesii was 0.9%, while the average uncorrected p-distances between G. reevesii and their counterfeits was 6.3% (at a minimum). According to phylogenetic analysis and genetic distances, the genuine G. reevesii samples collected in this study constitute a monophyly that can be distinguished from its counterfeits in TCM formulations, including G. gecko (red-spotted tokay geckos), which have very similar morphology. Thus, the short 16S rRNA barcode provides an effective tool for distinguishing G. reevesii from its counterfeits, ensuring the safety and efficacy of clinical medications containing components from G. reevesii in TCM.},
}

@article {pmid40872302,
year = {2025},
author = {Wisely, SM and Torhorst, CW and Botero-Cañola, S and Atsma, H and Burkett-Cadena, ND and Reeves, LE},
title = {Evaluation of Mosquito Blood Meals as a Tool for Wildlife Pathogen Surveillance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/pathogens14080792},
pmid = {40872302},
issn = {2076-0817},
support = {7004318//United States Department of Agriculture/ ; },
mesh = {Animals ; *Animals, Wild/virology/blood ; *Culicidae/virology/physiology ; Swine ; Deer/blood/virology ; Florida ; Turkeys/blood ; DNA Barcoding, Taxonomic ; },
abstract = {Mosquito blood meals provide a biological sample of host blood which can then be used in downstream applications including host-pathogen detection. We conducted DNA barcoding to identify the host species of blood meals from 4557 blood engorged mosquitoes collected in south central Florida, USA. We identified 314 blood meals from invasive wild pigs, 219 wild turkey blood meals, and 1046 white-tailed deer blood meals. From a subset of these host blood meals, we used molecular assays to detect the nucleic acids of Torque teno sus virus 1 (TTSuV1) in wild pig blood meals, Lymphoproliferative virus (LPDV) in wild turkey blood meals, and bluetongue virus (BTV) in white-tailed deer blood meals. None of these wildlife pathogens are transmitted by mosquitoes, but viral nucleic acids circulate in the peripheral blood of host species during or post infection. Prevalence of TTSuV1 in wild pig blood meals was 34%; in wild turkey blood meals the prevalence of LPDV was 2.7%, and BTV prevalence in blood meals of white-tailed deer was 3.6%. These prevalence values were similar to estimates obtained from peripheral blood collected directly from these hosts in Florida. Our analysis suggests that mosquito blood meals are a valuable sampling tool for the detection of wildlife pathogens. We suggest that this type of exogenous xenosurveillance, using mosquitoes to infer information about the vertebrate host, is distinct from endogenous xenosurveillance in which the goal is to understand the role of the arthropod in vectoring a pathogen.},
}

Animals
*Animals, Wild/virology/blood
*Culicidae/virology/physiology
Swine
Deer/blood/virology
Florida
Turkeys/blood
DNA Barcoding, Taxonomic

@article {pmid40870646,
year = {2025},
author = {Ma, S and Dai, L and Lv, H and Wei, Y and Zhang, X},
title = {Discobola Osten Sacken, 1865 (Diptera, Limoniidae) in China: Taxonomic Review, Updated Distribution, and DNA Barcoding.},
journal = {Insects},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/insects16080845},
pmid = {40870646},
issn = {2075-4450},
support = {32470481//the National Natural Science Foundation of China/ ; },
abstract = {The genus Discobola Osten Sacken, 1865 from China is taxonomically reviewed using an integrative approach that combines detailed morphological examination and molecular analysis. Discobola parvispinula (Alexander, 1947), a species widely distributed across the Palaearctic region, is newly recorded from China. Updated distributional data are presented for species known from China: D. annulata (Linnaeus, 1758), D. armorica (Alexander, 1942), D. margarita Alexander, 1924, and D. taivanella (Alexander, 1930). Detailed redescriptions and illustrations, including intraspecific morphological variation, are provided for these species. An identification key to Chinese Discobola species is also presented. Geographical analysis reveals a higher species richness in southern China and the Qinghai-Tibet region, with a progressive decline toward northern and northwestern China. The first DNA barcode reference library for Chinese Discobola is established, comprising 15 mt COI sequences from five species. These sequences, analyzed alongside an additional 101 mt COI sequences from Discobola species in other countries, show that intraspecific divergence within the genus remains below 7.4%, while interspecific divergence ranges from 7.6% to 17.7%. These findings provide important insights into the taxonomy, species delimitation, and biogeography of Discobola in China, contributing to a more comprehensive understanding of Discobola diversity across the region.},
}

@article {pmid40870559,
year = {2025},
author = {Nedeljković, Z and Mengual, X and Ricarte, A},
title = {Revision of the North African Hoverflies of the Genus Xanthogramma Schiner, 1861 (Diptera: Syrphidae), with Description of a New Species.},
journal = {Insects},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/insects16080758},
pmid = {40870559},
issn = {2075-4450},
support = {PGC2018-095851-A-C65//Ministerio de Ciencia, Innovación y Universidades/ ; Fauna y aves marinas exp P2C4I1.S000A2//Tragsatec/ ; },
abstract = {North Africa has a poorly and unevenly known hoverfly fauna. Xanthogramma Schiner, 1861 (Syrphinae, Syrphini) is represented in this territory by some scattered records of four species, Xanthogramma dives (Rondani, 1857), Xanthogramma evanescens Becker & Stein, 1913 (endemic to North Africa), Xanthogramma marginale (Loew, 1854), and Xanthogramma pedissequum (Harris, 1776). After examination of old Xanthogramma material collected in Tanger, Morocco, from the 'Museo Nacional de Ciencias Naturales, Madrid, Spain (MNCN)', specimens with distinctive morphology were spotted and found to be different from a syntype of X. evanescens collected in the same locality. Consequently, we revised all the available material of Xanthogramma from North Africa, characterised a new species, proposed a lectotype for X. evanescens, and provided an identification key to the North African species of this genus. The new species is also found in Tunisia and differs from X. evanescens in facial width, colour of the thoracic pleura, length of mesonotum hairs, wing pollinosity, and shape of the yellow maculae on tergum 2.},
}

@article {pmid40869309,
year = {2025},
author = {Zhang, Z and Liu, C and Gong, J and Su, C and Liu, Z and Li, J and Zhang, H},
title = {Distinct Phosphorylation Patterns of AT1R by Biased Ligands and GRK Subtypes.},
journal = {International journal of molecular sciences},
volume = {26},
number = {16},
pages = {},
doi = {10.3390/ijms26167988},
pmid = {40869309},
issn = {1422-0067},
mesh = {Phosphorylation ; *Receptor, Angiotensin, Type 1/metabolism/genetics/chemistry ; Humans ; Ligands ; HEK293 Cells ; Angiotensin II/metabolism/pharmacology ; *G-Protein-Coupled Receptor Kinases/metabolism ; Signal Transduction ; Amino Acid Motifs ; Mutation ; },
abstract = {G protein-coupled receptors (GPCRs) transmit through G proteins upon agonist activation, followed by phosphorylation by GPCR kinases (GRKs) to initiate β-arrestin signaling. However, the molecular mechanisms underlying GPCR signaling regulation by distinct agonists, GRK subtypes, and phosphorylation patterns remain poorly understood. The angiotensin II (AngII) type 1 receptor (AT1R), a prototypical GPCR, serves as an ideal model for studying biased ligands and signaling. Here, we investigated the wild-type (WT) AT1R and mutants of three potential phosphorylation motifs at its C-terminus (Motif I: S326/S328/S331, Motif II: T332/S335/T336/S338, and Motif III: S346/S347/S348/T349) using unbiased agonist AngII, β-arrestin-biased agonist TRV026, and G protein-biased agonist TRV056, along with GRK2/3/5/6 subtypes. We employed phosphorylation assays, β-arrestin pull-down experiments, molecular dynamics simulations, and AlphaFold3 predictions to dissect these mechanisms. Our results reveal that GRK2-mediated AT1R phosphorylation is abolished by mutations in Motifs I and II, with Motif II exhibiting a more pronounced effect. This phosphorylation was enhanced by Gβγ subunits. In contrast, GRK3-mediated phosphorylation remained unaffected by any mutations. GRK5 specifically phosphorylated Motif II, while GRK6 phosphorylated Motif II with the unbiased agonist AngII and both Motifs I and II with biased agonists TRV026 and TRV056. Notably, Motif II mutations reduced β-arrestin1/2 recruitment by GRK5/6 but not GRK2/3. Molecular dynamics simulations demonstrated that Motif II phosphorylation minimized steric hindrance, facilitating stable β-arrestin interactions, whereas Motif I phosphorylation increased intramolecular contacts that potentially impede recruitment. AlphaFold3 models provided detailed insights into the interactions between Motif II and β-arrestin1/2. Collectively, our findings elucidate diverse AT1R phosphorylation patterns driven by different agonists and GRK subtypes, offering a framework for developing signaling-biased AT1R therapeutics by decoding GRK-specific phosphorylation barcodes.},
}

Phosphorylation
*Receptor, Angiotensin, Type 1/metabolism/genetics/chemistry
Humans
Ligands
HEK293 Cells
Angiotensin II/metabolism/pharmacology
*G-Protein-Coupled Receptor Kinases/metabolism
Signal Transduction
Amino Acid Motifs
Mutation

@article {pmid40868840,
year = {2025},
author = {Tian, C and Li, J and Zhang, Y and Zhang, J and Gao, X and Yin, X and Yang, L and Feng, H},
title = {Involvement of Gonolabis distincta in the Control of Root Maggots in Garlic Fields.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/life15081192},
pmid = {40868840},
issn = {2075-1729},
support = {232103810016//Scientific and technological breakthrough foundation of Henan Province/ ; :254000510002//Project of Central Plains scholars/ ; },
abstract = {Garlic root maggots are the main pest of garlic in Qi County, Henan Province, China, which has become an important factor restricting the development of the garlic industry. Earwigs play an important role in controlling root maggots because of their similar ecological niches. In this study, through DNA barcoding and morphological identification, the following root maggots and main earwigs species from Qi County were quickly identified: Delia platura (Meigen), Bradysia odoriphaga Yang et Zhang, Delia antiqua (Meigen), Muscina angustifrons (Loew), Lucilia sericata (Meigan), and the main species of earwigs was Gonolabis marginalis (Dohrn). D. platura was the dominant species and accounted for 98% among all garlic root maggots. The predation ability for each stage of G. distincta on the larvae and pupae of D. platura showed that G. distincta at different developmental stages preyed on both the the larvae and the entire pupae of D. platura. Among them, female adults had the strongest predation ability and the largest daily predation on first instar larvae of gray D. platura (71.25 ± 0.66). First instar nymphs of G. distincta also had a certain predation ability with the daily predation of first instar larvae being (1.85 ± 0.13). The predation ability of G. distincta at different instars on the larvae of the same instar of D. platura increased with the increasing of the instar. For the first to second instar larvae of D. platura, the female adult of G. distincta had the strongest predation ability, followed by the male adult of G. distincta, and then the fifth instar nymph of G. distincta. There was no significant difference in the predation ability between the male and female adults of G. distincta, but the adults' predation capacities were significantly higher than that of the fifth instar nymph of G. distincta. The capacity of the fifth instar nymph of G. distincta was significantly higher than the fourth instar nymph of G. distincta, the fourth instar nymph of G. distincta was significantly higher than the first to third instar nymphs, and there was no significant difference in the predation amount among the first to third instar nymphs. The predation selection experiment indicated that the fifth instar nymphs and the male and female adults of G. distincta showed a positive preference for the first to third instar larvae of D. platura and a negative preference for the pupae of D. platura. Our study provided a preliminary scientific basis for green prevention and control of garlic root maggot.},
}

@article {pmid40867097,
year = {2025},
author = {Ye, J and Yu, L and Wang, YJ and Li, XX and Sun, YQ and Zheng, ST},
title = {Giant 3d-4f Heterometallic Polyoxoniobates of {Na2Zn29Ln12Nb122},
{Zn10Eu8Nb60},
and {Zn16Ln8Nb88}
with Photonic Barcodes.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e06482},
doi = {10.1002/smll.202506482},
pmid = {40867097},
issn = {1613-6829},
support = {22171046//NSF of China/ ; 2024J01234//Natural Science Foundation of Fujian Province/ ; },
abstract = {The integration of the rich electronic properties of 3d-4f heterometallic clusters with rigid and diamagnetic polyoxometalates is of great interest and is expected to yield novel materials with enhanced properties due to synergistic effects. For the first time, the study succeeds in introducing fluorescent Zn-Ln heterometallic clusters into polyoxoniobates (PONbs), forming a family of rare giant heterometallic PONbs with various architectures, including 78-metal {Zn10Eu8Nb60},
112-metal {Zn16Ln8Nb88}
(Ln = La, Y), and 165-metal {Na2Zn29Ln12Nb122}
(Ln = Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho). These heterometallic PONbs exhibit many appealing structural features and unique building blocks. Particularly, they are the largest 3d-4f heterometallic PONbs and also the PONbs incorporating the largest number of 3d-4f metal ions and the highest-nuclearity 3d-4f clusters known to date. Furthermore, the combination of PONbs and Zn-Ln clusters renders these new-type heterometallic PONbs multicolor luminescent characteristics and high fluorescence quantum yields, making them promising candidate cluster molecules for responsive photonic barcodes.},
}

@article {pmid40867047,
year = {2025},
author = {Ocari, T and Zin, EA and Tekinsoy, M and Van Meter, T and Desrosiers, M and Cammarota, C and Dalkara, D and Nemoto, T and Ferrari, U},
title = {Optimal sequencing depth for measuring the concentrations of molecular barcodes.},
journal = {Nucleic acids research},
volume = {53},
number = {16},
pages = {},
doi = {10.1093/nar/gkaf793},
pmid = {40867047},
issn = {1362-4962},
support = {ANR-10-LABX-65//Agence Nationale de la Recherches/ ; ANR-18-IAHU-01//Agence Nationale de la Recherches/ ; 863214 - NEUROPA//H2020 European Research Council/ ; I-Démo//Bpifrance/ ; REGE-NETHER 639888//Union Nationale des Aveugles et Déficients Visuels/ ; 22K17994//Japan Society for the Promotion of Science/ ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods/standards ; Gene Library ; *DNA Barcoding, Taxonomic/methods ; *Sequence Analysis, DNA/methods ; Humans ; Polymerase Chain Reaction ; DNA ; },
abstract = {In combinatorial genetic engineering experiments, next-generation sequencing (NGS) allows for measuring the concentrations of barcoded or mutated genes within highly diverse libraries. When designing and interpreting these experiments, sequencing depths are thus important parameters to take into account. Service providers follow established guidelines to determine NGS depth depending on the type of experiment, such as RNA sequencing or whole genome sequencing. However, guidelines specifically tailored for measuring barcode concentrations have not yet reached an accepted consensus. To address this issue, we combine the analysis of NGS datasets from barcoded libraries with a mathematical model taking into account the polymerase chain reaction amplification in library preparation. We demonstrate on several datasets that noise in the NGS counts increases with the sequencing depth; consequently, beyond certain limits, deeper sequencing does not improve the precision of measuring barcode concentrations. We propose, as rule of thumb, that the optimal sequencing depth should be about ten times the initial amount of barcoded DNA molecules before any amplification step.},
}

*High-Throughput Nucleotide Sequencing/methods/standards
Gene Library
*DNA Barcoding, Taxonomic/methods
*Sequence Analysis, DNA/methods
Humans
Polymerase Chain Reaction
DNA

@article {pmid40866952,
year = {2025},
author = {Broche, J and Kelemen, O and Sekar, A and Schütz, L and Muyas, F and Forschner, A and Schroeder, C and Ossowski, S},
title = {GeneBits: ultra-sensitive tumour-informed ctDNA monitoring of treatment response and relapse in cancer patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {964},
pmid = {40866952},
issn = {1479-5876},
abstract = {BACKGROUND: Circulating tumour DNA (ctDNA) in liquid biopsies has emerged as a powerful biomarker in cancer patients. Its relative abundance in cell-free DNA serves as a proxy for the overall tumour burden. Here we present GeneBits, a method for cancer therapy monitoring and relapse detection. GeneBits employs tumour-informed enrichment panels targeting 20-100 somatic single-nucleotide variants (SNVs) in plasma-derived DNA, combined with ultra-deep sequencing and unique molecular barcoding. In conjunction with the newly developed computational method umiVar, GeneBits enables accurate detection of molecular residual disease and early relapse identification.

RESULTS: To assess the performance of GeneBits and umiVar, we conducted benchmarking experiments using three different commercial cell-free DNA reference standards. These standards were tested with targeted next-generation sequencing (NGS) workflows from both IDT and Twist, allowing us to evaluate the consistency and accuracy of our approach across different oligo-enrichment strategies. GeneBits achieved comparable depth of coverage across all target sites, demonstrating robust performance independent of the enrichment kit used. For duplex reads with ≥ 4x UMI-family size, umiVar achieved exceptionally low error rates, ranging from 7.4×10[-7] to 7.5×10[-5]. Even when including mixed consensus reads (duplex & simplex), error rates remained low, between 6.1×10[-6] and 9×10[-5]. Furthermore, umiVar enabled variant detection at a limit of detection as low as 0.0017%, with no false positive calls in mutation-free reference samples. In a reanalysed melanoma cohort, variant allele frequency kinetics closely mirrored imaging results, confirming the clinical relevance of our method.

CONCLUSION: GeneBits and umiVar enable highly accurate therapy and relapse monitoring in plasma as well as identification of molecular residual disease within four weeks of tumour surgery or biopsy. By leveraging small, tumour-informed sequencing panels, GeneBits provides a targeted, cost-effective, and scalable approach for ctDNA-based cancer monitoring. The benchmarking experiments using multiple commercial cell-free DNA reference standards confirmed the high sensitivity and specificity of GeneBits and umiVar, making them valuable tools for precision oncology. UmiVar is available at https://github.com/imgag/umiVar .},
}

@article {pmid40865182,
year = {2025},
author = {Song, ZT and Sun, KY and Hou, L and Wu, JJ and Hu, WT and Zhou, S and Zhang, CY and Song, J and Lan, HB and Wei, F and Feng, CP},
title = {3D printable phase change information storage label films for dynamic and multi-level anti-counterfeiting.},
journal = {Journal of colloid and interface science},
volume = {701},
number = {},
pages = {138694},
doi = {10.1016/j.jcis.2025.138694},
pmid = {40865182},
issn = {1095-7103},
abstract = {Anti-counterfeiting technology demands continuous innovation to address escalating global counterfeiting challenges. This study introduces 3D printable phase change information storage label films for dynamic, multi-level anti-counterfeiting applications. Utilizing extrusion-based 3D printing, customizable anti-counterfeiting labels with complex encrypted information such as barcodes and QR codes were fabricated. These labels leverage the thermal responsiveness of phase change materials (PCMs) to reveal hidden information under infrared thermography at specific temperature and specific duration, while remaining concealed at ambient or elevated temperatures. Notably, a multi-level encryption strategy is achieved by integrating PCMs with distinct phase transition temperatures (30 °C and 53 °C), enabling sequential decryption of information at different temperature intervals. This approach significantly enhances anti-counterfeiting complexity and security. The work demonstrates the potential of PCM-based 3D printing for high-capacity information storage and adaptable anti-counterfeiting solutions, offering a versatile platform for diverse industrial applications.},
}

@article {pmid40864172,
year = {2025},
author = {Wade, RM and Ogushi, R and Gabrielson, PW and Hind, KR and Hughey, JR and Lindstrom, SC and Miller, KA and Martone, PT},
title = {Type-assisted taxonomy and biogeography of Corallina (Corallinales, Rhodophyta) in the eastern Pacific: Corallina americana sp. nov., C. bathybentha, C. hommersandiorum sp. nov., and C. saundersii sp. nov.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70078},
pmid = {40864172},
issn = {1529-8817},
support = {//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; //Hakai Institute/ ; },
abstract = {The articulated coralline genus Corallina is common in temperate rocky ecosystems and provides settlement substrate and refugia for other organisms. However, our ability to understand species-specific traits and interactions has been confounded by overlapping morphological characteristics among species. DNA sequences from type specimens and recently collected specimens have begun to address these issues by clarifying phylogenetic species boundaries and geographic distributions. We sequenced an rbcL gene barcode from a paratype specimen of Corallina bathybentha (type locality: 0.5 miles south of the west end of Anacapa Is., California, United States) and have provided an updated description. Three cryptic species have been described: C. hommersandiorum and C. saundersii are endemic to the northeastern Pacific, whereas C. americana is anti-tropical in the eastern Pacific. Haplotype network analyses using the COI locus suggested that C. americana naturally dispersed from North to South America; it was not likely a recent or human-mediated introduction. To explore species boundaries, stepwise discriminant models were used to analyze morphological and ecological traits and were visualized in canonical multidimensional plots. Every species overlapped in canonical space with at least one other species, further illustrating that morphological identifications of Corallina species are challenging and unreliable. This work completes the taxonomic study of the currently known diversity of Corallina in the northeast Pacific for which we have access to type specimens. Given that this region is likely the center of origin and home to three-quarters of the known Corallina species, these taxonomic studies, including this one, make a significant contribution to our understanding of coralline diversity.},
}

@article {pmid40864133,
year = {2025},
author = {Barretto, M and Olson, A and Alemayehu, D and Clausnitzer, R and Haas-Stapleton, EJ},
title = {Barcoding Quantitative PCR Assay to Distinguish Between Aedes aegypti and Aedes sierrensis.},
journal = {Tropical medicine and infectious disease},
volume = {10},
number = {8},
pages = {},
pmid = {40864133},
issn = {2414-6366},
support = {FY2024.6503//Alameda County Mosquito Abatement District/ ; },
abstract = {The accurate identification of mosquito species is critical for effective mosquito surveillance and control, especially when presented with morphologically similar species like Aedes aegypti and Aedes sierrensis. Damaged specimens and morphologically similar life stages such as eggs and larvae make it difficult to distinguish Aedes aegypti from Aedes sierrensis using microscopy and taxonomic keys. To address this, the AegySierr.ID-qPCR assay, a multiplex quantitative PCR assay that utilizes single-nucleotide polymorphisms within the mitochondrial cytochrome oxidase subunit I gene, was developed to distinguish between these two species. The assay was tested on DNA extracted from the eggs, larvae, and adults of both species, as well as from environmental DNA (eDNA) collected from natural mosquito reproduction sites. It demonstrated a high diagnostic accuracy across multiple life stages, with a sensitivity exceeding 95% for most groups and specificity exceeding 90%, except for field-collected adult Ae. sierrensis (75%). For eDNA samples, the assay achieved 100% sensitivity and 94% specificity for samples classified as Ae. sierrensis and 91% sensitivity and 86% specificity for Ae. aegypti. A two-graph receiver operating characteristic analysis was also used as an alternate method with which to establish Ct thresholds for interpreting results from unknown samples. The AegySierr.ID-qPCR assay enables the rapid and sensitive identification of Ae. aegypti and Ae. sierrensis from specimens and eDNA, and may be of use in mosquito surveillance programs.},
}

@article {pmid40860682,
year = {2025},
author = {Bakmaz, D and Sönmez, S and Korkmaz, EM},
title = {Evaluating COI and ITS2 dual barcoding for molecular delimitation and taxonomic insights in Arenosetella Wilson, 1932 (Harpacticoida: Ectinosomatidae) along Turkish Coasts.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19870},
pmid = {40860682},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Electron Transport Complex IV/genetics ; Turkey ; Phylogeny ; *Copepoda/genetics/classification ; Haplotypes ; Genetic Variation ; *DNA, Ribosomal Spacer/genetics ; },
abstract = {BACKGROUND: Accurate species delimitation is essential in morphologically conservative taxa such as harpacticoid copepods, in which cryptic diversity may go unnoticed without molecular data. The genus Arenosetella, common along the Turkish coastline, comprises two species: Arenosetella germanica and A. lanceorostrata, with overlapping ranges and subtle morphological differences. This study aimed to assess species boundaries and uncover potential hidden diversity within Arenosetella using the dual-marker DNA barcoding approach.

METHODS: Specimens of Arenosetella were collected from the Mediterranean, Aegean, and Black Sea coasts of Türkiye. Nuclear DNA from a total of 46 individuals were amplified and sequenced for both mitochondrial cytochrome oxidase I (COI) and nuclear internal transcribed spacer 2 (ITS2) markers. COI sequences were analysed for haplotype diversity, phylogenetic relationship, and species delimitations. ITS2 sequences were subjected to evaluation with regard to nucleotide diversity, secondary structure, and compensatory base changes (CBCs), using both sequence- and structure-based approaches. The concatenated dataset and species tree reconstruction (StarBEAST2) were employed to test gene tree-species tree congruence.

RESULTS: The COI analyses revealed a high level of haplotype diversity (21 haplotypes) and the presence of three molecular operational taxonomic units (MOTUs) within A. germanica and one MOTU within A. lanceorostrata, consistent with the geographic distribution patterns. ITS2 sequences exhibited relatively more conservation with nine haplotypes. These sequences revealed informative structural variation, including CBCs among candidate species. The species delimitation approaches reliably supported the identification of four to seven MOTUs, which corresponded to geographic populations. The analyses of the concatenated dataset supported four well-supported candidate species, and yielded congruent species trees, with high posterior probabilities. Morphological comparisons among MOTUs revealed subtle differences in female P5 structure and anal somite ornamentation among A. germanica lineages, while A. lanceorostrata MOTUs were morphologically indistinguishable.

CONCLUSION: This study provides the first integrative application of COI and ITS2 barcoding in Arenosetella and within Harpacticoida overall, combining DNA sequences and structure, and morphological data for species delimitation. The results demonstrate that COI is effective for detecting geographic differentiation and haplotype diversity, whereas ITS2 contributes structural resolution and potential markers of reproductive isolation through CBCs. These findings suggest the presence of a species complex within A. germanica and confirm the distinct status of A. lanceorostrata. Dual-marker barcoding, particularly incorporating ITS2 secondary structure, represents a valuable tool for taxonomic studies in morphologically conservative copepod groups.},
}

*DNA Barcoding, Taxonomic/methods
Animals
*Electron Transport Complex IV/genetics
Turkey
Phylogeny
*Copepoda/genetics/classification
Haplotypes
Genetic Variation
*DNA, Ribosomal Spacer/genetics

@article {pmid40860566,
year = {2025},
author = {Arnau, V and Ortiz-Maiques, A and Valero-Tebar, J and Mora-Quilis, L and Kurmauskaite, V and Campos Dopazo, L and Domingo-Calap, P and Džunková, M},
title = {CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf134},
pmid = {40860566},
issn = {2730-6151},
abstract = {Split-and-pool barcoding generates thousands of unique barcode strings through sequential ligations in 96-well plates, making single-cell omics more accessible, thus advancing microbial ecology, particularly in studies of bacterial interactions with plasmids and bacteriophages. While the wet-lab aspects of the split-and-pool barcoding are well-documented, no universally applicable bioinformatic tool exists for demultiplexing single cells barcoded with this approach. We present CleanBar (https://github.com/tbcgit/cleanbar), a flexible tool for demultiplexing reads tagged with sequentially ligated barcodes, accommodating variations in barcode positions and linker lengths while preventing misclassification of natural barcode-like sequences and handling diverse ligation errors. It also provides statistics useful for optimizing laboratory procedures. We demonstrate CleanBar's performance with the Atrandi platform for microbial single-cell genomics, coupled with PacBio sequencing, to reach a cell throughput comparable with traditional bulk metagenomics, but overcoming its limitations in studying phage-bacteria interactions. In four Klebsiella strains infected with their corresponding phages and a control phage, the single-cell genomics revealed infection heterogeneity and enabled phage copy number estimation per cell. By combining efficiency, adaptability, and precision, CleanBar, when applied to the Atrandi split-and-pool barcoding platform and PacBio sequencing, serves as a powerful high-throughput tool for advancing microbial single-cell genomics and understanding microbial ecology and evolution.},
}

@article {pmid40860319,
year = {2025},
author = {Moser, M and Vasilița, C and Haas-Renninger, M and Pirvu, E and Haas, M and Krogmann, L},
title = {German Barcode of Life reveals unexpected diversity of Ceraphronoidea (Hymenoptera).},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e159561},
pmid = {40860319},
issn = {1314-2828},
abstract = {Insect populations still experience marked declines globally, contributing to the ongoing biodiversity crisis. Counteracting these declines requires sound taxonomic and ecological knowledge on all levels of biodiversity, from genes to species to ecosystems. The superfamily Ceraphronoidea (Hymenoptera) has remained relatively obscure due to complex challenges in exploring its diversity and ecological roles. Despite their ecological importance as parasitoids or hyperparasitoids, these wasps are under-represented in scientific exploration and conservation. In a case study within the German Barcode of Life (GBOL) Dark Taxa project, we aim to bridge this knowledge gap through a comprehensive taxonomic investigation covering 2,136 specimens of Ceraphronoidea across 18 locations in the putatively well-studied State of Baden-Württemberg (south-western Germany). Our study identifies a surprising species richness of at least 193 conjectural species, based on COI-barcoding clusters, extrapolates key species richness estimators for the German ceraphronoid fauna and records a species new to the German fauna: Creatorspissicornis (Hellén, 1966). By setting a foundational benchmark for Ceraphronoidea biodiversity, our research advocates for the inclusion of dark taxa in broader insect biodiversity assessments, contributing meaningfully to the discourse on conservation priorities and strategies.},
}

@article {pmid40857085,
year = {2025},
author = {Mamane-Logsdon, A and Zane, I and Chong, JS and Chou, OHI and Huang, J and Rawal, M and Gillman, AC and Wongwiwat, W and Saleban, M and Donovan-Banfield, I and Matthews, DA and White, RE},
title = {A direct RNA-seq-based EBV latency transcriptome offers insights into the biogenesis of EBV gene products.},
journal = {The Journal of general virology},
volume = {106},
number = {8},
pages = {},
doi = {10.1099/jgv.0.002134},
pmid = {40857085},
issn = {1465-2099},
mesh = {*Herpesvirus 4, Human/genetics/physiology ; Humans ; *Virus Latency/genetics ; *Transcriptome ; Epstein-Barr Virus Nuclear Antigens/genetics ; RNA-Seq ; *Viral Proteins/genetics/biosynthesis ; Epstein-Barr Virus Infections/virology ; Gene Expression Regulation, Viral ; B-Lymphocytes/virology ; Cell Line ; Alternative Splicing ; Promoter Regions, Genetic ; RNA, Viral/genetics ; MicroRNAs/genetics ; },
abstract = {Epstein-Barr virus (EBV) ubiquitously infects humans, establishing lifelong persistence in B cells. In vitro, EBV-infected B cells can establish a lymphoblastoid cell line (LCL). EBV's transcripts in LCLs (latency III) produce six nuclear proteins [EBV nuclear antigens (EBNAs)], two latency membrane proteins (LMPs) and various microRNAs and putative long non-coding RNAs [BamHI A rightward transcripts (BARTs)]. The BART and EBNA transcription units are characterized by extensive alternative splicing. We generated LCLs with B95-8 EBV-BACs, including one engineered with 'barcodes' in the first and last repeat of internal repeat 1 (IR1), and analysed their EBV transcriptomes using long-read nanopore direct RNA-seq. Our pipeline ensures appropriate mapping of the W promoter (Wp) 5' exon and corrects W1-W2 exon counts that misalign to IR1. This suggests that splicing across IR1 largely includes all W exons and that Wp-derived transcripts more frequently encode the EBNA-LP start codon than Cp transcripts. Analysis identified a short variant of exon W2 and a novel polyadenylation site before EBNA2, provided insights into BHRF1 miRNA processing and suggested co-ordination between polyadenylation and splice site usage, although improved read depth and integrity are required to confirm this. The BAC region disrupts the integrity of BART transcripts through premature polyadenylation and cryptic splice sites in the hygromycin expression cassette. Finally, a few transcripts extended across established gene boundaries, running from EBNA to BART to LMP2 gene regions, sometimes including novel exons between EBNA1 and the BART promoter. We have produced an EBV annotation based on these findings to help others better characterize EBV transcriptomes in the future.},
}

*Herpesvirus 4, Human/genetics/physiology
Humans
*Virus Latency/genetics
*Transcriptome
Epstein-Barr Virus Nuclear Antigens/genetics
RNA-Seq
*Viral Proteins/genetics/biosynthesis
Epstein-Barr Virus Infections/virology
Gene Expression Regulation, Viral
B-Lymphocytes/virology
Cell Line
Alternative Splicing
Promoter Regions, Genetic
RNA, Viral/genetics
MicroRNAs/genetics

@article {pmid40854923,
year = {2025},
author = {Intharuksa, A and Prasertwitayakij, N and Yanaso, S and Phrutivorapongkul, A and Charoensup, W and Thongkhao, K and Sasaki, Y and Wongcharoen, W},
title = {Uncovering the poisonous aconitine containing plants in homemade herbal liquor using a convergent approach.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31286},
pmid = {40854923},
issn = {2045-2322},
abstract = {Human exposure to toxic plants is a global concern, with numerous reported cases of accidental poisoning. In this study, a patient experienced poisoning after inadvertently consuming an herbal preparation preserved in alcohol. The patient exhibited characteristic electrocardiogram abnormalities, prompting further investigation into the toxic plant responsible. A relative provided the suspected herbal sample for identification. Symptomatic treatment was administered, successfully stabilizing the patient. Given the suspicion of aconitine toxicity-despite the absence of naturally occurring Aconitum species in Thailand-a multi-approach methodology was employed to identify the plant source. Macroscopic and microscopic analyses were performed to characterize the morphological and histological features of the specimens. Organoleptic assessment revealed blackish-brown, shrunken surfaces with longitudinal wrinkles and a pale alcoholic-like odor. Microscopic examination identified three major structural layers: metaderm and cortex, vascular tissues, and a parenchyma-rich central pith, consistent with Aconitum storage roots. Chemical identification using thin-layer chromatography (TLC) compared the patient samples (SX1 and SX2) with standard aconitine and Aconitum crude drugs (AC1-AC5). The TLC chromatograms confirmed the presence of aconitine in SX1 and SX2, as evidenced by matching Rf values and characteristic color reactions. Further molecular analysis utilizing DNA barcoding targeted the trnH-psbA region to determine the genetic origin of the specimens. PCR successfully amplified DNA from SX1, SX2, and Aconitum reference samples, generating approximately 150 bp amplicons. BLAST analysis revealed a 99.07% sequence identity with Aconitum species, and phylogenetic analysis clustered the patient specimens with authenticated Aconitum species. Given that Aconitum, Delphinium, and Consolida species are not naturally distributed in Thailand, this case highlights the risks associated with imported medicinal plants containing aconitine. The integration of macroscopic, microscopic, chemical, and molecular techniques provided definitive identification of the toxic plant material. These findings underscore the importance of public health initiatives to raise awareness of aconitine poisoning and the need for regulatory measures to ensure the safe use of medicinal plants.},
}

@article {pmid40854664,
year = {2025},
author = {Azzam, CR and Rizk, MS and Mostafa, SSM and Arafa, RA and Al-Nabawi, MS and Morsi, NAA and Nasr El-Din, MM and Taher, EH and Khaled, KA},
title = {Characterization of two novel chia (Salvia hispanica L.) white and black genotypes via DNA barcoding, physiological, and agronomic traits.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {3},
pages = {100545},
doi = {10.1016/j.jgeb.2025.100545},
pmid = {40854664},
issn = {2090-5920},
abstract = {BACKGROUND: Chia (Salvia hispanica L.) is recognized for its nutritional value and health-promoting compounds, including flavonoids.

AIM: This study utilized DNA barcoding to identify and differentiate two novel chia genotypes, CACH-W and CACH-B, providing insights for breeding programs and genetic resource conservation (CA refers to the developer and CH refer to Chia).

METHODS: DNA was extracted from controlled samples and analyzed using five barcode markers: trnH-psbA, matK, rpoC1, rbcL, and ITS. Genetic diversity was evaluated through phylogenetic analysis with appropriate bioinformatics tools.

RESULTS: DNA barcoding using five markers (trnH-psbA, matK, rpoC1, rbcL, and ITS) successfully amplified sequences of 930 bp, 1520 bp, 2295 bp, 1910 bp, and 1630 bp, respectively. Among them, rbcL, rpoC1, and ITS effectively differentiated the two genotypes, and phylogenetic analysis confirmed their genetic identity and relationship with existing (Salvia hispanica L.) sequences. Functional analyses highlighted the conserved roles of key genes, including rbcL (carbon fixation), rpoC1 (chloroplast transcription), and matK (RNA splicing). The white genotype (CACH-W) outperformed the black genotype (CACH-B) in germination, physiological, and agronomic traits, achieving a higher seedling vigor index (11.68 vs. 8.51), longer radicle (6.94 cm vs. 5.02 cm), and greater total phenolic content (31.92 mg/g vs. 28.95 mg/g). Agronomically, CACH-W showed superior plant height, spike weight, and seed yield (1003.83 kg/feddan vs. 606.46 kg/feddan), making it a promising candidate for cultivation and breeding.

CONCLUSION: This study demonstrates the effectiveness of certain plastome gene sequences in identifying and distinguishing chia varieties, offering a reliable tool for breeding, quality control, and germplasm conservation. The white genotype (CACH-W) outperformed the black genotype (CACH-B) in germination, physiological, and agronomic traits, achieving a higher seedling vigor index, longer radicle, and greater total phenolic content. Agronomically, CACH-W showed superior plant height, spike weight, and seed yield, making it a promising candidate for cultivation and breeding. The results also support the integration of marker-assisted selection for developing chia varieties with improved traits, enhancing their commercial and agricultural value.},
}

@article {pmid40851185,
year = {2025},
author = {Shastay, A and Bertagnoli, S},
title = {Difficult-to-scan barcodes on intravenous bags need to be escalated.},
journal = {Nursing},
volume = {55},
number = {9},
pages = {55},
doi = {10.1097/NSG.0000000000000258},
pmid = {40851185},
issn = {1538-8689},
}

@article {pmid40850985,
year = {2025},
author = {Asaf, S and Williams, YA and Lubna, and Riethoven, JM and Eslamieh, J and Al-Rawahi, A and Al-Harrasi, A and Khan, AL},
title = {Plastome structure, evolution and diversity of Frankincense-producing Boswellia genus.},
journal = {Functional & integrative genomics},
volume = {25},
number = {1},
pages = {172},
pmid = {40850985},
issn = {1438-7948},
mesh = {*Boswellia/genetics/classification ; *Genome, Plastid ; *Evolution, Molecular ; Phylogeny ; Genetic Variation ; },
abstract = {The genus Boswellia is famous for its commercially important frankincense production. Additionally, it has unique ecological and taxonomic importance. However, the Boswellia species often face natural hybridization, and the lack of genomic datasets frequently contributes to taxonomic uncertainties. Here, we sequenced and analyzed the complete plastid genomes (plastomes) of six Boswellia species (B. carteri, B. bullata, B. dioscoridis, B. elongata, B. serrata, B. frereana, and a hybrid variant of B. sacra (B. sacra var. supersacra). The genome size of Boswellia plastomes is between 159,189 bp and 160,743 bp, displaying a typical structure with large single-copy (LSC; 86,811-88,054), small single-copy (SSC; 26,666-26,763), and inverted repeat (IR; 26,544-26,763) regions. The IR regions (~ 25,000 bp) are highly conserved across species, contributing to the stability of the plastome structure. Our study identified consistent gene content, typical of angiosperms, and showed that the IR boundaries remained unchanged across species. The simple sequence repeats revealed a range between 43 and 52 across the plastomes, with B. sacra exhibiting the highest count. We detected long, repetitive sequences that could serve as useful genetic markers for species differentiation. Nucleotide diversity analysis highlighted significant gene variations (matK, rbcL, rpl14, and rpoC2). The results showed substantial genetic divergence in regions (rpl14, matK, and rpoC2), demonstrating distinct variations among species. In evolutionary history, the B. carteri diverged around 4.2 million years ago (mya), while B. sacra and B. serrata separated by approximately 7.0 mya. The phylogenomic analysis supported the distinction between B. carteri and B. sacra, challenging prior claims that these are synonymous. These findings contribute to a deeper understanding of species boundaries within Boswellia and offer valuable resources for future DNA barcoding efforts.},
}

*Boswellia/genetics/classification
*Genome, Plastid
*Evolution, Molecular
Phylogeny
Genetic Variation

@article {pmid40849035,
year = {2025},
author = {Banerjee, N and Mazumdar, SM and Bellis, G and Mazumdar, A},
title = {New species, country records, DNA barcoding and host blood meal analysis of some Indian species of Culicoides Latreille subgenus Trithecoides Wirth and Hubert (Diptera: Ceratopogonidae).},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107798},
doi = {10.1016/j.actatropica.2025.107798},
pmid = {40849035},
issn = {1873-6254},
abstract = {Light trap collections from four states in India revealed the presence of four species belonging to Culicoides (Trithecoides). Included were a new species from the macfiei group, Culicoides tenebrus sp. nov., which is diagnosed with a dark mid-knee and a yellow scutum featuring a dark anterior quarter, two new country records for India: Culicoides paraflavescens Wirth and Hubert, 1959, and Culicoides laoensis Howarth, 1985, and some variants of the widely distributed species Culicoides palpifer Das Gupta and Ghosh, 1956. Collections contained blood-fed specimens of each of these species, and host blood meal analysis using 16S rRNA revealed that all specimens had fed on cattle. DNA barcodes obtained from some specimens of these species were analysed along with other species from Culicoides (Trithecoides), and a phylogenetic tree based on these sequences supported the status of each of these species. Considerable variation was observed within C. palpifer both in morphology and DNA barcodes, suggesting that this species requires some taxonomic revision. The apparent preference of these four species for cattle hosts suggests that studies into their vector potential are warranted; however, the status of the species of Trithecoides requires clarification before any vector potential studies.},
}

@article {pmid40847262,
year = {2025},
author = {Stern, N and Milstein, D and Bollous, M and Morov, AR},
title = {Comparative performance of eDNA and conventional capture-based monitoring approaches to detect riverine fish assemblages.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {9},
pages = {1036},
pmid = {40847262},
issn = {1573-2959},
mesh = {Animals ; *Environmental Monitoring/methods ; *Fishes/classification ; *DNA, Environmental/analysis ; Biodiversity ; Rivers/chemistry ; DNA Barcoding, Taxonomic ; Israel ; Ecosystem ; Fresh Water ; },
abstract = {Monitoring biodiversity constitutes a fundamental element in assessing the ecological status of sensitive and vulnerable habitats such as inland freshwater bodies. Although conventional capture-based methodologies in fish monitoring are still widely used, the development of alternative strategies is being vigorously pursued. The use of environmental DNA (eDNA) to detect species' presence is now a standard practice in aquatic ecology and is generating considerable attention within the scientific community. Here, we present the first eDNA metabarcoding study of the Israeli freshwater ecosystems, aiming to detect and compare fish assemblages of previously surveyed sites. Four riverine systems with different characteristics and known fish fauna were sampled, in parallel to the preparation of a complete 12S rRNA barcode reference library for the Israeli freshwater ichthyofauna. In total, 25 fish species belonging to 15 families were detected from 63 water samples using 12S eDNA metabarcoding. Comparisons with previous capture-based data have shown that eDNA surveys provided better species coverage, including the first documentation of two non-indigenous species and regardless of water characteristics or volume of filtered water. Lastly, we explain and discuss discrepancies in false-negative and false-positive results between the two methods.},
}

Animals
*Environmental Monitoring/methods
*Fishes/classification
*DNA, Environmental/analysis
Biodiversity
Rivers/chemistry
DNA Barcoding, Taxonomic
Israel
Ecosystem
Fresh Water

@article {pmid40846697,
year = {2025},
author = {Brunet, L and Alexandre, D and Lee, J and Blanquer-Rosselló, MDM and Bracquemond, D and Guernet, A and Chhouri, H and Goupil, M and Kherrouche, Z and Arabo, A and Mancini, M and Cartier, D and Yao, S and Godefroy, D and Dehedin, J and Li, JR and Duparc, C and Jamme, P and Vinchent, A and Bérard, C and Tulasne, D and Arena, S and Bardelli, A and Cheng, C and Cho, BC and Wurtz, O and Coulouarn, C and Maraver, A and Aaronson, SA and Cortot, AB and Anouar, Y and Grumolato, L},
title = {Prolonging lung cancer response to EGFR inhibition by targeting the selective advantage of resistant cells.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7853},
pmid = {40846697},
issn = {2041-1723},
support = {PLBIO 2017-159//Institut National Du Cancer (French National Cancer Institute)/ ; METROPOLIS-158530//Agence Nationale de la Recherche (French National Research Agency)/ ; PJA20161205119//Fondation ARC pour la Recherche sur le Cancer (ARC Foundation for Cancer Research)/ ; },
mesh = {Humans ; *Drug Resistance, Neoplasm/drug effects/genetics ; *Lung Neoplasms/drug therapy/pathology/genetics/metabolism ; ErbB Receptors/antagonists & inhibitors/metabolism/genetics ; Sorafenib/pharmacology ; Animals ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/genetics/metabolism ; *Protein Kinase Inhibitors/pharmacology/therapeutic use ; Xenograft Model Antitumor Assays ; Cell Line, Tumor ; Mice ; STAT3 Transcription Factor/metabolism ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism/genetics ; Phosphorylation/drug effects ; Female ; Mice, Nude ; },
abstract = {Non-small cell lung cancers (NSCLCs) treated with tyrosine kinase inhibitors (TKIs) of the epidermal growth factor receptor (EGFR) almost invariably relapse in the long term, due to the emergence of subpopulations of resistant cells. Through a DNA barcoding approach, we show that the clinically approved drug sorafenib specifically abolishes the selective advantage of EGFR-TKI-resistant cells, while preserving the response of EGFR-TKI-sensitive cells. Sorafenib is active against multiple mechanisms of resistance/tolerance to EGFR-TKIs and its effects depend on early inhibition of MAPK-interacting kinase (MKNK) activity and signal transducer and activator of transcription 3 (STAT3) phosphorylation, and later down-regulation of MCL1 and EGFR. Using different xenograft and allograft models, we show that the sorafenib-EGFR-TKI combination can delay tumor growth and promote the recruitment of inflammatory cells. Together, our findings indicate that sorafenib can prolong the response to EGFR-TKIs by targeting NSCLC capacity to adapt to treatment through the emergence of resistant cells.},
}

Humans
*Drug Resistance, Neoplasm/drug effects/genetics
*Lung Neoplasms/drug therapy/pathology/genetics/metabolism
ErbB Receptors/antagonists & inhibitors/metabolism/genetics
Sorafenib/pharmacology
Animals
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology/genetics/metabolism
*Protein Kinase Inhibitors/pharmacology/therapeutic use
Xenograft Model Antitumor Assays
Cell Line, Tumor
Mice
STAT3 Transcription Factor/metabolism
Myeloid Cell Leukemia Sequence 1 Protein/metabolism/genetics
Phosphorylation/drug effects
Female
Mice, Nude

@article {pmid40845955,
year = {2025},
author = {McPhail, BA and Tomusiak, S and Veinot, H and Dodds, N and Hanington, PC},
title = {Reclaimed wetlands support rich trematode and host diversity: Findings from a four-year survey.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijpara.2025.08.006},
pmid = {40845955},
issn = {1879-0135},
abstract = {Snail hosts play a central role in structuring trematode communities. To test how snail hosts shape parasite diversity in central Alberta, we built upon a previous snail-trematode survey conducted at six lakes in central Alberta from 2013-2015 that uncovered 79 trematode species. However, analyses suggested that additional species remained to be uncovered. To build on this baseline, we conducted further snail-trematode collections from 2019 to 2022 at eight reclaimed wetland sites in various stages of reclamation, along with one established lake in Alberta. Across the nine sites, we collected 22,397 snails, of which 1,981 were infected with digenetic trematodes. We also documented broader biodiversity at these sites using traditional survey techniques. Through DNA barcoding, we identified 74 trematode species infecting five snail species. Among these were 23 trematode species not previously reported in central Alberta and nine provisionally-named lineages with no matches to species in publicly available databases. In addition, we observed several previously unreported snail-trematode interactions. While trematode richness did not vary significantly with the wetland reclamation stage, host identity did influence richness: Physa gyrina hosted significantly more trematode species than Planorbella trivolvis. When combined with data from the earlier survey, sample completeness analyses indicate that we captured 100% of the dominant species and 99% of the typical species, but only 63% of the overall species diversity in central Alberta. These findings underscore that trematode diversity in central Alberta remains incompletely characterized and highlight the continued value of long-term and host-inclusive sampling efforts.},
}

@article {pmid40844265,
year = {2025},
author = {Bogaerts, B and Maex, M and Commans, F and Goeders, N and Van den Bossche, A and De Keersmaecker, SCJ and Roosens, NHC and Ceyssens, P-J and Mattheus, W and Vanneste, K},
title = {Oxford Nanopore Technologies R10 sequencing enables accurate cgMLST-based bacterial outbreak investigation of Neisseria meningitidis and Salmonella enterica when accounting for methylation-related errors.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0041025},
doi = {10.1128/jcm.00410-25},
pmid = {40844265},
issn = {1098-660X},
abstract = {UNLABELLED: Core-genome multi-locus sequence typing (cgMLST) is a well-established and standardized method for genomics-based cluster detection and phylogenomic analysis of bacteria. The reduced error rate of Oxford Nanopore Technologies (ONT) R10 sequencing has prompted many laboratories to explore incorporating this technology into their activities. However, conflicting reports exist on the performance of ONT R10 sequencing for cgMLST analysis. This study evaluates the suitability of ONT R10 data for cgMLST allele calling and cluster detection for bacterial outbreak investigation. ONT and Illumina sequencing data were generated for 24 Neisseria meningitidis and 24 Salmonella enterica isolates. For ONT, both the rapid barcoding kit (RBK) and the rapid PCR barcoding kit (RPB) were used. The percentage of loci called in the ONT-only assemblies was very high for both species. However, the proportion of mismatched alleles to the hybrid assemblies was substantially higher for the Neisseria ONT-only assemblies with the RBK kit, resulting in incorrect cluster assignments. The large majority of these mismatched alleles were due to incorrect base calls at methylated positions, which did not affect the ONT data generated using the RPB kit or any of the Salmonella ONT-only assemblies. In conclusion, ONT R10 sequencing shows great potential as a viable method for cgMLST analysis, but methylation-related errors can affect performance for certain species and strains. When properly corrected for, ONT R10 had the same performance for cgMLST analysis as Illumina, and both could be used interchangeably. These results support the integration of ONT R10 sequencing into routine public health and clinical workflows.

IMPORTANCE: This study evaluates the suitability of Oxford Nanopore Technologies R10 sequencing for core-genome multi-locus sequence typing (cgMLST), a widely used method in (clinical) outbreak investigation and bacterial strain tracking. We have sequenced 24 Neisseria meningitidis and 24 Salmonella enterica strains, including confirmed outbreak cases, using Illumina and ONT R10 sequencing to evaluate the performance for cgMLST analysis. We used a PCR-based and native barcoding protocol for the ONT sequencing, which enabled us to demonstrate a substantial species-dependent impact of methylation-related errors on the performance. However, we demonstrate that when these errors are properly addressed, ONT R10 can be used for accurate cgMLST-based clustering, including integration with strains sequenced using Illumina. Our findings support the use of ONT R10 as an alternative to Illumina sequencing for cgMLST analysis in routine public health practice.},
}

@article {pmid40844238,
year = {2025},
author = {Wang, C and Zheng, J and Xiong, Z and Yin, W and Zhao, Y and Wu, H and Liang, S and Zhang, L and Yao, C and Deng, Z and Liu, Y and Song, Q and Zhou, G and Zou, B},
title = {Voltage-Programmed Sequential Fluorescence Encoding (VPSFE) Enables Multiplexed In Situ Proteo-Imaging with Electric-Field Turing Patterns.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202511629},
doi = {10.1002/anie.202511629},
pmid = {40844238},
issn = {1521-3773},
support = {82404581//National Natural Science Foundation of China/ ; 82173780//National Natural Science Foundation of China/ ; BE2023843//Jiangsu Province Key R&D Program Social Development Project/ ; BK20241591//Natural Science Foundation of Jiangsu Province/ ; S202510316086//National Innovation and Entrepreneurship Training Program for Undergraduate/ ; S202510316087//National Innovation and Entrepreneurship Training Program for Undergraduate/ ; 3322400176//National Innovation and Entrepreneurship Training Program for Undergraduate/ ; },
abstract = {DNA barcode-based immunolabeling has revolutionized single-cell protein profiling. However, conventional multiplexed imaging methods are hindered by laborious probe exchange procedures involving buffer washing-based probe removal and prolonged hybridization cycles (requiring tens of minutes to 1.5 h per cycle), which limit throughput, specificity, and universality. Here, we introduce an electrophoresis-based in situ probe removal method that achieves high-specificity iterative probe imaging without washing steps, utilizing 2-min low-voltage electrophoresis for excess probes removal and 3-min high-voltage electrophoresis for hybridized probes dissociation. The robustness was validated through 19 rounds of cyclic electrophoresis, 10 rounds of repetitive imaging, and simultaneous processing of 14 probes (µM-level) across five rounds of multiprobe exchange, demonstrating exceptional specificity and efficiency. Applied to sequential color coding-based multiplexed imaging, this approach establishes voltage-programmed sequential fluorescence encoding (VPSFE), enabling multiplexed imaging of epithelial-mesenchymal transition (EMT)-related proteins. Furthermore, we developed a VPSFE-based Turing pattern coding strategy for multiplexed detection that requires only a single multicolor probe hybridization step. Using three voltage conditions and three fluorescence channels, this system generates 27 unique fluorescence Turing patterns to encode 27 distinct targets. This electric-field Turing pattern coding strategy represents a novel probe exchange-free approach for rapid, universal, and highly specific multiplexed in situ imaging.},
}

@article {pmid40844198,
year = {2025},
author = {Feng, Y and Xu, Q and Ouyang, C and Wei, Y and Gan, Z and Liu, Y and Yu, L and Xiao, Y},
title = {Dual-Enhanced Lanthanide MOF-Based Fluorescent Bio-Barcode via Conformational Regulation for Ultrasensitive Detection of DNA Epigenetic Biomarker.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e04246},
doi = {10.1002/smll.202504246},
pmid = {40844198},
issn = {1613-6829},
support = {82273895//National Natural Science Foundation of China/ ; 82304440//National Natural Science Foundation of China/ ; 82073811//National Natural Science Foundation of China/ ; },
abstract = {Aberrant epigenetic modifications (EMs) serve as critical biomarkers but remain challenging to detect due to their low abundance in biological samples. A lanthanide metal-organic framework (Ln-MOF) bio-barcode method integrating the dual actions of ultrahigh DNA loading density and anion-π interaction-driven fluorescence enhancement for the ultrasensitive detection of EMs, such as 5-formylcytosine (5fC), is developed. The system employs streptavidin-functionalized magnetic beads to selectively capture biotinylated 5fC-modified nucleic acids, which then capture Er-organic framework probes (UiO-66 (Er)) tagged with thousands of quenched fluorescent oligonucleotides (FAM-ODN). After magnetic separation, phosphate-induced desorption restores the fluorescence of oligonucleotides, signaling the presence of 5fC. Subsequently, free phosphate, functioning as both a strong base and an anion, further amplifies fluorescence by altering the conformation of FAM molecules. This dual-action mechanism combines high nucleic acid loading capacity of Ln-MOF and conformation-regulated fluorescence enhancement enables the fluorescent bio-barcode to achieve a detection limit of 0.0225% content. The detection results of 5fC in cellular and thyroid cancer tissue samples confirm global 5fC downregulation as a robust epigenetic hallmark of cancer. The enzyme- and amplification-free design ensures robustness and cost-efficiency, while modular probe architecture enables adaptation to diverse low-abundance targets, from epigenetic modifications to protein biomarkers.},
}

@article {pmid40836224,
year = {2025},
author = {Xu, J and Zheng, W and Ou, X and He, H and Yang, C and Guo, L and Xiao, C and Jiang, W and Shu, G and Zhou, T},
title = {Identification and functional analysis of novel precursor genes in cyclic peptide biosynthesis in Pseudostellaria heterophylla.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1103},
pmid = {40836224},
issn = {1471-2229},
abstract = {BACKGROUND: Pseudostellaria heterophylla, a member of the Caryophyllaceae family, is widely used in traditional Chinese medicine due to its bioactive cyclic peptides (CPs) with immunomodulatory functions. Caryophyllaceae- like CPs, one of the largest types plant-derived CPs, typically consist of 5–12 amino acids and are derived from ribosomally synthesized peptide precursors. The diversity of CPs arises from variations in their core peptide sequences. However, the precursor genes responsible for Caryophyllaceae-like CPs biosynthesis in P. heterophylla remain largely uncharacterized.

RESULTS: In this study, barcoding PCR combined with high-throughput sequencing was used to efficiently genotype precursor genes encoding CPs in P. heterophylla. This approach enabled the identification of known and novel precursor genes, including prePhHB_1, prePhHB_2, prePhPE and prePhPN. The core peptide regions showed high variability, while the leader and follower regions were relatively conserved, with a few nucleotide mutations. Tissue-specific expression analysis revealed that prePhHB was predominantly expressed in the phloem and fibrous roots, while prePhPE was specifically expressed in the xylem. prePhPN exhibited low expression level and was mainly detected in the phloem and stem. Moreover, the expression of these precursor genes was responsive to abscisic acid and nitrogen stress. RNA in situ hybridization revealed that prePhPE transcripts were primarily localized in the xylem and phellem of the roots. Transient co-expression in Nicotiana benthamiana indicated that prePhPE is involved in the biosynthesis of Pseudostellarin E (PE).

CONCLUSIONS: Barcoding PCR combined with high-throughput sequencing provides an effective strategy for investigating CP precursor genes, including those with low expression. The results reveal conserved features in CP precursor genes and highlight a previously unrecognized mechanism contributing to CP diversity. The prePhPE gene was identified as the precursor gene of PE, which accumulates mainly in the xylem of P. heterophylla roots. prePhPN may be a precursor gene for a novel CP.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-06972-2.},
}

@article {pmid40833964,
year = {2025},
author = {Wisitrassameewong, K and Adamčík, S and Adamčíková, K and Tang, SM and Tangthirasunun, N and Chuankid, B and Raspé, O},
title = {Russula orientalovirescens sp. nov., a common Southeast Asian edible fungus is different from the European look-alike R. virescens.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0322545},
doi = {10.1371/journal.pone.0322545},
pmid = {40833964},
issn = {1932-6203},
mesh = {Phylogeny ; *Basidiomycota/genetics/classification ; Asia, Southeastern ; DNA, Fungal/genetics ; Europe ; },
abstract = {Green-cracking Russulas are edible fungi that are widely consumed and traded in Southeast Asia. Asian collections of this morphotype were frequently identified as R. virescens in local literature. Multilocus phylogenetic analyses of ITS nrDNA, rpb2 and tef1 regions presented in this study strongly supported that the majority of green cracking Russula collections from Southeast Asia represent a species different from European R. virescens and these collections are described here as R. orientalovirescens sp. nova. Analysis of ITS barcoding region confirmed that published sequence data from China, Laos and Myanmar reported this species as R. virescens. In addition, this analysis showed that the species is widely distributed in Southeast Asia from Malayan Peninsula to Japan, preferring areas with dry season, and is associated with coniferous and deciduous trees as well as heterotrophic plants. Morphological analyses and detailed comparison with recent collections of R. virescens showed that R. orientalovirescens differs from the latter by larger spores and shorter and more abundant pileocystidia. Green-cracking Russula species with distinctly areolate pileus formed a monophyletic lineage where our new species is grouped with Asian R. viridirubrolimbata, European R. virescens and North American R. parvovirescens. Few publicly available ITS sequences from Southeast Asia clustered with either European or North American species suggesting that the phylogenetic lineage of green-cracking Russulas urgently require further attention.},
}

Phylogeny
*Basidiomycota/genetics/classification
Asia, Southeastern
DNA, Fungal/genetics
Europe

@article {pmid40833555,
year = {2025},
author = {Hurwitz, SN},
title = {Mapping Hematopoietic Fate after Transplantation.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {40833555},
issn = {2629-3277},
abstract = {Hematopoietic stem and progenitor cells (HSPCs) form the foundation of lifelong blood cell production and immune function. Understanding their fate, including how they differentiate, self-renew, and respond to environmental cues has long been a cornerstone of stem cell biology and regenerative medicine. This knowledge is especially vital in the context of therapeutic hematopoietic stem and progenitor cell transplantation, where the diverse behavior of transplanted HSPCs directly impacts patient outcomes. Advances in single-cell omics, lineage barcoding, and in situ tracking now allow us to directly trace the developmental trajectories and clonal contributions of individual HSPCs. These tools are reshaping our understanding of hematopoiesis not as a rigid hierarchy but as a dynamic and adaptive system. This review highlights key technologies that enable fate mapping of HSPCs, integrates insights into clonal behavior during both transplantation and native hematopoiesis, and discusses how these findings are likely to inform future diagnostic and therapeutic strategies. CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid40832237,
year = {2025},
author = {Aleksandrovic, E and Fross, SR and Golomb, SM and Liu, X and Zhao, Z and Das, NM and Reese, TC and Ma, W and Lopez, J and Stack, MS and Zhao, M and Zhang, S},
title = {Temporal Clonal Tracing and Functional Perturbation Reveal Niche-Adaptive and Tumor-Intrinsic IFNγ Dependencies Driving Ovarian Cancer Metastasis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.13.669778},
pmid = {40832237},
issn = {2692-8205},
abstract = {Metastasis is an emergent continuum, driven by evolving reciprocal adaptations between continuously disseminating tumor cells (DTCs) and the specialized metastatic niches of distant organs. The interplay between intrinsic and niche-driven mechanisms that enables DTCs to survive and home to distant organs remains incompletely understood. Here, using MetTag, a single-cell barcoding and transcriptome profiling approach with time-stamped BC.IDs, we mapped temporal, clonal dynamics of DTCs and the immune cell landscape across ovarian cancer metastatic niches. Deep sequencing of barcodes revealed preferred enrichment of early-disseminated clones across metastatic niches. Mechanistically, single-cell RNA sequencing (scRNA-seq) coupled with velocity analyses in ascites and metastasis-bearing omentums uncovered an emergent, distinct interferon-gamma (IFNγ) centric transcriptional trajectory, enriched among early seeding clones. Moreover, in vivo CRISPR/Cas9 screening of metastatic niche-specific signatures demonstrated that genes belonging to the ascites IFNγ signature, including Marco, Gbp2b, and Slfn1, are functionally important for peritoneal metastasis. Knockout of IFNγ receptor 1 (Ifngr1) in tumor cells significantly reduced metastatic burden and extended survival, underscoring the importance of tumor cell intrinsic IFNγ signaling in ovarian cancer metastasis. Furthermore, we identified that the tumor intrinsic IFNγ response and ascites-derived tumor-associated macrophages (TAMs) protect cancer cells from anoikis-mediated death within the IFNγ-rich ascites environment. Our study resolves temporal dynamics of disseminating tumor cells and highlights an ascites-driven, IFNγ program as a necessary pro-metastatic adaptation in the ovarian metastasis cascade.},
}

@article {pmid40830572,
year = {2025},
author = {Foyt, D and Brown, D and Zhou, S and Moser, B and Zhu, Q and Gartner, ZJ and Huang, B},
title = {HybriSeq: probe-based device-free single-cell RNA profiling.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1250},
pmid = {40830572},
issn = {2399-3642},
support = {R01DK127421//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; CRI5054//Cancer Research Institute (CRI)/ ; },
abstract = {We have developed the HybriSeq method for single-cell RNA profiling, which utilizes in situ hybridization of multiple probes for targeted transcripts, followed by split-pool barcoding and sequencing analysis of the probes. We have shown that HybriSeq can achieve high sensitivity for RNA detection with multiple probes and profile entire transcripts without an end bias. The utility of HybriSeq is demonstrated in characterizing cell-to-cell heterogeneities of a panel of 196 genes in peripheral blood mononuclear cells and the detection of missed annotations of transcripts.},
}

@article {pmid40830305,
year = {2025},
author = {Maetens, H and Mukungilwa, PN and Kasangaki, A and Boom, AF and Nshimiyumuremyi, T and Munyandamutsa, PS and Clausnitzer, V and Vranken, N and Snoeks, J and Van Steenberge, M},
title = {An ichthyological borderland: The fishfauna of Nyungwe National Park and surroundings (Rwanda, East Africa).},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70185},
pmid = {40830305},
issn = {1095-8649},
support = {B2/202/P1/KEAFish//Belgian Science Policy Office/ ; 1128222N//Fonds Wetenschappelijk Onderzoek/ ; //Volkswagen Foundation/ ; },
abstract = {Nyungwe National Park (NP) is a mountainous region situated in the southwestern part of Rwanda on Congo-Nile watershed. In spite of the high biodiversity in primates, birds and plants, no fish were reported to occur in the park, probably because of the cold temperatures of the rivers. An expedition in 2022 examined the fish diversity within the Nyungwe NP and its buffer zones. Additional sampling was performed in the main river draining the park into Lake Kivu: the Kamiranzovu. Three hundred and twenty specimens belonging to 13 species were collected. Specimens were collected only in the western part of the park, draining towards the Congo basin. The diversity within the park proper was limited to two putative species within the complex of Amphilius cf. kivuensis, which were caught on either side of the Kivu-Rusizi watershed. In contrast, a higher fish diversity, including one clariid species and two species of Enteromius, was observed in the rivers at a lower altitude of the buffer zone. However, the highest species diversity was found near the mouth of Kamiranzovu River, including 11 species, of which 4 were non-native: the guppy Poecilia reticulata, Astatotilapia burtoni, the blue-spotted tilapia Oreochromis leucosticus and the Egyptian mouth-brooder Pseudocrenilabrus multicolor.},
}

@article {pmid40827881,
year = {2025},
author = {Guan, W and Liu, S and Chen, Y and Chu, C and Peng, G and Wang, J and Weng, Q and Fu, Y and Li, J},
title = {HPVPool-Seq: a genotype-guided pooling strategy for cost-effective next-generation sequencing detection of HPV integration in cervical samples.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0139925},
doi = {10.1128/spectrum.01399-25},
pmid = {40827881},
issn = {2165-0497},
abstract = {UNLABELLED: Integration of high-risk human papillomavirus (hrHPV) DNA is a critical event in carcinogenesis and a promising biomarker for risk stratification. However, the high cost of next-generation sequencing (NGS) limits its widespread clinical adoption. We developed HPVPool-Seq, an innovative pooling strategy that leverages the inherent diversity of HPV genotypes as natural barcodes, enabling cost-effective, scalable integration detection. Samples were pooled based on qPCR-derived HPV genotypes and viral loads prior to targeted NGS and bioinformatic decoding. A web-based automation tool was implemented to streamline pooling and decoding workflows. In a proof-of-concept study of 175 clinical specimens, HPVPool-Seq achieved 77.1% exact genotype concordance and 97.1% combined sensitivity compared with qPCR. Cost simulations demonstrated a 60% reduction in per-sample sequencing expenses. Self-correcting capability through targeted retesting further enhanced reliability. HPVPool-Seq offers a novel, traceable, and economically viable solution for high-throughput HPV integration profiling, balancing cost, scalability, and clinical precision. This strategy sets a new framework for molecular screening in HPV-associated cancers.

IMPORTANCE: Accurate detection of high-risk HPV integration is critical for identifying individuals at true risk of progression to malignancy. However, the high cost of next-generation sequencing (NGS) has limited its widespread clinical application. Here, we propose HPVPool-Seq, a novel pooling-based sequencing strategy that uses HPV genotypes as intrinsic barcodes to guide sample pooling without compromising detection sensitivity. This method dramatically reduces sequencing costs while maintaining genotype-level traceability and offers a built-in mechanism for selective retesting of discordant cases. By addressing both technical and economic barriers, our approach provides a scalable, clinically applicable solution for HPV integration profiling in large cohorts, with important implications for precision screening, triage, and epidemiological surveillance.},
}

@article {pmid40827760,
year = {2025},
author = {Dhami, MK and Matheson, P and Bird, S and Walker, L and Hohaia, H and McGaughran, A},
title = {Revisiting Genetic Data Stewardship Practices in Aotearoa New Zealand: A Call to Action on Integrating Māori Data Sovereignty.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70021},
doi = {10.1111/1755-0998.70021},
pmid = {40827760},
issn = {1755-0998},
support = {2223-44-010//New Zealand Biological Heritage National Science Challenge/ ; },
abstract = {Genetic data, including environmental DNA (eDNA), are regularly used to monitor escalating biodiversity concerns globally. In Aotearoa New Zealand, biodiversity is unique and cherished-many species are taonga (treasured) and cared for by kaitiaki (guardians with customary responsibilities), specifically mana whenua with custodial rights (Māori; the Indigenous people of New Zealand). Discussions are currently underway regarding the development of a reference DNA barcode database for biodiversity in Aotearoa New Zealand to improve outcomes for biosecurity surveillance and biodiversity assessment. A priority of these discussions is that the database development and eventual implementation accords with Te Tiriti o Waitangi (The Treaty of Waitangi). Here, we evaluate current practices for storing genetic data from samples collected in Aotearoa New Zealand by examining two major public data repositories-the National Centre for Biotechnology Information (NCBI) GenBank and the Barcode of Life Data System (BOLD). We find that current database practices limit opportunities for Māori data sovereignty, with DNA from many taonga species uploaded to public repositories with no associated restrictions or guidelines over use. This is an important finding that will help shape the development of a future DNA reference database for Aotearoa New Zealand that integrates the rights and interests of Indigenous communities.},
}

@article {pmid40827628,
year = {2025},
author = {von der Heyden, S},
title = {'It's not much, but it's honest work': The status of environmental DNA analyses of fish biodiversity in southern Africa.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70187},
pmid = {40827628},
issn = {1095-8649},
support = {SRUG2204041792//National Research Foundation/ ; },
abstract = {Environmental DNA (eDNA) biodiversity surveys have the power to transform the detection of species in natural environments, which is crucial for the conservation and management of freshwater, estuarine and marine environments. Globally, eDNA-based analyses have increased significantly, with fishes being the most widely studied aquatic organisms. However, the extent of work and the current status of eDNA-based surveys for southern Africa are unclear. A literature search for studies with a focus on fishes was carried out for Botswana, Namibia, Mozambique, South Africa and Zimbabwe and retrieved 16 papers. Most of these were from South Africa (n = 14), with one paper each from Botswana and Mozambique. No papers were found for Namibia and Zimbabwe. Eleven papers utilized metabarcoding to detect fish communities, whereas four utilized species-specific primers to detect rare (e.g., coelacanth, pipefishes, endangered and vulnerable freshwater fishes) or invasive (silver carp) species and one consisted of a diet study. There were five papers from freshwater and 11 studies applying eDNA-based surveys in estuaries or marine systems. A scan of some of the technical aspects of the eDNA workflow (biological replication filtration, inclusion of negative controls, primer choice and technical replication) showed a wide range of approaches, highlighting the need for standardization of the eDNA workflow and the reporting of its data. Unsurprisingly, one of the largest challenges remains the lack of referenced barcodes, which limits the ability to determine species distributions and associated ecological inferences. Building on the exciting work highlighted here and to fully realize the power of eDNA will require increasing collaborations across all aspects of the eDNA workflow. Further, exploring pathways for the meaningful integration of data derived from eDNA surveys to support conservation and management decisions, not only for fishes but also for all the incredible biodiversity of southern Africa, is crucial.},
}

@article {pmid40806250,
year = {2025},
author = {Dang, Z and Wu, Q and Zhou, Y and Wang, L and Liu, Y and Yang, C and Liu, M and Xie, Q and Chen, C and Ma, S and Shan, B},
title = {Comparative Transcriptomic Analysis for Identification of Environmental-Responsive Genes in Seven Species of Threadfin Breams (Nemipterus).},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
pmid = {40806250},
issn = {1422-0067},
support = {NO. 42206109//National Natural Science Foundation of China/ ; Modern fishery cooperation between China and neighboring countries around the South China Sea//Asia Cooperation Fund Project/ ; NO.2023TD93//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {Members of the genus Nemipterus are economically important fish species distributed in the tropical and subtropical Indo-West Pacific region. The majority of species in this genus inhabit waters with sandy-muddy substrates on the continental shelf, although different species are found at slightly varying water depths. In this study, we sequenced seven species within the genus Nemipterus after identifying the specimens using complementary morphological analysis and DNA barcoding. Each species yielded over 40,000,000 clean reads, totaling over 300,000,000 clean reads across the seven species. A total of 276,389 unigenes were obtained after de novo assembly and a total of 168,010 (60.79%) unigenes were annotated in the protein database. The comprehensive functional annotation based on the KOG, GO, and KEGG databases revealed that these unigenes are mainly associated with numerous physiological, metabolic, and molecular processes, and that the seven species exhibit similarity in these aspects. By constructing a phylogenetic tree and conducting divergence time analysis, we found that N. bathybius and N. virgatus diverged most recently, approximately during the Neogene Period (14.9 Mya). Compared with other species, N. bathybius and N. virgatus are distributed in deeper water layers. Therefore, we conducted selection pressure analysis using these two species as the foreground branches and identified several environmental-responsive genes. The results indicate that genes such as aqp1, arrdc3, ISP2, Hip, ndufa1, ndufa3, pcyt1a, ctsk, col6a2, casp2 exhibit faster evolutionary rates during long-term adaptation to deep-water environments. Specifically, these genes are considered to be associated with adaptation to aquatic osmoregulation, temperature fluctuations, and skeletal development. This comprehensive analysis provides valuable insights into the evolutionary biology and environmental adaptability of threadfin breams, contributing to the conservation and sustainable management of these species.},
}

@article {pmid39677764,
year = {2024},
author = {Cho, S and Moon, W and Martino, N and Yun, SH},
title = {Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39677764},
issn = {2692-8205},
support = {R01 EB033155/EB/NIBIB NIH HHS/United States ; R01 EB034687/EB/NIBIB NIH HHS/United States ; },
abstract = {Laser particles (LPs) emitting narrowband spectra across wide spectral ranges are highly promising for high-multiplex optical barcoding. Here, we present LPs based on indium phosphide (InP) nanodisks, operating in the near-infrared wavelength range of 740-970 nm. Utilizing low-order whispering gallery resonance modes in size-tuned nanodisks, we achieved an ultrawide color palette with 27% bandwidth utilization and nanometer-scale linewidth. The minimum laser size was 430 nm in air and 560 nm within the cytoplasm, operating at mode order 4 or 5. We further demonstrated spectral detection of laser peaks with high signal-to-background ratios in highly-scattering media, including 1-cm-thick chicken breast tissue and blood vessels in live mice.},
}

@article {pmid39416107,
year = {2024},
author = {Chen, J and Nilsen, ED and Chitboonthavisuk, C and Mo, CY and Raman, S},
title = {Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416107},
issn = {2692-8205},
support = {R21 AI156785/AI/NIAID NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; },
abstract = {Understanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.},
}

@article {pmid39203446,
year = {2024},
author = {Darienko, T and Rad-Menéndez, C and Pröschold, T},
title = {The New Genus Caulinema Revealed New Insights into the Generic Relationship of the Order Ulotrichales (Ulvophyceae, Chlorophyta).},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
pmid = {39203446},
issn = {2076-2607},
support = {P 34416-B//FWF Austrian Science Fund/ ; },
abstract = {Traditionally, the order Ulotrichales comprised green algae of an unbranched, uniseriate, filamentous morphology. However, since the establishment of ultrastructural features, the circumscription of this order has dramatically changed. Some genera and species have been excluded from this order and others with different morphologies (sarcinoid, branched filaments or even parenchymatous taxa) have been included. Phylogenetic analyses have confirmed the monophyly of this order, but its differentiation from the Ulvales and Acrosiphoniales remains difficult because of the lack of synapomorphies at every level (morphology, molecular signatures). To demonstrate the difficulties of placement into genera and orders, we investigated two sarcinoid taxa with the absence of zoospore formation. SSU and ITS rDNA tree topology and the ITS-2/CBC approach revealed that both strains SAG 2661 and CCAP 312/1 belong to Ulosarcina terrestrica and the newly erected genus Caulinema, respectively. The species conception using this approach was evaluated by sequencing the plastid-coding gene tufA, a commonly used barcode marker for green algae. All three molecular markers resulted in similar topologies at the generic and species levels, which is consistent with the ITS-2/CBC approach and tufA for barcoding. The reevaluation of the ultrastructural features revealed that the presence of organic scales on the surfaces of motile cells is characteristic for the order Ulotrichales and can be used for separation from the closely related orders. As a consequence of our study, we propose the new genus Caulinema for strain CCAP 312/1.},
}

@article {pmid38002986,
year = {2023},
author = {Gao, T and Shi, Y and Xiao, J},
title = {Comparative Mitogenomics Reveals Cryptic Species in Sillago ingenuua McKay, 1985 (Perciformes: Sillaginidae).},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
pmid = {38002986},
issn = {2073-4425},
support = {41976083//National Natural Science Foundation of China/ ; 41776171//National Natural Science Foundation of China/ ; 2021C0204//the Province Key Research and Development Program of Zhejiang/ ; },
mesh = {Animals ; Phylogeny ; Thailand ; *Fishes/genetics ; *Perciformes/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {It is unreliable to identify marine fishes only by external morphological features. Species misidentification brings great challenges to fishery research, resource monitoring and ecomanagement. Sillago ingenuua is an important part of commercial marine fishes, and in which, the morphological differences between different groups are not obvious. Here, we compared different geographical groups of S. ingenuua which were collected from Xiamen, Dongshan, Keelung, Songkhla and Java. The results showed that all samples of S. ingenuua were similar in external morphological characteristics and the shape of the swim bladder, but there were two distinctive lineages which were flagged as cryptic species based on DNA barcoding. The comparative mitogenomic results showed that S. ingenuua A and S. ingenuua B were identical in structural organization and gene arrangement. Their nucleotide composition and codon usage were also similar. A phylogenetic analysis was performed based on 13 concatenated PCGs from eight Sillago species. The results showed that the genetic distance between S. ingenuua A and S. ingenuua B was large (D = 0.069), and this genetic distance was large enough to reveal that S. ingenuua A and S. ingenuua B might be different species.},
}

Animals
Phylogeny
Thailand
*Fishes/genetics
*Perciformes/genetics
Sequence Analysis, DNA/methods

@article {pmid36123605,
year = {2022},
author = {Maes, T and De Corte, Z and Vangestel, C and Virgilio, M and Smitz, N and Djuikwo-Teukeng, FF and Papadaki, MI and Huyse, T},
title = {Large-scale and small-scale population genetic structure of the medically important gastropod species Bulinus truncatus (Gastropoda, Heterobranchia).},
journal = {Parasites & vectors},
volume = {15},
number = {1},
pages = {328},
pmid = {36123605},
issn = {1756-3305},
support = {1S86319N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; *Bulinus/parasitology ; *Gastropoda/genetics ; Genetics, Population ; Humans ; Phylogeny ; Schistosoma haematobium/genetics ; },
abstract = {BACKGROUND: Gastropod snails remain strongly understudied, despite their important role in transmitting parasitic diseases. Knowledge of their distribution and population dynamics increases our understanding of the processes driving disease transmission. We report the first study to use high-throughput sequencing (HTS) to elucidate the population genetic structure of the hermaphroditic snail Bulinus truncatus (Gastropoda, Heterobranchia) on a regional (17-150 km) and inter-regional (1000-5400 km) scale. This snail species acts as an intermediate host of Schistosoma haematobium and Schistosoma bovis, which cause human and animal schistosomiasis respectively.

METHODS: Bulinus truncatus snails were collected in Senegal, Cameroon, Egypt and France and identified through DNA barcoding. A single-end genotyping-by-sequencing (GBS) library, comprising 87 snail specimens from the respective countries, was built and sequenced on an Illumina HiSeq 2000 platform. Reads were mapped against S. bovis and S. haematobium reference genomes to identify schistosome infections, and single nucleotide polymorphisms (SNPs) were scored using the Stacks pipeline. These SNPs were used to estimate genetic diversity, assess population structure and construct phylogenetic trees of B. truncatus.

RESULTS: A total of 10,750 SNPs were scored and used in downstream analyses. The phylogenetic analysis identified five clades, each consisting of snails from a single country but with two distinct clades within Senegal. Genetic diversity was low in all populations, reflecting high selfing rates, but varied between locations due to habitat variability. Significant genetic differentiation and isolation by distance patterns were observed at both spatial scales, indicating that gene flow is not strong enough to counteract the effects of population bottlenecks, high selfing rates and genetic drift. Remarkably, the population genetic differentiation on a regional scale (i.e. within Senegal) was as large as that between populations on an inter-regional scale. The blind GBS technique was able to pick up parasite DNA in snail tissue, demonstrating the potential of HTS techniques to further elucidate the role of snail species in parasite transmission.

CONCLUSIONS: HTS techniques offer a valuable toolbox to further investigate the population genetic patterns of intermediate schistosome host snails and the role of snail species in parasite transmission.},
}

Animals
*Bulinus/parasitology
*Gastropoda/genetics
Genetics, Population
Humans
Phylogeny
Schistosoma haematobium/genetics

@article {pmid36080967,
year = {2022},
author = {Khan, G and Hegge, A and Gemeinholzer, B},
title = {Development and Testing of the A1 Volumetric Air Sampler, an Automatic Pollen Trap Suitable for Long-Term Monitoring of eDNA Pollen Diversity.},
journal = {Sensors (Basel, Switzerland)},
volume = {22},
number = {17},
pages = {},
pmid = {36080967},
issn = {1424-8220},
support = {01LC19031//Federal Ministry of Education and Research/ ; },
mesh = {*Air Pollutants/analysis ; Biodiversity ; *Environmental Monitoring/methods ; Humans ; Pollen/chemistry ; },
abstract = {Airborne pollen surveys provide information on various aspects of biodiversity and human health monitoring. Such surveys are typically conducted using the Burkard Multi-Vial Cyclone Sampler, but have to be technically optimized for eDNA barcoding. We here developed and tested a new airborne pollen trap, especially suitable for autonomous eDNA-metabarcoding analyses, called the A1 volumetric air sampler. The trap can sample pollen in 24 different tubes with flexible intervals, allowing it to operate independently in the field for a certain amount of time. We compared the efficiency of the new A1 volumetric air sampler with another automated volumetric spore trap, the Burkard Multi-Vial Cyclone Sampler, which features shorter and fewer sampling intervals to evaluate the comparability of ambient pollen concentrations. In a sterile laboratory environment, we compared trap performances between the automated volumetric air samplers by using pure dry pollen of three species-Fagus sylvatica, Helianthus annuus and Zea mays-which differ both by exine ornamentation and pollen size. The traps had a standard suction flow rate of 16.5 L/min, and we counted the inhaled pollen microscopically after a predefined time interval. Our results showed that though we put three different pollen types in the same container, both the traps inhaled all the pollens in a statistically significant manner irrespective of their size. We found that, on average, both traps inhaled equal an number of pollens for each species. We did not detect any cross-contamination between tubes. We concluded that the A1 volumetric air sampler has the potential to be used for longer and more flexible sampling intervals in the wild, suitable for autonomous monitoring of eDNA pollen diversity.},
}

*Air Pollutants/analysis
Biodiversity
*Environmental Monitoring/methods
Humans
Pollen/chemistry

@article {pmid34646477,
year = {2021},
author = {Hurtado, G and Mayer, G and Mabry, KE},
title = {Does urbanization ameliorate the effect of endoparasite infection in kangaroo rats?.},
journal = {Ecology and evolution},
volume = {11},
number = {19},
pages = {13390-13400},
pmid = {34646477},
issn = {2045-7758},
support = {R25 GM061222/GM/NIGMS NIH HHS/United States ; },
abstract = {Urban development can fragment and degrade remnant habitat. Such habitat alterations can have profound impacts on wildlife, including effects on population density, parasite infection status, parasite prevalence, and body condition. We investigated the influence of urbanization on populations of Merriam's kangaroo rat (Dipodomys merriami) and their parasites. We predicted that urban development would lead to reduced abundance, increased parasite prevalence in urban populations, increased probability of parasite infection for individual animals, and decreased body condition of kangaroo rats in urban versus wildland areas. We live trapped kangaroo rats at 5 urban and 5 wildland sites in and around Las Cruces, NM, USA from 2013 to 2015, collected fecal samples from 209 kangaroo rats, and detected endoparasites using fecal flotation and molecular barcoding. Seven parasite species were detected, although only two parasitic worms, Mastophorus dipodomis and Pterygodermatites dipodomis, occurred frequently enough to allow for statistical analysis. We found no effects of urbanization on population density or probability of parasite infection. However, wildland animals infected with P. dipodomis had lower body condition scores than infected animals in urban areas or uninfected animals in either habitat. Our results suggest that urban environments may buffer Merriam's kangaroo rats from the detrimental impacts to body condition that P. dipodomis infections can cause.},
}

@article {pmid29115074,
year = {2017},
author = {Cho, YC and Lee, SH and Cho, YH and Choy, YB},
title = {Adapter-based Safety Injection System for Prevention of Wrong Route and Wrong Patient Medication Errors.},
journal = {Journal of Korean medical science},
volume = {32},
number = {12},
pages = {1938-1946},
pmid = {29115074},
issn = {1598-6357},
mesh = {Catheters ; Equipment Design ; Humans ; Injections/instrumentation/*methods ; Medication Errors/*prevention & control ; Printing, Three-Dimensional ; },
abstract = {Wrong-route or -patient medication errors due to human mistakes have been considered difficult to resolve in clinical settings. In this study, we suggest a safety injection system that can help to prevent an injection when a mismatch exists between the drug and route or patient. For this, we prepared two distinct adapters with key and keyhole patterns specifically assigned to a pair of drug and route or patient. When connected to a syringe tip and its counterpart, a catheter injection-port, respectively, the adapters allowed for a seamless connection only with their matching patterns. In this study, each of the adapters possessed a specific key and keyhole pattern at one end and the other end was shaped to be a universal fit for syringe tips or catheter injection-ports in clinical use. With the scheme proposed herein, we could generate 27,000 patterns, depending on the location and shape of the key tooth in the adapters. With a rapid prototyping technique, multiple distinct pairs of adapters could be prepared in a relatively short period of time and thus, we envision that a specific adapter pair can be produced on-site after patient hospitalization, much like patient identification barcodes.},
}

Catheters
Equipment Design
Humans
Injections/instrumentation/*methods
Medication Errors/*prevention & control
Printing, Three-Dimensional

@article {pmid40823546,
year = {2025},
author = {Rodríguez-Flores, PC and Bracken-Grissom, HD and Lemaitre, R and Felder, DL and Nizinski, MS},
title = {A new squat lobster (Crustacea, Decapoda, Munidopsidae) from the western Atlantic with redescription of Munidopsisexpansa Benedict, 1902 and several range extensions.},
journal = {ZooKeys},
volume = {1248},
number = {},
pages = {321-340},
pmid = {40823546},
issn = {1313-2989},
abstract = {The western Atlantic Ocean harbors a rich fauna of deep-sea squat lobsters that have been intensively studied during the last two centuries. We revise material recently collected by trawls, ROV and submersibles on several expeditions in the Gulf of Mexico and the Caribbean Sea. Using an integrative taxonomy approach, we describe Munidopsismessingi sp. nov. and redescribe M.expansa Benedict, 1902, the latter species known only from a few records. Additionally, we report a new record of M.turgida Rodríguez-Flores, Macpherson & Machordom, 2018 for the Gulf of Mexico. This rare species was previously known from only the holotype, collected in the Guadeloupe Islands, Caribbean Sea. We apply micro-CT scanning in the course of morphological illustrations and report barcode data as available.},
}

@article {pmid40823049,
year = {2025},
author = {Zaman, M and Faraz, A and Azad, R and Khan, IA and Faheem, B and Rafiq, N and Khan, A and Shilin, T and ALmunqedhi, BM and Ali, HM},
title = {Updating the Systematic Status of Genus Heterotermes (Rhinotermitidae: Isoptera: Blattodea) by Combining Morphometric Analysis, Distribution Mapping, and DNA Barcoding Approaches.},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71993},
pmid = {40823049},
issn = {2045-7758},
abstract = {Termites are eusocial insects, found widely in the tropics of the world. They are known as serious pests to agriculture, forestry, and structures, but they also act as key ecological engineers in the wild. We assessed termites diversity in three districts (Buner, Swabi and Haripur), which belong to various agro-ecological regions of Khyber Pakhtunkhwa (Pakistan; Oriental region). Sampling was done either by breaking visible mud galleries or by using modified NIFA termaps. Fourteen characters/indices were assessed for species morphometrics and Principal Component Analysis (PCA), and DNA was extracted from the identified soldier caste in each sample for MtDNA COII barcoding. An identification key and distribution map were made for Heterotermes gretudae (MZ018116.1) and Heterotermes indicola (MZ055400.1). H. gretudae is a true species endemic to India but is recorded in Pakistan for the first time (Buner and Swabi districts) on new feeding host substrates, while H. indicola has a new locality record. PCA analysis (74.9% variation) and MtDNA COII barcoding (Maximum Likelihood analyses) were used to validate the species. Novel COII sequences were submitted to the GenBank.},
}

@article {pmid40822413,
year = {2025},
author = {Kim, S and Sohn, J and Lee, M and Kim, H},
title = {First records of the genera Aclitus and Protaphidius (Hymenoptera, Braconidae, Aphidiinae) from South Korea.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e161563},
pmid = {40822413},
issn = {1314-2828},
abstract = {BACKGROUND: The aphidiine genera Aclitus Förster, 1863 and Protaphidius Ashmead, 1900 (Hymenoptera, Braconidae, Aphidiinae) each contain only a few species worldwide. In this study, we report the first records of Aclitus and Protaphidius from Korea, based on specimens of Aclitussappaphis Takada & Shiga, 1974 and Protaphidiusnawaii (Ashmead, 1906).

NEW INFORMATION: We provide detailed morphological characters, diagnostic characters, and photographic documentation for both species. A new host record, Hamamelistesbetulinus (de Horváth, 1896), of Aclitussappaphis is provided. To support species identification and future phylogenetic studies, mitochondrial (COI, COII, ND1, Cytb) and nuclear (28SD2, EF1A1, Wingless) gene sequences for both species are also provided.},
}

@article {pmid40817273,
year = {2025},
author = {Kaifu, K and Han, YS and Shiraishi, H},
title = {Global consumption of threatened freshwater eels revealed by integrating DNA barcoding, production data, and trade statistics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29968},
pmid = {40817273},
issn = {2045-2322},
support = {JP22H00371//Japan Society for the Promotion of Science/ ; NSTC 111-2313-B-002-016-MY3//National Science and Technology Council/ ; },
abstract = {Fisheries resources depend on natural ecosystems, yet their sustainable management is often limited by uneven regional capacities and the pressures of international trade. High demand from certain regions can lead to overexploitation in others, highlighting the need to understand global consumption patterns of key aquatic species. This study introduces an integrated approach that combines DNA barcoding of freshwater eel (Anguilla spp.) products collected from end markets in 11 countries/regions with global production and trade statistics. We estimate that over 99% of eels consumed worldwide belong to three IUCN-listed threatened species: the American eel, Japanese eel, and European eel. Consumption was heavily concentrated in East Asia-particularly China, Japan, and South Korea-where supply volumes far exceed those of other regions. Our approach yields the most comprehensive quantitative global estimate to date of eel species composition in consumption, offering essential insights for the conservation and sustainable management of this highly exploited group.},
}

@article {pmid40816522,
year = {2025},
author = {Meng, XQ and Xu, XL and Gao, Y and Deng, SL},
title = {Establishment of CRISPR/Cas9 lineage tracking technology for pig embryos.},
journal = {Molecular and cellular probes},
volume = {},
number = {},
pages = {102046},
doi = {10.1016/j.mcp.2025.102046},
pmid = {40816522},
issn = {1096-1194},
abstract = {Understanding tissue development in pigs is critical for biomedical research and genetic engineering, particularly for modeling human disease. However, tracing developmental origins and reconstructing lineage trees for pig cells remains a significant challenge. Here, we present a high-resolution lineage tracing system that combines molecular barcoding with single-cell transcriptomics in pigs. Our system combines two key components: DNA barcodes (three CRISPR/Cas9 target sites and an 8-base pair intBC) integrated into the genome via piggyBac transposition, and a constitutive Cas9-EGFP cassette stably integrated at the Rosa26 locus using CRISPR/Cas12a. By combining lineage barcodes with single-cell RNA sequencing (scRNA-seq), we constructed an evolutionary lineage recorder that captures distinct cell states across developmental or differentiation trajectories. This system provides an essential tool for the subsequent construction of complete porcine cell fate maps. Our work provides a tool for studying porcine developmental biology, but also helps to optimize regenerative medicine strategies and improve the design of genetically engineered animal models.},
}

@article {pmid40815071,
year = {2025},
author = {Silva, RGD and Teixeira, AAM and Chaves, RECRF and Ribeiro, SC and Ferreira, RR and Vasconcellos, A and Almeida, WO},
title = {Integrative taxonomy of Raillietiella gigliolii Hett, 1924 (Pentastomida: Raillietiellidae) - molecular and morphological evidence from Neotropical Amphisbaenians.},
journal = {Journal of helminthology},
volume = {99},
number = {},
pages = {e94},
doi = {10.1017/S0022149X25100655},
pmid = {40815071},
issn = {1475-2697},
support = {BMD-0008-02422.01.18/24//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; PVS-0215-00125.01.00/23//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; BP5-0197-00161.01.00/22)//Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico/ ; 308534/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 309820/2020-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.929233/2023-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88887.950422/2024-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {This study provides a comprehensive analysis of the morphology and genetics of Raillietiella gigliolii, an endoparasitic pentastomid found in amphisbaenians. The research was based on specimens deposited in the Universidade Regional do Cariri (URCA), as well as newly collected individuals from the Brazilian Caatinga. Detailed morphological descriptions were carried out, including measurements of the hooks, cephalothorax, tail, buccal cadre, and the copulatory spicule in males. In parallel, the first molecular characterisation of this species was performed, targeting the mitochondrial COI gene (barcode region). All specimens exhibited consistent morphotypes, particularly in the shape of the hooks, with no observable variation between males and females, nor between individuals parasitising different hosts (Amphisbaena alba and A. vermicularis). Molecular analyses revealed a well-supported monophyletic clade, with no detectable genetic divergence among individuals, confirming both the morphological stability and genetic delimitation of the species. These findings support the recognition of R. gigliolii as a clearly delineated species, currently restricted to amphisbaenians, which does not exhibit significant morphological variability, in contrast to other congeners.},
}

@article {pmid40813494,
year = {2025},
author = {Yan, R and Zeng, Y and Chen, C and Rab, A and Li, H and Ullah, R and Islam, M and Cui, Y and Liu, M and Tian, X},
title = {Molecular evolution of chloroplast genome in Triumfetta (Grewioideae, Malvaceae).},
journal = {Planta},
volume = {262},
number = {4},
pages = {82},
pmid = {40813494},
issn = {1432-2048},
support = {2060302//The Ability Establishment of Sustainable Use for Valuable Chinese Medicine Resources/ ; },
abstract = {This study provides insights into the chloroplast genome evolution of Triumfetta, identifies polymorphic loci for molecular marker development, and offers preliminary phylogenomic evidence on the evolutionary relationships within the genus. The genus Triumfetta Plum. ex L. (Grewioideae, Malvaceae) is a pantropical group comprising approximately 177 species. Despite its diversity, its chloroplast (cp) genomics remain unstudied. To investigate evolutionary dynamics and phylogenetic relationships within Triumfetta, complete cp genomes of eight species were de novo assembled and compared with two publicly available genomes. These cp genomes were 160,075 to 160,604 base pairs (bp) long and consisted of a large single-copy region (89,006-89,386 bp), a small single-copy region (20,142-20,266 bp), and a pair of inverted repeats (IRa and IRb, 25,440-25,498 bp), encoding 112 unique genes (78 protein-coding, 30 transfer RNA, and 4 ribosomal RNA). Comparative analyses showed high similarity in GC content, IR contraction/expansion, codon usage, substitution patterns, and repeat structures. An inversion was identified in the LSC region of Triumfetta tomentosa, reversing six genes: trnC, petN, psbM, trnD, trnY, and trnE, without gene loss. Six genes (psbK, rpl20, rpl23, rps16, rps7, and ycf2) showed signatures of positive selection, suggesting potential roles in adaptation. Ten polymorphic loci were identified across intergenic and coding regions, including trnR-atpA, rpl33-rps18, ccsA-ndhD, clpP, rpl22, and ycf1, representing useful markers for DNA barcoding and population genetics. Phylogenetic analysis revealed Triumfetta is monophyletic and closely related to Corchorus L. Triumfetta species formed two distinct clades, reflecting a clear biogeographic divergence: one comprising African and Asian species, and the other consisting exclusively of Australian species. This study provides the first insights into cp genome variation and phylogenetic relationships in Triumfetta, offering resources for further phylogenetic, barcoding, and conservation research.},
}

@article {pmid40813104,
year = {2025},
author = {Chou, WC and Canchola, A and Zhang, F and Lin, Z},
title = {Machine Learning and Artificial Intelligence in Nanomedicine.},
journal = {Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology},
volume = {17},
number = {4},
pages = {e70027},
pmid = {40813104},
issn = {1939-0041},
support = {R01 EB031022/EB/NIBIB NIH HHS/United States ; R03 EB035643/EB/NIBIB NIH HHS/United States ; R01EB031022/EB/NIBIB NIH HHS/United States ; R03EB035643/EB/NIBIB NIH HHS/United States ; },
abstract = {Nanomedicine harnesses nanoscale materials, such as lipid, polymeric, and inorganic nanoparticles, to deliver diagnostic or therapeutic agents for cancer, infectious disease, and neurological disorders, among others. However, translating promising nanoparticle designs into clinically approved products remains a challenge. Factors such as particle size, surface chemistry, and payload interactions must be optimized, and preclinical results often fail to predict human efficacy. In recent years, artificial intelligence (AI) and machine learning (ML) have emerged as transformative tools to address these hurdles at every stage of nanomedicine development. By rapidly screening extensive libraries and extracting structure-function relationships, AI-driven models can rationalize nanoparticle formulation, predict biodistribution, and guide optimal design. Techniques like high-throughput DNA barcoding and automated liquid handling facilitate robust, large-scale data collection, feeding into computational pipelines that expedite discovery while reducing reliance on resource-intensive trial-and-error experiments. AI-based platforms also enable improved modeling of protein corona formation, which profoundly affects nanoparticle immunogenicity and cellular uptake. Despite these advances, challenges persist in data standardization, model generalizability, and establishing a clear regulatory framework since no dedicated U.S. Food and Drug Administration (FDA) guidance addresses the intersection of AI and nanomedicine. Overcoming these limitations requires harmonized data sharing, rigorous in vivo validation, and clear ethical and regulatory guidelines. This review summarizes the rapidly evolving landscape of AI in nanomedicine, highlighting key successes in design and preclinical prediction, as well as persistent obstacles to full-scale clinical integration. By illuminating these dynamics, we aim to chart a more efficient path forward in developing next-generation nanomedicine.},
}

@article {pmid40809554,
year = {2025},
author = {Zhang, J and Xing, Y and Yu, H and Li, S},
title = {Six new species of the spider genus Clubiona Latreille, 1804 (Araneae, Clubionidae) from subtropical forests of Sichuan Province, China.},
journal = {ZooKeys},
volume = {1248},
number = {},
pages = {61-91},
pmid = {40809554},
issn = {1313-2989},
abstract = {Six new species, belonging to three species groups of Clubiona Latreille, 1804 are described from both males and females: C.huntianling Yu & Li, sp. nov., C.rouqiu Yu & Li, sp. nov. and C.yinyangjian Yu & Li, sp. nov. from the corticalis group; C.huojianqiang Yu & Li, sp. nov. and C.qiankunquan Yu & Li, sp. nov. from the trivialis group; C.nezha Yu & Li, sp. nov. from the zilla group. These species are currently known to occur only in subtropical forests, Sichuan, China. The DNA barcodes of all species were obtained for species delimitation, matching of sexes and future use.},
}

@article {pmid40809552,
year = {2025},
author = {Fang, Y and van Achterberg, C and Tang, P and Chen, XX},
title = {Revision of genus Zele Curtis (Hymenoptera, Braconidae, Euphorinae) from China, with description of nineteen new species.},
journal = {ZooKeys},
volume = {1248},
number = {},
pages = {125-208},
pmid = {40809552},
issn = {1313-2989},
abstract = {Zele Curtis is a braconid parasitoid wasp genus within the subfamily Euphorinae (Hymenoptera, Braconidae), consisting of only 30 species worldwide. The Chinese species of the genus Zele are revised and 29 species are now recognised, including 19 species new to science: Z.aquilus Fang, van Achterberg & Chen, sp. nov., Z.carinatus Fang, van Achterberg & Chen, sp. nov., Z.confusus Fang, van Achterberg & Chen, sp. nov., Z.cristatus Fang, van Achterberg & Chen, sp. nov., Z.curvatus Fang, van Achterberg & Chen, sp. nov., Z.curvinervis Fang, van Achterberg & Chen, sp. nov., Z.densipunctatus Fang, van Achterberg & Chen, sp. nov., Z.extensus Fang, van Achterberg & Chen, sp. nov., Z.fulgidus Fang, van Achterberg & Chen, sp. nov., Z.fuscatus Fang, van Achterberg & Chen, sp. nov., Z.impolitus Fang, van Achterberg & Chen, sp. nov., Z.inclinator Fang, van Achterberg & Chen, sp. nov., Z.irregularis Fang, van Achterberg & Chen, sp. nov., Z.petiolatus Fang, van Achterberg & Chen, sp. nov., Z.rugulosus Fang, van Achterberg & Chen, sp. nov., Z.sculpticoxis Fang, van Achterberg & Chen, sp. nov., Z.shaanxiensis Fang, van Achterberg & Chen, sp. nov., Z.syntomus Fang, van Achterberg & Chen, sp. nov., and Z.vacatus Fang, van Achterberg & Chen, sp. nov. 31 barcode region sequences of mitochondrial cytochrome c oxidase I (COI) from the genus Zele were obtained and combined with 102 sequences from BOLD. They were used to validate new species and to get an indication of similarity among species. Three species are reinstated: Zeleperonatus (Shestakov, 1940), Z.romani (Fahringer, 1929), and Z.rufulus (Thomson, 1895). In addition, an identification key for the Zele species recorded in China (plus one expected species) is provided.},
}

@article {pmid40809550,
year = {2025},
author = {Gallardo Salamanca, MLÁ and Asorey, C and Macpherson, E},
title = {A new species of Galathea (Decapoda, Galatheidae) from the seamounts of the Easter Island area (Southeast Pacific Ocean Ridge) associated with a sea urchin.},
journal = {ZooKeys},
volume = {1248},
number = {},
pages = {111-123},
pmid = {40809550},
issn = {1313-2989},
abstract = {Galatheatukitukimea sp. nov. is described from the seamounts near Rapa Nui (Easter Island) and represents the first record of the genus for this region of the Pacific Ocean and for Chilean territory. The new species belongs to the group of species having the carapace with median protogastric and cardiac spines. G.tukitukimea has always been observed associated with the sea urchin Stereocidarisnascaensis. This potential mimicry-based association is uncommon in squat lobsters, which warrants further study.},
}

@article {pmid40809456,
year = {2025},
author = {Guo, Y and Zhang, L and Zhao, X and Xu, C and Li, Y and Gao, Z and Ou, G and Chen, P and Zheng, W and Pei, H and Liu, X and Liu, BF and Li, Y},
title = {Toti-N-glycan Recognition Enables Universal Multiplexed Single-Nucleus RNA Sequencing.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0678},
pmid = {40809456},
issn = {2639-5274},
abstract = {Sample barcoding-based multiplex single-cell and single-nucleus sequencing (sc/sn-seq) offers substantial advantages by reducing costs, minimizing batch effects, and identifying artifacts, thereby advancing biological and biomedical research. Despite these benefits, universal sample barcoding has been hindered by challenges such as inhomogeneous expression of tagged biomolecules, limited tagging affinity, and insufficient genetic insertion. To overcome these limitations, we developed Toti-N-Seq, a universal sample multiplex method, by tagging Toti-N-glycan on cell surfaces or nuclear membranes via our engineered streptavidin-Fbs1 GYR variant fusion protein, which could be used not only for sc-seq but also for sn-seq. Instead of targeting lipids or proteins, we focused on targeting the ubiquitous N-glycans found on any species with accessible membranes, which minimizes the exchange between barcoded samples and avoids biased barcoding. Our technology can be broadly applied to multiple species and nearly all eukaryotic cell types, with an overall classification accuracy of 0.969 for sc-seq and of 0.987 for sn-seq. As a demonstration with clinical human peripheral blood mononuclear cells, our Toti-N-Seq achieved rapid one-step sample preparation (<3 min) for easily scaling up while keeping high fidelity of sample ratios, removing artifacts, and detecting rare cell populations (~0.5%). Consequently, we offer a versatile platform suitable for various cell types and applications.},
}

@article {pmid40808602,
year = {2025},
author = {Grigoryeva, MA and Khrenova, MG and Zvereva, MI},
title = {NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency.},
journal = {Journal of bioinformatics and computational biology},
volume = {23},
number = {4},
pages = {2550011},
doi = {10.1142/S0219720025500118},
pmid = {40808602},
issn = {1757-6334},
abstract = {In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation.},
}

@article {pmid40808235,
year = {2025},
author = {Hansen, ML and Kordatos, KIT and Nørgaard, JK and Peter Bredal Jørgensen, J and Strube, ML and Schostag, MD and Yang, L and Jelsbak, L},
title = {Genetic Memory Devices to Detect Specialized Metabolites in Plant and Soil Microbiomes.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00073},
pmid = {40808235},
issn = {2161-5063},
abstract = {Root-associated microbiomes significantly influence plant growth and resilience through intricate chemical dialogues mediated by plant- and microbe-derived specialized metabolites. These metabolites play pivotal roles in shaping the assembly, dynamics, and ecological functions of soil microbiomes. Despite advances in in vitro and DNA sequencing studies, a comprehensive understanding of in situ chemical signaling within plant and soil microbiomes remains elusive due to experimental constraints. To address this gap, we developed and tuned a set of five whole-cell biosensors in Escherichia coli for spatiotemporal, nondisruptive detection of biologically relevant specialized metabolites, including 2,4-diacetylphloroglucinol, pyoluteorin, tetracycline, salicylic acid, and naringenin. Four of these biosensors were successfully adapted to the soil-compatible Pseudomonas putida KT2440 Δall-Φ strain. Additionally, the four sensors were shown to respond to their cognate ligand in a nonsterile soil extract medium containing a diverse microbiome extracted from soil. By employing genetic memory devices with DNA barcodes for readouts, our approach provides a scalable platform for sensing additional specialized metabolites in the future. This work demonstrates the potential of biosensor technologies to unravel the complex chemical interactions driving soil microbiome ecology, with implications for sustainable agricultural practices.},
}

@article {pmid40806377,
year = {2025},
author = {Ghosh, M and Bayat, AH and Pearse, DD},
title = {Small Extracellular Vesicles in Neurodegenerative Disease: Emerging Roles in Pathogenesis, Biomarker Discovery, and Therapy.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
pmid = {40806377},
issn = {1422-0067},
abstract = {Neurodegenerative diseases (NDDs) such as Alzheimer's, Parkinson's, ALS, and Huntington's pose a growing global challenge due to their complex pathobiology and aging demographics. Once considered as cellular debris, small extracellular vesicles (sEVs) are now recognized as active mediators of intercellular signaling in NDD progression. These nanovesicles (~30-150 nm), capable of crossing the blood-brain barrier, carry pathological proteins, RNAs, and lipids, facilitating the spread of toxic species like Aβ, tau, TDP-43, and α-synuclein. sEVs are increasingly recognized as valuable diagnostic tools, outperforming traditional CSF biomarkers in early detection and disease monitoring. On the therapeutic front, engineered sEVs offer a promising platform for CNS-targeted delivery of siRNAs, CRISPR tools, and neuroprotective agents, demonstrating efficacy in preclinical models. However, translational hurdles persist, including standardization, scalability, and regulatory alignment. Promising solutions are emerging, such as CRISPR-based barcoding, which enables high-resolution tracking of vesicle biodistribution; AI-guided analytics to enhance quality control; and coordinated regulatory efforts by the FDA, EMA, and ISEV aimed at unifying identity and purity criteria under forthcoming Minimal Information for Studies of Extracellular Vesicles (MISEV) guidelines. This review critically examines the mechanistic roles, diagnostic potential, and therapeutic applications of sEVs in NDDs, and outlines key strategies for clinical translation.},
}

@article {pmid40806300,
year = {2025},
author = {Thongkhao, K and Intharuksa, A and Phrutivorapongkul, A},
title = {Unveiling Adulteration in Herbal Markets: MassARRAY iPLEX Assay for Accurate Identification of Plumbago indica L.},
journal = {International journal of molecular sciences},
volume = {26},
number = {15},
pages = {},
pmid = {40806300},
issn = {1422-0067},
abstract = {The root of Plumbago indica L. is commercially available in herbal markets in both crude and powdered forms. P. indica root is a key ingredient in numerous polyherbal formulations. However, P. indica has two closely related species, P. zeylanica L. and P. auriculata Lam. Since only P. indica is traditionally used in Thai polyherbal products, adulteration with other species could potentially compromise the therapeutic efficacy and overall effectiveness of these formulations. To address this issue, a MassARRAY iPLEX assay was developed to accurately identify and differentiate P. indica from its closely related species. Five single nucleotide polymorphism (SNP) sites-positions 18, 112, 577, 623, and 652-within the internal transcribed spacer (ITS) region were selected as genetic markers for species identification. The assay demonstrated high accuracy in identifying P. indica and was capable of detecting the species at DNA concentrations as low as 0.01 ng/µL. Additionally, the assay successfully identified P. zeylanica in commercial crude drug samples, highlighting potential instances of adulteration. Furthermore, it was able to distinguish P. indica in mixed samples containing P. indica, along with either P. zeylanica or P. auriculata. The developed MassARRAY iPLEX assay proves to be a reliable and effective molecular tool for authenticating P. indica raw materials. Its application holds significant potential for ensuring the integrity of herbal products by preventing misidentification and adulteration.},
}

@article {pmid40805713,
year = {2025},
author = {Amin, A and Park, S},
title = {Harnessing Molecular Phylogeny and Chemometrics for Taxonomic Validation of Korean Aromatic Plants: Integrating Genomics with Practical Applications.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805713},
issn = {2223-7747},
abstract = {Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts.},
}

@article {pmid40805682,
year = {2025},
author = {Romadanova, NV and Altayeva, NA and Zemtsova, AS and Artimovich, NA and Shevtsov, AB and Kakimzhanova, A and Nurtaza, A and Tolegen, AB and Kushnarenko, SV and Bettoni, JC},
title = {Geobotanical Study, DNA Barcoding, and Simple Sequence Repeat (SSR) Marker Analysis to Determine the Population Structure and Genetic Diversity of Rare and Endangered Prunus armeniaca L.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805682},
issn = {2223-7747},
support = {project 0123РК01118//Ministry of Science and Higher Education of Kazakhstan Republic/ ; },
abstract = {The ongoing genetic erosion of natural Prunus armeniaca populations in their native habitats underscores the urgent need for targeted conservation and restoration strategies. This study provides the first comprehensive characterization of P. armeniaca populations in the Almaty region of Kazakhstan, integrating morphological descriptors (46 parameters), molecular markers, geobotanical, and remote sensing analyses. Geobotanical and remote sensing analyses enhanced understanding of accession distribution, geological features, and ecosystem health across sites, while also revealing their vulnerability to various biotic and abiotic threats. Of 111 morphologically classified accessions, 54 were analyzed with 13 simple sequence repeat (SSR) markers and four DNA barcoding regions. Our findings demonstrate the necessity of integrated morphological and molecular analyses to differentiate closely related accessions. Genetic analysis identified 11 distinct populations with high heterozygosity and substantial genetic variability. Eight populations exhibited 100% polymorphism, indicating their potential as sources of adaptive genetic diversity. Cluster analysis grouped populations into three geographic clusters, suggesting limited gene flow across Gorges (features of a mountainous landscape) and greater connectivity within them. These findings underscore the need for site-specific conservation strategies, especially for genetically distinct, isolated populations with unique allelic profiles. This study provides a valuable foundation for prioritizing conservation targets, confirming genetic redundancies, and preserving genetic uniqueness to enhance the efficiency and effectiveness of the future conservation and use of P. armeniaca genetic resources in the region.},
}

@article {pmid40801815,
year = {2025},
author = {Taylor, KE and Saunders, GW},
title = {Assessment of rhodolith-forming species diversity in British Columbia uncovers novel cryptic diversity in the genera Boreolithothamnion and Rhodolithia gen. nov. (Florideophyceae, Rhodophyta) and the occurrence of hybrid rhodoliths.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70066},
pmid = {40801815},
issn = {1529-8817},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Northeast Algal Society Development Committee/ ; //New Brunswick Innovation Foundation/ ; //Canada Foundation for Innovation/ ; },
abstract = {Rhodolith collections in British Columbia have historically been limited, and published regional species diversity data are poor. The acquisition of recent collections, notably from rhodolith beds in Haida Gwaii, provided an opportunity to assess diversity in these waters. The DNA barcode markers COI-5P, rbcL-3P, and psbA were used to identify unique genetic groups, which were then placed into a phylogenetic context with other coralline algae and subsequently observed anatomically. These analyses uncovered six rhodolith-forming species: two known, viz. Boreolithothamnion phymatodeum and Boreolithothamnion soriferum; a species provisionally called Boreolithothamnion sp. 1heterocladum; and three novel species described here, viz. Boreolithothamion astragaloi sp. nov., Boreolithothamnion tanuense sp. nov., and Rhodolithia gracilis gen. et. sp. nov., which comprises three varieties. Of particular interest, sequences of the ITS rDNA region showed the variety Rhodolithia gracilis var. gracilis × ramosa var. nov. to be a hybrid of the other two varieties: Rhodolithia gracilis var. gracilis var. nov. and Rhodolithia gracilis var. ramosa var. nov. Although understanding the full extent of BC rhodolith beds will require additional sampling, these findings indicate that rhodoliths are widespread and diverse in British Columbia.},
}

@article {pmid40800620,
year = {2025},
author = {Partanen, V and Dekić Rozman, S and Karkman, A and Muurinen, J and Hiltunen, T and Virta, M},
title = {Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf113},
pmid = {40800620},
issn = {2730-6151},
abstract = {One of the most important knowledge gaps in the antimicrobial resistance crisis is the lack of understanding regarding how genes spread from their environmental origins to bacteria pathogenic to humans. In this study our aim was to create a system that allows the conduction of experiments in laboratory settings that mimic the complexity of natural communities with multiple resistance genes and mobile genetic elements circulating at the same time. Here we report a new sequence-based barcode system that allows simultaneous tracking of the spread of antimicrobial resistance genes from multiple genetic origins. We tested this concept with an experiment in which we added an antimicrobial resistance gene to different genetic environments in alive and dead donors and let the gene spread naturally in an artificial microbial community under different environmental conditions to provide examples of factors that can be investigated. We used emulsion, paired-isolation, and concatenation polymerase chain reaction to detect the new gene carriers and metagenomic analysis to see changes in the genetic environment. We observed the genes moving and were able to recognise the barcode from the gene sequences, thus validating the idea of barcode use. We also saw that temperature and gene origin had effects on the number of new host species. Our results confirmed that our system worked and can be further developed for more complicated experiments.},
}

@article {pmid40799287,
year = {2025},
author = {Choi, H and Favret, C and Lee, S},
title = {First record of the tropical aphid Schoutedeniaralumensis (Hemiptera, Aphididae) from Cambodia, with a re-description of the oviparous females and DNA barcoding.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e159374},
pmid = {40799287},
issn = {1314-2828},
abstract = {BACKGROUND: Schoutedenia Rübsaamen, 1905 (Hemiptera, Aphididae, Greenideinae) is a small aphid genus associated with woody Euphorbiaceae and Phyllanthaceae. Of its two recognised species, Schoutedeniaralumensis Rübsaamen, 1905 is widely distributed across Southeast Asia, India, Africa and along the eastern coast of Australia. Taxonomic difficulties arise from subtle morphological differences and an unusual life cycle in which all morphs may occur simultaneously. Moreover, the oviparous female remains inadequately described, limiting reliable identification and comparative analyses.

NEW INFORMATION: Schoutedeniaralumensis is newly recorded from Cambodia on Phyllanthus sp. (Phyllanthaceae). The poorly-known morphology of oviparous females is re-described with live photographs, biometric measurements and photomicrographic illustrations. Additionally, DNA barcoding, based on mitochondrial cytochrome c oxidase (COI) sequences, was performed on the Cambodian specimen and compared with available sequences, including one of S.emblica. Additionally, we propose the synonymisation of S.emblica under S.ralumensis as a conspecific variant. These findings expand the known distribution of S.ralumensis and contribute to a better understanding of aphid diversity in Cambodia.},
}

@article {pmid40796904,
year = {2025},
author = {Nowak, KH and Hartop, E and Prus-Frankowska, M and Buczek, M and Kolasa, MR and Roslin, T and Ovaskainen, O and Łukasik, P},
title = {What lurks in the dark? An innovative framework for studying diverse wild insect microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {186},
pmid = {40796904},
issn = {2049-2618},
support = {2016-203 4.3//Swedish Taxonomy Initiative/ ; 856506//Horizon 2020/ ; 336212//Research Council of Finland/ ; PPN/PPO/2018/1/00015//Narodowa Agencja Wymiany Akademickiej/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; },
abstract = {BACKGROUND: Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain poorly understood in natural insect communities, especially in 'dark taxa'-hyperdiverse yet understudied clades.

RESULTS: Here, we implemented a novel multi-target amplicon sequencing approach to study microbiota in complex, species-rich communities. It combines four methodological innovations: (1) To establish a host taxonomic framework, we sequenced amplicons of the host marker gene (COI) and reconstructed barcodes alongside microbiota characterisation using 16S-V4 rRNA bacterial gene amplicons. (2) To assess microbiota abundance, we incorporated spike-in-based quantification. (3) To improve the phylogenetic resolution for the dominant endosymbiont, Wolbachia, we analysed bycatch data from the COI amplicon sequencing. (4) To investigate the primary drivers of host-microbe associations in massive multi-dimensional datasets, we performed Hierarchical Modelling of Species Communities (HMSC). Applying this approach to 1842 wild-caught scuttle flies (Diptera: Phoridae) from northern Sweden, we organised them into 480 genotypes and 186 species and gained unprecedented insights into their microbiota. We found orders-of-magnitude differences in bacterial abundance and massive within-population variation in microbiota composition. Patterns and drivers differed among microbial functional categories: the distribution and abundance of facultative endosymbionts (Wolbachia, Rickettsia, Spiroplasma) were shaped by host species, genotype, and sex. In contrast, many other bacterial taxa were broadly distributed across species and sites.

CONCLUSIONS: This study highlights facultative endosymbionts as key players in insect microbiota and reveals striking variations in distributional patterns of microbial clades. It also demonstrates the power of integrative sequencing approaches in uncovering the ecological complexity and significance of symbiotic microorganisms in multi-species natural communities. Video Abstract.},
}

@article {pmid40796813,
year = {2025},
author = {Shehata, DHM and El-Mahdy, MM and Ibrahim, M and El Araby, MMI and El-Akkad, SS and Ellmouni, FY},
title = {Analytical assessment of physical characteristics, metabolic processes, and molecular investigations of selected wheat (Triticum spp.) cultivars.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1067},
pmid = {40796813},
issn = {1471-2229},
abstract = {BACKGROUND: Wheat, a primary cereal crop, is crucial in addressing global food security. Understanding genetic diversity and conserving wheat germplasm is essential for developing cultivars resilient to climate change. This study investigates grain quality, nutritional profiles, and genetic diversity across a selection of Egyptian and internationally sourced wheat cultivars. Physical and chemical analyses were conducted to assess grain/flour quality, hardness, and micronutrient content. Genetic diversity was evaluated using protein profiling, SCoT markers, and rbcL chloroplast DNA barcoding, chosen for its highly conserved nature and proven utility in plant species identification and phylogenetic analysis, making it a reliable marker for assessing genetic relationships among wheat cultivars. The findings from this study revealed distinct patterns of genetic variation and highlight valuable traits within the germplasm, providing crucial information for developing wheat cultivars adapted to diverse climatic conditions.

RESULTS: Physical and biochemical analyses revealed that two Egyptian cultivars, Sohag 5 and Misr 1, exhibited superior quality and nutritional value among the nine evaluated wheat cultivars. Both showed favorable physical properties (e.g., grain weight, falling number, gluten content). Sohag 5 was notably rich in carbohydrates, protein content, and essential minerals (zinc, calcium, magnesium), while Misr 1 also maintained healthy carbohydrate and gluten levels. Genetic diversity analysis, employing SDS-PAGE protein profiling and SCoT markers, effectively differentiated the wheat cultivars. These molecular markers consistently grouped the cultivars, generally distinguished between bread wheat and durum wheat varieties, and provided insights into the genetic relationships between Egyptian and imported lines. While the specific clustering patterns varied between marker types, particularly with rbcL sequences providing a distinct grouping since the rbcL chloroplast gene exhibited limited resolution for differentiating closely related cultivars. The combined genetic data confirmed significant diversity within the germplasm. Overall, the analysis identified two primary genetic groups among the cultivars, with Group I comprising seven diverse cultivars and Group II containing two distinct cultivars (Benisuif 6 and Sohag 5).

CONCLUSIONS: Overall, the investigated Egyptian wheat cultivars demonstrated competitive or superior performance in standard physical and nutritional parameters compared to the imported varieties, with Sohag 5 and Misr 1 notably excelling in grain quality and micronutrient content. The genetic diversity analysis, incorporating protein profiling, SCoT markers, and rbcL chloroplast DNA barcoding, effectively characterized the genetic landscape of the cultivars. A key finding was the consistent genetic distinction of specific Egyptian cultivars, notably Sohag 5 and Benisuif 6, which clustered uniquely, aligning with their classification as durum wheat varieties. This revealed genetic relationships, alongside the identified superior traits (e.g., in Sohag 5), provides valuable insights that can be strategically utilized in breeding programs to develop new wheat cultivars with enhanced quality and adaptability to diverse climatic conditions.},
}

@article {pmid40796554,
year = {2025},
author = {Okkelman, IA and Zhou, H and Borisov, SM and Debruyne, AC and Lefebvre, AEYT and Leomil Zoccoler, M and Chen, L and Devriendt, B and Dmitriev, RI},
title = {Visualizing the internalization and biological impact of nanoplastics in live intestinal organoids by Fluorescence Lifetime Imaging Microscopy (FLIM).},
journal = {Light, science & applications},
volume = {14},
number = {1},
pages = {272},
pmid = {40796554},
issn = {2047-7538},
support = {101073507//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101073507//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Increased micro- and nanoplastic (MNP) pollution poses significant health risks, yet the mechanisms of their accumulation and effects on absorptive tissues remain poorly understood. Addressing this knowledge gap requires tractable models coupled to dynamic live cell imaging methods, enabling multi-parameter single cell analysis. We report a new method combining adult stem cell-derived small intestinal organoid cultures with live fluorescence lifetime imaging microscopy (FLIM) to study MNP interactions with gut epithelium. To facilitate this, we optimized live imaging of porcine and mouse small intestinal organoids with an 'apical-out' topology. Subsequently, we produced a set of pristine MNPs based on PMMA and PS (<200 nm, doped with deep-red fluorescent dye) and evaluated their interaction with organoids displaying controlled epithelial polarity. We found that nanoparticles interacted differently with apical and basal membranes of the organoids and showed a species-specific pattern of cellular uptake. Using a phasor analysis approach, we demonstrate improved sensitivity of FLIM over conventional intensity-based microscopy. The resulting 'fluorescence lifetime barcoding' enabled distinguishing of different types of MNP and their interaction sites within organoids. Finally, we studied short (1 day)- and long (3 day)-term exposure effects of PMMA and PS-based MNPs on mitochondrial function, total cell energy budget and epithelial inflammation. We found that even pristine MNPs could disrupt chemokine production and mitochondrial membrane potential in intestinal epithelial cells. The presented FLIM approach will advance the study of MNP toxicity, their biological impacts on gastrointestinal tissue and enable the tracing of other fluorescent nanoparticles in live organoid and 3D ex vivo systems.},
}

@article {pmid40794723,
year = {2025},
author = {Muffett, KM and Labonté, JM and Miglietta, MP},
title = {Florida Keys Cassiopea host benthos-like external microbiomes and a gut dominated by Vibrio, Endozoicomonas and Mycoplasma.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0330180},
pmid = {40794723},
issn = {1932-6203},
mesh = {Animals ; Florida ; RNA, Ribosomal, 16S/genetics ; *Mycoplasma/genetics/isolation & purification/classification ; *Vibrio/genetics/isolation & purification ; *Scyphozoa/microbiology ; *Microbiota ; Phylogeny ; *Gastrointestinal Microbiome ; Symbiosis ; },
abstract = {Interactions with microbial communities fundamentally shape metazoans' physiology, development, and health across marine ecosystems. This is especially true in zooxanthellate (symbiotic algae-containing) cnidarians. In photosymbiotic anthozoans (e.g., shallow water anemones and corals), the key members of the associated microbiota are increasingly well studied, however there is limited data on photosymbiotic scyphozoans (true jellyfish). Using 16S rRNA barcoding, we sampled the internal and external mucus of the zooxanthellate Upside-Down Jellyfish, Cassiopea xamachana during August throughout eight sites covering the full length of the Florida Keys. We find that across sites, these medusae have low-diversity internal microbiomes distinct from the communities of their external surfaces and their environment. These internal communities are dominated by only three taxa: Endozoicomonas cf. atrinae, an uncultured novel Mycoplasma, and Vibrio cf. coralliilyticus. In addition, we find that Cassiopea bell mucosal samples were high diversity and conform largely to the communities of surrounding sediment with the addition of Endozoicomonas cf. atrinae. The microbial taxa we identify associated with wild Florida Keys Cassiopea bear a strong resemblance to those found within photosymbiotic anthozoans, increasing the known links in ecological position between these groups.},
}

Animals
Florida
RNA, Ribosomal, 16S/genetics
*Mycoplasma/genetics/isolation & purification/classification
*Vibrio/genetics/isolation & purification
*Scyphozoa/microbiology
*Microbiota
Phylogeny
*Gastrointestinal Microbiome
Symbiosis

@article {pmid40792566,
year = {2025},
author = {Mehdizadeh, M and Omidi, A and Morya, S and Abideen, Z},
title = {Combating saffron fraud: a systematic review of adulteration practices, detection technologies, recommendations and challenges.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/10408398.2025.2544767},
pmid = {40792566},
issn = {1549-7852},
abstract = {Saffron, the world's most valuable spice, faces pervasive threats from food fraud, compromising its authenticity, economic value, and consumer safety. This systematic review synthesizes evidence from 23 studies to evaluate the prevalence, methods, impacts, and detection strategies of saffron adulteration. Following PRISMA guidelines, peer-reviewed articles from PubMed, Scopus, and ScienceDirect (2015-2025) were analyzed. Findings reveal that 20-30% of commercial saffron is adulterated globally, though with significant regional disparities (e.g., 3.5% in regulated EU markets vs. 60% in India), driven by economic incentives and regulatory gaps. Common fraudulent practices include substitution with safflower, marigold, or turmeric; dilution with extraneous plant materials; and the addition of hazardous synthetic dyes such as Sudan compounds and auramine-O. Advanced detection technologies including DNA barcoding, spectroscopy, hyperspectral imaging, and machine learning demonstrate high accuracy but face barriers in cost, accessibility, and real-world applicability. Health risks, such as exposure to carcinogenic dyes, and economic losses for legitimate producers underscore the urgency of addressing supply chain vulnerabilities. The review highlights fragmented regulatory frameworks and emphasizes the need for harmonized ISO standards, blockchain-enabled traceability, and consumer education to combat fraud. Emerging portable tools, such as smartphone-based spectroscopy and AI-driven platforms, offer promising solutions for on-site authentication.},
}

@article {pmid40792429,
year = {2025},
author = {Zhou, P and Mills, CB and Dong, ZM and Barber, BR and Beronja, S},
title = {Barcoded Orthotopic Patient-Derived Head & Neck Squamous Cell Carcinoma Model Demonstrating Clonal Stability and Maintenance of Cancer Driver Mutational Landscape.},
journal = {Cancer medicine},
volume = {14},
number = {15},
pages = {e71137},
pmid = {40792429},
issn = {2045-7634},
support = {//Fred Hutchinson Cancer Research Center/ ; //Dick and Loraine Burger Pilot Funding/ ; //AAO-HNSF Resident Research Grant/ ; },
mesh = {Humans ; Animals ; Mice ; *Squamous Cell Carcinoma of Head and Neck/genetics/pathology ; *Head and Neck Neoplasms/genetics/pathology ; *Mutation ; Disease Models, Animal ; Female ; Xenograft Model Antitumor Assays ; Mice, SCID ; Exome Sequencing ; Male ; *DNA Barcoding, Taxonomic ; },
abstract = {OBJECTIVE: To illustrate a new barcoded orthotopic patient-derived xenograft (PDX) mouse model where one can investigate phenotypic effects of single-cell level gene manipulation in a pooled format. To address some concerns of current PDX mouse models of head and neck squamous cell carcinoma (HNSCC): (1) genomic evolution with passage by generating high-purity cancer cells, which can also be utilized for other downstream applications, including cell culture-based studies, and (2) cost-effectiveness of current PDX models.

METHODS: Two-millimeter tumor cubes from nine patients were implanted into immunodeficient mouse flanks subcutaneously. Purified tumor cells were obtained from subcutaneous xenografts. Various numbers of purified tumor cells were then injected into the lingual tissue of immunodeficient mice, and the lowest amount of cells needed to achieve a 100% orthotopic engraftment rate were identified. Clonal stability was tested using a lentiviral barcoding system. The orthotopic PDXs' genetic landscapes were characterized using whole exome sequencing.

RESULTS: This approach yielded an overall engraftment rate of 88.9%. The purification process increased cancer cell purity from 34% to 92%. Lingual injection of 100,000 purified tumor cells achieved a 100% orthotopic engraftment rate from purified subcutaneous PDX tumor cells while maintaining clonal and genetic stability.

CONCLUSION: Our study presents a barcoded orthotopic patient-derived xenograft model for head and neck squamous cell carcinoma with clonal stability. This model provides a way to study phenotypic effects of single cell level gene manipulation in a pooled format. The method can be adapted for in vitro work as well.},
}

Humans
Animals
Mice
*Squamous Cell Carcinoma of Head and Neck/genetics/pathology
*Head and Neck Neoplasms/genetics/pathology
*Mutation
Disease Models, Animal
Female
Xenograft Model Antitumor Assays
Mice, SCID
Exome Sequencing
Male
*DNA Barcoding, Taxonomic

@article {pmid40792070,
year = {2025},
author = {Lyu, H and Li, Y and Wu, S and Fu, L and Liang, X and Liu, E},
title = {Editorial: Expanding insights into structure, function, and disorder of genome by the power of artificial intelligence in bioinformatics.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1649410},
doi = {10.3389/fgene.2025.1649410},
pmid = {40792070},
issn = {1664-8021},
}

@article {pmid40791109,
year = {2025},
author = {Yuan, H and Han, J and Yang, M and Chen, S and Pang, X},
title = {DNA Metabarcoding: Current Applications and Challenges.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c06002},
pmid = {40791109},
issn = {1520-5118},
abstract = {DNA metabarcoding is a versatile approach that combines high-throughput sequencing (HTS) with DNA barcoding and enables the simultaneous identification of multiple species in complex DNA samples. With the rapid development of high-throughput sequencing (HTS), DNA meta-barcoding has been widely applied in many fields. This review summarizes the current state of research on DNA metabarcoding, focusing on recent advances in its application in several major fields. DNA metabarcoding can effectively analyze community biodiversity and contribute significantly to the foundation of ecological research. In terms of food safety, it can detect food-derived ingredients to ensure the accuracy of food labeling and prevent adulteration. It can reveal the dietary analysis of animals and provide a scientific foundation for biodiversity protection. It can also identify species in trace samples and help solve crimes in forensic research. Additionally, the challenges ahead and potential developments in DNA meta-barcoding are considered. This review provides comprehensive information about DNA metabarcoding and its multifaceted applications, which could facilitate interdisciplinary communication and improve methodological standardization.},
}